Molecular structure of cyclopentadiene from its NMR spectrum in a nematic solvent

The NMR spectrum of cyclopentadiene partially oriented in a nematic phase has been measured and the proton geometry has been determined. The results are compared with those deduced from microwave spectroscopy.     

Synthesizing an inorganic-rich solid electrolyte interphase by tailoring solvent chemistry in carbonate electrolyte for enabling high-voltage lithium metal batteries

High-voltage(>4.0 V) lithium metal battery(LBM) is considered to be one of the most promising candidates for next-generation high-energy batteries. However, the commercial carbonate electrolyte delivers a poor compatibility with Li metal anode, and its organic dominated solid electrolyte interphase(SEI) shows a low interfacial energy and a slow Li⁺diffusion ability. In this work, an inorganic LiF-Li₃N rich SEI is designed to enable high-voltage LBM by introducing nano-cu...     

Implicit solvent models for micellization of ionic surfactants

We propose a method for parametrization of implicit solvent models for the simulation of the self-assembly of ionic surfactants into micelles. The parametrization is carried out in two steps. The first step involves atomistic molecular dynamics simulations of headgroups and counterions with explicit solvent to determine structural properties. An implicit solvent model of the headgroup/counterion system is obtained by matching structural quantities between explicit solvent and implicit solvent systems. In the second step, we identify the solvophobic attractions between the tail beads. We determine the solvophobic parameters using grand canonical Monte Carlo simulations with histogram reweighting techniques. The matching objective for the identification of solvophobic attractions is the critical micelle concentration (cmc). We choose sodium dodecyl sulfate as the reference system. On the basis of hydrophobic parameters obtained from this particular model, we study specific ion effects (lithium and potassium instead of sodium) as well as the effect of cationic headgroups (dodecyltrimethylammonium bromide/chloride). Furthermore, the chain length dependence of micellization properties is investigated for sodium alkyl sulfate, with alkyl lengths between 6 and 14. All cases considered give results in broad agreement with experimental data, confirming the transferability of parameters and the generality of the approach.     

Implicit solvent models: Combining an analytical formulation of continuum electrostatics with simple models of the hydrophobic effect

The recent development of approximate analytical formulations of continuum electrostatics opens the possibility of efficient and accurate implicit solvent models for biomolecular simulations. One such formulation (ACE, Schaefer & Karplus, J. Phys. Chem., 1996, 100:1578) is used to compute the electrostatic contribution to solvation and conformational free energies of a set of small solutes and three proteins. Results are compared to finite-difference solutions of the Poisson equation (FDPB) and explicit solvent simulations and experimental data where available. Small molecule solvation free energies agree with FDPB within 1–1.5 kcal/mol, which is comparable to differences in FDPB due to different surface treatments or different force field parameterizations. Side chain conformation free energies of aspartate and asparagine are in qualitative agreement with explicit solvent simulations, while 74 conformations of a surface loop in the protein Ras are accurately ranked compared to FDPB. Preliminary results for solvation free energies of small alkane and polar solutes suggest that a recent Gaussian model could be used in combination with analytical continuum electrostatics to treat nonpolar interactions. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 322–335, 1999     

Review on multi-scale models of solid-electrolyte interphase formation

Electrolyte reduction products form the solid-electrolyte interphase (SEI) on negative electrodes of lithium-ion batteries. Even though this process practically stabilizes the electrode–electrolyte interface, it results in continued capacity-fade limiting lifetime and safety of lithium-ion batteries. Recent atomistic and continuum theories give new insights into the growth of structures and the transport of ions in the SEI. The diffusion of neutral radicals has emerged as a prominent candidate for the long-term growth mechanism, because it predicts the observed potential dependence of SEI growth.     

Molecular structure of biphenyl in an argon matrix

The infrared spectrum of biphenyl was measured in an Ar matrix at 20 K. A comparison of the results with the spectra of this molecule in the solid liquid states shows that the structure of biphenyl in the matrix is similar to that in the liquid state, that is, the molecule is non-planar.     

Comparison of implicit solvent models for the simulation of protein-surface interactions

Empirical force field-based molecular simulations can provide valuable atomistic-level insights into protein-surface interactions in aqueous solution. While the implicit treatment of solvation effects is desired as a means of improving simulation efficiency, existing implicit solvent models were primarily developed for the simulation of peptide or protein behavior in solution alone, and thus may not be appropriate for protein interactions with synthetic material surfaces. The objective of this research was to calculate the change in free energy as a function of surface-separation distance for peptide-surface interactions using different empirical force field-based implicit solvation models (ACE, ASP, EEF1, and RDIE with the CHARMM 19 force field), and to compare these results with the same calculations conducted using density functional theory (DFT) combined with the self-consistent reaction field (SCRF) implicit solvation model. These comparisons show that distinctly different types of behavior are predicted with each implicit solvation method, with ACE providing the best overall agreement with DFT/SCRF calculations. These results also identify areas where ACE is in need of improvement for this application and provide a basis for subsequent parameter refinement.     

Molecular dynamics simulations of the Li-ion diffusion in the amorphous solid electrolyte interphase

The solid electrolyte interphase (SEI), a passivation film covering the electrode surface, is crucial to the lifetime and efficiency of the lithium-ion (Li-ion) battery. Understanding the Li-ion diffusion mechanism within possible components in the mosaic-structured SEI is an essential step to improve the Li-ion conductivity and thus the battery performance. Here, we investigate the Li-ion diffusion mechanism within three amorphous SEI components (i.e., the inorganic inner layer, organic outer layer, and their mixture with 1:1 molar ratio) via ab initio molecular dynamic (AIMD) simulations. Our simulations show that the Li-ion diffusion coefficient in the inorganic layer is two orders of magnitude faster than that in the organic layer. Therefore, the inorganic layer makes a major contribution to the Li-ion diffusion. Furthermore, we find that the Li-ion diffusivity in the organic layer decreases slightly with the increase of the carbon chain from the methyl to ethyl owing to the steric hindrance induced by large groups. Overall, our current work unravels the Li-ion diffusion mechanism, and provides an atomic-scale insight for the understanding of the Li-ion transport in the SEI components.     

Molecular structure of hyaluronan: an introduction

Hyaluronan is an unbranched polysaccharide of repeating disaccharides consisting of d-glucuronic acid and N-acetyl-d-glucosamine. Its strong water-retaining ability and visco-elastic properties have been broadly utilized in medical applications. Hyaluronan is an important constituent of the extracellular matrix whose physiological functions are manifested both as the substance is by itself as well as when it is being linked to various proteins. Compared with other biopolymers, such as nucleic acids and proteins, the structural chemistry of hyaluronan is much less developed. The scarce information about the metrical aspects of its structure shows no unusual features. Its secondary structure is characterized by intramolecular hydrogen bonding that is hard to distinguish from hydrogen bonding involving water molecules when hyaluronan is in aqueous medium. The tertiary structure of hyaluronan is sensitively dependent on its environment. The relative rigidity of the glycosidic bond and the intramolecular hydrogen bonds would tend to restrict rotational freedom and thus conformational variability. This, however, seems to be overwritten by the impact of molecular environment leading to a great variability of tertiary structure. A large number of conformations are possible and may be present as witnessed by their rather small free energy differences. Of the plethora of physical techniques and computational methods, X-ray crystallography and molecular dynamics calculations have proved to be the most fruitful so far. There are untapped possibilities in NMR spectroscopy for structural studies and quantum chemical calculations are also expected to contribute substantially to the structural chemistry of hyaluronan. There are many basic data as well as structural intricacies of hyaluronan that have so far eluded the researchers of its molecular structure. Dedicated to Endre A. Balazs, pioneer in hyaluronan research.     

Effect of an aprotic solvent on the properties and structure of ion-exchange membranes

The effect of the aprotic solvent dimethylacetamide on the equilibrium and transport properties of heterogeneous (MK-40, MA-40, and MA-41) and homogeneous (MF-4SK) ion-exchange membranes is investigated. On the basis of concentration dependences of the conductivity and diffusion permeability of membranes, model calculations of transport-structural parameters that reflect the structural and kinetic characteristics of conducting phases of the swollen polymer are performed. The effect of the aprotic solvent on the flow of current through the structural fragments of the ion-exchange material is estimated. The causes of changes that are induced in the properties of the membranes by the aprotic solvent are ascertained.     

Molecular organization of the coupling agent interphase of fiber-glass reinforced plastics

The structure of the silane coupling agent interphase of fiber-glass reinforced plastics has been studied by Fourier transform infrared and laser Raman spectroscopy. It is found that there is a degree of order in the molecular organization of the coupling agent interphase for the vinyl and cyclohexyl functional silane coupling agents. When a cyclohexyl functional silane is used, crystalline layers of silanetriol on the glass fibers are observed. The extent of order is determined by the structure of the adsorbed species, which is influenced by the structure of the silane in the treating solution. Two factors introducing disorder in the interphase are the magnitude of aggregation of the silanes in solution and irregularities in the topology of the glass surface.     

Molecular radical models for the muonium centres in solids

Molecular radical models are presented for the various muonium-related paramagnetic centres observed in the elemental and compound semiconductors, and for those which are currently being reported in other crystalline solids, notably halides. The measured coupling constants are shown to place tight constraints on the intrinsic geometries which need be considered, i.e. on the crystallographic sites and local relaxation of the lattice, as well as on the nature of the singly occupied molecular orbital. The role of tunnelling states is emphasized.     

Implementation of solvent reaction fields for electronic structure

 Methods are described to incorporate solvent reaction field effects into solute electronic structure calculations. Included are several old and new approaches based on approximate solutions of Poisson's equation through boundary element methods, wherein the solutions are represented in terms of certain apparent surface charge or apparent surface dipole distributions. Practical algorithms to set up and solve the requisite equations are described and implemented in a new general reaction field computer program. Illustrative computational results are presented to show the performance of the program. Received: 2 July 2001 / Accepted: 11 September 2001 / Published online: 19 December 2001     

Treatment of charge singularities in implicit solvent models

This paper presents a novel method for solving the Poisson-Boltzmann (PB) equation based on a rigorous treatment of geometric singularities of the dielectric interface and a Green's function formulation of charge singularities. Geometric singularities, such as cusps and self-intersecting surfaces, in the dielectric interfaces are bottleneck in developing highly accurate PB solvers. Based on an advanced mathematical technique, the matched interface and boundary (MIB) method, we have recently developed a PB solver by rigorously enforcing the flux continuity conditions at the solvent-molecule interface where geometric singularities may occur. The resulting PB solver, denoted as MIBPB-II, is able to deliver second order accuracy for the molecular surfaces of proteins. However, when the mesh size approaches half of the van der Waals radius, the MIBPB-II cannot maintain its accuracy because the grid points that carry the interface information overlap with those that carry distributed singular charges. In the present Green's function formalism, the charge singularities are transformed into interface flux jump conditions, which are treated on an equal footing as the geometric singularities in our MIB framework. The resulting method, denoted as MIBPB-III, is able to provide highly accurate electrostatic potentials at a mesh as coarse as 1.2 A for proteins. Consequently, at a given level of accuracy, the MIBPB-III is about three times faster than the APBS, a recent multigrid PB solver. The MIBPB-III has been extensively validated by using analytically solvable problems, molecular surfaces of polyatomic systems, and 24 proteins. It provides reliable benchmark numerical solutions for the PB equation.     

Treatment of geometric singularities in implicit solvent models

Geometric singularities, such as cusps and self-intersecting surfaces, are major obstacles to the accuracy, convergence, and stability of the numerical solution of the Poisson-Boltzmann (PB) equation. In earlier work, an interface technique based PB solver was developed using the matched interface and boundary (MIB) method, which explicitly enforces the flux jump condition at the solvent-solute interfaces and leads to highly accurate biomolecular electrostatics in continuum electric environments. However, such a PB solver, denoted as MIBPB-I, cannot maintain the designed second order convergence whenever there are geometric singularities, such as cusps and self-intersecting surfaces. Moreover, the matrix of the MIBPB-I is not optimally symmetrical, resulting in the convergence difficulty. The present work presents a new interface method based PB solver, denoted as MIBPB-II, to address the aforementioned problems. The present MIBPB-II solver is systematical and robust in treating geometric singularities and delivers second order convergence for arbitrarily complex molecular surfaces of proteins. A new procedure is introduced to make the MIBPB-II matrix optimally symmetrical and diagonally dominant. The MIBPB-II solver is extensively validated by the molecular surfaces of few-atom systems and a set of 24 proteins. Converged electrostatic potentials and solvation free energies are obtained at a coarse grid spacing of 0.5 A and are considerably more accurate than those obtained by the PBEQ and the APBS at finer grid spacings.     

Secondary structure bias in generalized Born solvent models: comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit solvation

The effects of the use of three generalized Born (GB) implicit solvent models on the thermodynamics of a simple polyalanine peptide are studied via comparing several hundred nanoseconds of well-converged replica exchange molecular dynamics (REMD) simulations using explicit TIP3P solvent to REMD simulations with the GB solvent models. It is found that when compared to REMD simulations using TIP3P the GB REMD simulations contain significant differences in secondary structure populations, most notably an overabundance of alpha-helical secondary structure. This discrepancy is explored via comparison of the differences in the electrostatic component of the free energy of solvation (DeltaDeltaG(pol)) between TIP3P (via thermodynamic Integration calculations), the GB models, and an implicit solvent model based on the Poisson equation (PE). The electrostatic components of the solvation free energies are calculated using each solvent model for four representative conformations of Ala10. Since the PE model is found to have the best performance with respect to reproducing TIP3P DeltaDeltaG(pol) values, effective Born radii from the GB models are compared to effective Born radii calculated with PE (so-called perfect radii), and significant and numerous deviations in GB radii from perfect radii are found in all GB models. The effect of these deviations on the solvation free energy is discussed, and it is shown that even when perfect radii are used the agreement of GB with TIP3P DeltaDeltaG(pol) values does not improve. This suggests a limit to the optimization of the effective Born radius calculation and that future efforts to improve the accuracy of GB models must extend beyond such optimizations.