Diamond nucleation by energetic pure carbon bombardment

Deposition of 1000 eV pure carbon ions onto Si(001) held at 800 degrees C led to direct nucleation of diamond crystallites, as proven by high-resolution transmission electron microscopy and electron energy loss spectroscopy. Molecular dynamic simulations show that diamond nucleation in the absence of hydrogen can occur by precipitation of diamond clusters in a dense amorphous carbon matrix generated by subplantation. Once the diamond clusters are formed, they can grow by thermal annealing consuming carbon atoms from the amorphous matrix. The results are applicable to other materials as well.

Can the scaling behavior of electric conductivity be used to probe the self-organizational changes in solution with respect to the ionic liquid structure? The case of [C8MIM][NTf2]

Electrical conductivity of the supercooled ionic liquid [C8MIM][NTf2], determined as a function of temperature and pressure, highlights strong differences in its ionic transport behavior between low and high temperature regions. To date, the crossover effect which is very well known for low molecular van der Waals liquids has been rarely described for classical ionic liquids. This finding highlights that the thermal fluctuations could be dominant mechanisms driving the dramatic slowing down of ion motions near Tg. An alternative way to analyze separately low and high temperature dc-conductivity data using a density scaling approach was then proposed. Based on which a common value of the scaling exponent [gamma] = 2.4 was obtained, indicating that the applied density scaling is insensitive to the crossover effect. By comparing the scaling exponent [gamma] reported herein along with literature data for other ionic liquids, it appears that [gamma] decreases by increasing the alkyl chain length on the 1-alkyl-3-methylimidazolium-based ionic liquids. This observation may be related to changes in the interaction between ions in solution driven by an increase in the van der Waals type interaction by increasing the alkyl chain length on the cation. This effect may be related to changes in the ionic liquid nanostructural organization with the alkyl chain length on the cation as previously reported in the literature based on molecular dynamic simulations. In other words, the calculated scaling exponent [gamma] may be then used as a key parameter to probe the interaction and/or self-organizational changes in solution with respect to the ionic liquid structure.

Beschreibung von Oberflächenphänomenen durch relativistische Clusterrechnungen unter Verwendung eines Einbettungsverfahrens

For the theoretical investigation of local phenomena (adsorption at surfaces, defects or impurities within a crystal, etc.) one can assume that the effects caused by the local disturbance are only limited to the neighbouring particles. With this model, that is well-known as cluster-approximation, an infinite system can be simulated by a much smaller segment of the surface (Cluster). The size of this segment varies strongly for different systems. Calculations to the convergence of bond distance and binding energy of an adsorbed aluminum atom on an Al(100)-surface showed that more than 100 atoms are necessary to get a sufficient description of surface properties. However with a full-quantummechanical approach these system sizes cannot be calculated because of the effort in computer memory and processor speed. Therefore we developed an embedding procedure for the simulation of surfaces and solids, where the whole system is partitioned in several parts which itsself are treated differently: the internal part (cluster), which is located near the place of the adsorbate, is calculated completely self-consistently and is embedded into an environment, whereas the influence of the environment on the cluster enters as an additional, external potential to the relativistic Kohn-Sham-equations. The basis of the procedure represents the density functional theory. However this means that the choice of the electronic density of the environment constitutes the quality of the embedding procedure. The environment density was modelled in three different ways: atomic densities; of a large prepended calculation without embedding transferred densities; bulk-densities (copied). The embedding procedure was tested on the atomic adsorptions of 'Al on Al(100) and Cu on Cu(100). The result was that if the environment is choices appropriately for the Al-system one needs only 9 embedded atoms to reproduce the results of exact slab-calculations. For the Cu-system first calculations without embedding procedures were accomplished, with the result that already 60 atoms are sufficient as a surface-cluster. Using the embedding procedure the same values with only 25 atoms were obtained. This means a substantial improvement if one takes into consideration that the calculation time increased cubically with the number of atoms. With the embedding method Infinite systems can be treated by molecular methods. Additionally the program code was extended by the possibility to make molecular-dynamic simulations. Now it is possible apart from the past calculations of fixed cores to investigate also structures of small clusters and surfaces. A first application we made with the adsorption of Cu on Cu(100). We calculated the relaxed positions of the atoms that were located close to the adsorption site and afterwards made the full-quantummechanical calculation of this system. We did that procedure for different distances to the surface. Thus a realistic adsorption process could be examined for the first time. It should be remarked that when doing the Cu reference-calculations (without embedding) we begun to parallelize the entire program code. Only because of this aspect the investigations for the 100 atomic Cu surface-clusters were possible. Due to the good efficiency of both the parallelization and the developed embedding procedure we will be able to apply the combination in future. This will help to work on more these areas it will be possible to bring in results of full-relativistic molecular calculations, what will be very interesting especially for the regime of heavy systems.

Synthesis and properties of polyaromatic dendrimers possessing a repetitive amide-ester coupling sequence

A series of novel polyaromatic dendrimers that feature tris-(2-ethylamino)amine as the central core unit has been synthesized up to the third generation by employing a convergent growth strategy. The building blocks 1,3-diamino-2-hydroxypropane and 4-carboxybenzaldehyde were used for dendron construction, a process that involved the cyclic repetition of esterification, oxidation and selective amidation steps. Molecular modelling of this class of dendrimers has been used to predict potential solution state conformations employing molecular mechanics and molecular dynamic simulations. In addition, the results of preliminary metal binding studies using the first generation dendritic system are also outlined. (C) 2003 Elsevier Science Ltd. All rights reserved.

Kinetic multi-layer model of gas-particle interactions in aerosols and clouds (KM-GAP): linking condensation, evaporation and chemical reactions of organics, oxidants and water

We present a novel kinetic multi-layer model for gas-particle interactions in aerosols and clouds (KM-GAP) that treats explicitly all steps of mass transport and chemical reaction of semi-volatile species partitioning between gas phase, particle surface and particle bulk. KM-GAP is based on the PRA model framework (Pöschl-Rudich-Ammann, 2007), and it includes gas phase diffusion, reversible adsorption, surface reactions, bulk diffusion and reaction, as well as condensation, evaporation and heat transfer. The size change of atmospheric particles and the temporal evolution and spatial profile of the concentration of individual chemical species can be modelled along with gas uptake and accommodation coefficients. Depending on the complexity of the investigated system, unlimited numbers of semi-volatile species, chemical reactions, and physical processes can be treated, and the model shall help to bridge gaps in the understanding and quantification of multiphase chemistry and microphysics in atmo- spheric aerosols and clouds. In this study we demonstrate how KM-GAP can be used to analyze, interpret and design experimental investigations of changes in particle size and chemical composition in response to condensation, evaporation, and chemical reaction. For the condensational growth of water droplets, our kinetic model results provide a direct link between laboratory observations and molecular dynamic simulations, confirming that the accommodation coefficient of water at 270 K is close to unity. Literature data on the evaporation of dioctyl phthalate as a function of particle size and time can be reproduced, and the model results suggest that changes in the experimental conditions like aerosol particle concentration and chamber geometry may influence the evaporation kinetics and can be optimized for eðcient probing of specific physical effects and parameters. With regard to oxidative aging of organic aerosol particles, we illustrate how the formation and evaporation of volatile reaction products like nonanal can cause a decrease in the size of oleic acid particles exposed to ozone.

Kinetic multi-layer model of gas-particle interactions in aerosols and clouds (KM-GAP): linking condensation, evaporation and chemical reactions of organics, oxidants and water

We present a novel kinetic multi-layer model for gas-particle interactions in aerosols and clouds (KMGAP) that treats explicitly all steps of mass transport and chemical reaction of semi-volatile species partitioning between gas phase, particle surface and particle bulk. KMGAP is based on the PRA model framework (P¨oschl-Rudich- Ammann, 2007), and it includes gas phase diffusion, reversible adsorption, surface reactions, bulk diffusion and reaction, as well as condensation, evaporation and heat transfer. The size change of atmospheric particles and the temporal evolution and spatial profile of the concentration of individual chemical species can be modeled along with gas uptake and accommodation coefficients. Depending on the complexity of the investigated system and the computational constraints, unlimited numbers of semi-volatile species, chemical reactions, and physical processes can be treated, and the model shall help to bridge gaps in the understanding and quantification of multiphase chemistry and microphysics in atmospheric aerosols and clouds. In this study we demonstrate how KM-GAP can be used to analyze, interpret and design experimental investigations of changes in particle size and chemical composition in response to condensation, evaporation, and chemical reaction. For the condensational growth of water droplets, our kinetic model results provide a direct link between laboratory observations and molecular dynamic simulations, confirming that the accommodation coefficient of water at 270K is close to unity (Winkler et al., 2006). Literature data on the evaporation of dioctyl phthalate as a function of particle size and time can be reproduced, and the model results suggest that changes in the experimental conditions like aerosol particle concentration and chamber geometry may influence the evaporation kinetics and can be optimized for efficient probing of specific physical effects and parameters. With regard to oxidative aging of organic aerosol particles, we illustrate how the formation and evaporation of volatile reaction products like nonanal can cause a decrease in the size of oleic acid particles exposed to ozone.

Modeling of human P450 oxidoreductase structure by in silico mutagenesis and MD simulation

P450 oxidoreductase (POR) is the obligate electron donor for microsomal cytochrome P450s and mutations in POR cause several metabolic disorders. We have modeled the structure of human P450 oxidoreductase by in silico amino acid replacements in the rat POR crystal structure. The rat POR has 94% homology with human POR and 38 amino acids were replaced to make its sequence identical to human POR. Several rounds of molecular dynamic simulations refined the model and removed structural clashes from side chain alterations of replaced amino acids. This approach has the advantage of keeping the cofactor contacts and structural features of the core enzyme intact which could not be achieved by homology based approaches. The final model from our approach was of high quality and compared well with experimentally determined structures of other PORs. This model will be used for analyzing the structural implications of mutations and polymorphisms in human POR.

Sulfamethoxazole induces a switch mechanism in T cell receptors containing TCRVβ20-1, altering pHLA recognition

T cell receptors (TCR) containing Vβ20-1 have been implicated in a wide range of T cell mediated disease and allergic reactions, making it a target for understanding these. Mechanics of T cell receptors are largely unexplained by static structures available from x-ray crystallographic studies. A small number of molecular dynamic simulations have been conducted on TCR, however are currently lacking either portions of the receptor or explanations for differences between binding and non-binding TCR recognition of respective peptide-HLA. We performed molecular dynamic simulations of a TCR containing variable domain Vβ20-1, sequenced from drug responsive T cells. These were initially from a patient showing maculopapular eruptions in response to the sulfanilamide-antibiotic sulfamethoxazole (SMX). The CDR2β domain of this TCR was found to dock SMX with high affinity. Using this compound as a perturbation, overall mechanisms involved in responses mediated by this receptor were explored, showing a chemical action on the TCR free from HLA or peptide interaction. Our simulations show two completely separate modes of binding cognate peptide-HLA complexes, with an increased affinity induced by SMX bound to the Vβ20-1. Overall binding of the TCR is mediated through a primary recognition by either the variable β or α domain, and a switch in recognition within these across TCR loops contacting the peptide and HLA occurs when SMX is present in the CDR2β loop. Large binding affinity differences are induced by summed small amino acid changes primarily by SMX modifying only three critical CDR2β loop amino acid positions. These residues, TYRβ57, ASPβ64, and LYSβ65 initially hold hydrogen bonds from the CDR2β to adjacent CDR loops. Effects from SMX binding are amplified and traverse longer distances through internal TCR hydrogen bonding networks, controlling the overall TCR conformation. Thus, the CDR2β of Vβ20-1 acts as a ligand controlled switch affecting overall TCR binding affinity.

Developments in the Theory of X-ray Absorption and Compton Scattering.

Thesis (Ph.D.)--University of Washington, 2016-06

Design and characterization of zeolite membranes for fluid separation

Experimental and theoretical methods have been used to study zeolite structures, properties and applications as membranes for separation purposes. Thin layers of silicalite-1 and Na-LTA zeolites have been synthesised onto carbon-graphite supports using a hydrothermal synthesis procedure. The separation behaviour of the composite membranes was characterized by gas permeation studies of pure, binary and ternary mixtures of methane, ethane and propane. The influence of temperature and feed gas mixture composition on the separation and selectivity performance of the membranes was also investigated. It was found that the silicalite-1 composite membranes synthesised onto the 4 hour oxidized carbon-graphite supports showed the most promising separation behaviour of all the composite membranes investigated. Molecular simulation methods were used to gain an understanding of how hydrocarbon molecules behave both within the pores and on the surfaces of silicalite-1, mordenite and LTA zeolites. Molecular dynamic simulations were used to investigate the influence of temperature and molecular loadings on the diffusional behaviour of hydrocarbons in zeolites. Both hydroxylated (surface termination with hydroxyl groups) and non-hydroxylated silicalite-1 and Na-mordenite surfaces were generated. For both zeolites the most stable surfaces correspond to the {010} surface. For the silicalite-1 {010} surface the adsorption of hydrocarbons and molecular water onto the hydroxylated surface showed a favourable exothermic adsorption process compared to adsorption on the non-hydroxylated surface. With the Na-mordenite {010} surface the adsorption of hydrocarbons onto both the hydroxylated and non-hydroxylated surfaces had a combination of favourable and non-favourable adsorption energies, while the adsorption of molecular water onto both types of surface was found to be a favourable adsorption process.

Interdependent lateral interactions, hydrophobicity and acid strength and their influence on the catalytic activity of nanoporous sulfonic acid silicas

A series of propylsulfonic (MCM-SOH) and octyl co-functionalised propylsulfonic (MCM-Oc-SOH) catalysts have been prepared by post modification of MCM-41 with mercaptopropyltrimethoxysilane (MPTS) to achieve SOH surface coverages spanning the range 0.12-1 monolayer. Within the MCM-Oc-SOH series, samples with submonolayer MPTS coverages were further grafted with octyltrimethoxysilane to cap bare hydroxyl sites and tune the hydrophobicity of the support. For the MCM-SO H series NH calorimetry revealed acid strength increases as a function of sulfonic acid loading, with -ΔH(NH ) increasing from 87 to 118 kJ mol. In contrast, MCM-Oc-SOH exhibits a dramatic enhancement of acid strength for submonolayer SOH coverages, with -ΔH(NH ) found to increase to 103 kJ mol. In line with these acid strength measurements the per-site activity of the MCM-SOH series in the esterification of butanol with acetic acid was found to increase with SOH content. Incorporation of octyl groups further promotes esterification activity of all the samples within the MCM-Oc-SOH series, such that the turn over frequency of the sample with the lowest loading of SOH more than doubles. Molecular dynamic simulations indicate that the interaction of isolated sulfonic acid groups with the pore walls is the primary cause of the decrease in acid strength and activity of submonolayer samples within the MCM-SOH series. Incorporation of octyl groups results in a combination of increased hydrophobicity and lateral interactions between adjacent sulfonic acid head groups, resulting in a striking enhancement of acid strength and esterification activity. © 2010 The Royal Society of Chemistry.

The (Un)Folding of Multidomain Proteins Through the Lens of Single-molecule Force-spectroscopy and Computer Simulation

Proteins are specialized molecules that catalyze most of the reactions that can sustain life, and they become functional by folding into a specific 3D structure. Despite their importance, the question, "how do proteins fold?" - first pondered in in the 1930's - is still listed as one of the top unanswered scientific questions as of 2005, according to the journal Science. Answering this question would provide a foundation for understanding protein function and would enable improved drug targeting, efficient biofuel production, and stronger biomaterials. Much of what we currently know about protein folding comes from studies on small, single-domain proteins, which may be quite different from the folding of large, multidomain proteins that predominate the proteomes of all organisms.

In this thesis I will discuss my work to fill this gap in understanding by studying the unfolding and refolding of large, multidomain proteins using the powerful combination of single-molecule force-spectroscopy experiments and molecular dynamic simulations.

The three model proteins studied - Luciferase, Protein S, and Streptavidin - lend insight into the inter-domain dependence for unfolding and the subdomain stabilization of binding ligands, and ultimately provide new insight into atomistic details of the intermediate states along the folding pathway.

Crowding, molecular volume and plasticity: An assessment involving crystallography, NMR and simulations

The discrepancy between the X-ray and NMR structures of Mycobacterium tuberculosis peptidyl-tRNA hydrolase in relation to the functionally important plasticity of the molecule led to molecular dynamics simulations. The X-ray and the NMR studies along with the simulations indicated an inverse correlation between crowding and molecular volume. A detailed comparison of proteins for which X-ray and the NMR structures appears to confirm this correlation. In consonance with the reported results of the investigations in cellular compartments and aqueous solution, the comparison indicates that the crowding results in compaction of the molecule as well as change in its shape, which could specifically involve regions of the molecule important in function. Crowding could thus influence the action of proteins through modulation of the functionally important plasticity of the molecule. Selvaraj M, Ahmad R, Varshney U and Vijayan M 2012 Crowding, molecular volume and plasticity: An assessment involving crystallography, NMR and simulations. J. Biosci. 37 953-963] DOI 10.1007/s12038-012-9276-5

Molecular dynamics and simulations study on the vibrational and electronic solvatochromism of benzophenone

Solvent plays a key role in diverse physico-chemical and biological processes. Therefore, understanding solute-solvent interactions at the molecular level of detail is of utmost importance. A comprehensive solvatochromic analysis of benzophenone (Bzp) was carried out in various solvents using Raman and electronic spectroscopy, in conjunction with Density Functional Theory (DFT) calculations of supramolecular solute-solvent clusters generated using classical Molecular Dynamics Simulations (c-MDSs). The >C=O stretching frequency undergoes a bathochromic shift with solvent polarity. Interestingly, in protic solvents this peak appears as a doublet: c-MDS and ad hoc explicit solvent ab initio calculations suggest that the lower and higher frequency peaks are associated with the hydrogen bonded and dangling carbonyl group of Bzp, respectively. Additionally, the dangling carbonyl in methanol (MeOH) solvent is 4 cm(-1) blue-shifted relative to acetonitrile solvent, despite their similar dipolarity/polarizability. This suggests that the cybotactic region of the dangling carbonyl group in MeOH is very different from its bulk solvent structure. Therefore, we propose that this blue-shift of the dangling carbonyl originates in the hydrophobic solvation shell around it resulting from extended hydrogen bonding network of the protic solvents. Furthermore, the 1(1)n pi* (band I) and 1(1)pi pi* (band II) electronic transitions show a hypsochromic and bathochromic shift, respectively. In particular, these shifts in protic solvents are due to differences in their excited state-hydrogen bonding mechanisms. Additionally, a linear relationship is obtained for band I and the >C=O stretching frequency (cm(-1)), which suggests that the different excitation wavelengths in band I correspond to different solvation states. Therefore, we hypothesize that the variation in excitation wavelengths in band I could arise from different solvation states leading to varying solvation dynamics. This will have implications for ultrafast processes associated with electron-transfer, charge transfer, and also the photophysical aspects of excited states. (C) 2016 AIP Publishing LLC.

Atomistic simulations of crack nucleation and intergranular fracture in bulk nanocrystalline nickel

We report large scale molecular dynamics simulations of dynamic cyclic uniaxial tensile deformation of pure, fully dense nanocrystalline Ni, to reveal the crack initiation, and consequently intergranular fracture is the result of coalescence of nanovoids by breaking atomic bonds at grain boundaries and triple junctions. The results indicate that the brittle fracture behavior accounts for the transition from plastic deformation governed by dislocation to one that is grain-boundary dominant when the grain size reduces to the nanoscale. The grain-boundary mediated plasticity is also manifested by the new grain formation and growth induced by stress-assisted grain-boundary diffusion observed in this work. This work illustrates that grain-boundary decohesion is one of the fundamental deformation mechanisms in nanocrystalline Ni.