Search

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. There are only scant results concerning lateral diffusion of ions on aquated membrane surfaces (and strong belief that this occurs through binding to a diffusing lipid). We performed classical molecular dynamics (MD) simulations of monovalent ions, Na+, K+, and Cl−, near the surface of the zwitterionic palmitoyl-oleoyl-phosphatidylcholine (POPC) membrane. Realistic force-fields for lipids (Amber's Lipid17 and Lipid21) and water (TIP4P-Ew) are tested for the mass and charge densities and the electrostatic potential across the membrane. These calculations reveal that the chloride can bind to the choline moiety through an intervening water molecule by forming a CH⋯OH hydrogen bond, while cations bind to both the phosphatic and carbonyl oxygens of phosphatidylcholine moieties. Upon transitioning from the bulk to the interface, a cation sheds some of its hydration water, which are replaced by headgroup atoms. Notably, an interfacial cation can bind 1–4 headgroup atoms, which is a key to understanding its surface hopping mechanism. We find that cation binding to three headgroup atoms immobilizes it, while binding to four energizes it. Consequently, the lateral cation diffusion rate is only 15–25 times slower than in the bulk, and 4–5 times faster than lipid self-diffusion. K+ diffusion is notably more anomalous than Na+, switching from sub- to super-diffusion after about 2 ns. [ABSTRACT FROM AUTHOR]

Sometimes, all that remains from the history of a place is its name. Thus, toponyms may provide valuable information. Moving backward in time, we trace the ancient history of the Arab/Crusader village Bēt ˁAṭab in western Judea, with remains from Middle-Bronze II (MB II), Iron III and Hellenistic periods. In Roman times it was Eusebius' Ēnadab, 'Spring of ˁaṭab', identified near the spring of this name mentioned in the Survey of Western Palestine. While missing from Masoretic Biblical town lists, Tatami of the Septuagint derives by dropping the b- from reconstructed batˁaṭami, traced to Northwest Semitic languages exhibiting the ay>ā diphthong contraction. The MB II final -i is analysed as an enclitic -mi, found also in the Execration Text (ET) Shechem, and as enclitic -ma in personal names from Alalaḫ VII. The 'prince' of nearby ET 'Ashnah (=Beth Shemesh) had an identical name as later Niqmi-epuh, King of Yamḫad, suggesting settlers from Yamḫad/Alalaḫ during the early 2nd millennium bce. In Bronze Age Bēt-X toponyms X was a deity. Thus, batˁaṭami = 'place of the vulture-goddess shrine'. This, and additional evidence, suggest that Egyptian king Senwosret III could have set a shrine to goddess Nekhbet on Bēt ˁAṭab's summit during his Shechem campaign. [ABSTRACT FROM AUTHOR]

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. Here we adopt a "bottom-up" approach of obtaining these distances from quantum chemistry calculations [full MP2 with the 6-31++G(d,p) and cc-pVTZ basis-sets] of gas-phase Na + ( H 2 O) n clusters, as a function of the sodium coordination number (CN = 2–6). The bulk limit is obtained by the polarizable continuum model, which acts to increase the interatomic distances at small CN, but has a diminishing effect as the CN increases. This extends the CN dependence of the sodium-water distances from crystal structures (CN = 4–12) to lower CN values, revealing a switch between two power laws, having a small exponent at small CNs and a larger one at large CNs. We utilize Bader's theory of atoms in molecules to bisect the Na+–O distances into Na+ and water radii. Contrary to common wisdom, the water radius is not constant, decreasing even more than that of Na+ as the CN decreases. We also find that the electron density at the bond critical point increases exponentially as the sodium radius decreases. [ABSTRACT FROM AUTHOR]

The molecular dynamics (MD) simulations, which are based on the multistate empirical valence-bond methodology (MS-EVB) of Schmitt and Voth, are used to investigate the hydrogen-bond (HB) enthalpies and entropies for the hydronium solvation shells in liquid water. The systematic bond-energy differences have agreed with infrared (IR) study on proton hydration.

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-(H2O)2 clusters. To understand the temperature (T) effect, we have revisited the structure and spectroscopy of phenol- (H2O)2 at all T. While older quantum chemistry work concluded that the cyclic isomers are the most stable, the inclusion of dispersion interactions reveals that they are nearly isoenergetic with isomers forming π-HBs with the phenyl ring. Whereas the OH-stretch bands were previously assigned to purely local modes, we show that at low T they involve a concerted component. We have calculated the (static) anharmonic IR spectra for all low-lying isomers, showing that at the MP2 level, one can single out one isomer (udu) as accounting for the low-T spectrum to 3 cm-1 accuracy. Yet no isomer can explain the substantial blueshift of the phenyl-OH band at elevated temperatures. We describe the temperature effect using ab initio molecular dynamics with a density functional and basis-set (B3LYP-D3/aug-cc-pVTZ) that provide a realistic description of OH. . .O vs. OH. . . π HBing. From the dipole moment autocorrelation function, we obtain good description for both low- and high-T spectra. Trajectory visualization suggests that the ring structure remains mostly intact even at high T, with intermittent switching between OH. . .O and OH. . . π, HBing and lengthening of all 3 HBs. The phenyl-OH blueshift is thus attributed to strengthening of its OH bond. A model for three beads on a ring suggests that this shift is partly offset by the elimination of coupling to the other OH bonds in the ring, whereas for the two water molecules these two effects nearly cancel. [ABSTRACT FROM AUTHOR]

A combined effort of the experimental, theory, and the simulations revealed the elementary steps involved in the phenomenon of the photoacidity of ROH-type photoacids. The excitations triggered an intramolecular charge transfer to the ring system, which is more prominent for the anionic base than the acid.

The translational diffusion origin of preferential solvation is described. The main aspects of concentration and time dependence of spectral shifts are examined.

The solvatochromism of 2-naphthol (2OH) and 2-methoxynaphthalene (2OMe) have been studied by measuring the excitation and emission fluorescence spectra in a series of pure solvents. The empirical solvatochromic scale of Kamlet and Taft was used since it provides accurate values for dipolarity interactions as well as the HB accepting and donating power of the solvent. Results reveal that solvatochromism of 2OH is dominated by HBing rather than polarity effects. Both molecules have a small dipole moment in their ground electronic state which increases the excited (S1) state.

Research was conducted to examine the structure of concentrated HCl solutions. A pentagonal ring composed of four water molecules, one proton and one chloride anion, is proposed as the basic structural unit of HCl(H2O) and (HCl)2(H2O)6 in solution. It has bridged H5O2+ and Cl- ions, each of them having a coordination number around four. Results indicate that the ring structure is a likely candidate for the structure of protonated HCl clusters in the gas phase and for the contact ion-pair formed following HCl dissociation in solution.

The MbCO kinetics in trehalose was analyzed through the aid of a quantitative model involving diffusion on a temperature-dependent potential space. Studies revealed that the reaction of MbCO-rebinding kinetics in trehalose glass becomes faster with increasing temperature secondary to the absence of protein collapse, rather than the absence of protein relaxation.m It was also shown that there was an absence of protein collapse in room temperature trehalose as well as the presence of an enhanced reactivity of MbCO.

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. Here, multi-state empirical valence bond molecular dynamics simulations in conjunction with complex network analysis are applied to study proton transfer in liquid water. Making use of a transition network formalism, this approach takes into account the time evolution of several coordinates simultaneously. Our results provide evidence for a strong dependence of proton transfer on the length of the hydrogen bond solvating the Zundel complex, with proton transfer enhancement as shorter bonds are formed at the acceptor site. We identify six major states (nodes) on the network leading from the "special pair" to a more symmetric Zundel complex required for transferring the proton. Moreover, the second solvation shell specifically rearranges to promote the transfer, reiterating the idea that solvation beyond the first shell of the Zundel complex plays a crucial role in the process. [ABSTRACT FROM AUTHOR]

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. We show that integrals of this solution over the reaction sphere agree with previously obtained solutions. [ABSTRACT FROM AUTHOR]

We provide an analytic solution for diffusion-influenced geminate reaction with multiple (N) reversible binding sites (of which one may be irreversible). The solution obtained in the Laplace domain, for two different initial conditions, is valid for the case when the sites are overlapping spheres with no long-range interactions with the diffusing particle. The possibility to invert into the time domain is determined by a characteristic polynomial. When all its roots are distinct, it is possible to apply the Lagrange interpolation formula and obtain a partial-fraction expansion that can be termwise inverted. At long times the occupancy of all sites, and for all initial conditions, decays as t-3/2. The behavior at short times depends on the initial condition: when starting from contact, the binding probability rises as t1/2, but if the particle is initially bound to one of the sites, the occupancy of the others rises as t3/2. In between these two power laws we observe an intermediate-time kinetics consisting of N decaying exponentials. Those which are slower than a characteristic diffusion time are in the reaction-control regime and fit a discrete-state kinetic approximation with no adjustable parameters, whereas the faster kinetic steps are diffusion controlled. The model solved herein may depict a wide range of physical situations, from multisite proton transfer kinetics to hydrogen-bond dynamics of liquid water. [ABSTRACT FROM AUTHOR]

The (history independent) autocorrelation function for a hydrogen-bonded water molecule pair, calculated from classical molecular dynamics trajectories of liquid water, exhibits a t-3/2 asymptotic tail. Its whole time dependence agrees quantitatively with the solution for reversible diffusion-influenced geminate recombination derived by Agmon and Weiss [J. Chem. Phys. 91, 6937 (1989)]. Agreement with diffusion theory is independent of the precise definition of the bound state. Given the water self-diffusion constant, this theory enables us to determine the dissociation and bimolecular recombination rate parameters for a water dimer. (The theory is indispensable for obtaining the bimolecular rate coefficient.) Interestingly, the activation energies obtained from the temperature dependence of these rate coefficients are similar, rather than differing by the hydrogen-bond (HB) strength. This suggests that recombination requires displacing another water molecule, which meanwhile occupied the binding site. Because these activation energies are about twice the HB strength, cleavage of two HBs may be required to allow pair separation. The autocorrelation function without the HB angular restriction yields a recombination rate coefficient that is larger than that for rebinding to all four tetrahedral water sites (with angular restrictions), suggesting the additional participation of interstitial sites. Following dissociation, the probability of the pair to be unbound but within the reaction sphere rises more slowly than expected, possibly because binding to the interstitial sites delays pair separation. An extended diffusion model, which includes an additional binding site, can account for this behavior. [ABSTRACT FROM AUTHOR]

We report accurate Brownian simulation results for the kinetics of the pseudo-first-order diffusion-influenced excited-state reversible transfer reaction A*+B⇋C*+D with two different lifetimes using two different propagation algorithms. The results are used to test approximate solutions for this many-particle problem. Available theories fail when one of the two reactions or (decay) rate constants is large. To remedy this situation, we develop two uniform approximations, which are based on introducing a generalized Smoluchowski term into the relaxation-time approximation. The best of these is the extended unified theory of reversible target reactions, which reduces correctly in all limits and exhibits superior agreement with simulations. [ABSTRACT FROM AUTHOR]

Bond-order analysis is introduced to facilitate the study of cooperative many-molecule effects on proton mobility in liquid water, as simulated using the multistate empirical valence-bond methodology. We calculate the temperature dependence for proton mobility and the total effective bond orders in the first two solvation shells surrounding the H5O2+ proton-transferring complex. We find that proton-hopping between adjacent water molecules proceeds via this intermediate, but couples to hydrogen-bond dynamics in larger water clusters than previously anticipated. A two-color classification of these hydrogen bonds leads to an extended mechanism for proton mobility.© 2005 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Several recent theories of the kinetics of diffusion influenced excited-state association–dissociation reactions are tested against accurate Brownian dynamics simulation results for a wide range of parameters. The theories include the relaxation time approximation (RTA), multiparticle kernel decoupling approximations and the so-called kinetic theory. In the irreversible limit, none of these theories reduce to the Smoluchowski result. For the pseudo-first-order target problem, we show how the RTA can be modified so that the resulting formalism does reduce correctly in the irreversible limit. We call this the unified Smoluchowski approximation, because it unites modern theories of reversible reactions with Smoluchowski’s theory of irreversible reactions. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

We discuss two fundamental reversible diffusion influenced reactions: (i) A+B⇋C and (ii) A+B⇋C+D. In the pseudo-unimolecular case, we prove that reaction (i) is a special case of (ii), which thus constitutes a unified reversible problem of multiparticle kinetics. For static A and C (the “target” limit), we suggest to treat this problem as follows. First we generalize the Smoluchowski theory to reaction (ii). In Laplace space, we combine this with a power-law theory, determining the combination coefficient so that the unified theory reduces correctly in all known limits. We also show how to rewrite it in the time domain, with the generalized Smoluchowski theory as the leading term. Comparison with Brownian simulations shows near perfect agreement for both versions of our theory under all conditions.© 2003 American Institute of Physics. [ABSTRACT FROM AUTHOR]

We report a microscopic simulation for the reversible A+B⇌ C1D reaction in its pseudo-unimolecular limit. The simulations are used to assess the validity of various approximate theories for the time dependence of the approach to equilibrium, up to its long-time asymptotic behavior. To available theories we have added a new theory, the generalized multiparticle kernel 1 (GMPK1) theory. It is shown to be in very good agreement with our simulations than all other theories. The asymptotic behavior of both simulations and GMPK1 agrees with that derived by Gopich and Szabo [Chem. Phys. 284, 91 (2002)]. [ABSTRACT FROM AUTHOR]

We obtain exact analytic solution for the Green functions and survival probabilities of the reversible, geminate diffusion-influenced reaction A+B↔C+D in Laplace space, and in the time domain for various spatial dimensionalities. The asymptotic behavior (in one and three dimensions) goes as t[sub -½], like in the irreversible case, but approach to this limit may occur from either above or below. The implications of these results are demonstrated and discussed. [ABSTRACT FROM AUTHOR]

We report a first microscopic simulation for the diffusional kinetics of a reversible excited-state reaction, A+B+ ↔ AB, where A and AB have different lifetimes and the B-particles are in excess. When the excited species equilibrate fast compared with the excited-state lifetimes, one obtains the pre-equilibrium approximation. The full time-dependence in this case is approximated by a shifted infinite-lifetime expression, and this allows us to derive an analytic expression for the asymptotic exponent. Multiplying this exponential is a t[sup -3/2] term. When the excited-state decay of AB is fast, we obtain the quasistationary approximation. Quantitative comparison between various theories and simulation is presented. [ABSTRACT FROM AUTHOR]

We report three-dimensional simulations of the reversible reaction A+B↔C for a single static A molecule and a uniform initial concentration of noninteracting B-molecules. The results are compared with various analytic approximations for the time-dependence of the binding probability. They are in excellent agreement with a recent theory of Sung and Lee [J. Chem. Phys. 111, 796 (1999)] for all times and rate parameters. The second-order term in the long-time expansion of this theory is incorrect, yet it explains an apparent kinetic transition observed when the B-concentration increases. We also investigate the concentration profiles near the reversible trap. [ABSTRACT FROM AUTHOR]

The article presents a complete description of the x-ray structure of the proton antenna present in a high-resolution green fluorescent protein structure (GFP). The analyses reveal the presence of a strong correlation between the resolution and the water content of the structure.

The modern theories for many-body effects on diffusion-influenced reactions were used to derive approximate analytical expressions for the steady-state profile and the Laplace transform of the transient concentration profiles. The steady-state profiles were observed to have hyperbolic dependence on the distance of the substrate from the enzyme, with a prefactor containing the complexity of the manybody effects.