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Structure and atom labeling of the organic and halogenated organic molecules previously included in the SE100 database.
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The determination of accurate equilibrium molecular structures plays a fundamental role for understanding many physical–chemical properties of molecules, ranging from the precise evaluation of the electronic structure to the analysis of the role played by dynamical and environmental effects in tuning their overall behavior. For small semi-rigid sys...
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... Oxygen and Nitrogen Atoms. The LRA parameters for CO and CN bond lengths have been obtained from 48 and 39 data points, respectively, and they are reported in Table 2 while LR plots are shown in Figure S1 Bond lengths in Å, angles in °; N: number of points in the linear fit; MD: mean deviation; Neg.: largest negative error; Pos.: largest positive error; MAD: mean absolute deviation; for angles, only the most important parameterizations are reported; B (or A) = 0 means that the parameter has been fixed to zero; for the full list, see Table S2 of Supporting Information. ...
Citations
... Results show that both trans-and cis-configurations are planar (figure 1), with different geometric parameters due to lone pair electrons around N atom. Detailed geometric parameters and electron energy calculated by different theoretical levels were summarized in tables 1, 2. Results of bond length and bond angle of trans-formaldoxime obtained by the CCSD(T)/aug-cc-pVTZ theoretical level reproduce well with the Semi-experimental data [40]. Since the reported cis-formaldoxime configuration is a metastable structure with an energy of around 6 kcal mol −1 higher than trans-formaldoxime [3], there are no relevant cis-structural parameters provided in experiment. ...
Formaldoxime (CH2NOH) belongs to the possible interstellar molecules. Its isomerization, spectroscopic properties as well as the potential for pumped laser action has long received a lot of attention. Herein, the benchmark database of the spectroscopic constants and anharmonic force fields has been achieved for trans- and cis- formaldoxime. Evaluation is done by using the coupled-cluster theory [CCSD(T)] and density functional theory (B3LYP and B2PLYP), and different basis sets [cc-pVTZ, aug-cc-pVTZ, 6-311+G**, 6-311++G (3df,3pd)] are utilized. The calculated spectroscopic constants commendably reproduce previous experimental results. Besides, a series of vital anharmonic parameters such as vibration-rotation interaction constants, etc, has been provided, which is used for the in-depth study of high-resolution rovibronic spectrum of formaldoxime.
... If these are kept fixed at the revDSD/junTZ level, one then resorts to the TM model. If the linkage distances are corrected using the LR parameters reported in Ceselin et al. (2021), one then resorts to the TM+LR model. The reader is referred to Ye et al. (2022) for a thorough account of the improvement obtained once moving from TM to TM+LR. ...
The gas-phase reactions of methanimine (CH 2 NH) with small radicals, such as CN, CP, CCH, and OH, have been extensively studied theoretically in the literature, and the presence of a common, general reaction mechanism has been postulated. Since methanimine is considered the main precursor of complex imines in the interstellar medium (ISM), the present study extends the investigation of its reaction with other small radicals that have already been detected in the ISM. These are SiN, SH, NO, NS, HCO, HCS, and C 3 N. The corresponding products are easily formulated on the basis of the aforementioned general mechanism, and to understand whether they can be formed in the ISM, a preliminary thermochemical study has been carried out. The only exothermic addition reaction is that occurring between CH 2 NH and the C 3 N radical. This reaction has been further investigated in order to accurately characterize its reactive potential energy surface, which has then been employed in ab initio transition state theory calculations to derive global rate coefficients. The products of the CH 2 NH + C 3 N reaction are new potential interstellar species, namely, the Z and E isomers of HNCHCCCN and CH 2 NCCCN. For the first time, their structural characterization has been reported. In addition, this work investigates the possibility of H-abstraction processes for each radical species considered, and re-examines the CH 2 NH + CP reaction to derive the corresponding rate constants, that were still missing in the literature.
... We now focus our attention on the comparison of rotational constants calculated using various DFT methods across the rungs of Jacob's Ladder [83]. We also refer the reader to several related benchmark studies which considered other species [84][85][86][87]. We will primarily compare the DFT results to the best level of the theory in Table 1, namely ae-CC/cc-pwCVTZ for isomers 2 and 5, and ae-CC/cc-pCVQZ for isomers 3 and 8 (for a comparison between the DFT results and the semi-experimental values, see the Supplementary Materials). ...
... Furthermore, for half of the rotational constants, the percentage errors are below the 0.2% mark. Together with previous findings [84][85][86]88,89], these results place DSD-PBEP86-D3BJ as an excellent functional for the prediction of geometrical and spectroscopic properties. However, we note that this excellent performance comes with a significant increase in the computational cost. ...
We evaluate the accuracy of CCSD(T) and density functional theory (DFT) methods for the calculation of equilibrium rotational constants (Ae, Be, and Ce) for four experimentally detected low-lying C5H2 isomers (ethynylcyclopropenylidene (2), pentatetraenylidene (3), ethynylpropadienylidene (5), and 2-cyclopropen-1-ylidenethenylidene (8)). The calculated rotational constants are compared to semi-experimental rotational constants obtained by converting the vibrationally averaged experimental rotational constants (A0, B0, and C0) to equilibrium values by subtracting the vibrational contributions (calculated at the B3LYP/jun-cc-pVTZ level of the theory). The considered isomers are closed-shell carbenes, with cumulene, acetylene, or strained cyclopropene moieties, and are therefore highly challenging from an electronic structure point of view. We consider both frozen-core and all-electron CCSD(T) calculations, as well as a range of DFT methods. We find that calculating the equilibrium rotational constants of these C5H2 isomers is a difficult task, even at the CCSD(T) level. For example, at the all-electron CCSD(T)/cc-pwCVTZ level of the theory, we obtain percentage errors ≤0.4% (Ce of isomer 3, Be and Ce of isomer 5, and Be of isomer 8) and 0.9–1.5% (Be and Ce of isomer 2, Ae of isomer 5, and Ce of isomer 8), whereas for the Ae rotational constant of isomers 2 and 8 and Be rotational constant of isomer 3, high percentage errors above 3% are obtained. These results highlight the challenges associated with calculating accurate rotational constants for isomers with highly challenging electronic structures, which is further complicated by the need to convert vibrationally averaged experimental rotational constants to equilibrium values. We use our best CCSD(T) rotational constants (namely, ae-CCSD(T)/cc-pwCVTZ for isomers 2 and 5, and ae-CCSD(T)/cc-pCVQZ for isomers 3 and 8) to evaluate the performance of DFT methods across the rungs of Jacob’s Ladder. We find that the considered pure functionals (BLYP-D3BJ, PBE-D3BJ, and TPSS-D3BJ) perform significantly better than the global and range-separated hybrid functionals. The double-hybrid DSD-PBEP86-D3BJ method shows the best overall performance, with percentage errors below 0.5% in nearly all cases.
... For the accurate determination of the equilibrium structure of the fragments, we employ the so-called semi-experimental (SE) structures (Pulay et al., 1978;Piccardo et al., 2015;Demaison et al., 2016), which are determined by a linear least-squares fit of the SE equilibrium rotational constants of different isotopologues (these are obtained by correcting the experimental B i 0 constants for the computed ΔB i vib corrections; Pulay et al., 1978). To correct the linkage between different fragments, the linear regression (LR) model is then employed , thereby exploiting the database from Ceselin et al. (2021). In the following, we refer to the "Lego brick" approach as TM+LR, or only TM whenever LR is not applied. ...
The chemistry of the interstellar medium occurs under extreme conditions and can lead to the formation of exotic molecules. These are species that on Earth are unstable and/or highly reactive. Their discovery in space is usually based on the astronomical observation of their rotational fingerprints, which requires an accurate laboratory investigation. This is based on a strategy that starts from the interplay of experiment and theory. State-of-the-art quantum-chemical calculations are used to predict the relevant spectroscopic information required to guide the spectral recording, analysis and assignment. Rotational spectra measurements are then performed in the centimeter-/millimeter-/submillimeter-wave region, thereby exploiting efficient on-the-fly production protocols for exotic molecules. Subsequently, the spectral analysis leads to accurate spectroscopic parameters, which are then used for setting up accurate line catalogs for astronomical searches and detections. This review is based on the strategy developed and the results obtained at the ROT&Comp Lab of the University of Bologna.
... 32 The nature of the minima connected by the TSs obtained in this way was determined by following IRCs at the same level of theory. Several studies have shown that this combination of functional and basis set provides accurate geometrical structures 33,34 and vibrational frequencies. 35 The results of the simulations were analyzed using amk_tools, 36 a graphic visualizer that allows for the examination of the extremely complex reaction networks generated by AMK. ...
Vinyl alcohol (Vy) and hydroxyl radical (OH) are involved in several processes, which take place in environments characterized by very different physical−chemical conditions, ranging from the low pressures and temperatures typical of the interstellar medium (ISM) up to the high temperatures of interest for combustion processes. A gas-phase reaction mechanism involving Vy and OH has been proposed as a possible path for the formation of (Z)-1,2-ethenediol (Et), a molecule recently identified in the ISM. Et, the enolic form of glycolaldehyde, is considered a key precursor for the formation of sugars in both interstellar and prebiotic chemistry. We have therefore undertaken a detailed quantum chemical study of possible reaction channels starting from the interaction between the OH radical and both conformers of Vy (syn and anti). The formation of a prereactive complex always represents the first step of the reaction, which can then proceed through the attack to the C�C double bond (leading in turn to the formation of different dissociation products) or through hydrogen abstraction, which eventually produces a radical species and water. Then, a master equation approach based on ab initio transition state theory has been employed to calculate the reaction rate constants of different products for temperatures up to 500 K. A comparison of the kinetic results for the different reaction channels shows that hydrogen abstraction is strongly favored for both Vy conformers and leads to the formation of water and CH 2 CHO radical. As a matter of fact, formation of Et is strongly disfavored under the harsh conditions of the ISM from both kinetic and thermodynamic points of view because of the high activation energy and strong endothermicity of the corresponding reaction path.
... 37 In the specific case of rotational spectroscopy, improved equilibrium rotational constants are obtained by refining the optimized geometries by a linear regression approach. 20,38 Among the main biomolecule building blocks, natural αamino acids, which exist exclusively in neutral form in the gas phase, represent a particularly appealing playground because their rich conformational landscape is tuned by the competition among different kinds of intramolecular hydrogen bonds. At the same time, MW results are available for several conformers of most natural α-amino acids, 39−50 which represent very demanding benchmarks for the a priori prediction of structural and spectroscopic parameters. ...
... The typical MUEs of rDSD bond lengths (0.003 Å) and valence angles (0.003 radians, i.e., 0.15°) observed in the large SE100 database 38 are largely sufficient to obtain accurate relative electronic energies of different conformers by singlepoint energy evaluations using composite methods rooted in the coupled cluster (CC) ansatz. 68 In particular, the CC model including single, double, and perturbative estimate of triple excitations (CCSD(T)) 69 is considered the gold standard for this kind of computations provided that complete basis set (CBS) extrapolation and core valence (CV) correlation are taken into the proper account. ...
... However, the systematic nature of the errors permits geometrical parameters to be obtained and, thus, equilibrium rotational constants, rivaling the accuracy of the jun-ChSF12 counterparts by the linear regression approach (LRA). In this model, the computed geometrical parameters (r comp ) are corrected for systematic errors by means of scaling factors (a) and offset values (b) depending on the nature of the involved atoms and determined once for ever from a large database of accurate semiexperimental (SE) equilibrium geometries: 38,92 (2) ...
The accurate characterization of prototypical bricks of life can strongly benefit from the integration of high resolution spectroscopy and quantum mechanical computations. We have selected a number of representative amino acids (glycine, alanine, serine, cysteine, threonine, aspartic acid and asparagine) to validate a new computational setup rooted in quantum-chemical computations of increasing accuracy guided by machine learning tools. Together with low-lying energy minima, the barriers ruling their interconversion are evaluated in order to unravel possible fast relaxation paths. Vibrational and thermal effects are also included in order to estimate relative free energies at the temperature of interest in the experiment. The spectroscopic parameters of all the most stable conformers predicted by this computational strategy, which do not have low-energy relaxation paths available, closely match those of the species detected in microwave experiments. Together with their intrinsic interest, these accurate results represent ideal benchmarks for more approximate methods.
... To improve the optimized geometries obtained from double-hybrid functionals, one can resort to the the so-called linear regression approach (LRA) [71][72][73][74]. This corrects the computed bond lengths (r comp ) for systematic errors by means of scaling factors (a) and offset values (b) that have been derived from the comparison of DFT and accurate semi-experimental (SE) equilibrium geometries for a large database: ...
... with the a and b parameters depending not only on the functional considered, but also on the nature of the atoms involved. These are available in [73]. As mentioned above, the equilibrium rotational constants contribute more than 99% to the parameters derived from experiments and only depend on the molecular structure and isotopic composition [75]. ...
... When employing explicitly-correlated methods, the computational cost of the ChS methodology can be further reduced by omitting the CBS extrapolation step. To inspect this, a validation of the junChS and CCF12+CV models (for CCF12, we considered the DZCCF12, TZCCF12 and junCCF12 variants) has been performed by comparing their results with accurate SE equilibrium geometries from the SE100 database [73]. The subset considered includes 24 molecules containing hydrogen, second-and third-row atoms: CH 4 , CO 2 , HCN, HNC, H 2 O, NH 3 , C 2 H 2 , C 2 H 4 , H 2 CO, t-HCOOH, CH 2 NH, BH 3 NH 3 , BH 2 OH, C 2 H 4 O (oxirane), C 2 H 4 NH (aziridine), C 3 H 6 (cyclopropane), H 2 O 2 , SO 2 , H 2 S, PH 3 , H 2 CS, CH 2 PH, C 2 H 4 S (tiirane) and H 2 S 2 . ...
The interplay of high-resolution rotational spectroscopy and quantum-chemical computations plays an invaluable role in the investigation of biomolecule building blocks in the gas phase. However, quantum-chemical methods suffer from unfavorable scaling with the dimension of the system under consideration. While a complete characterization of flexible systems requires an elaborate multi-step strategy, in this work, we demonstrate that the accuracy obtained by quantum-chemical composite approaches in the prediction of rotational spectroscopy parameters can be approached by a model based on density functional theory. Glycine and serine are employed to demonstrate that, despite its limited cost, such a model is able to predict rotational constants with an accuracy of 0.3% or better, thus paving the way toward the accurate characterization of larger flexible building blocks of biomolecules.
... When these combinations of functional/basis set are used, only the acronym of the functional is indicated explicitly. The accuracy of computed geometries can be further improved by means of the so-called linear regression approach (LRA) (86,87). This makes use of the large database of accurate semiexperimental (SE) equilibrium structures (see Section 2.2.1 for definition), which allowed the derivation of reliable linear regressions for key geometric parameters to be used for correcting density functional theory (DFT) systematic errors. ...
... This makes use of the large database of accurate semiexperimental (SE) equilibrium structures (see Section 2.2.1 for definition), which allowed the derivation of reliable linear regressions for key geometric parameters to be used for correcting density functional theory (DFT) systematic errors. The LRA leads to equilibrium geometries rivaling those issuing from the most refined (and costly) QC schemes (86,87). Another approach that allows for improving DFT structures is the template model approach (TMA) (87,88), which implies the direct transfer of corrections to geometric parameters from suitable fragments to the molecular system under consideration. ...
... Another approach that allows for improving DFT structures is the template model approach (TMA) (87,88), which implies the direct transfer of corrections to geometric parameters from suitable fragments to the molecular system under consideration. The combination of the TMA and the LRA has recently led to the definition of a fully black-box tool, referred to as nano-LEGO (86). (89,90). ...
Gas-phase molecular spectroscopy is a natural playground for accurate quantum-chemical computations. However, the molecular bricks of life (e.g., DNA bases or amino acids) are challenging systems because of the unfavorable scaling of quantum-chemical models with the molecular size (active electrons) and/or the presence of large-amplitude internal motions. From the theoretical point of view, both aspects prevent the brute force use of very accurate but very expensive state-of-the-art quantum-chemical methodologies. From the experimental point of view, both features lead to congested gas-phase spectra, whose assignment and interpretation are not at all straightforward. Based on these premises, this review focuses on the current status and perspectives of the fully a priori prediction of the spectral signatures of medium-sized molecules (containing up to two dozen atoms) in the gas phase with special reference to rotational and vibrational spectroscopy of some representative molecular bricks of life.
Expected final online publication date for the Annual Review of Physical Chemistry, Volume 74 is April 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
... 9,16−18 The accuracy of reference structures can be further enhanced by the recently introduced nano-LEGO approach, which employs well-chosen fragments (synthons) and linear regression analyses based on large databases of accurate structures. 19 Next, solvent effects come into play, which require the generation of a sufficient number of representative structures by means of stochastic approaches, in the present context Molecular Dynamics (MD), possibly followed by suitable unsupervised learning procedures aimed to reduce the number of different structures and descriptive coordinates (features in Machine Learning jargon) needed to obtain well converged average results. In this connection, the fast and very effective polarizable continuum model (PCM) 20,21 can be profitably employed in the absence of strong and specific solute−solvent interactions or to include bulk electrostatic effects in atomistic simulations employing non periodic boundary conditions (NPBC). ...
... 45 Within the latter, systematic errors affecting bond lengths and valence angles are corrected based on linear regressions, whose parameters were derived from a large database of accurate semiexperimental equilibrium geometries. 19 Since the NO bond length is not included in the above database, we employ the difference between the rDSD and accurate value for the dimethylnitroxide radical. 24 Atomic charges to be used in MD computations were obtained by the CM5 recipe 46 from B3LYP/jul-cc-pVDZ 41,42,47 Kohn−Sham orbitals and splitting the oxygen charges between the atomic center and two lone-pairs according to a previously described procedure. ...
... Then, the structure of the solute can be taken from a database of accurate semiexperimental equilibrium geometries or optimized at the rDSD level and then corrected by the accurate yet effective nano-LEGO approach. 19 Once the periodic structure of the environment and the molecular structure of the solute have been loaded, it is possible to replicate the molecules of the environment so as to cover the space surrounding the solute up to a maximum distance (r max ). In the case of simulations enforcing NPBC, it is necessary to select the environmental molecules occupying a sphere of radius r max (chosen by the user) and centered at the solute center of mass. ...
The ongoing integration of quantum chemistry, statistical mechanics, and artificial intelligence is paving the route toward more effective and accurate strategies for the investigation of the spectroscopic properties of medium-to-large size chromophores in condensed phases. In this context we are developing a novel workflow aimed at improving the generality, reliability, and ease of use of the available computational tools. In this paper we report our latest developments with specific reference to unsupervised atomistic simulations employing non periodic boundary conditions (NPBC) followed by clustering of the trajectories employing optimized feature spaces. Next accurate variational computations are performed for a representative point of each cluster, whereas intracluster fluctuations are taken into account by a cheap yet reliable perturbative approach. A number of methodological improvements have been introduced including, e.g., more realistic reaction field effects at the outer boundary of the simulation sphere, automatic definition of the feature space by continuous perception of solute-solvent interactions, full account of polarization and charge transfer in the first solvation shell, and inclusion of vibronic contributions. After its validation, this new approach has been applied to the challenging case of solvatochromic effects on the UV-vis spectra of a prototypical nitroxide radical (TEMPO) in different solvents. The reliability, effectiveness, and robustness of the new platform is demonstrated by the remarkable agreement with experiment of the results obtained through an unsupervised approach characterized by a strongly reduced computational cost as compared to that of conventional quantum mechanics and molecular mechanics models without any accuracy reduction.
... The spectroscopic parameters relevant for rotational spectroscopy, specifically equilibrium and ground state rotational constants as well as quartic centrifugal distortion terms, are summarized in Table 2, where theoretical predictions are compared against the experimental data in the I r representation of the Watson's A reduced Hamiltonian. 81 A well consolidated procedure was followed, 30,38,80 and the best estimates of ground state rotational constants have been obtained by augmenting those of the equilibrium configuration computed according to the CCSD(T)/CBS+CV composite scheme through rev-DSDPBEP86-D3/jun-cc-pVTZ vibrational corrections. The resulting parameters are in very good agreement with the corresponding experimental counterparts with discrepancies of 0.06%, thus confirming the accuracy of the CCSD(T)/CBS+CV equilibrium geometry as well as the reliability of the rev-DSDPBEP86 vibrational contributions. ...
Very short-lived substances have recently been proposed as replacements for hydrofluorocarbons (HFCs), in turn being used in place of ozone-depleting substances, in refrigerant applications. In this respect, hydro-fluoro-olefins (HFOs) are attracting particular interest because, due to their reduced global warming potential, they are supposed to be environmentally friendlier. Notwithstanding this feature, they represent a new class of compounds whose spectroscopic properties and reactivity need to be characterized to allow their atmospheric monitoring and to understand their environmental fate. In the present work, the structural, vibrational, and ro-vibrational properties of trifluorothene (HFO-1123, F2C = CHF) are studied by state-of-the-art quantum chemical calculations. The equilibrium molecular structure has an expected error within 2 mÅ and 0.2° for bond lengths and angles, respectively. This represents the first step toward the computation of highly accurate rotational constants for both the ground and first excited fundamental vibrational levels, which reproduce the available experimental data well within 0.1%. Centrifugal distortion parameters and vibrational-rotational coupling terms are computed as well and used to solve some conflicting experimental results. Simulation of the vibrational transition frequencies and intensities beyond the double harmonic approximation and up to three quanta of vibrational excitation provides insights into the couplings ruling the vibrational dynamics and guides the characterization of the gas-phase infrared spectrum experimentally recorded in the range of 200-5000 cm-1. The full characterization of the IR features is completed with the experimental determination of the absorption cross sections over the 400-5000 cm-1 region from which the radiative forcing and global warming potential of HFO-1123 are derived.
