Computational study of solvent effects and the vibrational spectra of Anderson polyoxometalates

The structures and vibrational frequencies of the type II Anderson heteropolyanions [TeMo6O24]6- and [IMo6O24]5- have been calculated by using density functional theory using a number of common functionals and basis sets. For the first time, Raman intensities have been calculated and the effect of solvent on the modeling has been investigated. The calculated IR and Raman spectral traces are in good agreement with experiment allowing the characteristic group frequencies for this class of polyoxometalate to be identified. The stretching vibrations of the molybdenum-oxygen bonds are predicted to occur at somewhat lower frequencies than in the type I polyoxometalates. Stretching of the heteroatom-oxygen bonds occurs at significantly lower frequencies than in the Keggin anions as a simple consequence of the higher coordination number of the central heteroatom in the Anderson systems. For the [Mo2O7]2- and [Mo6O19]2- ions, the relatively low negative charge leads to small structural changes when solvent is included. In these systems, solvent leads to an increase in the bond polarity and a decrease in the covalent bond orders, resulting in decreases in the calculated frequencies. For the Anderson anions, the higher negative charges leads to greater solvent effects with contraction of the clusters and increases in the frequencies of bands due to stretching of the two, cis-related molybdenum-oxygen bonds.     

Structure effects on isomerization pathways and vibrational spectra of epoxysaccharides: a numerical study

Results of a comparative analysis of conformational possibilities of the hexopyranose ring of six epoxysaccharides differing from each other by the position of the oxirane ring within the limits of the hexapyranose ring and having different orientations of substituents and different positions of the oxirane ring with respect to the skeleton plane of the molecules are presented. Numerical simulations based on the Wiberg and Boyd method made it possible to determine all the stationary forms in which anhydropyranose rings can exist. The effect of various structural factors on the character of conformational transformations, heights of transition barriers, and the energy of stationary forms has been investigated. Normal vibrational modes of the stationary forms of the compounds were calculated using molecular mechanics. Based on results of our simulations, we predict a strong effect of steric factors on the vibrational spectra of sugar epoxides. Received: 24 March 1998 / Accepted: 3 September 1998 / Published online: 17 December 1998     

Ab initio studies of solvent effect on molecular conformation and vibrational spectra of diacetamide

The conformational equilibria and vibrational spectra of diacetamide have been investigated by ab initio molecular orbital studies using the basis sets 6-31g(d,p) and 6-31++g(d,p) at Hartree-Fock and MP2 levels. The vibrational spectra of diacetamide have been satisfactorily interpreted taking into consideration the agreement between the calculated harmonic vibrational frequencies, infrared and Raman band intensities and shifts in deuterated molecules with those observed. The solvent effects were investigated by the self-consistent reaction field (SCRF) theory. The effect of solvent on the conformational equilibria and vibrational spectra is discussed. The calculated changes in the geometry and vibrational spectra on going from the gas phase to the solvent medium are in accord with the increasing weight of the dipolar resonance structure of the amide group in more polar solvents.     

Infrared and vibrational CD spectra of partially solvated alpha-helices: DFT-based simulations with explicit solvent

Theoretical simulations are used to investigate the effects of aqueous solvent on the vibrational spectra of model alpha-helices, which are only partly exposed to solvent to mimic alpha-helices in proteins. Infrared absorption (IR) and vibrational circular dichroism (VCD) amide I' spectra for 15-amide alanine alpha-helices are simulated using density functional theory (DFT) calculations combined with the property transfer method. The solvent is modeled by explicit water molecules hydrogen bonded to the solvated amide groups. Simulated spectra for two partially solvated model alpha-helices, one corresponding to a more exposed and the other to a more buried structure, are compared to the fully solvated and unsolvated (gas phase) simulations. The dependence of the amide I spectra on the orientation of the partially solvated helix with respect to the solvent and effects of solvation on the amide I' of 13C isotopically substituted alpha-helices are also investigated. The partial exposure to solvent causes significant broadening of the amide I' bands due to differences in the vibrational frequencies of the explicitly solvated and unsolvated amide groups. The different degree of partial solvation is reflected primarily in the frequency shifts of the unsolvated (buried) amide group vibrations. Depending on which side of the alpha-helix is exposed to solvent, the simulated IR band-shapes exhibit significant changes, from broad and relatively featureless to distinctly split into two maxima. The simulated amide I' VCD band-shapes for the partially solvated alpha-helices parallel the broadening of the IR and exhibit more sign variation, but generally preserve the sign pattern characteristic of the alpha-helical structures and are much less dependent on the alpha-helix orientation with respect to the solvent. The simulated amide I' IR spectra for the model peptides with explicitly hydrogen-bonded water are consistent with the experimental data for small alpha-helical proteins at very low temperatures, but overestimate the effects of solvent on the protein spectra at ambient temperatures, where the peptide-water hydrogen bonds are weakened by thermal motion.     

Solvent and solvent isotope effects on the vibrational cooling dynamics of a DNA base derivative

Vibrational cooling by 9-methyladenine was studied in a series of solvents by femtosecond transient absorption spectroscopy. Signals at UV and near-UV probe wavelengths were assigned to hot ground state population created by ultrafast internal conversion following electronic excitation by a 267 nm pump pulse. A characteristic time for vibrational cooling was determined from bleach recovery signals at 250 nm. This time increases progressively in H2O (2.4 ps), D2O (4.2 ps), methanol (4.5 ps), and acetonitrile (13.1 ps), revealing a pronounced solvent effect on the dissipation of excess vibrational energy. The trend also indicates that the rate of cooling is enhanced in solvents with a dense network of hydrogen bonds. The faster rate of cooling seen in H2O vs D2O is noteworthy in view of the similar hydrogen bonding and macroscopic thermal properties of both liquids. We propose that the solvent isotope effect arises from differences in the rates of solute-solvent vibrational energy transfer. Given the similarities of the vibrational friction spectra of H2O and D2O at low frequencies, the solvent isotope effect may indicate that a considerable portion of the excess energy decays by exciting relatively high frequency (>/=700 cm-1) solvent modes.     

Machine learning of solvent effects on molecular spectra and reactions

Fast and accurate simulation of complex chemical systems in environments such as solutions is a long standing challenge in theoretical chemistry. In recent years, machine learning has extended the boundaries of quantum chemistry by providing highly accurate and efficient surrogate models of electronic structure theory, which previously have been out of reach for conventional approaches. Those models have long been restricted to closed molecular systems without accounting for environmental influences, such as external electric and magnetic fields or solvent effects. Here, we introduce the deep neural network FieldSchNet for modeling the interaction of molecules with arbitrary external fields. FieldSchNet offers access to a wealth of molecular response properties, enabling it to simulate a wide range of molecular spectra, such as infrared, Raman and nuclear magnetic resonance. Beyond that, it is able to describe implicit and explicit molecular environments, operating as a polarizable continuum model for solvation or in a quantum mechanics/molecular mechanics setup. We employ FieldSchNet to study the influence of solvent effects on molecular spectra and a Claisen rearrangement reaction. Based on these results, we use FieldSchNet to design an external environment capable of lowering the activation barrier of the rearrangement reaction significantly, demonstrating promising venues for inverse chemical design.

A machine learning approach for modeling the influence of external environments and fields on molecules has been developed, which allows the prediction of various types of molecular spectra in vacuum and under implicit and explicit solvation.     

Excitonic effects in two-dimensional vibrational spectra of liquid formamide

The linear and two-dimensional infrared (2DIR) responses of the amide I vibrational mode in liquid formamide are investigated experimentally and theoretically using molecular dynamics simulations. The recent method based on the numerical integration of the Schr?dinger equation is employed to calculate the 2DIR spectra. Special attention is devoted to the interplay of the structural dynamics and the excitonic nature of the amide I modes in determining the optical response of the studied system. In particular, combining experimental data, simulated spectra and analysis of the simulated atomic trajectory in terms of a transition dipole coupling model, we provide a convincing explanation of the peculiar features of the 2DIR spectra, which show a substantial increase of the antidiagonal bandwidth with increasing frequency. We point out that, at variance with liquid water, the 2DIR spectral profile of formamide is determined more by the excitonic nature of the vibrational states than by the fast structural dynamics responsible for the frequency fluctuations.     

Calculation of polymer blend compositions from vibrational spectra: A simple method

In this work, the application of a new approach for quantitative analysis, originally developed for Raman spectroscopy, is extended to IR spectroscopy. The attractive features of this methodology are its simplicity and ease of use in comparison with traditional approaches. Unlike other methods, rich spectral information containing several overlapped peaks can be used in the calculations. A robust and well‐conditioned calculation scheme renders precise results, which are independent of the operator's decisions. The method was applied to study the chemical compositions of homogeneous polymer blends made of polystyrene and poly(vinyl methyl ether). Raman and IR blend spectra were acquired with confocal Raman microspectroscopy and attenuated total reflection/Fourier transform infrared, respectively. The blend compositions were calculated from the corresponding vibrational spectra with the proposed strategy, and excellent agreement between those values and the true ones was found for both techniques. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 1144–1151, 2005     

Dynamical effects on vibrational and electronic spectra of hydroperoxyl radical water clusters

We have carried out ab initio molecular-dynamics studies on hydroperoxyl water clusters. Our studies are complemented by optimization, frequency, and excited-state calculations. The three main results we obtained are (a) the dynamically averaged energy gap between the highest-occupied molecular orbital and the lowest-unoccupied molecular orbital monotonically decreases as the number of water molecules is increased in a hydroperoxyl water cluster system, (b) the dynamical averaging of the potential-energy surface at finite temperature broadens the electronic excitation spectrum and changes the infrared spectrum in nontrivial ways, and (c) the structural analysis of our dynamics simulation indicates that the oxygen-oxygen distance in a solvated hydroperoxyl-water cluster is very similar to that found in protonated water clusters (Zundel: H5O2+) inspite of the fact that the latter possesses a positive charge and the hydroperoxyl-water cluster does not. Dynamical charge analysis and the weak acidity of HO2 are used to justify this result.     

Vibrational spectra of 2-methylpropanal: Assignments,self-associations and solvent effects

Raman and infrared spectra of 2-methylpropanal (CH₃)₂CHCHO, (CH₃)₂CDCHO and (CH₃)₂CHCDO in different physical states (liquid, solid and solution) have been investigated between 4000 and 40 cm⁻¹. A complete assignment is carried out on the basis of one predominant conformer (anticlinal) in equilibrium with another less stable one (synperiplanar). Some vibrational modes of the synperiplanar form are identified. The CO stretching region is carefully examined. The complex structure of this band as a function of the physical state of the pure aldehyde and the polarity of the solvent for solutions is discussed. The structure can be explained by Fermi resonances between combinations and the fundamental νCO mode. In the pure liquid, as well as in solution, the broadness of the band can be due to random dipolar interactions. In polar basic solvents (CH₃CN and DMSO), these interactions implicate both aldehyde and solvent. When the solvent is slightly acidic (HCCl₃), weak hydrogen bonds between the aldehydic group and the solvent may occur. Moving from the liquid to the solid state, in addition to the fact that the less stable conformer disappears, molecular association between the CO groups by charge transfer may account for the observed changes.     

NIR vibrational overtone spectra of toluidines-evidence for steric and electronic effects in o-toluidine

The near infrared vibrational overtone absorption spectra of liquid phase toluidines are reported. The analysis of the observed CH and NH local mode mechanical frequency values shows that there exists steric and electronic interaction between the amino and methyl groups in o-toluidine. This observation supports the conclusions drawn from structural studies of toluidines by resonance two-photon ionization (R2PI) spectroscopy, ab initio calculations and laser induced fluorescence studies reported earlier.     

A study of the anharmonic effects on the vibrational spectra of a realistic retinal chromophore model

Ab initio and vibrational self-consistent field (VSCF) computations are used to investigate the vibrational normal coordinates of the protonated Schiff base (PSB) 4-cis-gamma,eta-dimethyl-C9H9 NH2+. The ground and the first excited states are investigated. Both harmonic and anharmonic frequencies for the first three overtones of the ground and first excited states are reported. Special attention is payed to the discussion of the normal coordinates modes that involve the central C=C bond which plays a significant role in the isomerization process.     

Substituent and solvent effects on electronic spectra of some substituted phenoxyacetic acids

The effects of substituents and solvents have been studied through the absorption spectra of nearly 19 para- and ortho-substituted phenoxyacetic acids in the range of 200-400 nm. The effects of substituent on the absorption spectra of compounds under present investigation are interpreted by correlation of absorption frequencies with simple and extended Hammett equations. Effect of solvent polarity and hydrogen bonding on the absorption spectra are interpreted by means of Kamlet equation and the results are discussed.     

Electrochemistry of aluminum phthalocyanine: solvent and anion effects on UV-visible spectra and reduction mechanisms

The electrochemistry and UV-vis spectral properties of neutral and electroreduced Al(III) phthalocyanine, (Pc)AlCl, were characterized in four different nonaqueous solvents (THF, DMSO, DMF, and pyridine) containing tetra-n-butylammonium perchlorate, as well as in THF containing 0.4 M TBAP and the more strongly coordinating Cl-, F-, OH-, or CN- anions added to solution in the form of a tetra-n-butylammonium salt. The initial phthalocyanine added to solution is represented as (Pc)AlCl, but the actual electroactive form of the compound varied as a function of both the solvent and type or number of bound anionic axial ligands. An uncharged (Pc)AlCl(THF) or (Pc)Al(CN)(THF) complex is present in THF solutions containing 0.4 M TBAP and excess Cl- or CN-, while transient mu-oxo dimers are spectroscopically observed upon addition of OH- or F- to (Pc)AlCl(THF) in THF followed by the ultimate formation of stable six-coordinate anionic species represented as [(Pc)Al(OH)2]- or [(Pc)AlF2]-. Each phthalocyanine undergoes three reversible one-electron additions at the conjugated Pc macrocycle within the negative potential limit of the solvent, and the UV-vis spectral changes obtained during the first two reductions were recorded in a thin-layer cell to evaluate the prevailing electron-transfer mechanisms.     

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     

Modeling vibrational spectra using the self-consistent charge density-functional tight-binding method. I. Raman spectra

An extension of the self-consistent charge density-functional tight-binding (SCC-DFTB) method is presented that allows for calculating intensities of peaks in vibrational Raman spectra for very large molecules. The extension is based on a simple ansatz: an extra term, which describes interaction of an external electric field with induced atomic charges, is added to the SCC-DFTB energy expression. We apply the modified SCC-DFTB formalism for reproducing vibrational Raman spectra of 17 organic molecules. The calculated spectra are compared with experiment and with spectra obtained from density functional theory (DFT) calculations. We find that the SCC-DFTB method is capable of reproducing most of the features of experimental Raman spectra. Limitations and advantages of this approach are analyzed and suggestions for interpreting calculated SCC-DFTB Raman spectra are given.     

Infrared spectra of permanganate anions in potassium perchlorate matrices: vibrational anharmonicity,effective symmetry and vibrational mode mixing effects

Fourier transform infrared spectra of MnO4- anions isomorphously isolated in potassium perchlorate matrices were recorded at room and low temperature (LT, approximately 100 K). On the basis of the detected second-order vibrational transitions involving the dopant species nu3 mode components, anharmonicity constants and harmonic eigenvalues for these modes were calculated. Despite the fact that, rigorously speaking, the appearance of the spectra of dopant permanganate anions may be explained in terms of a Cs site symmetry, the nu3 stretching region resembles an approximate A1+E splitting (characteristic for a local C3nu or even higher symmetry), which is not expected, even within the latent symmetry approach. We explain such spectral patterns on the basis of vibrational mode mixing (a 'Fermi-like' resonance) of the MnO4- nu1 mode with the nu3, site-group component. With the results of degenerate case stationary perturbation theory, we show that in the present case the Fermi-like resonance is predominantly responsible for the observed spectral features. The appearance of the region of second-order vibrational transitions in the spectra of dopant permanganate anions may be better explained in terms of the (rigorous) crystallographic Cs site group (corresponding to the crystallographic Pnma space group), instead of the 'latent' (effective) symmetry site group C2nu (corresponding to the latent symmetry space group Imma).     

Empirical solvent correction for multiple amide group vibrational modes

Previously proposed solvent correction to the amide I peptide vibration was extended so that it can be applied to a general solvated chromophore. The combined molecular and quantum mechanics (MMQM) method is based on a linear dependence of harmonic force field and intensity tensor components of the solute on solvent electrostatic field. For N-methylacetamide, realistic solvent frequency and intensity changes as well as inhomogeneous band widths were obtained for amide A, I, II , and III modes. A rather anomalous basis set size dependence was observed for the amide A and I vibrations, when bigger basis lead to narrowing of spectral bands and lesser molecular sensibility to the environment. For a model alpha-helical peptide, a W-shape of the vibrational circular dichroism signal observed in deuterated solvent for the amide I band was reproduced correctly, unlike with previous vacuum models.