Search results for "molecular dynamics"
showing 10 items of 1075 documents
Reversible hydrogen bond network dynamics: molecular dynamics simulations of calix[4]arene-catenanes.
2011
We present detailed molecular dynamics (MD) simulations of mechanically interlocked calix[4]arene-catenanes under external force. Single-molecule force spectroscopy experiments revealed that the separation of dimers with two aliphatic loops results in reversible hydrogen bond breakage through an intermediate in a triple-well potential, while the tetra-loop species separates in a one-step manner (Janke, M.; et al. Nat. Nanotechnol. 2009, 4, 225). MD simulations show that calix[4]arenes interlocked by four loops (1) display a complete restructuring of the hydrogen bond network under mechanical force. All hydrogen bonds of the closed structure open, and new ones are formed in the extended stru…
Metal complex-DNA binding: Insights from molecular dynamics and DFT/MM calculations.
2012
Molecular dynamics (MD) simulations, followed by density functional theory/molecular mechanics (DFT/MM) calculations, provided a detailed structure of the binding site between the cationic metallointercalator (dipyrido [3,2-a:2',3'-c]phenazine)(glycinato)copper(II), [Cu(gly)(dppz)](+), and the two dodeca-deoxynucleotide duplexes [dodeca(dG-dC)]2 and [dodeca(dA-dT)]2. Three simultaneous DNA binding types were detected in the fully optimized DFT/MM structures: 1) metal coordination through exocyclic oxygen atoms of nitrogen bases; 2) intercalation of the dppz chromophore between stacked Watson-Crick AT-AT and GC-GC bases; and 3) hydrogen bonding between the glycinato ligand and amine groups o…
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 …
N- and O-methylation of sphingomyelin markedly affects its membrane properties and interactions with cholesterol
2011
We have prepared palmitoyl sphingomyelin (PSM) analogs in which either the 2-NH was methylated to NMe, the 3-OH was methylated to OMe, or both were methylated simultaneously. The aim of the study was to determine how such modifications in the membrane interfacial region of the molecules affected interlipid interactions in bilayer membranes. Measuring DPH anisotropy in vesicle membranes prepared from the SM analogs, we observed that methylation decreased gel-phase stability and increased fluid phase disorder, when compared to PSM. Methylation of the 2-NH had the largest effect on gel-phase instability (T(m), was lowered by similar to 7 degrees C). Atomistic molecular dynamics simulations sho…
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…
Thermal evolution of the CO stretching band in carboxy-myoglobin in the light of neutron scattering and molecular dynamics simulations
2008
Abstract As it is well known, the thermal behaviour of the CO stretching band in MbCO reflects the interconversion among protein’s taxonomic and lower tier substates. We compare here FTIR data on the thermal behaviour of the CO stretching band in MbCO embedded in non-liquid, water–trehalose matrixes, and neutron scattering data on dry and hydrated proteins and nucleic acids. The comparison, also in the light of simulative data, gives relevant information on the relationship between the mean square displacements of hydrogen atoms and the heme pocket thermal rearrangements in MbCO, as experienced by the bound CO, in the temperature region 100–200 K, and at higher temperature when large scale …
H2 hitting on graphene supported palladium cluster: molecular dynamics simulations
2016
Dissociative adsorption of impinging gas-phase molecular hydrogen (H2) on a palladium cluster (Pd4) supported on defective graphene (C47) was studied by periodic density functional theory molecular dynamics simulations. The H2 on Pd4/C47 collision dynamics were investigated without any particular constraint, except for the Born–Oppenheimer approximation. The study, which had mostly method-testing aims, provided, anyway, valuable information about the collision kinetics of gas-phase molecular hydrogen. This was treated as an impacting projectile having different kinetic energy values. At lower kinetic energies, sticking was ruled by steering effects imputable to the Pd cluster that easily re…