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Ab initio molecular dynamics simulations were performed in order to study chemisorption, electronic properties, and desorption of glycine at wet pyrite surfaces focusing on the role of surface point defects. Results showed that the formation of such point defects has an appreciable impact on the electronic structure and reactivity of this surface.

Using density functional theory study was conducted on the interaction of alkanethiolates with small coinage metal clusters of copper and gold. The relativistic origin of differences between Cu and Au is discussed, and an analysis ob bonding considerations is presented.

Isomers of 2-(2',4'-dinitrobenzyl)-pyridine (DNBP) in both the gas phase and the crystalline phase were investigated.

In this Focus Review, we put the spotlight on very recent insights into the fascinating world of wet chemistry in the realm offered by nanoconfinement of water in mechanically rather rigid and chemically inert planar slit pores wherein only monolayer and bilayer water lamellae can be hosted. We review the effect of confinement on different aspects such as hydrogen bonding, ion diffusion, and charge defect migration of H+(aq) and OH–(aq) in nanoconfined water depending on slit pore width. A particular focus is put on the strongly modulated local dielectric properties as quantified in terms of anisotropic polarization fluctuations across such extremely confined water films and their putative effects on chemical reactions therein. The stunning findings disclosed only recently extend wet chemistry in particular and solvation science in general toward extreme molecular confinement conditions. [ABSTRACT FROM AUTHOR]

Car-Parrinello molecular dynamics are used to study the mechanism of specific acid-catalyzed glycosidic bond formation between methanol and alpha-D-glucopyranoside in aqueous solution at 300 K. The reaction proceeded through a non-solvent equilibrated oxacarbenium cation intermediate characterized by the loss of a hydrogen-bonding interaction between the ring oxygen and solvating water.

The analysis on the role played by aliphatic polymer chains in the transduction of external forces to mechanophores being at the heart of force spectroscopy and sonication experiments is presented. The studies have highlighted the necessity of considering the polymer chains explicitly when thinking about mechanochemical manipulation and have also announced the possibility of tuning the properties of mechanoresponsive polymers by tailoring the force-transducing chain molecules.

Ab initio molecular dynamics are used for examining the mechanisms and free energetics underlying the formation of peptides from [alpha]-amino acids and [alpha]-amino acid N-carboxyanhydrides (NCAs) in bulk water at both ambient and extreme temperatures. The results have helped in understanding the affect of elevated temperatures and increased pressures on organic reactions in aqueous solutions and also on peptide bond formation and peptide hydrolysis in aqueous media.

The ab initio molecular dynamics studies are conducted to explain the various mechanisms involved in the activation of amino acids in bulk water in ambient, as well as extreme temperature-pressure thermodynamic conditions. The analysis proves that the formation of such activated species is highly favored by the extreme conditions.

Peptide synthesis is examined in various aqueous environments, which has provided details of free energy profiles and pathways that are at the center of amino acid activation via N-carboxyanhydrides (NCAs) and subsequent elongation. Pyrite surfaces have acted as catalysts, thus leading to remarkable reductions of free energy barriers by scaffolding immobilization of reactants.

Ab initio molecular dynamics simulations are used for studying the properties of perdeuterated HCl[([H.sub.2]O).sub.n] aggregates with n = 1, 2, ..., 6 water molecules. Zwitterionic species have shown differences in the hydronium region, whereas the D-Cl stretching regime has distinguished neutral aggregates.

The inverse temperature transition of a biomimetic model for elastin, capped GVG(VPGVG) in liquid water is investigated with a comprehensive classical molecular dynamics study. The temperature dependence of the solvation structure and dynamics of the octapeptide are compared using three common force fields, CHARMM, GROMOS, and OPLS.

Three popular density functionals have been used to perform a virtual experiment on how different proposed solvation patterns for OH-(aq) influence the microscopic transport mechanism. It suggests that the solvation pattern of OH (super -) (aq) is not analogues to that of H+ (aq), implying that its structural diffusion mechanism cannot be a simple mirror image picture of the later.

On the basis of ab initio Gibbs ensemble Monte Carlo simulations, we map the liquid-vapor phase diagram of water described by the RPBE density functional supplemented by D3 dispersion corrections and estimate the critical point by density extrapolation. Knowing the approximate location of the critical point, two sets of ab initio molecular dynamics simulations at gas-like and liquid-like densities deep in the supercritical phase of water are carried out where particular attention is payed to ergodic sampling in view of large correlation lengths and long correlation times. Structural, H-bonding, and dipolar properties of RPBE-D3 water are analyzed along the liquid-vapor coexistence curve upon moving toward the critical point and compared to those in the supercritical state. The properties of high-density supercritical water are astonishingly similar to those of the liquid on the coexistence curve under subcritical conditions at comparable density. Upon decomposing the molecular dipole moments into purely configurational and electronic polarization/charge-transfer contributions, it is demonstrated that the latter play a decreasing role in liquid water upon approaching the critical point on the coexistence curve. Moreover, these many-body effects are systematically suppressed in supercritical water due to the significantly reduced H-bonding network. [ABSTRACT FROM AUTHOR]

The Staudinger reaction yielding β-lactam rings via [2 + 2] cycloaddition is a torquoselective reaction where the stereochemistry of the product can be steered by suitable substituents. Although the mechanochemical ring-opening of β-lactams has been investigated recently, the force-assisted synthesis of this important functional four-ring motif remains unexplored. As it will be computationally demonstrated, mechanochemical activation greatly reduces the barrier of the rate-limiting ring-closure step while, at the same time, preserves its torquoselectivity. This finding strongly suggests that strained four-membered rings can be readily incorporated in chain molecules using sonication techniques that greatly enhance reactivity while conserving selectivity. [ABSTRACT FROM AUTHOR]

Ab initio molecular dynamics (MD) simulations of the amino acid, glycine at the water/pyrite interface, which can be carried out at the Iron-Sulfur World (ISW) is used for understanding the pyrite assisted peptide bond formation, which is the adsorption of GLY on the pyrite surface and its possible activation. It is seen that the GLY easily desorbs from a pyrite/water interface through hydrogen-bond assistance.

The quinizarin chemisorbed on the basal-plane (0001) surface of alpha-Al2O3 is perpendicular on the surface and forms chelate bonds with surface aluminum atoms at exposed sites. This was observed ab initio calculations. The results also shows that the electronic characteristics due to long-range surface effects cannot explain the improved spectral hole-burning properties of chemisorbed quinizarin.

The article discusses various aspects of mechanochemistry in formation of covalent bonds through coupling of mechanical forces and chemical reactivity. It highlights the theoretical concepts which outline different mechanical forces that determine electronic structure of different molecular systems. The computational chemistry approach along with application of mechanochemistry to molecular nanomechanics for chemical and biological detection of components is also included.

The impact of sampling methods on spectral broadening in the gas phase and on the convergence of spectra in aqueous solution when using microsolvation, continuum solvation, and hybrid models is studied using pyrazine as a test case. For the sake of comparing classical Maxwell-Boltzmann and Wigner samplings in the gas phase, static and time-resolved X-ray absorption spectra after photoexcitation to the lowest 1 B 2 u ( ππ *) state, as well as the static UV-vis absorption spectrum, are considered. In addition, the UV-vis absorption spectrum of pyrazine in aqueous solution is also computed in order to systematically investigate its convergence with the number of explicitly included solvent shells with and without taking bulk solvation effects into account with the conductor-like screening model to represent implicit water beyond such explicit solute complexes. Concerning the static and time-resolved X-ray absorption spectra of pyrazine at the carbon K-edge as well as its UV-vis absorption spectrum in the gas phase, we find that these spectra obtained with Wigner and Maxwell-Boltzmann samplings substantially agree. For the UV-vis absorption spectrum in the aqueous solution, only the first two energetically low-lying bands converge quickly with the size of the explicitly included solvation shells, either with or without an additional continuum solvation taken into account. In stark contrast, calculations of the higher-lying excitations relying on finite microsolvated clusters without additional continuum solvation severely suffer from unphysical charge-transfer excitations into Rydberg-like orbitals at the cluster/vacuum interface. This finding indicates that computational UV-vis absorption spectra covering sufficiently high-lying states converge only if continuum solvation of the explicitly microsolvated solutes is included in the models.