Interplay of intrinsic and environmental effects on the magnetic properties of free radicals issuing from H-atom addition to cytosine.

Possible radical reaction products issuing from H-atom addition to cytosine have been characterized and analyzed by means of a comprehensive quantum mechanical approach including density functional computations (B3LYP), together with simulation of the solvent by the polarizable continuum model (PCM), and averaging of spectroscopic properties over the most important vibrational motions. The hyperfine couplings of the semirigid 5,6-dihydrocytos-6yl radical computed at the optimized geometry are in good agreement with their experimental counterparts. On the other hand, vibrational averaging is mandatory for obtaining an effectively planar structure for the 5,6-dihydrocytos-5yl radical with the consequent equivalence of beta-hydrogens. Finally, only proper consideration of environmental effects restores the agreement between computed and experimental couplings for the base anion protonated at N3.     

Approximate inclusion of four-mode couplings in vibrational coupled-cluster theory

The vibrational coupled cluster (VCC) equations are analyzed in terms of vibrational Mo?ller-Plesset perturbation theory aiming specifically at the importance of four-mode couplings. Based on this analysis, new VCC methods are derived for the calculation of anharmonic vibrational energies and vibrational spectra using vibrational coupled cluster response theory. It is shown how the effect of four-mode coupling and excitations can be efficiently and accurately described using approximations for their inclusion. Two closely related approaches are suggested. The computational scaling of the so-called VCC[3pt4F] method is not higher than the fifth power in the number of vibrational degrees of freedom when up to four-mode coupling terms are present in the Hamiltonian and only fourth order when only up to three-mode couplings are present. With a further approximation, one obtains the VCC[3pt4] model which is shown to scale with at most the fourth power in the number of vibrational degrees of freedom for Hamiltonians with both three- and four-mode coupling levels, while sharing the most important characteristics with VCC[3pt4F]. Sample calculations reported for selected tetra-atomic molecules as well as the larger dioxirane and ethylene oxide molecules support that the new models are accurate and useful.     

Conformational properties of and a reorientation triggered by sugar-water vibrational resonance in the hydroxymethyl group in hydrated beta-glucopyranose

In this paper, we discuss the conformational properties of the hydroxymethyl group of beta-glucopyranose in aqueous solution and its reorientation mechanism. First, using the values for the hydroxymethyl torsion (O5-C5-C6-O6) angle obtained by our ab initio simulations, we reestimate the experimental ratio of the hydroxymethyl rotamer populations. The reestimated ratio is found to be in agreement with those previously reported in several computational studies, which probably partly explains the discrepancies between theoretical and experimental studies that have been discussed in the literature. Second, our time-frequency analysis on a reorientation in the hydroxymethyl group in an ab initio molecular dynamics trajectory suggests that, before the reorientation, the O6-H6 stretching mode is vibrationally coupled with a proton-accepting first-hydration-shell water molecule, whereas the C6-O6 stretching mode is vibrationally coupled with a proton-donating one. The amount of the total vibrational energy induced by these vibrational couplings is estimated to be comparable to typical values for the potential barriers between hydroxymethyl rotamers. To elucidate the vibrational couplings, we investigate the hydrogen-bonding properties around the hydroxymethyl group during the pretransition period. The implications, validity, and limitation of a possible reorientation mechanism based on these findings are also discussed.     

A Self-consistent Reaction Field Model of Solvation Using Distributed Multipoles. II: Second Energy Derivatives and Application to Vibrational Spectra

The use of distributed multipoles in the formalism of the reaction field factors allowed us to develop a computational scheme adapted to quantum chemical computations on a molecule solvated by a dielectric continuum. The algorithm used to compute the second energy derivatives is developed and, after its implementation in a quantum chemical computational code, permits the computation of the vibrational frequencies of the solute. This approach has been tested successfully on two test molecules and applied to the study of the solvent effect on the structure and the vibrational spectrum of a series of parasubstituted benzonitriles.     

Ab initio vibrational state calculations with a quartic force field: applications to H2CO, C2H4, CH3OH, CH3CCH, and C6H6

For polyatomic molecules, n-mode coupling representations of the quartic force field (nMR-QFF) are presented, which include terms up to n normal coordinate couplings in a fourth-order polynomial potential energy function. The computational scheme to evaluate third-and fourth-order derivatives by finite differentiations of the energy is fully described. The code to generate the nMR-QFF has been implemented into GAMESS program package and interfaced with the vibrational self-consistent field (VSCF) and correlation corrected VSCF (cc-VSCF) methods. As a demonstration, fundamental frequencies have been calculated by the cc-VSCF method based on 2MR-QFF for formaldehyde, ethylene, methanol, propyne, and benzene. The applications show that 2MR-QFF is a highly accurate potential energy function, with errors of 1.0-1.9% relative to the experimental value in fundamental frequencies. This approach will help quantitative evaluations of vibrational energies of a general molecule with a reasonable computational cost.     

The D 1Sigma+ state of 7LiH: comparison of observations with vibronic theory

The excited D (1)Sigma(+) electronic state of (7)LiH has been observed up to near its dissociation limit by a pulsed optical-optical double resonance fluorescence depletion spectroscopic technique. An extensive vibronic calculation has been performed with a diabatic approach with purely potential couplings involving a set of eight diabatic states of (1)Sigma(+) symmetry, corresponding to seven neutral states and one ionic state. Twenty-six new vibrational levels have been observed. Both the derived vibrational energy spacings and the vibronic ones are similarly irregular. The observed spectral linewidths and vibronic resonance widths are found to vary similarly with increasing energy. Observed asymmetric spectral lineshapes may be attributed to the strong radial couplings between the discrete levels of the D (1)Sigma(+) electronic state and the continuum states of the C (1)Sigma(+) electronic state. The mutual agreement between the spectral results and the vibronic results demonstrates that the D (1)Sigma(+) electronic state of (7)LiH is better characterized by the vibronic approach.     

On the number of significant mode-mode anharmonic couplings in vibrational calculations: Correlation-corrected vibrational self-consistent field treatment of di-, tri-, and tetrapeptides

A computational study is made of the number of important anharmonic mode-mode couplings in the context of vibrational calculations for di-, tri-, and tetrapeptides. The method employed is the correlation-corrected vibrational self-consistent field (CC-VSCF) algorithm, which includes correlation effects between different vibrational modes. It is found that results of good accuracy can be obtained in calculations that include only N log N mode-mode coupling terms, where N is the number of modes. This simplification significantly accelerates CC-VSCF calculations for large molecules. A criterion based on the characteristics of the normal-mode displacements is employed to predict a priori unimportant coupling terms. The criterion is tested statistically using Spearman's rank correlation coefficient. The results are illustrated by calculations for several di-, tri-, and tetrapeptides using semiempirical PM3 potential surfaces. These results are analyzed and a statistical model for error estimation is given. The decrease in the number of included coupling from N(2) to N log N opens possibilities of anharmonic vibrational calculations for large peptides.     

Is styrene planar in liquid phases?

The proton NMR spectra of two (13)C-labeled isotopomers of styrene dissolved in two liquid crystalline solvents have been obtained and analyzed to yield four sets each of 24 dipolar couplings. These couplings were then used to investigate the structure of the ring and the ene fragments of the molecule, and the position of the maximum, phi(0), in the ring-ene bond rotational probability distribution. To do this, the effect on the dipolar couplings of small-amplitude vibrational motion was taken into account using vibrational wave functions calculated by molecular orbital and density functional methods. It is concluded that the NMR data are consistent with the ring fragment, averaged over the ring-ene rotation, planar, while the ene fragment is not. The value of phi(0) is found to be 18.0 degrees +/-0.2 degrees for the two solutions, compared with a value of 27 degrees calculated by the molecular method MP2/6-31G(*).     

Complete structural and magnetic characterization of biological radicals in solution by an integrated quantum mechanical approach: glycyl radical as a case study

An integrated quantum mechanical approach for the structural and magnetic characterization of flexible free radicals in solution has been applied to a model of the glycyl radical engaged in peptidic chains. The hyperfine couplings computed using hybrid density functionals and purposely tailored basis sets are in good agreement with experiment when vibrational averaging effects from low frequency motions and solvent effects (both direct H bonding and bulk) are taken into the proper account. The g tensor shows a smaller dependence on the specific form of the density functional, the extension of the basis set over a standard double-zeta+polarization level, vibrational averaging, and bulk solvent effects. However, hydrogen bridges with solvent molecules belonging to the first solvation shell play a significant role. Together with their intrinsic interest, our results show that a comprehensive and reliable computational approach is becoming available for the complete characterization of open-shell systems of biological interest in their natural environment.     

Two-dimensional Raman and infrared vibrational spectroscopy for a harmonic oscillator system nonlinearly coupled with a colored noise bath

Multidimensional vibrational response functions of a harmonic oscillator are reconsidered by assuming nonlinear system-bath couplings. In addition to a standard linear-linear (LL) system-bath interaction, we consider a square-linear (SL) interaction. The LL interaction causes the vibrational energy relaxation, while the SL interaction is mainly responsible for the vibrational phase relaxation. The dynamics of the relevant system are investigated by the numerical integration of the Gaussian-Markovian Fokker-Planck equation under the condition of strong couplings with a colored noise bath, where the conventional perturbative approach cannot be applied. The response functions for the fifth-order nonresonant Raman and the third-order infrared (or equivalently the second-order infrared and the seventh-order nonresonant Raman) spectra are calculated under the various combinations of the LL and the SL coupling strengths. Calculated two-dimensional response functions demonstrate that those spectroscopic techniques are very sensitive to the mechanism of the system-bath couplings and the correlation time of the bath fluctuation. We discuss the primary optical transition pathways involved to elucidate the corresponding spectroscopic features and to relate them to the microscopic sources of the vibrational nonlinearity induced by the system-bath interactions. Optical pathways for the fifth-order Raman spectroscopies from an "anisotropic" medium were newly found in this study, which were not predicted by the weak system-bath coupling theory or the standard Brownian harmonic oscillator model.     

Synthesis,Spectroscopy, and Computational Analysis of Photoluminescent Bis(aminophenyl)‐Substituted Thiophene Derivatives

Substituted oligothiophenes have a long history in the field of organic electronics, as they often combine outstanding electro‐optical properties with the ease of synthesis. To assist the rational selection of the most promising structures to be synthesized, there is the demand for tools that allow prediction of the properties of the materials. In this study, we present strategies for synthesis and computational characterization, with respect to the fluorescence behavior of oligothiophene‐based materials for organoelectronic applications. In a combined approach, sophisticated computational methodologies are directly compared to experimental results. The M06‐2X functional in combination with the polarizable continuum model in a state‐specific formulation for excited‐state solvation proved to be particularly reliable. In addition, a semiclassical approach for describing the vibrational broadening of the spectra is employed. As a result, a robust procedure for the prediction of the fluorescence spectra of oligothiophene derivatives is presented.     

Molecules with large-amplitude torsional motion partially oriented in a nematic liquid crystal: ethane and isotopomers

An NMR study on ethane and five isotopomers dissolved in the nematic liquid crystal Merck ZLI 1132 is performed. A consistent set of dipolar and quadrupolar couplings is obtained. The dipolar couplings are corrected for harmonic vibrational effects, while the contribution from the torsional motion is incorporated classically. The corrected dipolar couplings cannot be understood in terms of a reasonable molecular structure unless effects of the reorientation-vibration interaction are taken into account. Assuming that the reorientation-vibration contributions that are known for the methyl group in methyl fluoride are transferable to ethane, excellent agreement between observed and calculated dipolar couplings is obtained on the basis of the ethane gas-phase structure. The observed and calculated deuterium quadrupolar couplings show discrepancies supporting the notion that average electric field gradients are important in liquid-crystal solvents. An important consequence of the transferability of the reorientation-vibration correlation is that in other molecules with a methyl group the same procedure as for ethane can be followed. Inclusion of this effect generally removes the need to interpret changes in observed dipolar couplings in terms of elusive chemical effects.     

Semiclassical initial value series representation in the continuum limit: application to vibrational relaxation

A recently formulated continuum limit semiclassical initial value series representation (SCIVR) of the quantum dynamics of dissipative systems is applied to the study of vibrational relaxation of model harmonic and anharmonic oscillator systems. As is well known, the classical dynamics of dissipative systems may be described in terms of a generalized Langevin equation. The continuum limit SCIVR uses the Langevin trajectories as input, albeit with a quantum noise rather than a classical noise. Combining this development with the forward-backward form of the prefactor-free propagator leads to a tractable scheme for computing quantum thermal correlation functions. Here we present the first implementation of this continuum limit SCIVR series method to study two model problems of vibrational relaxation. Simulations of the dissipative harmonic oscillator system over a wide range of parameters demonstrate that at most only the first two terms in the SCIVR series are needed for convergence of the correlation function. The methodology is then applied to the vibrational relaxation of a dissipative Morse oscillator. Here, too, the SCIVR series converges rapidly as the first two terms are sufficient to provide the quantum mechanical relaxation with an estimated accuracy on the order of a few percent. The results in this case are compared with computations obtained using the classical Wigner approximation for the relaxation dynamics.     

Dynamical effects in line shapes for coupled chromophores: time-averaging approximation

For an isolated resonance of an isolated chromophore in a condensed phase, the absorption line shape is often more sharply peaked than the distribution of transition frequencies as a result of motional narrowing. The latter arises from the time-dependent fluctuations of the transition frequencies. It is well known that one can incorporate these dynamical effects into line shape calculations within a semiclassical approach. For a system of coupled chromophores, both the transition frequencies and the interchromophore couplings fluctuate in time. In principle one can again solve this more complicated problem with a related semiclassical approach, but in practice, for large numbers of chromophores, the computational demands are prohibitive. This has led to the development of a number of approximate theoretical approaches to this problem. In this paper we develop another such approach, using a time-averaging approximation. The idea is that, for a single chromophore, a motionally narrowed line shape can be thought of as a distribution of time-averaged frequencies. This idea is developed and tested on both stochastic and more realistic models of isolated chromophores, and also on realistic models of coupled chromophores, and it is found that in all cases this approximation is quite satisfactory, without undue computational demands. This approach should find application for the vibrational spectroscopy of neat liquids, and also for proteins and other complicated multichromophore systems.     

Anharmonic vibrational modes of nucleic acid bases revealed by 2D IR spectroscopy

Polarization-dependent two-dimensional infrared (2D IR) spectra of the purine and pyrimadine base vibrations of five nucleotide monophosphates (NMPs) were acquired in D(2)O at neutral pH in the frequency range 1500-1700 cm(-1). The distinctive cross-peaks between the ring deformations and carbonyl stretches of NMPs indicate that these vibrational modes are highly coupled, in contrast with the traditional peak assignment, which is based on a simple local mode picture such as C═O, C═N, and C═C double bond stretches. A model of multiple anharmonically coupled oscillators was employed to characterize the transition energies, vibrational anharmonicities and couplings, and transition dipole strengths and orientations. No simple or intuitive structural correlations are found to readily assign the spectral features, except in the case of guanine and cytosine, which contain a single local CO stretching mode. To help interpret the nature of these vibrational modes, we performed density functional theory (DFT) calculations and found that multiple ring vibrations are coupled and delocalized over the purine and pyrimidine rings. Generally, there is close correspondence between the experimental and computational results, provided that the DFT calculations include explicit waters solvating hydrogen-bonding sites. These results provide direct experimental evidence of the delocalized nature of the nucleotide base vibrations via a nonperturbative fashion and will serve as building blocks for constructing a structure-based model of DNA and RNA vibrational spectroscopy.     

Stochastic Liouville equation simulation of multidimensional vibrational line shapes of trialanine

The line shapes detected in coherent femtosecond vibrational spectroscopies contain direct signatures of peptide conformational fluctuations through their effect on vibrational frequencies and intermode couplings. These effects are simulated in trialanine using a Green's function solution of a stochastic Liouville equation constructed for four collective bath coordinates (two Ramachandran angles affecting the mode couplings and two diagonal energies). We find that fluctuations of the Ramachandran angles which hardly affect the linear absorption can be effectively probed by two-dimensional spectra. The signal generated at k(1)+k(2)-k(3) is particularly sensitive to such fluctuations.     

Solvent effects on the vibrational frequencies of the phenolate anion, the para-cresolate anion, and their radicals

The effects of aqueous solvation on the structure and vibrational frequencies of phenol, para-cresol, and their respective radicals are calculated at the B3LYP/6-31+G(d,p) level of theory using the conductor-like polarizable continuum model (C-PCM) alone and in combination with an explicit water molecule H-bonded to the phenolic oxygen. Calculated vibrational frequencies are compared to experimental frequencies obtained in aqueous buffer at high pH. For all models, the C-PCM provides the best overall agreement between theory and experiment at a modest computational effort, as demonstrated by the lowest mean absolute deviations in the computed frequencies. In addition, the C-PCM provides anion Wilson mode 7a (18)O isotope shifts in excellent agreement with experiment and improves agreement between the computed and observed radical Wilson mode 7a (2)H isotope shift. On the basis of a quantitative comparison of the anion and radical normal modes by vibrational projection analysis and total energy decomposition, an alternative criterion for distinguishing the anion and radical Wilson modes 7a and 19a using the relative phasing of the carbon-oxygen and carbon-carbon bond stretches is presented.     

Approximate vibrational corrections for NMR spectral parameters of partially oriented molecules

The NMR spectral parameters of partially oriented molecules, such as indirect couplings, chemical shifts and quadrupolar couplings, should be corrected for effects due to vibrational motions. A practicable method of correction, applicable to cases where the parameters are determined approximately by axially symmetric bonds, is described.