Testing a two-state model of nanoconfined liquids: conformational equilibrium of ethylene glycol in amorphous silica pores

Molecular dynamics simulations of the conformational equilibrium of ethylene glycol in roughly cylindrical nanoscale amorphous silica pores are presented and analyzed in the context of a two-state model of confined liquids. This model assumes that an observable property of a confined liquid can be decomposed into a weighted average arising from two subensembles with distinct physical attributes: molecules at the surface and molecules in the interior of the pore. It is further assumed that the molecules in the interior exhibit behavior that is indistinguishable from that of the bulk liquid. However, the present simulation results are not consistent with this two-state model. Neither the assumption of two distinct subensembles nor the assumption that the interior molecules possess bulk-like behavior is supported.     

Molecular dynamics studies of nanoconfined water in clinoptilolite and heulandite zeolites

The complete periodic series of alkali and alkaline earth cation variants (Li(+), Na(+), K(+), Rb(+), Cs(+), Mg(2+), Ca(2+), Sr(2+), and Ba(2+)) of clinoptilolite (Si : Al=5) and heulandite (Si : Al=3.5) aluminosilicate zeolites are examined by large-scale molecular dynamics utilizing a flexible SPC water and aluminosilicate force field. Calculated hydration enthalpies, radial distribution functions, and ion coordination environments are used to describe the energetic and structural components of extra-framework species while power spectra are used to examine the intermolecular dynamics. These data are correlated to evaluate the impact of ion-zeolite, ion-water, and water-zeolite interactions on the behavior of nanoconfined water. Analysis of the correlated data clearly indicates that the charge density of extra-framework cations appears to have the greatest influence on librational motions, while the anionic charge of the framework (i.e. Si:Al ratios) has a lesser impact.     

A two-state stochastic model for the dynamics of constrained water in reversed micelles

Translational diffusion leads the tagged water molecule to explore regions of the reversed micelle with a varying degree of space hindrance, thereby modulating the rotational relaxation process. A two-state modulation is shown to result in satisfactory agreement with the NMR experimental data on the rotational correlation time as a function of the micelle radius.     

Hydrophobic molecules slow down the hydrogen-bond dynamics of water

We study the spectral and orientational dynamics of HDO molecules in solutions of tertiary-butyl-alcohol (TBA), trimethyl-amine-oxide (TMAO), and tetramethylurea (TMU) in isotopically diluted water (HDO:D(2)O and HDO:H(2)O). The spectral dynamics are studied with femtosecond two-dimensional infrared spectroscopy and the orientational dynamics with femtosecond polarization-resolved vibrational pump-probe spectroscopy. We observe a strong slowing down of the spectral diffusion around the central part of the absorption line that increases with increasing solute concentration. At low concentrations, the fraction of water showing slow spectral dynamics is observed to scale with the number of methyl groups, indicating that this effect is due to slow hydrogen-bond dynamics in the hydration shell of the methyl groups of the solute molecules. The slowing down of the vibrational frequency dynamics is strongly correlated with the slowing down of the orientational mobility of the water molecules. This correlation indicates that these effects have a common origin in the effect of hydrophobic molecular groups on the hydrogen-bond dynamics of water.     

Effects of hydrogen-bond environment on single particle and pair dynamics in liquid water

We have performed molecular dynamics simulations of liquid water at 298 and 258 K to investigate the effects of hydrogen-bond environment on various single-particle and pair dynamical properties of water molecules at ambient and supercooled conditions. The water molecules are modelled by the extended simple point charge (SPC/E) model. We first calculate the distribution of hydrogen-bond environment in liquid water at both temperatures and then investigate how the self-diffusion and orientational relaxation of a single water molecule and also the relative diffusion and relaxation of the hydrogen-bond of a water pair depend on the nature of the hydrogen-bond environment of the tagged molecules. We find that the various dynamical quantities depend significantly on the hydrogen-bond environment, especially at the supercooled temperature. The present study provides a molecular-level insight into the dynamics of liquid water under ambient and supercooled conditions.     

Maximum Caliber: a variational approach applied to two-state dynamics

We show how to apply a general theoretical approach to nonequilibrium statistical mechanics, called Maximum Caliber, originally suggested by E. T. Jaynes [Annu. Rev. Phys. Chem. 31, 579 (1980)], to a problem of two-state dynamics. Maximum Caliber is a variational principle for dynamics in the same spirit that Maximum Entropy is a variational principle for equilibrium statistical mechanics. The central idea is to compute a dynamical partition function, a sum of weights over all microscopic paths, rather than over microstates. We illustrate the method on the simple problem of two-state dynamics, A<-->B, first for a single particle, then for M particles. Maximum Caliber gives a unified framework for deriving all the relevant dynamical properties, including the microtrajectories and all the moments of the time-dependent probability density. While it can readily be used to derive the traditional master equation and the Langevin results, it goes beyond them in also giving trajectory information. For example, we derive the Langevin noise distribution rather than assuming it. As a general approach to solving nonequilibrium statistical mechanics dynamical problems, Maximum Caliber has some advantages: (1) It is partition-function-based, so we can draw insights from similarities to equilibrium statistical mechanics. (2) It is trajectory-based, so it gives more dynamical information than population-based approaches like master equations; this is particularly important for few-particle and single-molecule systems. (3) It gives an unambiguous way to relate flows to forces, which has traditionally posed challenges. (4) Like Maximum Entropy, it may be useful for data analysis, specifically for time-dependent phenomena.     

Molecular dynamics of a short-range ordered smectic phase nanoconfined in porous silicon

4-n-octyl-4-cyanobiphenyl has been recently shown to display an unusual sequence of phases when confined into porous silicon (PSi). The gradual increase of oriented short-range smectic (SRS) correlations in place of a phase transition has been interpreted as a consequence of the anisotropic quenched disorder induced by confinement in PSi. Combining two quasielastic neutron scattering experiments with complementary energy resolutions, the authors present the first investigation of the individual molecular dynamics of this system. A large reduction of the molecular dynamics is observed in the confined liquid phase, as a direct consequence of the boundary conditions imposed by the confinement. Temperature fixed window scans reveal a continuous glasslike reduction of the molecular dynamics of the confined liquid and SRS phases on cooling down to 250 K, where a solidlike behavior is finally reached by a two-step crystallization process.     

Irreversibility,decay, and asymptotic dynamics

Ab initio molecular-orbital theory has been used to study the 1,3-sigmatropic hydrogen rearrangements: propene → propene, formic acic → formic acid, and vinyl alcohol → acetaldehyde. Fully optimized structures of stable molecules and transition states have been determined using gradient procedures and the 4-31G basis set. Improved energies have been obtained using a variety of techniques with basis sets up to the size of double-ζ plus polarization (DZP ) and electron correlation up to the CEPA /DZP level. Although both polarization functions and electron correlation lead to a lowering of the calculated barriers, the values remain substantial for all three rearrangements.     

Controlled incorporation of water molecules into carboxy hydrogen-bond networks: a designed approach

The incorporation of water molecules into the hydrogen-bonded pattern of condensed organic materials implies an unfavorable entropic tradeoff resulting from water ordering. Here we show for a family of diacids of general structure (+/-)-1 that extended chains of anhydrous or hydrated structures can be prepared by controlling the steric factors that lead to the closest packing of individual components.     

Shear response of nanoconfined water on muscovite mica: role of cations

By monitoring the thermal noise of a vertically oriented micromechanical force sensor, we detect the viscoelastic response to shear for water in a subnanometer confinement. Measurements in pure water as well as under acidic and high-ionic-strength conditions relate this response to the effect of surface-adsorbed cations, which, because of their hydration, act as pinning centers restricting the mobility of the confined water molecules.     

Testing the core/shell model of nanoconfined water in reverse micelles using linear and nonlinear IR spectroscopy

A core/shell model has often been used to describe water confined to the interior of reverse micelles. The validity of this model for water encapsulated in AOT/isooctane reverse micelles ranging in diameter from 1.7 to 28 nm (w0 = 2-60) and bulk water is investigated using four experimental observables: the hydroxyl stretch absorption spectra, vibrational population relaxation times, orientational relaxation rates, and spectral diffusion dynamics. The time dependent observables are measured with ultrafast infrared spectrally resolved pump-probe and vibrational echo spectroscopies. Major progressive changes appear in all observables as the system moves from bulk water to the smallest water nanopool, w0 = 2. The dynamics are readily distinguishable for reverse micelle sizes smaller than 7 nm in diameter (w0 = 20) compared to the response of bulk water. The results also demonstrate that the size dependent absorption spectra and population relaxation times can be quantitatively predicted using a core-shell model in which the properties of the core (interior of the nanopool) are taken to be those of bulk water and the properties of the shell (water associated with the headgroups) are taken to be those of w0 = 2. A weighted sum of the core and shell components reproduces the size dependent spectra and the nonexponential population relaxation dynamics. However, the same model does not reproduce the spectral diffusion and the orientational relaxation experiments. It is proposed that, when hydrogen bond structural rearrangement is involved (orientational relaxation and spectral diffusion), dynamical coupling between the shell and the core cause the water nanopool to display more homogeneous dynamics. Therefore, the absorption spectra and vibrational lifetime decays can discern different hydrogen bonding environments whereas orientational and spectral diffusion correlation functions predict that the dynamics are size dependent but not as strongly spatially dependent within a reverse micelle.     

Ionization energies and hydrogen-bond strength of the water clusters

The first vertical ionization energies of the water clusters (H₂O)_n for n = 1–8 have been evaluated from ab initio SCF MO calculations. The values obtained for n = 5 and 8 are in reasonable agreement with the experimental values of ice. The stability of the clusters is examined in terms of the hydrogen-bond strength per bond (B_h).     

Mono- and bichromatic electron dynamics: LiH, a test case

This paper describes an electron dynamics method where the time dependence of an external oscillating electric field is the perturbing part of the Hamiltonian. Application of the electric field induces charge movement inside the molecule and electronic transitions between the molecular orbitals. The test system is the neutral LiH molecule. The method is applied to wave functions calculated using the B3LYP (hybrid) density functional, with the STO-3G and the 6-31+G basis sets. The molecule undergoes full population inversion between the HOMO and the LUMO when the electric field is in resonance with the HOMO-LUMO energy gap. The magnitude of the electric field directly affects the rate at which electronic transitions occur and the rate at which charges move between lithium and hydrogen atoms. The method is used to model both monochromatic and bichromatic multiphoton effects in LiH. Monochromatic one-, two- and three-photon transitions occur between the HOMO, LUMO and two other virtual orbitals. There is evidence of both [1+2] direct and [1+1+1] stepwise multiphoton transitions. Bichromatically, two "laser" pulses are applied at different frequencies. Electronic transitions can be fine-tuned to occur via pre-specified pathways of virtual molecular orbitals.     

Nonadiabatic decay dynamics of a benzylidene malononitrile

The photoinduced nonadiabatic decay dynamics of 2-[4-(dimethylamino)benzylidene]malononitrile (DMN) in the gas phase is investigated at the semiempirical OM2/MRCI level using surface hopping simulations. A lifetime of 1.2 ps is predicted for the S(1) state, in accordance with experimental observation. The dominant reaction coordinate is found to be the twisting around the C7═C8 double bond accompanied by pronounced pyramidalization at the C8 atom. Motion along this coordinate leads to the lowest-energy conical intersection (CI(01α)). Several other S(0)/S(1) conical intersections have also been located by full optimization but play no role in the dynamics. The time-resolved fluorescence spectrum of DMN is simulated by computing emission energies and oscillator strengths along the trajectories. It compares well with the experimental spectrum. The use of different active spaces in the OM2/MRCI calculations yields similar results and thus demonstrates their internal consistency.     

New model pair potential for water. Effect of inclusion of specific O⋯H interactions on the topology and dynamics of the hydrogen-bond network

Classical molecular dynamics was used to calculate the topologic and dynamic characteristics of H-bond networks in water, using various model potentials. The explicit inclusion of intermolecular interactions of oxygen and hydrogen atoms leads to a model involving additional stabilization of tetrahedrally coordinated molecules and, as a consequence, increased number of such molecules in the system. The H-bond lifetimes point to a strongly correlated molecular motion in the immediate environment.     

Evaluating hydrogen-bond propensity,hydrogen-bond coordination and hydrogen-bond energy as tools for predicting the outcome of attempted co-crystallisations

ABSTRACT

Two different structure-informatics based methods and one approach based on hydrogen-bond interaction energies were evaluated for their abilities to predict the experimental outcomes of attempted co-crystallisations between two known drug molecules, Nevirapine and Diclofenac, and a series of potential co-formers. The hydrogen-bond propensity (HBP) tool gave the correct result in 26 out of 30 cases, whereas a hydrogen-bond coordination (HBC) method predicted the correct outcome in 22 out of 30 cases. Finally, calculated hydrogen-bond energies (HBE) using a simple electrostatic model, gave the correct result in 23 out of 30 experiments. In those cases, where the crystal structure of a co-crystal of either Nevirapine or Diclofenac was known, we also examined how well the three methods predicted which primary hydrogen-bond interactions were present in the crystal structure. HBP correctly predicted 6 out of 6 cases, HBC could not predict any of the synthon formations correctly, and HBE successfully predicted 1 out of 6 cases.     

A parametric variant of resonant activation: two-state model approach

Mean first passage time of a periodically driven particle for its escape over a fluctuating barrier with wells remaining unbiased exhibits a resonance when the frequency of the driving field is varied. This parametric variant of resonant activation and associated features of noise induced transition are realized in terms of a two-state model to estimate analytically several quantifiers of the escape event. Numerical simulation on a continuous double-well model collaborates our theoretical analysis.     

Analytical theory of hysteresis in ion channels: two-state model

Channel-forming proteins in a lipid bilayer of a biological membrane usually respond to variation of external voltage by changing their conformations. Periodic voltages with frequency comparable with the inverse relaxation time of the protein produce hysteresis in the occupancies of the protein conformations. If the channel conductance changes when the protein jumps between these conformations, hysteresis in occupancies is observed as hysteresis in ion current through the channel. We develop an analytical theory of this phenomenon assuming that the channel conformational dynamics can be described in terms of a two-state model. The theory describes transient behavior of the channel after the periodic voltage is switched on as well as the shape and area of the hysteretic loop as functions of the frequency and amplitude of the applied voltage. The area vanishes as the voltage period T tends to zero and infinity. Asymptotic behaviors of the loop area A in the high- and low-frequency regimes, respectively, are A approximately T and A approximately T(-1).     

Direct observation and control of hydrogen-bond dynamics using low-temperature scanning tunneling microscopy

Hydrogen(H)-bond dynamics are involved in many elementary processes in chemistry and biology. Because of its fundamental importance, a variety of experimental and theoretical approaches have been employed to study the dynamics in gas, liquid, solid phases, and their interfaces. This review describes the recent progress of direct observation and control of H-bond dynamics in several model systems on a metal surface by using low-temperature scanning tunneling microscopy (STM). General aspects of H-bond dynamics and the experimental methods are briefly described in chapter 1 and 2. In the subsequent four chapters, I present direct observation of an H-bond exchange reaction within a single water dimer (chapter 3), a symmetric H bond (chapter 4) and H-atom relay reactions (chapter 5) within water–hydroxyl complexes, and an intramolecular H-atom transfer reaction (tautomerization) within a single porphycene molecule (chapter 6). These results provide novel microscopic insights into H-bond dynamics at the single-molecule level, and highlight significant impact on the process from quantum effects, namely tunneling and zero-point vibration, resulting from the small mass of H atom. Additionally, local environmental effect on H-bond dynamics is also examined by using atom/molecule manipulation with the STM.