http://www.mtdna.or.kr/neowiz/board/up_files/files_17/Chitin_Chitosan_polymers_chemistrySolubilityFiberFormation.pdf

Chitin and chitosan polymers: Chemistry, solubility and fiber formation

A new derivation of the GLYCAM06 force field, which removes its previous specificity for carbohydrates, and its dependency on the AMBER force field and parameters, is presented. All pertinent force field terms have been explicitly specified and so no default or generic parameters are employed. The new GLYCAM is no longer limited to any particular class of biomolecules, but is extendible to all molecular classes in the spirit of a small-molecule force field. The torsion terms in the present work were all derived from quantum mechanical data from a collection of minimal molecular fragments and related small molecules. For carbohydrates, there is now a single parameter set applicable to both alpha- and beta-anomers and to all monosaccharide ring sizes and conformations. We demonstrate that deriving dihedral parameters by fitting to QM data for internal rotational energy curves for representative small molecules generally leads to correct rotamer populations in molecular dynamics simulations, and that this approach removes the need for phase corrections in the dihedral terms. However, we note that there are cases where this approach is inadequate. Reported here are the basic components of the new force field as well as an illustration of its extension to carbohydrates. In addition to reproducing the gas-phase properties of an array of small test molecules, condensed-phase simulations employing GLYCAM06 are shown to reproduce rotamer populations for key small molecules and representative biopolymer building blocks in explicit water, as well as crystalline lattice properties, such as unit cell dimensions, and vibrational frequencies.

/pdf/glycam06-a-generalizable-biomolecular-force-field-2f07t7094q.pdf

GLYCAM06: a generalizable biomolecular force field. Carbohydrates.

Two decades have passed since the discovery in liver microsomes of a haemprotein that forms a reduced-CO complex with the absorptive maximum of the Soret at 450 nm (Klingenberg, 1958; Garfinkel, 1958) and the identification of this protein as a new cytochrome: pigment cytochrome, P-450 (Omura and Sato, 1962, 1964a). In the intervening years, the study of cytochrome P-450 dependent monoxygenases has expanded exponentially. From the first crude attempts to solubilise a P-450 (Omura and Sato, 1963, 1964b) to the determination of the primary, secondary, and tertiary structure of cytochrome P-450cam by amino acid sequencing (Haniu et al., 1982a,b) and x-ray crystallography (Poulos et al., 1984) our understanding of this unique family of proteins has been advancing on all fronts. Since, perhaps, the greatest understanding of the structure and mechanism of P-450s has come from concentrated study of P-450cam of the Pseudomonas putida camphor-5-exo-hydroxylase, this review will concentrate on findings with P-450cam; attention will be drawn to parallel and contrasting examples from other P-450s as appropriate.

Structure and Chemistry of Cytochrome P450

: The unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio. Harmonic force fields are obtained using Density Functional Theory (DFT), MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set. DFT calculations use the Local Spin Density Approximation (LSDA), BLYP, and Becke3LYP (B3LYP) density functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with experiment. The MP2 force field yields spectra in slightly worse agreement with experiment than the B3LYP force field. The SCF force field yields spectra in poor agreement with experiment.The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreements with experiment. jg

Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields

A self-consistent system of additive covalent radii, R(AB)=r(A) + r(B), is set up for the entire periodic table, Groups 1-18, Z=1-118. The primary bond lengths, R, are taken from experimental or theoretical data corresponding to chosen group valencies. All r(E) values are obtained from the same fit. Both E-E, E-H, and E-CH 3 data are incorporated for most elements, E. Many E-E' data inside the same group are included. For the late main groups, the system is close to that of Pauling. For other elements it is close to the methyl-based one of Suresh and Koga [J. Phys. Chem. A 2001, 105, 5940] and its predecessors. For the diatomic alkalis MM' and halides XX', separate fits give a very high accuracy. These primary data are then absorbed with the rest. The most notable exclusion are the transition-metal halides and chalcogenides which are regarded as partial multiple bonds. Other anomalies include H 2 and F 2 . The standard deviation for the 410 included data points is 2.8 pm.

Molecular single-bond covalent radii for elements 1-118.

The noble gases have a particularly stable electronic configuration, comprising fully filled s and p valence orbitals. This makes these elements relatively non-reactive, and they exist at room temperature as monatomic gases. Pauling predicted1 in 1933 that the heavier noble gases, whose valence electrons are screened by core electrons and thus less strongly bound, could form stable molecules. This prediction was verified in 1962 by the preparation of xenon hexafluoroplatinate, XePtF6, the first compound to contain a noble-gas atom2,3. Since then, a range of different compounds containing radon, xenon and krypton have been theoretically anticipated and prepared4,5,6,7,8. Although the lighter noble gases neon, helium and argon are also expected to be reactive under suitable conditions9,10, they remain the last three long-lived elements of the periodic table for which no stable compound is known. Here we report that the photolysis of hydrogen fluoride in a solid argon matrix leads to the formation of argon fluorohydride (HArF), which we have identified by probing the shift in the position of vibrational bands on isotopic substitution using infrared spectroscopy. Extensive ab initio calculations indicate that HArF is intrinsically stable, owing to significant ionic and covalent contributions to its bonding, thus confirming computational predictions11,12,13 that argon should form a stable hydride species with properties similar to those of the analogous xenon and krypton compounds reported before14,15,16,17,18.

A stable argon compound

Ultraviolet‐irradiation of hydrogen halide containing rare gas matrices yields the formation of linear centrosymmetric cations of type (XHX)+, (X=Ar, Kr, Xe). Annealing of the irradiated doped solids produces, along with thermoluminescence, extremely strong absorptions in the 1700–1000 cm−1 region. Based on isotopic substitution and halogen dependence of these bands, the presence of hydrogen and halogen atom(s) in these species is evident. In the present paper we show the participation of rare gas atom(s) in these new compounds. The evidence is based on studies of the thermally generated species in mixed rare gas matrices. The new species are assigned as neutral charge‐transfer molecules HX+Y− (Y=halogen), and their vibrational spectra are discussed and compared with those calculated with ab initio methods. This is the first time hydrogen and a rare gas atom has been found to make a chemical bond in a neutral stable compound. The highest level ab initio calculations on the existence of compounds of type HXY corroborate the experimental observations. The mechanism responsible for the formation of these species is also discussed.

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Neutral rare-gas containing charge-transfer molecules in solid matrices. I. HXeCl, HXeBr, HXeI, and HKrCl in Kr and Xe

Noble-gas chemistry has been undergoing a renaissance in recent years, due in large part to noble-gas hydrides, HNgY, where Ng = noble-gas atom and Y = electronegative fragment. These molecules are exceptional because of their relatively weak bonding and large dipole moments, which lead to strongly enhanced effects of the environment, complexation, and reactions. In this Account, we discuss the matrix-isolation synthesis of noble-gas hydrides, their spectroscopic and structural properties, and their stabilities. This family of species was discovered in 1995 and now has 23 members that are prepared in noble-gas matrices (HXeBr, HKrCl, HXeH, HXeOH, HXeO, etc.). The preparations of the first neutral argon molecule, HArF, and halogen-free organic noble-gas molecules (HXeCCH, HXeCC, HKrCCH, etc.) are important highlights of the field. These molecules are formed by the neutral H + Ng + Y channel. The first addition reaction involving HNgY molecules was HXeCC + Xe + H → HXeCCXeH, and this led to the first hydrid...

/pdf/noble-gas-hydrides-new-chemistry-at-low-temperatures-x8o76bw3le.pdf

Noble-gas hydrides: new chemistry at low temperatures.

IR Spectrum of the Other Rotamer of Formic Acid, cis-HCOOH

Three novel Xe-containing organic compounds, HXeCCH, HXeCC (open-shell species), and HXeCCXeH, are identified using infrared absorption spectroscopy. They are prepared in a low-temperature Xe matrix using UV photolysis of acetylene and subsequent annealing at 40−45 K. The experimental observations are supported by extensive ab initio calculations. This work demonstrates a new way to activate the H−C⋮C− group without use of XeF2, which can extend the range of organoxenon compounds.

/pdf/fluorine-free-organoxenon-chemistry-hxecch-hxecc-and-1c3k0xpm5g.pdf

Markku Räsänen

Papers

A stable argon compound

Neutral rare-gas containing charge-transfer molecules in solid matrices. I. HXeCl, HXeBr, HXeI, and HKrCl in Kr and Xe

Noble-gas hydrides: new chemistry at low temperatures.

IR Spectrum of the Other Rotamer of Formic Acid, cis-HCOOH

Fluorine-free organoxenon chemistry: HXeCCH, HXeCC, and HXeCCXeH.