Search results for "quantum theory"
showing 10 items of 234 documents
Structure of bottle-brush brushes under good solvent conditions: a molecular dynamics study.
2011
We report a simulation study for bottle-brush polymers grafted on a rigid backbone. Using a standard coarse-grained bead-spring model extensive molecular dynamics simulations for such macromolecules under good solvent conditions are performed. We consider a broad range of parameters and present numerical results for the monomer density profile, density of the untethered ends of the grafted flexible backbones and the correlation function describing the range that neighboring grafted bottle-brushes are affected by the presence of the others due to the excluded volume interactions. The end beads of the flexible backbones of the grafted bottle-brushes do not access the region close to the rigid…
Self-Assembling of Peptide/Membrane Complexes by Atomistic Molecular Dynamics Simulations
2007
Abstract Model biological membranes consisting of peptide/lipid-bilayer complexes can nowadays be studied by classical molecular dynamics (MD) simulations at atomic detail. In most cases, the simulation starts with an assumed state of a peptide in a preformed bilayer, from which equilibrium configurations are difficult to obtain due to a relatively slow molecular diffusion. As an alternative, we propose an extension of reported work on the self-organization of unordered lipids into bilayers, consisting of including a peptide molecule in the initial random configuration to obtain a membrane-bound peptide simultaneous to the formation of the lipid bilayer. This strategy takes advantage of the…
A quantum mechanics/molecular mechanics study of the protein-ligand interaction for inhibitors of HIV-1 integrase.
2007
Human immunodeficiency virus type-1 integrase (HIV-1 IN) is an essential enzyme for effective viral replication. Diketo acids such as L-731,988 and S-1360 are potent and selective inhibitors of HIV-1 IN. In this study, we used molecular dynamics simulations, within the hybrid quantum mechanics/molecular mechanics (QM/MM) approach, to determine the protein-ligand interaction energy between HIV-1 IN and L-731,988 and 10 of its derivatives and analogues. This hybrid methodology has the advantage that it includes quantum effects such as ligand polarisation upon binding, which can be very important when highly polarisable groups are embedded in anisotropic environments, as for example in metal-c…
Enzyme molecular mechanism as a starting point to design new inhibitors: a theoretical study of O-GlcNAcase.
2011
O-Glycoprotein 2-acetamino-2-deoxy-β-d-glucopyranosidase (O-GlcNAcase) hydrolyzes O-linked 2-acetamido-2-deoxy-β-d-glucopyranoside (O-GlcNAc) residues from post-translationally modified serine/threonine residues of nucleocytoplasmic protein. The chemical process involves substrate-assisted catalysis, where two aspartate residues have been identified as the two key catalytic residues of O-GlcNAcase. In this report, the first step of the catalytic mechanism used by O-GlcNAcase involving substrate-assisted catalysis has been studied using a hybrid quantum mechanical/molecular mechanical (QM/MM) Molecular Dynamics (MD) calculations. The free energy profile shows that the formation of the oxazol…
Substituent effects in nitro derivatives of carbazoles investigated by comparison of low-temperature crystallographic studies with density functional…
2014
The crystal structure of 9H-carbazole, C12H9N, (I), has been redetermined at low temperature for use as a reference structure in a comparative study with the structures of 1-nitro-9H-carbazole, C12H8N2O2, (II), and 9-nitrocarbazole, C12H8N2O2, (III). The molecule of (I) has crystallographically imposed mirror symmetry (Z′ = 0.5). All three solid-state structures are slightly nonplanar, the dihedral angles between the planes of the arene and pyrrole rings ranging from 0.40 (7)° in (III) to 1.82 (18)° in (II). Nevertheless, a density functional theory (DFT) study predicts completely planar conformations for the isolated molecules. To estimate the influence of nitro-group substitution on aroma…
Efficient photoinduced electron transfer in a porphyrin tripod-fullerene supramolecular complex via pi-pi interactions in nonpolar media.
2010
A novel porphyrin tripod (TPZn(3)) was synthesized via "click chemistry". Three porphyrin moieties of TPZn(3) are geometrically close and linked by a flexible linker. The electron-transfer oxidation of TPZn(3) results in intramolecular pi-dimer formation between porphyrin moieties as indicated by electrochemical, vis-NIR, and ESR measurements. The cyclic voltammogram of TPZn(3) exhibited stepwise one-electron oxidation processes of three porphyrin moieties in the range from 0.58 to 0.73 V (vs SCE in CH(2)Cl(2)). When TPZn(3) was oxidized by tris(2,2'-bipyridyl)-ruthenium(III) ([Ru(bpy)(3)](3+)), the oxidized species (TPZn(3))(n+) (0n/= 3) exhibited a charge resonance band in the NIR region …
Otherwise than quantum
2022
AbstractThe paper focuses on two problems with Alexander Wendt's unification of physical and social ontology on the basis of quantum theory. Firstly, by endowing social phenomena with an ontological foundation in physical reality defined in quantum terms Wendt risks reducing a plurality of worlds as ‘fields of sense’, ordered by their immanent rules, to the physical world ordered by the laws of quantum theory. Secondly, by defining his quantum social science as an ontology Wendt risks excluding from consideration all that which violates ontological laws, yet may still be said to exist or take place: event, potentiality, and alterity. Although the advantages of a scientific ontology are indi…
Structural Origin of Metal Specificity in Isatin Hydrolase from Labrenzia aggregata Investigated by Computer Simulations.
2017
We performed quantum-chemical calculations, ab initio molecular dynamics, hybrid quantum mechanics/molecular mechanics (QM/MM) and enhanced sampling metadynamics simulations to investigate the origin of metal specificity in isatin hydrolase from Labrenzia aggregata. The peculiar octahedral binding geometry of the Mn2+ ion in the Michaelis complex includes both the isatin substrate and the catalytic water within the first coordination shell of the cation. Our calculations show that the same arrangement of the ligands cannot be efficiently achieved in the presence of other small divalent metal cations such as Zn2+ or Cu2+ . On the contrary, bulkier alkaline-earth cations such as Mg2+ , which …
All-Possible-Couplings Approach to Measuring Probabilistic Context.
2013
From behavioral sciences to biology to quantum mechanics, one encounters situations where (i) a system outputs several random variables in response to several inputs, (ii) for each of these responses only some of the inputs may "directly" influence them, but (iii) other inputs provide a "context" for this response by influencing its probabilistic relations to other responses. These contextual influences are very different, say, in classical kinetic theory and in the entanglement paradigm of quantum mechanics, which are traditionally interpreted as representing different forms of physical determinism. One can mathematically construct systems with other types of contextuality, whether or not …
Comparison of different theory models and basis sets in the calculation of 13C NMR chemical shifts of natural products.
2004
The influence of the calculation method in mimicking experimental 13C NMR chemical shifts of 15 low-polarity natural products singularly containing 10–20 carbon atoms was investigated by employing different quantum chemistry approaches and basis sets, both in the preliminary geometry optimizations and in the following single-point 13C GIAO calculations of the NMR chemical shifts. The geometries of the involved species were optimized at the PM3, HF, B3LYP and mPW1PW91 levels whereas the 13C NMR parameters were determined at the HF, B3LYP and mPW1PW91 levels. Different combinations of basis sets were also tested. The consistency and efficiency of the considered combinations of geometry optimi…