Simulation of vibrational spectra of polymers by molecular dynamics calculations

Molecular dynamics is used to study the vibrational spectra (infrared and Raman) of polyethylene and polytetrafluoroethylene. The calculated frequencies are in good agreement with results of normal mode analyses. The calculated intensities lead to the conclusion that, while satisfactory relative intensities can be expected from simple models, quantitative determination of the intensities necessitates the use of complete sets of electro-optical parameters.     

Relaxation in excited vibrational levels of NH3 by infrared triple-resonance spectroscopy

A two step optical pumping technique in combination with transient diode laser absorption is described which provides a powerful tool for preparing sel     

Interpretation of nuclear resonant vibrational spectra of rubredoxin using a combined quantum mechanics and molecular mechanics approach

Nuclear resonant vibrational spectra of the reduced and oxidized form of a mutant of rubredoxin from Pyrococcus abyssii were measured and are compared with simulated spectra that were calculated by a combined quantum mechanics (QM) and molecular mechanics (MM) method. Density functional theory was used for the QM level. Calculations were performed for different models of rubredoxin. Realistic spectra were simulated with reduced models that include at least the iron center, the four cysteins coordinating it, and the residues connected to the cysteins together with a QM layer that comprises the first two coordination shells of the iron center. Larger QM layers did not lead to significant changes of the simulated spectra.     

Rotational dynamics of solvated carbon dioxide studied by infrared, Raman, and time-resolved infrared spectroscopies and a molecular dynamics simulation

Rotational dynamics of solvated carbon dioxide (CO(2)) has been studied. The infrared absorption band of the antisymmetric stretch mode in acetonitrile is found to show a non-Lorentzian band shape, suggesting a non-exponential decay of the vibrational and/or rotational correlation functions. A combined method of a molecular dynamics (MD) simulation and a quantum chemical calculation well reproduces the observed band shape. The analysis suggests that the band broadening is almost purely rotational, while the contribution from the vibrational dephasing is negligibly small. The non-exponential rotational correlation decay can be explained by a simple rotor model simulation, which can treat large angle rotations of a relatively small molecule. A polarized Raman study of the symmetric stretch mode in acetonitrile gives a rotational bandwidth consistent with that obtained from the infrared analysis. A sub-picosecond time-resolved infrared absorption anisotropy measurement of the antisymmetric stretch mode in ethanol also gives a decay rate that is consistent with the observed rotational bandwidths.     

Anharmonic infrared and Raman spectra in Car-Parrinello molecular dynamics simulations

The infrared and Raman spectra of naphthalene crystal with inclusion of anharmonic effects have been calculated by adopting the generalized variational density functional perturbation theory in the framework of Car-Parrinello molecular dynamics simulations. The computational approach has been generalized for cells of arbitrary shape. The intermolecular interactions have been analyzed with and without the van der Waals corrections, showing the importance of such interactions in the naphthalene crystal to reproduce the structural, dynamical, and spectroscopic properties.     

Molecular hydrophobic attraction and ion-specific effects studied by molecular dynamics

Much is written about "hydrophobic forces" that act between solvated molecules and nonpolar interfaces, but it is not always clear what causes these forces and whether they should be labeled as hydrophobic. Hydrophobic effects roughly fall in two classes, those that are influenced by the addition of salt and those that are not. Bubble adsorption and cavitation effects plague experiments and simulations of interacting extended hydrophobic surfaces and lead to a strong, almost irreversible attraction that has little or no dependence on salt type and concentration. In this paper, we are concerned with hydrophobic interactions between single molecules and extended surfaces and try to elucidate the relation to electrostatic and ion-specific effects. For these nanoscopic hydrophobic forces, bubbles and cavitation effects play only a minor role and even if present cause no equilibration problems. In specific, we study the forced desorption of peptides from nonpolar interfaces by means of molecular dynamics simulations and determine the adsorption potential of mean force. The simulation results for peptides compare well with corresponding AFM experiments. An analysis of the various contributions to the total peptide-surface interactions shows that structural effects of water as well as van der Waals interactions between surface and peptide are important. Hofmeister ion effects are studied by separately determining the effective interaction of various ions with hydrophobic surfaces. An extension of the Poisson-Boltzmann equation that includes the ion-specific potential of mean force yields surface potentials, interfacial tensions, and effective interactions between hydrophobic surfaces. There, we also analyze the energetic contributions to the potential of mean force and find that the most important factor determining ion-specific adsorption at hydrophobic surfaces can best be described as surface-modified ion hydration.     

Depth profiling of water molecules at the liquid-liquid interface using a combined surface vibrational spectroscopy and molecular dynamics approach

The studies presented here combine experimental and computational approaches to provide new insights into how water structures and penetrates into the organic phase at two different liquid-liquid systems: the interfaces of carbon tetrachloride-water (CCl4-H2O) and 1,2-dichloroethane-water (DCE-H2O). In particular, molecular dynamics simulations are performed to generate computational spectral intensities of the CCl4-H2O and DCE-H2O interfaces that are directly comparable with experimental measurements. These simulations are then applied toward the generation of spectral profiles, responses that vary as functions of both frequency and interfacial depth. These studies emphasize the similarities and differences in the structure, orientation, and bonding of interfacial water as a function of interfacial depth for these two liquid-liquid systems and demonstrate the differing behavior of water monomers that penetrate into the organic phase.     

Quantum wavepacket ab initio molecular dynamics: an approach for computing dynamically averaged vibrational spectra including critical nuclear quantum effects

We have introduced a computational methodology to study vibrational spectroscopy in clusters inclusive of critical nuclear quantum effects. This approach is based on the recently developed quantum wavepacket ab initio molecular dynamics method that combines quantum wavepacket dynamics with ab initio molecular dynamics. The computational efficiency of the dynamical procedure is drastically improved (by several orders of magnitude) through the utilization of wavelet-based techniques combined with the previously introduced time-dependent deterministic sampling procedure measure to achieve stable, picosecond length, quantum-classical dynamics of electrons and nuclei in clusters. The dynamical information is employed to construct a novel cumulative flux/velocity correlation function, where the wavepacket flux from the quantized particle is combined with classical nuclear velocities to obtain the vibrational density of states. The approach is demonstrated by computing the vibrational density of states of [Cl-H-Cl]-, inclusive of critical quantum nuclear effects, and our results are in good agreement with experiment. A general hierarchical procedure is also provided, based on electronic structure harmonic frequencies, classical ab initio molecular dynamics, computation of nuclear quantum-mechanical eigenstates, and employing quantum wavepacket ab initio dynamics to understand vibrational spectroscopy in hydrogen-bonded clusters that display large degrees of anharmonicities.     

Vibrational and rotational relaxation of NH3 studied in a molecular jet by infrared-infrared double resonance

Infrared-infrared double resonance is applied to an expanding jet of NH₃. Molecules in the a(3,3) rotational level of the vibrational ground state are excited with a CO₂-laser into the s(4,3) level of the υ₂ vibrational state, 2s(4,3). Rotational distributions in the ground and υ₂ state are probed by the infrared absorption of color-center-laser radiation producing transitions to the υ₁ and υ₁ + υ₂ states. The time delay between pumping and probing is determined by the distance between the CO₂ laser focus and the color-center-laser focus, along the jet axis. The results indicate an average relaxation time of vibration to rotation/translation of 280 (50) ns Torr* over the temperature range 50–110 K. In that temperature range the population difference between ortho and para species comes into equilibrium within 425(190) ns Torr*, and the relaxation between (3,3) and other ortho ground state levels occurs within 56(20) ns Torr* and between the 2s(4,3) and 2s(3,3) levels within 20(8) ns Torr*. The inversion relaxation time between a(3,3) and s(3,3) is determined to 7.6 (20) ns Torr*, at 50 K. (Here 1 Torr* indicates a density, 1 Torr* = 3.27 × 10²² molecules/m³).     

Ultrafast vibrational dynamics of SCN(-) and N3(-) in polar solvents studied by nonlinear infrared spectroscopy

In this paper, we report on our investigation into the vibrational dynamics of the antisymmetric stretching modes of SCN(-) and N(3)(-) in several polar solvents. We used an infrared (IR) pump-probe method to study orientational relaxation processes. In two aprotic solvents (N,N-dimethylformamide (DMF) and dimethyl sulfoxide (DMSO)), the anisotropy decay shows a bimodal feature, whereas in other solvents the anisotropy decay can be fitted well by a single exponential function. We consider that the relative contribution of fast-decaying components is smaller in the other solvents than in DMF and DMSO. We discuss the possible origins of the different anisotropy decay behavior in different solvents. From the three-pulse IR photon echo measurements for SCN(-) and N(3)(-), we found that the time-correlation functions (TCFs) of vibrational frequency fluctuations decay on two different time scales, one of which is less than 100 fs and the other is approximately 3-6 ps. In aprotic solvents, the fast-decaying components of the TCFs on a <100 fs time scale play an important role in the vibrational frequency fluctuation, although the contribution of collective solvent reorganization in aprotic solvents was clearly observed to have small amplitudes. On the other hand, we found that the amplitude of components that decay in a few picoseconds and/or the constant offset of the TCF in protic solvents is relatively large compared with that in aprotic solvents. With the formation and dissociation of hydrogen bonds between ion solute and solvent molecules, the spectra of different solvated species are exchanged with each other and merged into one band. We considered that this exchange may be an origin of slow-decaying components of the TCFs and that the decay of the TCFs corresponds to the time scales of the exchange for protic solvents such as formamide. The mechanism of vibrational frequency fluctuations for the antisymmetric stretching modes of SCN(-) and N(3)(-) is discussed in terms of the difference between protic and aprotic solvents.     

Strong vibrational exciton coupling effects in polarized IR spectra of the hydrogen bond in 2-thiopyridone crystals

This paper presents the results of investigation on polarized IR spectra of the hydrogen bond in 2-thiopyridone crystals. The spectra were measured in the frequency range of the NH and ND bond stretching vibrations, for two different crystalline forms, having developed ab or bc crystal faces. The spectra exhibited extremely strong vibrational exciton coupling effects characterized by a large Davydov-splitting (correlation field splitting), whose existence was confirmed by a strong difference between the polarized spectra of the two forms of 2-thiopyridone crystals. It was shown that extremely strong exciton interactions involving the translationally non-equivalent hydrogen bonds in the unit cell are responsible for these effects. Isotopic dilution in the crystals caused the disappearance of the spectral effects, ascribed to the inter-dimer exciton couplings, and the simultaneous retaining of the dimeric character of the “residual” ν_NH and ν_ND bands. This spectral behavior of the isotopically diluted crystals was interpreted as the result of the dynamical co-operative interactions involving the hydrogen bonds in the lattice. These interactions lead to a non-random distribution of the protons and deuterons in the cyclic hydrogen bond dimeric systems and in consequence to the so-called H/D isotopic “self-organization” effects in the crystal spectra. The fine structure of the “residual” ν_NH and ν_ND bands is also influenced by such non-conventional spectral effects as the selection rule breaking for IR transitions, as well as the “reversal” exciton coupling effect for centrosymmetric hydrogen bonded dimers. This statement is supported by model calculations of the analyzed band shapes. They are performed in terms of the “strong-coupling” theory which assumes a strong anharmonic coupling involving different frequency hydrogen bond normal vibrations in the dimers, namely the high-frequency NH stretching and the low-frequency ν_N⋯S hydrogen bond stretching vibrations.     

Effects of tert-butyl halide molecular siting in crystalline NaX faujasite on the infrared vibrational spectra

Experimental, analytical, and modeling techniques employed in this study elucidate interactions between adsorbate molecules and the interior surfaces of the porous host faujasite. The vibrational spectroscopies of guest and host offer opportunities to locate the guest site in the host. We present Fourier transform (FT) infrared (IR) studies of sodium-X (NaX) faujasite supercage-included tert-butyl halides, (CH(3))(3)C-X (X=Cl, Br, I) in comparison with the adsorbate molecular gas-phase and host solid-state spectra at 295 K. Four observations of guest (nu(5,) nu(6), nu(7), and {nu(3), nu(16), nu(17)}) vibrational mode changes, three of them concomitant with host mode changes, together with modeling studies, point to a particular preferred siting of the guest molecules at host hexagonal prisms (D6R). The siting involved simultaneous interactions of the host with methyl group axial protons and the halide atom. All three methyl group axial protons interact preferentially with a single D6R O1 oxygen atom via C-H...O bonding. The halide atom also interacts with a site III' Na cation. The cation, in turn, is coordinated by three O atoms (two O1 and an O4). Two of these O atoms (O1) bridge the double six-rings that form the hexagonal prism part of the NaX substructure. O4 connects the two D6R units.     

On the vibrational structure in inner-shell ionization spectra by a many-body approach

The vibrational structure due to the ionization of inner-shell electrons is calculated for methane and carbon monoxide. The vibrational coupling constants are renormalized by going up to second order perturbation theory. It is found that for core electrons the renormalization is essential. The results are compared with experimental spectra.     

Nonequilibrium molecular dynamics simulations with a backward-forward trajectories sampling for multidimensional infrared spectroscopy of molecular vibrational modes

A full molecular dynamics (MD) simulation approach to calculate multidimensional third-order infrared (IR) signals of molecular vibrational modes is proposed. Third-order IR spectroscopy involves three-time intervals between three excitation and one probe pulses. The nonequilibrium MD (NEMD) simulation allows us to calculate molecular dipoles from nonequilibrium MD trajectories for different pulse configurations and sequences. While the conventional NEMD approach utilizes MD trajectories started from the initial equilibrium state, our approach does from the intermediate state of the third-order optical process, which leads to the doorway-window decomposition of nonlinear response functions. The decomposition is made before the second pump excitation for a two-dimensional case of IR photon echo measurement, while it is made after the second pump excitation for a three-dimensional case of three-pulse IR photon echo measurement. We show that the three-dimensional IR signals are efficiently calculated by using the MD trajectories backward and forward in time for the doorway and window functions, respectively. We examined the capability of the present approach by evaluating the signals of two- and three-dimensional IR vibrational spectroscopies for liquid hydrogen fluoride. The calculated signals might be explained by anharmonic Brownian model with the linear-linear and square-linear system-bath couplings which was used to discuss the inhomogeneous broadening and dephasing mechanism of vibrational motions. The predicted intermolecular librational spectra clearly reveal the unusually narrow inhomogeneous linewidth due to the one-dimensional character of HF molecule and the strong hydrogen bond network.     

Raman and infrared spectra of phase transition in CH3NH3ClO4

Studies on the temperature variation of infrared and Raman spectra in the range 298 to 460K have shown the presence of two structural phase transitions at 321 and 451K. Phase III

transition is of first order. Phase I exhibits isotropic reorientational motion of the cations and anions.     

Assigning vibrational spectra of ferryl-oxo intermediates of cytochrome C oxidase by periodic orbits and molecular dynamics

Complexity is inherent in biological molecules not only because of the large number of atoms but also because of their nonlinear interactions responsible for chaotic behaviours, localized motions, and bifurcation phenomena. Thus, versatile spectroscopic techniques have been invented to achieve temporal and spatial resolution to minimize the uncertainties in assigning the spectra of complex molecules. Can we associate spectral lines to specific chemical bonds or species in a large molecule? Can energy stay localized in a bond for a substantial period of time to leave its spectroscopic signature? These longstanding problems are investigated by studying the resonance Raman spectra of ferryl-oxo intermediates of cytochrome c oxidase. The difference spectra of isotopically substituted ferryl oxygen ((16)O minus (18)O) in the cytochrome c oxidase recorded in several laboratories show one or two prominent positive peaks which have not been completely elucidated yet. By applying the hierarchical methods of nonlinear mechanics, and particularly the study of periodic orbits in the active site of the enzyme, in conjunction with molecular dynamics calculations of larger systems which include the embraced active site by the protein and selected protonated/deprotonated conformations of amino acids, we translate the spectral lines to molecular motions. It is demonstrated that for the active site stable periodic orbits exist for a substantial energy range. Families of periodic orbits which are associated with the vibrations of Fe(IV)=O bond mark the regions of phase space where nearby trajectories remain localized, as well as assign the spectral bands of the active site in the protein matrix. We demonstrate that proton movement adjacent to active site, which occurs during the P --> F transition, can lead to significant perturbations of the Fe(IV)=O isotopic difference vibrational spectra in cytochrome c oxidase, without a change in oxidation state of the metal sites. This finding links spectroscopic characteristics to protonation events occurring during enzymatic turnover.     

Calculation of the infrared spectrum and density of the vibrational states of an SiO2 melt by molecular dynamics

The density of the vibrational states of an SiO₂ melt under various PT conditions, the distributions of the Si-O-Si and O-Si-O angles in it, and its IR absorption spectra have been calculated by molecular dynamics with the use of a pairwise additive Born-Mayer potential. A comparison with the experimental data reveals that the ionic approximation selected is capable of basically reproducing the structural and spectroscopic properties of the melt, but the distributions of the bond angles are considerably broader than the experimentally determined distributions, and the absorption band caused by the stretching vibrations is not displayed in the calculated spectrum. The disparities indicated are apparently due to the isotropic nature of the potential of the interparticle interactions.V. I. Vernadskii Institute of Geochemistry and Analytical Chemistry, Academy of Sciences of the USSR, Moscow. Translated from Teoreticheskaya i Éksperimental'naya Khimiya, Vol. 27, No. 4, pp. 467–470, July–August, 1991. Original article submitted October 12, 1990.     

Extraordinary exciton polaritons in the optical spectra of molecular crystals

The highly anisotropic reflectivity spectra of molecular crystals (cyanine dye, TCNQ⁰) are discussed in terms of macroscopic dielectric theory. The resonance energies defined as the maxima in the ?₂-spectra depend on the relative orientation of the wavevector of the light and the transition moment. These directional effects are quantitatively explained by directional dispersion of the extraordinary polariton modes. Vibrational satellites are responsible for the detailed structure of the reflectance bands. Strong mixing of the various polariton branches shows up as additional broadening of the peaks in the ?₂-spectra.     

Electronic absorption spectra of pyridine and nicotine in aqueous solution with a combined molecular dynamics and polarizable QM/MM approach

The electronic absorption spectra of pyridine and nicotine in aqueous solution have been computed using a multistep approach. The computational protocol consists in studying the solute solvation with accurate molecular dynamics simulations, characterizing the hydrogen bond interactions, and calculating electronic transitions for a series of configurations extracted from the molecular dynamics trajectories with a polarizable QM/MM scheme based on the fluctuating charge model. Molecular dynamics simulations and electronic transition calculations have been performed on both pyridine and nicotine. Furthermore, the contributions of solute vibrational effect on electronic absorption spectra have been taken into account in the so called vertical gradient approximation. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.