Umbrella sampling of solute vibrational line shifts in mixed quantum-classical molecular dynamics simulations

An umbrella sampling approach for vibrational frequency line shifts is presented. The technique allows for efficient sampling of the solvent configurations corresponding to frequency shifts of a solute in mixed quantum-classical simulations. The approach is generally applicable and can also be used within traditional perturbation theory calculations of frequency shifts. It is particularly useful in the extraction of detailed mechanistic information about the solute-solvent interactions giving rise to the frequency shifts. The method is illustrated by application to the simple I2 in a liquid Xe system, and the advantages are discussed.     

Vibrational solvatochromism and electrochromism of infrared probe molecules containing C≡O, C≡N, C=O, or C-F vibrational chromophore

Solvatochromic vibrational frequency shifts of a few different infrared (IR) probe molecules have been studied by carrying out quantum chemistry calculations for a number of their water clusters. We are particularly focused on the vibrational solvatochromic and electrochromic effects on the CO, CN, and CF stretch modes in carbon monoxide, acetone, 4-cyanopyridine, p-tolunitrile, fluorobenzene, and 3-fluoropyridine. Using multiple interaction site antenna model, we show that their solvatochromic vibrational frequency shifts can be successfully described by considering spatially nonuniform electrostatic potential generated by the surrounding water molecules. It turns out that the CO and CF stretch mode frequencies are approximately proportional to the solvent electric field projected onto the bond axes, whereas the vibrational frequencies of the nitrile stretch mode in 4-cyanopyridine and p-tolunitrile are not. Consequently, it is confirmed that the vibrational Stark tuning rates of the CO and CF stretching modes can be directly used to describe their solvatochromic frequency shifts in condensed phases. However, the nitrile stretch mode frequency shift induced by solvent electrostatic potential appears to be more complicated than its electrochromic phenomenon. To examine the validity of the distributed interaction site model for solvatochromic frequency shifts of these vibrational chromophores, we thus calculated the vibrational Stark tuning rates of the CO, CN, and CF stretch modes and found that they are in good agreement with the experimental results found in literatures. This confirms that a collection of properly chosen distributed interaction sites can be an excellent electric antenna sensing local electrostatics that affects on vibrational frequencies of IR probe modes.     

Correlation between solvent-induced vibrational frequency shifts of the CO moiety and solvent electron acceptor numbers: tetramethylurea

The CO stretching frequencies in the Raman spectra of 0.10 M solutions of tetramethylurea in seventeen solvents have been recorded. These frequencies exhibit a linear relationship with the solvent electron acceptor number. Comparison of the slopes of these lines and those obtained from analyzing literature data of ν(CO) reveals a correlation with the bond polarity. A linear correlation between (ν_hexane −ν_soln)/ν_hexane and the solvent acceptor number is also shown. The slopes of these latter plots can be related to ν_hexane and it is suggested that this approach be used to explain the specific solvent—solute interaction contributions to solvent-induced vibrational frequency shifts. This method is compared with the solvato-chromic method and it is shown that solvent acidity strongly influences the observed vibrational frequency shifts for the CO moiety of tetramethylurea.     

Hydrogen bond of radicals: Interaction of HNO with HCO,HNO, and HOO

Ab initio quantum mechanics methods are employed to investigate hydrogen bonding interactions between HNO and HCO, HOO radicals, and closed‐shell HNO. The systems were calculated at MP2/6‐311++G (2d, 2p) level and G2MP2 level. The topological and NBO analysis were investigated the origin of hydrogen bonds red‐ or blue‐shifts. In addition, the comparisons were performed between HNO‐opened‐shell radical (HCO, HOO) complexes and HNO‐corresponding closed‐shell molecule (H₂CO, HOOH) complexes. It is found that the stabilities of complexes increase from HNO‐HCO to HNO‐HOO. There are blue‐shifts of N? H, C? H stretching vibrational frequencies and a red‐shift of O? H stretching vibrational frequency in the complexes. Rehybridization and electron density redistribution contribute to the blue‐shifts of C? H and N? H stretching vibrational frequencies. Compared with the closed‐shell H₂CO, HCO is weaker proton donor and weaker proton acceptor. For the HOO, it is stronger proton donor and weaker proton acceptor than the HOOH is. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Environmental effects on vibrational properties of carotenoids: experiments and calculations on peridinin

Carotenoids are employed in light-harvesting complexes of dinoflagellates with the two-fold aim to extend the spectral range of the antenna and to protect it from radiation damage. We have studied the effect of the environment on the vibrational properties of the carotenoid peridinin in different solvents by means of vibrational spectroscopies and QM/MM molecular dynamics simulations. Three prototypical solvents were considered: cyclohexane (an apolar/aprotic solvent), deuterated acetonitrile (a polar/aprotic solvent) and methanol (a polar/protic solvent). Thanks to effective normal mode analysis, we were able to assign the experimental Raman and IR bands and to clarify the effect of the solvent on band shifts. In the 1500-1650 cm(-1) region, seven vibrational modes of the polyene chain were identified and assigned to specific molecular vibrations. In the 1700-1800 cm(-1) region a strong progressive down-shift of the lactonic carbonyl frequency is observed passing from cyclohexane to methanol solutions. This has been rationalized here in terms of solvent polarity and solute-solvent hydrogen bond interactions. On the basis of our data we propose a classification of non-equivalent peridinins in the Peridinin-Chlorophyll-Proteins, light-harvesting complexes of dinoflagellates.     

Solvent effects on the electrochemical p-doping of PEDOT

EQCM experiments were carried out on PEDOT films exposed to TEABF(4)/CH(3)CN and TEABF(4)/CH(2)Cl(2) under permselective conditions and subjected to cyclic voltammetry in the potential range corresponding to p-doping. Current and frequency responses were used to obtain time-resolved ion and solvent flux data as functions of potential. Normalization of these fluxes with potential scan rate distinguishes thermodynamically (ir)reversible elementary steps in the overall redox process. The specific mechanisms are different in the two solvents, although both show mechanistic switches at partial redox conversion during both p-doping and undoping. These different mechanistic signatures are characterized according to the solvent identity, by different patterns of deviation from scan rate normalization for the experimentally measured ion and solvent fluxes. Comparison of these ion and solvent fluxes demonstrates that the rates of solvent expulsion (during doping) and entry (during undoping) are key determinants of mechanism. In both switching directions there are changes between kinetically limiting and rapid solvent transfer that depend upon solvent identity, i.e. the mechanism depends substantially upon charge state, switching direction and solvent. These mechanistic pathways and shifts can be visualized by a scheme-of-cubes representation.     

Vibrational spectroscopy and dynamics of azide ion in ionic liquid and dimethyl sulfoxide water mixtures

Steady-state and time-resolved infrared spectroscopy of the azide (N(3)-) anion has been used to characterize aqueous mixtures both with the ionic liquid (IL) 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF(4)]) and with dimethyl sulfoxide (DMSO). In the DMSO-water mixtures, two anion vibrational bands are observed for low water mole fractions (0 > X(w) > 0.25), which indicates a heterogeneous ion solvation environment. The band at 2000 cm(-1) observed for neat DMSO does not shift but decreases in amplitude as the amount of water is increased. Another band appears at slightly higher frequency at low X(w) (=0.05). As the amount of water is increased, this band shifts to higher frequency and becomes stronger and is attributed to azide with an increasing degree of hydration. At intermediate and high X(w), a single band is observed that shifts almost linearly with water mole fraction toward the bulk water value. The heterogeneity is evident from the infrared pump-probe studies in which the decay times depend on probe frequency at low mole fraction. For the azide spectra in IL-water mixtures, a single azide band is observed for each mole fraction mixture. The azide band shifts almost linearly with mole fraction, indicating nearly ideal mixing behavior. As with the DMSO-water mixtures, the time-resolved IR decay times are probe-frequency-dependent at low mole fraction, again indicating heterogeneous solvation. In both the DMSO and IL mixtures with water, the relaxation times are slower than would be expected from ideal mixing, suggesting that vibrational relaxation of azide is more sensitive than its vibrational frequency to the solvent structure. The results are discussed in terms of preferential solvation and the degree to which the azide shift and vibrational relaxation depend on the degree of water association in the mixtures.     

混合量子-经典动力学方法研究反胶团水池中I2分子的振动频率位移

结合Monte Carlo模拟技术, 提出了一种反胶团溶液的快速数学建模新方法. 利用量子-经典动力学模拟方法, 考察了I2分子受限于两个不同尺寸的反胶团水池中振动频率的诱导位移及谱分布. 结果表明, 相比于体相水, 受限于反胶团水池中I2分子的诱导位移表现为蓝移, 且蓝移大小随水池尺寸变化不大. 通过对I2分子与周围环境相互作用的分解分析, 得到了水池水、表面活性剂以及有机溶剂分子对I2分子振动频率诱导位移的瞬态贡献, 揭示了I2分子振动弛豫的微观作用机制. 此外, 对于受限水池中水分子的诱导贡献及空间分布的研究表明, I2分子振动频率位移的诱导贡献主要来自于第一溶剂层, 它是由4个水分子蓝移贡献和2个水分子红移贡献组成.     

Intramolecular vibrational coupling contribution to temperature dependence of vibrational mode frequencies

High-frequency vibrational modes in molecules in solution are sensitive to temperature and shift either to lower or higher frequencies with the temperature increase. These frequency shifts are often attributed to specific interactions of the molecule and to the solvent polarization effect. We found that a substantial and often dominant contribution to sensitivity of vibrational high-frequency modes to temperature originates from anharmonic interactions with other modes in the molecule. The temperature dependencies were measured for several modes in ortho-, meta-, and para-isomers of acetylbenzonitrile in solution and in a solid matrix and compared to the theoretical predictions originated from the intramolecular vibrational coupling (IVC) evaluated using anharmonic density functional theory calculations. It is found that the IVC contribution is essential for temperature dependencies of all high-frequency vibrational modes and is dominant for many modes. As such, the IVC contribution alone permits predicting the main trend in the temperature dependencies, especially for vibrational modes with smaller transition dipoles. In addition, an Onsager reaction field theory was used to describe the solvent contribution to the temperature dependencies.     

Solute-solvent interaction in liquids. I. Long-range forces and vibrational solvent shifts

The model of solute— solvent interaction based on dipole-induced-dipole forces (Kirkwood-Bauer-Magat) has been generalized, yielding an expression for the energy as a function of solute position and orientalion within a spherical cavity in a dielectric medium. An analogous relation has been derived for the dispersion energy. Barriers to rotation of the solute molecule and shifts in its vibrational frequency are calculated as functions of cavity radius and eccentricity for the case of dilute solutions of HCl in CCl₄. It is found that the effect of dispersion forces on the vibrational frequency of HCl is two-to-three times more important than the traditional dipole-induced-dipole contribution.     

Vibrational recognition of adsorption sites for CO on platinum and platinum-ruthenium surfaces

We have studied the vibrational properties of CO adsorbed on platinum and platinum-ruthenium surfaces using density-functional perturbation theory within the Perdew-Burke-Ernzerhof generalized-gradient approximation. The calculated C-O stretching frequencies are found to be in excellent agreement with spectroscopic measurements. The frequency shifts that take place when the surface is covered with ruthenium monolayers are also correctly predicted. This agreement for both shifts and absolute vibrational frequencies is made more remarkable by the frequent failure of local and semilocal exchange-correlation functionals in predicting the stability of the different adsorption sites for CO on transition metal surfaces. We have investigated the chemical origin of the C-O frequency shifts introducing an orbital-resolved analysis of the force and frequency density of states, and assessed the effect of donation and backdonation on the CO vibrational frequency using a GGA+molecular U approach. These findings rationalize and establish the accuracy of density-functional calculations in predicting absolute vibrational frequencies, notwithstanding the failure in determining relative adsorption energies, in the strong chemisorption regime.     

Intermolecular Hydrogen Bonds Formed Between Amino Acid Molecules in Aqueous Solution Investigated by Temperature-jump NanosecondTime-resolved Transient Mid-IR Spectroscopy

Carboxyl (COO?) vibrational modes of two amino acids histidine and glycine in D2O solution were investigated by temperature-dependent FTIR spectroscopy and temperature-jump nanosecond time-resolved IR di?erence absorbance spectroscopy. The results show that hydrogen bonds are formed between amino acid molecules as well as between the amino acid molecule and the solvent molecules. The asymmetric vibrational frequency of COO? around 1600-1610 cm?1 is blue shifted when raising temperature, indicating that the strength of the hydrogen bonds becomes weaker at higher temperature. Two bleaching peaks at 1604 and 1612 cm?1 were observed for histidine in response to a temperature jump from 10 ±C to 20 ±C. The lower vibrational frequency at 1604 cm?1 is assigned to the chain COO? group which forms the intermolecular hydrogen bond with NH3+ group, while the higher frequency at 1612 cm?1 is assigned to the end COO? group forming hydrogen bonds with the solvent molecules. This is because that the hydrogen bonds in the former are expected to be stronger than the latter. In addition the intensities of these two bleaching peaks are almost the same. In contrast, only the lower frequency at 1604 cm?1 bleaching peak has been observed for glycine. The fact indicates that histidine molecules form a dimer-like intermolecular chain while glycine forms a relatively longer chain in the solution. The rising phase of the IR absorption kinetics in response to the temperature-jump detected at 1604 cm?1 for histidine is about 30§10 ns, within the resolution limit ofour instrument, indicating that breaking or weakening the hydrogen bond is a very fast process.     

Solvent-dependent vibrational frequencies and reorganization energies of two merocyanine chromophores

Absorption and resonance Raman spectra have been measured over a wide range of solvents for two merocyanine dyes containing the indoline ("Fischer" base) electron donor group with different accepting groups. One appears to be near the cyanine limit (equal contributions of the neutral and zwitterionic resonance forms to both ground- and excited-state structures) based on electrooptic absorption data showing a very small dipole moment change upon electronic excitation. The resonance Raman spectra of both molecules show significant frequency shifts and intensity redistributions that evolve monotonically with increasing solvent polarity and are consistent with increasing zwitterionic character of the ground-state structure. The vibrational reorganization energies of both molecules, obtained by simulating the absorption band shapes, are smaller in polar solvents than in nonpolar or weakly polar ones, consistent with a more cyanine-like structure at higher solvent polarities. However, the vibrational reorganization energies of both molecules exceed 700 cm(-1) in all solvents, larger than in many true cyanine dyes, and the optical absorption maxima do not correlate well with either solvent polarity or vibrational reorganization energy. This indicates some limitations to the structural conclusions that can be reached from the two-state model for pi-conjugated donor-acceptor systems.     

Solvent effects on IR and VCD spectra of helical peptides: DFT-based static spectral simulations with explicit water

Simulations of IR and VCD spectra are carried out for model alpha-helical, 3(10)-helical, and 3(1)-helical (polyProII-like) oligopeptides, with up to 21 amide groups, and including explicit consideration of effects of directly hydrogen-bonded solvent (water). Parameters used were obtained from ab initio density functional theory (DFT) computations of force field, atomic polar and axial tensors for oligopeptides of 5 to 7 amides, whose structures were constrained in (phi,psi) to target the secondary structure type but otherwise fully optimized. By comparison with experimental data as well as with calculations for identical but isolated (gas phase) peptides, the computed effects of an inner shell of aqueous solvent on the vibrational spectra of helical oligopeptides are illustrated. The interaction with solvent causes significant frequency shifts of the amide bands, but only minor changes in the characteristic IR intensity distributions and splittings and the VCD band shapes. Better agreement with experimental band shapes is achieved for the alpha-helical amide I' (N-deuterated) VCD by inclusion of explicit solvent in the calculations. Some improvements are also observed in theoretical VCD predictions for 13C labeled alpha-helical peptides when solvated models are used. However, the qualitative isotopic splitting patterns are preserved and just shifted in frequency due to consistent, solvent independent interamide coupling constants. The critical match of experiment and theory for relative positions of transitions in peptides with specifically separated 13C=O labels, including and neglecting solvent, confirms the stability of the coupling interactions. Despite these solvation effects, the calculated VCD band shape of the amide I mode is shown to be a reliable conformational probe, since it remains basically insensitive to frequency shifts caused by environment. Thus theoretical VCD simulations, even vacuum calculations, are shown to provide useful spectral predictions for solution-phase peptides.     

The O-H stretching mode of a prototypical photoacid as a local dielectric probe

We investigate the OH stretch vibrational frequency shifts of a prototype photoacid, 2-naphthol (2N), when dissolved in solvents of low polarity. We combine femtosecond mid-infrared spectroscopy and a theoretical model based on the Pullin-van der Zwan-Hynes perturbative approach to explore vibrational solvatochromic effects in the ground S(0) and the first electronically excited (1)L(b) states. The model is parametrized using density functional theory (DFT), at the B3LYP/TZVP and TD-B3LYP/TZVP levels for the 2N chromophore in the S(0) and (1)L(b) states, respectively. From the agreement between experiment and theory we conclude that vibrational solvatochromic effects are dominated by the instantaneous dielectric response of the solvent, while time-dependent nuclear rearrangements are of secondary importance.     

Vibrational spectroscopic determination of local solvent electric field, solute-solvent electrostatic interaction energy, and their fluctuation amplitudes

IR probes have been extensively used to monitor local electrostatic and solvation dynamics. Particularly, their vibrational frequencies are highly sensitive to local solvent electric field around an IR probe. Here, we show that the experimentally measured vibrational frequency shifts can be inversely used to determine local electric potential distribution and solute-solvent electrostatic interaction energy. In addition, the upper limits of their fluctuation amplitudes are estimated by using the vibrational bandwidths. Applying this method to fully deuterated N-methylacetamide (NMA) in D(2)O and examining the solvatochromic effects on the amide I' and II' mode frequencies, we found that the solvent electric potential difference between O(═C) and D(-N) atoms of the peptide bond is about 5.4 V, and thus, the approximate solvent electric field produced by surrounding water molecules on the NMA is 172 MV/cm on average if the molecular geometry is taken into account. The solute-solvent electrostatic interaction energy is estimated to be -137 kJ/mol, by considering electric dipole-electric field interaction. Furthermore, their root-mean-square fluctuation amplitudes are as large as 1.6 V, 52 MV/cm, and 41 kJ/mol, respectively. We found that the water electric potential on a peptide bond is spatially nonhomogeneous and that the fluctuation in the electrostatic peptide-water interaction energy is about 10 times larger than the thermal energy at room temperature. This indicates that the peptide-solvent interactions are indeed important for the activation of chemical reactions in aqueous solution.     

On the use of the Bayliss-McRae dispersion model in NMR solvent effects

The use of the Bayliss-McRae theory on the solvent induced electronic frequency shifts for NMR dispersion shifts is criticized. It is suggested that the NMR shifts should actually be proportional to the square of the Bayliss-McRae function. It is shown that the methane gas-to-liquid shifts in eleven halo-methanes as solvents are indeed proportional to this squared function; ?σ_m(CH₄) = 9.62 (n₂²?1)²/(2n₂²+1)² ppm, where n₂ is the refractive index of the solvent. The relation between this solvent factor and several existing continuum models for NMR medium shifts is discussed.     

Quasiharmonic treatment of infrared and raman vibrational frequency shifts induced by tensile deformation of polymer chains. II. Application to the polyoxymethylene and isotactic polypropylene single chains and the three-dimensional orthorhombic polyethylene crystal

Quasiharmonic equations are derived for stress-induced vibrational frequency shifts in the infrared and Raman spectra of polymer chains subjected to a tensile stress. The expressions are applied to the helical chains of polyoxymethylene and isotactic polypropylene. Observed frequency shifts can be reproduced well by using reasonable anharmonic force constants. A semiquantitative interpretation is given for the close relationship between stress-induced vibrational frequency shifts and the deformation mechanism of the polymer chains. Stress-induced frequency shifts are also calculated for an orthorhombic polyethylene crystal subjected to uniaxial tension along the chain axis or to hydrostatic pressure. The results consistently and reasonably reproduce observed data, not only for the intramolecular vibrational modes but also for the external lattice modes. © 1992 John Wiley & Sons, Inc.     

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.