Fatty acid influence on zinc and uranyl ion binding to human serum albumin: an all atoms molecular dynamics investigation.

The potential health risks associated with radionuclides, particularly actinides, have prompted investigations into their interactions with body fluids in living organisms. Human serum albumin (HSA), a plenteous plasma protein with extraordinary binding capacities, is a key player in these interactions. The present study is intended at understanding the interplay between metal ions, namely, zinc and uranyl ions and fatty acids binding with HSA, using all atom equilibrium and non-equilibrium molecular dynamics simulations.

Experimental and theoretical validation for transmutation of palladium at electrochemical interfaces.

Electrolysis of DO may be used as a portable neutron source with numerous applications without the complexity of huge reactor operations. Herein, we report reproducible fast neutron generation by electrolysis of DO using palladium cathode and platinum anode, which was detected with diamond detector, gas filled He detectors after thermalisation with high density polythene, as well as novel epoxy resin and CR-39 detectors. Notably, a highly reproducible neutron generation at electrochemical surfaces of palladium electrode was observed and signature transmutation via Pd (d, n) Ag was corroborated.

Linkage Isomers of Triangular Pd Metallacycles and Catalysis in Aqueous Suzuki Coupling Reaction.

The water-soluble trinuclear Pd metallacycles [Pd(tmeda)(4-Spy)](X) (tmeda = tetramethylethylenediamine, X = OTf, ; NO, ) were synthesized from the ambidentate ligand 4-pyridylthiolate (Spy) and [Pd(tmeda)X] in 80 and 70% yield, respectively. Two possible linkage isomers are found in solution (slow interconversion found in the NMR) and in the solid state. Density functional calculations showed that the energy of the isomer with a D-symmetric arrangement of the SPy ligand and all Pd atoms having N∧NPdSN coordination is only 7 kcal/mol lower.

Binding of human serum albumin with uranyl ion at various pH: an all atom molecular dynamics study.

Uranium is routinely handled in various stages of nuclear fuel cycle and its association with human serum albumin (HSA) has been reported in literature, however, their binding characteristics still remains obscure. The present study aims to understand interaction of uranium with HSA by employing all atom molecular dynamics simulation of the HSA-metal ion complex. His67, His247 and Asp249 residues constitute the major binding site of HSA, which capture the uranyl ion (UO).

Heat-induced transitions of an empty minute virus of mice capsid in explicit water: all-atom MD simulation.

The capsid-like structure of the virus-based protein nanoparticles (NPs) can serve as bionanomaterials, with applications in biomedicines and nanotechnology. Release of packaged material from these nanocontainers is associated with subtle conformational changes of the NP structure, which , is readily accomplished by heating. Characterizing the structural changes as a function of temperature may provide fresh insights into nanomaterial/antiviral strategies.

Temperature Induced Dynamical Transition of Biomolecules in Polarizable and Nonpolarizable TIP3P Water.

Temperature induced dynamical transition (DT), associated with a sharp rise in molecular flexibility, is well-known to be exhibited between 270 and 280 K in glycerol to 200-230 K in hydrated biomolecules and is controlled by diffusivity (viscosity) of the solvation layer. In the molecular dynamics (MD) community, especially for water as a solvent, this has been an intense area of research despite decades of investigations. However, in general, water in these studies is described by empirical nonpolarizable force fields in which electronic polarizability is treated implicitly with effective charges and related parameters.

Xantphos-Capped Pd(II) and Pt(II) Macrocycles of Aryldithiolates: Structural Variation and Catalysis in C-C Coupling Reaction.

The self-assembly of Xantphos-capped M(OTf) (M = cis-[M'(Xantphos)]; M' = Pd, Pt) with bridging ligands 1,4-benezenedithiol or 4,4'-biphenyldithiol has been investigated. The reactions have yielded complexes [M{S(CH) SH}](OTf) (I) and [M{S(CH) S}](OTf) (II) ( n = 1 or 2). The equilibrium between I and II has been established in platinum complexes for n = 2, whereas the analogous Pd complex exclusively exist as II.

Effect of pH on the hinge region of influenza viral protein: a combined constant pH and well-tempered molecular dynamics study.

Despite the knowledge that the influenza protein, hemagglutinin, undergoes a large conformational change at low pH during the process of fusion with the host cell, its molecular mechanism remains elusive. The present constant pH molecular dynamics (CpHMD) study identifies the residues responsible for large conformational change in acidic condition. Based on the pKa calculations, it is predicted that His-106 is much more responsible for the large conformational change than any other residues in the hinge region of hemagglutinin protein.

Unbinding of fluorinated oxime drug from the AChE gorge in polarizable water: a well-tempered metadynamics study.

Despite the fact that fluorination makes a drug more lipophilic, the molecular level understanding of protein-fluorinated drug interactions is very poor. Due to their enhanced ability to penetrate the blood brain barrier, they are suitable for reactivation of organophosphorus inactivated acetylcholinesterase (AChE) in the central nervous system. We systematically studied the unbinding of fluorinated obidoxime (FOBI) and non-fluorinated obidoxime (OBI) from the active site gorge of the serine hydrolase AChE in mean field polarizable water by employing all atom molecular dynamics simulations.

An ab Initio Study on the Structure, Energetics, and Spectra of Cl···(CO) Clusters.

Structures, energetics, and photoelectron spectral properties of Cl···(CO) (n = 1-8) clusters are studied by ab initio electronic structure methods, namely, Møller-Plesset second-order perturbation theory (MP2) correlated consistent, aug-cc-pvtz basis functions. The most stable structure for each size is evaluated by using both bottom-up and top-down approaches. It is observed that CO molecules approach to the chloride anion in an asymmetric way except for Cl···(CO) cluster.

Ortho-7 bound to the active-site gorge of free and OP-conjugated acetylcholinesterase: cation-π interactions.

Despite the immense importance of cation-π interactions prevailing in bispyridinium drug acetylcholinesterase (AChE) complexes, a precise description of cation-π interactions at molecular level has remained elusive. Here, we consider a bispyridinium drug, namely, ortho-7 in three different structures of AChE, with and without complexation with organophosphorus (OP) compounds for detailed investigation using all atom molecular dynamics simulation. By quantum mechanical calculations, Y72, W86, Y124, W286, Y337, and Y341 aromatic residues of the enzyme are investigated for possible cation-π interactions with ortho-7.

A theoretical study on structures, energetics, and spectra of Br-.nCO2 clusters: towards bridging the gap between micro-domain and macro-domain.

Structures, energetics, and spectra of Br(-).nCO(2) (n = 1-8) clusters are studied based on ab initio electronic structure theory. The geometry of each size of clusters is evaluated by employing second-order Moller-Plesset (MP2) perturbation theory.

Conformationally averaged vertical detachment energy of finite size NO3(-)·nH2O clusters: a route connecting few to many.

We report conformationally averaged VDEs (VDE(w)(n)) for different sizes of NO(3)(-)·nH(2)O clusters calculated by using uncorrelated HF, correlated hybrid density functional (B3LYP, BHHLYP) and correlated ab intio (MP2 and CCSD(T)) theory. It is observed that the VDE(w)(n) at the B3LYP/6-311++G(d,p), B3LYP/Aug-cc-Pvtz and CCSD(T)/6-311++G(d,p) levels is very close to the experimentally measured VDE. It is shown that the use of calculated results of the conformationally averaged VDE for small-sized solvated negatively-charged clusters and a microscopic theory-based general expression for the same provides a route to obtain the VDE for a wide range of cluster sizes, including bulk.

Global minimum-energy structure and spectroscopic properties of I2(*-) x n H2O clusters: a Monte Carlo simulated annealing study.

The vibrational (IR and Raman) and photoelectron spectral properties of hydrated iodine-dimer radical-anion clusters, I(2)(*-) x n H(2)O (n=1-10), are presented. Several initial guess structures are considered for each size of cluster to locate the global minimum-energy structure by applying a Monte Carlo simulated annealing procedure including spin-orbit interaction. In the Raman spectrum, hydration reduces the intensity of the I-I stretching band but enhances the intensity of the O-H stretching band of water.