Molecular Dynamics Study of Hydrogen Bond Structure and Tensile Strength for Hydrated Amorphous Cellulose.

Molecular dynamics (MD) simulations were conducted to investigate the hydrogen-bond (H-bond) structure and its impact on the tensile strength of hydrated amorphous cellulose. The study identifies a stable intramolecular H-bond between the hydroxyl group at position 3 and the ether oxygen at position 5 (OH3···O5). Intermolecularly, the hydroxyl groups at positions 2 (OH2) and 6 (OH6) form stable H-bonds. Young's modulus, maximum tensile strength, and corresponding strain were calculated as functions of moisture content, while the H-bond network, water cluster formation, and cellulose chain orientation during tensile simulations were analyzed to elucidate mechanical properties. The substitution effect of cellulose on Young's modulus is also examined, revealing that the substitution of OH3 for a hydrophobic group minimally affects Young's modulus, but substitutions at OH2 and OH6 significantly reduce tensile strength due to their roles as key intermolecular H-bond donor sites.

Molecular dynamics study of N,N'-di-n-alkyl-3,4,9,10-perylenetetracarboxylic diimide (PTCDI)/rubrene interface: Why the charge transfer at the interface is optimized depending on the alkyl chain length of PTCDI.

Molecular dynamics simulations were performed to investigate the interfacial structure of the N,N'-di-n-alkyl-3,4,9,10-perylenetetracarboxylic diimide (PTCDI)/rubrene interface, which represents the donor/acceptor interface in new types of organic light-emission diodes. In particular, the interfacial structure was examined for different alkyl chain lengths of PTCDI (Cn-PTCDI) at n = 4, 8, and 13, in order to elucidate the observed maximum charge transfer efficiency at the C8-PTCDI/rubrene interface in a recent experiment. The results revealed that the molecular conformation of the acceptor (Cn-PTCDI) molecules at the interface undergoes changes depending on the alkyl chain length when interacting with the rubrene molecule. It was found that the closest complex between Cn-PTCDI and rubrene is formed at n = 8, consistent with the experimental observation. In addition, the interfacial structures of Cn-PTCDI/air and rubrene/air were examined and compared to gain insights into the inherent stability associated with the intermolecular interactions at the interface.

Formation of Long-Lived Dark States during Electronic Relaxation of Pyrimidine Nucleobases Studied Using Extreme Ultraviolet Time-Resolved Photoelectron Spectroscopy.

Ultrafast electronic relaxation of nucleobases from 1ππ* states to the ground state (S0) is considered essential for the photostability of DNA. However, transient absorption spectroscopy (TAS) has indicated that some nucleobases in aqueous solutions create long-lived 1nπ*/3ππ* dark states from the 1ππ* states with a high quantum yield of 0.4-0.5. We investigated electronic relaxation in pyrimidine nucleobases in both aqueous solutions and the gas phase using extreme ultraviolet (EUV) time-resolved photoelectron spectroscopy. Femtosecond EUV probe pulses cause ionization from all electronic states involved in the relaxation process, providing a clear overview of the electronic dynamics. The 1nπ* quantum yields for aqueous cytidine and uracil (Ura) derivatives were found to be considerably lower (<0.07) than previous estimates reported by TAS. On the other hand, aqueous thymine (Thy) and thymidine exhibited a longer 1ππ* lifetime and a higher quantum yield (0.12-0.22) for the 1nπ* state. A similar trend was found for isolated Thy and Ura in the gas phase: the 1ππ* lifetimes are 39 and 17 fs and the quantum yield for 1nπ* are 1.0 and 0.45 for Thy and Ura, respectively. The result indicates that single methylation to the C5 position hinders the out-of-plane deformation that drives the system to the conical intersection region between 1ππ* and S0, providing a large impact on the photophysics/photochemistry of a pyrimidine nucleobase. The significant reduction of 1nπ* yield in aqueous solution is ascribed to the destabilization of the 1nπ* state induced by hydrogen bonding.

Why the Photochemical Reaction of Phenol Becomes Ultrafast at the Air-Water Interface: The Effect of Surface Hydration.

Photochemical reactions at the air-water interface can show remarkably different rates from those in bulk water. The present study elucidates the reaction mechanism of phenol characteristic at the air-water interface by the combination of molecular dynamics simulation and quantum chemical calculations of the excited states. We found that incomplete hydrogen bonding to phenol at the air-water interface affects excited states associated with the conical intersection and significantly reduces the reaction barrier, resulting in the distinctively facilitated rate in comparison with the bulk phase. The present study indicates that the reaction dynamics can be substantially different at the interfaces in general, reflecting the difference in the stabilization energy of the electronic states in markedly different solvation at the interface.

Reply to the 'Comment on "Bi-layering at ionic liquid surfaces: a sum-frequency generation vibrational spectroscopy- and molecular dynamics simulation-based study"' by M. Deutsch, O. M. Magnussen, J. Haddad, D. Pontoni, B. M. Murphy and B. M. Ocko, Phys. Chem. Chem. Phys., 2021, DOI.

In our recent paper titled "Bi-layering at ionic liquid surfaces: a sum-frequency generation vibrational spectroscopy- and molecular dynamics simulation-based study" co-authored by T. Iwahashi, T. Ishiyama, Y. Sakai, A. Morita, D. Kim, and Y. Ouchi, Phys. Chem. Chem. Phys., 2020, 22, 12565 (hereafter referred to as IW), the sum-frequency (SF) spectra for a homologous series of 1-alkyl-3-methylimidazolium bis(trifluoromethanesulfonyl)amide ([Cnmim][TFSA] n = 4, 6, 8, 10, and 12) were reported. In particular, a clear decrease in the SF signals from the [TFSA]- anions with increasing chain length of the [Cnmim]+ cation (Fig. 5 of IW) was explained in terms of "head-to-head" bi-layer formation at the air/ionic liquid (IL) interface. A comment by M. Deutsch et al. (hereafter referred to as DE) questioned this report, claiming that our proposed structure is not consistent with a multilayered electron density (ED) profile obtained by X-ray reflectivity (XR).

Energy relaxation path of excited free OH vibration at an air/water interface revealed by nonequilibrium ab initio molecular dynamics simulation.

Nonequilibrium ab initio molecular dynamics (NE-AIMD) simulations are conducted at an air/water interface to elucidate the vibrational energy relaxation path of excited non-hydrogen-bonded (free) OH. A recent time-resolved vibrational sum frequency generation (TR-VSFG) spectroscopy experiment revealed that the relaxation time scales of free OH at the surface of pure water and isotopically diluted water are very similar to each other. In the present study, the dynamics of free OH excited at the surface of pure water and deuterated water are examined with an NE-AIMD simulation, which reproduces the experimentally observed features. The relaxation paths are examined by introducing constraints for the bonds and angles of water molecules relevant to specific vibrational modes in NE-AIMD simulations. In the case of free OH relaxation at the pure water surface, stretching vibrational coupling with the conjugate bond makes a significant contribution to the relaxation path. In the case of the isotopically diluted water surface, the bend (HOD)-stretching (OD) combination band couples with the free OH vibration, generating a relaxation rate similar to that in the pure water case. It is also found that the reorientation of the free OH bond contributes substantially to the relaxation of the free OH vibrational frequency component measured by TR-VSFG spectroscopy.

Ab initio molecular dynamics study on energy relaxation path of hydrogen-bonded OH vibration in bulk water.

The vibrational energy relaxation paths of hydrogen-bonded (H-bonded) OH excited in pure water and in isotopically diluted (deuterated) water are elucidated via non-equilibrium ab initio molecular dynamics (NE-AIMD) simulations. The present study extends the previous NE-AIMD simulation for the energy relaxation of an excited free OH vibration at an air/water interface [T. Ishiyama, J. Chem. Phys. 154, 104708 (2021)] to the energy relaxation of an excited H-bonded OH vibration in bulk water. The present simulation shows that the excited OH vibration in pure water dissipates its energy on a timescale of 0.1 ps, whereas that in deuterated water relaxes on a timescale of 0.7 ps, consistent with the experimental observations. To decompose these relaxation energies into the components due to intramolecular and intermolecular couplings, constraints are introduced on the vibrational modes except for the target path in the NE-AIMD simulation. In the case of pure water, 80% of the total relaxation is attributed to the pathway due to the resonant intermolecular OH⋯OH stretch coupling, and the remaining 17% and 3% are attributed to intramolecular couplings with the bend overtone and with the conjugate OH stretch, respectively. This result strongly supports a significant role for the Förster transfer mechanism of pure water due to the intermolecular dipole-dipole interactions. In the case of deuterated water, on the other hand, 36% of the total relaxation is due to the intermolecular stretch coupling, and all the remaining 64% arises from coupling with the intramolecular bend overtone.

Energy relaxation dynamics of hydrogen-bonded OH vibration conjugated with free OH bond at an air/water interface.

Vibrational energy relaxation dynamics of the excited hydrogen-bonded (H-bonded) OH conjugated with free OH (OD) at an air/water (for both pure water and isotopically diluted water) interface are elucidated via non-equilibrium ab initio molecular dynamics (NE-AIMD) simulations. The calculated results are compared with those of the excited H-bonded OH in bulk liquid water reported previously. In the case of pure water, the relaxation timescale (vibrational lifetime) of the excited H-bonded OH at the interface is T1 = 0.13 ps, which is slightly larger than that in the bulk (T1 = 0.11 ps). Conversely, in the case of isotopically diluted water, the relaxation timescale of T1 = 0.74 ps in the bulk decreases to T1 = 0.26 ps at the interface, suggesting that the relaxation dynamics of the H-bonded OH are strongly dependent on the surrounding H-bond environments particularly for the isotopically diluted conditions. The relaxation paths and their rates are estimated by introducing certain constraints on the vibrational modes except for the target path in the NE-AIMD simulation to decompose the total energy relaxation rate into contributions to possible relaxation pathways. It is found that the main relaxation pathway in the case of pure water is due to intermolecular OH⋯OH vibrational coupling, which is similar to the relaxation in the bulk. In the case of isotopically diluted water, the main pathway is due to intramolecular stretch and bend couplings, which show more efficient relaxation than in the bulk because of strong H-bonding interactions specific to the air/water interface.

Bi-layering at ionic liquid surfaces: a sum-frequency generation vibrational spectroscopy- and molecular dynamics simulation-based study.

Room-temperature ionic liquids (RTILs) are being increasingly employed as novel solvents in several fields, including chemical engineering, electrochemistry, and synthetic chemistry. To further increase their usage potential, a better understanding of the structure of their surface layer is essential. Bi-layering at the surfaces of RTILs consisting of 1-alkyl-3-methylimidazolium ([Cnmim]+; n = 4, 6, 8, 10, and 12) cations and bis(trifluoromethanesulfonyl)amide ([TFSA]-) anions was demonstrated via infrared-visible sum-frequency generation (IV-SFG) vibrational spectroscopy and molecular dynamics (MD) simulations. It was found that the sum-frequency (SF) signal from the [TFSA]- anions decreases as the alkyl chain length increases, whereas the SF signal from the r+ mode (the terminal CH3 group) of the [Cnmim]+ cations is almost the same regardless of chain length. MD simulations show the formation of a bi-layered structure consisting of the outermost first layer and a submerged second layer in a "head-to-head" molecular arrangement. The decrease in the SF signals of the normal modes of the [TFSA]- anions is caused by destructive and out-of-phase interference of vibrations of corresponding molecular moieties oriented toward each other in the first and second layers. In contrast, the r+ mode of [Cnmim]+ does not experience destructive interference because the peak position of the r+ mode differs marginally at the surface and in the bulk. Our conclusions are not limited to the system presented here. Similar bi-layered structures can be expected for the surfaces of conventional RTILs, which necessitates the consideration of bi-layering in the design and application.

Existence of weakly interacting OH bond at air/water interface.

Ab initio molecular dynamics simulations at the air/water interface are carried out and elucidate a clear bump-like shoulder band at ∼3600 cm-1 in the imaginary part of the second order nonlinear susceptibility measured by phase-sensitive or heterodyne-detected vibrational sum frequency generation spectroscopy. The structure of the weakly interacting (WI) OH bond producing this band is found by first-principles simulation. WI OH is the OH bond directing toward the vapor phase and is somewhat buried in the Gibbs dividing surface of water, which is a characteristic structure at the air/water interface. The WI OH vibration tends to couple with the combination band between a neighboring hydrogen-bonded OH vibration and its bonding intermolecular oxygen-oxygen vibration.

Experimental and theoretical evidence for bilayer-by-bilayer surface melting of crystalline ice.

On the surface of water ice, a quasi-liquid layer (QLL) has been extensively reported at temperatures below its bulk melting point at 273 K. Approaching the bulk melting temperature from below, the thickness of the QLL is known to increase. To elucidate the precise temperature variation of the QLL, and its nature, we investigate the surface melting of hexagonal ice by combining noncontact, surface-specific vibrational sum frequency generation (SFG) spectroscopy and spectra calculated from molecular dynamics simulations. Using SFG, we probe the outermost water layers of distinct single crystalline ice faces at different temperatures. For the basal face, a stepwise, sudden weakening of the hydrogen-bonded structure of the outermost water layers occurs at 257 K. The spectral calculations from the molecular dynamics simulations reproduce the experimental findings; this allows us to interpret our experimental findings in terms of a stepwise change from one to two molten bilayers at the transition temperature.

Molecular structure and vibrational spectra at water/poly(2-methoxyethylacrylate) and water/poly(methyl methacrylate) interfaces: A molecular dynamics simulation study.

Classical molecular dynamics simulations at the interfaces of two (meth)acrylate polymers, poly(2-methoxyethylacrylate) (PMEA) and poly(methyl methacrylate) (PMMA), upon contact with water are performed to elucidate interfacial molecular structures from the interface-specific nonlinear spectroscopic point of view. PMEA has methoxy oxygen in the side chain, while PMMA does not have it, and its impacts on the interfacial structure are particularly focused on. The force fields of PMEA and PMMA used in the classical simulation are modeled so as to reproduce the radial distribution functions and the vibrational density of states calculated by ab initio molecular dynamics simulations, where a stronger hydrogen-bonding interaction between water and methoxy oxygen of PMEA than the conventional molecular modeling predicts is found. The imaginary part of the second order nonlinear susceptibility is theoretically calculated for these two interfaces, showing a definite difference between them. The origin of the spectral difference is discussed on the basis of the decomposition analysis of the spectra and the interfacial molecular structures.

Computational Analysis of Vibrational Sum Frequency Generation Spectroscopy.

Vibrational sum frequency generation (VSFG) spectroscopy is a widely used probe of interfaces and, having ideal surface sensitivity and selectivity, is particularly powerful when applied to wet and soft interfaces. Although VSFG spectroscopy can sensitively detect molecular details of interfaces, interpretation of observed spectra has, until recently, been challenging and often ambiguous. The situation has been greatly improved by remarkable advances in computational VSFG analysis on the basis of molecular modeling and molecular dynamics simulation. This article reviews the basic idea of computational VSFG analysis and recent applications to both aqueous and organic interfaces.

Structure at the air/water interface in the presence of phenol: a study using heterodyne-detected vibrational sum frequency generation and molecular dynamics simulation.

Many kinds of organic compounds pollute the aquatic environment, and they change the properties of the water surface due to their high surface affinity. Chemical reactions at the water surface are key in environmental chemistry because, for instance, reactions occurring at the surface of aqueous aerosols play essential roles in the atmosphere. Therefore, it is very important to elucidate how organic compounds affect the properties of water surfaces. Here, we choose phenol as an organic pollutant prototype and report how phenol affects the molecular-level structure of the air/water interface. Interface-selective vibrational spectra, i.e., the imaginary part of second-order nonlinear susceptibility (Im χ(2)), of the air/water-phenol mixture interface in the OH stretch region were collected using heterodyne-detected vibrational sum frequency generation (HD-VSFG) spectroscopy, and the observed Im χ(2) spectra were interpreted with the aid of molecular dynamics (MD) simulation. The Im χ(2) spectra observed via HD-VSFG drastically change as a function of phenol concentration in water, and exhibit two isosbestic points. In the spectra, a positive OH band appears at 3620 cm-1, which is assigned to an OH group of water that forms an OHπ hydrogen-bond (H-bond) with the aromatic ring of phenol, and a strong negative OH band appears around 3200 cm-1, which is attributed to a water that accepts a H-bond from the phenol OH, while pointing its OH groups toward the bulk water side. It was concluded that two types of unique water molecules hydrate a phenol molecule: (1) water that forms an OHπ H-bond; and (2) water that accepts a H-bond from a phenol OH group. Each phenol molecule adsorbed at the air/water forms a specific hydration structure, which causes a large change in the interfacial water structure. The present study provides a clear example demonstrating that even such a simple organic pollutant as phenol can drastically alter the interfacial water structure.

Molecular dynamics study of structure and vibrational spectra at zwitterionoic lipid/aqueous KCl, NaCl, and CaCl2 solution interfaces.

Molecular dynamics (MD) simulations of KCl, NaCl, and CaCl2 solution/dipalmytoylphosphatidylcholine lipid interfaces were performed to analyze heterodyne-detected vibrational sum frequency generation (HD-VSFG) spectra in relation to the interfacial water structure. The present MD simulation well reproduces the experimental spectra and elucidates a specific cation effect on the interfacial structure. The K+, Na+, and Ca2+ cation species penetrate in the lipid layer more than the anions in this order, due to the electrostatic interaction with negative polar groups of lipid, and the electric double layer between the cations and anions cancels the intrinsic orientation of water at the water/lipid interface. These mechanisms explain the HD-VSFG spectrum of the water/lipid interface and its spectral perturbation by adding the ions. The lipid monolayer reverses the order of surface preference of the cations at the solution/lipid interface from that at the solution/air interface.

Theoretical and experimental examination of SFG polarization analysis at acetonitrile-water solution surfaces.

Sum frequency generation (SFG) spectroscopy is widely used to observe molecular orientation at interfaces through a combination of various types of polarization. The present work thoroughly examines the relation between the polarization dependence of SFG signals and the molecular orientation, by comparing SFG measurements and molecular dynamics (MD) simulations of acetonitrile/water solutions. The present SFG experiment and MD simulations yield quite consistent results on the ratios of χ(2) elements, supporting the reliability of both means. However, the subsequent polarization analysis tends to derive more upright tilt angles of acetonitrile than the direct MD calculations. The reasons for discrepancy are examined in terms of three issues; (i) anisotropy of the Raman tensor, (ii) cross-correlation, and (iii) orientational distribution. The analysis revealed that the issues (i) and (iii) are the main causes of errors in the conventional polarization analysis of SFG spectra. In methyl CH stretching, the anisotropy of Raman tensor cannot be estimated from the simple bond polarizability model. The neglect of the orientational distribution is shown to systematically underestimate the tilt angle of acetonitrile. Further refined use of polarization analysis in collaboration with MD simulations should be proposed.

Theoretical Investigation of C-H Vibrational Spectroscopy. 1. Modeling of Methyl and Methylene Groups of Ethanol with Different Conformers.

A flexible and polarizable molecular model of ethanol is developed to extend our investigation of thermodynamic, structural, and vibrational properties of the liquid and interface. A molecular dynamics (MD) simulation with the present model confirmed that this model well reproduces a number of properties of liquid ethanol, including density, heat of vaporization, surface tension, molecular dipole moment, and trans/gauche ratio. In particular, the present model can describe vibrational IR, Raman, and sum frequency generation (SFG) spectra of ethanol and partially deuterated analogues with reliable accuracy. The improved accuracy is largely attributed to proper modeling of the conformational dependence and the intramolecular couplings including Fermi resonance in C-H vibrations. Precise dependence of torsional motions is found to be critical in representing vibrational spectra of the C-H bending. This model allows for further vibrational analysis of complicated alkyl groups widely observed in various organic molecules with MD simulation.

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.

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

IR-visible sum-frequency generation (IV-SFG) vibrational spectroscopy and a molecular dynamics (MD) simulation were used to study the local layering order at the interface of 1-butanol-d9 and 1-butyl-3-methylimidazolium hexafluorophosphate ([bmim]PF6), a room-temperature ionic liquid (RTIL). The presence of a local non-polar layer at the interface of the two polar liquids was successfully demonstrated. In the SFG spectra of 1-butanol-d9, we observed significant reduction and enhancement in the strength of the CD3 symmetric stretching (r(+)) mode and the antisymmetric stretching (r(-)) mode peaks, respectively. The results can be well explained by the presence of an oppositely oriented quasi-bilayer structure of butanol molecules, where the bottom layer is strongly bound by hydrogen-bonding with the PF6(-) anion. MD simulations reveal that the hydrogen-bonding of butanol with the PF6(-) anion causes the preferential orientation of the butanols; the restriction on the rotational distribution of the terminal methyl group along their C3 axis enhances the r(-) mode. As for the [bmim](+) cations, the SFG spectra taken within the CH stretch region indicate that the butyl chain of [bmim](+) points away from the bulk RTIL phase to the butanol phase at the interface. Combining the SFG spectroscopy and MD simulation results, we propose an interfacial model structure of layering, in which the butyl chains of the butanol molecules form a non-polar interfacial layer with the butyl chains of the [bmim](+) cations at the interface.