QM/MM calculation of solvent effects on absorption spectra of guanine

Electronic spectra of guanine in the gas phase and in water were studied by quantum mechanical/molecular mechanical (QM/MM) methods. Geometries for the excited‐state calculations were extracted from ground‐state molecular dynamics (MD) simulations using the self‐consistent‐charge density functional tight binding (SCC‐DFTB) method for the QM region and the TIP3P force field for the water environment. Theoretical absorption spectra were generated from excitation energies and oscillator strengths calculated for 50 to 500 MD snapshots of guanine in the gas phase (QM) and in solution (QM/MM). The excited‐state calculations used time‐dependent density functional theory (TDDFT) and the DFT‐based multireference configuration interaction (DFT/MRCI) method of Grimme and Waletzke, in combination with two basis sets. Our investigation covered keto‐N7H and keto‐N9H guanine, with particular focus on solvent effects in the low‐energy spectrum of the keto‐N9H tautomer. When compared with the vertical excitation energies of gas‐phase guanine at the optimized DFT (B3LYP/TZVP) geometry, the maxima in the computed solution spectra are shifted by several tenths of an eV. Three effects contribute: the use of SCC‐DFTB‐based rather than B3LYP‐based geometries in the MD snapshots (red shift of ca. 0.1 eV), explicit inclusion of nuclear motion through the MD snapshots (red shift of ca. 0.1 eV), and intrinsic solvent effects (differences in the absorption maxima in the computed gas‐phase and solution spectra, typically ca. 0.1–0.3 eV). A detailed analysis of the results indicates that the intrinsic solvent effects arise both from solvent‐induced structural changes and from electrostatic solute–solvent interactions, the latter being dominant. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010     

Implementation of the analytic energy gradient for the combined time-dependent density functional theory/effective fragment potential method: application to excited-state molecular dynamics simulations

Excited-state quantum mechanics/molecular mechanics molecular dynamics simulations are performed, to examine the solvent effects on the fluorescence spectra of aqueous formaldehyde. For that purpose, the analytical energy gradient has been derived and implemented for the linear-response time-dependent density functional theory (TDDFT) combined with the effective fragment potential (EFP) method. The EFP method is an efficient ab initio based polarizable model that describes the explicit solvent effects on electronic excitations, in the present work within a hybrid TDDFT/EFP scheme. The new method is applied to the excited-state MD of aqueous formaldehyde in the n-π* state. The calculated π*→n transition energy and solvatochromic shift are in good agreement with other theoretical results.     

Excited States of Xanthene Analogues: Photofragmentation and Calculations by CC2 and Time‐Dependent Density Functional Theory

Action spectroscopy has emerged as an analytical tool to probe excited states in the gas phase. Although comparison of gas‐phase absorption properties with quantum‐chemical calculations is, in principle, straightforward, popular methods often fail to describe many molecules of interest—such as xanthene analogues. We, therefore, face their nano‐ and picosecond laser‐induced photofragmentation with excited‐state computations by using the CC2 method and time‐dependent density functional theory (TDDFT). Whereas the extracted absorption maxima agree with CC2 predictions, the TDDFT excitation energies are blueshifted. Lowering the amount of Hartree–Fock exchange in the DFT functional can reduce this shift but at the cost of changing the nature of the excited state. Additional bandwidth observed in the photofragmentation spectra is rationalized in terms of multiphoton processes. Observed fragmentation from higher‐lying excited states conforms to intense excited‐to‐excited state transitions calculated with CC2. The CC2 method is thus suitable for the comparison with photofragmentation in xanthene analogues.     

QM/MM study of the absorption spectra of DsRed.M1 chromophores

We report geometries and vertical excitation energies for the red and green chromophores of the DsRed.M1 protein in the gas phase and in the solvated protein environment. Geometries are optimized using density functional theory (DFT, B3LYP functional) for the isolated chromophores and combined quantum mechanical/molecular mechanical (QM/MM) methods for the protein (B3LYP/MM). Vertical excitation energies are computed using DFT/MRCI, OM2/MRCI, and TDDFT as QM methods. In the case of the red chromophore, there is a general blue shift in the excitation energies when going from the isolated chromophore to the protein, which is caused both by structural changes and by electrostatic interactions with the environment. For the lowest ππ* transition, these two factors contribute to a similar extent to the overall DFT/MRCI shift of 0.4 eV. An enlargement of the QM region to include active‐site residues does not change the DFT/MRCI excitation energies much. The DFT/MRCI results are closest to experiment for both chromophores. OM2/MRCI and TDDFT overestimate the first vertical excitation energy by 0.3–0.5 and 0.2–0.4 eV, respectively, relative to the experimental or DFT/MRCI values. The experimental gap of 0.35 eV between the lowest ππ* excitation energies of the red (cis‐acylimine) and green (trans‐peptide) forms is well reproduced by DFT/MRCI and TDDFT (0.32 and 0.37 eV, respectively). A histogram spectrum for an equal mixture of the two forms, generated by OM2/MRCI calculations on 450 snapshots along molecular dynamics trajectories, matches the experimental spectrum quite well, with a gap of 0.23 eV and an overall blue shift of about 0.3 eV. DFT/MRCI appears as an attractive choice for calculating excitation energies in fluorescent proteins, without the shortcomings of TDDFT and computationally more affordable than CASSCF‐based approaches. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Theoretical Studies on the Intramolecular Electron Transfer in Some Aromatic Systems

1 INTRODUCTION As early as forty years ago, Lippert et al. found that there is a double-fluorescence phenomenon of the compound 4-(N,N-dimethylamino)benzonitrile (4DMAB-CN)[1]. Subsequently, similar phenomenon was observed in the same kind of compounds[2～5]. Two bands exist in these fluorescence spectra, repre- senting respectively that the minor and macro axis polarizations are hardly and easily affected by the polar solvent. This phenomenon can be explained by the intramolecular e…     

Solvent-induced shift of the lowest singlet π → π* charge-transfer excited state of p-nitroaniline in water: an application of the TDDFT/EFP1 method

The combined time-dependent density functional theory effective fragment potential method (TDDFT/EFP1) is applied to a study of the solvent-induced shift of the lowest singlet π → π* charge-transfer excited state of p-nitroaniline (pNA) from the gas to the condensed phase in water. Molecular dynamics simulations of pNA with 150 EFP1 water molecules are used to model the condensed-phase and generate a simulated spectrum of the lowest singlet charge-transfer excitation. The TDDFT/EFP1 method successfully reproduces the experimental condensed-phase π → π* vertical excitation energy and solvent-induced red shift of pNA in water. The largest contribution to the red shift comes from Coulomb interactions, between pNA and water, and solute relaxation. The solvent shift contributions reflect the increase in zwitterionic character of pNA upon solvation.     

Cover Picture: QM/MM Car‐Parrinello Molecular Dynamics Study of the Solvent Effects on the Ground State and on the First Excited Singlet State of Acetone in Water (ChemPhysChem 11/2003)

The cover picture shows …?‥the solvent effect of water upon the lowest‐lying singlet excitation in acetone. The transition, which involves the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO), is blue‐shifted in water (sol) with respect to the gas phase (vac), since the HOMO is stronger stabilized in water than the LUMO. The authors calculate the absorption and fluorescence spectra of acetone in water with a hybrid Car–Parrinello quantum chemical/classical molecular dynamics approach and investigate the influence of the solvent. The lower part of the picture shows the excitation energy during a simulation. One configuration with a very high excitation energy (three hydrogen bonds, short C?O bond) and one configuration with a very low excitation energy (two hydrogen bonds, long C?O bond) are shown in detail. Find out more in the article by Rothlisberger and co‐workers on pages pp. 1177–1182.     

Relaxation of the CH stretch in liquid CHBr3: solvent effects and decay rates using classical nonequilibrium simulations

This article addresses two questions regarding the decay of the CH stretch in liquid CHBr3. The first is whether the initial steps of the relaxation primarily involve energy redistribution within the excited molecule alone. Gas phase quantum mechanical and classical calculations are performed to examine the role of the solvent in this process. At the fundamental excitation level, it is found that CH stretch decay is, in fact, strongly solvent driven. The second question is on the applicability of a fully classical approach to the calculation of CH stretch condensed phase decay rates. To this end, nonequilibrium molecular dynamics simulations are performed. The results are compared with quantum mechanical rates computed previously. The two methods are found to be in fair agreement with each other. However, care must be exercised in the interpretation of the classical results.     

Theoretical investigations of the perylene electronic structure: Monomer,dimers, and excimers

The structural and electronic properties of perylene molecule, dimers, and excimers have been computationally studied. The present work represents the first systematic study of perylene molecule and dimer forms by means of long‐range corrected time‐dependent density functional theory (TDDFT) approaches. Initially, the study explores the photophysical properties of the molecular species. Vertical transitions to many excited singlet states have been computed and rationalized with different exchange‐correlation functionals. Differences between excitation energies are discussed and compared to the absorption spectrum of perylene in gas phase and diluted solution. De‐excitation energy from the relaxed geometry of the lowest excited singlet is in good agreement with the experimental fluorescence emission. Optimization of several coplanar forms of the perylene pair prove that, contrary to generalized gradient approximation (GGA) and hybrid exchange‐correlation functionals, corrected TDDFT is able to bind the perylene dimer in the ground state. Excitation energies from different dimer conformers point to dimer formation prior to photoexcitation. The fully relaxed excimer geometry belongs to the perfectly eclipsed conformation with D_2h symmetry. The excimer equilibrium intermolecular distance is shorter than the separation found for the ground state, which is an indication of stronger interchromophore interaction in the excimer state. Excimer de‐excitation energy is in rather good agreement with the excimer band of perylene in concentrated solution. The study also scans the energy profiles of the ground and lowest excited states along several geometrical distortions. The nature of the interactions responsible for the excimer stabilization is explored in terms of excitonic and charge resonance contributions. © 2015 Wiley Periodicals, Inc.     

UV‐photoexcitation and ultrafast dynamics of HCFC‐132b (CF2ClCH2Cl)

The UV‐induced photochemistry of HCFC‐132b (CF₂ClCH₂Cl) was investigated by computing excited‐state properties with time‐dependent density functional theory (TDDFT), multiconfigurational second‐order perturbation theory (CASPT2), and coupled cluster with singles, doubles, and perturbative triples (CCSD(T)). Excited states calculated with TDDFT show good agreement with CASPT2 and CCSD(T) results, correctly predicting the main excited‐states properties. Simulations of ultrafast nonadiabatic dynamics in the gas phase were performed, taking into account 25 electronic states at TDDFT level starting in two different spectral windows (8.5 ± 0.25 and 10.0 ± 0.25 eV). Experimental data measured at 123.6 nm (10 eV) is in very good agreement with our simulations. The excited‐state lifetimes are 106 and 191 fs for the 8.5 and 10.0 eV spectral windows, respectively. Internal conversion to the ground state occurred through several different reaction pathways with different products, where 2Cl, C‐Cl bond breakage, and HCl are the main photochemical pathways in the low‐excitation region, representing 95% of all processes. On the other hand, HCl, HF, and C‐Cl bond breakage are the main reaction pathways in the higher excitation region, with 77% of the total yield. © 2015 Wiley Periodicals, Inc.     

Absorption Spectrum of A–T DNA Unraveled by Quantum Mechanical Calculations in Solution on the (dA)2⋅(dT)2 Tetramer

The absorption spectrum of A–T DNA is computed for the first time in aqueous solution by means of quantum mechanical calculations performed on realistic models, thereby accounting for both stacking and base pairing interactions and including solvent effects through the polarizable continuum model. The computed and experimental spectra are in close agreement. Our analysis allows the identification of all the electronic transitions hidden in the broad absorption spectrum of A–T DNA, thus determining their most relevant properties and providing an explanation for the most significant experimental features, such as the small blue shift of the band maximum and the appearance of a shoulder on the red wing of the absorption band. The lowest‐energy dark excited state corresponds to a charge‐transfer state between two stacked adenine bases.     

A Theoretical Study on Hydrogen‐Bonded Complex of Proflavine Cation and Water: The Site‐dependent Feature of Hydrogen Bond Strengthening and Weakening

The intermolecular hydrogen‐bonds between proflavine cation (PC) and water molecules are investigated by density functional theory (DFT) and time‐dependent density functional theory (TDDFT) methods. The ground‐state geometry optimizations, electronic excitation energies and corresponding oscillation strengths of the low‐lying electronically excited states for the isolated proflavine cation, the hydrogen‐bonded PC–H2O dimer and PC–(H2O)2 trimer are calculated. Intermolecular hydrogen bonds at the central site of proflavine molecule are found to be stronger than the peripheral site. The hydrogen bond N–H???O for the hydrogen‐bonded dimer are indicated to be weakened in the excited states, since the excitation energy is increased slightly comparing to the monomer. Hydrogen bonds of PC–(H2O)2 trimer with the same type as the dimer are strengthened in the excited state, which is demonstrated by the decrease of the excited energies. Thus, hydrogen bond strengthening and weakening are observed to reveal site dependent feature in proflavine molecule. Furthermore, the hydrogen bond at central site induces the blue‐shift of the absorption spectrum, while the ones at peripheral site induce red‐shift. Hydrogen bonds with the same type at peripheral and central sites of proflavine molecule provide different effects on the photochemical and photophysical properties of proflavine.     

On low‐lying excited states of extended nanographenes

Low‐lying excited states of planarly extended nanographenes are investigated using the long‐range corrected (LC) density functional theory (DFT) and the spin‐flip (SF) time‐dependent density functional theory (TDDFT) by exploring the long‐range exchange and double‐excitation correlation effects on the excitation energies, band gaps, and exciton binding energies. Optimizing the geometries of the nanographenes indicates that the long‐range exchange interaction significantly improves the C C bond lengths and amplify their bond length alternations with overall shortening the bond lengths. The calculated TDDFT excitation energies show that long‐range exchange interaction is crucial to provide accurate excitation energies of small nanographenes and dominate the exciton binding energies in the excited states of nanographenes. It is, however, also found that the present long‐range correction may cause the overestimation of the excitation energy for the infinitely wide graphene due to the discrepancy between the calculated band gaps and vertical ionization potential (IP) minus electron affinity (EA) values. Contrasting to the long‐range exchange effects, the SF‐TDDFT calculations show that the double‐excitation correlation effects are negligible in the low‐lying excitations of nanographenes, although this effect is large in the lowest excitation of benzene molecule. It is, therefore, concluded that long‐range exchange interactions should be incorporated in TDDFT calculations to quantitatively investigate the excited states of graphenes, although TDDFT using a present LC functional may provide a considerable excitation energy for the infinitely wide graphene mainly due to the discrepancy between the calculated band gaps and IP–EA values. © 2017 Wiley Periodicals, Inc.     

Solvatochromism and preferential solvation of Brooker's merocyanine in water–methanol mixtures

The excitation energy of Brooker's merocyanine in water–methanol mixtures shows nonlinear behavior with respect to the mole fraction of methanol, and it was suggested that this behavior is related to preferential solvation by methanol. We investigated the origin of this behavior and its relation to preferential solvation using the three‐dimensional reference interaction site model self‐consistent field method and time‐dependent density functional theory. The calculated excitation energies were in good agreement with the experimental behavior. Analysis of the coordination numbers revealed preferential solvation by methanol. The free energy component analysis implied that solvent reorganization and solvation entropy drive the preferential solvation by methanol, while the direct solute–solvent interaction promotes solvation by water. The difference in the preferential solvation effect on the ground and excited states causes the nonlinear excitation energy shift. © 2017 Wiley Periodicals, Inc.     

Excited‐State Deactivation of Branched Phthalocyanine Compounds

The excited‐state relaxation dynamics and chromophore interactions in two phthalocyanine compounds (bis‐ and trisphthalocyanines) are studied by using steady‐state and femtosecond transient absorption spectral measurements, where the excited‐state energy‐transfer mechanism is explored. By exciting phthalocyanine compounds to their second electronically excited states and probing the subsequent relaxation dynamics, a multitude of deactivation pathways are identified. The transient absorption spectra show the relaxation pathway from the exciton state to excimer state and then back to the ground state in bisphthalocyanine (bis‐Pc). In trisphthalocyanine (tris‐Pc), the monomeric and dimeric subunits are excited and the excitation energy transfers from the monomeric vibrationally hot S1 state to the exciton state of a pre‐associated dimer, with subsequent relaxation to the ground state through the excimer state. The theoretical calculations and steady‐state spectra also show a face‐to‐face conformation in bis‐Pc, whereas in tris‐Pc, two of the three phthalocyanine branches form a pre‐associated face‐to‐face dimeric conformation with the third one acting as a monomeric unit; this is consistent with the results of the transient absorption experiments from the perspective of molecular structure. The detailed structure–property relationships in phthalocyanine compounds is useful for exploring the function of molecular aggregates in energy migration of natural photosynthesis systems.     

First-principles simulation of the photoreaction of a capped azobenzene: the rotational pathway is feasible.

We present first-principles molecular dynamics simulations of azobenzene and a sterically hindered derivative in the first excited state. The restricted open-shell Kohn-Sham (ROKS) approach is employed to describe the motion in the lowest excited state. The rotational pathway is observed in the molecular dynamics simulations for both azobenzene and its azacrown ether capped derivative.     

The merits of the frozen-density embedding scheme to model solvatochromic shifts

We investigate the usefulness of a frozen-density embedding scheme within density-functional theory [J. Phys. Chem. 97, 8050 (1993)] for the calculation of solvatochromic shifts. The frozen-density calculations, particularly of excitation energies have two clear advantages over the standard supermolecule calculations: (i) calculations for much larger systems are feasible, since the time-consuming time-dependent density functional theory (TDDFT) part is carried out in a limited molecular orbital space, while the effect of the surroundings is still included at a quantum mechanical level. This allows a large number of solvent molecules to be included and thus affords both specific and nonspecific solvent effects to be modeled. (ii) Only excitations of the system of interest, i.e., the selected embedded system, are calculated. This allows an easy analysis and interpretation of the results. In TDDFT calculations, it avoids unphysical results introduced by spurious mixings with the artificially too low charge-transfer excitations which are an artifact of the adiabatic local-density approximation or generalized gradient approximation exchange-correlation kernels currently used. The performance of the frozen-density embedding method is tested for the well-studied solvatochromic properties of the n-->pi(*) excitation of acetone. Further enhancement of the efficiency is studied by constructing approximate solvent densities, e.g., from a superposition of densities of individual solvent molecules. This is demonstrated for systems with up to 802 atoms. To obtain a realistic modeling of the absorption spectra of solvated molecules, including the effect of the solvent motions, we combine the embedding scheme with classical molecular dynamics (MD) and Car-Parrinello MD simulations to obtain snapshots of the solute and its solvent environment, for which then excitation energies are calculated. The frozen-density embedding yields estimated solvent shifts in the range of 0.20-0.26 eV, in good agreement with experimental values of between 0.19 and 0.21 eV.     

Influence of Solvent Polarity and Hydrogen Bonding on the Electronic Transition of Coumarin 120: A TDDFT Study

The characteristics of the electronic transition energy of Coumarin 120 (C120) and its H‐bonded complexes in various solvents have been examined by time‐dependent density functional theory (TDDFT) in combination with a polarizable continuum solvent model (PCM). Molecular structures of C120 and its H‐bonded complexes are optimized with the B3LYP method in PCM solution, and the dihedral angle H14? N13? C7? H15 is dependent on solvent polarity and the type of H‐bond. A linear correlation of the absorption maximum of C120 with the solvent polarity function is revealed with the PCM model for all solvents except DMSO. The experimental absorption maximum of C120 in nine solvents is well described by a PCM–TDDFT scheme augmented with explicit inclusion of a few H‐bonded solvent molecules, and quantitative agreement between our calculated results and experimental measurements is obtained with an average error of less than 2 nm. H‐bonding at three different sites shifts the absorption wavelength of C120 either to the blue or to the red, that is, a significant role is played by solvent molecules in the first solvation shell in determining the electronic transition energy of C120. The dependence on the H‐bonding site and solvent polarity is examined by using the Kamlet–Taft equation for solvatochromism.