Search results for " Simulation"
showing 10 items of 4034 documents
Monte Carlo Tests of Nucleation Concepts in the Lattice Gas Model
2013
The conventional theory of homogeneous and heterogeneous nucleation in a supersaturated vapor is tested by Monte Carlo simulations of the lattice gas (Ising) model with nearest-neighbor attractive interactions on the simple cubic lattice. The theory considers the nucleation process as a slow (quasi-static) cluster (droplet) growth over a free energy barrier $\Delta F^*$, constructed in terms of a balance of surface and bulk term of a "critical droplet" of radius $R^*$, implying that the rates of droplet growth and shrinking essentially balance each other for droplet radius $R=R^*$. For heterogeneous nucleation at surfaces, the barrier is reduced by a factor depending on the contact angle. U…
Synthesis, photophysical properties and structures of organotin-Schiff bases utilizing aromatic amino acid from the chiral pool and evaluation of the…
2017
Abstract Five new organotin(IV) complexes of compositions [Me 2 SnL 1 ] ( 1 ), [Me 2 SnL 2 ] n ( 2 ), [Me 2 SnL 3 ] ( 3 ), [Ph 3 SnL 1 H] n ( 4 ) and [Ph 3 SnL 3 H] ( 5 ) (where L 1 = (2 S )-2-(( E )-(( Z )-4-hydroxypent-3-en-2-ylidene)amino)-3-(1 H -indol-3-yl)propanoate, L 2 = (2 S )-( E )-2-((2-hydroxybenzylidene)amino)-3-(1 H -indol-3-yl)propanoate and L 3 = (2 S )-( E )-2-((1-(2-hydroxyphenyl)ethylidene)amino)-3-(1 H -indol-3-yl)propanoate were synthesized and spectroscopically characterized. The crystal structures of 1 – 4 were determined. For the dimethyltin derivative 2 , a polymeric chain structure was observed as a result of a long Sn∙∙∙O contact involving the exocyclic carbony…
Protein NMR Structures Refined with Rosetta Have Higher Accuracy Relative to Corresponding X-ray Crystal Structures
2014
We have found that refinement of protein NMR structures using Rosetta with experimental NMR restraints yields more accurate protein NMR structures than those that have been deposited in the PDB using standard refinement protocols. Using 40 pairs of NMR and X-ray crystal structures determined by the Northeast Structural Genomics Consortium, for proteins ranging in size from 5-22 kDa, restrained Rosetta refined structures fit better to the raw experimental data, are in better agreement with their X-ray counterparts, and have better phasing power compared to conventionally determined NMR structures. For 37 proteins for which NMR ensembles were available and which had similar structures in solu…
Computational simulation of the lifetime of the methoxymethyl cation in water. A simple model for a glycosyl cation: when is an intermediate an inter…
2010
A two-dimensional free-energy surface is constructed for transfer of the methoxymethyl cation between two water molecules. These atoms are treated quantum mechanically within a box of >1000 classical solvent water molecules, and the molecular dynamics of the whole system is considered at 300 K. This provides a simple model for glycosyl transfer in water. The best surface obtained (MPWB1K/6-31+G(d,p) corrected AMI/TIP3P) contains a shallow free-energy well corresponding to an oxacarbenium ion intermediate in a stepwise mechanism. Molecular dynamics analysis at three temperatures leads to a classical estimate of the lifetime of the methoxymethyl cation in water; when quantum corrections fo…
Mechanistic insights into the phosphoryl transfer reaction in cyclin-dependent kinase 2: a QM/MM study
2019
AbstractCyclin-dependent kinase 2 (CDK2) is an important member of the CDK family exerting its most important function in the regulation of the cell cycle. It catalyzes the transfer of the gamma phosphate group from an ATP (adenosine triphosphate) molecule to a Serine/Threonine residue of a peptide substrate. Due to the importance of this enzyme, and protein kinases in general, a detailed understanding of the reaction mechanism is desired. Thus, in this work the phosphoryl transfer reaction catalyzed by CDK2 was revisited and studied by means of hybrid quantum mechanics/molecular mechanics (QM/MM) calculations. Our results show that the base-assisted mechanism is preferred over the substrat…
Unraveling the role of protein dynamics in dihydrofolate reductase catalysis
2013
Protein dynamics have controversially been proposed to be at the heart of enzyme catalysis, but identification and analysis of dynamical effects in enzyme-catalyzed reactions have proved very challenging. Here, we tackle this question by comparing an enzyme with its heavy ((15)N, (13)C, (2)H substituted) counterpart, providing a subtle probe of dynamics. The crucial hydride transfer step of the reaction (the chemical step) occurs more slowly in the heavy enzyme. A combination of experimental results, quantum mechanics/molecular mechanics simulations, and theoretical analyses identify the origins of the observed differences in reactivity. The generally slightly slower reaction in the heavy e…
Self-assembly of janus dendrimers into uniform dendrimersomes and other complex architectures
2010
Janus Drug Delivery Vehicle Efficient drug delivery vehicles need to be produced in a limited size range and with uniform size distribution. The self-assembly of traditional small-molecule and polymeric amphiphiles has led to the production of micelles, liposomes, polymeric micelles, and polymersomes for use in drug delivery applications. Now, Percec et al. (p. 1009 ) describe the self-assembly of Janus-type (i.e., two-headed) dendrimers to produce monodisperse supramolecular constructs, termed “dendrimersomes,” and other complex architectures. The structures, which showed long-term stability as well as very narrow size distributions, were easily produced by the injection of an ethanolic so…
Template-Assembled Synthetic G-Quadruplex (TASQ): A Useful System for Investigating the Interactions of Ligands with Constrained Quadruplex Topologies
2010
A new biomolecular device for investigating the interactions of ligands with constrained DNA quadruplex topologies, using surface plasmon resonance (SPR), is reported. Biomolecular systems containing an intermolecular-like G-quadruplex motif 1 (parallel G-quadruplex conformation), an intramolecular G-quadruplex 2, and a duplex DNA 3 have been designed and developed. The method is based on the concept of template-assembled synthetic G-quadruplex (TASQ), whereby quadruplex DNA structures are assembled on a template that allows precise control of the parallel G-quadruplex conformation. Various known G-quadruplex ligands have been used to investigate the affinities of ligands for intermolecular…
Electron Microscopy of Human Erythrocyte Catalase: New Two-Dimensional Crystal Forms
1993
Abstract Using the mica-spreading "negative staining-carbon film" procedure, human erythrocyte catalase has been shown to create a number of different periodic or crystalline two-dimensional (2-D) arrays which differ in the arrangement of molecules in the repeating units and the lattice type. Digital image processing has been performed with a 2-D array which contains regularly arranged "undulating" rows of molecules and also with a 2-D crystal form, exhibiting pgg (p22 1 2 1 ) symmetry and lattice parameters of a = 12.7 nm, b = 44 nm, and γ= 92°. The data are compared with our previous analysis of a different human erythrocyte catalase 2-D crystal, and the effect of partial-depth negative s…
Role of Solvent on Nonenzymatic Peptide Bond Formation Mechanisms and Kinetic Isotope Effects
2013
Based on the hypothesis that similar mechanisms are involved in the peptide bond formation in aqueous solution and in the ribosome, the aminolysis of esters in aqueous solution has been the subject of numerous studies as the reference reaction for the catalyzed process. The mechanisms proposed in the literature have been explored in the present paper by hybrid QM/MM molecular dynamics simulations. The free energy profiles have been computed with the QM region of the system described at semiempirical AM1 level and by DFT within the M06-2X functional. According to the results, the formation of adduct zwitterion species is a preliminary step required for all possible mechanisms. Then, from dif…