Phenol-benzene complexation dynamics: quantum chemistry calculation, molecular dynamics simulations, and two dimensional IR spectroscopy

Molecular dynamics (MD) simulations and quantum mechanical electronic structure calculations are used to investigate the nature and dynamics of the phenol-benzene complex in the mixed solvent, benzene/CCl4. Under thermal equilibrium conditions, the complexes are continuously dissociating and forming. The MD simulations are used to calculate the experimental observables related to the phenol hydroxyl stretching mode, i.e., the two dimensional infrared vibrational echo spectrum as a function of time, which directly displays the formation and dissociation of the complex through the growth of off-diagonal peaks, and the linear absorption spectrum, which displays two hydroxyl stretch peaks, one for the complex and one for the free phenol. The results of the simulations are compared to previously reported experimental data and are found to be in quite reasonable agreement. The electronic structure calculations show that the complex is T shaped. The classical potential used for the phenol-benzene interaction in the MD simulations is in good accord with the highest level of the electronic structure calculations. A variety of other features is extracted from the simulations including the relationship between the structure and the projection of the electric field on the hydroxyl group. The fluctuating electric field is used to determine the hydroxyl stretch frequency-frequency correlation function (FFCF). The simulations are also used to examine the number distribution of benzene and CCl4 molecules in the first solvent shell around the phenol. It is found that the distribution is not that of the solvent mole fraction of benzene. There are substantial probabilities of finding a phenol in either a pure benzene environment or a pure CCl4 environment. A conjecture is made that relates the FFCF to the local number of benzene molecules in phenol's first solvent shell.     

Argon cluster-ion sputter yield: Molecular dynamics simulations on silicon and equation for estimating total sputter yield

Argon Gas Cluster-Ion Beam sources have become widely-used on X-ray photoelectron spectroscopy (XPS) and secondary ion mass spectrometry (SIMS) instruments in recent years, but there is little reference data on sputter yields in the literature as yet. Total sputter yield reference data is needed in order to calibrate the depth scale, of XPS or SIMS depth profiles. We previously published a semi-empirical ‘Threshold’ equation for estimating cluster total sputter yield from the energy-per-atom of the cluster and the effective monatomic sputter threshold of the material. This has been shown to agree extremely well with sputter yield measurements on a range or organic and inorganic materials for clusters of around a thousand atoms. Here we use the molecular dynamics (MD) approach to explore a wider range of energy and cluster size than is easy to do experimentally to high precision. We performed MD simulations using the ‘Large-scale Atomic/Molecular Massively Parallel Simulator’ (LAMMPS) parallel MD code on high-performance computer (HPC) systems. We performed 1150 simulations of individual collisions with a silicon (100) surface as an archetypal inorganic substrate, for cluster sizes between 30 and 3000 argon atoms and energies in the range 5 to 40 eV per atom. This corresponds to the most important regime for experimental cluster depth-profiling in SIMS and XPS. Our MD results show a dependence on cluster size as well as energy-per-atom. Using the exponent previously suggested by Paruch et al., we modified the Threshold model equation published previously to take this into account. The modified Threshold equation fits all our MD results extremely well, building on its success in fitting experimental sputter yield measurements. This work is submitted to the volume dedicated to Dr. Martin P Seah, MBE, who was a great influence on the early career of one of the authors (PJC) and who himself made many valuable contributions to the literature on sputtering as it relates to surface and interface analysis.     

A powerful computational crystallography method to study ice polymorphism

Classical molecular dynamics (MD) simulations are employed as a tool to investigate structural properties of ice crystals under several temperature and pressure conditions. All ice crystal phases are analyzed by means of a computational protocol based on a clustering approach following standard MD simulations. The MD simulations are performed by using a recently published classical interaction potential for oxygen and hydrogen in bulk water, derived from neutron scattering data, able to successfully describe complex phenomena such as proton hopping and bond formation/breaking. The present study demonstrates the ability of the interaction potential model to well describe most ice structures found in the phase diagram of water and to estimate the relative stability of 16 known phases through a cluster analysis of simulated powder diagrams of polymorphs obtained from MD simulations. The proposed computational protocol is suited for automated crystal structure identification.     

Microscopic approaches to liquid nitromethane detonation properties

In this paper, thermodynamic and chemical properties of nitromethane are investigated using microscopic simulations. The Hugoniot curve of the inert explosive is computed using Monte Carlo simulations with a modified version of the adaptative Erpenbeck equation of state and a recently developed intermolecular potential. Molecular dynamic simulations of nitromethane decomposition have been performed using a reactive potential, allowing the calculation of kinetic rate constants and activation energies. Finally, the Crussard curve of detonation products as well as thermodynamic properties at the Chapman-Jouguet (CJ) point are computed using reactive ensemble Monte Carlo simulations. Results are in good agreement with both thermochemical calculations and experimental measurements.     

Molecular dynamics simulation of structure H clathrate-hydrates of binary guest molecules

Molecular dynamics (MD) simulations are performed to study the stability of structure H clathrate-hydrates of methane+large-molecule guest substance (LMGS) at temperatures of 270, 273, 278 and 280 K under canonical (NVT-) ensemble condition in a 3×3×3 structure H unit cell replica with 918 TIP4P water molecules. The studied LMGS are 2-methylbutane (2-MB), 2,3-dimethylbutane (2,3-DMB), neohexane (NH), methylcyclohexane (MCH), adamantane and tert-butyl methyl ether (TBME). In the process of MD simulation, achieving equilibrium of the studied system is recognized by stability in calculated pressure for NVT-ensemble. So, for the accuracy of MD simulations, the obtained pressures are compared with the experimental phase diagrams. Therefore, the obtained equilibrium pressures by MD simulations are presented for studying the structure H clathrate-hydrates. The results show that the calculated temperature and pressure conditions by MD simulations are consistent with the experimental phase diagrams. Also, the radial distribution functions (RDFs) of host-host, host-guest and guest-guest molecules are used to analysis the characteristic configurations of the structure H clathrate-hydrate.     

Molecular dynamics simulations of structure and dynamics of organic molecular crystals

A set of model compounds covering a range of polarity and flexibility have been simulated using GAFF, CHARMM22, OPLS and MM3 force fields to examine how well classical molecular dynamics simulations can reproduce structural and dynamic aspects of organic molecular crystals. Molecular structure, crystal structure and thermal motion, including molecular reorientations and internal rotations, found from the simulations have been compared between force fields and with experimental data. The MM3 force field does not perform well in condensed phase simulations, while GAFF, CHARMM and OPLS perform very similarly. Generally molecular and crystal structure are reproduced well, with a few exceptions. The atomic displacement parameters (ADPs) are mostly underestimated in the simulations with a relative error of up to 70%. Examples of molecular reorientation and internal rotation, observed in the simulations, include in-plane reorientations of benzene, methyl rotations in alanine, decane, isopropylcyclohexane, pyramidal inversion of nitrogen in amino group and rotation of the whole group around the C-N bond. Frequencies of such dynamic processes were calculated, as well as thermodynamic properties for reorientations in benzene and alanine. We conclude that MD simulations can be used for qualitative analysis, while quantitative results should be taken with caution. It is important to compare the outcomes from simulations with as many experimental quantities as available before using them to study or quantify crystal properties not available from experiment.     

Statistical mechanically averaged molecular properties of liquid water calculated using the combined coupled cluster/molecular dynamics method

Liquid water is investigated theoretically using combined molecular dynamics (MD) simulations and accurate electronic structure methods. The statistical mechanically averaged molecular properties of liquid water are calculated using the combined coupled cluster/molecular mechanics (CC/MM) method for a large number of configurations generated from MD simulations. The method includes electron correlation effects at the coupled cluster singles and doubles level and the use of a large correlation consistent basis set. A polarizable force field has been used for the molecular dynamics part in both the CC/MM method and in the MD simulation. We describe how the methodology can be optimized with respect to computational costs while maintaining the quality of the results. Using the optimized method we study the energetic properties including the heat of vaporization and electronic excitation energies as well as electric dipole and quadrupole moments, the frequency dependent electric (dipole) polarizability, and electric-field-induced second harmonic generation first and second hyperpolarizabilities. Comparisons with experiments are performed where reliable data are available. Furthermore, we discuss the important issue on how to compare the calculated microscopic nonlocal properties to the experimental macroscopic measurements.     

Molecular simulation study of adsorption and diffusion on silicalite for a benzene/CO2 mixture

The adsorption and diffusion of a binary mixture of supercritical CO2 and benzene on silicalite (MFI-type) have been studied through the grand canonical Monte Carlo and molecular dynamics (MD) simulations. The adsorption behavior of pure CO2 on silicalite was discussed in detail from the adsorption isotherms, adsorption sites, interaction energies, and isosteric heats of adsorption. For the mixture, the influences of temperature, pressure and composition on the adsorption isotherms have been examined. The adsorption site behavior of the mixture has been analyzed, and benzene molecules get adsorbed preferentially in the more spacious channel intersection positions. These simulation results suggest that SC-CO2 fluid can be used as an efficient desorbent of larger aromatics in the zeolite material. The diffusion characteristic for the benzene/CO2 mixture was studied on the basis of MD simulation. It was found that the large coadsorbed benzene molecule has a pronounced effect on the CO2 diffusion in the mixture, while the mobility of benzene molecules is very small due to geometrical restrictions.     

Development of a molecular dynamics-based coalescence model for DSMC simulations of ammonia condensate flows

A coalescence model for homogeneous condensation of ammonia in supersonic expansions to vacuum has been developed using molecular dynamics trajectory calculations. The MD calculations show that the sticking probability increases as the ammonia cluster size increases or the cluster temperature decreases. In addition, the sensitivity of the sticking probability to cluster size decreases as the temperature decreases. Comparison of the Ashgriz-Poo semiempirical coalescence model with MD simulations show that for cluster sizes larger than 100 the former model may be used. To model homogeneous nucleation in an ammonia jet, direct simulation Monte Carlo (DSMC) simulations were performed for different stagnation pressure conditions using the MD simulation outcomes for smaller cluster-cluster collisions and the Ashgriz-Poo model for cluster sizes larger than 100. We found that, by including the combined coalescence model, the average cluster sizes and size distributions predicted by DSMC agree reasonably well with experiment.     

Atomistic molecular dynamics simulations of shock compressed quartz

Atomistic non-equilibrium molecular dynamics simulations of shock wave compression of quartz have been performed using the so-called BKS semi-empirical potential of van Beest, Kramer, and van Santen [Phys. Rev. B 43, 5068 (1991)] to construct the Hugoniot of quartz. Our scheme mimics the real world experimental set up by using a flyer-plate impactor to initiate the shock wave and is the first shock wave simulation that uses a geometry optimised system of a polar slab in a three-dimensional system employing periodic boundary conditions. Our scheme also includes the relaxation of the surface dipole in the polar quartz slab which is an essential pre-requisite to a stable simulation. The original BKS potential is unsuited to shock wave calculations and so we propose a simple modification. With this modification, we find that our calculated Hugoniot is in good agreement with experimental shock wave data up to 25 GPa, but significantly diverges beyond this point. We conclude that our modified BKS potential is suitable for quartz under representative pressure conditions of the Earth core, but unsuitable for high-pressure shock wave simulations. We also find that the BKS potential incorrectly prefers the β-quartz phase over the α-quartz phase at zero-temperature, and that there is a β → α phase-transition at 6 GPa.     

Surface relaxation in water clusters: evidence from theoretical analysis of the oxygen 1s photoelectron spectrum

We present a theoretical interpretation of the oxygen 1s photoelectron spectrum published by Ohrwall et al. [J. Chem. Phys. 123, 054310 (2005)]. A water cluster that contains 200 molecules was simulated at 215 K using the polarizable AMOEBA force field. The force field predicts longer O...O distances at the cluster surface than in the bulk. Comparisons to ab initio molecular dynamics (MD) simulations indicate that the force field underestimates the degree of surface relaxation. By comparing cluster lineshape models, computed from MD simulations, to the experimental spectrum we find further evidence of surface relaxation.     

Phase transition and chemical decomposition of shocked CO-N(2) mixture

Using quantum molecular dynamics simulations based on density functional theory including dispersion corrections (DFT-D), we have studied the thermophysical properties of liquid carbon monoxide and nitrogen (CO-N(2)) mixture under extreme conditions. Density functional theory (DFT) method significantly overestimates the pressure as compared to DFT-D. It is demonstrated that the van der Waals (vdW) interaction has a negative contribution to the pressure and tends to reduce the overestimation of the equilibrium volume. We also demonstrate that a negative slope of Hugoniot curve could possibly be caused by both the absorption of dissociation energy and the uncertainties in composition. As density and temperature increase along the Hoguniot curve, the system appears to undergo a continuous transition and provides for a much richer set of dissociation products. The influence of dissociated carbon and oxygen atoms on nitrogen molecules is also discussed.     

Hydroxamate类抑制剂与MMP-3的结合自由能的计算

用自由能微扰方法(FEP)计算了两种hydroxamate类的抑制剂和MMP-3的相对结合自由能。在计算中,对于催化区的锌离子与其共价结合的配体(包括抑制和组氨酸)采用了键合的模型,抑制剂和周围配体的部分电荷的计算采用两步静电势收敛方法。自由能计算采用了慢增长(Slowgrowth)和固定窗口增长(Fixedwidthwindowgrowth)两种方法,并且在每次计算中都采用了双向采样(Double-widesampling)的策略。两种方法计算得到的相对结合自由能都能和实验值很好的符合。同时从动力学模拟的得到的分子轨迹得到了抑制剂和受体之间相互作用模式,抑制剂的P1部分可以和受体的S1'口袋形成很强范德华和疏水相互作用,P1上的苯环可以和Tyr223上的苯环形成较好的π键堆积相互作用。     

Coarse-grained molecular dynamics simulations of the sphere to rod transition in surfactant micelles

Surfactant molecules self-assemble in aqueous solutions to form various micellar structures such as spheres, rods, or lamellae. Although phase transitions in surfactant solutions have been studied experimentally, their molecular mechanisms are still not well understood. In this work, we show that molecular dynamics (MD) simulations using the coarse-grained (CG) MARTINI force field and explicit CG solvent, validated against atomistic MD studies, can accurately represent micellar assemblies of cetyltrimethylammonium chloride (CTAC). The effect of salt on micellar structures is studied for aromatic anionic salts, e.g., sodium salicylate, and simple inorganic salts, e.g., sodium chloride. Above a threshold concentration, sodium salicylate induces a sphere to rod transition in the micelle. CG MD simulations are shown to capture the dynamics of this shape transition and support a mechanism based on the reduction in the micelle-water interfacial tension induced by the adsorption of the amphiphilic salicylate ions. At the threshold salt concentration, the interface is nearly saturated with adsorbed salicylate ions. Predictions of the effect of salt on the micelle structure in different CG solvent models, namely, single-site standard water and three-site polarizable water, show qualitative agreement. This suggests that phase transitions in aqueous micelle solutions could be investigated by using standard CG water models which allow for 3 orders of magnitude reduction in the computational time as compared to that required for atomistic MD simulations.     

First principles and classical molecular dynamics simulations of solvated benzene

We have performed extensive ab initio and classical molecular dynamics (MD) simulations of benzene in water in order to examine the unique solvation structures that are formed. Qualitative differences between classical and ab initio MD simulations are found and the importance of various technical simulation parameters is examined. Our comparison indicates that nonpolarizable classical models are not capable of describing the solute-water interface correctly if local interactions become energetically comparable to water hydrogen bonds. In addition, a comparison is made between a rigid water model and fully flexible water within ab initio MD simulations which shows that both models agree qualitatively for this challenging system.     

Peptide Conformation from Coupling Constants: Scalar Couplings as Restraints in MD Simulations

The question of how far one can go in the determination of conformation with the sole use of coupling constants as restraints in MD simulations was addressed. Couplings are being used ever more frequently as constraints as measuring heteronuclear long-range coupling constants becomes easier. For this investigation, cyclosporin A, which has previously been extensively examined with NOE-restrained simulations, is used as a model system. Many additional one-and three-bond coupling constants have been measured. The MD simulations were carried out with the addition of a potential-energy penalty function based directly on the Karplus curve. It is shown that, for dihedral angles with more than one coupling, the restraints are very efficient, in agreement with the structure observed from NOEs. However, it turned out that the structure of CsA is not adequately described, when only J couplings are used.     

Multiple Proton Confinement in the M2 Channel from the Influenza A Virus

The tetrameric M2 protein bundle of the influenza A virus is the proton channel responsible for the acidification of the viral interior, a key step in the infection cycle. Selective proton transport is achieved by successive protonation of the conserved histidine amino acids at position 37. A recent X-ray structure of the tetrameric transmembrane (TM) domain of the protein (residues 22-46) resolved several water clusters in the channel lumen, which suggest possible proton pathways to the His37 residues. To explore this hypothesis, we have carried out molecular dynamics (MD) simulations of a proton traveling towards the His37 side chains using MD with classical and quantum force fields. Diffusion through the first half of the channel to the "entry" water cluster near His37 may be hampered by significant kinetic barriers due to electrostatic repulsion. However, once in the entry cluster, a proton can move to one of the acceptor His37 in a nearly barrierless fashion, as evidenced both by MD simulations and a scan of the potential energy surface (PES). Water molecules of the entry cluster, although confined in the M2 pore and restricted in their motions, can conduct protons with a rate very similar to that of bulk water.     

Searching for nanostructures of the cubic mesophase of liquid crystal molecules, BABH8

Nanostructures of a thermotropic cubic phase forming liquid crystal compound, 1,2-bis-[4-n-octyloxy-benzoyl]-hydrazine was studied by molecular dynamics (MD) simulations. A model for its cubic phase structure was proposed, which was constructed from the building unit of a locally orientational ordered "bundle" consistent with the cell parameter and the space group (Ia3d) from the recent x-ray results. Stability of the model structure was studied by multinanosecond MD simulations. A periodic nanostructure with 2.6 nm periodicity [coincides with the Ia3d (211) reflection] was kept up to 60 ns in the reduced pressure simulation which realizes the experimental value of density. However, the calculated fourth-rank order parameter shows that the simulated final state above does not have cubic orientational symmetry but rather isotropic symmetry.