Papers by Keyword: Molecular Modeling

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Authors: Vincent B.C. Tan, M. Deng, Tong Earn Tay
Abstract: The interface of fiber and matrix strongly influences the performance and strength of fiber-reinforced composite materials. Due to the limitations of continuum mechanics at the nanometer length scale, atomistic level computer simulation has started to play an important role in the understanding of such interfacial systems. Our study focuses on a typical crosslinked interfacial system of glass-epoxy composite with the presence of silanes. To explore the mechanical properties of the interfacial network system, Coarse-grained Molecular Dynamics is used. Currently it is not possible to study mechanical properties of interfacial systems purely through ab initio molecular dynamics simulations because of the huge computational resources required. Although pure atomistic classical molecular dynamics simulations have been used to study systems comprising billions of atoms, classical MD simulation do not take into account the effects of crosslinking of molecular chains. A new force field, which combines the Lennard-Jones potential and a finiteextensible nonlinear elastic attractive potential, is proposed and incorporated in a bead-spring model to simulate glass/epoxy interfacial system with the crosslinked structure of silanes. The finite-extensible nonlinear elastic attractive potential is included to control the motion and breakage of polymer chains. Interfacial adhesion and mechanical properties were studied through the simulation of mechanically separating the interfacial system.
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Authors: Song Li, Lei Fang
Abstract: Molecular conformation and binding modeling were built by Hyperchem 8.0 computational chemistry package and the optimum molecular conformation was obtained by molecular mechanics optimizer. It was found that there were two types of binding sites for norfloxacin on the molecular imprinted particles (MIPs).One was the hydrogen bonds between oxygen atom of MIPs with the carbonyl group of norfloxacin and the other one was the hydrogen bonds between oxygen atom of MIPs with the hydroxyl group of norfloxacin. Moreover, the energies change of the molecules were1.69 x106 J/mol, 1.80x106 J/mol and 5.37x106 J/mol and 2.54 x106 J/mol during the binding process of the norfloxacin (NOR), ciprofloxacin (CIP), bisphenol A (BPA) and tonalide (TON) onto the MIPs, respectively. The result indicated that the MIPs had a good selectivity for NOR and CIP than BPA and TON.
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Authors: Ming Hui Zhou, Wen Jie Sun
Abstract: Many gas-condensate reservoirs experience a sharp drop in gas production owing to condensation near the wellbore as pressure drops lower than the dew point. It has been a challenge for a long time to develop cheaper chemical to stop the dramatic decline in gas production. In this study several molecule formulas are designed, properties of two chemicals for wettability alteration are predicted using molecular modeling method and then synthesized. Analysis result shows high conformity between the prediction and experimental properties.
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Authors: Liu Sen, Xiao Hong Ma
Abstract: Tumor necrosis factor-alpha converting enzyme (TACE) is a very important membrane-bound proteinase, and it can cut a lot of membrane proteins to their released form. Many of the substrates of TACE are critical protein factors, such as IL-6, TNF-alpha, EGF receptor. Therefore, TACE has been a hopeful drug targets in many diseases. However, selective inhibitors against TACE with high specificity has yet been developed successfully, partly due to the lack of the understanding of the TACE substrate interaction details. To solve this problem, here we build a computational complex model of the TACE catalytic domain and its substrate peptide using the protein design software Rosetta. To further optimize the complex model, molecular dynamics analysis was performed in NAMD with explicit water molecules. The result showed that our complex model is a pretty reliable intermediate model for TACE and its peptide substrate. This complex model could be very useful for further study of the substrate specificity and selectivity of TACE.
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Authors: Dieter Hofmann, Maria Entrialgo, Jürgen Reiche, Karl Kratz, Andreas Lendlein
Abstract: Biodegradable polymers are applied in temporary implants, such as surgical sutures and controlled drug delivery systems. They are also of relevance in biomaterial-based Regenerative Therapies, where they provide a temporary substitute of the extra-cellular matrix. A major limitation of established degradable implant materials is the fact, that their degradation behavior can not be reliably predicted applying existing experimental methodologies. Therefore a knowledge-based approach is clearly needed to overcome this problem and to enable the tailored design of biodegradable polymers. Here we describe two methods, which can be applied in this approach: molecular modeling combining atomistic bulk and interface models with quantum chemical studies and experimental investigations of macromolecule degradation in Langmuir monolayers. The polymers utilized to exemplarily illustrate the concepts are aliphatic (co)polyesters [e.g. poly(-caprolactone) (PCL), polyglycolide (PGA), poly(rac-lactide) (PDLLA), poly[(rac-lactide)-co-glycolide] (PLGA)] and copoly(ether)esteruretanes as multiblock copolymers. The molecular modeling approach permits to efficiently investigate the influence of micro-structural properties like free volume distribution, cohesive energy density and concentration of polar functional groups on the bulk water uptake as one constituent part of hydrolytic degradation. The Langmuir monolayer investigations on polymer degradation on the other hand yield the dynamics of bond splitting during degradation within hours separately from time consuming diffusion processes, which may take months in bulk samples.
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Authors: Jie Cheng, Jing Chuan Zhu, Bo Liu
Abstract: Four kinds of dimers from cyclic peptide [-(1R, 3S)-γ-Acc-D-Phe]3 were investigated using molecular modeling based on the density functional theory (DFT), molecular mechanics (MM) and molecular dynamics (MD). The equilibrium dimer structures reveal that these dimers can be divided into two different types according to stacking formation, in which one type dimer is more stable due to the effect of side chain groups. In each type of dimers, only one can transport CHCl3. When the terminal N-substituent methyl is introduced, the transport character is reversed. Analysis of 500 ps MD trajectory suggests that the inner and terminal sizes of the dimers are the main factor that affects the transport of CHCl3. The modeling results can provide a new way for designing and synthesizing cyclic peptide transport channels.
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Authors: Muhamad Fitri Othman, Nornizar Anuar, Noor Fitrah Abu Bakar
Abstract: . In this paper, L-alanine crystal was crystallized in the presence and absence of glycine additive using slow evaporation method, in association with a simulation technique using ab-initio quantum mechanical method used to predict the crystal morphology of L-alanine. Comparison between the experimental and simulated lattice energies have shown a good agreement with the 8% error, thus validating the set of force field and the partial atomic charges used. Attachment energy method used by the simulation to predict the morphology of L-alanine crystal, revealed a prismatic crystal morphology bounded with 10 dominant faces: (110), ( 0), ( 10), (1 0), (020), (0 0) (011), (0 ), (0 1) and (01 ), which is in good agreement with the experimental morphology. Crystallization of L-alanine in the presence of glycine in the solution also resulted in prismatic crystal morphology, but elongated in the z-axis direction. This result was further explained by intermolecular bonding analysis of glycine on the morphological faces of L-alanine crystal, which suggested that glycine was preferentially adsorbed on the (0 ) and (1 0) faces of L-alanine crystal morphology.
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Authors: Rui Jie, Quan Zhou, Jin Song Wang, Yun He Liang, Ting Ting Liao, Jin Hui Yu, De Li Liu, Hui Geng
Abstract: Human α-enolase (ENO1), an evolutionarily conserved and multifunctional protein, is a target self-antigen of rheumatoid arthritis (RA). Rheumatoid arthritis (RA) is genetically associated with MHC class II molecules, such as DRB1*0101, DRB1*0401 and DRB1*0404 allele. Among these DRB1 alleles, DRB1*0401 show the most correlation with RA. However, strong binding ability polypeptide of ENO1 with HLA-DRB1*0401 is still largely unknown. In this study, we used NetMHCII prediction method to predict the strong binding ability polypeptide with HLA-DRB1*0401. Among the 434 predicted fragment peptide, ENO1129-141: PLYRHIADLAGNS showed strong binding with HLA-DR4 and peptide ENO1281-293 KSFIKDYPVVSIE is the second candidate peptide. Based on these result, we choosed EON1129-141 and EON1281-293 polypeptides to do the molecular modeling, and used the molecular dynamics to optimize the three-dimensional structural model. The molecular dynamics results showed that ENO1129-141: PLYRHIADLAGNS and ENO1281-293: KSFIKDYPVVSIE have strong binding ability with HLA-DR4* 0401. In the shared epitope, both ENO1129-141and ENO1281-293 have the very near distance 3.15Å and 3.10Å with K71 of the β1 chain. The main-chain conformations of ENO1129-141 sit more deeply with β1 chain. All together, results indicated that ENO1129-141 and ENO1281-293 bind strong with HLA-DR4 and would be potential T cell epitopes of human α-enolase that induced RA.
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Authors: Zulfahmi Lukman, Nornizar Anuar, Norazah Abdul Rahman
Abstract: Crystal morphology remains an important aspect in pharmaceutical industries and thus lengthy experimentally determined morphology becomes a routine. This leads to advancement of molecular modeling to assist in crystal morphology determination. Morphology of racemic ibuprofen can be grown in PEG 300 solvent and simulated via molecular modeling, the computational technique. The resulting morphology dictates its feasibility and prepares for further necessary control to produce desired morphology. Tuning up the morphology can be done by rationalizing out via molecular modeling the effect of the solvent and crystallization method. Solvent effect persists to influence crystal morphology mainly via interaction of hydrogen bond specific at different facets. However, the influence of solvent-surface interaction in enhancing or inhibiting crystal growth is still not completely resolved. To date, racemic ibuprofen grown in PEG 300 solvent is the first ever reported. The objective of this study is to compare experimental and predicted morphology of racemic ibuprofen using selected potential functions and charge set in vacuum condition. Racemic ibuprofen crystal morphology was grown in PEG 300 solvent via cooling at ambient temperature and predicted via attachment energy (AE) method using molecular modeling. It was found that the experimental morphology is tabular hexagonal while the predicted one is tabular octagonal. The facets were cleaved and its surface chemistry was explained. The predicted lattice energy with lowest percentage error of 0.02% is dominated by van der Waals force rather than electrostatic force.
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Authors: D. Jehnichen, D. Pospiech, L. Häußler, P. Friedel, A. Gottwald, S. Kummer
Abstract: Alkyl-perfluoroalkyl compounds are known to form a microphase-separated structure due to the thermodynamic immiscibility between the fluorinated and the protonated segments [1,2]. Many similarities between bulk and surface structures of such polymers were found in the past [2,3,4] which can be explained by both microphase separation in the bulk as well as surface segregation of the fluorinated parts. Basing on this concept, polymers with chemically different main chains were attached with alkylperfluoroalkyl side chains (particularly, oxydecylperfluorodecyl chains, -O-(CH2) 10-(CF 2) 9-CF 3). Combined investigations by means of temperature-dependent X-ray scattering, molecular modeling and DSC measurements were performed to characterize the bulk structure in dependence on the flexibility of the main chain as well as the density of side chains. The polymers under investigation show one or more phase transitions in the temperature range from room temperature to 300 °C which can be assigned as transitions between different smectic structures. These phases are characterized to have positive as well as negative expansion coefficients, respectively, indicating changes of the tilt angle of the side chains and/or the degree of interdigitation. The polymer melts feature a high memory behavior evidenced by reversed imaging of the scattering patterns in the heating and cooling runs.
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