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.

Adsorption Energetics of Amino Acid Analogs on Polymer/Water Interfaces Studied by All-Atom Molecular Dynamics Simulation and a Theory of Solutions.

Energetics of adsorption was addressed with all-atom molecular dynamics simulation on the interfaces of poly(2-methoxyethyl acrylate) (PMEA), poly(methyl methacrylate) (PMMA), and poly(butyl acrylate) (PBA) with water. A wide variety of adsorbate solutes were examined, and the free energy of adsorption was computed with the method of energy representation. It was found that the adsorption free energy was favorable (negative) for all the combinations of solute and polymer, and among PMEA, PMMA, and PBA, the strongest adsorption was observed on PMMA for the hydrophobic solutes and on PMEA for the hydrophilic ones. According to the decomposition of the adsorption free energy into the contributions from polymer and water, it was seen that the polymer contribution is larger in magnitude with the solute size. The total free energy of adsorption was correlated well with the solvation free energy in bulk water only for hydrophobic solutes. The roles of the intermolecular interaction components such as electrostatic, van der Waals, and excluded-volume were further studied, and the electrostatic component was influential only in determining the polymer dependences of the adsorption propensities of hydrophilic solutes. The extent of adsorption was shown to be ranked by the van der Waals component in the solute-polymer interaction separately over the hydrophilic and hydrophobic solutes, with the excluded-volume effect from water pointed out to also drive the adsorption.

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.

Molecular Structure and Vibrational Spectra of Water Molecules Sorbed in Poly(2-methoxyethylacrylate) Revealed by Molecular Dynamics Simulation.

Molecular dynamics (MD) simulations of water sorption in poly(2-methoxyethylacrylate) (PMEA) are carried out to elucidate the hydrogen bonding (H-bonding) structures of the water molecules and the side chains of PMEA. A PMEA model incorporating lone-pair virtual sites on the carbonyl and methoxy oxygens of the side chain of PMEA, which are the key interaction sites in a biocompatible polymer, is newly developed. The PMEA model well reproduces the experimentally observed features in the infrared spectra of the hydrated polymer, as well as the radial distribution function of the water molecules in contact with the polymer, as calculated by ab initio MD simulations. The MD simulation results reveal that water molecules tend to form H-bonds with the carbonyl oxygen and the methoxy oxygen of the side chain of PMEA simultaneously, which enhance the "head-to-tail" stacking structure of the side chains at a low concentration range of water. Further penetration of water into the PMEA structure gradually increases the water-water H-bonding state and promotes the formation of water clusters even below the equilibrium water content.

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.

Stimuli-Responsive Self-Assembly of π-Conjugated Liquids Triggers Circularly Polarized Luminescence.

We developed novel room-temperature stimuli-responsive N-heteroacene-based liquid materials bearing a chiral alkyl chain. When these liquid materials were exposed to HCl vapor as an external stimulus, a disordered-ordered state change occurred immediately to yield self-assembled solid states from fluidic liquids. The self-assembly mechanism during this state change was evaluated by experimental in situ observations and molecular dynamics simulations over various spatiotemporal scales. These self-assembled structures led to supramolecular chirality through the influence of the chiral alkyl chain. As a result, circularly polarized luminescence (CPL) was triggered in the solid state, which was absent in the precursor liquid, thereby rendering this the first report on a stimuli-responsive CPL on/off liquid material. In addition, the initial state was recovered by exposure to air or upon heating. Moreover, the synergy between the experimental and the theoretical studies opens a new avenue to develop a novel class of stimuli-responsive materials and to discover novel phenomena in such materials.

Exploration of Gas-Liquid Interfaces for Liquid Water and Methanol Using Extreme Ultraviolet Laser Photoemission Spectroscopy.

We present a study using extreme UV (EUV) photoemission spectroscopy of the valence electronic structures of aqueous and methanol solutions using a 10 kHz EUV light source based on high-order harmonic generation and a magnetic bottle time-of-flight electron spectrometer. Two aspects of the observed spectra are highlighted in this study. One is variation of the vertical ionization energy (VIE) for liquids as a function of the solute concentration, which is closely related to surface dipoles at the gas-liquid interface. The experimental results show that the VIE of liquid water increases slightly with increasing concentrations of NaCl and NaI and decreases with NaOH. The VIE of liquid methanol was also found to change slightly with NaI. On the other hand, tetrabutylammonium iodide (TBAI) and butylamine (BA) clearly reduce the VIE for liquid water, which is attributed to the formation of an electric double layer (EDL) by segregated solutes at the gas-liquid interface. As evidence for this, when the pH of an aqueous BA solution is reduced to protonate BA, the VIE shift gradually decreases because the protonated BA moves into the bulk to suppress the influence of the EDL. We computed the surface potentials for these solutions using molecular dynamics simulations, and the results supported our interpretation of the experimental results. Another observation is the variation of the relative energy and shape of individual photoelectron bands for solvents, which is related to alteration of the structure and constituents of the first solvation shell of ionized solvent molecules. All of the solutes cause changes in the photoelectron spectra at high concentration, one of the most prominent of which is the degree of splitting of the 3a1 band for liquid water and the 7a' band for liquid methanol, which are sensitive to hydrogen bonding in the liquids. The 3a1 splitting decreases with the increasing concentration of NaI, NaCl, and NaOH, indicating that Na+ penetrates into the hydrogen-bonding network to coordinate to a nonbonding electron of a water molecule. On the other hand, TBAI and BA cause smaller changes in the 3a1 splitting. Full interpretation of these spectroscopic features awaits extensive quantum chemical calculations and is beyond the scope of this study. However, these results illustrate the strong potential of EUV laser photoemission spectroscopy of liquids for exploration of interfacial and solution chemistry.

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 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.

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).

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.

Nuclear Quantum Effect on the χ(2) Band Shape of Vibrational Sum Frequency Generation Spectra of Normal and Deuterated Water Surfaces.

In the vibrational sum frequency generation (VSFG) spectrum of the air/water interface, there is an open question whether the imaginary spectrum of nonlinear susceptibility Im[χ(2)] has a positive band in the low-frequency tail of the OH stretching band. We previously elucidated by molecular dynamics (MD) analysis of the VSFG spectrum that the positive band could arise from particularly strong hydrogen-bonded water pairs at the water surface. This mechanism should be emphasized in OD stretching in comparison to OH, because OD forms stronger hydrogen bonds. Therefore, we calculated the Im[χ(2)] spectra of normal and deuterated water surfaces by MD simulation including the nuclear quantum effect and demonstrated that the low-frequency positive feature could arise in the tail of the OD stretching band. This positive feature is sensitive to the oxygen-oxygen distance of hydrogen-bonding pairs at the surface and hence the temperature and disappears with increasing temperature.

Stimuli-Responsive Room-Temperature N-Heteroacene Liquid: In Situ Observation of the Self-Assembling Process and Its Multiple Properties.

A novel stimuli-responsive room-temperature photoluminescent liquid 1 based on the N-heteroacene framework is developed and analyzed by several experiments such as differential scanning calorimetry, X-ray diffraction, dynamic viscoelasticity measurement, in situ observation by optical and polarized optical microscopes, UV-vis absorption and fluorescence spectroscopy, and by theoretical methods such as ab initio calculation and molecular dynamics (MD) computer simulation techniques. In contrast to stimuli-responsive solid materials reported previously, liquid 1 in response to HCl vapor as a single stimulus can involve dramatically multiple changes in physical properties such as rheological behavior, morphology, as well as photoluminescence. The present ab initio calculation and microsecond-timescale MD simulations reveal that the complexation of 1 and HCl molecules induces a large dipole moment, leading to the formation of stacking structures because of their dipole-dipole interaction. Upon exposure to HCl vapor, in situ microscopic observation of the stimuli-responsive liquid elucidates a self-assembling process involving the formation of the wrinkle structure in a micrometer scale, indicating disorder-order phase transition. Further exposure of 1 to HCl vapor from seconds to hours has an influence on the macroscopic physical properties such as viscosity, viscoelasticity, and photoluminescent colors. The synergy between the experimental and theoretical investigations opens a new strategy to develop a novel class of stimuli-responsive materials showing multiple changes in physical properties.

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.

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.

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.

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.

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.