Lateral diffusion of ions near membrane surface.

Biological membranes isolate living cells from their environment, while allowing selective molecular transport between the inner and outer realms. For example, Na and K permeability through ionic channels contributes to neural conduction. Whether the ionic currents arise directly from cations in the bulk, or from the interface, is currently unclear.

Collagen Structured Hydration.

Collagen is a triple-helical protein unique to the extracellular matrix, conferring rigidity and stability to tissues such as bone and tendon. For the [(PPG)10]3 collagen-mimetic peptide at room temperature, our molecular dynamics simulations show that these properties result in a remarkably ordered first hydration layer of water molecules hydrogen bonded to the backbone carbonyl (bb-CO) oxygen atoms. This originates from the following observations.

Temperature and Nuclear Quantum Effects on the Stretching Modes of the Water Hexamer.

The water hexamer has many low-lying isomers, e.g., ring, book, cage, and prism, shifting from two- to three-dimensional structures.

Thermally Induced Hydrogen-Bond Rearrangements in Small Water Clusters and the Persistent Water Tetramer.

Small water clusters absorb heat and catalyze pivotal atmospheric reactions. Yet, experiments produced conflicting results on water cluster distribution under atmospheric conditions. Additionally, it is unclear which "phase transitions" such clusters exhibit, at what temperatures, and what are their underlying molecular mechanisms.

Temperature Dependence of Intramolecular Vibrational Bands in Small Water Clusters.

Cyclic water clusters are pivotal for understanding atmospheric reactions as well as liquid water, yet the temperature () dependence of their dynamics and spectroscopy is poorly studied. The development of highly accurate water potentials, such as MB-pol, partly rectifies this. It remains to account for the quantum nuclear effects (NQE), because quantum nuclear dynamics become increasingly inaccurate at low temperatures.

Ionic radii of hydrated sodium cation from QTAIM.

The sodium cation is ubiquitous in aqueous chemistry and biological systems. Yet, in spite of numerous studies, the (average) distance between the sodium cation and its water ligands, and the corresponding ionic radii, are still controversial. Recent experimental values in solution are notably smaller than those from previous X-ray studies and ab initio molecular dynamics.

Structure, spectroscopy, and dynamics of the phenol-(water) cluster at low and high temperatures.

Aqueous solutions are complex due to hydrogen bonding (HBing). While gas-phase clusters could provide clues on the solution behavior, most neutral clusters were studied at cryogenic temperatures. Recent results of Shimamori and Fujii provide the first IR spectrum of warm phenol-(HO) clusters.

Isoelectronic Theory for Cationic Radii.

Ionic radii play a central role in all branches of chemistry, in geochemistry, solid-state physics, and biophysics. While authoritative compilations of experimental radii are available, their theoretical basis is unclear, and no quantitative derivation exists. Here we show how a quantitative calculation of ionic radii for cations with spherically symmetric charge distribution is obtained by charge-weighted averaging of outer and inner radii.

Origin of proton affinity to membrane/water interfaces.

Proton diffusion along biological membranes is vitally important for cellular energetics. Here we extended previous time-resolved fluorescence measurements to study the time and temperature dependence of surface proton transport. We determined the Gibbs activation energy barrier ΔG that opposes proton surface-to-bulk release from Arrhenius plots of (i) protons' surface diffusion constant and (ii) the rate coefficient for proton surface-to-bulk release.

Reinvestigation of the Infrared Spectrum of the Gas-Phase Protonated Water Tetramer.

Gas-phase HO has been considered an archetypal Eigen cation, HO(HO). Yet ab initio molecular dynamics (AIMD) suggested that its infrared spectrum is explained by a linear-chain Zundel isomer, alone or in a mixture with the Eigen cation. Recently, hole-burning experiments suggested a single isomer, with a second-order vibrational perturbation theory (VPT2) spectrum agreeing with the Eigen cation.

Proton Wire Dynamics in the Green Fluorescent Protein.

Inside proteins, protons move on proton wires (PWs). Starting from the highest resolution X-ray structure available, we conduct a 306 ns molecular dynamics simulation of the (A-state) wild-type (wt) green fluorescent protein (GFP) to study how its PWs change with time. We find that the PW from the chromophore via Ser205 to Glu222, observed in all X-ray structures, undergoes rapid water molecule insertion between Ser205 and Glu222.

Reversible Excited-State Proton Geminate Recombination: Revisited.

About three decades ago, Pines and Huppert found that the excited-state proton transfer to water from a photoacid (8-hydroxy-1,3,6-pyrene trisulfonate (HPTS)) is followed by an efficient diffusion-assisted reversible geminate-recombination of the proton. To model the reaction, Pines, Huppert, and Agmon used the Debye-Smoluchowski equation with boundary conditions appropriate for reversible contact reaction kinetics. This reaction model has been used successfully to quantitatively fit the experimental data of the time-resolved fluorescence of HPTS and several commonly used photoacids.

Protons and Hydroxide Ions in Aqueous Systems.

Understanding the structure and dynamics of water's constituent ions, proton and hydroxide, has been a subject of numerous experimental and theoretical studies over the last century. Besides their obvious importance in acid-base chemistry, these ions play an important role in numerous applications ranging from enzyme catalysis to environmental chemistry. Despite a long history of research, many fundamental issues regarding their properties continue to be an active area of research.

Complete Assignment of the Infrared Spectrum of the Gas-Phase Protonated Ammonia Dimer.

The infrared (IR) spectrum of the ammoniated ammonium dimer is more complex than those of the larger protonated ammonia clusters due to close-lying fundamental and combination bands and possible Fermi resonances (FR). To date, the only theoretical analysis involved partial dimensionality quantum nuclear dynamic simulations, assuming a symmetric structure (D3d) with the proton midway between the two nitrogen atoms. Here we report an extensive study of the less symmetric (C3v) dimer, utilizing both second order vibrational perturbation theory (VPT2) and ab initio molecular dynamics (AIMD), from which we calculated the Fourier transform (FT) of the dipole-moment autocorrelation function (DACF).

Structure and Spectroscopy of Hydrated Sodium Ions at Different Temperatures and the Cluster Stability Rules.

The sodium cation plays an important role in several physiological processes. Understanding its solvation may help understanding ion selectivity in sodium channels that are pivotal for nerve impulses. This paper presents a thorough investigation of over 75 isomers of gas-phase Na(+)(H2O)(n=1-8) clusters, whose optimized structures, energies, and (harmonic) vibrational frequencies were computed quantum mechanically at the full MP2/6-31++G(d,p) level of theory.

The hole in the barrel: water exchange at the GFP chromophore.

Internal water molecules in proteins are conceivably part of the protein structure, not exchanging easily with the bulk. We present a detailed molecular dynamics study of the water molecule bound to the green fluorescent protein (GFP) chromophore that conducts its proton following photoexcitation. It readily exchanges above 310 K through a hole that forms between strands 7 and 10, due to fluctuations in the 6-7 loop.

Protonated water dimer on benzene: standing Eigen or crouching Zundel?

Protonated water clusters that are hydrogen-bonded to a neutral benzene molecule are a reductionist model for protons at hydrophobic surfaces, which are of fundamental importance in biological energy transduction processes. Of particular interest is the protonated water dimer ("Zundel ion") on benzene, whose gas-phase messenger IR spectrum has been previously interpreted in terms of an asymmetric binding of the protonated water dimer to the benzene ring through a single water molecule. This "standing Eigen" isomer has a hydronium core.

Network analysis of proton transfer in liquid water.

Proton transfer in macromolecular systems is a fascinating yet elusive process. In the last ten years, molecular simulations have shown to be a useful tool to unveil the atomistic mechanism. Notwithstanding, the large number of degrees of freedom involved make the accurate description of the process very hard even for the case of proton diffusion in bulk water.

Deciphering the infrared spectrum of the protonated water pentamer and the hybrid Eigen-Zundel cation.

Traditionally, infrared band assignment for the protonated water clusters, such as H(+)(H2O)5, is based on their lowest energy isomer. Recent experiments extend the observation spectral window to lower frequencies, for which such assignment appears to be inadequate. Because this hydrogen-bonded system is highly anharmonic, harmonic spectral calculations are insufficient for reliable interpretation.

Statistics of language morphology change: from biconsonantal hunters to triconsonantal farmers.

Linguistic evolution mirrors cultural evolution, of which one of the most decisive steps was the "agricultural revolution" that occurred 11,000 years ago in W. Asia. Traditional comparative historical linguistics becomes inaccurate for time depths greater than, say, 10 kyr.

Both Zundel and Eigen isomers contribute to the IR spectrum of the gas-phase H9O4+ cluster.

The "Eigen cation", H3O+(H2O)3, is the most prevalent protonated water structure in the liquid phase and the most stable gas-phase isomer of the H+(H2O)4 cluster. Nevertheless, its 50 K argon predissociation vibrational spectrum contains unexplainable low frequency peak(s). We have simulated the IR spectra of 10 gas-phase H+(H2O)4 isomers, that include zero to three argon ligands, using dipole autocorrelation functions from ab initio molecular dynamics with the CP2K software.

On the origin of proton mobility suppression in aqueous solutions of amphiphiles.

Recent experiments reported that proton mobility in tetramethylurea (TMU) solutions is much slower than in urea solutions of the same molarity, and this (as well as the significantly retarded water reorientation) was ascribed to hydrophopic effects. In order to further explore the mechanism of proton transport in these solutions, reactive molecular dynamics simulations using a multistate empirical valence bond model were conducted. The simulations showed that the hydrophobic effect of the TMU methyl groups is weaker than believed.

A 'clusters-in-liquid' method for calculating infrared spectra identifies the proton-transfer mode in acidic aqueous solutions.

In liquid water the transfer of an excess proton between two water molecules occurs through the Zundel cation, H(2)O···H(+)···OH(2). The proton-transfer mode is the asymmetric stretch of the central O···H(+)···O moiety, but there is no consensus on its identification in the infrared spectra of acidic aqueous solutions. Also, in experiments with protonated gas-phase water clusters, its position shifts with cluster size, which makes its relationship with solution spectra unclear.

Green's function for reversible geminate reaction with volume reactivity.

The kinetics of a diffusing particle near a reversible trap may be described by an extension of the Feynman-Kac equation to the case of reversible binding, which can occur within a finite reaction sphere. We obtain the Green's function solution for the Laplace transform of this equation when the particle is initially either bound or unbound. We study the solution in the time-domain by either inverting the Laplace transform numerically or propagating the partial differential equation in the time-domain.