Search results for "molecular dynamics"

Elucidating the ligand shell structure and dynamics of Au683MBA32 gold nanocluster using molecular dynamics simulations

2017

Synthesising novel gold nanoparticles and -clusters can be often easier than characterising them, and after experimental analysis many options for the possible molecular formula of the cluster may remain as equally valid options. These options may be investigated by quantum computational means, such as density functional theory, but since DFT includes the electronic interactions, this might take time and excessive effort if the amount of options is large. In this thesis a new way of easing the computational task is introduced by a novel method, that combines a guessing algorithm and molecular dynamics simulations. The algorithm produces possible structures by utilising existing structures o…

Virtual screening : development of a novel structure-based method

2013

The electric properties of ionic solutions: a molecular dynamics (preliminary) study

2011

Best Practices in Constant pH MD Simulations: Accuracy and Sampling

2022

Various approaches have been proposed to include the effect of pH in molecular dynamics (MD) simulations. Among these, the λ-dynamics approach proposed by Brooks and co-workers [Kong, X.; Brooks III, C. L. J. Chem. Phys.1996, 105, 2414−2423] can be performed with little computational overhead and hfor each typeence be used to routinely perform MD simulations at microsecond time scales, as shown in the accompanying paper [Aho, N. et al. J. Chem. Theory Comput.2022, DOI: 10.1021/acs.jctc.2c00516]. At such time scales, however, the accuracy of the molecular mechanics force field and the parametrization becomes critical. Here, we address these issues and provide the community with guidelines on…

Molecular dynamics simulations of heavy ion induced defects in SiC Schottky diodes

2018

Heavy ion irradiation increases the leakage current in reverse-biased SiC Schottky diodes. This letter demonstrates, via molecular dynamics simulations, that a combination of bias and ion-deposited energy is required to produce the degradation. Peer reviewed

Targeting Orthosteric and Allosteric Pockets of Aromatase via Dual-Mode Novel Azole Inhibitors

2020

[Image: see text] Breast cancer (BC) is the most diffused cancer type in women and the second leading cause of death among the female population. Effective strategies to fight estrogen responsive (ER+) BC, which represents 70% of all BC cases, rely on estrogen deprivation, via the inhibition of the aromatase enzyme, or the modulation of its cognate estrogen receptor. Current clinical therapies significantly increased patient survival time. Nevertheless, the onset of resistance in metastatic BC patients undergoing prolonged treatments is becoming a current clinical challenge, urgently demanding to devise innovative strategies. In this context, here we designed, synthesized, and performed in …

Structural, Thermodynamic, and Kinetic Traits of Antiestrogen-Compounds Selectively Targeting the Y537S Mutant Estrogen Receptor α Transcriptional Ac…

2019

The most frequently diagnosed cancers in women are the estrogen receptor (ER)-positive breast cancer subtypes, which are characterized by estrogen dependency for their growth. The mainstay of clinical treatment for this tumor relies on the modulation of ER action or on the suppression of estrogen biosynthesis via the administration of Selective ERα Modulators/Down-regulators (SERMs/SERDs) or aromatase inhibitors, respectively. Nevertheless, de novo and acquired resistance to these therapies frequently occurs and represents a major clinical concern for patient survival. Recently, somatic mutations affecting the hormone-binding domain of ERα (i. e. Y537S, Y537N, D538G) have been associated w…

Atomistic MD simulation of proteins in complex solvents

2009

Case-specific performance of MM-PBSA, MM-GBSA, and SIE in virtual screening.

2015

In drug discovery the reliable prediction of binding free energies is of crucial importance. Methods that combine molecular mechanics force fields with continuum solvent models have become popular because of their high accuracy and relatively good computational efficiency. In this research we studied the performance of molecular mechanics generalized Born surface area (MM-GBSA), molecular mechanics Poisson-Boltzmann surface area (MM-PBSA), and solvated interaction energy (SIE) both in their virtual screening efficiency and their ability to predict experimentally determined binding affinities for five different protein targets. The protein-ligand complexes were derived with two different app…

A magnetic look into the protecting layer of Au25 clusters

2016

The field of molecular metal clusters protected by organothiolates is experiencing a very rapid growth. So far, however, a clear understanding of the fine interactions between the cluster core and the capping monolayer has remained elusive, despite the importance of the latter in interfacing the former to the surrounding medium. Here, we describe a very sensitive methodology that enables comprehensive assessment of these interactions. Pulse electron nuclear double resonance (ENDOR) was employed to study the interaction of the unpaired electron with the protons of the alkanethiolate ligands in four structurally related paramagnetic Au25(SR)0 18 clusters (R ¼ ethyl, propyl, butyl, 2-methylpro…