A combined instantaneous normal mode and time correlation function description of the infrared vibrational spectrum of ambient water

Ab Initio Investigation of the Resonance Raman Spectrum of the Hydrated Electron

According to the conventional picture, the aqueous or "hydrated" electron, e^-(aq), occupies an excluded volume (cavity) in the structure of liquid water. However, simulations with certain one-electron models predict a more delocalized spin density for the unpaired electron, with no distinct cavity structure. It has been suggested that only the latter (non-cavity) structure can explain the hydrated electron's resonance Raman spectrum, although this suggestion is based on calculations using empirical frequency maps developed for neat liquid water, not for e^-(aq). All-electron ab initio calculations presented here demonstrate that both cavity and non-cavity models of e^-(aq) afford significant red-shifts in the O-H stretching region. This effect is nonspecific and arises due to electron penetration into frontier orbitals of the water molecules. Only the conventional cavity model, however, reproduces the splitting of the H-O-D bend (in isotopically mixed water) that is observed experimentally and arises due to the asymmetric environments of the hydroxyl moieties in the electron's first solvation shell. We conclude that the cavity model of e^-(aq) is more consistent with the measured resonance Raman spectrum than is the delocalized, non-cavity model, despite previous suggestions to the contrary. Furthermore, calculations with hybrid density functionals and with Hartree-Fock theory predict that non-cavity liquid geometries afford only unbound (continuum) states for an extra electron, whereas in reality this energy level should lie more than 3 eV below vacuum level. As such, the non-cavity model of e^-(aq) appears to be inconsistent with available vibrational spectroscopy, photoelectron spectroscopy, and quantum chemistry.

Pressure response of the THz spectrum of bulk liquid water revealed by intermolecular instantaneous normal mode analysis

The radial distribution functions of liquid water are known to change significantly their shape upon hydrostatic compression from ambient conditions deep into the kbar pressure regime. It has been shown that despite their eye-catching changes, the fundamental locally tetrahedral fourfold H-bonding pattern that characterizes ambient water is preserved up to about 10 kbar (1 GPa), which is the stability limit of liquid water at 300 K. The observed increase in coordination number comes from pushing water molecules into the first coordination sphere without establishing an H-bond, resulting in roughly two such additional interstitial molecules at 10 kbar. THz spectroscopy has been firmly established as a powerful experimental technique to analyze H-bonding in aqueous solutions given that it directly probes the far-infrared lineshape and thus the prominent H-bond network mode around 180 cm^-1. We, therefore, set out to assess pressure effects on the THz response of liquid water at 10 kbar in comparison to the 1 bar (0.1 MPa) reference, both at 300 K, with the aim to trace back the related lineshape changes to the structural level. To this end, we employ the instantaneous normal mode approximation to rigorously separate the H-bonding peak from the large background arising from the pronounced librational tail. By exactly decomposing the total molecular dynamics into hindered translations, hindered rotations, and intramolecular vibrations, we find that the H-bonding peak arises from translation-translation and translation-rotation correlations, which are successively decomposed down to the level of distinct local H-bond environments. Our utmost detailed analysis based on molecular pair classifications unveils that H-bonded double-donor water pairs contribute most to the THz response around 180 cm^-1, whereas interstitial waters are negligible. Moreover, short double-donor H-bonds have their peak maximum significantly shifted toward higher frequencies with respect to such long H-bonds. In conjunction with an increasing relative population of these short H-bonds versus the long ones (while the population of other water pair classes is essentially pressure insensitive), this explains not only the blue-shift of the H-bonding peak by about 20-30 cm^-1 in total from 1 bar to 10 kbar but also the filling of the shallow local minimum of the THz lineshape located in between the network peak and the red-wing of the librational band at 1 bar. Based on the changing populations as a function of pressure, we are also able to roughly estimate the pressure-dependence of the H-bond network mode and find that its pressure response and thus the blue-shifting are most pronounced at low kbar pressures.

Effects of protein-DNA complex formation on the intermolecular vibrational density of states of interfacial water

Single-stranded DNAs (ss-DNAs) are formed as intermediates during DNA metabolic processes. ss-DNA binding (SSB) proteins specifically bind to the single-stranded segments of the DNA and protect it from being degraded. We have performed room temperature molecular dynamics simulations of the aqueous solution of two DNA binding K homology (KH) domains (KH3 and KH4) of the far upstream element (FUSE) binding protein (FBP) complexed with two ss-DNA oligomers. Efforts have been made to explore the influence of complex formation on low-frequency vibrational density of states of the surface water molecules. It is revealed that increased back scattering of water confined around the complexed structures leads to significant blue shifts of the band corresponding to the O···O···O bending or restricted transverse motions of water, the effect being more for the bridged water molecules. Importantly, it is demonstrated that the formation of such complexed structures of a similar type may often influence the transverse and longitudinal degrees of freedom of the surrounding water molecules in a nonuniform manner.

On the interplay of the potential energy and dipole moment surfaces in controlling the infrared activity of liquid water

Infrared vibrational spectroscopy is a valuable tool for probing molecular structure and dynamics. However, obtaining an unambiguous molecular-level interpretation of the spectral features is made difficult, in part, due to the complex interplay of the dipole moment with the underlying vibrational structure. Here, we disentangle the contributions of the potential energy surface (PES) and dipole moment surface (DMS) to the infrared spectrum of liquid water by examining three classes of models, ranging in complexity from simple point charge models to accurate representations of the many-body interactions. By decoupling the PES from the DMS in the calculation of the infrared spectra, we demonstrate that the PES, by directly modulating the vibrational structure, primarily controls the width and position of the spectroscopic features. Due to the dependence of the molecular dipole moment on the hydration environment, many-body electrostatic effects result in a ∼100 cm(-1) redshift in the peak of the OH stretch band. Interestingly, while an accurate description of many-body collective motion is required to generate the correct (vibrational) structure of the liquid, the infrared intensity in the OH stretching region appears to be a measure of the local structure due to the dominance of the one-body and short-ranged two-body contributions to the total dipole moment.

Quantum calculations of the IR spectrum of liquid water using ab initio and model potential and dipole moment surfaces and comparison with experiment

The calculation and characterization of the IR spectrum of liquid water have remained a challenge for theory. In this paper, we address this challenge using a combination of ab initio approaches, namely, a quantum treatment of IR spectrum using the ab initio WHBB water potential energy surface and a refined ab initio dipole moment surface. The quantum treatment is based on the embedded local monomer method, in which the three intramolecular modes of each embedded H2O monomer are fully coupled and also coupled singly to each of six intermolecular modes. The new dipole moment surface consists of a previous spectroscopically accurate 1-body dipole moment surface and a newly fitted ab initio intrinsic 2-body dipole moment. A detailed analysis of the new dipole moment surface in terms of the coordinate dependence of the effective atomic charges is done along with tests of it for the water dimer and prism hexamer double-harmonic spectra against direct ab initio calculations. The liquid configurations are taken from previous molecular dynamics calculations of Skinner and co-workers, using the TIP4P plus E3B rigid monomer water potential. The IR spectrum of water at 300 K in the range of 0-4000 cm(-1) is calculated and compared with experiment, using the ab initio WHBB potential and new ab initio dipole moment, the q-TIP4P/F potential, which has a fixed-charged description of the dipole moment, and the TTM3-F potential and dipole moment surfaces. The newly calculated ab initio spectrum is in very good agreement with experiment throughout the above spectral range, both in band positions and intensities. This contrasts to results with the other potentials and dipole moments, especially the fixed-charge q-TIP4P/F model, which gives unrealistic intensities. The calculated ab initio spectrum is analyzed by examining the contribution of various transitions to each band.

Instantaneous normal mode analysis for intermolecular and intramolecular vibrations of water from atomic point of view

By exploiting the instantaneous normal mode (INM) analysis for models of flexible molecules, we investigate intermolecular and intramolecular vibrations of water from the atomic point of view. With two flexible SPC/E models, our investigations include three aspects about their INM spectra, which are separated into the unstable, intermolecular, bending, and stretching bands. First, the O- and H-atom contributions in the four INM bands are calculated and their stable INM spectra are compared with the power spectra of the atomic velocity autocorrelation functions. The unstable and intermolecular bands of the flexible models are also compared with those of the SPC/E model of rigid molecules. Second, we formulate the inverse participation ratio (IPR) of the INMs, respectively, for the O- and H-atom and molecule. With the IPRs, the numbers of the three species participated in the INMs are estimated so that the localization characters of the INMs in each band are studied. Further, by the ratio of the IPR of the H atom to that of the O atom, we explore the number of involved OH bond per molecule participated in the INMs. Third, by classifying simulated molecules into subensembles according to the geometry of their local environments or their H-bond configurations, we examine the local-structure effects on the bending and stretching INM bands. All of our results are verified to be insensible to the definition of H-bond. Our conclusions about the intermolecular and intramolecular vibrations in water are given.

Localization-delocalization transition of the instantaneous normal modes of liquid water

Despite the fact that the localization-delocalization transition (LDT) widely exists in wave systems, quantitative studies on its critical and multifractal properties are mainly focused on solids. In this work, these properties are investigated on the vibrational motions of liquid water. Simulations of up to 18000 molecules on the flexible extended simple point charge water model provide nearly 10(6) instantaneous normal modes. They are shown to undergo an LDT close to the translational transition and exhibit multifractal fluctuations while approaching the LDT. In combination with finite-size scaling, multifractal analysis predicts the critical frequency Im(ω(c))≈-131.6 cm(-1) for unstable modes at room temperature. The estimated critical exponent ν≈1.60 is close to those of other calculated systems in the same Wigner-Dyson class. At the LDT, the fractal spectrum f(α) and the most probable local vibrational intensity α(mc)≈4.04 coincide with those of the Anderson model, which might be additional universal properties of LDT in more general wave systems. The results extend the validity of the multifractal scaling approach beyond Andersonian systems to a Hessian system.

Dual-modulator broadband infrared Mueller matrix ellipsometry

A broadband mid-infrared Mueller matrix ellipsometer is described based on two photoelastic modulators and a step-scan interferometer. The data are analyzed using a combination hardware-software double Fourier transformation. Obtaining spectra of the Mueller matrix elements requires that the infrared wavelength-dependent retardation amplitude of the modulators be known through calibration and subsequently incorporated into the data processing. The spectroscopic capability of the instrument is demonstrated in transmission and reflection geometries by the measured Mueller matrices of air, an anisotropic quartz crystal, and the ZnSe-water interface, each from 2500-4000 cm(-1).

Quantitative Assessment of Force Fields on Both Low-Energy Conformational Basins and Transition-State Regions of the (ϕ-ψ) Space

The free energy surfaces (FESs) of alanine dipeptide are studied to illustrate a new strategy to assess the performance of classical molecular mechanics force field on the full range of the (ϕ-ψ) conformational space. The FES is obtained from metadynamics simulations with five commonly used force fields and from ab initio density functional theory calculations in both gas phase and aqueous solution. The FESs obtained at the B3LYP/6-311+G(2d,p)//B3LYP/6-31G(d,p) level of theory are validated by comparison with previously reported MP2 and LMP2 results as well as with experimentally obtained probability distribution between the C5-β (or β-PPII) and αR states. A quantitative assessment is made for each force field in three conformational basins, LeRI (C5-β-C7eq), LeRII (β2-αR), and LeRIII(αL-C7ax-αD) as well as three transition-state regions linking the above conformational basins. The performance of each force field is evaluated in terms of the average free energy of each region in comparison with that of the ab initio results. We quantify how well a force field FES matches the ab initio FES through the calculation of the standard deviation of a free energy difference map between the two FESs. The results indicate that the performance varies largely from region to region or from force field to force field. Although not one force field is able to outperform all others in all conformational areas, the OPLSAA/L force field gives the best performance overall, followed by OPLSAA and AMBER03. For the three top performers, the average free energies differ from the corresponding ab initio values from within the error range (<0.4 kcal/mol) to ∼1.5 kcal/mol for the low-energy regions and up to ∼2.0 kcal/mol for the transition-state regions. The strategy presented and the results obtained here should be useful for improving the parametrization of force fields targeting both accuracy in the energies of conformers and the transition-state barriers.

Fourier transformed infrared spectral investigations of molecular interactions in propionic acid-2-propanol binary system

FTIR spectra of propionic acid (PA), 2-propanol (PROH) and its binary mixtures with varying molefraction of the PA were recorded in the region 500-3500 cm(-1), to investigate the formation of hydrogen bonded complexes in a mixed system. The observed features in nu(CO), nu(CO) and delta(COH) of PA, nu(CO) of PROH and delta(COH) of PA+PROH have been explained in terms of the hydrogen bonding interactions between PROH and PA and dipole-dipole interaction. The dipole moment derivative for the above mentioned vibrational modes have also been predicted from the integrated absorbance. The intrinsic linewidth for the vibrational modes nu(CO) and delta(COH) of PA has been elucidated using Bondarev and Mardaeva model.

Analysis of anisotropic local field in sum frequency generation spectroscopy with the charge response kernel water model

A new flexible and polarizable water model based on the charge response kernel (CRK) theory is developed for the analysis of sum frequency generation (SFG) spectroscopy. The CRK model well describes several bulk water properties and SFG spectrum by molecular dynamics (MD) calculations. While the flexible and polarizable MD simulation generally adopts the short-range damping of intermolecular interaction, it is found that the same procedure is not adequate for the calculation of transition dipole in strongly hydrogen bonding environment. Accordingly, the improved calculation of the nonlinear susceptibility of water surface results in the positive imaginary part in the 3000-3200 cm(-1) region, which is consistent with recent phase-sensitive experiments. The mechanism of the positive region is attributed to the anisotropic local field effect induced by the orientational correlation of surface water.

Hydrogen-Bond Disruption by Vibrational Excitations in Water

An excitation of the OH-stretch nu(OH) of water has unique disruptive effects on the local hydrogen bonding. The disruption is not an immediate vibrational predissociation, which is frequently the case with hydrogen-bonded clusters, but instead is a delayed disruption caused by a burst of energy from a vibrationally excited water molecule. The disruptive effects are the result of a fragile hydrogen-bonding network subjected to a large amount of vibrational energy released in a short time by the relaxation of nu(OH) stretching and delta(H2O) bending excitations. The energy of a single nu(OH) vibration distributed over one, two, or three (classical) water molecules would be enough to raise the local temperature to 1100, 700, or 570 K, respectively. Our understanding of the properties of the metastable water state having this excess energy in nearby hydrogen bonds, termed H2O*, has emerged as a result of experiments where a femtosecond IR pulse is used to pump nu(OH), which is probed by either Raman or IR spectroscopy. These experiments show that the H2O* spectrum is blue-shifted and narrowed, and the spectrum looks very much like supercritical water at approximately 600 K, which is consistent with the temperature estimates above. The H2O* is created within approximately 400 fs after nu(OH) excitation, and it relaxes with an 0.8 ps lifetime by re-formation of the disrupted hydrogen-bond network. Vibrationally excited H2O* with one quantum of excitation in the stretching mode has the same 0.8 ps lifetime, suggesting it also relaxes by hydrogen-bond re-formation.

A time correlation function theory describing static field enhanced third order optical effects at interfaces

Sum vibrational frequency spectroscopy, a second order optical process, is interface specific in the dipole approximation. At charged interfaces, there exists a static field, and as a direct consequence, the experimentally detected signal is a combination of enhanced second and static field induced third order contributions. There is significant evidence in the literature of the importance/relative magnitude of this third order contribution, but no previous molecularly detailed approach existed to separately calculate the second and third order contributions. Thus, for the first time, a molecularly detailed time correlation function theory is derived here that allows for the second and third order contributions to sum frequency vibrational spectra to be individually determined. Further, a practical, molecular dynamics based, implementation procedure for the derived correlation functions that describe the third order phenomenon is also presented. This approach includes a novel generalization of point atomic polarizability models to calculate the hyperpolarizability of a molecular system. The full system hyperpolarizability appears in the time correlation functions responsible for third order contributions in the presence of a static field.

Instantaneous normal mode analysis of orientational motions in liquid water: local structural effects

We have investigated the effects of local structures on the orientational motions in liquid water in terms of the instantaneous normal mode (INM) analysis. The local structures of a molecule in liquid water are characterized by two different kinds of index: the asphericity parameter of its Voronoi polyhedron and the numbers of the H bonds donated and accepted by the molecule. According to the two kinds of index, the molecules in the simulated water are classified into subensembles, for which the rotational contributions to the INM spectrum are calculated. Our results indicate that by increasing the asphericity, the rotational contribution has a shift toward the high-frequency end in the real spectrum and a decrease in the fraction of the imaginary modes. Furthermore, we find that this shift essentially relies on the number of the donated H bonds of a molecule, but has almost nothing to do with that of the accepted H bonds. The local structural effects resulting from the geometry of water molecule are also discussed.

Induction model for molecular electrostatics: Application to the infrared spectroscopy of CO liquid

Far-infrared intermolecular and midinfrared vibrational spectra of CO liquid have been calculated by Fourier transforming the quantum-corrected classical dipole correlation. The time dependence of the coordinates is determined from a standard nonpolarizable force field, and the dipole is determined from the coordinates with a "spectroscopic model" proposed herein. The model includes intramolecular induction and atomic charges, polarizabilities, and permanent dipoles. A good agreement with available experimental spectra is achieved. Our results demonstrate that the use of an anharmonic potential is necessary to reproduce the experimentally observed shift upon going from gas to liquid. The behavior of the simulated dipole time correlation functions suggests that CO liquid at 80 K exhibits aspects of both free rotation and solidlike caging. The proposition of some free rotation present in CO liquid supports Ewing's experimental hypothesis.

Theoretical Investigation of the Temperature Dependence of the Fifth-Order Raman Response Function of Fluid and Liquid Xenon

The temperature dependence of the fifth-order Raman response function, R(5)(t1,t2), is calculated for fluid xenon by employing a recently developed time-correlation function (TCF) theory. The TCF theory expresses the two-dimensional (2D) Raman quantum response function in terms of a two-time, computationally tractable, classical TCF. The theory was shown to be in excellent agreement with existing exact classical MD calculations for liquid xenon as well as reproducing line shape characteristics predicted by earlier theoretical work. It is applied here to investigate the temperature dependence of the fifth-order Raman response function in fluid xenon. In general, the characteristic line shapes are preserved over the temperature range investigated (for the reduced temperature points T* = 0.5, 1.0, and 2.0); differences in the signal decay times and a large decline in intensity with decreasing temperature (and associated anharmonicity) are observed. In addition, there are some signature features that were not observed in earlier results for T* = 1. The most dramatic difference in line shape is observed for the polarization condition, xxzzxx, that shows a vibrational echo peak. In contrast, the fully polarized signal changes mainly in magnitude.

A theoretical description of the polarization dependence of the sum frequency generation spectroscopy of the water/vapor interface

An improved time correlation function (TCF) description of sum frequency generation (SFG) spectroscopy was developed and applied to theoretically describing the spectroscopy of the ambient water/vapor interface. A more general TCF expression than was published previously is presented-it is valid over the entire vibrational spectrum for both the real and imaginary parts of the signal. Computationally, earlier time correlation function approaches were limited to short correlation times that made signal processing challenging. Here, this limitation is overcome, and well-averaged spectra are presented for the three independent polarization conditions that are possible for electronically nonresonant SFG. The theoretical spectra compare quite favorably in shape and relative magnitude to extant experimental results in the O-H stretching region of water for all polarization geometries. The methodological improvements also allow the calculation of intermolecular SFG spectra. While the intermolecular spectrum of bulk water shows relatively little structure, the interfacial spectra (for polarizations that are sensitive to dipole derivatives normal to the interface--SSP and PPP) show a well-defined intermolecular mode at 875 cm(-1) that is comparable in intensity to the rest of the intermolecular structure, and has an intensity that is approximately one-sixth of the magnitude of the intense free O-H stretching peak. Using instantaneous normal mode methods, the resonance is shown to be due to a wagging mode localized on a single water molecule, almost parallel to the interface, with two hydrogens displaced normal to the interface, and the oxygen anchored in the interface. We have also uncovered the origin of another intermolecular mode at 95 cm(-1) for the SSP and PPP spectra, and at 220 cm(-1) for the SPS spectra. These resonances are due to hindered translations perpendicular to the interface for the SSP and PPP spectra, and translations parallel to the interface for the SPS spectra. Further, by examining the real and imaginary parts of the SFG signal, several resonances are shown to be due to a single spectroscopic species while the "donor" O-H region is shown to consist of three distinct species-consistent with an earlier experimental analysis.

IR spectra of N-methylacetamide in water predicted by combined quantum mechanical/molecular mechanical molecular dynamics simulations

We applied the combined quantum mechanical (QM)/molecular mechanical (MM) molecular dynamics (MD) simulation method in assessing IR spectra of N-methylacetamide and its deuterated form in aqueous solutions. The model peptide is treated at the Austin Model 1 (AM1) level and the induced dipole effects by the solvent are incorporated in fluctuating solute dipole moments, which are calculated using partial charges from Mulliken population analyses without resorting to any available high-level ab initio dipole moment data. Fourier transform of the solute dipole autocorrelation function produces in silico IR spectra, in which the relative peak intensities and bandwidths of major amide bands are quantitatively compatible with experimental results only when both geometric and electronic polarizations of the peptide by the solvent are dealt with at the same quantum-mechanical level. We cast light on the importance of addressing dynamic charge fluctuations of the solute in calculating IR spectra by comparing classical and QM/MM MD simulation results. We propose the adjustable scaling factors for each amide mode to be directly compared with experimental data.

Identification of a wagging vibrational mode of water molecules at the water/vapor interface

An improved time correlation function description of sum frequency generation (SFG) spectroscopy was applied to theoretically describe the water/vapor interface. The resulting spectra compare favorably in shape and relative magnitude to extant experimental results in the O-H stretching region of water. Further, the SFG spectra show a well-defined intermolecular mode at 875 cm(-1) that has significant intensity. The resonance is due to a wagging mode localized on a single water molecule. It represents a well-defined population of water molecules at the interface that, along with the free O-H modes, represent the dominant interfacial species.

A time correlation function theory of two-dimensional infrared spectroscopy with applications to liquid water

A theory describing the third-order response function R((3))(t(1),t(2),t(3)), which is associated with two-dimensional infrared (2DIR) spectroscopy, has been developed. R((3)) can be written as sums and differences of four distinct quantum mechanical dipole (multi)time correlation functions (TCF's), each with the same classical limit; the combination of TCF's has a leading contribution of order variant Planck's over 2pi (3) and thus there is no obvious classical limit that can be written in terms of a TCF. In order to calculate the response function in a form amenable to classical mechanical simulation techniques, it is rewritten approximately in terms of a single classical TCF, B(R)(t(1),t(2),t(3))=micro(j)(t(2)+t(1))micro(i)(t(3)+t(2)+t(1))micro(k)(t(1))micro(l)(0), where the subscripts denote the Cartesian dipole directions. The response function is then given, in the frequency domain, as the Fourier transform of a classical TCF multiplied by frequency factors. This classical expression can then further be quantum corrected to approximate the true response function, although for low frequency spectroscopy no correction is needed. In the classical limit, R((3)) becomes the sum of multidimensional time derivatives of B(R)(t(1),t(2),t(3)). To construct the theory, the response function's four TCF's are rewritten in terms of a single TCF: first, two TCF's are eliminated from R((3)) using frequency domain detailed balance relationships, and next, two more are removed by relating the remaining TCF's to each other within a harmonic oscillator approximation; the theory invokes a harmonic approximation only in relating the TCF's and applications of theory involve fully anharmonic, atomistically detailed molecular dynamics (MD). Writing the response function as a single TCF thus yields a form amenable to calculation using classical MD methods along with a suitable spectroscopic model. To demonstrate the theory, the response function is obtained for liquid water with emphasis on the OH stretching portion of the spectrum. This approach to evaluating R((3)) can easily be applied to chemically interesting systems currently being explored experimentally by 2DIR and to help understand the information content of the emerging multidimensional spectroscopy.

Vibrational spectra from atomic fluctuations in dynamics simulations. I. Theory, limitations, and a sample application

Hybrid molecular dynamics (MD) simulations, which combine density functional theory (DFT) descriptions of a molecule with a molecular mechanics (MM) modeling of its solvent environment, have opened the way towards accurate computations of solvation effects in the vibrational spectra of molecules. Recently, Wheeler et al. [ChemPhysChem 4, 382 (2002)] have suggested to compute these spectra from DFT/MM-MD trajectories by diagonalizing the covariance matrix of atomic fluctuations. This so-called principal mode analysis (PMA) allegedly can replace the well-established approaches, which are based on Fourier transform methods or on conventional normal mode analyses. By scrutinizing and revising the PMA approach we identify five conditions, which must be guaranteed if PMA is supposed to render exact vibrational frequencies. Besides specific choices of (a) coordinates and (b) coordinate systems, these conditions cover (c) a harmonic intramolecular potential, (d) a complete thermal equilibrium within the molecule, and (e) a molecular Hamiltonian independent of time. However, the PMA conditions [(c)-(d)] and [(c)-(e)] are generally violated in gas phase DFT-MD and liquid phase DFT/MM-MD trajectories, respectively. Based on a series of simple analytical model calculations and on the analysis of MD trajectories calculated for the formaldehyde molecule in the gas phase (DFT) and in liquid water (DFT/MM) we show that in both phases the violation of condition (d) can cause huge errors in PMA frequency computations, whereas the inevitable violations of conditions (c) and (e), the latter being generic to the liquid phase, imply systematic and sizable underestimates of the vibrational frequencies by PMA. We demonstrate that the huge errors, which are caused by an incomplete thermal equilibrium violating (d), can be avoided if one introduces mode-specific temperatures T(j) and calculates the frequencies from a "generalized virial" (GV) expression instead from PMA. Concerning ways to additionally remove the remaining errors, which GV still shares with PMA, we refer to Paper II of this work [M. Schmitz and P. Tavan, J. Chem. Phys. 121, 12247 (2004)].

A molecular dynamics method for calculating molecular volume changes appropriate for biomolecular simulation

Photothermal methods permit measurement of molecular volume changes of solvated molecules over nanosecond timescales. Such experiments are an important tool in investigating complex biophysical phenomena including identifying transient species in solution. Developing a microscopic understanding of the origin of volume changes in the condensed phase is needed to complement the experimental measurements. A molecular dynamics (MD) method exploiting available simulation methodology is demonstrated here that both mimics experimental measurements and provides microscopic resolution to the thermodynamic measurements. To calculate thermodynamic volume changes over time, isothermal-isobaric (NPT) MD is performed on a solution for a chosen length of time and the volume of the system is thus established. A further simulation is then performed by "plucking" out a solute molecule of interest to determine the volume of the system in its absence. The difference between these volumes is the thermodynamic volume of the solute molecule. NPT MD allows the volume of the system to fluctuate over time and this results in a statistical uncertainty in volumes that are calculated. It is found in the systems investigated here that simulations lasting a few nanoseconds can discern volume changes of approximately 1.0 ml/mole. This precision is comparable to that achieved empirically, making the experimental and theoretical techniques synergistic. The technique is demonstrated here on model systems including neat water, both charged and neutral aqueous methane, and an aqueous beta-sheet peptide.

Attenuated total reflection surface-enhanced infrared absorption spectroscopy of carboxyl terminated self-assembled monolayers on gold

A new recipe for surface-enhanced infrared absorption (SEIRA) active island Au films with improved adhesion in aqueous solution, low resistivity, and enhancement of the infrared (IR) absorption of about 300 was developed. The Au films prepared were utilized in studies of the ionization of self-assembled monolayers of 11-mercaptoundecanoic acid in Na2SO4 aqueous solutions by attenuated total reflection surface-enhanced infrared absorption (ATR-SEIRA) spectroscopy. It was found that the carboxyl end groups of the self-assembled monolayer turn into carboxylate anions on going from anodic to cathodic potentials or from acidic to alkaline pH. The water molecules close to the self-assembled monolayer in acidic solutions or at anodic potentials are preferentially aligned with their dipole moments parallel to the interface. This type of alignment can be ascribed to the dipole-dipole interaction between the carboxyl groups and the water molecules. On the other hand, in alkaline solutions or at cathodic potentials the structure of water close to the self-assembled monolayer is essentially bulk-like, with randomly oriented water molecules. This observation suggests that in alkaline solutions or at cathodic potentials the charge of the carboxylate anions is almost completely compensated for by strongly adsorbed counter cations. As a result, the electric field close to the surface of the ionized self-assembled monolayer is weak and has little influence on the orientation and hydrogen bonding of the water molecules.