A computational model of the nicotinic acetylcholine binding site

We have derived a model of the nicotinic acetylcholine binding site. This was accomplished by using three known agonists (acetylcholine, nicotine and epibatidine) as templates around which polypeptide side chains, found to be part of the receptor cavity from published molecular biology studies, are allowed to flow freely in molecular dynamics simulations and mold themselves around these templates. The resulting supramolecular complex should thus be a complement, both in terms of steric effects as well as electronic effects, to the agonists and it should be a good estimation of the true receptor cavity structure. The shapes of those minireceptor cavities equilibrated rapidly on the simulation time scale and their structural congruence is very high, implying that a satisfactory model of the nicotinic acetylcholine binding site has been achieved. The computational methodology was internally tested against two rigid and specific antagonists (dihydro--erytroidine and erysoidine), that are expected to give rise to a somewhat differently shaped binding site compared to that derived from the agonists. Using these antagonists as templates there were structural reorganizations of the initial receptor cavities leading to distinctly different cavities compared to agonists. This indicates that adequate times and temperatures were used in our computational protocols to achieve equilibrium structures for the agonists. Overall, both minireceptor geometries for agonists and antagonists are similar with the exception of one amino acid (ARG209).     

Solubility enhancement of triflumizole by host-guest interaction with β-cyclodextrin

Summary The solubility enhancement of triflumizole, a systemic fungicide, by -cyclodextrin inclusion complexation was investigated by electron absorption spectroscopy. The respective association constant determined by different methods was estimated to 470±20M ^–1 in aqueous solution. A model for the host-guest complexation was deduced by molecular calculations.

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Löslichkeitsverbesserung von Triflumizole durchHost-Guest-Complexierung mit -Cyclodextrin

Zusammenfassung Die Löslichkeitsverbesserung des systemischen Fungizids Triflumizole durch Komplexierung mit -Cyclodextrin wurde mittels Elektronenabsorptionsspektroskopie untersucht. Die entsprechende Stabilitätskonstante wurde durch verschiedene Methoden erfaßt und betrug im wäßrigen Medium 470±20M ^–1. Ein Model für denHost-Guest-Complex wurde durch Molekülrechnungen erstellt.

     

Ab initio study of the ground state and conformational stability of peroxyacetyl nitrate in internal rotation about the peroxide bond

The molecular and electronic structure of the ground state of peroxyacetyl nitrate (PAN) was calculated by the unrestricted Hartree-Fock-Roothaan method with the use of the standard 3–21G and 6–31G basis set. The potential curve of the internal rotation about the peroxide bond of PAN was calculated with the 6–31G basis set. The curve contains two maxima. The ground state of PAN is characterized by a structure in which groups of atoms adjacent to the peroxide bond lie in planes that are perpendicular to each other (the dihedral angle ϱ(COON) is 89.9°). The calculated barriers to rotation are 19.6 and 66.8 kJ mol⁻¹. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 600–604, April, 1998.     

A force field study of diacetylene molecule by kinetic constant method

The potential constants of diacetylene molecule has been evaluated using kinetic constants. The other molecular constants such as the generalised vibrational mean amplitudes, shrinkage constants, Coriolis coupling constants and centrifugal distortion constants are also calculated using the vibrational frequencies and the results discussed.     

Linear scaling local correlation approach for solving the coupled cluster equations of large systems

A linear scaling local correlation approach is proposed for approximately solving the coupled cluster doubles (CCD) equations of large systems in a basis of orthogonal localized molecular orbitals (LMOs). By restricting double excitations from spatially close occupied LMOs into their associated virtual LMOs, the number of significant excitation amplitudes scales only linearly with molecular size in large molecules. Significant amplitudes are obtained to a very good approximation by solving the CCD equations of various subsystems, each of which is made up of a cluster associated with the orbital indices of a subset of significant amplitudes and the local environmental domain of the cluster. The combined effect of these two approximations leads to a linear scaling algorithm for large systems. By using typical thresholds, which are designed to target an energy accuracy, our numerical calculations for a wide range of molecules using the 6-31G or 6-31G* basis set demonstrate that the present local correlation approach recovers more than 98.5% of the conventional CCD correlation energy.     

1,2,4-三苯基环戊二烯的合成及其烷基化反应

测定了颇哪醇在酸性条件下所得的脱水产物的分子结构.结果表明,在酸性条件下颇哪醇的脱水反应优于重排反应,由此合成了1,2,4-三苯基环戊二烯.该环戊二烯衍生物的烷基化反应,在通常条件下优先发生在碳环的第5位碳原子上,但在苛刻的剧烈反应条件下,进而发生在碳环的第3位碳原子上.讨论了脱水反应和烷基化反应的机理.     

Determination of extremely localized molecular orbitals in the framework of density functional theory

Extremely localized molecular orbitals are rigorously localized on only a preselected set of atoms and do not have any tails outside the localization region. The importance of these orbitals lies in their ability to be transferred from one molecule to another one. A new algorithm to determine extremely localized molecular orbitals in the framework of the density functional theory method is presented. This could also be a valuable tool in the quantum mechanics/molecular mechanics methodology where localized molecular orbitals are used to describe covalent bonds across the frontier region. The present approach is used to build up the electron density of thymopentin, a polypeptide constituted by five residues, starting from extremely localized molecular orbitals determined on a set of model molecules. The results obtained confirm good transferability properties for these orbitals.Proceedings of the 11th International Congress of Quantum Chemistry satellite meeting in honor of Jean-Louis Rivail     

In silico engineering of tailored ink-binding ability at molecular printboards.

Molecular recognition between guest ink molecules and beta-cyclodextrin (beta-CD) cavities at self-assembled monolayers provides a molecular printboard for nanopatterning applications. We recently used molecular dynamics (MD) simulations to describe the specificity of ink-printboard binding and here extend the simulations to include charged cyclodextrin hosts, necessary to broaden the chemistry of molecular printboards and bind charged inks such as the ferrocenium cation. Shifting to high pH, or alternatively grafting a charged sidearm onto beta-CD, created three distinct types of anionic beta-CD cavity and we used electronic structure calculations and MD simulations to measure host-guest charge transfer and binding strengths. We find that steric recognition of uncharged organic molecules is retained at the charged printboards, and that improved guest-host electrostatic contacts can strengthen binding of larger inks while penalising small inks, enhancing the level of discrimination. A prudent choice of complementary host-guest shape and charge states thus provides a means of tuning both ink binding strength and specificity at molecular printboards.     

The characterization of silica microparticles by electrophoretic mobility measurements

Summary Electrophoretic mobility measurements in the pH 2‐10 range are described for several commercial HPLC silica microparticles and a laboratory-produced product. The content of metal impurities for the silicas was also determined by AAS. An acidic/hydrothermal treatment was used to generate a more homogenous surface for some of the silicas. The zero points of charge (zpc) for both a native and a treated silica plus several commercial HPLC silicas were compared. The electrophoretic mobility method may be useful in predicting the utility of certain types of silica supports for chromatographic separations.