Molecular dynamics simulation of liquid methanol. I. Molecular modeling including C–H vibration and fermi resonance

Molecular dynamics simulations reliably identify vibrational modes in far-IR spectra of phospholipids

The properties of self-assembled phospholipid membranes are of essential importance in biochemistry and physical chemistry, providing a platform for many cellular life functions. Far-infrared (far-IR) vibrational spectroscopy, on the other hand, is a highly information-rich method to characterize intermolecular interactions and collective behaviour of lipids that can help explain, e.g., chain packing, thermodynamic phase behaviour, and sequestration. However, reliable interpretation of the far-IR spectra is still lacking. Here we present a molecular dynamics (MD) based approach to simulate vibrational modes of individual lipids and in an ensemble. The results are a good match to synchrotron far-IR measurements and enable identification of the molecular motions corresponding to each vibrational mode, thus allowing the correct interpretation of membrane spectra with high accuracy and resolving the longstanding ambiguities in the literature in this regard. Our results demonstrate the feasibility of using MD simulations for interpreting far-IR spectra broadly, opening new avenues for practical use of this powerful method.

Molecular dynamics simulations of the dielectric constants of salt-free and salt-doped polar solvents

We develop a Stockmayer fluid model that accounts for the dielectric responses of polar solvents (water, MeOH, EtOH, acetone, 1-propanol, DMSO, and DMF) and NaCl solutions. These solvent molecules are represented by Lennard-Jones (LJ) spheres with permanent dipole moments and the ions by charged LJ spheres. The simulated dielectric constants of these liquids are comparable to experimental values, including the substantial decrease in the dielectric constant of water upon the addition of NaCl. Moreover, the simulations predict an increase in the dielectric constant when considering the influence of ion translations in addition to the orientation of permanent dipoles.

An in silico osmotic pressure approach allows characterization of pressure-area isotherms of lipid monolayers at low molecular areas

Surface pressure-area isotherms of lipid monolayers at the air-water interface provide essential information about the structure and mechanical behaviour of lipid membranes. These curves can be readily obtained through Langmuir trough measurements and, as such, have been collected for decades in the field of membrane biochemistry. However, it is still challenging to directly observe and understand nanoscopic features of monolayers through such experiments, and molecular dynamics (MD) simulations are generally used to provide a molecular view of such interfaces. In MD simulations, the surface pressure-area (Π-A) isotherms are generally computed using the Kirkwood-Irving formula, that relies on the evaluation of the pressure tensor. This approach, however, has intrinsic limitations when the molecular area in the monolayer is low (typically < 60 Ų per lipid). Recently, an alternative method to compute Π-A isotherms of surfactants, based on the calculation of the three-dimensional osmotic pressure via the implementation of semipermeable barriers was proposed. In this work, we investigate the feasibility of this approach for long-chain surfactants such as phospholipids. We identify some discrepancies between the computed values and experimental results, and we propose a semi-empirical correction based on the molecular structure of the surfactants at the monolayer interface. To validate the potential of this new approach, we simulate several phosphatidylcholine and phosphatidylethanolamine lipids at various temperatures using all-atom and coarse-grained force fields, and we compute the corresponding Π-A isotherms. Our results show that the Π-A isotherms obtained using the new method are in very good agreement with experiments and far superior to the canonical pressure tensor-based method at low molecular areas. This corrected osmotic pressure method allows for accurate characterization of the molecular packing in monolayers in various physical phases.

Sum-frequency vibrational spectroscopy of methanol at interfaces due to Fermi resonance

We present a theoretical method of studying sum-frequency vibrational spectroscopy for the CH3 group of methanol at interfaces due to Fermi resonance, which provides a novel and untraditional point of view with respect to traditional approaches.

How many methanol molecules effectively solvate an excess proton in the gas phase? Infrared spectroscopy of H+(methanol)n-benzene clusters

An excess proton in a hydrogen-bonded system enhances the strength of hydrogen bonds of the surrounding molecules. The extent of this influence can be a measure of the number of molecules effectively solvating the excess proton. Such extent in methanol has been discussed by the observation of the π-hydrogen-bonded OH stretch bands of the terminal sites of protonated methanol clusters, H⁺(methanol)_n, in benzene solutions, and it has been concluded that ∼8 molecules effectively solvate the excess proton (Stoyanov et al., Chem. Eur. J. 2008, 14, 3596-3604). In the present study, we performed infrared spectroscopy of H⁺(methanol)_n-benzene clusters in the gas phase. The cluster size and hydrogen-bonded network structure are identified by the tandem mass spectrometric technique and the comparison of the observed infrared spectra with density functional theory calculations. Though changes of the preferred hydrogen bond network type occur with the increase of cluster size in the gas phase clusters, the observed size dependence of the π-hydrogen bonded OH frequency agrees well with that in the benzene solutions. This means that the observations in both the gas and condensed phases catch the same physical essence of the excess proton solvation by methanol.

Electric Field and Temperature Effects on the Ab Initio Spectroscopy of Liquid Methanol

Although many H-bonded systems have been extensively investigated by means of infrared (IR) spectroscopy, the vibrational response to externally applied electric fields of polar liquids remains poorly investigated. However, local electric fields along with quantum-mechanical interactions rule the behavior of H-bonded samples at the molecular level. Among the many H-bonded systems, liquid methanol holds a key place in that it exhibits a very simple H-bond network where, on average, each molecule acts as a single H-bond donor and, at the same time, as a single H-bond acceptor. Here we report on the IR spectra emerging from a series of state-of-the-art ab initio molecular dynamics simulations of bulk liquid methanol under the action of static and homogeneous electric fields. In addition, the same analysis is here conducted in the absence of the external field and for different temperatures. Although some electric-field-induced effects resemble the response of other polar liquids (such as the global contraction of the IR spectrum upon field exposure), it turns out that, distinctly from water, the “electrofreezing” phenomenon is unlikely to happen in liquid methanol. Finally, we provide atomistic analyses magnifying the completely different nature of electric-field- and temperature-induced effects on bulk liquid methanol and on its vibrational response.

Development of quadrupole susceptibility automatic calculator in sum frequency generation spectroscopy and application to methyl C-H vibrations

Sum frequency generation (SFG) spectroscopy has been established as a powerful interface probe technique based on the electric dipole approximation, while possible signals of quadrupole and bulk origin have also been known for a long time. In this work, we developed a computational tool, namely, Qsac (quadrupole susceptibility automatic calculator), to evaluate the comprehensive contributions of the dipole/quadrupole and interface/bulk in the arbitrary vibrational bands of SFG spectra. The calculations of relevant susceptibility terms are performed on the basis of the theory of energy representation using quantum chemical calculation and molecular dynamics simulation, which allows for semi-quantitative comparison among these terms on the same footing. We applied the Qsac to the methyl C-H stretching bands of organic molecules and found a general trend that the weak asymmetric bands are more sensitive to the bulk contribution than the symmetric ones. The phases of interface and bulk terms tend to cancel in the asymmetric band, which results in the reduced band intensity in the SFG spectra.

Effects of mixing between short-chain and branched-chain alcohols in protonated clusters

The previous analysis of the neat protonated branched-chain alcohol clusters revealed the impact of steric repulsion and dispersion of the bulky alkyl group on the hydrogen-bonded (H-bonded) structures and their temperature-dependence. To further understand the influence of the alkyl groups in H-bonded clusters, we studied the mixing of the two extremes of alcohols, methanol (MeOH) and tert-butyl alcohol (t-BuOH), with an excess proton. Infrared spectroscopy and a structural search of first principles calculations on the size-selected clusters H⁺(MeOH)_m(t-BuOH)_t (m + t = 4 and 5) were conducted. Temperature-dependence of the dominant H-bonded structures was explored by the Ar-tagging technique and quantum harmonic superposition approach. By introducing the dispersion-corrected density functional theory methods, it was shown that the effects of dispersion due to the bulky alkyl groups in the mixed clusters cannot be ignored for t≥ 2. The computational results qualitatively depicted the characteristics of the observed IR spectra, but overestimation of the temperature-dependence with dispersion correction was clearly seen due to the unbalanced correction between linear H-bonded structures and compact cyclic ones. These results demonstrate the importance of extensive investigation and benchmarks on different levels of theory, and that a properly sampled structure database is crucial to evaluate theoretical models.

Facet-specific interaction between methanol and TiO2 probed by sum-frequency vibrational spectroscopy

The facet-specific interaction between molecules and crystalline catalysts, such as titanium dioxides (TiO2), has attracted much attention due to possible facet-dependent reactivity. Using surface-sensitive sum-frequency vibrational spectroscopy, we have studied how methanol interacts with different common facets of crystalline TiO2, including rutile(110), (001), (100), and anatase(101), under ambient temperature and pressure. We found that methanol adsorbs predominantly in the molecular form on all of the four surfaces, while spontaneous dissociation into methoxy occurs preferentially when these surfaces become defective. Extraction of Fermi resonance coupling between stretch and bending modes of the methyl group in analyzing adsorbed methanol spectra allows determination of the methanol adsorption isotherm. The isotherms obtained for the four surfaces are nearly the same, yielding two adsorbed Gibbs free energies associated with two different adsorption configurations singled out by ab initio calculations. They are (i) ∼-20 kJ/mol for methanol with its oxygen attached to a low-coordinated surface titanium, and (ii) ∼-5 kJ/mol for methanol hydrogen-bonded to a surface oxygen and a neighboring methanol molecule. Despite similar adsorption energetics, the Fermi resonance coupling strength for adsorbed methanol appears to depend sensitively on the surface facet and coverage.

Sum-frequency vibrational spectroscopy of limonene chiral liquids due to the nonadiabatic effect

Using quantum computations we study sum-frequency vibrational spectroscopy of limonene chiral liquids due to the nonadiabatic effect in the non-resonant case for the first time. The nonadiabatic effect has an important impact on non-resonant antisymmetric polarizability and chiral sum-frequency vibrational spectroscopy. The theoretical spectroscopy agrees with the experimental spectroscopy. However, the nonadiabatic effect only has a small influence on non-resonant Raman. Bulk sum-frequency vibrational spectroscopy may become a powerful method of investigating the nonadiabatic effect and the nonradiative transition between excited electronic states for chiral molecules.

Chain length effects on the vibrational structure and molecular interactions in the liquid normal alkyl alcohols

Alkyl alcohols are widely used in academia, industry, and our everyday lives, e.g. as cleaning agents and solvents. Vibrational spectroscopy is commonly used to identify and quantify these compounds, but also to study their structure and behavior. However, a comprehensive investigation and comparison of all normal alkanols that are liquid at room temperature has not been performed, surprisingly. This study aims at bridging this gap with a combined experimental and computational effort. For this purpose, the alkyl alcohols from methanol to undecan-1-ol have been analyzed using infrared and Raman spectroscopy. A detailed assignment of the individual peaks is presented and the influence of the alkyl chain length on the hydrogen bonding network is discussed. A 2D vibrational mapping allows a straightforward visualization of the effects. The conclusions drawn from the experimental data are backed up with results from Monte Carlo simulations using the simulation package Cassandra.

Hydrogen bond network structures of protonated short-chain alcohol clusters

Protonated alcohol clusters enable extraction of the physical essence of the nature of hydrogen bond networks.

Theoretical Investigation of C-H Vibrational Spectroscopy. 2. Unified Assignment Method of IR, Raman, and Sum Frequency Generation Spectra of Ethanol

Using the flexible and polarizable model in the preceding paper, we performed comprehensive analysis of C-H stretching vibrations of ethanol and partially deuterated ones by molecular dynamics (MD) simulation. The overlapping band structures of the C-H stretching region including (i) methyl and methylene, (ii) the number of modes with Fermi resonances, and (iii) different trans/gauche conformers are disentangled by various analysis methods, such as isotope exchange, empirical potential parameter shift analysis, and separate calculations of conformers. The present analysis with MD simulation revealed unified assignment of infrared, Raman, and sum frequency generation (SFG) spectra. The analysis confirmed that the different conformers have significant influence on the assignment of CH₂ vibrations. Band components and their signs in the imaginary χ⁽²⁾ spectra of SFG under various polarizations are also understood from the common assignment with the infrared and Raman spectra.

Simultaneous Acquisition of the Polarized and Depolarized Raman Signal with a Single Detector

Polarization-resolved Raman spectroscopy provides much more information than its conventional counterpart. However, it usually either requires a complicated setup with two spectrographs and detectors or two measurements must be performed sequentially. This study presents a simple and straightforward approach to recording both polarization components simultaneously with a single spectrograph and detector. The vertically and a horizontally polarized laser beam exiting a Wollaston prism are focused into the sample with a small spatial separation. The scattered light from both beams is imaged onto the slit of an imaging spectrograph as two spatially separated signals, i.e., the polarized and the depolarized Raman signal. Eventually, both spectra are acquired on a single CCD chip simultaneously. Experimental data of ethanol and dimethyl sulfoxide are shown as proof-of-concept. The new method has a number of advantages, for example, laser intensity fluctuations and the polarization dependence of the diffraction grating do not play a role. The proposed approach will be useful for an improved structural analysis and it will be the enabling technology for temporally resolved enantioselective Raman (esR) spectroscopy.

Liquid/liquid interface layering of 1-butanol and [bmim]PF6 ionic liquid: a nonlinear vibrational spectroscopy and molecular dynamics simulation study

IV-SFG vibrational spectroscopy and MD simulation studies reveal a local polar/nonpolar layering structure at the interface of 1-butanol-d₉ and 1-butyl-3-methylimidazolium hexafluorophosphate ([bmim]PF₆).

Critical analysis of the accuracy of models predicting or extracting liquid structure information

This work aims at a critical assessment of properties predicting or extracting information on the density and structure of liquids. State-of-the-art NVT and NpT molecular dynamics (MD) simulations have been performed on five liquids: methanol, chloroform, acetonitrile, tetrahydrofuran, and ethanol. These simulations allow the computation of properties based on first principles, including the equilibrium density and radial distribution functions (RDFs), characterizing the liquid structure. Refinements have been incorporated in the MD simulations by taking into account basis set superposition errors (BSSE). An extended BSSE model for an instantaneous evaluation of the BSSE corrections has been proposed, and their impact on the liquid properties has been assessed. If available, the theoretical RDFs have been compared with the experimentally derived RDFs. For some liquids, significant discrepancies have been observed, and a profound but critical investigation is presented to unravel the origin of these deficiencies. This discussion is focused on tetrahydrofuran where the experiment reveals some prominent peaks completely missing in any MD simulation. Experiments providing information on liquid structure consist mainly of neutron diffraction measurements offering total structure factors as the primary observables. The splitting of these factors in reciprocal space into intra- and intermolecular contributions is extensively discussed, together with their sensitivity in reproducing correct RDFs in coordinate space.

Ultrafast dynamics of liquid water: frequency fluctuations of the OH stretch and the HOH bend

Frequency fluctuations of the OH stretch and the HOH bend in liquid water are reported from the third-order response function evaluated using the TTM3-F potential for water. The simulated two-dimensional infrared spectra of the OH stretch are similar to previously reported theoretical results. The present study suggests that the frequency fluctuation of the HOH bend is faster than that of the OH stretch. The ultrafast loss of the frequency correlation of the HOH bend is due to the strong couplings with the OH stretch as well as the intermolecular hydrogen bond bend.

Analysis of the basis set superposition error in molecular dynamics of hydrogen-bonded liquids: application to methanol

An efficient protocol is presented to compensate for the basis set superposition error (BSSE) in DFT molecular dynamics (MD) simulations using localized Gaussian basis sets. We propose a classical correction term that can be added a posteriori to account for BSSE. It is tested to what extension this term will improve radial distribution functions (RDFs). The proposed term is pairwise between certain atoms in different molecules and was calibrated by fitting reference BSSE data points computed with the counterpoise method. It is verified that the proposed exponential decaying functional form of the model is valid. This work focuses on hydrogen-bonded liquids, i.e., methanol, and more specific on the intermolecular hydrogen bond, but in principle the method is generally applicable on any type of interaction where BSSE is significant. We evaluated the relative importance of the Grimme-dispersion versus BSSE and found that they are of the same order of magnitude, but with an opposite sign. Upon introduction of the correction, the relevant RDFs, obtained from MD, have amplitudes equal to experiment.