Solvent effects in the hydrogenation of 2-butanone

In liquid-phase reaction systems, the role of the solvent is often limited to the simple requirement of dissolving and/or diluting substrates. However, the correct choice, either pure or mixed, can significantly influence both reaction rate and selectivity. For multi-phase heterogeneously catalysed reactions observed variations may be due to changes in mass transfer rates, reaction mechanism, reaction kinetics, adsorption properties and combinations thereof. The liquid-phase hydrogenation of 2-butanone to 2-butanol over a Ru/SiO catalyst, for example, shows such complex rate behaviour when varying water/isopropyl alcohol (IPA) solvent ratios. In this paper, we outline a strategy which combines measured rate data with physical property measurements and molecular simulation in order to gain a more fundamental understanding of mixed solvent effects for this heterogeneously catalysed reaction. By combining these techniques, the observed complex behaviour of rate against water fraction is shown to be a combination of both mass transfer and chemical effects. © 2012 Elsevier Inc. All rights reserved.

PLUMED 2: New feathers for an old bird

Enhancing sampling and analyzing simulations are central issues in molecular simulation. Recently, we introduced PLUMED, an open-source plug-in that provides some of the most popular molecular dynamics (MD) codes with implementations of a variety of different enhanced sampling algorithms and collective variables (CVs). The rapid changes in this field, in particular new directions in enhanced sampling and dimensionality reduction together with new hardware, require a code that is more flexible and more efficient. We therefore present PLUMED 2 here a,complete rewrite of the code in an object-oriented programming language (C++). This new version introduces greater flexibility and greater modularity, which both extends its core capabilities and makes it far easier to add new methods and CVs. It also has a simpler interface with the MD engines and provides a single software library containing both tools and core facilities. Ultimately, the new code better serves the ever-growing community of users and contributors in coping with the new challenges arising in the field.

Program summary

Program title: PLUMED 2

Catalogue identifier: AEEE_v2_0

Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEEE_v2_0.html

Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland

Licensing provisions: Yes

No. of lines in distributed program, including test data, etc.: 700646

No. of bytes in distributed program, including test data, etc.: 6618136

Distribution format: tar.gz

Programming language: ANSI-C++.

Computer: Any computer capable of running an executable produced by a C++ compiler.

Operating system: Linux operating system, Unix OSs.

Has the code been vectorized or parallelized?: Yes, parallelized using MPI.

RAM: Depends on the number of atoms, the method chosen and the collective variables used.

Classification: 3, 7.7, 23. Catalogue identifier of previous version: AEEE_v1_0.

Journal reference of previous version: Comput. Phys. Comm. 180 (2009) 1961.

External routines: GNU libmatheval, Lapack, Bias, MPI. (C) 2013 Elsevier B.V. All rights reserved.

Extraordinary mechanical properties of monatomic C3N2 chain

One-dimensional monatomic chains are promising candidates for technical applications in the field of nanoelectronics due to their unique mechanical, electrical and optical properties. In particular, we investigate the mechanical properties including Young's modulus, ultimate strength and ultimate strain, which are necessities for the stability of the materials by the Car-Parrinello molecular dynamics in this work. The comparative studies for the alternating carbon-nitrogen (C₃N₂) chain and carbon chains (carbyne) of different lengths show that the carbon-nitrogen (C-N) chain is obviously stronger and stiffer than carbynes. Thus the C-N chain, which has been found in decomposition products of the nitromethane explosive simulations, could be a superior nano-mechanical material than the carbyne chain. Furthermore, it is found that the bond order of weakest bond in monatomic chains is positively correlated with Young's modulus and ultimate strength of materials.

Ab initio molecular dynamics simulation of a room temperature ionic liquid

Ab initio molecular dynamics simulations have been performed for the first time on the room-temperature organic ionic liquid dimethyl imidazolium chloride [DMIM][Cl] using density functional theory. The aim is to compare the local liquid structure with both that obtained from two different classical force fields and from neutron scattering experiments. The local structure around the cation shows significant differences compared to both the classical calculations and the neutron results. In particular, and unlike in the gas-phase ion pair, chloride ions tend to be located near a ring C-H proton in a position suggesting hydrogen bonding. The results are used to suggest ways in which the classical potentials may be improved.

Molecular dynamics simulation of ionic liquids: The effect of electronic polarizability

An electronically polarizable model has been developed for the ionic liquid 1-ethyl-3-methylimidazolium nitrate (EMIM+/NO3-), Molecular dynamics simulation studies were then performed on both the polarizable and nonpolarizable versions of the model. Comparisons of shear viscosity and diffusion constants at 400 K show that the effects of polarizability are quite substantial and the polarizable model results are in better agreement with the experimental values.

Binding modes of diketo-acid inhibitors of HIV-1 integrase: A comparative molecular dynamics simulation study

HIV-1 integrase (IN) has become an attractive target since drug resistance against HIV-1 reverse transcriptase (RT) and protease (PR) has appeared. Diketo acid (DKA) inhibitors are potent and selective inhibitors of HIV-1 IN: however the action mechanism is not well understood. Here, to study the inhibition mechanism of DKAs we performed 10 ns comparative molecular dynamics simulations on HIV-1 IN bound with three most representative DMA inhibitors: Shionogi inhibitor, S-1360 and two Merck inhibitors L-731,988 and L-708,906. Our simulations show that the acidic part of S-1360 formed salt bridge and cation-pi interactions with Lys159. In addition, the catalytic Glu152 in S-1360 was pushed away from the active site to form an ion-pair interaction with Arg199. The Merck inhibitors can maintain either one or both of these ion-pair interaction features. The difference in potencies of the DMA inhibitors is thus attributed to the different binding modes at the catalytic site. Such structural information at atomic level, not only demonstrates the action modes of DMA inhibitors but also provides a novel starting point for structural-based design of HIV-1 IN inhibitors.

Molecular dynamics simulation model for the quantitative assessment of tool wear during single point diamond turning of cubic silicon carbide

Silicon carbide (SiC) is a material of great technological interest for engineering applications concerning hostile environments where silicon-based components cannot work (beyond 623 K). Single point diamond turning (SPDT) has remained a superior and viable method to harness process efficiency and freeform shapes on this harder material. However, it is extremely difficult to machine this ceramic consistently in the ductile regime due to sudden and rapid tool wear. It thus becomes non trivial to develop an accurate understanding of tool wear mechanism during SPDT of SiC in order to identify measures to suppress wear to minimize operational cost.

In this paper, molecular dynamics (MD) simulation has been deployed with a realistic analytical bond order potential (ABOP) formalism based potential energy function to understand tool wear mechanism during single point diamond turning of SiC. The most significant result was obtained using the radial distribution function which suggests graphitization of diamond tool during the machining process. This phenomenon occurs due to the abrasive processes between these two ultra hard materials. The abrasive action results in locally high temperature which compounds with the massive cutting forces leading to sp3–sp2 order–disorder transition of diamond tool. This represents the root cause of tool wear during SPDT operation of cubic SiC. Further testing led to the development of a novel method for quantitative assessment of the progression of diamond tool wear from MD simulations.

Molecular dynamics simulation of nanoindentation of Fe3C and tetrahedral Fe4C

Study of nanomechanical response of iron carbides is important because presence of iron carbides greatly influences the performance and longevity of steel components. This work contributes to the literature by exploring nanoindentation of nanocrystalline Fe3C and tetrahedral-Fe4C using molecular dynamics simulation. The chemical interactions of iron and carbon were described through an analytical bond order inter-atomic potential (ABOP) energy function. The indentations were performed at an indentation speed of 50 m/sec and a repeat trial was performed at 5 m/sec. Load-displacement (P-h) curve for both these carbides showed residual indentation depth and maximum indentation depth (hf/hmax) ratio to be higher than 0.7 i.e. a circumstance where Oliver and Pharr method was not appropriate to be applied to evaluate the material properties. Alternate evaluation revealed Fe3C to be much harder than Fe4C. Gibbs free energy of formation and radial distribution function, coupled with state of the average local temperature and von Mises stresses indicate the formation of a new phase of iron-carbide. Formation of this newer phase was found to be due to deviatoric strain rather than the high temperature induced in the substrate during nanoindentation

Nanoindentation of polysilicon and single crystal silicon: Molecular dynamics simulation and experimental validation

This paper presents novel advances on the deformation behaviour of polycrystalline and single crystal silicon using molecular dynamics (MD) simulation and validation of the same via nanoindentation experiments. In order to unravel the mechanism of deformation, four simulations were performed: Indentation of polycrystalline silicon substrate with a (i) Berkovich pyramidal and a (ii) spherical (arc) indenter, and indentation of a single crystal silicon substrate with these two indenters. The simulation results reveal that high pressure phase transformation (HPPT) in silicon (Si-I to Si-II phase transformation) occurred in all cases, however, its extent and the manner in which it occurred differed significantly between polycrystalline silicon and single crystal silicon, and was the main driver of differences in nanoindentation deformation behaviour between the two types of silicon. An interesting observation was that in polycrystalline silicon, the HPPT was observed to occur preferentially along the grain boundaries than across the grain boundaries. An automated dislocation extraction algorithm (DXA) revealed no dislocations in the deformation zone, suggesting HPPT to be the primary mechanism in inducing plasticity in silicon.