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Ab initio investigation on the photophysics of indole
Abstract
Reaction paths and potential-energy profiles for detachment of the hydrogen atom of the NH group in excited singlet states of indole have been investigated using the CIS, CASSCF and CASPT2 ab initio methods. The potential-energy profile of the lowest excited singlet state is found to be essentially repulsive. It crosses the potential-energy functions of the and excited states of character as well as those of the ground state. The resulting multiple conical intersections can provide the mechanism for efficient internal conversion to the ground state. The polarities of the excited states are remarkably different, indicating a complex interplay of internal conversion and solvation dynamics of photoexcited indole in polar solvents.
... Although both 1 L a and 1 L b are of ππ* character, their static dipoles are markedly different. 31 In the gas phase, the maximum of 1 L a absorption always lies above the maximum of 1 L b which makes 1 L b the fluorescent state according to Kasha's rule. But dissolved in solvent, the relative energy separation between 1 L a and 1 L b in indole strongly depends on the dielectric constant of the medium. ...
... This results in the lowering of 1 L a relative to 1 L b to an extent where 1 L a now becomes the state where emission originates and the fluorescence spectrum exhibits a large Stokes shift. [31][32][33] Figure 1b shows the resolution of the excitation spectrum of indole along with the relative contribution of the 1 L a and 1 L b states. 34,35 There is still a debate in the literature whether the reversal of energy order for 1 L a and 1 L b happens before or after excitation. ...
... Several computational studies performed on indole in water reveal that the polar nature of water mainly affects the emission properties of indole leading to inversion of the energy order of 1 L a and 1 L b ; 1 L a becomes the emitting state in water. 31,32,62 The inversion of the solvent-relaxed electronic states can be explained based on the argument of the higher permanent dipole moment of 1 L a state; the 1 L a state becomes lower in energy due to enhanced dipole-dipole interaction in water. 32 Although the relaxed state ordering is inverted compared to the gas phase, the state ordering is unchanged at the level of the vertical excitation energy from the ground state of indole. ...
Understanding how the electronic structure of an aqueous solute is intricately bound up with the arrangement of a host liquid provides insight into how non-adiabatic photochemistry takes place in the condensed phase. For example, the presence of water provides additional solute-solvent interactions compared to non-polar solvents, changing the stability of ionized products; modifying the energies of low-lying excited valence states as well as moving the point of intersection between potential surfaces. Thus, the locations and topology of conical intersections between these surfaces also change. The overall impact of the aqueous environment can be to modify the intricate photochemical and non-radiative pathways taking place after photoexcitation. Time-resolved photoelectron spectroscopy (TRPES) in a liquid microjet is here implemented to investigate the influence of water on the electronic structure and dynamics of indole, the chromophore of the amino acid tryptophan. TRPES is used to establish ultrafast relaxation pathways that vary as a function of excitation wavelength. In our experiment, aqueous indole was excited with femtosecond pulses centered at 292 nm and 266 nm. The vertical excitation energy (VIE) of aqueous indole is extracted and found to be lowered by 0.5 eV in water relative to the gas phase. In the TRPES study, the spectral signature of ¹La and evidence of solvated electron formation on an ultrafast timescale are observed. Our data also points to a possible contribution of the dissociative πσ* state, which can be accessed by a conical intersection (CI) with the ¹La state.
... [19] Upon extension of the NH or OH bond of these photoacids, the σ* orbital collapses to the compact 1 s orbital of the free H-atom, which is the reason for the pronounced stabilization of the πσ* energy by NH or OH bond stretching. [19] The vertical electronic excitation spectrum of HzH exhibits similarities with the excitation spectrum of indole (two absorbing ππ* states, followed by a dark πσ* state), [80] but the excitation energies of HzH are much lower, as expected for a radical. The PE crossings along the NH stretching coordinate in HzH also are qualitatively similar to indole, but are located at much lower electronic excitation energies. ...
... [19] Compared to the S 1 (ππ*) state in the phenol···H 2 O complex, the D 1 (ππ*) and D 2 (ππ*) states in the HzH···H 2 O complex are much lower in energy and the 2 πσ*-2 ππ* energy crossing occurs at much larger bond distances. Like in phenol···(H 2 O) n complexes, [80,82] the conical intersection of the energy of the πσ* state with the energy of the electronic ground state along the H-atom detachment coordinate, which exists in free phenol and free HzH, is eliminated in the HzH···H 2 O and HzH···(H 2 O) 4 complexes. Phenol and indole are known as photoacids with a comparatively high yield of hydrated electrons when excited to their S 1 or S 2 states. ...
Ab initio computational methods are employed to explore whether hydrated electrons can be produced by the photodetachment of the excess hydrogen atom of the heptazinyl radical (HzH) in finite‐size HzH⋅⋅⋅(H2O)n clusters. The HzH radical is an intermediate species in the photocatalytic oxidation of water with the heptazine (Hz) chromophore. Hz (heptaazaphenalene) is the monomer of the ubiquitous polymeric water‐oxidation photocatalyst graphitic carbon nitride (g‐C3N4). The energy profiles of minimum‐energy excited‐state reaction paths for proton‐coupled electron transfer from HzH to water molecules were computed for the HzH⋅⋅⋅H2O and HzH⋅⋅⋅(H2O)4 complexes with the CASPT2 method. The results reveal that the photodetachment of the excess H‐atom from the HzH radical is a barrierless reaction in these hydrogen‐bonded complexes, resulting in the formation of H3O and H3O(H2O)3 radicals, respectively, which are finite‐size models of the hydrated electron. The computational results suggest that the photocatalytic formation of hydrated electrons from water with visible light could be possible in principle.
... [29][30][31] For indoles with the methoxy substituent connected at positions C 5 and C 6 , we have shown that excitation of the first overtone of the NH stretching vibration (in the near-infrared) leads to a change of the conformation of the remotely located methoxy substituent, constituting the first firm experimental evidence of occurrence of long-range intramolecular vibrational energy transfer. 29 Photochemistry and photophysics of the parent indole has been extensively investigated, 28,[32][33][34][35][36][37][38][39][40][41][42][43] while analogous studies on methoxy substituted derivatives are not so numerous. 25,31,40,[44][45][46][47] Recently, we found that the dominant UV-induced transformations of matrix-isolated monomeric 6-methoxyindole are initiated by photodetachment of the hydrogen atom from the N-H bond. ...
... UV-irradiations at higher energies should promote excitations comparable with the energy of the s* ' p (S 2 ' S 0 ) transition. Despite the s* ' p excitations in indole are electric dipole forbidden, they are vibronically allowed, 25,39 and gain oscillator strength by borrowing intensity from the p* ' p ( 1 L b ) states by means of vibronic coupling, 33 resulting in the 1 pp* -1 ps* population transfer. 25 It has been shown that the ps* potential energy surface has dissociative character along the NH stretching coordinate in indole 84 and in substituted indoles. ...
Monomers of 4-methoxyindole and 5-methoxyindole trapped in low-temperature xenon matrices (15-16 K) were characterized by IR spectroscopy, in separate experiments. Each compound was shown to adopt the most stable 1H-tautomeric form. The photochemistry of the matrix-isolated compounds was then investigated by exciting the matrices with narrowband UV light with λ ≤ 305 nm. Two main photoproducts, similar for each compound, have been detected: (1) 4-methoxy- or 5-methoxy-indolyl radical, resulting from cleavage of the N-H bond; (2) 3H-tautomers (4-methoxy- or 5-methoxy-) with the released hydrogen atom reconnected at the C3 ring carbon atom. The presence of the two types of photoproducts in the UV-irradiated matrices was confirmed by comparison of their B3LYP/6-311++G(d,p) calculated IR spectra with the experimental spectra emerging upon the irradiations. The mechanism of the observed phototransformations was elucidated by Natural Bond Orbital and Natural Resonance Theory computations on the methoxy-substituted indolyl radicals resulting from the N-H bond cleavage. The highest natural atomic spin densities were predicted at the C3 and N1 positions of the indolyl ring, corresponding to a predominance of the resonance structures with the radical centres located at these two atoms. As a whole, the obtained experimental and theoretical data allowed establishing a general pattern for the photochemistry of methoxyindoles under matrix-isolation conditions.
... [20][21][22][23][24][25][26][27][28] Also theory provided important details for the classification of these states. 7,10,11,[29][30][31][32] Domcke and Sobolewski have shown that the photophysics of indoles can be influenced by the existence of a ps* state, which is dissociative along the NH coordinate. 2,6,7,33 Much less fundamental investigations on the 1 L a and 1 L b states has been performed for the cyanoindoles. ...
... 7,10,11,[29][30][31][32] Domcke and Sobolewski have shown that the photophysics of indoles can be influenced by the existence of a ps* state, which is dissociative along the NH coordinate. 2,6,7,33 Much less fundamental investigations on the 1 L a and 1 L b states has been performed for the cyanoindoles. Rotationally resolved electronic spectra of 5-cyanoindole have been presented. ...
The rotationally resolved electronic Stark spectrum of 4-cyanoindole and some N-D and C-D deuterated isotopologues has been measured and analyzed.
... 3 Indole, as the chromophore of the aromatic amino acid tryptophane, has been extensively studied, mainly regarding the location of the higher electronically excited 1 L a state relative to the lowest 1 L b state, both experimentally 4-12 as well as theoretically. [13][14][15][16][17][18] Exchange of one hydrogen atom in the chromophore for the highly polar cyano group, changes the fluorescence properties of the indole chromophore considerably. 19,20 5-Cyanotryptophane is used as a fluorescence probe of protein hydration. ...
... Sobolewski and Domcke have shown, that along with the lowest two excited singlet 1 L a and 1 L b states, which are of pp* character, a third state of ps* character plays a crucial role in the photophysics of these chromophores. 17,[53][54][55] This ps* state is repulsive along the OH coordinate for phenol and along the NH coordinate for indole and forms conical intersections with the directly excited state and subsequently with the electronic ground state. For excitations above the threshold, a rapid decay channel is open, which connects the primarily excited pp* state through a conical intersection (CI) with the ps* state, and subsequently through a second CI with the ground state. ...
The rotationally resolved electronic spectra of the origin bands of 3-cyanoindole, cyanoindole(d1), and the 3-cyanoindole-(H2O)1 cluster have been measured and analyzed using evolutionary algorithms. For the monomer, permanent dipole moments of 5.90 D for the ground state, and of 5.35 D for the lowest excited singlet state have been obtained from electronic Stark spectroscopy. The orientation of the transition dipole moment is that of an $^1$L$_b$ state for the monomer. The water moiety in the water cluster could be determined to be trans-linearly bound to the NH group of 3-cyanoindole, with an NH...O hydrogen bond length of 201.9 pm in the electronic ground state. Like the 3-cyanoindole monomer, the 3-cyanoindole-water cluster also shows an ¹Lb-like excited singlet state. The excited state life time of isolate 3-cyanoindole in the gas phase has been determined to 9.8 ns, that of 3-cyanoindole(d1) has found to be 14.8 ns, while that of the 1:1 water cluster is considerably shorter (3.6 ns). The excited state life time of 3-cyanoindole(d1) in D2O solution has found to be smaller than 20 ps.
... Calculation of the time-dependent fluorescence anisotropy requires simulation of dynamics in the excited state, and tracking the transition dipole as a function of time. Fluorescence from the indole group of tryptophan is produced by excitation of two closely lying excited singlet states, L a and L b , of which transition dipole moments to the S 0 state are almost orthogonal to each other [74][75][76][77]. Since it is believed that the excited indole quickly relaxes to the L a state before fluorescence in polar solvents [75,78], the excited state calculations were performed in the L a state, and fluorescence anisotropy obtained by monitoring the S 0 -L a transition dipole at the instant of photoexcitation and after the system evolves for a time t on the excited L a state surface. ...
... Since it is believed that the excited indole quickly relaxes to the L a state before fluorescence in polar solvents [75,78], the excited state calculations were performed in the L a state, and fluorescence anisotropy obtained by monitoring the S 0 -L a transition dipole at the instant of photoexcitation and after the system evolves for a time t on the excited L a state surface. We approximate the photoexcited molecule in the L a state by altering the partial charges on indole group to those calculated for the excited L a state by Sobolewski and Domcke [77]. This model, previously developed by some of us [79,80] and fully described in Section S.1 of the supplementary information, was shown to give good agreement with experimental data for KWK in aqueous solution [79,80]. ...
We investigate binding of the tripeptides Lys-Trp-Lys (KWK) and Glu-Trp-Glu (EWE) to the amorphous silica surface using atomistic simulations. These peptides were chosen because they were previously utilized in experiments measuring binding affinity and steady-state fluorescence anisotropy from the indole chromophore of the tryptophan residue. Our simulations were performed using silica with surface change density of −0.8 elementary charges per square nanometer, which is expected at neutral pH. Even though positive charged KWK binds more strongly to the negatively charged silica surface, EWE also forms bound complexes with the surface that are stable for at least 15ns of simulation, in agreement with the experiments which revealed evidence for binding of both KWK and EWE to silica. Binding mechanisms include a wide variety of electrostatic interactions, as well as hydrophobic interactions between the indole group and hydrophobic areas of the heterogeneous silica surface. The long-time limit of the fluorescence anisotropy of tryptophan is calculated from the simulations in order to help interpret the recent experiments. We identify several factors which control the magnitude of the fluorescence anisotropy for each binding configuration.
... 13,14 Indole became one of the widely studied model systems to understand the photochemistry of heteroaromatic systems, in particular, the role of the πσ* states. 1 The excited states and photodynamics of gaseous indole were studied by a large variety of techniques, including high-resolution spectroscopy, 8,9,15 pump−probe laser spectroscopy, 16,17 ion imaging, 18 and ab initio calculations. 19 Radiation below 300 nm has the potential to cause pyrimidine dimerization, e.g., leading to melanoma. 20 The most damaging is radiation around 250 nm, corresponding to a minimum of the indole absorption spectrum. ...
Solvent interactions, particularly hydration, are vital in chemical and biochemical systems. Model systems reveal microscopic details of such interactions. We uncover a specific hydrogen-bonding motif of the biomolecular building block indole (C8H7N), tryptophan’s chromophore, in water: a strong localized N–H···OH2 hydrogen bond, alongside unstructured solvent interactions. This insight is revealed from a combined experimental and theoretical analysis of the electronic structure of indole in aqueous solution. We recorded the complete X-ray photoemission and Auger spectrum of aqueous-phase indole, quantitatively explaining all peaks through ab initio modeling. The efficient and accurate technique for modeling valence and core photoemission spectra involves the maximum-overlap method and the nonequilibrium polarizable-continuum model. A two-hole electron-population analysis quantitatively describes the Auger spectra. Core–electron binding energies for nitrogen and carbon highlight the specific interaction with a hydrogen-bonded water molecule at the N–H group and otherwise nonspecific solvent interactions.
... The photoexcitation is modeled by modifying the point charges of the indole-group atoms in both Trp residues in the protein. The charge differences between ground and excited state are based on multi-reference quantum chemistry (CASSCF/CASPT2) electronic structure calculations performed by Sobolewski and coworkers [38]. This procedure has been applied in several previous studies in our group and has been found to give good agreement with experiments [28,29]. ...
The microscopic origins of terahertz (THz) vibrational modes in biological systems are an active and open area of current research. Recent experiments [Physical Review X 8, 031061 (2018)] have revealed the presence of a pronounced mode at ∼0.3 THz in fluorophore-decorated bovine serum albumin (BSA) protein in aqueous solution under nonequilibrium conditions induced by optical pumping. This result was heuristically interpreted as a collective elastic fluctuation originating from the activation of a low-frequency phonon mode. In this work, we show that the sub-THz spectroscopic response emerges in a statistically significant manner (> 2σ) from such collective behavior, illustrating how photoexcitation can alter specific THz vibrational modes. We revisit the theoretical analysis with proof-of-concept molecular dynamics that introduce optical excitations into the simulations. Using information theory techniques, we show that these excitations can give rise to a multiscale response involving two optically excited chromophores (tryptophans), other amino acids in the protein, ions, and water. Our results motivate new experiments and fully nonequilibrium simulations to probe these phenomena, as well as the refinement of atomistic models of Fröohlich condensates that are fundamentally determined by nonlinear interactions in biology.
... Furthermore, the close-lying electronic excited states of indole indicate the importance of vibronic coupling in the excited state properties of the indole chromophore. Due to its interesting excited state properties, indole has been extensively studied both experimentally and theoretically [3,[81][82][83][84][85][86]. Comparison of vibronic spectra of Indole calculated using time-independent (blue, red) and time-dependent (green) methods with available experimental spectra (black) [87]. ...
Electronic and vibrational spectroscopic studies of molecules are of crucial importance to characterizing a molecule and detecting the molecular species in different environments. In this review article, we summarized some important theoretical methods to calculate high-resolution electronic spectra and ro-vibrational states for small molecular systems with the inclusion of vibronic and ro-vibrational couplings, respectively. We have also reviewed a number of theoretical studies exploring some interesting organic chromophores like indole, isoalloxazine, transition metal trifluoride CoF 3 and NiF 3 , and molecular ions like protonated rare gases and azido ions. These studies involve the calculation of spectroscopic features based on analytical potential energy surfaces constructed using high-level ab initio energies. The topology of the potential energy surfaces has been explored for these selected systems. The vibronic spectra and ro-vibrational states calculated using various theoretical methods and their comparison to available experimental results are reported in this review.
... This depopulation goes along with the fluorescence decay. The solvent dependence of the time constant 2 can be rationalized by a crossing of the L b state with a 1 πσ* one as put forth by Domcke and Sobolewski [43,44]. The 1 πσ* state gets stabilized in polar solvents, thereby reducing the barrier for the IC transition. ...
The photophysics of 2-cyanoindole (2-CI) in solution (water, 2,2,2-trifluoroethanol, acetonitrile‚ and tetrahydrofuran) was investigated by steady-state as well as time resolved fluorescence and absorption spectroscopy. The fluorescence quantum yield of 2-cyanoindole is strongly sensitive to the solvent. In water the quantum yield is as low as 4 . 4 × 10 –4 . In tetrahydrofuran, it amounts to a yield of 0.057. For 2-CI dissolved in water, a bi-exponential fluorescence decay with time constants of ∼1 ps and ∼8 ps is observed. For short wavelength excitation (266 nm) the initial fluorescence anisotropy is close to zero. For excitation with 310 nm it amounts to 0.2. In water, femtosecond transient absorption reveals that the fluorescence decay is solely due to internal conversion to the ground state. In aprotic solvents, the fluorescence decay takes much longer (acetonitrile: ∼900 ps, tetrahydrofuran: ∼2.6 ns) and intersystem crossing contributes.
Graphical abstract
... The charge differences between ground and excited state are based on multi-reference quantum chemistry (CASSCF/CASPT2) electronic structure calculations performed by Sobolewski and coworkers. 57 This procedure has been applied in several previous studies in our group and has been found to give good agreement with experiments. 45,58 Terahertz Spectra Analysis ...
The microscopic origins of terahertz (THz) vibrational modes in biological systems are an active and open area of current research. Recent experiments [Physical Review X 8, 031061 (2018)] have revealed the presence of a pronounced mode at $\sim$0.3 THz in fluorophore-decorated bovine serum albumin (BSA) protein in aqueous solution under nonequilibrium conditions induced by optical pumping. This result was heuristically interpreted as a collective elastic fluctuation originating from the activation of a low-frequency phonon mode. In this work, we show that the sub-THz spectroscopic response emerges in a statistically significant manner (> 2$\sigma$) from such collective behavior, illustrating how specific THz vibrational modes can be triggered through optical excitations and other charge reorganization processes. We revisit the theoretical analysis with proof-of-concept molecular dynamics that introduce optical excitations into the simulations. Using information theory techniques, we show that these excitations can induce a multiscale response involving the two optically excited chromophores (tryptophans), other amino acids in the protein, ions, and water. Our results motivate new experiments and fully nonequilibrium simulations to probe these phenomena, as well as the refinement of atomistic models of Fr\"ohlich condensates that are fundamentally determined by nonlinear interactions in biology.
... The existence of a strong vibronic coupling required for an efficient IC was demonstrated by Brand et al. 26,27 Relying on nonadiabatic dynamics in explicit solvent using time-dependent density functional theory, Wohlgemuth et al. 19 obtained a time constant of 45 fs for the L a → L b IC, along with a minor repopulation of the ground state (GS) through a πσ* state accessed from L a . 10,32 These studies suggest the intriguing idea that the early excited-state dynamics in Trp are characterized by a sub-ps, CI-assisted, solvent-sensitive, and back-and-forth population transfer between L a and L b . ...
By combining UV transient absorption spectroscopy with sub-30-fs temporal resolution and CASPT2/MM calculations, we present a complete description of the primary photoinduced processes in solvated tryptophan. Our results shed new light on the role of the solvent in the relaxation dynamics of tryptophan. We unveil two consecutive coherent population transfer events involving the lowest two singlet excited states: a sub-50-fs nonadiabatic La → Lb transfer through a conical intersection and a subsequent 220 fs reverse Lb → La transfer due to solvent-assisted adiabatic stabilization of the La state. Vibrational fingerprints in the transient absorption spectra provide compelling evidence of a vibronic coherence established between the two excited states from the earliest times after photoexcitation and lasting until the back-transfer to La is complete. The demonstration of response to the environment as a driver of coherent population dynamics among the excited states of tryptophan closes the long debate on its solvent-assisted relaxation mechanisms and extends its application as a local probe of protein dynamics to the ultrafast time scales.
... Photodynamics simulations are very powerful to decipher the mechanisms underlying photoexcitation and to provide explanations of experimental observables. While tryptophan, tyrosine and phenylalanine have been studied experimentally [14][15][16][17] , theoretical simulations of their excited states are extremely expensive, such that only the smaller chromophores of these molecules (such as benzene, phenol and indole) are often the focus of theoretical investigations 15,[18][19][20] . However, size-dependent deactivation pathways suggested by experiments question the use of chromophores as model systems to study the photochemistry of the respective amino acids 14,16,17 . ...
Amino acids are among the building blocks of life, forming peptides and proteins, and have been carefully ‘selected’ to prevent harmful reactions caused by light. To prevent photodamage, molecules relax from electronic excited states to the ground state faster than the harmful reactions can occur; however, such photochemistry is not fully understood, in part because theoretical simulations of such systems are extremely expensive—with only smaller chromophores accessible. Here, we study the excited-state dynamics of tyrosine using a method based on deep neural networks that leverages the physics underlying quantum chemical data and combines different levels of theory. We reveal unconventional and dynamically controlled ‘roaming’ dynamics in excited tyrosine that are beyond chemical intuition and compete with other ultrafast deactivation mechanisms. Our findings suggest that the roaming atoms are radicals that can lead to photodamage, offering a new perspective on the photostability and photodamage of biological systems. Amino acids are one of the major building blocks of life, but the ways in which they respond to light excitation are not fully understood. Now, the photochemistry of tyrosine has been studied using physically inspired deep neural networks, leading to the observation of unconventional dynamically controlled reactivity that involves ‘roaming’ radicals that can cause photodamage.
... Indole became one of the widely studied model systems to understand the photochemistry of heteroaromatic systems, in particular, the role of the πσ * states [1]. The excited states and photodynamics of gaseous indole were studied by a large variety of techniques, including high-resolution spectroscopy [8,9,16], pump-probe laser spectroscopy [17,18], ion imaging [19], and ab initio calculations [20]. Radia-tion below 300 nm has the potential to cause pyrimidine dimerization, e. g., leading to melanoma [21]. ...
Solvent interactions and specifically hydration are of utmost importance in chemical and biochemical systems. Model systems enable us to unravel the relevance of microscopic details of these interactions. Here, we characterized the electronic structure of the prototypical biomolecular chromophore indole (\ind) in aqueous solution and disentangled the specific and non-specific effects of the solvent on indole's electronic structure. The complete photoelectron-emission spectrum of indole\textsubscript{aq} in a liquid microjet was measured using 600~eV synchrotron radiation. The first valence photoelectron peak corresponds to the ionization from the HOMO and HOMO$-$1 orbitals, for which we assigned the binding energies to 7.38 and 7.93~eV. The solvent shifts for these peaks indicate the presence of simultaneous specific and non-specific effects of the aqueous environment. The valence photoemission data were also compared to available data to determine the reorganization energy of aqueous-phase indole associated with its ionization. The core-electron binding energies for nitrogen and carbon demonstrated a distinct interaction of the water solvent with these atoms: a strong $\text{N-H}\cdots\text{OH}_2$ hydrogen bond and an unstructured interaction of the water solvent with the carbon atoms. Auger-electron contributions to the spectra are also reported and discussed. The experimental data were interpreted with the aid of extensive \emph{ab initio} modeling. The combination of the maximum-overlap method with the non-equilibrium polarizable-continuum model was demonstrated as an efficient and accurate technique for a modeling of both the valence and core peaks in the spectra. The two-hole electron-population analysis is shown to provide a quantitative theoretical description of Auger spectra.
... It raises the question whether these modes are dominating the spectrum because they gain intensity via vibronic coupling to the . Another possibility is that other vibrations are suppressed due to the potential influence of a dissociative state [34]. Such a coupling has been observed for indole and several of its derivatives in the gas phase before [19,25,35,36]. ...
Vibronic couplings between the two lowest excited singlet states of the neurotransmitter serotonin are studied both experimentally and theoretically. Using rotationally resolved electronic spectroscopy, we observe a mode-dependent rotation of the S1 transition dipole moment (TDM). This is rationalized as a coupling of the S1 (1Lb) to the S2 (1La) state, lying about 3300 cm−1 higher in energy.
... (i) Photoreaction, by photodissociation, which constitutes the dominant decay mechanism for many small heterocyclic molecules in the gas phase. Much studied examples include phenol [2,4,[16][17][18][19][20][21][22][23][24][25], pyrrole [26][27][28][29][30][31][32][33][34] and indole [35][36][37][38]; ...
Melanins are skin-centered molecular structures that block harmful UV radiation from the sun and help protect chromosomal DNA from UV damage. Understanding the photodynamics of the chromophores that make up eumelanin is therefore paramount. This manuscript presents a multi-reference computational study of the mechanisms responsible for the experimentally observed photostability of a melanin-relevant model heterodimer comprising a catechol (C)–benzoquinone (Q) pair. The present results validate a recently proposed photoinduced intermolecular transfer of an H atom from an OH moiety of C to a carbonyl-oxygen atom of the Q. Photoexcitation of the ground state C:Q heterodimer (which has a π-stacked “sandwich” structure) results in population of a locally excited ππ* state (on Q), which develops increasing charge-transfer (biradical) character as it evolves to a “hinged” minimum energy geometry and drives proton transfer (i.e., net H atom transfer) from C to Q. The study provides further insights into excited state decay mechanisms that could contribute to the photostability afforded by the bulk polymeric structure of eumelanin
... Water molecules and possibly nearby charged residues stabilize the tryptophan 1 L a excited state, which has a large dipole moment. 35 As shown in Fig. 1f, there are overlapping regions between absorption and emission spectra of 3 Trp groups, leading to possible RET. The tryptophan spectra in Fig. 1e reveal an energetic ordering that favors excitation-energy ow from 6W d to 3W p /4W c and from 3W p to 4W c . ...
Photosynthetic pigments form light-harvesting networks to enable nearly perfect quantum efficiency in photosynthesis via excitation energy transfer. However, similar light-harvesting mechanisms have not been reported in light sensing processes in other classes of photoreceptors during light-mediated signaling. Here, based on our earlier report, we mapped out a striking energy-transfer network composed of 26 structural tryptophan residues in the plant UV-B photoreceptor UVR8. The spectra of the tryptophan chromophores are tuned by the protein environments, funneling all excitation energy to a cluster of four tryptophan residues, a pyramid center, where the excitation-induced monomerization is initiated for cell signaling. With extensive site-directed mutagenesis, various time-resolved fluorescence techniques, and combined QM/MM simulations, we determined the energy-transfer rates for all donor–acceptor pairs, revealing the time scales from tens of picoseconds to nanoseconds. The overall light harvesting quantum efficiency by the pyramid center is significantly increased to 73%, compared to a direct excitation probability of 35%. UVR8 is the only photoreceptor discovered so far using a natural amino-acid tryptophan without utilizing extrinsic chromophores to form a network to carry out both light harvesting and light perception for biological functions.
... Charge transfer (CT) complexes of biologically significant quinones with a variety of donors have been studied in recent years, because of their wide applications ranging from different fields [1][2][3][4]. In the field of material science which can be used as organic semiconductors, photocatalysts and redox reagents [5][6][7][8][9]. In natural biological systems quinones present in the form of substituted p-benzoquinones such as plastoquinones [10], Vitamin K [11], ubiquinones [12], etc. ...
Molecular charge-transfer interaction of a series of electron π-acceptors of 1,4-benzoquinone (BQ), 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ) and Tetracyanoquinodimethane (TCNQ) with selected donors of 1-phenyl-1,2,3,4-tetrahydroisoquinoline (PTHIQ) and 4-aminoacetanilide (ACE) have been studied in methanol at room temperature. The stoichiometry of the complexes was determined by photometric titration method and was found to be 1:1, in all the cases. Spectro-kinetic interaction studies along with rate constants and observed formation constants (K) indicated that the strength of the complex formations is PTHIQ-BQ < PTHIQ-DDQ < PTHIQ-TCNQ. Also, Similar observations happened in ACE-BQ and < ACE-DDQ < ACE-TCNQ systems. FT-IR results indicated that the point of interaction was identifying in NH moiety of PTHIQ and NH2 moiety of ACE with series of π-acceptor complexes. The experimental results were compared with Ab initio DFT calculations at the B3LYP/6-31 + G(d) level of theory. The increasing order of the experimentally measured formation constant of CT-complexes (PTHIQ and ACE with series of acceptors) was well supported by theoretical HOMO-LUMO energy gap and drastically changes in Mulliken charges of NH moiety of PTHIQ, NH2 moiety of ACE with complexation with acceptors.
... The photochemistry and photophysics of isolated heteroaromatic molecules has been the subject of many experimental and theoretical studies [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16][17][18]. This interest has been driven in part because molecules in this class are considered as useful, tractable models for the DNA nucleobases and, by extension, nucelotides. ...
Following on from previous experimental and theoretical work [Neville et al., Nat. Commun. 7, 11357 (2016)], we report the results of a combined electronic structure theory and quantum dynamics study of the excited state dynamics of the pyrrole dimer following excitation to its first two excited states. Employing an exciton-based analysis of the Ã(π3s/σ*) and B̃(π3s/3p/σ*) states, we identify an excited-state electron transfer pathway involving the coupling of the Ã(π3s/σ*) and B̃(π3s/3p/σ*) states and driven by N–H dissociation in the B̃(π3s/3p/σ*) state. This electron transfer mechanism is found to be mediated by vibronic coupling of the B̃ state, which has a mixed π3s/3p Rydberg character at the Franck-Condon point, to a high-lying charge transfer state of the πσ* character by the N–H stretch coordinate. Motivated by these results, quantum dynamics simulations of the excited-state dynamics of the pyrrole dimer are performed using the multiconfigurational time-dependent Hartree method and a newly developed model Hamiltonian. It is predicted that the newly identified electron transfer pathway will be open following excitation to both the Ã(π3s/σ*) and B̃(π3s/3p/σ*) states and may be the dominant relaxation pathway in the latter case.
... Parallels can be drawn between these results and the behavior of the 1 L b absorption band of indole. 64,65 Callis 63 observed negative lobes to be present in the 2PA tensor of pure indole, which were then reduced significantly upon the addition of a single methyl group to the pyrole ring. The difference in the 2PA tensors of the short and long lifetime species of NAD(P)H clearly cannot be attributed to differing substituent groups. ...
Two-photon absorption (2PA) finds widespread application in biological systems, which frequently exhibit heterogeneous fluorescence decay dynamics corresponding to multiple species or environments. By combining polarised 2PA with time-resolved fluorescence intensity and anisotropy decay measurements, we show how the two-photon transition tensors for the components of a heterogeneous population can be separately determined, allowing structural differences between the two fluorescent states of the redox cofactor NAD(P)H to be identified. The results support the view that the two states correspond to alternate configurations of the nicotinamide ring, rather than folded and extended conformations of the entire molecule.
... Whilst this state cannot be directly accessed, its position relative to the 1 ππ * state dictates the dynamics that occurs and the location of the crossing points. This has been observed in a variety of planar organic molecules [9,11]. This difference in positions of the two states and the effect becomes apparent when comparing the photodissociation of phenol with pyrrole [10,12,13]. ...
The photoelectron spectrum for the two lowest ionisation bands of phenol has been simulated using quantum dynamic methods. A vibronic coupling Hamiltonian was set up consisting of seven vibrational modes and the first two ionised states. Parameters for the model are obtained by fitting adiabatic surfaces to a series of points calculated using ab initio methods. Such a model allows non-adiabatic couplings between the states to be included. CASSCF calculations used in this work provide reliable quantum chemical information for the model and the calculated photoelectron spectrum shows good agreement to experiment. The vibrational fine structure of both bands are reassessed and different assignments to those previously reported are detailed. The existence of a conical intersection between the ionised states is reported and its role in the dynamics of phenol upon ionisation is examined.
... In the past, computational studies of isolated chromophores' photochemistry demonstrated that population of the low-lying repulsive ps* states leads to N-H and O-H bond ssion processes resulting in the formation of a ps*/S 0 conical intersection. [32][33][34][35][36][37] The character of this repulsive state is changed in solution through direct interactions of a chromophore with solvent molecules, such as water or ammonia, which leads to charge-transfer-to-solvent (CTTS) phenomenon and formation of a solvated electron. 32,33 The latter might be followed by a consecutive proton transfer from a chromophore to a nearby water molecule yielding a hydronium cation and a radical form of a chromophore. ...
2-aminoimidazole (2-AIM) was proposed as a plausible nucleotide activating group in a nonenzymatic copying and polymerization of short RNA sequences under prebiotically plausible conditions. One of the key selection factors controlling the lifespan and importance of organic molecules on the early Earth is ultraviolet radiation from the young Sun. Therefore, to assess suitability of 2-AIM for prebiotic chemistry, we performed non-adiabatic molecular dynamics simulations and static explorations of potential energy surface of the photoexcited 2-AIM-(H2O)5 cluster by means of the algebraic diagrammatic construction method to the second-order [ADC(2)]. Our quantum mechanical simulations demonstrate that ¹πσ∗ excited states play a crucial role in the radiationless deactivation of UV-excited 2-AIM-(H2O)5 system. More precisely, electron-driven proton transfer (EDPT) along water wires is the only photorelaxation pathway leading to the formation of ¹πσ∗/S0 conical intersections. The availability of this mechanism and lack of destructive photochemistry indicate that microhydrated 2-AIM is characterized by substantial photostability and resistance to prolonged UV irradiation.
... It is believed that the ultrafast internal conversion and energy redistribution processes provide the pathways for the photostability of biomolecules and help them survive through UV radiation. 1-6 The investigation of the photostability of peptides [7][8][9] and amino acids [10][11][12][13] leads to the photochemical study of phenol, [14][15][16][17][18][19][20][21][22] indole, [23][24][25][26][27][28][29][30] pyrrole, 24,[31][32][33][34] and imidazole, [35][36][37][38][39] the chromophore component in tyrosine, tryptophan, and histidine that dominates the ultraviolet absorption spectra of many biological molecules. ...
Phenol is an important model molecule for the theoretical and experimental investigation of dissociation in the multistate potential energy surfaces. Recent theoretical calculations [X. Xu et al., J. Am. Chem. Soc. 136, 16378 (2014)] suggest that the phenoxyl radical produced in both the X and A states from the O–H bond fission in phenol can contribute substantially to the slow component of photofragment translational energy distribution. However, current experimental techniques struggle to separate the contributions from different dissociation pathways. A new type of time-resolved pump-probe experiment is described that enables the selection of the products generated from a specific time window after molecules are excited by a pump laser pulse and can quantitatively characterize the translational energy distribution and branching ratio of each dissociation pathway. This method modifies conventional photofragment translational spectroscopy by reducing the acceptance angles of the detection region and changing the interaction region of the pump laser beam and the molecular beam along the molecular beam axis. The translational energy distributions and branching ratios of the phenoxyl radicals produced in the X, A, and B states from the photodissociation of phenol at 213 and 193 nm are reported. Unlike other techniques, this method has no interference from the undissociated hot molecules. It can ultimately become a standard pump-probe technique for the study of large molecule photodissociation in multistates.
... [14][15][16] More recently, it has been theoretically predicted that the lowest 1 πσ* excited state of dissociative character plays an important role in the hydrogen-atom photodetachment from the N1− −H bond. [17][18][19] This prediction was confirmed by photofragment translational spectroscopy and pump-probe experiments, where slow and fast hydrogen atoms were observed to dissociate from UV-excited molecules of a) Author to whom correspondence should be addressed: mjnow@ifpan.edu.pl indole seeded in supersonic jet expansions. ...
Photochemical transformations were studied for monomers of indole and 3-formylindole isolated in low-temperature noble-gas matrices. Upon UV (λ > 270 nm) irradiation of indole trapped in argon and neon matrices, the initial 1H-form of the compound converted into the 3H-tautomer. Alongside this photoinduced hydrogen-atom transfer, an indolyl radical was also generated by photodetachment of the hydrogen atom from the N1–H bond. Excitation of 3-formylindole isolated in an argon matrix with UV (λ > 335 nm) light led to interconversion between the two conformers of the 1H-tautomer, differing from each other in the orientation of the formyl group (cis or trans). Parallel to this conformational phototransformation, the 3H-form of the compound was generated in the 1H → 3H phototautomeric conversion. The photoproducts emerging upon UV irradiation of indole and 3-formylindole were identified by comparison of their infrared spectra with the spectra calculated for candidate structures.
... 108,265,266 Needless to say, such progress in photobiology was dependent on progress on the theoretical photochemistry front. For instance, Domcke, 258,267 Koppel, 268 Cederbaum, 269 and Martínez 270 and co-workers, among others, played a vital role in rigorously demonstrating how ultrafast decay occurs at CIs. The demonstration, by quantum dynamics calculations, that few vibrational degrees of freedom are sufficient for irreversible radiationless decay at CIs led to a fundamental change of paradigms in radiationless decay theory. ...
Ultrafast processes in light-absorbing proteins have been implicated in the primary step in the light-to-energy conversion and the initialization of photoresponsive biological functions. Theory and computations have played an instrumental role in understanding the molecular mechanism of such processes, as they provide a molecular-level insight of structural and electronic changes at ultrafast time scales that often are very difficult or impossible to obtain from experiments alone. Among theoretical strategies, the application of hybrid quantum mechanics and molecular mechanics (QM/MM) models is an important approach that has reached an evident degree of maturity, resulting in several important contributions to the field. This review presents an overview of state-of-the-art computational studies on subnanosecond events in rhodopsins, photoactive yellow proteins, phytochromes, and some other photoresponsive proteins where photoinduced double-bond isomerization occurs. The review also discusses current limitations that need to be solved in future developments.
The photoionization dynamics of indole, the ultraviolet-B chromophore of tryptophan, were explored in water and ethanol using ultrafast transient absorption spectroscopy with 292, 268, and 200 nm excitation. By studying the femtosecond-to-nanosecond dynamics of indole in two different solvents, a new photophysical model has been generated that explains many previously unsolved facets of indole’s complex solution phase photochemistry. Photoionization is only an active pathway for indole in aqueous solution, leading to a reduction in the fluorescence quantum yield in water-rich environments, which is frequently used in biophysical experiments as a key signature of the protein-folded state. Photoionization of indole in aqueous solution was observed for all three pump wavelengths but via two different mechanisms. For 200 nm excitation, electrons are ballistically ejected directly into the bulk solvent. Conversely, 292 and 268 nm excitation populates an admixture of two ¹ππ* states, which form a dynamic equilibrium with a tightly bound indole cation and electron–ion pair. The ion pair dissociates on a nanosecond time scale, generating separated solvated electrons and indole cations. The charged species serve as important precursors to triplet indole production and greatly enhance the overall intersystem crossing rate. Our proposed photophysical model for indole in aqueous solution is the most appropriate for describing photoinduced dynamics of tryptophan in polypeptide sequences; tryptophan in aqueous pH 7 solution is zwitterionic, unlike in peptides, and resultantly has a competitive excited state proton transfer pathway that quenches the tryptophan fluorescence.
We investigate the molecular origin of the fluorescence Stokes shift in an aqueous liquid. By examining the speed of energy change, the solvation response function is explicitly projected onto the translational and rotational motions of water molecules for both nonequilibrium relaxation and equilibrium fluctuations. Molecular dynamics simulations of a tryptophan solution show that these two processes have highly consistent dynamics, not only for the total response function but also for the decomposed components in terms of specific molecular movements. We found that the rotational mode governs the relaxation of the Stokes shift, whereas the translational mode contributes non-negligibly with slower dynamics. This consistency implies the similarity of the underlying translational and rotational movements of water molecules as the system is far away from and at equilibrium, supporting the validity of the linear response theory at the molecular level. The decomposition methodology is also applicable to a rigid solvent.
The rotationally resolved electronic spectrum of the S1←S0 electronic origin band of 6-methylindole (6-MI) has been measured in a molecular beam and has been fit to rigid asymmetric rotor Hamiltonians in both electronic states using evolutionary strategies. Rotational constants, dipole moments in both electronic states, and orientation of the transition dipole moment in the inertial frame of the molecule have been determined and compared to the results of ab initio calculations. Both the values of the permanent dipole moments as of the transition dipole moment point to an Lb-state as lowest electronically excited state in 6-MI.
In this work, we report the photophysical properties of three thiol derivatives, commonly used as
photoinitiators in thiol–ene free radical polymerization, the ultimate goal being to rationalize the main
reason behind the photoinitiation efficiency. For this aim, time dependent density functional theory is
used to simulate the absorption spectra of alkyl thiol (R–SH), thiophenol (PhSH) and p-(trifluoromethyl)
thiophenol (p-CF3PhSH), describe their excited state topologies, and explore their potential energy
surfaces along the S–H dissociation. Excited state calculations have shown that the S–H photolysis is
achieved through the triplet excited states following intersystem crossing from the originally populated
singlet manifolds. More specifically, while in aromatic thiol derivatives dissociation is mainly triplet-state
mediated, the first excited singlet state and first triplet state of alkyl thiol are both dissociative and hence
potentially capable of generating the photoinduced radical species. We have also justified the
experimental findings concerning the photoinitiator efficiency considering both their potential energy
surface topologies and the absorption intensity, in the lowest energy region.
Although the amino acid tyrosine is among the main building blocks of life, its photochemistry is not fully understood. Traditional theoretical simulations are neither accurate enough, nor computationally efficient to provide the missing puzzle pieces to the experimentally observed signatures obtained via time-resolved pump-probe spectroscopy or mass spectroscopy. In this work, we go beyond the realms of possibility with conventional quantum chemical methods and develop as well as apply a new technique to shed light on the photochemistry of tyrosine. By doing so, we discover roaming atoms in tyrosine, which is the first time such a reaction is discovered in biology. Our findings suggest that roaming atoms are radicals that could play a fundamental role in the photochemistry of peptides and proteins, offering a new perspective. Our novel method is based on deep learning, leverages the physics underlying the data, and combines different levels of theory. This combination of methods to obtain an accurate picture of excited molecules could shape how we study photochemical systems in the future and how we can overcome the current limitations that we face when applying quantum chemical methods.
The excited state dipole moment of the lowest excited singlet state of 2,3-benzofuran in ethylacetate solution is determined using thermochromic spectroscopy and compared to the values, obtained for the isolated molecule from electronic Stark spectroscopy (M.-L. Hebestreit, et al., J. Mol. Struct., 2020, 1210, 127992) and to the results of ab initio calculations at coupled cluster level of theory. It is shown that the dipole moment from thermochromic shifts in solution deviates considerably from that of the isolated molecule. This finding can be traced back to a field induced mixing by the strong reaction field of the solvent, which exceeds the external Stark field applied in gas phase measurements by a factor of 10.000. Depending on the dipole moments of the perturbing state and its energy gap to the excited state, dipole moments from thermochromic shifts (and consequently also of solvatochromic shifts) might be considerably different to gas phase values. However, the alteration of the electronic configuration of the molecule via the reaction field of the solvent can be deperturbed in the high-field limit.
In this work, we adopt theoretical calculation manner to explore excited state dynamical behaviors of intramolecular hydrogen bond and proton transfer (ESIPT) process for a novel organic 3-(benzo[d]thiazol-2-yl)-2-hydroxy-5-methoxybenzaldehyde (BTHMB) system. Insights into changes of chemical geometries and infrared (IR) vibrational behaviors, we judge excited state hydrogen bonding strengthening for BTHMB. Our estimated hydrogen bonding energies further check the intramolecular hydrogen bond of BTHMB should be strengthened much stronger in polar solvent. Photo-induced charge reorganization and negative charges concentrated on N moiety facilitate ESIPT reaction for BTHMB. Probing into frontier molecular gap, we infer in polar solvent, intramolecular hydrogen bonding activities and molecular reactional kinetic initiatives become more obvious. By means of restricted optimization, we further construct potential energy curves (PECs) along with ESIPT direction. In addition, via searching reactional transition state (TS) and IRC simulations, we present the ultrafast ESIPT reaction of BTHMB could be regulated via solvent polarity.
Aggregation-induced emission (AIE), usually referring to the phenomenon in which molecules emit more strongly in the aggregate state than in the solution state, is intriguing and promising in various optoelectronic and biosensing applications. In this Perspective, the basic principles that can lead to AIE and experimental evidence to reveal the AIE mechanism of tetraphenyl ethylene (TPE)-type molecules are discussed. AIE is the consequence of two factors: (1) the fast energy dissipation by crossing a conical intersection (CI) in solutions but not in solids results in low luminescence efficiencies in the solutions, and (2) the weak intermolecular coupling and thus slow intermolecular energy/charge transfers in the AIE solids effectively prevent quenching and result in relatively high luminescence efficiencies. The key to AIE is that the luminescence efficiency is tuned by controlling molecules to cross or not to cross a CI by changing the phase of molecules. How fast a molecule can cross a CI is dependent on the energy barrier of isomerization, which can be tuned in many ways, including mechanical or electrical stimuli, in addition to changing phases. Barrier-dependent crossing CI also results in a very important consequence: excitation-wavelength-dependent fluorescence yield within one electronic excited state, an anti-Vavilov's rule phenomenon. In principle, there can be an alternative way to tune luminescence efficiency by manipulating the formation of CIs instead of crossing or not crossing them. This approach relies on the fact that the electronic ground state and the excited state have many different properties, e.g., dipole moment. By tuning the environment, e.g., dielectric constant, to favor or disfavor one state, one may be able to lift or lower the potential surface of one state so that the potential surfaces of two states can vary between intersected and not contacted.
The photodissociation dynamics of pyrrole-ammonia clusters (PyHÁ(NH 3) n , n = 2-6) has been studied using a combination of velocity map imaging and non-resonant detection of the NH 4 (NH 3) nÀ1 products. The excited state hydrogen-atom transfer mechanism (ESHT) is evidenced through delayed ionization and presents a threshold around 236.6 nm, in agreement with previous reports. A high resolution determination of the kinetic energy distributions (KEDs) of the products reveals slow (B0.15 eV) and structured distributions for all the ammonia cluster masses studied. The low values of the measured kinetic energy rule out the existence of a long-lived intermediate state, as it has been proposed previously. Instead, a direct N-H bond rupture, in the fashion of the photodissociation of bare pyrrole, is proposed. This assumption is supported by a careful analysis of the structure of the measured KEDs in terms of a discrete vibrational activity of the pyrrolyl co-fragment.
We present an overview of experimental and theoretical investigations exploring the dynamical evolution of Rydberg-to-valence character in the electronically excited states of small polyatomic molecules. Time-resolved photoelectron imaging (TRPEI), in conjunction with high-level quantum chemistry calculations, permits detailed insight into the non-adiabatic processes operating in these systems and we review several case studies drawn from our own work in this area over the last few years. Electronically excited Rydberg states that develop significant valence character along specific molecular coordinates provide potentially important pathways for the rapid and efficient redistribution of excess energy following ultraviolet absorption. As such, there is considerable interest in developing better understanding of role of these states play within a broad range of different photochemical environments. A central theme of this review considers the way in which key energy – and angle-resolved observables in TRPEI measurements are influenced by different aspects of transitory Rydberg-to-valence behaviour. Several themes are discussed within a coherent narrative, drawing on experimental and theoretical findings in a selected series of small organic species containing nitrogen heteroatoms. Critically, many of the effects we highlight will also be generalisable to related studies interrogating non-adiabatic processes within a much broader range of molecular systems.
The rotationally resolved electronic spectra of the origin band of 2,3-benzofuran has been measured and analyzed. Using electronic Stark spectroscopy, the dipole moments in the ground and electronically excited state have been determined. From the values for the permanent dipole moments, the orientation of the transition dipole moment and from the geometry changes upon excitation, the lowest excited singlet state could be shown to be of ¹Lb symmetry. These results are compared to those of indole in particular. Moreover, the excited state lifetime of isolate 2,3-benzofuran in the gas phase has been determined to be 14 ns and compared to the excited state lifetime of 2,3-benzofuran in ethylacetate solution of 4 ns
An analytic full-dimensional diabatic potential energy matrix (DPEM) for the lowest three singlet states of thiophenol (C6H5SH) at geometries accessible during photodissociation is constructed using the anchor points reactive potential (APRP) scheme. The data set used for modeling is obtained from electronic structure calculations including dynamic correlation via excitations into the virtual space of a three-state multiconfiguration self-consistent field calculation. The resulting DPEM is a function of all the internal coordinates of thiophenol. The DPEM as a function of the S−H bond stretch and C−C−S−H torsion and the diabatic couplings along two in-plane bend modes and nine out-of-plane distortion modes are computed using extended multiconfigurational quasidegenerate perturbation theory followed by the fourfold way determination of diabatic molecular orbitals and model space diabatization by configurational uniformity, and this dependence of the DPEM is represented by general functional forms. Potentials along 31 tertiary internal degrees of freedom are modeled with system-dependent, primary-coordinate-dependent nonreactive molecular mechanics-type force fields that are parameterized by Cartesian Hessians calculated by generalized Kohn-Sham density functional theory. Adiabatic potential energy surfaces (PESs) and nonadiabatic couplings are obtained by a transformation of the DPEM. The topography of the APRP PESs is characterized by vertical excitation energies, equilibrium geometries, vibrational frequencies, and conical intersections, and we find good agreement with available reference data. This analytic DPEM is suitable for full-dimensional electronically nonadiabatic molecular dynamics calculations of the photodissociation of thiophenol with analytic gradients in either the adiabatic or diabatic representation.
The nonradiative deactivation mechanisms of the lowest ¹ππ excited states in four protonated isomers of the 7H- and 9H-xanthine, based on the MP2, CC2, ADC(2) and CASSCF theoretical methods have been investigated. It has been predicted that out-of-plane driving coordinates are effectively responsible for photostability of these systems at the Franck-Condon region of the ¹ππ* excited state, while the NH or OH stretching coordinates can be suggested to play the deactivation role in the higher energetic range based on the ¹πσ* state. The different deactivation mechanisms provide significant supports for photostability of protonated xanthine in the wide range of UV radiation as well as its neutral homologue. Also, from spectroscopy points of view, no significant alteration in the ¹ππ*-S0 electronic transition has been predicted to occur following protonation.
A detailed understanding of radiative and nonradiative processes in peptides containing an aromatic chromophore requires the knowledge of the nature and energy level of low-lying excited states that could be coupled to the bright 1ππ* excited state. Isolated aromatic amino acids and short peptides provide benchmark cases to study, at the molecular level, the photoinduced processes that govern their excited state dynamics. Recent advances in gas phase laser spectroscopy of conformer-selected peptides have paved the way to a better, yet not fully complete, understanding of the influence of intramolecular interactions on the properties of aromatic chromophores. This review aims at providing an overview of the photophysics and photochemistry at play in neutral and charged aromatic chromophore containing peptides, with a particular emphasis on the charge (electron, proton) and energy transfer processes. A significant impact is exerted by the experimental progress in energy- and time-resolved spectroscopy of protonated species, which leads to a growing demand for theoretical supports to accurately describe their excited state properties.
The photoinduced S–H (D) bond fission dynamics of four ortho-substituted thiophenols: 2-fluoro, 2-chloro, 2-bromo, and 2-methoxythiophenol at the pump wavelength of 243 nm, have been investigated by velocity-map imaging and high-level electronic structure calculations. The D atom images of the deuterated ortho-substituted thiophenols show much reduced X ̃/Ã branching ratios of the co-fragment radicals over that of bare thiophenol. The angular distributions of the D fragment display negative anisotropies, indicating that transition dipole moments are perpendicular to the fast dissociating S–D bond axis. Initial excitation at 243 nm occurs directly to the 1πσ* state or to the 21ππ* state followed by efficient coupling to the 1πσ* state. The calculated potential energy curves for the 1πσ* or 21ππ* excited states of the ortho-substituted thiophenols along the CCS–D torsion angle (ϕ) display minima at the nonplanar structures, whereas all the states for bare thiophenol present minima at the planar geometries. This different topology of the ortho-substituted thiophenols in the excited states induces the wide spread of the reactive flux along the ϕ coordinate on the repulsive surface as it should experience significant torque with respect to ϕ during the fragmentation. This encourages the dissociating molecules to follow the adiabatic path at the conical intersection between the ground and 1πσ* states at extended S–D bond lengths, giving rise to decreased X ̃/Ã branching ratios, demonstrating that the excited-state molecular structure dictates the nonadiabatic transition probability.
Tetrahydropterins are essential biological cofactors, which play crucial role in DNA and RNA synthesis, NO synthesis, hydroxylation of aromatic amino acids, etc. In the last few years it was shown that 6-substituted “unconjugated” tetrahydropterins can also play a photoreceptor chromophoric role in plants and cyanobacteria. However, the nature of the initial light signal transduction act in which H4pterins participate is unknown. Our quantum chemical calculations have shown the possibility of fast internal conversion of excited states of H4pterins. It was demonstrated for the first time that the nature of the excited states of H4pterins is similar to the nature of excited states of guanine.
Absorption and luminescence spectra of 7-azaindole vapor were measured. The absorption spectrum in the range 240–300 nm had a broad band with a superimposed sequence of vibrational maxima. The luminescence spectrum exhibited two bands, one of which with λmax = 305 nm belonged to fast fluorescence and the second of which with λmax = 520 nm, to long-lived luminescence. The fluorescence spectrum with excitation near the 0–0-transition (λex = 289 nm) was quasilinear. The fluorescence spectrum was diffuse at other excitation wavelengths. Long-lived luminescence decaying in the microsecond range was interpreted as luminescence of free radicals formed as a result of triplet–triplet annihilation. Excited states of free radicals were populated by nonradiative energy transfer from 7-azaindole triplet states into free-radical doublet states.
The electronic spectrum of thiophenol was simulated by a normal-mode sampling approach combined with TDDFT in the Tamm-Dancoff approximation (TDA). The vertical excitation energies were compared with electronic structure calculations by completely renormalized equation-of-motion coupled cluster theory with single and double excitations and noniterative inclusion of connected triples (CR-EOM-CCSD(T)) and by multi-reference perturbation theory. Using multireference-perturbation-theory adiabatic wave functions and model-space diabatization by the fourfold way, diabatic potential energy surfaces of the lowest three singlet states (1ππ, 1ππ*, and 1nπσ*) were constructed along the S−H stretching coordinate, the C−C−S−H torsion coordinate, and the v16a and v16b normal coordinates. The first two of these two can serve as primary coordinates for constructing analytic full-dimensional potential energy surfaces, and the diabatic crossing seams of the three states were calculated and plotted as functions of the two coordinates. The other two coordinates are out-of-plane ring distortion modes studied to assess the extent of their role in coupling the states near the first conical intersection, and the v16a mode was shown to be an important coupling mode there.
Room‐temperature phosphorescence (RTP)‐based sensors have distinctive advantages over the fluorescence counterparts, such as larger Stokes shifts and longer lifetimes. Unfortunately, almost all RTP sensors are operated on quenching‐based mechanisms given the sensitive nature of the emissive triplet state. Here we report a type of thioether RTP molecules that shows RTP “turn‐on” when volatile acid vapors such as HCl are in contact. To elucidate the underlying mechanism, model thioethers containing different donor/acceptor combinations are investigated via fluorescence spectroscopy and theoretical calculations aided by molecular coordinates obtained from single‐crystal X‐ray diffraction. It is revealed that a charge‐transfer character in the phosphorescence state is crucial. The “turn‐on” design concept may significantly broaden the sensing application scope for organic RTP molecules.
Understanding the properties of electronically excited states is a challenging task that becomes increasingly important for numerous applications in chemistry, molecular physics, molecular biology, and materials science. A substantial impact is exerted by the fascinating progress in time-resolved spectroscopy, which leads to a strongly growing demand for theoretical methods to describe the characteristic features of excited states accurately. Whereas for electronic ground state problems of stable molecules the quantum chemical methodology is now so well developed that informed nonexperts can use it efficiently, the situation is entirely different concerning the investigation of excited states. This review is devoted to a specific class of approaches, usually denoted as multireference (MR) methods, the generality of which is needed for solving many spectroscopic or photodynamical problems. However, the understanding and proper application of these MR methods is often found to be difficult due to their complexity and their computational cost. The purpose of this review is to provide an overview of the most important facts about the different theoretical approaches available and to present by means of a collection of characteristic examples useful information, which can guide the reader in performing their own applications.
Electron Localization Function analysis reveals the details of a Charge Induced Hydrogen Detachment mechanism of 3-amino-1,2,4-triazole, identified recently as responsible for phototautomerization of the molecule. . In this process the vertical excitation to 1πσ* state is followed by the barrier-less migration of H atom along the N-H bond toward the conical intersection with S0 ground state. The most striking feature revealed for the 1πσ* state is partial ejection of σ* electron outside the molecule, even beyond the NH group, at the Franck-Condon point. Further gradual spatial localization of the electron around the proton moving along the N-H stretching coordinate gives a plausible explanation of the repulsive character of 1πσ* potential energy surface with the proton wadding through the region of space where some negative charge is accumulated (‘a virtual acceptor’) dragging some electron density. This mechanism resembles the one postulated for the hydrogen transfer from a donor molecule (D-H) to an acceptor one (A) in a class of vertically excited molecules with a preexisting inter- or intramolecular D-H···A motif, even though the acceptor molecule is not present. Present analysis demonstrate also that the bond evolution and changes in electron density along the excited state reaction path can be effectively studied with the use of an electron localization function.
Radiative and nonradiative decay paths from the first excited singlet electronic state (S1) in four heteroaromatics, indole, isoindole, quinoline, and isoquinoline, were systematically explored. Three decay processes, i.e., internal conversion (IC), intersystem crossing (ISC), and fluorescence emission (FE), were compared. Minimum energy conical intersection structures between the electronic ground and first excited states were investigated to determine the most preferred IC path. Minimum energy seam of crossing (MESX) geometries between S1 and lowest-lying triplet states and the spin–orbit couplings at these MESX structures were computed to identify the most feasible ISC path. The oscillator strength was calculated at each S1 local minimum to reveal the contribution of the FE process. The calculations clearly showed that indole had the highest fluorescent quantum yield, consistent with experimental data. The present calculations also explained other experimental properties of the heteroaromatics such as ISC quantum yields.
Hierarchy among the weak noncovalent interactions such as van der Waals, electrostatic, hydrogen bonding etc. dictates the secondary and tertiary structures of proteins as well as their interactions with various ligands. In this work, we investigate the competition between conventional (N−H···O), unconventional (C−H···O) hydrogen bonds, and van der Waals interaction in the model compounds of the chromophores of the amino acids, tryptophan and histidine. These include indole (IND), benzimidazole (BIM), and its N-methylated analog (N-methylbenzimidazole, MBIM) which present multiple docking sites. The binary complexes of these molecules with ethers (dimethyl ether, diethyl ether, and tetrahydrofuran) which possess high proton affinity but lack acidic protons (thereby only act as hydrogen bond acceptors) are investigated. The complexes are formed in a supersonic jet and jointly studied by electronic and vibrational spectroscopy as well as quantum chemical calculations. Only the N−H···O bound structures are observed for the complexes of IND and BIM with ethers, although computations predict reasonably competent C−H···O type of structures. Remarkably, IND and BIM produce three (N−H···O) conformers with Me2O but single conformers with Et2O and THF. In the case of MBIM, which lacks a conventional hydrogen bond donor, no evidence for C(2)−H···O hydrogen bonds is seen; instead, the complexes are found to be bound purely by van der Waals interactions. The results indicate that strong N−H···O and even weak van der Waals interactions are thermodynamically favored over C(2)−H···O bound structures in these binary gas-phase complexes.
The changes observed in the ultraviolet absorption spectra of indole and 1-methyl indole between the gaseous state and the solution, suggest the existence of a low-lying molecular Rydberg state.
The absorption and emission solvatochromism of five indole derivatives was studied by referring the shifts to the corresponding vapor-phase wave numbers. The emission results clearly demonstrate, in three cases, the change in the nature of the emitting state when the solvent polarity is increased. In absorption, a large red shift in the 1La band is observed in all polar solvents, and this cannot be explained by classical solvent–solute interaction forces. The temperature dependence of the emission shift in a viscous solvent (glycerol) confirms that most of the emission shift is due to solvent relaxation. The 1La–1Lb level inversion model applied to ground-state polar solvent–solute complex, can account for most of the solvatochromism features observed.
Absorption spectra and fluorescence spectra of indile, 5-methoxyindole, 1-methyl indole, and 2,3-dimethyloudole are reported. The mean nonradiative decay rates were deduced from the measured lifelime and quantum yield.(AIP)
Substitution of a methyl group around the indole ring has been used as a method for mildly perturbing the indole absorption spectrum. Comparison of the spectra of two methylindoles by a subtraction technique has allowed the separation of the overlapping 1La and 1Lb bands, whose oscillator strengths were found to be 0.123 and 0.045 respectively.
Two new split-valence basis sets, termed 6-21G and 3-21G, recently proposed for use in molecular orbital calculations on molecules containing first-row elements have been extended through the second row. The valence functions for the smaller representation (3-21G) have been taken directly from the larger (6-21G), preventing their collapse inwards to make up for deficiencies in the inner-shell region. This is necessary to ensure a good description of bonding interactions which necessarily involve overlap of valence functions. Equilibrium geometries, vibrational frequencies, relative energies, and electric dipole moments calculated with the use of the 3-21G basis set for a number of molecules containing second-row atoms are nearly identical with those obtained from the larger 6-21G representation. Compared to experiment they are consistently superior to properties derived from the STO-3G minimal basis set, and of comparable quality to those obtained from the larger 4-31G split-valence representation. The 3-21G basis set comprises the same number of primitive Gaussian functions as STO-3G (although a significantly greater number of basis functions), and should be nearly as efficient computationally as that representation for applications which require evaluation of energy derivatives as well as the energy itself (e.g., determination of equilibrium geometry and calculation of vibrational frequencies). It is significantly less costly to apply than the 4-31G basis set, and would appear to be the method of choice for split-valence level Hartree-Fock calculations on moderately sized molecules.
The complete active space (CAS) SCF method and multiconfigurational second-order perturbation theory (CASPT2) have been used in a theoretical analysis of the electronic spectrum of indole. The calculations comprise a large number of singlet and triplet valence and Rydberg excited states with the aim to obtain a full understanding of the electronic spectrum. In addition to the gas-phase spectra, solvatochromic shifts have been computed at the CASPT2 level for the low-lying singlet valence states using a continuum representation of the solvent with the solute in a spherical cavity. The results support the assignments of two low-lying π → π* valence singlet excited states, 1Lb and 1La, computed at 4.43 and 4.73 eV in the gas phase. The location of the 1La band origin 0.23 eV above the 1Lb band origin is in agreement with the most recent experimental studies. The most intense feature of the spectrum is obtained at 5.84 eV as a π → π* singlet excited valence state. In total 25 singlet states have been computed, including 2 Rydberg series and 7 valence excited states, and in addition 15 triplet excited states. The solvatochromic shifts in the absorption and emission bands for the 1Lb and 1La states show the large sensitivity of the 1La state to the polarity of the solvent. The change in the main fluorescing state on going from nonpolar (1Lb state) to polar solvents (1La state) is confirmed by the calculations.
Second-order perturbation theory based on a CASSCF reference state is derived and implemented. The first-order wave function includes the full space of interacting states. Expressions for the contributions to the second-order energy are obtained in terms of up to four-particle density matrices for the CASSCF reference state. The zeroth-order Hamiltonian reduces to the Møller-Plesset Hamiltonian for a closed-shell reference state. The limit of the implementation is given by the number of active orbitals, which determines the size of the density matrices. It is presently around 13 orbitals. The method is illustrated in a series of calculations on H 2, H 2O, CH 2, and F -, and the results are compared with corresponding full CI results.
A comprehensive study of the electronic spectra and decay dynamics of jet-cooled indole and substituted indoles has revealed the presence of an additional electronic state above the 1Lb, origin of 2,3-dialkylindoles. Results for indole, 1-methylindole, 3-methylindole, and 5-methoxyindole are found to be consistent with the presence of a single bound excited electronic state in the energy regions examined. However, for 2,3-dimethylindole and 1,2,3,4-hydrocarbazole, evidence for an additional electronic state has been found and assigned to the elusive 1La state. For these two molecules, electronic predissociation has been observed and attributed to coupling of the lowest energy excited state (1Lb) with a dissociative 1La state. Based on isotope effects and theoretical considerations, the dissociation pathway is suggested to be N-H bond cleavage. Formation of van der Waals molecules between jet-cooled indoles and the polar molecules methanol, trimethylamine, and ammonia demonstrates that the 1La state is stabilized to a much greater extent by polar solvent molecules than is the 1Lb state, in agreement with previous solution-phase studies. Implications of these results for future investigations of the 1La state of indoles are discussed.
The 1Lb and 1La excited state optimized energies and wave functions of indole are computed at the CIS/3-21G and CIS-MP2/3-21G levels. The 1Lb geometry is found to be compatible with experimental vibronic structure. The optimized ground state electronic wave function and energy were obtained using the HF and MP2 methods with several basis sets ranging in quality up to MP2/6-31G*. Vertical transition energies, oscillator strengths, and transition dipole vectors were obtained using the STO-3G, 3-21G, 6-31G, 6-31+G, 6-31G*, and 6-31+G* basis sets for the CIS and CIS-MP2 treatments of the excited states. Results are generally similar to those found from INDO/S studies, with higher excited configurations essential for approaching the experimental 1La-1Lb energy gap. The two energy surfaces exhibit an avoided crossing as the geometry is varied between the 1Lb and 1La minima. The apparent coupling between the diabatic states is quite weak, only about 50 cm-1.
A method is described to calculate the matrix elements of one- and two-electron operators for CASSCF wavefunctions employing individually optimized orbitals. The computation procedure is very efficient, and matrix elements between CAS wavefunctions with up to a few hundred thousand configurations are easily evaluated. An implementation of this method is presented, which sets up and solves the Hamiltonian secular problem in a basis of independently optimized CASSCF wavefunctions. In the program, the only restriction imposed is that the AO basis set and the number of active orbitals is the same for all states. The method is illustrated by calculations on π-excited states of some aromatic molecules.
Comparison of solvent behaviour upon indole, N-methylindole, 5-methoxyindole and benzimidazole, both at the first S1(1La, 1Lb) and second S2(1Bb) excited states, provides new information upon solvent interactions for the biologically important indole chromophore.
Two new split-valence basis sets, termed 6-21G and 3-21G, are proposed for use in molecular orbital calculations on molecules containing first-row elements. The valence functions for the smaller representation (3-21G) have been taken directly from the larger (6-21G), preventing their collapse inwards to make up for deficiencies in the inner-shell region. This is necessary to ensure a good description of bonding interactions which necessarily involve overlap of valence functions. Equilibrium geometries, vibrational frequencies, relative energies, and electric dipole moments calculated using the 3-21G basis set are nearly identical with those obtained from the larger 6-21G representation. Compared to experiment they are consistently superior to properties derived from the STO-3G minimal basis set, and of comparable quality to those obtained from the larger 4-21G and 4-31G representations. One notable exception is that the 4-31G basis set yields hydrogenation energies in significantly better agreement with experiment than those obtained from 3-21G. The 3-21G basis set comprises the same number of primitive Gaussian functions as STO-3G (although nearly twice the number of basis functions) and should be nearly as efficient computationally as that representation for applications which require evaluation of energy derivatives as well as the energy itself (e.g., determination of equilibrium geometry and calculation of vibrational frequencies). It is less costly to apply than either the 4-21G or 4-31G split-valence basis sets, and in those areas where the performance of the two is comparable it would appear to be the method of choice.
This work reviews the methodological and computational considerations necessary for the determination of the ab initio energy, wave function, and gradient of a molecule in an electronically excited state using molecular orbital theory. In particular, this paper reexamines a fundamental level of theory which was employed several years ago for the interpretation of the electronic spectra of simple organic molecules: configuration interaction (CI) among all singly substituted determinants using a Hartree-Fock reference state. This investigation presents several new enhancements to this general theory. First, it is shown how the "CI-singles" wave function can be used to compute efficiently the analytic first derivative of the energy in order to obtain accurate properties and optimized geometries for a wide range of molecules in their excited states. Second, a computer program is described which allows these computations to be done in a "direct" fashion, with no disk storage required for the two-electron repulsion integrals. This allows investigations of systems with large numbers of atoms (or large numbers of basis functions). Third, it is shown how the CI-singles approximation can be corrected via second-order Moller-Plesset perturbation theory to produce a level of theory for excited states which further includes some effects of electronic correlation. The relative success of the model as a function of basis set indicates that a judicious choice of basis set is needed in order to evaluate its performance adequately. Application of the method to the excited states of formaldehyde, ethylene, pyridine, and porphin demonstrates the utility of CI-singles theory.
A perturbation theory is developed for treating a system of n electrons in which the Hartree-Fock solution appears as the zero-order approximation. It is shown by this development that the first order correction for the energy and the charge density of the system is zero. The expression for the second-order correction for the energy greatly simplifies because of the special property of the zero-order solution. It is pointed out that the development of the higher approximation involves only calculations based on a definite one-body problem.
A general approach to dissecting the complex photophysics of tryptophan is presented and used to elucidate the effects of amino acid functional groups on tryptophan fluorescence. We have definitively identified the amino acid side chains that quench tryptophan fluorescence and delineated the respective quenching mechanisms in a simple model system. Steady-state and time-resolved fluorescence techniques, photochemical H-D exchange experiments, and transient absorption techniques were used to measure individual contributions to the total nonradiative rate for deactivation of the excited state, including intersystem crossing, solvent quenching, and excited-state proton and electron transfer rates. Eight amino acid side chains representing six functional groups quench 3-methylindole fluorescence with a 100-fold range in quenching rate constant. Lysine and tyrosine side chains quench by excited-state proton transfer; glutamine, asparagine, glutamic and aspartic acid, cysteine, and histidine side chains quench by excited-state electron transfer. These studies provide a framework for deriving detailed structural and dynamical information from tryptophan fluorescence intensity and lifetime data in peptides and proteins.
Version 4, User's Guide
- K Andersson