We present a novel approach to explore the conformational space of globular proteins near their native state. It combines advantages coarse-grained models with those all-atoms simulations, required treat molecular recognition processes. The comparison between calculated structural properties obtained dynamics simulations establishes accuracy model. Our method has potential be extended processes in systems whose characteristic size and time scale prevent an analysis based on dynamics.

More than 100 years since its discovery, the mechanism of Grignard reaction remains unresolved. Ambiguities arise from concomitant presence multiple organomagnesium species and competing mechanisms involving either nucleophilic addition or formation radical intermediates. To shed light on this topic, quantum-chemical calculations ab initio molecular dynamics simulations are used to study CH3MgCl in tetrahydrofuran with acetaldehyde fluorenone as prototypical reagents. All coexisting solution...

Significance This study resolves a long-standing question about the ability of humans to perceive near infrared radiation (IR) and identifies mechanism driving human IR vision. A few previous reports our expanded psychophysical studies here reveal that can detect at wavelengths longer than 1,000 nm it as visible light, finding has not received satisfactory physical explanation. We show light activates photoreceptors through nonlinear optical process. also caused photoisomerization purified...

The fundamental interactions underlying citrate-mediated chemical stability of metal nanoparticles, and their surface characteristics dictating particle dispersion/aggregation in aqueous solutions, are largely unclear. Here, we developed a theoretical model to estimate the stoichiometry small, charged ligands (like citrate) chemisorbed onto spherical metallic nanoparticles coupled it with atomistic molecular dynamics simulations define uncovered solvent-accessible area nanoparticle. Then,...

To better understand the complex photophysics of amino acid tryptophan, which is widely used as a probe protein structure and dynamics, we have measured electronic spectra protonated, gas-phase tryptophan solvated with controlled number water molecules cooled to ∼10 K. We observe that, even at this temperature, bare molecule exhibits broad spectrum, implying ultrafast, nonradiative decay excited state. Surprisingly, addition two sufficiently lengthens excited-state lifetime that obtain fully...

We have coupled hybrid quantum mechanics (density functional theory; Car-Parrinello)/molecular molecular dynamics simulations to a grand-canonical scheme, calculate the in situ redox potential of Cu(2+) + e(-) --> Cu(+) half reaction azurin from Pseudomonas aeruginosa. An accurate description at atomistic level environment surrounding metal-binding site and finite-temperature fluctuations protein structure are both essential for correct quantitative electronic properties this system. report...

Viral disinfection kinetics have been studied in depth, but the molecular-level inactivation mechanisms are not understood. Consequently, it is difficult to predict behavior of nonculturable viruses, even when related, culturable viruses available. The objective this work was determine how small differences composition viral genome and proteins impact disinfection. To end, we investigated three related bacteriophages (MS2, fr, GA) by UV254, singlet oxygen ((1)O2), free chlorine (FC), dioxide...

The Schlenk equilibrium is a complex reaction governing the presence of multiple chemical species in solution Grignard reagents. full characterization at molecular level transformation CH3MgCl into MgCl2 and Mg(CH3)2 tetrahydrofuran (THF) by means ab initio dynamics simulations with enhanced-sampling metadynamics presented. occurs via formation dinuclear bridged chlorine atoms. At room temperature, different involved accept solvation structures, two to four THF molecules that can coordinate...

A new strategy for the development of a compactly fused tetrathiafulvalene (TTF)-based sensitizer is reported, leading to best performance date TTF-sensitized solar cells.

The shape and size of self-assembled structures upon local organization their molecular building blocks are hard to predict in the presence long-range interactions. Combining small-angle X-ray/neutron scattering data, theoretical modelling, computer simulations, sodium dodecyl sulfate (SDS), over a broad range concentrations ionic strengths, was investigated. Computer simulations indicate that micellar changes associated with different binding counterions. By employing toy model based on...

The solubilization mechanism of lipid membranes in the presence Triton X-100 (TX-100) is investigated at molecular resolution using dynamics (MD) simulations. Thanks to large time and length scales accessible by hybrid particle-field formulation models employed here, complex process membrane has been studied, with goal verifying three stage model reported literature. DPPC bilayers vesicles have studied different concentrations TX-100 detergent employing coarse grained (CG) models. Systems up...

Abstract For decades, it was considered all but impossible to perform Stark spectroscopy on molecules in a liquid solution, because their concomitant orientation the applied electric field results overwhelming background signals. A way out immobilize solute by freezing solvent. While mitigating orientation, removes possibility study environments at ambient conditions. Here we demonstrate time-resolved THz spectroscopy, utilizing intense single-cycle terahertz pulses as source. At...

Abstract The centromere is a part of the chromosome that essential for even segregation duplicated chromosomes during cell division. It epigenetically defined by presence histone H3 variant CENP-A. CENP-A associates specifically with group 16 proteins form centromere-associated network (CCAN). In mitosis, kinetochore forms on CCAN to connect microtubules protruding from poles. Previous studies have shown replaces in nucleosomes, and recently structures CENP-A-containing nucleosomes complex...

Organozinc reagents play a critical role in synthesis, yet our comprehension of their structure-reactivity relationships is limited by lack information about structures solution. This study introduces computational workflow, validated X-ray absorption spectroscopy, to investigate organozinc The solvation states ZnCl2, ZnMeCl and ZnMe2 were explored using ab initio molecular dynamics (metadynamics Blue Moon sampling) within an explicit solvent cage. revealed the existence various at room...

Antimicrobial peptides (AMPs) are highly effective broad-spectrum antibiotics, found as components of the immune system in almost all forms life. It is well established that their primary target cell membrane where they hypothesized to permeabilize bilayer. However, it a long-standing question whether stable transmembrane and structural pores necessary, or if through transient channels. Here this addressed with simultaneous characterization structure, peptide partitioning, ion transport real...

The biological function of the aspartic protease from HIV-1 has recently been related to conformational flexibility its structural scaffold. Here, we use a multistep strategy investigate whether same mechanism affects functionality in pepsin-like fold. (i) We identify set conserved residues by using sequence-alignment techniques. These cluster three distinct regions: near cleavage-site cavity, four beta-sheets cross-linking two lobes, and solvent-exposed region below long beta-hairpin...

We present ab initio calculations of the excited state properties liquid water in framework many-body Green's function formalism. Snapshots taken from molecular dynamics simulations are used as input geometries to calculate electronic and optical spectra, results averaged over different configurations. The absorption spectra with inclusion excitonic effects calculated by solving Bethe-Salpeter equation. insensitivity screening a particular configuration make these feasible. resulting which...

Abstract The three‐component reaction of aryl boronic acids with 1,2,4,5‐tetrahydroxybenzene and 1,2‐bis(4‐pyridyl)ethylene or 4,4′‐bipyridine leads to the formation dark‐purple boronate ester polymers. Crystallographic analyses show that polymer strands have a zig–zag geometry, bis(dioxaborole) units are connected by dipyridyl linkers through dative B–N interactions. Upon dissolution polymers in hot chloroform, most connections broken, which indicates is reversible process. A computational...

We introduce a nonradial potential term for coarse-grained (CG) molecular simulations of proteins. This mimics the backbone dipole-dipole interactions and accounts needed directionality to form stable folded secondary structure elements. show that α-helical β-sheet peptide chains are correctly described in dynamics without need introducing any priori bias potentials or ad hoc parametrizations, which limit broader applicability CG Moreover, our model is able catch formation supersecondary...

Basic understanding of the means by which multidrug efflux systems can efficiently recognize and transport drugs constitutes a fundamental step toward development compounds able to tackle continuous outbreak new bacterial strains resistant traditional antibiotics. We applied series computational techniques, from molecular docking dynamics simulations free energy estimate methods, determine differences in binding properties imipenem meropenem, two potent antibiotics carbapenem family, MexB,...

Abstract Much research has been dedicated to understanding the molecular basis of UV damage biomolecules, yet many questions remain regarding specific pathways involved. Here we describe a genome‐mediated mechanism that causes site‐specific virus protein cleavage upon irradiation. Bacteriophage MS2 was disinfected with 254 nm UV, and characterized ESI‐ MALDI‐based FT‐ICR, Orbitrap, TOF mass spectroscopy. Top‐down spectrometry products identified backbone site as Cys46–Ser47 in capsid...

Molecular dynamics simulations were used to study the effect of mechanical and thermal stimuli on electrostatic properties collagen model helices. Our sequences based glycine proline hydroxyproline amino acids. We find that longitudinal strain induces significant variation polarization fibril. Such a phenomenon is determined by reorientation backbone polar groups, which are free respond solicitation. This non-negligible facilitated peculiar folding structure helix, characterized absence an...

Cellular membranes are fundamental constituents of living organisms. Apart from defining the boundaries cells, they involved in a wide range biological functions, associated with both their structural and dynamical properties. Biomembranes can undergo large-scale transformations when subject to specific environmental changes, including gel-liquid phase transitions, change aggregation structure, formation microtubules, or rupture into vesicles. All these processes dependent on delicate...

We present HylleraasMD (HyMD), a comprehensive implementation of the recently proposed Hamiltonian formulation hybrid particle-field molecular dynamics. The methodology is based on tunable, grid-independent length-scale coarse graining, obtained by filtering particle densities in reciprocal space. This enables systematic convergence energies and forces grid refinement, also eliminating nonphysical force aliasing. Separating time integration fast modes associated with internal motion from...

Hybrid particle–field molecular dynamics is a simulation strategy, wherein particles couple to density field instead of through ordinary pair potentials. Traditionally considered mean-field theory, momentum and energy-conserving hybrid formalism has recently been introduced, which was demonstrated approach the Gaussian Core model potential in grid-converged limit. Here, we expand on generalize correspondence between Hamiltonian method particle–particle Using spectral procedure suggested by...