Search results for " MOLECULAR DYNAMICS"
showing 10 items of 126 documents
CO rebinding kinetics and molecular dynamics simulations highlight dynamic regulation of internal cavities in human cytoglobin
2013
Abstract: Cytoglobin (Cygb) was recently discovered in the human genome and localized in different tissues. It was suggested to play tissue-specific protective roles, spanning from scavenging of reactive oxygen species in neurons to supplying oxygen to enzymes in fibroblasts. To shed light on the functioning of such versatile machinery, we have studied the processes supporting transport of gaseous heme ligands in Cygb. Carbon monoxide rebinding shows a complex kinetic pattern with several distinct reaction intermediates, reflecting rebinding from temporary docking sites, second order recombination, and formation (and dissociation) of a bis-histidyl heme hexacoordinated reaction intermediate…
Simulations of Glassforming Network Fluids: Classical Molecular Dynamics versus Car-Parrinello Molecular Dynamics
2010
Abstract Static and dynamic Properties of molten germanium dioxide are studied by two simulation methods, classical Molecular Dynamics (MD) using the Oeffner-Elliott (OE) potential, and “ab initio” Car-Parrinello Molecular Dynamics (CPMD). While CPMD provides a (presumably) more accurate description of the local structure and the forces, it severely suffers from finite size effects when the structure beyond the first neighbor shells is considered. For glassforming fluids, the demanding equilibrium needs are a further reason, why simply MD is still preferable, when a “good” effective potential is available.
Liquid structure of a water-based, hydrophobic and natural deep eutectic solvent: The case of thymol-water. A Molecular Dynamics study
2022
The structural organization of the first example of a water-based, type V, hydrophobic, natural deep eutectic solvent (DES) is investigated in this work, exploiting the synergy of X-ray scattering and compu- tational techniques. The stoichiometric mixture of thymol:water (4.8:1) has been recently reported to behave as a DES, with a melting point at 6 C, well below the one foreseen for the ideal liquid mixture. Our study provides an atomistic insight into the structural correlations in this system, highlighting the major role played by hydrogen bonding (HB) correlations in affecting morphology as well as the solid– liquid equilibrium. Thymol engages HB-mediated interactions with both thymol …
Structure and vibrational features of the protic ionic liquid 1,8-diazabicyclo[5.4.0]-undec-7-ene-8-ium bis(trifluoromethanesulfonyl)amide, [DBUH][TF…
2022
Abstract The Protic Ionic Liquid (PIL) formed by neutralization of the super-strong base 1,7-diazabicyclo[5.4.0]undec-7-ene (DBU) with the super-strong acid bis(trifluoromethanesulfonyl)-imide (TFSI), indicated as [DBUH][TFSI], has been investigated. Its chemical physical properties and structural features have been explored using a synergy of experimental and computational tools. Molecular Dynamics-rationalised X-ray diffraction patterns highlight the major role played by hydrogen bonding (HB) in affecting morphology in this PIL. A comparison between HB features in this and in related PILs has been presented, on the base of far-IR experiments and DFT analysis. Indications of a weaker HB in…
Molecular dynamics simulations of elementary chemical processes in liquid water using combined density functional and molecular mechanics potentials.…
1997
The first molecular dynamics (MD) simulation of a chemical process in solution with an ab initio description of the reactant species and a classical representation of the solvent is presented. We study the dynamics of proton (deuterium) transfer in strongly hydrogen-bonded systems characterized by an energy surface presenting a double well separated by a low activation barrier. We have chosen the hydroxyl-water complex in liquid water to analyze the coupling between the reactive system and the environment. The proton is transferred from one well to the other with a frequency close to 1 ps−1 which is comparable to the low-frequency band associated to hindered translations, diffusional transl…
Ab initio molecular dynamics study of overtone excitations in formic acid and its water complex
2018
In this article, we present results from ab initio molecular dynamics simulation of overtone excitation in formic acid monomer and its water complex in the gas phase. For the monomer, a conformation change is observed employing both OH and CH vibrational excitations, which supports experimental findings. In the formic acid–water complex, interconversion also takes place, but it proceeds via hydrogen exchange rather than via intramolecular reaction. Simulations raise a question on effect of quantum and matrix effects to the results. Also, a brief test of different computation methods was done on the system. peerReviewed
Vibrational Signature of Water Molecules in Asymmetric Hydrogen Bonding Environments
2013
The O–H stretching vibrational modes of water molecules are sensitive to their local environments. Here, we applied effective normal-mode analysis to isolate contributions of each of the two hydrogen atoms to the vibrational modes ν1 and ν3 of water molecules in the liquid phase. We demonstrate that the decoupling of the two contributions fd and the frequency splitting of the vibrational modes Δω13 are inextricably related to the symmetry of the hydrogen bonding environment. We show that ambient liquid water modeled at the density functional level of theory exhibits the characteristics of an asymmetric environment with an average decoupling of 0.82 and a splitting of 137 inverse centimeters…
Construction and characterization of models of hypercrosslinked polystyrene
2012
A simple algorithm involving classical molecular dynamics (MD) simulations is here suggested to build up models of hypercrosslinked polystyrene showing macroporous structure. The algorithm is composed by three consecutive stages: MD simulation of a single polystyrene coil, crosslink formation, and finally relaxation of the structure. The models, which are differentiated by the crosslinker concentration in the initial polystyrene chain, can be characterized by employing tools of the small angle neutron scattering analysis and procedures associated to the crosslinking algorithm, which allows one to discriminate among the different kinds of crosslinks between phenyl rings and to calculate the …
Liquid structure and dynamics in the choline acetate:urea 1:2 deep eutectic solvent
2021
We report on the thermodynamic, structural, and dynamic properties of a recently proposed deep eutectic solvent, formed by choline acetate (ChAc) and urea (U) at the stoichiometric ratio 1:2, hereinafter indicated as ChAc:U. Although the crystalline phase melts at 36-38 degrees C depending on the heating rate, ChAc:U can be easily supercooled at sub-ambient conditions, thus maintaining at the liquid state, with a glass-liquid transition at about -50 degrees C. Synchrotron high energy x-ray scattering experiments provide the experimental data for supporting a reverse Monte Carlo analysis to extract structural information at the atomistic level. This exploration of the liquid structure of ChA…
Exploring the non-covalent ligand-binding mechanism on immunoproteasome by enhanced Molecular Dynamics
2021
Selective inhibition of immunoproteasome is a valuable strategy to treat autoimmune and inflammatory diseases, and hematologic malignancies. In particular, non-covalent inhibition is strongly desirable because it is free of the drawbacks and side effects associated with covalent inhibition. Recently, a new series of amide derivatives with Ki values in the low/submicromolar ranges toward the β1i subunit have been identified as non-covalent inhibitors 1 . We investigated the binding mechanism of the most potent and selective inhibitor (1) to elucidate the steps from the ligand entrance into the binding pocket to the ligand-induced conformational changes. We carried out a total of 400ns of MD-…