Search results for " MOLECULAR DYNAMICS"
showing 10 items of 126 documents
Magic triangular and tetrahedral clusters
1997
Using the methods of density functional theory and the jellium model we show that clusters with triangular [in two dimensions (2D)] or tetrahedral [in three dimensions (3D)] shapes have a strong shell structure and enhanced stability. Moreover, the shell closings correspond to the lowest magic numbers of a 2D and 3D harmonic oscillator and at the same time to the number of divalent atoms in close-packed triangles and tetrahedrons. Ab initio molecular dynamics simulations for Na and Mg clusters support the results of the jellium model.
Revisiting the Nonadiabatic Process in 1,2-Dioxetane.
2015
Determining the ground and excited-state decomposition mechanisms of 1,2-dioxetane is essential to understand the chemiluminescence and bioluminescence phenomena. Several experimental and theoretical studies has been performed in the past without reaching a converged description. The reason is in part associated with the complex nonadiabatic process taking place along the reaction. The present study is an extension of a previous work (De Vico, L.; Liu, Y.-J.; Krogh, J. W.; Lindh, R. J. Phys. Chem. A 2007, 111, 8013-8019) in which a two-step mechanism was established for the chemiluminescence involving asynchronous O-O' and C-C' bond dissociations. New high-level multistate multi configurati…
Recent advances in computational design of potent aromatase inhibitors: open-eye on endocrine-resistant breast cancers.
2019
Introduction: The vast majority of breast cancers (BC) are estrogen receptor positive (ER+). The most effective treatments to fight this BC type rely on estrogen deprivation therapy, by inhibiting the aromatase enzyme, which performs estrogen biosynthesis, or on blocking the estrogens signaling path via modulating/degrading the estrogen's specific nuclear receptor (estrogen receptor-?, ER?). While being effective at early disease stage, patients treated with aromatase inhibitors (AIs) may acquire resistance and often relapse after prolonged therapies. Areas covered: In this compendium, after an overview of the historical development of the AIs currently in clinical use, and of the computati…
A quantum mechanics-molecular mechanics study of dissociative electron transfer : The methylchloride radical anion in aqueous solution
2002
The dissociative electron transfer reaction CH3Cl+e−→CH3•+Cl− in aqueous solution is studied by using a QM/MM method. In this work the quantum subsystem (a methylchloride molecule plus an electron) is described using density functional theory while the solvent (300 water molecules) is described using the TIP3P classical potential. By means of molecular dynamics simulations and the thermodynamic integration technique we obtained the potential of mean force (PMF) for the carbon–chlorine bond dissociation of the neutral and radical anion species. Combining these two free energy curves we found a quadratic dependence of the activation free energy on the reaction free energy in agreement with Ma…
Ab Initio Liquid Water Dynamics in Aqueous TMAO Solution
2015
Ab initio molecular dynamics (AIMD) simulations in trimethylamine N-oxide (TMAO)-D2O solution are employed to elucidate the effects of TMAO on the reorientational dynamics of D2O molecules. By decomposing the O-D groups of the D2O molecules into specific subensembles, we reveal that water reorientational dynamics are retarded considerably in the vicinity of the hydrophilic TMAO oxygen (O(TMAO)) atom, due to the O-D···O(TMAO) hydrogen-bond. We find that this reorientational motion is governed by two distinct mechanisms: The O-D group rotates (1) after breaking the O-D···O(TMAO) hydrogen-bond, or (2) together with the TMAO molecule while keeping this hydrogen-bond intact. While the orientatio…
The Catalytic Mechanism of Steroidogenic Cytochromes P450 from All-Atom Simulations: Entwinement with Membrane Environment, Redox Partners, and Post-…
2019
Cytochromes P450 (CYP450s) promote the biosynthesis of steroid hormones with major impact on the onset of diseases such as breast and prostate cancers. By merging distinct functions into the same catalytic scaffold, steroidogenic CYP450s enhance complex chemical transformations with extreme efficiency and selectivity. Mammalian CYP450s and their redox partners are membrane-anchored proteins, dynamically associating to form functional machineries. Mounting evidence signifies that environmental factors are strictly intertwined with CYP450s catalysis. Atomic-level simulations have the potential to provide insights into the catalytic mechanism of steroidogenic CYP450s and on its regulation by e…
New fitting scheme to obtain effective potential from Car-Parrinello molecular dynamics simulations: Application to silica
2008
A fitting scheme is proposed to obtain effective potentials from Car-Parrinello molecular dynamics (CPMD) simulations. It is used to parameterize a new pair potential for silica. MD simulations with this new potential are done to determine structural and dynamic properties and to compare these properties to those obtained from CPMD and a MD simulation using the so-called BKS potential. The new potential reproduces accurately the liquid structure generated by the CPMD trajectories, the experimental activation energies for the self-diffusion constants and the experimental density of amorphous silica. Also lattice parameters and elastic constants of alpha-quartz are well-reproduced, showing th…
Short hydrogen bonds enhance nonaromatic protein-related fluorescence
2021
Significance Intrinsic fluorescence of nonaromatic amino acids is a puzzling phenomenon with an enormous potential in biophotonic applications. The physical origins of this effect, however, remain elusive. Herein, we demonstrate how specific hydrogen bond networks can modulate fluorescence. We highlight the key role played by short hydrogen bonds, present in the protein structure, on the ensuing fluorescence. We provide detailed experimental and molecular evidence to explain these unusual nonaromatic optical properties. Our findings should benefit the design of novel optically active biomaterials for applications in biosensing and imaging.
Visualizing Solubilization by a Realistic Particle Model in Chemistry Education
2019
An application for the visualization of the mixing process of two different types of structureless interacting particles is presented. The application allows to demonstrate on a qualitative basis, as well as by quantitatively monitoring the time evolution of the fractions of aggregates of different sizes, that the formation of a homogeneous mixture is the result of favorable solute-solvent interactions as well as by temperature. It is suggested that, along with the use of suitable macroscopic examples, visualizations by the present application are useful in elucidating concepts related to miscibility/solubility. The application is based on a two-dimensional realistic dynamic model where ato…
Combined spectroscopic and theoretical analysis of the binding of a water-soluble perylene diimide to DNA/RNA polynucleotides and G-quadruplexes.
2021
We present here a combined spectroscopic and theoretical analysis of the binding of N,N’-bis(2-(1-piperazino)ethyl)-3,4,9,10-perylenetetracarboxylic acid diimide dichloride (PZPERY) to different biosubstrates. Absorbance titrations and circular dichroism experiments, melting studies and isothermal calorimetry (ITC) titrations reveal a picture where the binding to natural double-stranded DNA is very different from that to double and triple-stranded RNAs (poly(A)∙poly(U) and poly(U)∙poly(A)⁎poly(U)). As confirmed also by the structural and energetic details clarified by density functional theory (DFT) calculations, intercalation occurs for DNA, with a process driven by the combination of aggr…