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Reaction dynamics. Vibrational relaxation and microsolvation of DF after F-atom reactions in polar solvents
Abstract
Solvent-solute interactions influence the mechanisms of chemical reactions in solution, but the response of the solvent is often slower than the reactive event. Here, we report that exothermic reactions of fluorine (F) atoms in d3-acetonitrile and d2-dichloromethane involve efficient energy flow to vibrational motion of the deuterium fluoride (DF) product that competes with dissipation of the energy to the solvent bath, despite strong solvent coupling. Transient infrared absorption spectroscopy and molecular dynamics simulations show that after DF forms its first hydrogen bond on a subpicosecond time scale, DF vibrational relaxation and further solvent restructuring occur over more than 10 picoseconds. Characteristic dynamics of gas-phase F-atom reactions with hydrogen-containing molecules persist in polar organic solvents, and the spectral evolution of the DF products serves as a probe of solvent reorganization induced by a chemical reaction.
Copyright © 2015, American Association for the Advancement of Science.
... Nevertheless, it is only in recent years that the effect of solvent on the dynamics and energy relaxation of this kind of reaction has been explored experimentally. 38,45 Dunning et al. found that the nascent DF in the wake of the reaction (F + CD 3 CN or F + CD 2 Cl 2 ) is in an excited vibrational state with a lifetime of several picoseconds. 38 The nascent DF is experimentally observed to relax at a comparable rate in deuterated acetonitrile and dichloromethane. ...
... 38,45 Dunning et al. found that the nascent DF in the wake of the reaction (F + CD 3 CN or F + CD 2 Cl 2 ) is in an excited vibrational state with a lifetime of several picoseconds. 38 The nascent DF is experimentally observed to relax at a comparable rate in deuterated acetonitrile and dichloromethane. Reactive simulations for the case of the reaction between F and CD 3 CN showed that at short postreaction times, the vibrationally excited DF molecule is not yet hydrogen-bonded to the solvent molecules, a process that takes roughly 1 ps, with subsequent excess energy loss into the solvent bath taking several picoseconds (∼3−4 ps). ...
... Reactive simulations for the case of the reaction between F and CD 3 CN showed that at short postreaction times, the vibrationally excited DF molecule is not yet hydrogen-bonded to the solvent molecules, a process that takes roughly 1 ps, with subsequent excess energy loss into the solvent bath taking several picoseconds (∼3−4 ps). 37, 38 The experiment also observed a comparable relaxation timescale for IR-excited DF molecules and for the excited DF produced by the reaction. ...
Vibrationally excited deuterium fluoride (DF) formed by fluorine atom reaction with a solvent was found (Science, 2015, 347, 530) to relax rapidly (less than 10 ps) in acetonitrile-d3 (CD3CN) and dichloromethane-d2 (CD2Cl2). However, insights into how CD2Cl2 facilitates this energy relaxation have so far been lacking, given the weak interaction between DF and a single CD2Cl2. In this work, we report the results of reactive simulations with a two-state reactive empirical valence bond (EVB) potential to study the energy deposited into nascent DF after transition-state passage and of nonequilibrium molecular dynamics simulations using multiple different potential energy functions to model the relaxation dynamics. For these second simulations, we used the standard Merck molecular force field (MMFF) potential, an MMFF-based covalent-ionic empirical valence bond (EVB) potential (EVBCI), a newly developed potential [referred to as MMFF(rDF)] which extends upon the MMFF potential by making the DF/CD2Cl2 interaction depend on the value of the D—F bond stretching coordinate and by taking the anisotropic charge distribution of the solvent molecules into account, the polarizable atomic multipole optimized energetics for biomolecular applications (AMOEBA) potential, and the quantum mechanics/molecular mechanics (QM/MM) potential. The relaxation is revealed to be highly sensitive to the potential used. Neither standard MMFF nor EVBCI reproduces the experimentally observed rapid relaxation dynamics, and they also fail to provide a good description of the interaction potential between DF and CD2Cl2 as calculated using CCSD(T)-F12. This is attributed to the use of a point-charge model for the solute and to failing to model the anisotropic electrostatic properties of CD2Cl2. The MMFF(rDF), AMOEBA, and QM/MM potentials all reproduce the CCSD(T)-F12 two-body DF---CD2Cl2 interaction potential rather well but only with the QM/MM approach is fast vibrational relaxation obtained (lifetimes of ∼288, ∼186, and ∼8 ps, respectively), which we attribute to differences in the solute–solvent local structure. With QM/MM, a unique “many-body” interaction pattern in which DF is in close contact with two solvent Cl atoms and more than three solvent D atoms is found, but this structure is not seen with other potentials. The QM/MM dynamics also display enhanced solute–solvent interactions with vibrationally excited DF that induce a DF band redshift and hence a resonant overlap with solvent C—D modes, which facilitate the intermolecular energy transfer. Our work also suggests that potentials used to model energy relaxation need to capture the fine structure of solute–solvent interactions and not just the two-body part.
... Refs. [9][10][11][12][13][14][15][16][17][18][19][20][21][22]). The EVB approach is implemented into a number of software packages, including its original implementation into Warshel's MOLARIS simulation package [23], as well as AMBER [24], CHARMM [25] and Tinker [25,26]. ...
... This approach is extremely flexible in that once a given reference state (usually either the background reaction in vacuum or aqueous solution, or, for example, the wildtype enzyme compared to a series of mutant enzymes) has been parameterized, it is possible to move the same parameter set to a host of different environments, unchanged, without the need for further parametrization (see Ref. [62] for discussion of the phase-independence of the EVB off-diagonal term). In addition, while EVB simulations can be performed employing commonly used periodic boundary conditions [16], both MOLARIS [23,63] and Q [30] also allow for the use of spherical boundary conditions to describe the reacting system. In these software packages, the spherical boundary conditions are described in a stochastic multilayer model in which the inner region of the sphere (i.e. the reacting atoms and all atoms within the typically inner 85% of the sphere) is completely flexible, all atoms outside the explicit sphere are that the postprocessing for the free energy calculations (empirical valence bond and linear interaction energy calculations) is handled in a separate external module, Qcalc6. ...
Atomistic simulations have become one of the main approaches to study the chemistry and dynamics of biomolecular systems in solution. Chemical modelling is a powerful way to understand biochemistry, with a number of different programs available to perform specialized calculations. We present here Q6, a new version of the Q software package, which is a generalized package for empirical valence bond, linear interaction energy, and other free energy calculations. In addition to general technical improvements, Q6 extends the reach of the EVB implementation to fast approximations of quantum effects, extended solvent descriptions and quick estimation of the contributions of individual residues to changes in the activation free energy of reactions.
... The extent to which vibrational energy transfer dynamics can impact reaction outcomes in condensed phases remains an active research question. Over the past few years, a combination of molecular dynamics and master equation studies have provided examples of reaction outcomes in liquids which depend on energy transfer efficiencies [5][6][7][8]. Chemistry and reaction dynamics at the gas-surface interface [9][10][11] provide an interesting application domain for investigating the role that energy transfer plays in governing reaction outcomes because it offers an intermediate regime between the gas and liquid phases. ...
... Specifically, the atomic kinetic energies were summed to construct a kinetic energy time series KE(t) for the 'system' atoms in figure 7. The average total energy within the system as a function of time E(t) was calculated by the virial theorem as 2 KE(t) τ , where the angled brackets indicate averages, and τ is a user-specified time window over which the averaging is carried out. This is a strategy that we have used successfully in a number of previous studies [5,8,31,40], which has given quantitative agreement with experiment, so long as τ is chosen to span several of the slowest vibrational periods within the set of 'system' atoms. For this system, we found that our results more or less converged so long as τ was greater than 100 fs. . ...
The extent to which vibrational energy transfer dynamics can impact reaction outcomes beyond the gas phase remains an active research question. Molecular dynamics (MD) simulations are the method of choice for investigating such questions; however, they can be extremely expensive, and therefore it is worth developing cheaper models that are capable of furnishing reasonable results. This paper has two primary aims. First, we investigate the competition between energy relaxation and reaction at ‘hotspots’ that form on the surface of diamond during the chemical vapour deposition process. To explore this, we developed an efficient reactive potential energy surface by fitting an empirical valence bond model to higher-level ab initio electronic structure theory. We then ran 160 000 NVE trajectories on a large slab of diamond, and the results are in reasonable agreement with experiment: they suggest that energy dissipation from surface hotspots is complete within a few hundred femtoseconds, but that a small fraction of CH3 does in fact undergo dissociation prior to the onset of thermal equilibrium. Second, we developed and tested a general procedure to formulate and solve the energy-grained master equation (EGME) for surface chemistry problems. The procedure we outline splits the diamond slab into system and bath components, and then evaluates microcanonical transition-state theory rate coefficients in the configuration space of the system atoms. Energy transfer from the system to the bath is estimated using linear response theory from a single long MD trajectory, and used to parametrize an energy transfer function which can be input into the EGME. Despite the number of approximations involved, the surface EGME results are in reasonable agreement with the NVE MD simulations, but considerably cheaper. The results are encouraging, because they offer a computationally tractable strategy for investigating non-equilibrium reaction dynamics at surfaces for a broader range of systems.
This article is part of the themed issue ‘Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces’.
... As a result of these features, BXD has been successfully utilized to provide microscopic insight into a range of problems within condensed phase chemistry. 15,16,[18][19][20][21][22][23][24][25][26][27][28][29][30] The fact that BXD preserves the dynamics (unlike umbrella sampling, where dynamics is lost) has been experimentally conrmed for a growing set of systems. 18,[20][21][22]24 The fundamental idea in BXD is to accelerate dynamics simulations by introducing a set of hard boundaries within the hyperdimensional conguration space of the system being simulated. ...
... 15,16,[18][19][20][21][22][23][24][25][26][27][28][29][30] The fact that BXD preserves the dynamics (unlike umbrella sampling, where dynamics is lost) has been experimentally conrmed for a growing set of systems. 18,[20][21][22]24 The fundamental idea in BXD is to accelerate dynamics simulations by introducing a set of hard boundaries within the hyperdimensional conguration space of the system being simulated. When a trajectory passes a boundary, those components of the velocity vector that take the trajectory across the boundary are reected. ...
The past decade has seen the development of a new class of rare event methods in which molecular configuration space is divided into a set of boundaries/interfaces, and then short trajectories are run between boundaries. For all these methods, an important concern is how to generate boundaries. In this paper, we outline an algorithm for adaptively generating boundaries along a free energy surface in multi-dimensional collective variable (CV) space, building on the boxed molecular dynamics (BXD) rare event algorithm. BXD is a simple technique for accelerating the simulation of rare events and free energy sampling which has proven useful for calculating kinetics and free energy profiles in reactive and non-reactive molecular dynamics (MD) simulations across a range of systems, in both NVT and NVE ensembles. Two key developments outlined in this paper make it possible to automate BXD, and to adaptively map free energy and kinetics in complex systems. First, we have generalized BXD to multidimensional CV space. Using strategies from rigid-body dynamics, we have derived a simple and general velocity-reflection procedure that conserves energy for arbitrary collective variable definitions in multiple dimensions, and show that it is straightforward to apply BXD to sampling in multidimensional CV space so long as the Cartesian gradients ∇CV are available. Second, we have modified BXD to undertake on-the-fly statistical analysis during a trajectory, harnessing the information content latent in the dynamics to automatically determine boundary locations. Such automation not only makes BXD considerably easier to use; it also guarantees optimal boundaries, speeding up convergence. We have tested the multidimensional adaptive BXD procedure by calculating the potential of mean force for a chemical reaction recently investigated using both experimental and computational approaches - i.e., F + CD3CN → DF + D2CN in both the gas phase and a strongly coupled explicit CD3CN solvent. The results obtained using multidimensional adaptive BXD agree well with previously published experimental and computational results, providing good evidence for its reliability.
... Recently we have proposed [1] and applied [2,3] a theoreticalcomputational method for modelling, at the atomistic detail, the dynamics and the kinetics of the Vibrational Energy Relaxation (VER) [4][5][6][7] of a chromophore embedded in a complex molecular environment, e. g. a solvent and/or a biomacromolecular system. The proposed approach is performed by evaluating, at each frame of a semi-classical Molecular Dynamics (MD) simulation, the electric-field exerted by the environment onto the chromophore, represented by a subportion of the simulated system termed as the Quantum Center (QC). ...
A theoretical‐computational procedure, recently proposed for modelling Vibrational Energy Relaxation (VER) processes of a molecule (Quantum Center, QC) embedded in a complex atomic‐molecular system, is extended and applied for analyzing in detail the features of the QC density matrix (DM) temporal evolution. The results, obtained using aqueous azide ion as a case study, show the total lack of coherence in the DM, when the system is prepared to be initially in a pure vibrational eigenstate. This finding is fully in line with the statistical interpretation of the process typically adopted also in the experimental studies where the relaxation processes are all described within the typical schemes of chemical kinetics. Consistently, when the initial vibrational state corresponds to an eigenstate mixture, although initially coherent, the DM relaxes to a fully incoherent condition with a mean lifetime related to the one of the diagonal elements relaxation. These specific DM features turn out to be essentially governed by the thermal equilibrium condition of the atomic‐molecular classical coordinates which drive the ensemble of the quantum‐trajectories toward the observed statistical regime. Finally, from the analysis of a single long timescale quantum vibrational trajectory it also clearly emerges its ergodic behaviour.
... The continuum-based approaches naturally fail to provide a molecular description of solvent structural evolution. In fact, most practical solvents are polar ones, and polar solvents have a non-negligible effect on ion solvation dynamics [34][35], and their structural evolution coupled with ion diffusion should be properly accounted. ...
Herein the structural evolution of polar solvent coupled with single ion diffusion into charged nanopores is explored. The solvent dynamics is described with the dynamical molecular density functional theory while the solute ion diffusion is governed by Newton's equation of motion. This multiscale approach enables us to analyze the ion diffusion ability and selectivity under the conditions of different pore sizes and surface wettability. We find that the solvent force resulting from the inhomogeneous solvent structure plays an important role in modulating ion diffusion. When the pore size is specified, the solvophobic pore surface reduces the solvent resistance force, hence promoting ion diffusion. To enhance ion separation , however, a small nanopore with solvophilic pore surface should be chosen. The analysis on the ion-evoked current shows that the ion diffusion ability competes with the ion selectivity and large ion diffusion leads to low ion selectivity, and vice versa. This work unravels the underlying mechanism of solvent-evolution-coupled ion diffusion into charged nanopores and provides guidance towards the promotion of ion diffusion and selectivity efficiency.
... The system was OH + CH4, which we were simulating using a multi-state reactive EVB model. [41][42] This system, probably the best studied oxidation reaction in all of atmospheric chemistry, is one which I had only ever written algorithms to simulate, following the same standard protocol as every other computational chemist: input file preparation… batch submission… waiting… waiting… view & analyze output files… identify mistakes in input files…. Modify input files… batch submission… waiting… I went into VR, reached out, and used my wireless force probes to manipulate the OH using one hand and CH4 using the other. ...
Conceptually, the mechanics of nanoscale molecular objects arise through electrostatic forces acting on particles in non-uniform fields, and are relatively well characterized owing to decades of study. Nevertheless, because dynamics at this scale differ from the familiar mechanics of everyday objects, they are often non-intuitive, even for highly trained researchers. Moreover, because molecular systems have many of degrees of freedom, their motion involves a complicated, highly correlated, and 3D many-body dynamical choreography with few analogues in day-to-day experience. We recently described how advances in virtual reality (VR) enable researchers to manipulate real-time dynamics simulations of molecular structures in 3D. In this article, we discuss VR's design affordances, outline cognitive and perceptual principles for understanding how people experience VR, and provide an overview of efforts to use immersive technologies for the molecular sciences. We also introduce 'Narupa', a flexible, open-source, multi-person VR software framework designed to enable groups of researchers to simultaneously cohabit real-time simulation environments and interactively inspect, visualize, and manipulate the dynamics of complex molecular structures with atomic-level precision. We highlight the potential of VR to furnish insight into microscopic 3D dynamical concepts. We outline a range of application domains where VR is proving useful in enabling research and communication, including biomolecular conformational sampling, transport dynamics in materials, reaction discovery using 'on-the-fly' quantum chemistry, protein-ligand binding, and machine learning potential energy surfaces. We describe ongoing experiments using sound and proprioception to enable new forms of integrated multisensory molecular perception, and outline future applications for immersive technologies like VR in molecular science.
... Moreover, it has been known for some time that an accurate treatment of anharmonicity plays a crucial role in accurately treating inter and intra-molecular energy transfer rates. [12][13][14] Typically, bonding terms used in molecular mechanics force fields are polynomial expansions (up to fourth order), but this approximation breaks down for elongated bonds, e.g., during reactive events or in cases where molecules have significant internal energy. The primary motivation for treating bonds as harmonic rather than anharmonic in the past was one of computational efficiency, owing to the fact that force evaluations for a harmonic bond term are significantly cheaper than for a Morse type oscillator. ...
Methodologies for creating reactive potential energy surfaces from molecular mechanics force-fields are becoming increasingly popular. To date, molecular mechanics force-fields use harmonic expressions to treat bonding stretches, which is a poor approximation in reactive molecular dynamics simulations since bonds are displaced significantly from their equilibrium positions. For such applications there is need for a better treatment of anharmonicity. In this contribution Morse bonding potentials have been extensively parameterised for the atom types in the MM3 force field of Allinger and co-workers using high level CCSD(T)(F12*) energies. To our knowledge this is the first instance of a large-scale paramerization of Morse potentials in a popular force field.
... The temperature dependence of a chemical reaction in solution provides important information on the reaction rate and activation barrier 12,13 , whereas details on the RC, on the nuclear conformation and the dynamics of the reactive complex and its surroundings at the transition state (TS) are hard to obtain for ground-state reactions 15 . ...
Infrared (IR) excitation of vibrations that participate in the reaction coordinate of an otherwise thermally driven chemical reaction are believed to lead to its acceleration. Attempts at the practical realization of this concept have been hampered so far by competing processes leading to sample heating. Here we demonstrate, using femtosecond IR-pump IR-probe experiments, the acceleration of urethane and polyurethane formation due to vibrational excitation of the reactants for 1:1 mixtures of phenylisocyanate and cyclohexanol, and toluene-2,4-diisocyanate and 2,2,2-trichloroethane-1,1-diol, respectively. We measured reaction rate changes upon selective vibrational excitation with negligible heating of the sample and observed an increase of the reaction rate up to 24%. The observation is rationalized using reactant and transition-state structures obtained from quantum chemical calculations. We subsequently used IR-driven reaction acceleration to write a polyurethane square on sample windows using a femtosecond IR pulse.
... This reaction has been studied in the gas phase [21][22][23] and also in liquid CD 3 CN. 24,25 Of particular interest are the distributions of the vibrational and rotational quantum numbers, n and J, of the HF product. The simulation results for these distributions are compared with those found from 300 K experiments by Setser, Heydtmann, and co-workers. ...
Born-Oppenheimer direct dynamics simulations were performed to study atomistic details of the F + CH3CN → HF + CH2CN H-atom abstraction reaction. The simulation trajectories were calculated with a combined M06-2X/MP2 algorithm utilizing the 6-311++G** basis set. The experiments were performed at 300 K, and assuming the accuracy of transition state theory (TST), the trajectories were initiated at the F⋯HCH2CN abstraction TS with a 300 K Boltzmann distribution of energy and directed towards products. Recrossing of the TS was negligible, confirming the accuracy of TST. HF formation was rapid, occurring within 0.014 ps of the trajectory initiation. The intrinsic reaction coordinate (IRC) for reaction involves rotation of HF about CH2CN and then trapping in the CH2CN⋯HF post-reaction potential energy well of ∼10 kcal/mol with respect to the HF + CH2CN products. In contrast to this IRC, five different trajectory types were observed: the majority proceeded by direct H-atom transfer and only 11% approximately following the IRC. The HF vibrational and rotational quantum numbers, n and J, were calculated when HF was initially formed and they increase as potential energy is released in forming the HF + CH2CN products. The population of the HF product vibrational states is only in qualitative agreement with experiment, with the simulations showing depressed and enhanced populations of the n = 1 and 2 states as compared to experiment. Simulations with an anharmonic zero-point energy constraint gave product distributions for relative translation, HF rotation, HF vibration, CH2CN rotation, and CH2CN vibration as 5%, 11%, 60%, 7%, and 16%, respectively. In contrast, the experimental energy partitioning percentages to HF rotation and vibration are 6% and 41%. Comparisons are made between the current simulation and those for other F + H-atom abstraction reactions. The simulation product energy partitioning and HF vibrational population for F + CH3CN → HF + CH2CN resemble those for other reactions. A detailed discussion is given of possible origins of the difference between the simulation and experimental energy partitioning dynamics for F + CH3CN → HF + CH2CN. The F + CH3CN reaction also forms the CH3C(F)N intermediate, in which the F-atom adds to the C≡N bond. However, this intermediate and F⋯CH3CN and CH3CN⋯F van der Waals complexes are not expected to affect the F + CH3CN → HF + CH2CN product energy partitioning.
... This is exactly why the solvent relaxation time is involved in determining the actual trajectory that a reactive path follows. Recently, some post-TS dynamics was performed in the liquid phase, pointing out the appearance of dynamical effects [63][64][65][66][67]. The dynamics after the TS can be fast enough such that the solvent does not have time to rearrange and equilibrate according to the solute motion. ...
In this Introduction, we show the basic problems of non-statistical and non-equilibrium phenomena related to the papers collected in this themed issue. Over the past few years, significant advances in both computing power and development of theories have allowed the study of larger systems, increasing the time length of simulations and improving the quality of potential energy surfaces. In particular, the possibility of using quantum chemistry to calculate energies and forces ‘on the fly’ has paved the way to directly study chemical reactions. This has provided a valuable tool to explore molecular mechanisms at given temperatures and energies and to see whether these reactive trajectories follow statistical laws and/or minimum energy pathways. This themed issue collects different aspects of the problem and gives an overview of recent works and developments in different contexts, from the gas phase to the condensed phase to excited states.
This article is part of the themed issue ‘Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces’.
In this paper we apply a recently developed theoretical-computational procedure for modelling the Vibrational Energy Relaxation (VER) of solvated chromophores represented by small inorganic species. In particular we focus our attention on four different systems, all experimentally well characterized : aqueous cyanide ion and aqueous azide ion, nitrogen dioxide and water both in chloroform. Our method essentially reconstructs the whole vibrational relaxation kinetics (with the chromophore in the ground electronic state) by: (i) determining, through semiclassical Molecular Dynamics (MD) simulation, the electric field (perturbation) produced onto the chromophore by the solvent atom motions; (ii) using the electrostatic perturbation for directly determining the chromophore quantum vibrational dynamics;(iii) calculating the rate constant for the vibrational relaxation as occurring without quantum-classical energy exchange;(iv) introducing the latter effect, a posteriori, hence obtaining the actual relaxation kinetics. Our results, in satisfactory agreement with the available experimental data, show that the VER mechanism is almost entirely determined by the fluctuating perturbation field as produced by the time-dependent motions of the environment atoms (in these cases the solvent) similarly to the well-known effects of the electromagnetic wave causing absorption/emission processes.
Atomistic simulations using accurate energy functions can provide molecular-level insight into functional motions of molecules in the gas- and in the condensed phase. Together with recently developed and currently pursued efforts in integrating and combining this with machine learning techniques provides a unique opportunity to bring such dynamics simulations closer to reality. This perspective delineates the present status of the field from efforts of others in the field and some of your own work and discusses open questions and future prospects.
How solvent motions affect the dynamics of chemical reactions in which the solute undergoes a substantial shape change is a fundamental but elusive issue. This work utilizes reactive simulation and Grote-Hynes theory to explore the effect of solvent motions on the dynamics of the Diels–Alder reaction (in the reverse direction, this reaction involves very substantial solute expansion) in aprotic solvents. The results reveal that the solvent environment is not sufficiently constraining to influence transition state passage dynamics, with the calculated transmission coefficients being close to unity. Even when solvent motions are suppressed or artificially slowed down, the solvent only affects the reaction dynamics in the transition state region to a very small extent. The only notable effect of solvent occurs far from the transition state region and corresponds to caging of the reactants within the reactant well.
While understanding the mechanism of the solvation dynamics in polar liquid solvents is of fundamental importance, an efficient molecular theory that can capture the microscopic solvation structure and dynamics is still under development. Herein, we extend the dynamical density functional theory to describe the solvation dynamics in polar solvents by incorporating with the molecular version of classical density functional theory. The proposed theoretical model is then applied to probe the solvation dynamics of acetonitrile solvent near individual ionic solutes. Results show the heterogeneous effect of solvent orientation surrounding charged solute plays an important role in determining the characteristic of solvation dynamics. The orientation-dependent solvation free energy at solute-unfavored orientations monotonically decays, while that at solute-favored orientations reaches a minimum value rapidly by fast adsorption of solvent molecules and then increases to a plateau owning to solvent-solvent correlation. This unravels that the solvent translation and rotation are induced firstly by the solute-solvent interaction and then driven by the solvent-solvent correlation. This work not only casts molecular insights but also provides a feasible tool to explore the solvation dynamics in polar solvents.
A comparative investigation on the photophysical properties of a quinoxaline derivative 4,4'-((1E,1'E)-quinoxaline-2,3-diylbis(ethene-2,1-diyl))bis(N,N-dimethylaniline) (QDMA2) was performed by employing many spectroscopies. Based on the pump-dump/push-probe measurement, it is found that a solvent-stabilized charge-transfer state can participate in the relaxation of excited QDMA2 with increasing solvent polarity. Meanwhile, the aggregated QDMA2 molecules were engineered into the organic light-emitting diode test, which showed a correlated color temperature value of 1875 K. With the help of a diamond anvil cell, the pressure-dependent photoluminescence of aggregated QDMA2 shows that the intermolecular interaction can affect the color and intensity of photoluminescence through adjusting the band gap and irradiative channel of the aggregated molecules. These results are important for understanding the structure-property relationships and the rational design of functional materials for optoelectronic applications.
While solvation dynamics plays an important role in many processes, most available studies focus on the solvent response to the variations of charge distribution on dissolved solute, and the solvent response to the structural and geometrical variations of solute is rarely explored. Herein, by using dynamical density functional theory, we study the solvation dynamics of simple solvent in response to the variations of solute size and potential strength. We find that increasing solute size causes opposite effect of increasing its potential strength on solvation time. On the solvent structure, varying solute's potential strength brings a long-range yet weak influence while changing solute size generates a short-range yet strong effect, and therefore the penalty in solvent free energy is generally dominated by the change in solute's potential strength while the variations of coordination number and solvation shell radius are dominated by the change in solute size. This work unravels the nonpolar solvation dynamics in response to the variation of solute geometry, and casts helpful insights on the design and control of solvation-dynamics related applications in molecular engineering.
Spatial separation of water dimers from water monomers and larger water-clusters through the electric deflector is presented. A beam of water dimers with $93~\%$ purity and a rotational temperature of $1.5~$K was obtained. Following strong-field ionization using a 35~fs laser pulse with a wavelength centered around 800~nm and a peak intensity of $10^{14}~\Wpcmcm$ we observed proton transfer and $46~\%$ of ionized water dimers broke apart into hydronium ions \HHHOp and neutral OH.
The hydrogen abstraction from methanol (CH3OH) by F atoms presents an ideal proving ground to investigate dynamics of multi-channel reactions, because two types of hydrogen can be abstracted from the methanol molecule leading to the HF + CH3O and HF + CH2OH products. Using the quasi-classical trajectory approach on a globally accurate potential energy surfacebased on high-level ab initio calculations, this work reports a comprehensive dynamical investigation of this multi-channel reaction, yielding measurable attributes including integral and differential cross sections, as well as branching ratios. It is shown that while complex-forming and direct mechanisms coexist at low collision energies, these barrierless reaction channels are dominated at high energies by the direct mechanism, in which the reaction is only possible for trajectories entering into the respective dynamical cones of acceptance. Perhaps more importantly, the non-statistical product branching is found to be dictated by unique stereodynamics in the entrance channels.
As molecular scientists have made progress in their ability to engineer nanoscale molecular structure, we face new challenges in our ability to engineer molecular dynamics (MD) and flexibility. Dynamics at the molecular scale differs from the familiar mechanics of everyday objects because it involves a complicated, highly correlated, and three-dimensional many-body dynamical choreography which is often nonintuitive even for highly trained researchers. We recently described how interactive molecular dynamics in virtual reality (iMD-VR) can help to meet this challenge, enabling researchers to manipulate real-time MD simulations of flexible structures in 3D. In this article, we outline various efforts to extend immersive technologies to the molecular sciences, and we introduce "Narupa," a flexible, open-source, multiperson iMD-VR software framework which enables groups of researchers to simultaneously cohabit real-time simulation environments to interactively visualize and manipulate the dynamics of molecular structures with atomic-level precision. We outline several application domains where iMD-VR is facilitating research, communication, and creative approaches within the molecular sciences, including training machines to learn potential energy functions, biomolecular conformational sampling, protein-ligand binding, reaction discovery using "on-the-fly" quantum chemistry, and transport dynamics in materials. We touch on iMD-VR's various cognitive and perceptual affordances and outline how these provide research insight for molecular systems. By synergistically combining human spatial reasoning and design insight with computational automation, technologies such as iMD-VR have the potential to improve our ability to understand, engineer, and communicate microscopic dynamical behavior, offering the potential to usher in a new paradigm for engineering molecules and nano-architectures.
Spatial separation of water dimer from water monomer and larger water-clusters through the electric deflector is presented. A beam of water dimer with $93~\%$ purity and a rotational temperature of $1.5~$K was obtained. Following strong-field ionization using a $35~$fs laser pulse with a wavelength centered around $800~$nm and a peak intensity of $10^{14}~\text{W}/\text{cm}^2$ we observed proton transfer and $46~\%$ of the ionized water dimer broke apart into a hydronium ion $\text{H}_3\text{O}^+$ and OH.
Whilst the primary bottleneck to a number of computational workflows was not so long ago limited by processing power, the rise of machine learning technologies has resulted in an interesting paradigm shift, which places increasing value on issues related to data curation – i.e., data size, quality, bias, format, and coverage. Increasingly, data-related issues are equally as important as the algorithmic methods used to process and learn from the data. Here we introduce an open source GPU-accelerated neural network (NN) framework for learning reactive potential energy surfaces (PESs), and investigate the use of real-time interactive ab initio molecular dynamics in virtual reality (iMD-VR) as a new strategy which enables human users to rapidly sample geometries along reaction pathways which can subsequently be used to train NNs to learn efficient reactive PESs. Focussing on hydrogen abstraction reactions of CN radical with isopentane, we compare the performance of NNs trained using iMD-VR data versus NNs trained using a more traditional method, namely molecular dynamics (MD) constrained to sample a predefined grid of points along the hydrogen abstraction reaction coordinate. Both the NN trained using iMD-VR data and the NN trained using the constrained MD data reproduce important qualitative features of the reactive PESs, such as a low and early barrier to abstraction. Quantitative analysis shows that NN learning is sensitive to the dataset used for training. Our results show that user-sampled structures obtained with the quantum chemical iMD-VR machinery enable excellent sampling in the vicinity of the minimum energy path (MEP). As a result, the NN trained on the iMD-VR data does very well predicting energies which are close to the (MEP), but less well predicting energies for ‘off-path’ structures. The NN trained on the constrained MD data does better predicting high-energy ‘off-path’ structures, given that it included a number of such structures in its training set.
Methodologies for creating reactive potential energy surfaces from molecular mechanics force-fields are becoming increasingly popular. To date, molecular mechanics force-fields in biochemistry and small molecule organic chemistry tend to use harmonic expressions to treat bonding stretches, which is a poor approximation in reactive and non-equilibirum molecular dynamics simulations since bonds are often displaced significantly from their equilibrium positions. For such applications there is need for a better treatment of anharmonicity. In this contribution, Morse bonding potentials have been extensively parameterized for the atom types in the MM3 force field of Allinger and co-workers using high level CCSD(T)(F12*) energies. To our knowledge this is amongst the first instances of a comprehensive parametrization of Morse potentials in a popular organic chemistry force field. In the context of molecular dynamics simulations, this data will: (1) facilitate the fitting of reactive potential energy surfaces using empirical valence bond approaches, and (2) enable more accurate treatments of energy transfer.
The H-abstraction reaction between fluorine atom and deuterated acetonitrile (CD3CN) is highly exothermic and the resulting deuterium fluoride (DF) molecule is formed with a significant amount of energy that requires several picoseconds to relax into the solvent environment. Previous empirical valence bond (EVB) modelling work (J. Chem. Phys. 2015, 143, 044120) showed that reproducing the experimental relaxation timescale is quite sensitive to the potential energy surface (PES) used, and the physical effects responsible for cooling were not fully clear. Here, we study the rate of cooling on two new carefully designed PESs, and by comparison to behaviour on other PESs, this provides additional insight into these effects. The first PES is a MMFF (Merck Molecular Force Field) based covalent-ionic two-state EVB model constructed utilizing the valence-bond resonance structures of DF, which is shown to give a good description of the PES for interaction of hydrogen fluoride through hydrogen bonding with one acetonitrile molecule, but performs relatively poorly in predicting the vibrational relaxation rate in bulk solvent. The second new PES uses the polarizable AMOEBA force field formalism, and describes both the DF-acetonitrile dimer PES and the rate of vibrational cooling very well, with good computational efficiency. Comparison of those PESs shows that as well as a good description of the non-bonded interactions in the DF-acetonitrile dimer, successful prediction of cooling dynamics requires a good description of many-body effects involving the supramolecular complex formed by DF, the H-bonded CD3CN and nearby solvent molecules.
Solvation plays a critical role in various physicochemical and biological processes. Here, the rate of intersystem crossing (ISC) of benzophenone from its S1(nπ*) state to its triplet manifold of states is shown to be modified by hydrogen-bonding interactions with protic solvent molecules. We selectively photo-excite benzophenone with its carbonyl group either solvent coordinated or uncoordinated by tuning the excitation wavelength to the band center (λ = 340 nm) or the long-wavelength edge (λ = 380 nm) of its π*←n absorption band. A combination of ultrafast absorption and Raman spectroscopy shows that the hydrogen bonding interaction increases the time constant for ISC from < 200 fs to 1.7 ± 0.2 ps for benzophenone in CH3OH. The spectroscopic evidence suggests that the preferred pathway for ISC is from the S1(nπ*) to the T2(ππ*) state, with the rate of internal conversion from T2(ππ*) to T1(nπ*) controlled by solvent quenching of excess vibrational energy.
Using Born-Oppenheimer molecular dynamics (BOMD), we explore the nature of interactions between H2 and the activated carbonyl carbon, C(carbonyl), of the acetone-B(C6F5)3 adduct surrounded by an explicit solvent (1,4-dioxane). BOMD simulations at finite (non-zero) temperature with an explicit solvent produced long-lasting instances of significant vibrational perturbation of the H—H bond and H2-polarization at C(carbonyl). As far as the characteristics of H2 are concerned, the dynamical transient state approximates the transition-state of the heterolytic H2-cleavage. The culprit is the concerted interactions of H2 with C(carbonyl) and a number of Lewis basic solvent molecules—i.e., the concerted C(carbonyl)⋯H2⋯solvent interactions. On one hand, the results presented herein complement the mechanistic insight gained from our recent transition-state calculations, reported separately from this article. But on the other hand, we now indicate that an idea of the sufficiency of just one simple reaction coordinate in solution-phase reactions can be too simplistic and misleading. This article goes in the footsteps of the rapidly strengthening approach of investigating molecular interactions in large molecular systems via “computational experimentation” employing, primarily, ab initio molecular dynamics describing reactants-interaction without constraints of the preordained reaction coordinate and/or foreknowledge of the sampling order parameters.
The dynamics of chemical reactions in liquid solutions are now amenable to direct study using ultrafast laser spectroscopy techniques and advances in computer simulation methods. The surrounding solvent affects the chemical reaction dynamics in numerous ways, which include: (i) formation of complexes between reactants and solvent molecules; (ii) modifications to transition state energies and structures relative to the reactants and products; (iii) coupling between the motions of the reacting molecules and the solvent modes, and exchange of energy; (iv) solvent caging of reactants and products; and (v) structural changes to the solvation shells in response to the changing chemical identity of the solutes, on timescales which may be slower than the reactive events. This article reviews progress in the study of bimolecular chemical reaction dynamics in solution, concentrating on reactions which occur on ground electronic states. It illustrates this progress with reference to recent experimental and computational studies, and considers how the various ways in which a solvent affects the chemical reaction dynamics can be unravelled. Implications are considered for research in fields such as mechanistic synthetic chemistry.
4-hydroxy-2-nonenal (HNE) and 4-oxo-2-nonenal (ONE) are biologically important reactive aldehydes formed during oxidative stress in phospholipid bilayers. They are highly reactive species due to presence of several reaction centers and can react with amino acids in peptides and proteins, as well as phosphoethanolamine (PE) lipids, thus modifying their biological activity. The aim of this work is to study in a molecular detail the reactivity of HNE and ONE towards PE lipids in a simplified system containing only lipids and reactive aldehydes in dichloromethane as an inert solvent. We use a combination of quantum chemical calculations, (1)H-NMR measurements, FT-IR spectroscopy and mass spectrometry experiments and show that for both reactive aldehydes two types of chemical reactions are possible - formation of Michael adducts and Schiff bases. In the case of HNE, an initially formed Michael adduct can also undergo an additional cyclization step to a hemiacetal derivative, whereas no cyclization occurs in the case of ONE and a Michael adduct is identified. A Schiff base product initially formed when HNE is added to PE lipid can also further cyclize to a pyrrole derivative in contrast to ONE, where only a Schiff base product is isolated. The suggested reaction mechanism by quantum-chemical calculations is in a qualitative agreement with experimental yields of isolated products and is also additionally investigated by (1)H-NMR measurements, FT-IR spectroscopy and mass spectrometry experiments.
The use of EVB to study the dynamics of chemical reactions is reviewed. Both simple gas-phase systems and solution reactions are discussed. The history of EVB applications to dynamics is first considered, then the methodology we have used is described, followed by a detailed discussion of some applications, chosen to highlight the possibilities of the method. The chapter concludes with a description of strategies we have used for software implementation, with a particular focus on using existing molecular mechanics codes, and on parallelization.
We present evidence for vibrational enhancement of the rate of the bimolecular reactions of Br atoms with dimethylsulfoxide (DMSO) and methanol (CH3OH) in the condensed phase. The abstraction of a hydrogen atom from either of these solvents by a Br atom is highly endoergic: 3269 cm⁻¹ for DMSO and 1416 or 4414 cm⁻¹ for CH3OH, depending on the hydrogen atom abstracted. Thus, there is no thermal abstraction reaction at room temperature. Broadband electronic transient absorption shows that following photolysis of bromine precursors, Br atoms form van der Waals complexes with the solvent molecules in about 5 ps and this Br●-solvent complex undergoes recombination. To explore the influence of vibrational energy on the abstraction reactions, we introduce a near-infrared (IR) pump pulse following the photolysis pulse to excite the first overtone of the C-H (or O-H) stretch of the solvent molecules. Using single-wavelength detection, we observe a loss of the Br●-solvent complex that requires the presence of both the photolysis and near-IR pump pulses. Moreover, the magnitude of this loss depends on the near-IR wavelength. While this loss of reactive Br supports the notion of vibrationally driven chemistry, it is not concrete evidence of the hydrogen-abstraction reaction. To verify that the loss of reactive Br results from the vibrationally driven bimolecular reaction, we examine the pH dependence of the solution (as a measure of the formation of the HBr product) following long-time irradiation of the sample with both the photolysis and near-IR pump beams. We observe that when the near-IR beam is on-resonance, the hydronium ion concentration increases 4-fold as compared to when it is off-resonance, suggesting the formation of HBr via a vibrationally driven hydrogen-abstraction reaction in solution.
The vibrational relaxation of the C=O stretching mode of HCO2CH3 in CCl4 solution was measured using femtosecond infrared spectroscopy. Time-resolved spectra after excitation of the C=O stretching mode revealed a new absorption other than that of the excited C=O mode. Transient signals for the fundamental band and the absorption of the excited C=O mode showed nonexponential kinetics having a subpicosecond component. A three-state kinetic scheme showed that the excited C=O mode decayed via the v = 1 state of the C−O mode. The subpicosecond decay component might be due to fast equilibration of the excited state with the adjacent 2nd excited state of the O−CH3 stretching mode. Or it might be caused by solvent memory effects, which cause unusually rapid nonexponential absorption decay. As demonstrated herein, time-resolved infrared spectra with high spectral resolution and sensitivity can provide detailed relaxation pathways of vibrational energy.
A Cl atom can react with 2,3-dimethylbutane (DMB), 2,3-dimethyl-2-butene (DMBE), and 2,5-dimethyl-2,4-hexadiene (DMHD) in solution via a hydrogen-abstraction reaction. The large exoergicity of the reaction between a Cl atom and alkenes (DMBE and DMHD) makes vibrational excitation of the HCl product possible, and we observe the formation of vibrationally excited HCl (v=1) for both reactions. In CCl4, the branching fractions of HCl (v=1), Γ (v=1), for the Cl-atom reactions with DMBE and DMHD are 0.14 and 0.23, respectively, reflecting an increased amount of vibrational excitation in the products of the more exoergic reaction. In addition, Γ (v=1) for both reactions is larger in the solvent CDCl3, being 0.23 and 0.40, as the less viscous solvent apparently dampens the vibrational excitation of the nascent HCl less effectively. The bimolecular reaction rates for the Cl reactions with DMB, DMBE, and DMHD in CCl4 are diffusion limited (having rate constants of 1.5 × 10(10), 3.6 × (10), and 17.5 × 10(10) M(-1)s(-1), respectively). In fact, the bimolecular reaction rate for Cl + DMHD exceeds a typical diffusion-limited reaction rate, implying that the attractive intermolecular forces between a Cl atom and a C=C bond increase the rate of favorable encounters. The two-fold increase in the reaction rate of the Cl + DMBE reaction from that of the Cl + DMB reaction likely reflects the effect of the C=C bond, while both the number of C=C bonds and the molecular geometry likely play a role in the large reaction rate of the Cl + DMHD reaction.
Novel experimental techniques and computational methods have provided new insight into the behavior of reactive intermediates in solution. The results of these studies show that some of the earlier ideas about how reactive intermediates ought to behave in solution were incomplete or even incorrect. This perspective summarizes what the new experimental and computational methods are, and draws attention to the shortcomings that their application has brought to light in previous models. Key areas needing further research are highlighted.
Dynamics of collisions between structured molecular species quickly become complex as molecules become large. Reactions of methane with halogen and oxygen atoms serve as model systems for polyatomic molecule chemical dynamics, and replacing the atomic reagent with a diatomic radical affords further insights. A new, full-dimensional potential energy surface for collisions between CN + CH4 to form HCN + CH3 is developed and then used to perform quasi-classical simulations of the reaction. Coupled-cluster energies serve as input to an empirical valence bonding (EVB) model, which provides an analytical function for the surface. Efficient sampling permits simulating velocity map ion images and exploring dynamics over a range of collision energies. Reaction populates HCN vibration, and energy partitioning changes with collision energy. The reaction cross-section depends on the orientation of the diatomic CN radical. A two-dimensional extension of the cone of acceptance for an atom in the line-of-centers model appropriately describes its reactivity. The simulation results foster future experiments and diatomic extensions to existing atomic models of chemical collisions and reaction dynamics.
The bimolecular reactions that follow ultraviolet photolysis of ICN in acetonitrile solution have been studied using transient absorption spectroscopy on the picosecond timescale. Time-resolved electronic absorption spectroscopy (TEAS) in the ultraviolet and visible spectral regions observes rapid production and loss (with a decay time constant of 0.6 +/- 0.1 ps) of the photolytically generated free CN radicals. Some of these radicals convert to a solvated form which decays with a lifetime of 8.5 +/- 2.1 ps. Time-resolved vibrational absorption spectroscopy (TVAS) reveals that the free and solvated CN-radicals undergo geminate recombination with I atoms to make ICN and INC, H-atom abstraction reactions, and addition reactions to solvent molecules to make C3H3N2 radical species. These radical products have a characteristic absorption band at 2036 cm(-1) that shifts to 2010 cm(-1) when ICN is photolysed in CD3CN. The HCN yield is low, suggesting the addition pathway competes effectively with H-atom abstraction from CH3CN, but the delayed growth of the C3H3N2 radical band is best described by reaction of solvated CN radicals through an unobserved intermediate species. Addition of methanol or tetrahydrofuran as a co-solute promotes H-atom abstraction reactions that produce vibrationally hot HCN. The combination of TEAS and TVAS measurements shows that the rate-limiting process for production of ground-state HCN is vibrational cooling, the rate of which is accelerated by the presence of methanol or tetrahydrofuran.
The role solvent plays in reactions involving frustrated Lewis pairs (FLPs)-for example, the stoichiometric mixture of a bulky Lewis acid and a bulky Lewis base-still remains largely unexplored at the molecular level. For a reaction of the phosphorus/boron FLP and dissolved CO2 gas, first principles (Born-Oppenheimer) molecular dynamics with explicit solvent reveals a hitherto unknown two-step reaction pathway-one that complements the concerted (one-step) mechanism known from the minimum-energy-path calculations. The rationalization of the discovered reaction pathway-that is, the stepwise formation of PC and OB bonds-is that the environment (typical organic solvents) stabilizes an intermediate which results from nucleophilic attack of the phosphorus Lewis base on CO2 . This finding is significant because presently the concerted reaction-path paradigm predominates in the rationalization of FLP reactivity. Herein we point out how to attain experimental proof of our results.
We report a theoretical investigation of the CH4 + Cl hydrogen abstraction reaction in the framework of empirical valence bond (EVB) theory. The main purpose of this study is to benchmark the EVB method against previous experimental and theoretical work. Analytical potential energy surfaces for the reaction have been developed on which quasi-classical trajectory calculations were carried out. The surfaces agree well with ab initio calculations at stationary points along the reaction path and dynamically relevant regions outside the reaction path. The analysis of dynamical data obtained using the EVB method, such as vibrational, rotational, and angular distribution functions, shows that this method compares well to both experimental measurements and higher-level theoretical calculations, with the additional benefit of low computational cost.
Quasi-classical trajectory calculations on a newly constructed and full-dimensionality potential energy surface (PES) examine the dynamics of the reaction of Cl atoms with propene. The PES is an empirical valence bond (EVB) fit to high-level ab initio energies and incorporates deep potential energy wells for the 1-chloropropyl and 2-chloropropyl radicals, a direct H-atom abstraction route to HCl + allyl radical (CH2CHCH2·) products (∆rH298K(o) = -63.1 kJ mol(-1)), and a pathway connecting these regions. In total, 94000 successful reactive trajectories were used to compute distributions of angular scattering and HCl vibrational and rotational level populations. These measures of the reaction dynamics agree satisfactorily with available experimental data. The dominant reaction pathway is direct abstraction of a hydrogen atom from the methyl group of propene occurring in under 500 fs. Fewer than 10% of trajectories follow an addition-elimination route via the two isomeric chloropropyl radicals. Large amplitude motions of the Cl about the propene molecular framework couple the addition intermediates to the direct abstraction pathway. The EVB method provides a good description of the complicated PES for the Cl + propene reaction despite fitting to a limited number of ab initio points, with the further advantage that dynamics specific to certain mechanisms can be studied in isolation by switching off coupling terms in the EVB matrix connecting different regions of the PES.
We describe a parallelized linear-scaling computational framework developed to implement arbitrarily large multi-state empirical valence bond (MS-EVB) calculations within CHARMM and TINKER. Forces are obtained using the Hellmann-Feynman relationship, giving continuous gradients, and good energy conservation. Utilizing multi-dimensional Gaussian coupling elements fit to explicitly correlated coupled cluster theory, we built a 64-state MS-EVB model designed to study the F + CD3CN → DF + CD2CN reaction in CD3CN solvent (recently reported in Dunning et al. [Science 347(6221), 530 (2015)]). This approach allows us to build a reactive potential energy surface whose balanced accuracy and efficiency considerably surpass what we could achieve otherwise. We ran molecular dynamics simulations to examine a range of observables which follow in the wake of the reactive event: energy deposition in the nascent reaction products, vibrational relaxation rates of excited DF in CD3CN solvent, equilibrium power spectra of DF in CD3CN, and time dependent spectral shifts associated with relaxation of the nascent DF. Many of our results are in good agreement with time-resolved experimental observations, providing evidence for the accuracy of our MS-EVB framework in treating both the solute and solute/solvent interactions. The simulations provide additional insight into the dynamics at sub-picosecond time scales that are difficult to resolve experimentally. In particular, the simulations show that (immediately following deuterium abstraction) the nascent DF finds itself in a non-equilibrium regime in two different respects: (1) it is highly vibrationally excited, with ∼23 kcal mol(-1) localized in the stretch and (2) its post-reaction solvation environment, in which it is not yet hydrogen-bonded to CD3CN solvent molecules, is intermediate between the non-interacting gas-phase limit and the solution-phase equilibrium limit. Vibrational relaxation of the nascent DF results in a spectral blue shift, while relaxation of the post-reaction solvation environment results in a red shift. These two competing effects mean that the post-reaction relaxation profile is distinct from what is observed when Franck-Condon vibrational excitation of DF occurs within a microsolvation environment initially at equilibrium. Our conclusions, along with the theoretical and parallel software framework presented in this paper, should be more broadly applicable to a range of complex reactive systems.
Transient electronic and vibrational absorption spectroscopy unravel the mechanisms and dynamics of bimolecular reactions of CN radicals with acetone in deuterated chloroform solutions. The CN radicals are produced by ultrafast ultraviolet photolysis of dissolved ICN. Two reactive forms of CN radicals are distinguished by their electronic absorption bands: "free" (uncomplexed) CN radicals, and "solvated" CN radicals that are complexed with solvent molecules. The lifetimes of the free CN radicals are limited to a few picoseconds following their photolytic production because of geminate recombination to ICN and INC, complexation with CDCl3 molecules, and reaction with acetone. The acetone reaction occurs with a rate coefficient of (8.0 ± 0.5) × 10(10) M(-1) s(-1) and transient vibrational spectra in the C=N and C=O stretching regions reveal that both the nascent HCN and 2-oxo-propyl (CH3C(O)CH2) radical products are vibrationally excited. The rate coefficient for the reaction of solvated CN with acetone is 40 times slower than for free CN, with a rate coefficient of (2.0 ± 0.9) × 10(9) M(-1) s(-1) obtained from the rise in the HCN product v1(C=N stretch) IR absorption band. Evidence is also presented for CN-complexes with acetone that are more strongly bound than the CN-CDCl3 complexes because of CN interactions with the carbonyl group. The rates of reactions of these more strongly associated radicals are slower still.
Generating a reactive force field for a given chemical reaction is turned form a many-months project for experts into a task of a few hours for a non-specialist, by joining the newly developed quantum-mechanically derived force field (QMDFF) and Warshel's time-tested empirical valence bond (EVB) idea. Three first example applications demonstrate that this works not just for simple atom exchange but also for more complicated reactions.
Mechanisms of bimolecular chemical reactions in solution are amenable to study on picosecond timescales, both by transient absorption spectroscopy and by computer simulation. The dynamics of exothermic reactions of CN radicals and of Cl and F atoms with organic solutes in commonly used solvents are contrasted with the corresponding dynamics in the gas phase. Many characteristics of the gas-phase reaction dynamics persist in solution, such as efficient energy release to specific vibrational modes of the products. However, additional complexities associated with the presence of the solvent are open to investigation. These features of liquid-phase reactions include the role of solvent-solute complexes, solvent caging, coupling of the product motions to the solvent bath, thermalization of internally excited reaction products, incipient hydrogen bond formation, and involvement of charge-separated states that arise from proton transfer.
Time-resolved infra-red (IR) absorption spectroscopy is used to follow the production of HF from the reaction of fluorine atoms in liquid acetonitrile (CH3CN). Photolysis of dissolved XeF2 using ∼50 fs duration, 267 nm laser pulses generates F atoms and XeF on prompt (sub-ps) timescales, as verified by broadband transient electronic absorption spectroscopy. The fundamental vibrational band of HF in solution spans more than 400 cm(-1) around the band centre at 3300 cm(-1), and analysis of portions of the time-resolved spectra reveals time constants for the rise in HF absorption that become longer to lower wavenumber. The time constants for growth of 40 cm(-1) wide portions of the IR spectra centred at 3420, 3320 and 3240 cm(-1) are, respectively, 3.04 ± 0.26, 5.48 ± 0.24 and 7.47 ± 0.74 ps (1 SD uncertainties). The shift to lower wavenumber with time that causes these changes to the time constants is attributed to evolution of the micro-solvation environment of HF following the chemical reaction. The initial growth of the high-wavenumber portion of the band may contain a contribution from relaxation of initially vibrationally excited HF, for which a time constant of 2.4 ± 0.2 ps is deduced from IR pump and probe spectroscopy of a dilute HF solution in acetonitrile.
The cycloadditions of tetrazines with cyclopropenes and other strained alkenes have become among the most valuable bioorthogonal reactions. These reactions lead to bicyclic Diels-Alder adducts that spontaneously lose N2. We report quantum mechanical (QM) and quasi-classical molecular dynam-ics (QMD) simulations on a number of these reactions, with special attention to stereoelectronic and dynamic effects on spontaneous N2 loss from these adducts. QM calculations show that the barrier to N2 loss is low, and MD calculations show that the intermediate is frequently bypassed dynamically. There is a large preference for N2 loss anti to the cyclopropane moiety rather than syn from adducts formed from reactions with cyclopropenes. This is explained by the interactions of the Walsh orbit-als of the cyclopropane group with the breaking C-N bonds in N2 loss. Dynamical effects opposing the QM preferences have also been discovered involving the coupling of vibrations associated with the formation of the new C-C bonds in the cycloaddition step, and those of the breaking C-N bonds during subsequent N2 loss. This dynamic matching leads to pronounced non-statistical effects on the lifetimes of Diels-Alder intermediates. An unusual oscillatory behavior of the rate of decay of the intermediate has been identified and attributed to specific vibrational coupling.
Transient electronic absorption measurements with 1 ps time resolution follow XeF2 photoproducts in acetonitrile and chlorinated solvents. Ultraviolet light near 266 nm promptly breaks one Xe-F bond, and probe light covering 320-700 nm monitors the products. Some of the cleaved F atoms remain in close proximity to an XeF fragment and perturb the electronic states of XeF. The time evolution of a perturbed spectral feature is used to monitor the FXe-F complex population, which decays in less than 5 ps. Decay can occur through geminate recombination, diffusive separation or reaction of the complex with the solvent.
4-(4-Nitrobenzylideneamine)phenol was used in two strategies allowing the highly selective detection of F and CN. Firstly, the compound in acetonitrile acts as a chromogenic chemosensor based on the idea that more basic anions cause its deprotonation (colorless solution), generating a colored solution containing phenolate. The discrimination of CN over F was obtained by adding 1.4% water to acetonitrile: water preferentially solvates F, leaving the CN free to deprotonate the compound. Another strategy involved an assay comprised of the competition between phenolate dye and the analyte for calix[4]pyrrole in acetonitrile, a receptor highly selective for F. Phenolate and calix[4]pyrrole form a hydrogen-bonded complex, which changes the color of the medium. On the addition of various anions, only F was able to restore the original color corresponding to phenolate in solution due to the fact that the anion dislodges phenolate from the complexation site.
The prototypical F + H2 → HF + H reaction possesses a substantial energetic barrier (~800 K) and might therefore be expected to slow to a negligible rate at low temperatures. It is, however, the only source of interstellar HF, which has been detected in a wide range of cold (10-100 K) environments. In fact, the reaction does take place efficiently at low temperatures due to quantum-mechanical tunnelling. Rate constant measurements at such temperatures have essentially been limited to fast barrierless reactions, such as those between two radicals. Using uniform supersonic hydrogen flows we can now report direct experimental measurements of the rate of this reaction down to a temperature of 11 K, in remarkable agreement with state-of-the-art quantum reactive scattering calculations. The results will allow a stronger link to be made between observations of interstellar HF and the abundance of the most common interstellar molecule, H2, and hence a more accurate estimation of the total mass of astronomical objects.
Experimental limitations in vibrational excitation efficiency have previously hindered investigation of how vibrational energy
might mediate the role of dynamical resonances in bimolecular reactions. Here, we report on a high-resolution crossed-molecular-beam
experiment on the vibrationally excited HD(v = 1) + F → HF + D reaction, in which two broad peaks for backward-scattered HF(v′ = 2 and 3) products clearly emerge at collision energies of 0.21 kilocalories per mole (kcal/mol) and 0.62 kcal/mol from
differential cross sections measured over a range of energies. We attribute these features to excited Feshbach resonances
trapped in the peculiar HF(v′ = 4)–D vibrationally adiabatic potential in the postbarrier region. Quantum dynamics calculations on a highly accurate potential
energy surface show that these resonance states correlate to the HD(v′ = 1) state in the entrance channel and therefore can only be accessed by the vibrationally excited HD reagent.
Explicitly correlated MP2-F12 and CCSD(T)-F12 methods with orbital-pair-specific Slater-type geminals are proposed. The fixed amplitude ansatz of Ten-no is used, and different exponents of the Slater geminal functions can be chosen for core–core, core–valence, and valence–valence pairs. This takes care of the different sizes of the correlation hole and leads to improved results when inner-shell orbitals are correlated. The complications and the extra computational cost as compared to corresponding calculations with a single geminal are minor. The improved accuracy of the method is demonstrated for spectroscopic properties of Br2, As2, Ga2, Cu2, GaCl, CuCl, and CuBr, where the d-orbitals are treated as core.
Transient, broadband infra-red absorption spectroscopy with picosecond time resolution has been used to study the dynamics of reactions of CN radicals with tetrahydrofuran (THF) and d(8)-THF in liquid solutions ranging from neat THF to 0.5 M THF in chlorinated solvents (CDCl(3) and CD(2)Cl(2)). HCN and DCN products were monitored via their v(1) (C≡N stretching) and v(3) (C-H(D) stretching) vibrational absorption bands. Transient spectral features indicate formation of vibrationally excited HCN and DCN, and the onsets of absorption via the fundamental bands of HCN and DCN show short (5-15 ps) delays consistent with vibrational relaxation within the nascent reaction products. This interpretation is confirmed by non-equilibrium molecular dynamics simulations employing a newly derived analytic potential energy surface for the reaction in explicit THF solvent. The rate coefficient for reactive formation of HCN (as determined from measurements on both the 1(1)(0) and 3(1)(0) fundamental bands) decreases with increasing dilution of the THF in CDCl(3) or CD(2)Cl(2), showing pseudo-first order kinetic behaviour for THF concentrations in the range 0.5-4.5 M, and a bimolecular rate coefficient of (1.57 ± 0.12) × 10(10) M(-1) s(-1) is derived. Simultaneous analysis of time-dependent HCN 1(1)(0) and 3(1)(0) band intensities following reaction of CN with THF (3.0 M) in CD(2)Cl(2) suggests that C-H stretching mode excitation is favoured, and this deduction is supported by the computer simulations. The results extend our recent demonstration of nascent vibrational excitation of the products of bimolecular reactions in liquid solution to a different, and more strongly interacting class of organic solvents. They serve to reinforce the finding that dynamics (and thus the topology of the reactive potential energy surface) play an important role in determining the nascent product state distributions in condensed phase reactions.
The dynamics of reactions of CN radicals with cyclohexane, d(12)-cyclohexane, and tetramethylsilane have been studied in solutions of chloroform, dichloromethane, and the deuterated variants of these solvents using ultraviolet photolysis of ICN to initiate a reaction. The H(D)-atom abstraction reactions produce HCN (DCN) that is probed in absorption with sub-picosecond time resolution using ∼500 cm(-1) bandwidth infrared (IR) pulses in the spectral regions corresponding to C-H (or C-D) and C≡N stretching mode fundamental and hot bands. Equivalent IR spectra were obtained for the reactions of CN radicals with the pure solvents. In all cases, the reaction products are formed at early times with a strong propensity for vibrational excitation of the C-H (or C-D) stretching (v(3)) and H-C-N (D-C-N) bending (v(2)) modes, and for DCN products there is also evidence of vibrational excitation of the v(1) mode, which involves stretching of the C≡N bond. The vibrationally excited products relax to the ground vibrational level of HCN (DCN) with time constants of ∼130-270 ps (depending on molecule and solvent), and the majority of the HCN (DCN) in this ground level is formed by vibrational relaxation, instead of directly from the chemical reaction. The time-dependence of reactive production of HCN (DCN) and vibrational relaxation is analysed using a vibrationally quantum-state specific kinetic model. The experimental outcomes are indicative of dynamics of exothermic reactions over an energy surface with an early transition state. Although the presence of the chlorinated solvent may reduce the extent of vibrational excitation of the nascent products, the early-time chemical reaction dynamics in these liquid solvents are deduced to be very similar to those for isolated collisions in the gas phase. The transient IR spectra show additional spectroscopic absorption features centered at 2037 cm(-1) and 2065 cm(-1) (in CHCl(3)) that are assigned, respectively, to CN-solvent complexes and recombination of I atoms with CN radicals to form INC molecules. These products build up rapidly, with respective time constants of 8-26 and 11-22 ps. A further, slower rise in the INC absorption signal (with time constant >500 ps) is attributed to diffusive recombination after escape from the initial solvent cage and accounts for more than 2/3 of the observed INC.
Solvent collisions can often mask initial disposition of energy to the products of solution-phase chemical reactions. Here,
we show with transient infrared absorption spectra obtained with picosecond time resolution that the nascent HCN products
of reaction of CN radicals with cyclohexane in chlorinated organic solvents exhibit preferential excitation of one quantum
of the C-H stretching mode and up to two quanta of the bending mode. On time scales of approximately 100 to 300 picoseconds,
the HCN products undergo relaxation to the vibrational ground state by coupling to the solvent bath. Comparison with reactions
of CN radicals with alkanes in the gas phase, known to produce HCN with greater C-H stretch and bending mode excitation (up
to two and approximately six quanta, respectively), indicates partial damping of the nascent product vibrational motion by
the solvent. The transient infrared spectra therefore probe solvent-induced modifications to the reaction free energy surface
and chemical dynamics.
Partial View
Skilled billiard players can easily predict how spinning of one ball will affect the trajectory of the second ball it strikes in a collision. In principle, quantum mechanics can be used to predict the analogous impact of the angular momentum of reagents on the outcome of a chemical reaction. In practice, however, observation of most chemical reactions—even in the confines of a molecular beam apparatus—encompasses a vast number of collisions over multiple angular momentum distributions. Dong et al. (p. 1501 ; see the Perspective by Althorpe ) have honed their spectroscopic resolution sufficiently to distinguish the impact of subtle angular momentum variations on the reactivity of fluorine with hydrogen atoms. Their data agree with theory and reveal oscillating peaks in reaction probability, termed partial wave resonances.
CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. It has been developed over the last three decades with a primary focus on molecules of biological interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals, and membrane environments. For the study of such systems, the program provides a large suite of computational tools that include numerous conformational and path sampling methods, free energy estimators, molecular minimization, dynamics, and analysis techniques, and model-building capabilities. The CHARMM program is applicable to problems involving a much broader class of many-particle systems. Calculations with CHARMM can be performed using a number of different energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potential energy functions with explicit solvent and various boundary conditions, to implicit solvent and membrane models. The program has been ported to numerous platforms in both serial and parallel architectures. This article provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM article in 1983.
Exothermic chemical reaction dynamics at the gas-liquid interface have been investigated by colliding a supersonic beam of F atoms [E(com)=0.7(3) kcalmol] with a continuously refreshed liquid hydrocarbon (squalane) surface under high vacuum conditions. Absolute HF(v,J) product densities are determined by infrared laser absorption spectroscopy, with velocity distributions along the probe axis derived from high resolution Dopplerimetry. Nascent HF(v<or=3) products are formed in a highly nonequilibrium (inverted) vibrational distribution [E(vib)=13.2(2) kcalmol], reflecting insufficient time for complete thermal accommodation with the surface prior to desorption. Colder, but still non-Boltzmann, rotational state populations [E(rot)=1.0(1) kcalmol] indicate that some fraction of molecules directly scatter into the gas phase without rotationally equilibrating with the surface. Nascent HF also recoils from the liquid surface with excess translational energy, resulting in Doppler broadened linewidths that increase systematically with internal HF excitation. The data are consistent with microscopic branching in HF-surface dynamics following the reactive event, with (i) a direct reactive scattering fraction of newly formed product molecules leaving the surface promptly and (ii) a trapping desorption fraction that accommodates rotationally (though still not vibrationally) with the bulk liquid. Comparison with analogous gas phase F+hydrocarbon processes reveals that the liquid acts as a partial "heat sink" for vibrational energy flow on the time scale of the chemical reaction event.
Reaction resonances, or transiently stabilized transition-state structures, have proven highly challenging to capture experimentally.
Here, we used the highly sensitive H atom Rydberg tagging time-of-flight method to conduct a crossed molecular beam scattering
study of the F + H2 → HF + H reaction with full quantum-state resolution. Pronounced forward-scattered HF products in the v′ = 2 vibrational state were clearly observed at a collision energy of 0.52 kcal/mol; this was attributed to both the ground
and the first excited Feshbach resonances trapped in the peculiar HF(v′ = 3)-H′ vibrationally adiabatic potential, with substantial enhancement by constructive interference between the two resonances.
The reaction of F with H2 and its isotopomers is the paradigm for an exothermic triatomic abstraction reaction. In a crossed-beam scattering experiment, we determined relative integral and differential cross sections for reaction of the ground F(2P(3/2)) and excited F*(2P(1/2)) spin-orbit states with D2 for collision energies of 0.25 to 1.2 kilocalorie/mole. At the lowest collision energy, F* is approximately 1.6 times more reactive than F, although reaction of F* is forbidden within the Born-Oppenheimer (BO) approximation. As the collision energy increases, the BO-allowed reaction rapidly dominates. We found excellent agreement between multistate, quantum reactive scattering calculations and both the measured energy dependence of the F*/F reactivity ratio and the differential cross sections. This agreement confirms the fundamental understanding of the factors controlling electronic nonadiabaticity in abstraction reactions.
The transition state region of the F + H(2) reaction has been studied by photoelectron spectroscopy of FH(2)(-). New para and normal FH(2)(-)photoelectron spectra have been measured in refined experiments and are compared here with exact three-dimensional quantum reactive scattering simulations that use an accurate new ab initio potential energy surface for F + H(2). The detailed agreement that is obtained between this fully ab initio theory and experiment is unprecedented for the F + H(2) reaction and suggests that the transition state region of the F + H(2) potential energy surface has finally been understood quantitatively.
The objective in this work has been one which I have shared with the two other 1986 Nobel lecturers in chemistry. D.R. Herschbach and Y.T. Lee, as well as with a wide group of colleagues and co-workers who have been responsible for bringing this field to its current state. That state is summarized in the title; we now have some concepts relevant to the motions of atoms and molecules in simple reactions, and some examples of the application of these concepts. We are, however, richer in vocabulary than in literature. The great epics of reaction dynamics remain to be written. I shall confine myself to some simple stories.
We describe a parallel linear-scaling computational framework developed to
implement arbitrarily large multi-state empirical valence bond (MS-EVB)
calculations within CHARMM. Forces are obtained using the Hellman-Feynmann
relationship, giving continuous gradients, and excellent energy conservation.
Utilizing multi-dimensional Gaussian coupling elements fit to CCSD(T)-F12
electronic structure theory, we built a 64-state MS-EVB model designed to study
the F + CD3CN -> DF + CD2CN reaction in CD3CN solvent. This approach allows us
to build a reactive potential energy surface (PES) whose balanced accuracy and
efficiency considerably surpass what we could achieve otherwise. We use our PES
to run MD simulations, and examine a range of transient observables which
follow in the wake of reaction, including transient spectra of the DF
vibrational band, time dependent profiles of vibrationally excited DF in CD3CN
solvent, and relaxation rates for energy flow from DF into the solvent, all of
which agree well with experimental observations. Immediately following
deuterium abstraction, the nascent DF is in a non-equilibrium regime in two
different respects: (1) it is highly excited, with ~23 kcal mol-1 localized in
the stretch; and (2) not yet Hydrogen bonded to the CD3CN solvent, its
microsolvation environment is intermediate between the non-interacting
gas-phase limit and the solution-phase equilibrium limit. Vibrational
relaxation of the nascent DF results in a spectral blue shift, while relaxation
of its microsolvation environment results in a red shift. These two competing
effects result in a post-reaction relaxation profile distinct from that
observed when DF vibration excitation occurs within an equilibrium
microsolvation environment. The parallel software framework presented in this
paper should be more broadly applicable to a range of complex reactive systems.
Extracting meaningful kinetic traces from time-resolved absorption spectra is a non-trivial task, particularly for solution phase spectra where solvent interactions can substantially broaden and shift the transition frequencies. Typically, each spectrum is composed of signal from a number of molecular species (e.g., excited states, intermediate complexes, product species) with overlapping spectral features. Additionally, the profiles of these spectral features may evolve in time (i.e., signal nonlinearity), further complicating the decomposition process. Here, we present a new program for decomposing mixed transient spectra into their individual component spectra and extracting the corresponding kinetic traces: KOALA (Kinetics Observed After Light Absorption). The software combines spectral target analysis with brute-force linear least squares fitting, which is computationally efficient because of the small nonlinear parameter space of most spectral features. Within, we demonstrate the application of KOALA to two sets of experimental transient absorption spectra with multiple mixed spectral components. Although designed for decomposing solution-phase transient absorption data, KOALA may in principle be applied to any time-evolving spectra with multiple components.
Bimolecular reactions in the gas phase exhibit rich and varied dynamical behaviour, but whether a profound knowledge of the mechanisms of isolated reactive collisions can usefully inform our understanding of reactions in liquid solutions remains an open question. The fluctuating environment in a liquid may significantly alter the motions of the reacting particles and the flow of energy into the reaction products after a transition state has been crossed. Recent experimental and computational studies of exothermic reactions of CN radicals with organic molecules indicate that many features of the gas-phase dynamics are retained in solution. However, observed differences may also provide information on the ways in which a solvent modifies fundamental chemical mechanisms. This perspective examines progress in the use of time-resolved infra-red spectroscopy to study reaction dynamics in liquids, discusses how existing theories can guide the interpretation of experimental data, and suggests future challenges for this field of research.
The study of gas-phase reaction dynamics has advanced to a point where four-atom reactions are the proving ground for detailed comparisons between experiment and theory. Here, a combined experimental and theoretical study of the dissociation dynamics of the tetra-atomic FH2O system is presented, providing snapshots of the F + H2O → HF + OH reaction. Photoelectron-photofragment coincidence measurements of the dissociative photodetachment (DPD) of the F (H2O) anion revealed various dissociation pathways along different electronic states. A distinct photoelectron spectrum of stable FH-OH complexes was also measured and attributed to long-lived Feshbach resonances. Comparison to full-dimensional quantum calculations confirms the sensitivity of the DPD measurements to the subtle dynamics on the low-lying FH2O potential energy surfaces over a wide range of nuclear configurations and energies.
Molecular reaction dynamics is the study of chemical and physical transformations of matter at the molecular level. The understanding of how chemical reactions occur and how to control them is fundamental to chemists and interdisciplinary areas such as materials and nanoscience, rational drug design, environmental and astrochemistry. This book provides a thorough foundation to this area. The first half is introductory, detailing experimental techniques for initiating and probing reaction dynamics and the essential insights that have been gained. The second part explores key areas including photoselective chemistry, stereochemistry, chemical reactions in real time and chemical reaction dynamics in solutions and interfaces. Typical of the new challenges are molecular machines, enzyme action and molecular control. With problem sets included, this book is suitable for advanced undergraduate and graduate students, as well as being supplementary to chemical kinetics, physical chemistry, biophysics and materials science courses, and as a primer for practising scientists.
The reaction of atomic fluorine with dichloromethane has been studied by the diffusion cloud in a flow technique. Fluorine atoms were generated through F2 dissociation in a high-frequency discharge. The reaction products were detected mass spectrometrically, applying the technique of focusing the paramagnetic component of the molecular beam in an inhomogeneous magnetic field to detect radical species. Cl atoms and CHCl2 and CF3 free radicals have been identified among the reaction products. The initial step was shown to be hydrogen atom abstraction. The room temperature rate constant of this reaction was found to be k0 = (1.51 ± 0.28) X 10−11 cm3/s. The rate constant of the secondary reaction of fluorine atoms with dichloromethyl radicals, which is suggested to produce mainly HCl, was evaluated as 3 X 10−10 cm3/s.
Transient absorption spectroscopy is used to follow the reactive intermediates involved in the first steps in the photochemistry initiated by ultraviolet (266-nm wavelength) excitation of solutions of 1,5-hexadiene, isoprene and 2,3-dimethylbut-2-ene in carbon tetrachloride or chloroform. Ultraviolet and visible bands centred close to 330 nm and 500 nm in both solvents are assigned respectively to a charge transfer band of Cl-solvent complexes, and the strong absorption band of a higher energy isomeric form of the solvent molecules (iso-CCl3-Cl or iso-CHCl2-Cl). These assignments are supported by calculations of electronic excitation energies. The isomeric forms have significant contributions to their structures from charge-separated resonance forms, and offer a re-interpretation of previous assignments of the carriers of the visible bands that were based on pulsed radiolysis experiments. Kinetic analysis demonstrates that the isomeric forms are produced via the Cl-solvent complexes. Addition of the unsaturated hydrocarbons provides a reactive loss channel for the Cl-solvent complexes, and reaction radii and bimolecular rate coefficients are derived from analysis using a Smoluchowski theory model. For reactions of Cl with 1,5-hexadiene, isoprene and 2,3-dimethylbut-2-ene in CCl4, rate coefficients at 294 K are, respectively, (8.6 ± 0.8) × 10(9) M(-1) s(-1), (9.5 ± 1.6) × 10(9) M(-1) s(-1) and (1.7 ± 0.1) × 10(10) M(-1) s(-1). The larger reaction radius and rate coefficient for 2,3-dimethylbut-2-ene are interpreted as evidence for an H-atom abstraction channel that competes effectively with the channel involving addition of a Cl atom to a C=C bond. However, the addition mechanism appears to dominate the reactions of 1,5-hexadiene and isoprene. Two-photon excited CCl4 or CHCl3 can also ionize the diene or alkene solute.
The solvation dynamics of acetonitrile were characterized by a time resolved fluorescence shift measurement determined via the fluorescence upconversion technique. The solvation response is clearly two part in character. The fast initial relaxation accounts for ∼80% of the amplitude and is well fit by a Gaussian of 120 fs FWHM, giving a decay time of 70 fs. The slower tail is exponential with a decay time of ∼200 fs. Comparison of the results to molecular dynamics simulations performed by Maroncelli [J. Chem. Phys. 94, 2085 (1991)] reveal the fast initial part of the solvent response arises from small amplitude inertial rotational motion of molecules in the first solvation shell. The implications of a large amplitude, rapid inertial Gaussian component in the solvent response for theoretical descriptions of chemical reaction dynamics in solution are discussed.
Co-condensation of dilute Ar/HF and Ar/H2O samples at 12 K produces a number of sharp new infrared absorptions. The major species, which exhibits a strong 3554.7 cm−1 band and two quartets beginning at 753.1 and 635.6 cm−1, is identified as H2O– –HF. Isotopic substitution in the base submolecule changes the splitting in the latter multiplets and provides evidence for inversion doubling of the H–F librational modes in the H2O– –HF complex. The reverse complex HF– –HOH, identified at 3915.5 cm−1, exhibits a stronger interaction when HOH is replaced by DOD. Two H–F stretching fundamentals, which show small D2O shifts, increased markedly on sample warming and are assigned to the 1:2 complex H2O– –HF– –HF with an open structure.
Systematic measurements of the IR spectra of solutions of HF in N,N-dimethylformamide, acetone, and acetonitrile have been carried out for the first time in a wide range of variation of the molar ratio of the components (from 0:1 to 7:1, 8.9:1, and 10:1, respectively). This has not only scientific significance but also important applied significance. The absorption features of each of the binary liquid systems studied here and the spectral attributes of the heterocomplexes formed in it are analyzed. It is established that the molecular associates (HF)ns(CH3)2NCHO and (HF)ns(CH3)2CO contain the same large structural fragment the appearance of which is typical of solutions of HF in organic solvents.
A simple intermolecular potential function has been devised to yield good thermodynamic and structural results for liquid acetonitrile The function was tested in Monte Carlo statistical mechanics simulations for the liquid at temperatures of 25°C and 70°C at 1 atm. The average errors in the computed densities and heats of vaporization are 1–2 per cent. The structural results are presented by means of radial distribution functions and dipole-dipole correlation functions, and compared with prior findings. In addition, the importance of the electrostatic interactions in determining the liquid's structure is illustrated by the results of a simulation at 25°C with the partial charges set to zero.
An infrared spectral study of hydrogen bonding phenomena has been carried out on solutions of anhydrous HF (and in some cases DF) in the following solvents: diethyl ether, tetrahydrofuran, dioxane, ethanol, ethanol-d, trifluoroethanol, acetone, acetonitrile, diethyl sulfide, phenol, and nitrobenzene. In general three new broad regions of absorption appear centering around (a) 3000 cm-1, (b) 1800 cm-1, and (c) 800 cm-1, which are attributed respectively to (a) the stretching vibration of HF in a molecular complex, (b) the HF2- ion, (c) a hydrogen vibration in a molecular complex, probably the out-of-plane vibration in the X-H-F bond. There are also observed in many of the spectra new, sharp peaks which appear to be disturbances of the peaks due to the functional groups. These are attributed to the formation of molecular complexes.
Photodissociation of XeF2 with synchrotron light pulses (0.3 ns duration) has been used as the source of the XeF(B, C, and D) excited states. The time‐resolved profiles of the intensity of the resulting fluorescence have been recorded and partially analyzed. Most of the measurements were made in the strong XeF2 absorption band between 145 and 175 nm. The absorption cross section was redetermined out to 210 nm, with a maximum value of (5.9±0.5)×10−17 cm2 at 158 nm. By comparison with O(1S) signals from N2O photodissociation, quantum yields for XeF B, C, and D state production were determined. Radiative lifetimes of (14±1) and (100±10) ns were found for the B and C states. Rate coefficients for quenching by XeF2 are reported as are those for converting B to C by collision with Ne, Ar, and N2, along with upper limits for quenching of the C state by these gases.
The dynamics of the F+H2 reaction have been investigated in a high resolution crossed molecular beam study. Differential cross sections and kinetic energy distributions were obtained for each HF vibrational state. The v=1 and v=2 states were predominantly backward scattered, but substantial forward scattering was observed for HF (v=3) over the range of collision energies accessible in our apparatus, from 0.7 to 3.4 kcal/mol. The results strongly suggest that dynamical resonances play a significant role in the reaction dynamics of F+H2 and that resonance effects are most prominent in the v=3 product channel. Quantal reactive scattering calculations on F+H2 predict that the v=2 channel should be most strongly affected by resonances. This discrepancy is attributed to inadequacies in the potential energy surface used in the calculations, and several modifications to the surface are proposed based on the experimental results. Other features of the reaction are also discussed, including the integrated partial cross sections, the effect of H2 rotation, and the reactivity of F(2P1/2).
Molecular dynamics simulations are used to examine two key aspects of recent ultrafast infrared experiments on liquid water dynamics. It is found that the relation between the OH stretch frequency and the length of the hydrogen bond in which the OH is involved, currently assumed to be one-to-one, is instead characterized by considerable dispersion and that the time scale currently interpreted in terms of a stochastic modulation by the surrounding solvent of a highly frictionally damped hydrogen bond system is shown to be governed by hydrogen bond-breaking and -making dynamics, whereas the motion of an intact hydrogen-bonded complex is underdamped in character.
A simple and reliable empirical valence bond (EVB) approach for comparing potential surfaces of reaction in solution and in enzymes is developed. The method uses the valence bond concept of ionic-covalent resonance to obtain a Hamiltonian for the isolated molecule and then evaluates the Hamiltonian for the reaction in solution by adding the calculated solvation energies to the diagonal matrix elements of the ionic resonance forms. The resulting potential surface is then calibrated by using pKa measurements and other information about the reaction in solution. The calibrated potential surface provides a simple tool for comparing the activation energy of a reaction in solution with that in an enzyme by replacing the solvation energies of the ionic resonance forms by their interactions with the enzyme active site. The EVB method is illustrated by calculations of typical solution reactions including an ionic bond-breaking reaction, a proton-transfer reaction, and a general-acid catalysis reaction. The application of the EVB method to studies of enzymic reactions is demonstrated by calculating the potential surface for the rate-limiting step of the catalytic reaction of lysozyme and comparing the calculated activation energy to that of the reaction in solution.
Laser flash photolysis of xenon difluoride in 1,1,2-trichlorotrifluoroethane (Freon-113) yields atomic fluorine, which can be detected via its loose complex with the solvent. This complex, with an absorption maximum at 320 nm, has a lifetime at ambient temperature of about 200 ns and is quenched with rate constants near the diffusion controlled limit by most substrates. In neat hexafluorobenzene as solvent, the heptafluorocyclohexadienyl radical is observed. In addition to the fluorine atom, a second species formed with lambda(max) = 345 nm is assigned to be the XeF radical, with a lifetime of ca. 25 mu s in acetonitrile at ambient temperature.
The cocondensation reaction between acetonitrile and HF produced a linear 1:1 complex in solid argon at 12 K of the form CH3CN⋯HF. Warming the matrix above 20 K allowed diffusion of HF and produced 2:1 and 3:1 complexes CH3CN⋯(H-F)2 and CH3CN⋯(H-F)3. The HF submolecule stretching frequency of 1:1 complex was observed at 3482.8 cm-1, while the HF librational mode was centered at 680.5 cm-1, with an overtone at 1259.4 cm-1. The acetonitrile submolecule in the 1:1 complex showed a perturbed C-C≡N stretch at 938.8 cm-1, and a Fermi resonance doublet at 2315.5 and 2290.4 cm-1 for the perturbed v2 and v3 + v4 modes. The analogous 1:1 and 2:1 complexes were observed for the HCl and acetonitrile cocondensation reaction. The HCl submolecule frequency in the 1:1 complex was observed at 2662 cm-1 and the HCl libration was centered at 414 cm-1 with an overtone at 736 cm-1.
Time-resolved emission measurements of the solute coumarin 153 (C153) are used to probe the time dependence of solvation in 24 common solvents at room temperature. Significant improvements in experimental time resolution ({approx}100 fs instrument response) as well as corresponding improvements in analysis methods provide confidence that all of the spectral evolution (including both the inertial and the diffusive parts of the response) are observed in these measurements. Extensive data concerning the steady-state solvatochromism of C153, coupled to an examination of the effects of vibrational relaxation, further demonstrate that the spectral dynamics being observed accurately monitor the dynamics of nonspecific solvation. Comparisons to theoretical predictions show that models based on the dielectric response of the pure solvent provide a semiquantitative understanding of the dynamics observed. 156 refs., 26 figs., 5 tabs.
A number of methods proposed in the past few years have been aimed at accelerating the sampling of rare events in molecular dynamics simulations. We recently introduced a method called Boxed Molecular Dynamics (BXD) for accelerating the calculation of thermodynamics and kinetics ( J. Phys. Chem. B 2009, 113, 16603−16611). BXD relies upon confining the system in a series of adjacent “boxes” by inverting the projection of the system velocities along the reaction coordinate. The potential of mean force along the reaction coordinate is obtained from the mean first passage times (MFPTs) for exchange between neighboring boxes, simultaneously providing both kinetics and thermodynamics. In this paper, we investigate BXD in the context of its natural relation to a kinetic master equation and show that the BXD first passage times (FPTs) include different time scales—a fast short time decay due to correlated dynamical motion and slower long time decay arising from phase space diffusion. Correcting the FPTs to remove the fast correlated motion yields accurate thermodynamics and master equation kinetics. We also discuss interrelations between BXD and a recently described Markovian milestoning technique and use a simple application to show that, despite each method producing distinct nonstatistical effects on time scales on the order of dynamical decorrelation, both yield similar long-time kinetics.
A method of determination of the composition of heterocomplexes formed in a binary system is proposed that is based on the
analysis of the concentration dependence of the IR spectr of the system and is adequate to the law of mass action. The study
of solutions of HF in dimethylformamide, acetone, and acetonitrile with this method showed that molecular associates with
the soichiometric ratios 4:1, 6:1, and 4:1, respectively, form in the solutions. The correctness of the method proposed is
demonstrated by comparison of these results with analogous data obtained from the analysis of the concentration dependences
of the excessive density of solutions HF-(CH3)2NCHO, HF-(CH3)2CO, and HF-CH3CN.
The HF product state distributions from F+CH4(CD4), C2H6, CH4-nCln series, CH3F, CD3OH, CH3OD and H2S have been studied by the infrared chemiluminiscence technique in two different laboratories with two types of reactors: a fast-flow system with = 1 Torr of Ar buffer gas and a low-pressure, cold-wall system (usually called the arrested-relaxation method). The same HF Einstein coefficients were used in both laboratories to convert intensities to populations and emphasis is placed upon evaluation of the reliability of the resulting HF vibrational-rotational distributions. Arrested-relaxation data from Frankfurt for the F+D2O reaction, which populates DF(υ⩽2) are also presented. Well-behaved data were obtained for CH4(CD4), C2H6 and H2S in both laboratories and in both reactors. For the CH4-nCln series the HF(υ, J) distributions depend upon the design of the arrested-relaxation vessel and upon the operating conditions, especially flow rates. The lowest-pressure arrested-relaxation distributions strongly disagree with flow-reactor results. It is argued that the flowing-afterglow data provide initial HF(υ) distributions for 300 K Boltzmann reaction conditions. The AR data are compared to this work. One possibility for explaining the arrested-relaxation results, which fits many of the diagnostic tests, is the existence of two reaction channels: one directly gives HF, the second involves formation of adducts with F atoms, which subsequently react to give HF in low vibrational levels. For CH3F the discrepancy between flow-reactor and arrested-relaxation results most likely stems from an interfering secondary reaction. Unusually rapid HF(υ)/DF(υ) vibrational relaxation is observed for methanol. However, initial HF(υ)/DF(υ) vibrational distributions in the flow reactor were obtained. Arguments based on surprisal analysis suggest that the F+H2O and D2O systems yield inverted HF(υ)/DF(υ) primary distributions.
In the reactive systems F + CH3CN, F + CH3NC, F + CH3SCH3 and F + CH3SSCH3 infrared emission spectra were recorded from HF in the fundamental region under relaxation-free conditions. The reported vibrational distributions are for F+CH3CN:Nυ=1:Nυ=2:Nυ=3=0.38:0.42:0.20 for F+CH3NC:Nυ=1:Nυ=2:Nυ=3:Nυ=4:=0.46:0.32:0.17:0.05;for F+CH3SCH3:Nυ=1:Nυ=2:Nυ=3:=0.36:0.39:0.25;for F+CH3SSCH3:Nυ=1:Nυ=2:Nυ=3:Nυ=4:=0.43:0.35:0.19:0.04 Rotational distributions are drawn up and discussed for F + CH3CN and F + CH3SCH3. There is strong evidence for the existence of two microscopic channels in all four systems investigated.
This article introduces MMFF94, the initial published version of the Merck molecular force field (MMFF). It describes the objectives set for MMFF, the form it takes, and the range of systems to which it applies. This study also outlines the methodology employed in parameterizing MMFF94 and summarizes its performance in reproducing computational and experimental data. Though similar to MM3 in some respects, MMFF94 differs in ways intended to facilitate application to condensed-phase processes in molecular-dynamics simulations. Indeed, MMFF94 seeks to achieve MM3-like accuracy for small molecules in a combined “organic/protein” force field that is equally applicable to proteins and other systems of biological significance. A second distinguishing feature is that the core portion of MMFF94 has primarily been derived from high-quality computational data—ca. 500 molecular structures optimized at the HF/6-31G* level, 475 structures optimized at the MP2/6-31G* level, 380 MP2/6-31G* structures evaluated at a defined approximation to the MP4SDQ/TZP level, and 1450 structures partly derived from MP2/6-31G* geometries and evaluated at the MP2/TZP level. A third distinguishing feature is that MMFF94 has been parameterized for a wide variety of chemical systems of interest to organic and medicial chemists, including many that feature frequently occurring combinations of functional groups for which little, if any, useful experimental data are available. The methodology used in parameterizing MMFF94 represents a fourth distinguishing feature. Rather than using the common “functional group” approach, nearly all MMFF parameters have been determined in a mutually consistent fashion from the full set of available computational data. MMFF94 reproduces the computational data used in its parameterization very well. In addition, MMFF94 reproduces experimental bond lengths (0.014 Å root mean square [rms]), bond angles (1.2° rms), vibrational frequencies (61 cm⁻¹ rms), conformational energies (0.38 kcal/mol/rms), and rotational barriers (0.39 kcal/mol rms) very nearly as well as does MM3 for comparable systems. MMFF94 also describes intermolecular interactions in hydrogen-bonded systems in a way that closely parallels that given by the highly regarded OPLS force field. © 1996 John Wiley & Sons, Inc.
Vibrational energy flow into reactants, and out of products, plays a key role in chemical reactivity, so understanding the microscopic detail of the pathways and rates associated with this phenomenon is of considerable interest. Here, we use molecular dynamics simulations to model the vibrational relaxation that occurs during the reaction CN + c-C(6)H(12) → HCN + c-C(6)H(11) in CH(2)Cl(2), which produces vibrationally hot HCN. The calculations reproduce the observed energy distribution, and show that HCN relaxation follows multiple timescales. Initial rapid decay occurs through energy transfer to the cyclohexyl co-product within the solvent cage, and slower relaxation follows once the products diffuse apart. Re-analysis of the ultrafast experimental data also provides evidence for the dual timescales. These results, which represent a formal violation of conventional linear response theory, provide a detailed picture of the interplay between fluctuations in organic solvent structure and thermal solution-phase chemistry.
In this work, we report the first theoretical studies of post-transition state dynamics for reaction of CN with polyatomic organic species. Using electronic structure theory, a newly developed analytic reactive PES, a recently implemented rare-event acceleration algorithm, and a normal mode projection scheme, we carried out and analyzed quasi-classical and classical non-equilibrium molecular dynamics simulations of the reactions CN + propane (R1) and CN + cyclohexane (R2). For (R2), we carried out simulations in both the gas phase and in a CH(2)Cl(2) solvent. Analysis of the results suggests that the solvent perturbations to the (R2) reactive free energy surface are small, leading to product energy partitioning in the solvent that is similar to the gas phase. The distribution of molecular geometries at the respective gas and solution phase variational association transition states is very similar, leading to nascent HCN which is vibrationally excited in both its CH stretching and HCN bending coordinates. This study highlights the fact that significant non-equilibrium energy distributions may follow in the wake of solution phase bimolecular reactions, and may persist for hundreds of picoseconds despite frictional damping. Consideration of non-thermal distributions is often neglected in descriptions of condensed-phase reactivity; the extent to which the present intriguing observations are widespread remains an interesting question.
We use temperature-dependent ultrafast infrared spectroscopy of dilute HOD in H(2)O to study the picosecond reorganization of the hydrogen bond network of liquid water. Temperature-dependent two-dimensional infrared (2D IR), pump-probe, and linear absorption measurements are self-consistently analyzed with a response function formalism that includes the effects of spectral diffusion, population lifetime, reorientational motion, and nonequilibrium heating of the local environment upon vibrational relaxation. Over the range 278-345 K, we find the time scales of spectral diffusion and reorientational relaxation decrease from approximately 2.4 to 0.7 ps and 4.6 to 1.2 ps, respectively, which corresponds to barrier heights of 3.4 and 3.7 kcal/mol, respectively. We compare the temperature dependence of the time scales to a number of measures of structural relaxation and find similar effective activation barrier heights and slightly non-Arrhenius behavior, which suggests that the reaction coordinate for the hydrogen bond rearrangement in water is collective. Frequency and orientational correlation functions computed from molecular dynamics (MD) simulations over the same temperature range support our interpretations. Finally, we find the lifetime of the OD stretch is nearly the same from 278 K to room temperature and then increases as the temperature is increased to 345 K.
We report the development of a high-sensitivity time-resolved infrared and Raman spectrometer with exceptional experimental flexibility based on a 10-kHz synchronized dual-arm femtosecond and picosecond laser system. Ultrafast high-average-power titanium sapphire lasers and optical parametric amplifiers provide wavelength tuning from the ultraviolet (UV) to the mid-infrared region. Customized silicon, indium gallium arsenide, and mercury cadmium telluride linear array detectors are provided to monitor the probe laser intensity in the UV to mid-infrared wavelength range capable of measuring changes in sample absorbance of ΔOD ~ 10(-5) in 1 second. The system performance is demonstrated for the time-resolved infrared, two-dimensional (2D) infrared, and femtosecond stimulated Raman spectroscopy techniques with organometallic intermediates, organic excited states, and the dynamics of the tertiary structure of DNA.
The time dependent response of a polar solvent to a changing charge distribution is studied in solvation dynamics. The change in the energy of the solute is measured by a time domain Stokes shift in the fluorescence spectrum of the solute. Alternatively, one can use sophisticated non-linear optical spectroscopic techniques to measure the energy fluctuation of the solute at equilibrium. In both methods, the measured dynamic response is expressed by the normalized solvation time correlation function, S(t). The latter is found to exhibit unique features reflecting both the static and dynamic characteristics of each solvent. For water, S(t) consists of a dominant sub-50 fs ultrafast component, followed by a multi-exponential decay. Acetonitrile exhibits a sub-100 fs ultrafast component, followed by an exponential decay. Alcohols and amides show features unique to each solvent and solvent series. However, understanding and interpretation of these results have proven to be difficult, and often controversial. Theoretical studies and computer simulations have greatly facilitated the understanding of S(t) in simple systems. Recently solvation dynamics has been used extensively to explore dynamics of complex systems, like micelles and reverse micelles, protein and DNA hydration layers, sol-gel mixtures and polymers. In each case one observes rich dynamical features, characterized again by multi-exponential decays but the initial and final time constants are now widely separated. In this tutorial review, we discuss the difficulties in interpreting the origin of the observed behaviour in complex systems.
We present a simple, comprehensive technique for accelerating simulation of rare events and calculating free energy profiles in molecular dynamics (MD) simulations. The technique is based on two related and complementary methods (AXD and BXD), which provide both thermodynamic and kinetic information along some reaction coordinate. The idea is to slice the reaction coordinate into several "boxes", and then run trajectories, locking them consecutively within each box to generate kinetic rate coefficients for exchange between neighboring boxes. In this way, a reaction coordinate may be efficiently explored, including those regions that would otherwise be visited only rarely. Combined with a simple and exact method for renormalizing the statistics obtained within each box, the box-to-box rate coefficients permit efficient free energy mapping. Tests carried out on model peptides demonstrate the utility of the method as well as the validity of the detailed balance assumption that underpins the derivations.
In this paper, we present classical and coupled coherent states quantum dynamics simulations to investigate intramolecular vibrational energy redistribution (IVR) from an excited (v = 1-10) OH stretch within the HOSO(2) complex to the other molecular bath modes. Using an analytical PES derived from electronic structure theory calculations, the results obtained from both the classical and quantum simulations are in reasonable agreement. The dynamics results suggest that statistical models overpredict HOSO(2) dissociation k(E)s, and underpredict the amount of vibrational excitation in the nascent OH formed following complex dissociation. In order to understand the dynamics results, we utilize a simple analytical model for describing energy flow from excited modes to bath modes, and show that IVR limits complex dissociation at short times. We also consider qualitative mass affects on IVR, and consider the implications of this work on previous measurements of the OH + SO(2) association k(infinity) using the proxy method.
When a chemical reaction forms two molecular products, even if the state-resolved differential cross section (DCS) for each product is obtained individually, the coincident attributes of the coproducts are still lacking. We exploit a method that provides coincidence information by measuring the state-resolved, pair-correlated DCS. Exemplified by the reaction F + CD4 --> DF + CD3, a time-sliced ion velocity imaging technique was used to measure the velocity distribution of a state-selected CD3 product and to reveal the information of the coincident DF in a state-correlated manner. The correlation of different product state pairs shows a striking difference, which opens up a new way to unravel the complexity of a polyatomic reaction.
The excess proton in aqueous media is critical to many aspects of chemistry, biology, and materials science. This species is at the heart of the most elementary of chemical (e.g., acid-base) and biological (e.g., bioenergetics) concepts, yet to this day, it remains mysterious, surprising, and often misunderstood. In this Account, our efforts to describe excess proton solvation and transport through computer modeling and simulation will be described. Results will be summarized for several important systems, as obtained from the multistate empirical valence bond (MS-EVB) approach, which allows for the explicit treatment of (Grotthuss) proton shuttling and charge delocalization.