Solvent Influence on Cellulose 1,4‐β‐Glycosidic Bond Cleavage: A Molecular Dynamics and Metadynamics Study

We explore the influence of two solvents, namely water and the ionic liquid 1‐ethyl‐3‐methylimidazolium acetate (EmimAc), on the conformations of two cellulose models (cellobiose and a chain of 40 glucose units) and the solvent impact on glycosidic bond cleavage by acid hydrolysis by using molecular dynamics and metadynamics simulations. We investigate the rotation around the glycosidic bond and ring puckering, as well as the anomeric effect and hydrogen bonds, in order to gauge the effect on the hydrolysis mechanism. We find that EmimAc eases hydrolysis through stronger solvent–cellulose interactions, which break structural and electronic barriers to hydrolysis. Our results indicate that hydrolysis in cellulose chains should start from the ends and not in the centre of the chain, which is less accessible to solvent.     

Solvent‐Dependent Structure of the I3− Ion Derived from Photoelectron Spectroscopy and Ab Initio Molecular Dynamics Simulations

Ab initio molecular dynamics (MD) simulations of the solvation of LiI₃ in four different solvents (water, methanol, ethanol, and acetonitrile) are employed to investigate the molecular and electronic structure of the I₃^? ion in relation to X‐ray photoelectron spectroscopy (XPS). Simulations show that hydrogen‐bond rearrangement in the solvation shell is coupled to intramolecular bond‐length asymmetry in the I₃^? ion. By a combination of charge analysis and I 4 d core‐level XPS measurements, the mechanism of the solvent‐induced distortions has been studied, and it has been concluded that charge localization mediates intermolecular interactions and intramolecular distortion. The approach involving a synergistic combination of theory and experiment probes the solvent‐dependent structure of the I₃^? ion, and the geometric structure has been correlated with the electronic structure.     

Cover Picture: QM/MM Car‐Parrinello Molecular Dynamics Study of the Solvent Effects on the Ground State and on the First Excited Singlet State of Acetone in Water (ChemPhysChem 11/2003)

The cover picture shows …?‥the solvent effect of water upon the lowest‐lying singlet excitation in acetone. The transition, which involves the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO), is blue‐shifted in water (sol) with respect to the gas phase (vac), since the HOMO is stronger stabilized in water than the LUMO. The authors calculate the absorption and fluorescence spectra of acetone in water with a hybrid Car–Parrinello quantum chemical/classical molecular dynamics approach and investigate the influence of the solvent. The lower part of the picture shows the excitation energy during a simulation. One configuration with a very high excitation energy (three hydrogen bonds, short C?O bond) and one configuration with a very low excitation energy (two hydrogen bonds, long C?O bond) are shown in detail. Find out more in the article by Rothlisberger and co‐workers on pages pp. 1177–1182.     

Phase Behavior of Amphiphilic Molecules in the Presence of One Solvent: A Dissipative Particle Dynamics Study

We simulate the phase behavior of amphiphilic molecules in the presence of one solvent by DPD. In general, DPD has successfully captured most of the effects of composition of amphiphilic molecules, solvent selectivity, and solvent amount, on the phase transition behavior obtained by both SCMF calculations and experiments. When a neutral good solvent is added, the solutions undergo a lyotropic transition analogous to the thermotropic transition in the melts. Furthermore, the order‐disorder transition results obtained via DPD are in good agreement with theoretical predictions by including the fluctuation effects, as well as with experiments. In the selective solvents, various transitions from the “normal” phases (i.e., the minority blocks form the minor domains) to even the “inverted” phases (formed by the majority blocks) have been observed by varying solvent selectivity and solvent amount. Since the packing order of the spheres is greatly affected by the finite size of the simulation box, it becomes difficult to examine the most stable packing array of spheres via DPD as has been predicted by SCMF theory. However, DPD reveals a possible spherical order of A15, which has been ignored in current SCMF work but observed in some amphiphilic molecule systems.

     

Ether-Functionalized Pyrrolidinium-Based Room Temperature Ionic Liquids: Physicochemical Properties,Molecular Dynamics,and the Lithium Ion Coordination Environment

The physicochemical properties of room temperature ionic liquids (RTILs) consisting of bis(trifluoromethanesulfonyl)amide (TFSA⁻) combined with 1-hexyl-1-methylpyrrolidinium (Pyr_1,6⁺), 1-(butoxymethyl)-1-methylpyrrolidinium (Pyr_1,1O4⁺), 1-(4-methoxybutyl)-1-methyl pyrrolidinium (Pyr_1,4O1⁺), and 1-((2-methoxyethoxy)methyl)-1-methylpyrrolidinium (Pyr_1,1O2O1⁺) were investigated using both experimental and computational approaches. Pyr_1,1O2O1TFSA, which contains two ether oxygen atoms, showed the lowest viscosity, and the relationship between its physicochemical properties and the position and number of the ether oxygen atoms was discussed by a careful comparison with Pyr_1,1O4TFSA and Pyr_1,4O1TFSA. Ab initio calculations revealed the conformational flexibility of the side chain containing the ether oxygen atoms. In addition, molecular dynamics (MD) calculations suggested that the ion distributions have a significant impact on the transport properties. Furthermore, the coordination environments of the Li ions in the RTILs were evaluated using Raman spectroscopy, which was supported by MD calculations using 1000 ion pairs. The presented results will be valuable for the design of functionalized RTILs for various applications.     

Ion Interactions with the Carbon Nanotube Surface in Aqueous Solutions: Understanding the Molecular Mechanisms

We study the molecular mechanisms of alkali halide ion interactions with the single‐wall carbon nanotube surface in water by means of fully atomistic molecular dynamics simulations. We focus on the basic physical‐chemical principles of ion–nanotube interactions in aqueous solutions and discuss them in light of recent experimental findings on selective ion effects on carbon nanotubes.     

Solvent effect on the synthesis of clarithromycin: A molecular dynamics study

Clarithromycin (6-O-methylerythromycin A) is a 14-membered macrolide antibiotic which is active in vitro against clinically important gram-positive and gram-negative bacteria. The selectivity of the methylation of the C-6 OH group is studied on erythromycin A derivatives. To understand the effect of the solvent on the methylation process, detailed molecular dynamics (MD) simulations are performed in pure DMSO, pure THF and DMSO:THF (1:1) mixture by using the anions at the C-6, C-11 and C-12 positions of 2',4"-[O-bis(TMS)]erythromycin A 9-[O-(dimethylthexylsilyl)oxime] under the assumption that the anions are stable on the sub-nanosecond time scale. The conformations of the anions are not affected by the presence of the solvent mixture. The radial distribution functions are computed for the distribution of different solvent molecules around the 'O-' of the anions. At distances shorter than 5 A, DMSO molecules are found to cluster around the C-11 anion, whereas the anion at the C-12 position is surrounded by the THF molecules. The anion at the C-6 position is not blocked by the solvent molecules. The results are consistent with the experimental finding that the methylation yield at the latter position is increased in the presence of a DMSO:THF (1:1) solvent mixture. Thus, the effect of the solvent in enhancing the yield during the synthesis is not by changing the conformational properties of the anions, but rather by creating a suitable environment for methylation at the C-6 position.     

Counteractive Effects of Choline Geranate (CAGE) ILs and Ethanol on Insulin’s Stability—A Leap Forward towards Oral Insulin Formulation

Choline geranate (CAGE) ionic liquids (ILs) stabilize insulin, thereby aiding its oral delivery, whereas ethanol (EtOH) affects its stability by disrupting the hydrophobic interactions. In this study, cognizance of the stabilization mechanism of insulin dimer in the presence of both CAGE ILs and EtOH mixtures is achieved through biased and unbiased molecular dynamics (MD) simulations. Here, two order parameters are employed to study the insulin dimer dissociation using well-tempered metadynamics (WT-MetaD). The stability of insulin is found to be strongly maintained until a 0.20 mole fraction of EtOH. Besides, higher concentrations of EtOH marginally affect the insulin stability. Moreover, geranate anions form a higher number of H-bonding interactions with water molecules, which aids insulin stabilization. Conversely, the addition of EtOH minimizes the water-mediated H-bonding interactions of geranate. Additionally, geranate traps the EtOH molecules, thereby preventing the interactions between insulin and EtOH. Furthermore, the free energy landscape (FEL) reveals the absence of dimer dissociation along with noticeable deviations in the distances R and the number of contacts Q. The dimerization free energy of insulin was calculated to be −16.1 kcal/mol at a 0.20 mole fraction of EtOH. Moreover, increments in mole fractions of EtOH effectuate a decrease in the insulin stability. Thus, the present study represents CAGE ILs as efficient insulin dimer stabilizes at low concentrations of EtOH.     

Effect of Size and Temperature on Water Dynamics inside Carbon Nano-Tubes Studied by Molecular Dynamics Simulation

Water transport inside carbon nano-tubes (CNTs) has attracted considerable attention due to its nano-fluidic properties, its importance in nonporous systems, and the wide range of applications in membrane desalination and biological medicine. Recent studies show an enhancement of water diffusion inside nano-channels depending on the size of the nano-confinement. However, the underlying mechanism of this enhancement is not well understood yet. In this study, we performed Molecular Dynamics (MD) simulations to study water flow inside CNT systems. The length of CNTs considered in this study is 20 nm, but their diameters vary from 1 to 10 nm. The simulations are conducted at temperatures ranging from 260 K to 320 K. We observe that water molecules are arranged into coaxial water tubular sheets. The number of these tubular sheets depends on the CNT size. Further analysis reveals that the diffusion of water molecules along the CNT axis deviates from the Arrhenius temperature dependence. The non-Arrhenius relationship results from a fragile liquid-like water component persisting at low temperatures with fragility higher than that of the bulk water.     

Direct Derivation of Free Energies of Membrane Deformation and Other Solvent Density Variations From Enhanced Sampling Molecular Dynamics

We report a methodology to calculate the free energy of a shape transformation in a lipid membrane directly from a molecular dynamics simulation. The bilayer need not be homogeneous or symmetric and can be atomically detailed or coarse grained. The method is based on a collective variable that quantifies the similarity between the membrane and a set of predefined density distributions. Enhanced sampling of this “Multi-Map” variable re-shapes the bilayer and permits the derivation of the corresponding potential of mean force. Calculated energies thus reflect the dynamic interplay of atoms and molecules, rather than postulated effects. Evaluation of deformations of different shape, amplitude, and range demonstrates that the macroscopic bending modulus assumed by the Helfrich–Canham model is increasingly unsuitable below the 100-Å scale. In this range of major biological significance, direct free-energy calculations reveal a much greater plasticity. We also quantify the stiffening effect of cholesterol on bilayers of different composition and compare with experiments. Lastly, we illustrate how this approach facilitates analysis of other solvent reorganization processes, such as hydrophobic hydration. Published 2019. This article is a U.S. Government work and is in the public domain in the USA.     

Effect of Vacancy Defects on the Young's Modulus and Fracture Strength of Graphene: A Molecular Dynamics Study

The Young's modulus of graphene with various rectangular and circular vacancy defects is investigated by molecular dynamics simulation. By comparing with the results calculated from an effective spring model, it is demonstrated that the Young's modulus of graphene is largely correlated to the size of vacancy defects perpendicular to the stretching direction. And a linear reduction of Young's modulus with the increasing concentration of mono‐atomic‐vacancy defects (i.e., the slope of ?0.03) is also observed. The fracture behavior of graphene, including the fracture strength, crack initiation and propagation are then studied by the molecular dynamics simulation, the effective spring model, and the quantized fracture mechanics. The blunting effect of vacancy edges is demonstrated, and the characterized crack tip radius of 4.44 Å is observed.     

Effects of the Bead‐Solvent Interaction on the Dynamics of Macromolecules, 1

Summary: Hamiltonian dynamics and a chain model are used to study the dynamics of macromolecules immersed in a solution. From the Hamiltonian of the overall system, “macromolecule + solvent,” a master and a Fokker‐Planck equation are then derived for the phase‐space distribution of the macromolecule. In the Fokker‐Planck equation, all the information about the interaction among the beads of the macromolecule as well as the effects of the surrounding solvent is described by friction tensors, which are expressed in terms of the bead‐solvent interaction and the dynamic structure factor of the solvent. To explore the influence of the bead‐solvent potential on the dynamics of macromolecules, the friction tensors are calculated for a dumbbell molecule and for three choices of the interaction (Yukawa, Born‐Mayer, and Lennard‐Jones). Expressions are derived, in particular, for the friction tensor coefficients of the center‐of‐mass and the relative coordinates of the dumbbell. For the long‐term behaviour of the internal momentum autocorrelation function, moreover, an “algebraic decay” is found, in contrast to the (unphysical) exponential decay as known from phenomenological theory.

Yukawa, Born‐Mayer and Lennard‐Jones bead‐solvent interaction potentials.     

The Effect of Boron on the Properties of Glucomannan： An Experimental and Molecular Dynamics Simulation Study

1 INTRODUCTION gel using KGM and borax at 60 ℃, which can be used as slow-released reagent of theophylline and Generally, the mixture of Konjac Glucomanan dibucaine. And Hogi Tsuneo utilized KGM and tetra- (KGM) and salts that could be hydrolyzed to form valent boric acid to prepare artificial crystal[1]. This multi-hydroxyl hydrates leads to the generation of kind of crystal has good light transmission property, gelatum. Among the familiar salts, such as borate, elasticity, intensi…     

聚合物与表面活性剂相互作用的分子模拟研究进展

聚合物与表面活性剂复配体系已广泛应用于医药、生物、石油石化等领域。从微观上认识其相互作用机理对指导其生产实际有着重要作用,因而此方面的研究倍受关注。随着分子模拟技术的发展,聚合物与表面活性剂在分子水平上的相互作用机理研究已经被广泛开展,并获得了大量有用的信息。本文综述了耗散粒子动力学(DPD)和粗粒度分子动力学(CG-MD)在聚合物与表面活性剂相互作用方面的应用,分别对中性聚合物与离子型表面活性剂,以及带相反电荷的聚电解质和表面活性剂在溶液相和界面相的相互作用进行了阐述,并揭示了聚合物/表面活性剂聚集体结构形态的变化规律。     

Dynamic Behavior of Rotation Transmission Nano-System in Helium Environment: A Molecular Dynamics Study

The molecular dynamics (MD) method is used to investigate the influence of the shielding gas on the dynamic behavior of the heterogeneous rotation transmission nano-system (RTS) built on carbon nanotubes (CNTs) and boron nitride nanotube (BNNT) in a helium environment. In the heterogeneous RTS, the inner CNT acts as a rotor, the middle BNNT serves as a motor, and the outer CNT functions as a stator. The rotor will be actuated to rotate by the motor due to the interlayer van der Waals effects and the end effects. The MD simulation results show that, when the gas density is lower than a critical range, a stable signal of the rotor will arise on the output and the rotation transmission ratio (RRT) of RTS can reach 1.0, but as the gas density is higher than the critical range, the output signal of the rotor cannot be stable due to the sharp drop of the RRT caused by the large friction between helium and the RTS. The greater the motor input signal of RTS, the lower the critical working helium density range. The results also show that the system temperature and gas density are the two main factors affecting the RTS transmission behavior regardless of the size of the simulation box. Our MD results clearly indicate that in the working temperature range of the RTS from 100 K to 600 K, the higher the temperature and the lower the motor input rotation frequency, the higher the critical working helium density range allows.