scholarly journals Identification of new, well-populated amino-acid sidechain rotamers involving hydroxyl-hydrogen atoms and sulfhydryl-hydrogen atoms

2008 ◽  
Vol 8 (1) ◽  
pp. 41 ◽  
Author(s):  
Bosco K Ho ◽  
David A Agard
Keyword(s):  
Amino Acid ◽  
Hydrogen Atoms ◽  
Sidechain Rotamers ◽  
Hydroxyl Hydrogen

Studies Directed Towards the Total Synthesis of Anticapsin. X-Ray Crystal-Structure of (1RS,2SR,4RS,5RS,6SR)-5-Hydroxy-2-phthalimido-1-trimethylsilyloxy-bicyclo[2.2.2]octane-2,6-carbolactone

1990 ◽  
Vol 43 (11) ◽  
pp. 1827 ◽  
Author(s):  
MJ Crossley ◽  
TW Hambley ◽  
AW Stamford
Keyword(s):  
Crystal Structure ◽  
Amino Acid ◽  
Total Synthesis ◽  
Synthetic Approach ◽  
Hydrogen Atoms ◽  
Full Matrix ◽  
X Ray ◽  
X Ray Crystallography ◽  
Relative Stereochemistry ◽  
Atomic Parameters

The relative stereochemistry of methyl 2-phthalimido-1- trimethylsilyloxybicyclo[2.2.2]oct-5-ene-2-carboxylate (9) and its 5,6-epoxide (10), intermediates in a synthetic approach to the amino acid antibiotic anticapsin, were established by the TiCl4-mediated cyclization of (10) to the carbolactone (12); the structure of which was proved by single-crystal X-ray crystallography. Full-matrix least- squares refinement of all atomic parameters with individual isotropic thermal parameters for the hydrogen atoms by using 1446 reflections converged at R 0.036. Crystals of (12) are monoclinic, P21/c, a 12.342(3), b 12.239(2), c 13.405(3) Ǻ, β 99.34(2)°, Z 4.

(S)-2,2,5,5-Tetramethylthiazolidine-4-carboxylic acid: a compound which exists in the amino acid rather than the zwitterion form

1985 ◽  
Vol 63 (9) ◽  
pp. 2411-2419 ◽  
Author(s):  
Helen Elaine Howard-Lock ◽  
Colin James Lyne Lock ◽  
Philip Stuart Smalley
Keyword(s):  
Amino Acid ◽  
Carboxylic Acid ◽  
Raman Spectra ◽  
Cooh Group ◽  
Infrared And Raman Spectra ◽  
Acid Form ◽  
Hydrogen Atoms ◽  
Cell Dimensions ◽  
Amino Acid Form ◽  
C Nmr

The X-ray crystal structure of (S)-2,2,5,5-tetramethylthiazolidine-4-carboxylic acid, 1, has been determined. Crystals are monoclinic, P21, with cell dimensions a = 11.351(4) b = 8.303(2), c = 11.969(3) Å, β = 116.69(2)°, and Z = 4. The structure was solved by standard methods and refined to R1 = 0.0774, R2 = 0.0670 for 2388 independent reflections. Compound 1 exists in the amino-acid form as shown by two distinctly different C—O bond lengths, 1.209 and 1.309 Å, typical of the COOH group, and by the positions of the hydrogen atoms. The amino-acid form of 1 found in the solid also exists in solution as shown by infrared and Raman spectra. The mass spectra, and 1H and 13C nmr spectra are reported, as well as detailed infrared and Raman spectra for the title compound and several deuterated species.

Carbon-Centered Radicals Can Transfer Hydrogen Atoms between Amino Acid Side Chains

2012 ◽  
Vol 124 (12) ◽  
pp. 3014-3017 ◽  
Author(s):  
Quentin Raffy ◽  
David-Alexandre Buisson ◽  
Jean-Christophe Cintrat ◽  
Bernard Rousseau ◽  
Serge Pin ◽  
...  
Keyword(s):  
Amino Acid ◽  
Side Chains ◽  
Hydrogen Atoms ◽  
Amino Acid Side Chains

Investigations of the biosynthesis of the phytotoxin coronatine

1994 ◽  
Vol 72 (1) ◽  
pp. 86-99 ◽  
Author(s):  
Ronald J. Parry ◽  
Sunil V. Mhaskar ◽  
Ming-Teh Lin ◽  
Alan E. Walker ◽  
Robson Mafoti
Keyword(s):  
Amino Acid ◽  
Pseudomonas Syringae ◽  
Cyclopropane Ring ◽  
Carbonyl Oxygen ◽  
Oxidative Cyclization ◽  
Amide Bond ◽  
Hydrogen Atoms ◽  
Coronafacic Acid ◽  
Polyketide Chain ◽  
Oxygen Atoms

The biosynthesis of the phytotoxin coronatine has been investigated by administration of isotopically labeled precursors to Pseudomonas syringae pv. glycinea. The structure of coronatine contains two moieties of distinct biosynthetic origin, a bicyclic, hydrindanone carboxylic acid (coronafacic acid) and a cyclopropyl α-amino acid (coronamic acid). Investigations of coronafacic acid biosynthesis have shown that this compound is a polyketide derived from three acetate units, one butyrate unit, and one pyruvate unit. The two carbonyl oxygen atoms of coronafacic acid were found to be derived from the oxygen atoms of acetate. Additional experiments are described that rule out some possible modes for assembly of the polyketide chain. Coronamic acid is shown to be derived from L-isoleucine via the intermediacy of L-alloisoleucine. Examination of the mechanism of the cyclization of L-alloisoleucine to coronamic acid revealed that the formation of the cyclopropane ring takes place with the removal of only two hydrogen atoms from the amino acid, one at C-2 and the other at C-6. The nitrogen atom at C-2 of L-alloisoleucine is shown to be retained. On the basis of these observations, a mechanism is postulated for the cyclization reaction that involves the diversion of an enzymatic hydroxylation reaction into an oxidative cyclization. Finally, a precursor incorporation experiment with deuterium-labeled coronamic acid demonstrated that free coronamic acid can be efficiently incorporated into coronatine. This observation indicates that the cyclization of L-alloisoleucine to coronamic acid can occur before formation of the amide bond between coronafacic acid and coronamic acid.

scholarly journals Comparative Antibacterial Analysis of the Anthraquinone Compounds Based on the AIM Theory and Molecular Docking Analysis

2021 ◽  
Author(s):  
Yanjiao Qi ◽  
Mingyang Wang ◽  
Bo Zhang ◽  
Yue Liu ◽  
Hong Zhang ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Binding Energies ◽  
Hydrogen Atoms ◽  
Docking Analysis ◽  
Comprehensive Comparison ◽  
Molecular Potentials ◽  
Almost All ◽  
Atoms In Molecules Theory ◽  
Hydroxyl Hydrogen ◽  
Present Text

Abstract Hydroxyanthraquinones and anthraquinone glucoside derivatives are always considered as the active antibacterial components. In the present text, a comprehensive comparison and analysis of these compounds were performed for their structure characteristics and antibacterial effect by applying quantum chemical calculations, atoms in molecules theory and molecular docking procedure. The molecular geometric configuration, electrostatic potential, the frontier orbital energies and topological properties were analyzed. Once glucose ring is introduced into the hydroxyanthraquinone rings, almost all of the positive molecular potentials are distributed among the hydroxyl hydrogen atoms of the glucose rings. The anthraquinone glucoside compounds have generally higher intermolecular binding energies than the corresponding aglycones due to the strong interaction between the glucose rings and the surrounding amino acids. Once glucoside ring is introduced into the emodin, low electron density ρ(r) and positive Laplacian value of the O-H bond are the evidences of the highly polarized and covalently decreased bonding interactions. The type of carboxyl, hydroxyl, hydroxylmethyl groups on phenyl ring and the substituent glucose rings are important to the interactions with the topoisomerase type II enzyme DNA gyrase B.

The Fragmentation Mechanism of Cyclobutanol

1973 ◽  
Vol 51 (14) ◽  
pp. 2342-2346 ◽  
Author(s):  
John L. Holmes ◽  
Robin T. B. Rye
Keyword(s):  
Hydrogen Atom ◽  
Mass Spectra ◽  
Fragmentation Mechanism ◽  
Hydrogen Atoms ◽  
Specific Mechanism ◽  
Molecular Ion ◽  
Random Manner ◽  
Hydroxyl Hydrogen

The mass spectra of cyclobutanol and three 2H labelled analogs have been studied. The losses of C2H4 and C2H5• from the molecular ion involve specific fragmentations. Only CH3• loss from the α-cleaved molecular ion2 clearly involves hydrogen atom scrambling; this fragmentation also proceeds by a specific mechanism involving C-2 and hydroxyl hydrogen atoms. Loss of water from the molecular ion involves all the hydrogen atoms but in a complex, non-random manner.

Polymorphism in phenol under pressure: dielectric properties and molar polarizations of polycrystalline phenol I and II

1977 ◽  
Vol 55 (8) ◽  
pp. 1294-1302 ◽  
Author(s):  
John E. Bertie ◽  
Peter R. Tremaine
Keyword(s):  
Dielectric Properties ◽  
Temperature Dependence ◽  
Dielectric Relaxation ◽  
Applied Pressure ◽  
Thermal Expansivity ◽  
Hydrogen Atoms ◽  
Dielectric Parameters ◽  
Molar Volumes ◽  
Molar Polarization ◽  
Hydroxyl Hydrogen

The dielectric properties of phenol I have been measured as isothermal functions of pressure between 140 and 1520 bar and between +35 and −10 °C. No dielectric relaxation was observed. The static (50 kHz) permittivity at 10 °C is given with a precision of 0.3% by[Formula: see text]where P is in bar. The extrapolated value at 1 bar is 2.882 ± 0.009 which compares with literature values between 2.74 and 2.84. The 50 kHz molar polarization, [Formula: see text], at 10 °C is given by[Formula: see text]where V and Vo are the molar volumes at pressures P and 1 bar, respectively. At 10 °C and 1 bar, the electronic and atomic polarizations are estimated to be 26.9 ± 0.3 cm3 and 5.1 ± 0.4 cm3, respectively. Expressions for the isobaric temperature dependence of εo′ are reported for several pressures. Below 1500 bar, (∂εo′/∂T)P is negative, as expected from the density change but in contrast with previous results and with results obtained while varying the temperature under a constant applied pressure of 1 kbar. The accuracy of the temperature dependence at 1 bar is not high, judging from the thermal expansivity calculated from it.εo′ of phenol II at 10 °C and an estimated pressure of 2000 bar is 3.10 ± 0.06, with the corresponding molar polarization 30.75 ± 0.5 cm3. No intrinsic dielectric relaxation was observed in phenol II and the molar polarization shows no marked discontinuity at the transition. Phenol II is, therefore, like phenol I, a hydrogen-bonded solid in which the hydroxyl hydrogen atoms are ordered, either fully or in chains. The dielectric parameters and Arrhenius activation energies of two transient dispersions which appeared whenever phenol II formed are discussed.

Carbon-Centered Radicals Can Transfer Hydrogen Atoms between Amino Acid Side Chains

2012 ◽  
Vol 51 (12) ◽  
pp. 2960-2963 ◽  
Author(s):  
Quentin Raffy ◽  
David-Alexandre Buisson ◽  
Jean-Christophe Cintrat ◽  
Bernard Rousseau ◽  
Serge Pin ◽  
...  
Keyword(s):  
Amino Acid ◽  
Side Chains ◽  
Hydrogen Atoms ◽  
Amino Acid Side Chains

Examination of the molecular properties of D-fructose and L-sorbose by abinitio LCAO-MO calculations

1984 ◽  
Vol 62 (8) ◽  
pp. 1506-1511 ◽  
Author(s):  
Walter A. Szarek ◽  
Sirkka-Liisa Korppi-Tommola ◽  
Olivier R. Martin ◽  
Vedene H. Smith Jr.
Keyword(s):  
Point Charge ◽  
Population Analysis ◽  
Sweet Taste ◽  
Molecular Properties ◽  
Intramolecular Interactions ◽  
Mo Calculations ◽  
Hydrogen Atoms ◽  
Mulliken Population ◽  
Hydroxyl Hydrogen ◽  
Lcao Mo

Abinitio SCF LCAO-MO calculations at the STO-3G level have been performed on β-D-fructopyranose (1) and α-L-sorbopyranose (2) using crystallographic data as the geometrical input. Molecular properties of 1 and 2 are discussed in terms of orbital energies, total energy, ionization potentials, Mulliken population analysis, and electrostatic potentials, with a particular emphasis on the possible consequences of these features as regards the sweet taste of these two ketoses. No correlation was found, for example, with the electrostatic, point-charge distribution since the calculated hydrogen-bonding abilities would lead to the prediction of 2 being sweeter than 1. On the other hand, non-bonded overlap populations between oxygen and hydroxyl-hydrogen atoms reveal the presence of intramolecular interactions, which may have a determinant influence on the taste of these molecules and which could explain why D-fructose is much sweeter than its epimer at C-5, namely, L-sorbose.

Sign in / Sign up

Export Citation Format

Share Document