In this work, through a docking analysis of compounds from the ZINC chemical library on human β-tubulin using high performance computer cluster, we report new polycyclic aromatic compounds that bind with high energy on the colchicine binding site of β-tubulin, suggesting three new key amino acids. However, molecular dynamic analysis showed low stability in the interaction between ligand and receptor. Results were confirmed experimentally in in vitro and in vivo models that suggest that molecular dynamics simulation is the best option to find new potential β-tubulin inhibitors.
In this article, we explore, both theoretically and experimentally, the general reactivity of alkyl hydrogeno-phenylphosphinates with alcohols. We show that alcohol molecules act exclusively as nucleophilic species, and add to alkyl hydrogeno-phenylphosphinates, leading to pentacoordinated intermediates. These intermediates are shown to subsequently competitively undergo alcohol eliminations and/or Berry pseudorotations. This offers several possible routes for racemizations and/or alcohol exchange reactions. Transition standard Gibbs free energies predicted from DFT calculations for the overall alcohol exchange mechanism are shown to be compatible with those experimentally measured in case ethanol reacts with ethyl hydrogeno-phenylphosphinate (134.5～136.0 kJ mol?1 at 78 °C).
The addition of C2 to HCN is of relevant interest in astrochemistry. We studied the pathways of this addition to produce CCCN and estimated its reaction rate using the Master Equation in the circumstellar environment. From the results of this study, it was possible to show that a different pathway in the Surface Potential Energy-PES can also be investigated. In a circumstellar envelop environment, with temperatures varying between 1000 K and 2000 K, the abundances of these species are favorable to this kind of addition, and our branching ratio for the rate constant showed that the new pathway is more favorable in comparison with other possibilities for this range of temperatures in this environment, and must be taken into account in any computation of the rate constant.
Coarse-grained force field (CGFF) methods were applied to study the self-assembly of sodium dodecyl sulfate with fragrance additives. The CGFF parameters were parameterized and validated using experimental and all-atom simulation data. Direct molecular dynamics simulations were carried out to characterize the initial aggregation, partitioning of fragrances, and chemical potentials of the surfactant and fragrance molecules in aggregates of different sizes. The equilibrium critical micelle concentrations (CMCs) and micelle size distributions, which could not be obtained by direct simulation, were predicted using the calculated chemical potentials in combination with a thermodynamic model. The predicted partitioning of fragrances, CMCs, micelle sizes, and micelle structures agree well with previously reported experimental data.
Catalytic fields illustrate topology of the optimal charge distribution of a molecular environment reducing the activation energy for any process involving barrier crossing, like chemical reaction, bond rotation etc. Until now, this technique has been successfully applied to predict catalytic effects resulting from intermolecular interactions with individual water molecules constituting the first hydration shell, aminoacid mutations in enzymes or Si→Al substitutions in zeolites. In this contribution, hydrogen to fluorine (H→F) substitution effects for two model reactions have been examined indicating qualitative applicability of the catalytic field concept in the case of systems involving intramolecular interactions.
The present paper reports the analysis of surface decoration on the structural, electronic, and optical properties of (n,0) ZnO nanotubes, performed by means of a density function theory based ab-initio approach. Fe functionalization induced buckling in ZnO nanotubes affects its electronic and optical properties. Increase in Fe functionalization leads to better stability of ZnO nanotube and shows enhanced metallic character. The possibility of its use in optoelectronics has been analyzed in terms of dielectric constant, absorption coefficient, and refractive index. In another observation, the high sensitivity of the HCN molecule for the Fe-incorporated ZnO nanotube suggests it as a potential gas sensor.
Beryllium telluride (BeTe) with cubic zinc-blende (ZB) structure was studied using ab initio constant pressure method under high pressure. The ab initio molecular dynamics (MD) approach for constant pressure was studied and it was found that the first order phase transition occurs from the ZB structure to the nickel arsenide (NiAs) structure. It has been shown that the MD simulation predicts the transition pressure PT more than the value obtained by the static enthalpy and experimental data. The structural pathway reveals MD simulation such as cubic → tetragonal → orthorhombic → monoclinic → orthorhombic → hexagonal, leading the ZB to NiAs phase. The phase transformation is accompanied by a 10% volume drop and at 80 GPa is likely to be around 35 GPa in the experiment. In the present study, our obtained values can be compared with the experimental and theoretical results.
In this work, we address the effects of molecular doping on the electronic properties of fluorinated and chlorinated silicon nanowires (SiNWs), in comparison with those corresponding to hydrogen-passivated SiNWs. Adsorption of n-type dopant molecules on hydrogenated and halogenated SiNWs and their chemisorption energies, formation energies, and electronic band gap are studied by using density functional theory calculations. The results show that there are considerable charge transfers and strong covalent interactions between the dopant molecules and the SiNWs. Moreover, the results show that the energy band gap of SiNWs changes due to chemical surface doping and it can be further tuned by surface passivation. We conclude that a molecular based ex-situ doping, where molecules are adsorbed on the surface of the SiNW, can be an alternative path to conventional doping.
Hydrogen molecule adsorption on frameworks consisting of alkaline earth metal atoms (Be, Mg, or Ca) in LTL zeolite was investigated via density functional theory. A 24T zeolite cluster model was used in this study. HOMO and LUMO energy, chemical potential, chemical hardness, electronegativity, adsorption energy, and adsorption enthalpy values were calculated. The Mg-LTL and Ca-LTL clusters were found to have much lower chemical potentials and adsorption energies than those of the Be-LTL cluster. Additionally, the calculations indicated that the Mg-LTL and Ca-LTL clusters are softer (considering their lower chemical hardness values) and more chemically reactive than the Be-LTL cluster. The calculated hydrogen adsorption enthalpies were ?14.7 and ?9.4 kJ/mol for the Mg-LTL and Ca-LTL clusters, respectively, which are significantly larger than the enthalpy of liquefaction for the hydrogen molecule. These results imply that the Mg-LTL and Ca-LTL zeolite structures are promising cryoadsorbents for hydrogen storage.
Graphical abstract Hydrogen adsorption was theoretically investigated on Be-, Ca- and Mg-LTL clusters. Ca- and Mg-LTL zeolites are potential cryoadsorbent materials for hydrogen storage.
Elucidating the mechanical response of diamond is a difficult task due to its ultrahard nature. Here, we applied a molecular dynamics (MD) method to investigate the mechanical response of single-crystal diamond under nanoindentation. There was no obvious “pop in” phenomenon on the load–depth curve, and the elastic modulus deduced from the curve was 1128 GPa, which was similar to the value obtained from experimental measurements. Results from computed tomography (CT) and the coordination number showed that the distribution of the mismatched C atoms around the deformation zone took the form of a ‘double cross.’ The atoms around the indenter tip could be divided into two zones, a translation zone and a lattice distortion zone, based on their movements. Subsequent first-principles calculations revealed that the C-atom displacement barrier varied significantly with direction, which resulted in shear stress between the two zones and the formation of the double-cross splitting.
A post-calculation correction is established for PM7 band gaps of transition-metal oxides. The correction is based on the charge on the metal cation of interest, as obtained from MOPAC PM7 calculations. Application of the correction reduces the average error in the PM7 band gap from ~3 eV to ~1 eV. The residual error after correction is shown to be uncorrelated to the Hartree–Fock method upon which PM7 is based.
Graphical Abstract Comparison between calculated band gaps and experimental band gaps for binary oxides. The orange crosses are for corrected PM7 band gaps. Blue squares are uncorrected values. The orange crosses fall closer to the diagonal dashed line, showing an overall improvement of the accuracy of calculated values
Efficient design of ionic compounds requires a systematic understanding of cation–anion interactions. Weakening of electrostatic attraction is essential to increase the liquid range of the ionic compound and decrease its melting point. Here, we report simulations of the closest-approach cation–anion distances in a variety of ion pairs containing the tetrakis(pentafluorophenyl)borate (TFPB–) anion. Small alkali cations (Li+, Na+) penetrate the TFPB– core, whereas K+ and larger organic cations do not. In the latter case, the shortest possible distance from the cations to the boron atom of TFPB– ranges from 0.50 nm to 0.63 nm. TFPB– was shown to be substantially rigid, providing a steric hindrance to thermodynamically efficient cation–anion coordination. Our results prove that TFPB– is more efficient for electrostatic charge confinement than the tetraoctylammonium cation, whereas the perfluorophenyl group is more efficient than linear alkyl chains. These simulations will motivate development of TFPB–-based ionic liquids with low phase transition points.
Vitamin C is one of the most abundant exogenous antioxidants in the cell, and it is of the utmost importance to elucidate its mechanism of action against radicals. In this study, the reactivity of vitamin C toward OH and \( {HO}_2/{O}_2^{-} \) radicals in aqueous medium was analyzed by ab initio molecular dynamics using CPMD code. The simulations led to results similar to those of static studies or experiments for the pair of \( {HO}_2/{O}_2^{-} \) radicals but bring new insights for the reactivity with hydroxyl radical: the reaction takes place before the formation of an adduct and consists of two steps: first an electron is transferred to hydroxyl radical and then the ascorbyl radical loses a proton.
In this article, we explore the capacity of formed Schiff base complexes to trap metal atoms or ions, using their aromatic ends. The intrinsic geometry of each complex defines the process of substitution. Two cases were studied; one involving a trans Schiff base complex and the other considering how a salen ligand, with nickel systems traps chromium. We also assessed the nature of the new bonds and the frontier molecular orbitals.
The characterization of the seleno-sulfide-bromo systems and the isomerization process on the [H, S, Se, Br] potential energy surface were investigated using state-of-the-art theoretical methods. The CCSD(T) and the MP2 levels of theory were employed along with the series of correlation consistent basis sets extrapolated to the complete basis set (CBS) limit in the optimization of the geometrical parameters and computation of electronic energies. The relative stability, in kcal mol?1, at the CCSD(T)/CBS follows the trend: HSSeBr (0) > HSeSBr (9.51) > SSeHBr (24.02) > SeSHBr (25.42). This order was observed in the previous study of the [H, S, Se, Cl] species. The structural parameters and vibrational frequencies of the [H, S, Se, Br] species are reported. This research work should be helpful to experimentalists in order to gain insights into these novel heteroatom molecules.
Graphical abstract Relative energy profile (in kcal mol?1) using the CCSD(T)/CBS and MP2/CBS (in parentheses) method of the stationary states on the [H, S, Se, Br] PES.
