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Showing 1 to 20 of 109 for “"molecular mechanics"”.
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Molecular mechanics calculations of tin-bis (triphenylphosphine oxide) complexes
The capability of molecular mechanics for modeling the wide distribution of bond angles and bond lengths characteristic of coordination complexes was investigatecl. This was the preliminary step for future modeling of solvent extraction. Several tin-phosphine oxide COrnI)le:){es were selected as …
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Application of molecular mechanics polarization to fragment based drug design.
Polarization is a term that is often excluded from almost all virtual screening. Polarizability helps explain interactions between nonpolar atoms and electrically charged species. When studying fragments in FBDD these minor interactions could have large effect in changing how well a ligand will …
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A study of the molecular mechanics of wood cell walls
… matrix to provide a bottom-up description of the mechanics. We identify the mechanical behaviors for varying fibril angles, and in addition, for varying fibril lengths, plot force-strain relationships and compare the data with experimental results and theoretical predictions, providing insight …
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Molecular Mechanics Simulations of Instabilities in 3D Deformations of Gold Nanospecimens
We use molecular mechanics (MM) simulations with the tight-binding (TB) potential to study local and global instabilities in initially defect-free finite specimens of gold crystals deformed in shear, simple shear, tension/compression, simple tension/compression, and triaxial tension/compression. …
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Carbon Nanotube Mechanics: Continuum Model Development from Molecular Mechanics Virtual Experiments
… their material properties. We have used molecular mechanics (MM) simulations to conduct virtual experiments on single-wall and multi-wall carbon nanotubes (SWNTs and MWNTs respectively) similar to those performed in the mechanics of materials laboratory on a continuum structure. The …
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Molecular mechanics of DNA bricks: in situ structure, mechanical properties and ionic conductivity
… yet to be determined. Here, we use the all-atom molecular dynamic method to directly compare the structure, mechanical properties and ionic conductivity of DNA brick and DNA origami objects different only by internal connectivity of their consistituent DNA strands. In comparison to equivalent DNA …
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Molecular mechanics of cartilage : quantification of GAG electrostatic interactions via high-resolution force spectroscopy
Intermolecular repulsion forces between negatively charged glycosaminoglycan (CS-GAG) macromolecules are a major determinant of cartilage biomechanical properties. It is thought that the electrostatic component of the total intermolecular interaction is responsible for 50-75% of the equilibrium …
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Application of X-ray Diffraction Methods and Molecular Mechanics Simulations to Structure Determination and Cotton Fiber Analysis
… diffraction analyses, and in conjunction with molecular modeling of Cellulose IIII. Although each technique is different in its sampling, data acquisition, data treatment, and identification, the common denominator has been the use of x-rays. The single-crystal structure determination of …
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Secondary structure determination of insect neuropeptides using high-resolution nuclear magnetic resonance and various molecular mechanics calculations
… magnetic resonance (NMR) techniques and various molecular mechanics computations. The interproton distances and φ torsion angles obtained from the NMR data were used to constrain the peptides in subsequent Monte Carlo and molecular dynamics (simulated annealing) calculations. The results of these …
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Combined Application of Density Functional Theory and Molecular Mechanics Sampling Techniques to study Chemical Systems, from Intramolecular Rearrangements to Polymerization Reactions
… of higher computational resources. Methods like molecular mechanics (MM) are less computationally expensive, but fail to describe important features of chemical systems. While the study of chemical systems of relatively small size can often be carried out using methods like DFT, some of these …
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Elastic constants from molecular mechanics simulations of frequencies of free-free single-walled carbon nanotubes and clamped single-layer graphene sheets
… their free vibration characteristics using molecular mechanics (MM) simulations with the MM3 potential and finding their equivalent continuum structures (ECSs). The computational framework has been validated by comparing the presently computed basal plane stiffness and frequencies of radial …
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Part I. Studies of the substitution and formation reactions of rhenium carbonyl o-semiquinone compounds. Part II. Molecular mechanics studies of the steric interactions in chromium pentacarbonyl phosphine compounds
In part I, the thermal synthesis of (3,5-di-t-butyl-1,2-benzosemiquinone)Re(CO)$\sb4$ from the sodium semiquinone radical anion and Re(CO)$\sb5$Cl is reported. The substitution kinetics of (3,5-di-t-butyl-1,2-benzosemiquinone)Re(CO)$\sb4$ with P(n-Bu)$\sb3$ was studied by stopped-flow methods. The …
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A Computational Investigation of the Mechanism of CB1954 Reduction by E.coli Nitroreductase
… up the initial reduction step. Additionally, molecular mechanics and molecular dynamics have been used to examine the nature of the active site of the wild-type enzyme, as well as several mutants, and determine possible binding modes of the substrate. Finally, ONIOM calculations were utilised …
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Practical Applications of Molecular Modeling Pertaining to Oxidative Damage and Disease
Molecular modeling is a term referring to the study of proteins, nucleic acids, lipids, and other bio- or macro- or small molecules at the atomistic level using a combination of computational methods, physico-chemical principles, and mathematical functions. It can be generally sub-divided into two …
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Diamino diamide copper complexes as anti-arthritic agents
… electrode potentiometry, UV/VIS spectroscopy, molecular mechanics calculations, speciation modelling as well as X-ray crystallography. Animal experiments were also carried out.
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Molecular studies of natural products and related compounds.
… in this field are discussed. The applications of molecular mechanics calculations to molecular studies are presented along with the theoretical aspects of the method. Detailed structural information is given for several novel compounds, these having been solved using direct methods. The structures …
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Theoretical and experimental studies of slowly deacylating alpha-chymotrypsin acyl enzymes
… and 14 have been studied using the techniques of molecular mechanics and molecular dynamics. These studies indicate that the ketone side-chain of slowly deacylating acyl enzyme 13 is hydrogen bonded to the NH of Gly-216, and that the force of this hydrogen bond along with other non-bonded …
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Molecular Dynamics simulation of rock and clay minerals to estimate their mechanical properties
… is a need to study these materials using micro molecular mechanics. There is also a theory that failure in a rock mass is governed by the formation and propagation of microscopic cracks. The development of these can be observed and studied using the nanoscale analyses. A new science is emerging …
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Computer aided chemical speciation in designing metal-based potential anti-inflammatory agents
… associated with Rheumatoid Arthritis. Four low molecular ligands, N,Nt-di(aminoethylene)-2,6-pyridine dicarbonylamine (PrDH), Bis-(N,N-dimethylethyl)-2,6-pyridinedicarboxamide (PrDM), N,N'-bis[2(2-pyridyl)-methyl]pyridine-2,6-dicarboxamide (PrDPr) and …
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Stereoelectronic effects in brominations of cyclopropylarenes and 9-alkylanthracenes
… believed to be due to stereoelectronic effects. Molecular mechanics calculations and X-ray crystallography have been used to demonstrate that 9-cycIopropylanthracene, unlike other cyclopropylarenes, is effectively locked in a conformation which places the a-cyclopropyl C-H bond in alignment with …
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