Study of peptide conformation in terms of the ABEEM/MM method

The ABEEM/MM model (atom-bond electronegativity equalization method fused into molecular mechanics) is applied to study of the polypeptide conformations. The Lennard-Jones and torsional parameters were optimized to be consistent with the ABEEM/MM fluctuating charge electrostatic potential. The hydrogen bond was specially treated with an electrostatic fitting function. Molecular dipole moments, dimerization energies, and hydrogen bond lengths of complexes are reasonably achieved by our model, compared to ab initio results. The ABEEM/MM fluctuating charge model reproduces both the peptide conformational energies and structures with satisfactory accuracy with low computer cost. The transferability is tested by applying the parameters of our model to the tetrapeptide of alanine and another four dipeptides. The overall RMS deviations in conformational energies and key dihedral angles for four di- or tetrapeptide, is 0.39 kcal/mol and 7.7 degrees . The current results agree well with those by the accurate ab initio method, and are comparable to those from the best existing force fields. The results make us believe that our fluctuating charge model can obtain more promising results in protein and macromolecular modeling with good accuracy but less computer cost.     

A comparative theoretical study of dipeptide solvation in water

Molecular dynamics studies have been performed on the zwitterionic form of the dipeptide glycine-alanine in water, with focus on the solvation and electrostatic properties using a range of theoretical methods, from purely classical force fields, through mixed quantum mechanical/molecular mechanical simulations, to fully quantum mechanical Car-Parrinello calculations. The results of these studies show that the solvation pattern is similar for all methods used for most atoms in the dipeptide, but can differ substantially for some groups; namely the carboxy and aminoterminii, and the backbone amid NH group. This might have implications in other theoretical studies of peptides and proteins with charged -NH(3) (+) and -CO(2) (-) side chains solvated in water. Hybrid quantum mechanical/molecular mechanical simulations successfully reproduce the solvation patterns from the fully quantum mechanical simulations (PACS numbers: 87.14.Ee, 87.15.Aa, 87.15.He, 71.15.Pd).     

AFM studies of metal deposition: instantaneous nucleation and the growth of cobalt nanoparticles on boron-doped diamond electrodes.

In situ atomic force microscopy (AFM) is used to study the growth of cobalt nuclei on a boron doped diamond electrode under potentiostatic control. The rate of growth of the nuclei at the electrode surface is monitored using AFM as a function of time at different deposition potentials. The nucleation of cobalt nuclei is found to be "instantaneous" and the growth of the nuclei is shown to be kinetically rather than diffusionally controlled over periods of tens and hundreds of seconds. At very short times (<10 seconds) the kinetics of nucleation are apparent.     

Synthesis and Characterization of [(1,4‐diamine)dichloro]platinum(II) Compounds Preliminary Studies on their Biological Activity

Two 1,4‐diamine ligands were synthesized having 1,2‐bis(aminomethyl)‐cyclohexane and 1,2‐bis(aminomethyl)‐benzene structures. The two ligands have different electron density in the six‐membered ring: a cyclohexane versus a phenyl ring. The organic synthesis of the ligands was carried out by synthetic pathways of seven and four steps, respectively, starting from 1,2,3,6‐tetrahydrophthalic anhydride and diethyl phthalate. The coordination of platinum to these ligands afforded platinum(II) complexes which are analogue to the clinical drug cisplatin but form a seven‐membered chelate ring. The interaction of the platinum compounds with DNA was studied in order to know the relationship between the electron density of ligands and their capability to chelate DNA, by using three techniques: Circular Dichroism, Agarose Gel Electrophoresis and Atomic Force Microscopy. The degree of interaction of both compounds with DNA was slightly different, but both complexes showed a cisplatin‐like behaviour and are promising candidates to follow an extensive study of their cytotoxic activity.     

Nucleic acid reactivity: Challenges for next‐generation semiempirical quantum models

Semiempirical quantum models are routinely used to study mechanisms of RNA catalysis and phosphoryl transfer reactions using combined quantum mechanical (QM)/molecular mechanical methods. Herein, we provide a broad assessment of the performance of existing semiempirical quantum models to describe nucleic acid structure and reactivity to quantify their limitations and guide the development of next‐generation quantum models with improved accuracy. Neglect of diatomic differential overlap and self‐consistent density‐functional tight‐binding semiempirical models are evaluated against high‐level QM benchmark calculations for seven biologically important datasets. The datasets include: proton affinities, polarizabilities, nucleobase dimer interactions, dimethyl phosphate anion, nucleoside sugar and glycosidic torsion conformations, and RNA phosphoryl transfer model reactions. As an additional baseline, comparisons are made with several commonly used density‐functional models, including M062X and B3LYP (in some cases with dispersion corrections). The results show that, among the semiempirical models examined, the AM1/d‐PhoT model is the most robust at predicting proton affinities. AM1/d‐PhoT and DFTB3‐3ob/OPhyd reproduce the MP2 potential energy surfaces of 6 associative RNA phosphoryl transfer model reactions reasonably well. Further, a recently developed linear‐scaling “modified divide‐and‐conquer” model exhibits the most accurate results for binding energies of both hydrogen bonded and stacked nucleobase dimers. The semiempirical models considered here are shown to underestimate the isotropic polarizabilities of neutral molecules by approximately 30%. The semiempirical models also fail to adequately describe torsion profiles for the dimethyl phosphate anion, the nucleoside sugar ring puckers, and the rotations about the nucleoside glycosidic bond. The modeling of pentavalent phosphorus, particularly with thio substitutions often used experimentally as mechanistic probes, was problematic for all of the models considered. Analysis of the strengths and weakness of the models suggests that the creation of robust next‐generation models should emphasize the improvement of relative conformational energies and barriers, and nonbonded interactions. © 2015 Wiley Periodicals, Inc.     

The PyPES library of high quality semi‐global potential energy surfaces

In this article, we present a Python‐based library of high quality semi‐global potential energy surfaces for 50 polyatomic molecules with up to six atoms. We anticipate that these surfaces will find widespread application in the testing of new potential energy surface construction algorithms and nuclear ro‐vibrational structure theories. To this end, we provide the ability to generate the energy derivatives required for Taylor series expansions to sixth order about any point on the potential energy surface in a range of common coordinate systems, including curvilinear internal, Cartesian, and normal mode coordinates. The PyPES package, along with FORTRAN, C, MATLAB and Mathematica wrappers, is available at http://sourceforge.net/projects/pypes-lib . © 2015 Wiley Periodicals, Inc.     

The reaction force. A scalar property to characterize reaction mechanisms

The reaction force is a global property of a chemical reaction that arises when applying the Hellmann–Feynmann theorem to the potential energy surface that links reactants, products and transition states. In the present work, the reaction force is defined rigorously from the cartesian components coming out from all forces exerted over each atom of a molecular system during the chemical reaction; it is demonstrated that the reaction force is a scalar property. An erratum to this article can be found at     

Sol–gel synthesis,preparation and characterization of photoactive TIO<Subscript>2</Subscript> with ultrasound treatment

Titania was prepared by the sol–gel method from titanium isopropoxide with ultrasound influence (USI) by different pH (acetic acid (AA) or diethyl amine (DEA). Samples were represented in powder and films forms. The TiO₂ was characterized by X-ray diffraction (XRD), FTIR. XRD shows that TiO₂ prepared with diethyl amine has only the anatase phase, however the samples prepared with acetic acid–anatase and rutile phases both could be detected. Ultrasound influence increases the anatase content in comparison with its missing. Photo electromotive force (Photo EMF) datas of TiO₂ films were received in a three-electrode wet cell. It was found that the photo activity depended on the conditions of synthesis crystalline phases. Photo EMF for the TiO₂ films on the nickel electrode is 1.5 mV (TiO₂ with acetic acid conditions), 6.8 mV (TiO₂ with diethyl amine conditions) 8.0 mV (TiO₂ with acetic acid + USI conditions), 22.0 mV (TiO₂ with diethyl amine +USI conditions).