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PubMed2006

Molecular structure and conformations of benzenesulfonamide: gas electron diffraction and quantum chemical calculations.

The molecular structure and conformational properties of benzenesulfonamide, C6H5SO2NH2, were studied by gas electron diffraction (GED) and quantum chemical methods (MP2 and B3LYP with different basis sets). The calculations predict the presence of two stable conformers with the NH2 group eclipsing or staggering the SO2 group. The eclipsed form is predicted to be favored by about 0.5 kcal/mol. According to GED, the saturated vapor over solid benzenesulfonamide at a temperature of 150(5) degrees C consists of the eclipsed conformer. The GED intensities, however, possess a very low sensitivity toward the vapor composition, and contributions of the anti conformer of up to 75% (at the 0.05 level of significance) or up to 55% (at the 0.25 level of significance) cannot be excluded. The molecule possesses C(sS) symmetry with the S-N bond perpendicular to the ring plane.

Electrons↗
PubMed2004

The molecular structure and catalytic mechanism of a novel carboxyl peptidase from Scytalidium lignicolum.

The molecular structure of the pepstatin-insensitive carboxyl peptidase from Scytalidium lignicolum, formerly known as scytalidopepsin B, was solved by multiple isomorphous replacement phasing methods and refined to an R factor of 0.230 (R(free) = 0.246) at 2.1-A resolution. In addition to the structure of the unbound peptidase, the structure of a product complex of cleaved angiotensin II bound in the active site of the enzyme was also determined. We propose the name scytalidocarboxyl peptidase B (SCP-B) for this enzyme. On the basis of conserved, catalytic residues identified at the active site, we suggest the name Eqolisin for the enzyme family. The previously uninvestigated SCP-B fold is that of a beta-sandwich; each sheet has seven antiparallel strands. A tripeptide product, Ala-Ile-His, bound in the active site of SCP-B has allowed for identification of the catalytic residues and the residues in subsites S1, S2, and S3, which are important for substrate binding. The most likely hydrolytic mechanism involves nucleophilic attack of a general base (Glu-136)-activated water (OH(-)) on the si-face of the scissile peptide carbonylcarbon atom to form a tetrahedral intermediate. Electrophilic assistance and oxyanion stabilization is provided by the side-chain amide of Gln-53. Protonation of the leaving-group nitrogen is accomplished by the general acid function of the protonated carboxyl group of Glu-136.

Amino Acid Sequence↗
PubMed2002

Air-stable, electron-deficient Fe(II) catalytic porphyrins. Characterization and molecular structures of rare high spin Fe(II) hexacoordinated porphyrins.

The synthesis, characterization, and molecular structures of the first air-stable, hexacoordinated high spin Fe(II) porphyrins (1) with axial alcohols are reported (1 = Fe(II) meso-tetrakis(o-dichlorophenyl)-beta-octanitroporphyrin). The structure of 1 with two axial waters is also presented. The very different conformations and metrics observed with the two types of ligands illustrate the acute interplay between ligands, conformations, and spin states in Fe porphyrins.

Journal Article↗
PubMed1990

[Relationship between molecular structure of halogenated methane compounds and their hypotensive effect in rats].

In this study gases of twelve halogenated methane compounds were administered by inspiration to Wistar rats in order to elucidate the relationship between molecular structure of the compounds and their hypotensive effect, and to develop new inhalational circulatory control agents. The correlation between the hypotensive effect of the compounds evaluated from the experimental data and computed van der Waals volume as well as surface area following molecular mechanics calculations of structure and energy, was investigated. The results showed that the compounds with van der Waals volume and surface area more than 73 A3 and 100 A2, respectively, had the hypotensive effect. In conclusion, our data suggest that the hypotensive effect of inhalational agents requires greater molecular sizes than regular ones.

Administration, Inhalation↗
PubMed2006

Prediction of the sorption of organic compounds into soil organic matter from molecular structure.

A new model to estimate the soil-water partition coefficient of non-ionic organic compounds normalized to soil organic carbon, Koc, from the two-dimensional molecular structure is presented. Literature data of log Koc for 571 organic chemicals were fitted to 29 parameters with a squared correlation coefficient r2 of 0.852 and a standard error of 0.469 log units. The application domain includes the atom types C, H, N, O, P, S, F, Cl, and Br in various important compound classes. The multilinear model contains the variables molecular weight, bond connectivity, molecular E-state, an indicator for nonpolar and weakly polar compounds, and 24 fragment corrections representing polar groups. The prediction capability is evaluated through an initial two-step development using an 80%:20% split of the data into training and prediction, cross-validation, permutation, and application to three external data sets. The discussion includes separate analyses for subsets of H-bond donors and acceptors as well as for nonpolar and weakly polar compounds. Comparison with existing models including linear solvation energy relationships illustrates the superiority of the new model.

Absorption↗
PubMed2006

Solid-state NMR studies of the molecular structure of Taxol.

Solid-state 13C{1H} cross-polarization/magic angle spinning spectroscopy (CP/MAS) has been utilized to extract the molecular structure information of Taxol, which is an anti-tumor therapeutic medicine extracted from the yew bark. The 13C signals have chemical shift values quite consistent with those measured in solution phase, and the overall chemical shift range is over 200 ppm. Notably, most of the 13C resonances of the taxane ring have two clearly resolved spectral components except the resonance peaks of C-15, C-16 and C-17, which are located at the central part of the taxane ring. On the basis of our NMR data, we propose that these doublets originate from two slightly different molecular conformations of the taxane ring and still the central part of the ring remains structurally similar. Furthermore, it is demonstrated that the 13C chemical shift difference deduced from the doublet splittings can serve as a direct measure of the structural difference between the two conformations, which could possibly correlate with the anti-tumor activity of Taxol.

Antineoplastic Agents, Phytogenic↗
PubMed2005

Revealing structural effects, part II: the influence of molecular structure on the adsorption of butanol isomers on platinum.

The nature of the adsorbates formed when butanol isomers interact with platinum electrodes in a perchloric acid medium was investigated by the application of on-line differential electrochemical mass spectrometry (DEMS) and cyclic voltammetry. In this way, the reactivity of the residues remaining on the electrode surface after a flow-cell experiment was established for the different molecules. It was found that the four isomers form strongly adsorbed species on the electrode, which undergo both electro-oxidation and electroreduction, depending on the potential applied at the electrode. Oxidative stripping of the adsorbates produces CO2 as the only oxidation product, whereas propane and the corresponding butane isomer are obtained on platinum in the hydrogen adsorption potential region. The yields of these hydrocarbons were found to depend strongly on the nature of the butanol isomer and on the adsorption potential. According to these results, it can be concluded that fragmentation of the butanol isomers occurs during adsorption and reduction reactions. C4 alkene and acetyl species are proposed as the adsorbed intermediates in all cases.

Journal Article↗
PubMed2005

Approaching the basis set limit for transition metal compounds with highly polar bonds: a benchmark coupled-cluster study of the ScF3 and FeF3 molecular structures and spectra.

The molecular equilibrium geometries, quadratic and cubic force constants, vibrational frequencies, and infrared intensities of scandium and iron trifluorides are determined ab initio with a sequence of atomic natural orbital basis sets using the CCSD(T) treatment of electron correlation. The largest basis set of spdf ghi quality contains 462 contracted Gaussian functions. Relativistic corrections are applied to compute the equilibrium geometries and vibrational frequencies. The cubic force constants are used to estimate vibrational corrections to the effective r(g) internuclear distances determined in the gas electron diffraction experiments. The computed molecular properties are extrapolated to the complete basis-set limit. The predicted values are compared to the available experimental data; uncertainties and inconsistencies in these data are then discussed.

Journal Article↗
PubMed2005

The role of molecular structure in the crystal polymorphism of local anesthetic drugs: crystal polymorphism of local anesthetic drugs, part X.

PURPOSE: This report is the résumé of a comprehensive investigation on the solid-state properties and the crystal polymorphism of the structurally homogenous class of local anesthetic drugs. The goal is to explore the relationship between crystal polymorphism and molecular structural features. METHODS: A salt form (mostly the hydrochloride) as well as the free base of 24 local anesthetics has been characterized by means of thermomicroscopy, differential scanning calorimetry, pycnometry, Fourier transform infrared, Fourier transform Raman, and solid-state NMR spectroscopies, as well as X-ray diffraction methods (single crystal, powder). RESULTS: Based on the thermochemical data, the relative thermodynamic stabilities of the different crystal forms of each polymorphic system were evaluated and visualized as semiquantitative energy/temperature diagrams. CONCLUSION: This study is the first step in recognizing relationships between the structure and the solid-state properties within this limited group of active substances with common structural elements. The results clearly show that there are certain relationships, but, to understand the phenomenological behavior in more detail on a molecular level, more structural information must be collected and analyzed by computational methods.

Adsorption↗
PubMed1992

Molecular structure of the acyl-enzyme intermediate in beta-lactam hydrolysis at 1.7 A resolution.

The X-ray crystal structure of the molecular complex of penicillin G with a deacylation-defective mutant of the RTEM-1 beta-lactamase from Escherichia coli shows how these antibiotics are recognized and destroyed. Penicillin G is covalently bound to Ser 70 0 gamma as an acyl-enzyme intermediate. The deduced catalytic mechanism uses Ser 70 0 gamma as the attacking nucleophile during acylation. Lys 73 N zeta acts as a general base in abstracting a proton from Ser 70 and transferring it to the thiazolidine ring nitrogen atom via Ser 130 0 gamma. Deacylation is accomplished by nucleophilic attack on the penicilloyl carbonyl carbon by a water molecule assisted by the general base, Glu 166.

Acylation↗
PubMed1997

A new plug-in software architecture applied for a portable molecular structure browser.

A new software configuration method using plug-in style components was established for the tool with the incremental development of software used in protein structural study. Our memory database provides the interface of data and functions among plug-in modules and its host program. A molecular structure browser program was developed together with several plug-in modules on our programming library that maintains graphics portability and user interfaces. This plug-in software architecture is generally useful for large-scale software development and for prototyping parts of the system.

Computer Graphics↗
PubMed1993

The crystal and molecular structure of beta-D-fructofuranosyl alpha-D-xylopyranoside hemihydrate.

The crystal and molecular structure of beta-D-fructofuranosyl alpha-D-xylopyranoside (xylosucrose) hemihydrate, C11H20O10.0.5H2O, is orthorhombic, P2(1)2(1)2, with a = 20.919(5), b = 18.727(2), c = 7.071(1) A, V = 2770.1(2) A3, Z = 8, and Dx = 1.541 g.cm-3. The structure was solved by direct methods and refined to R = 0.040 for 2564 observed reflections. Two independent xylosucrose molecules exist in the unit cell, and their conformations about the 1-->2' glycosidic bond are similar to sucrose. The orientations of the primary hydroxyl groups in the two molecules differ. An O-1'...O-2 intramolecular hydrogen bond was observed in the one molecule, while an O-6'...O-5 intramolecular hydrogen bond was observed in the other involving disorder of O-6'.

Carbohydrate Sequence↗
PubMed2006

Using trifluoroacetic acid to augment studies of potato suberin molecular structure.

Systematically varied reaction times and concentrations of trifluoroacetic acid (TFA) have been used to remove polysaccharides associated with suberin isolated from potato wound periderm, thereby augmenting spectroscopic determinations of the molecular structure of this protective plant polyester. Treatments with dilute TFA left a residual insoluble material for which both solid-state 13C and 1H NMR spectra displayed significant improvements in resolution without compromising the integrity of the protective plant polyester, whereas higher concentrations of TFA made it possible to achieve controlled hydrolysis of the suberin aliphatic or aromatic domains. Among the isolated fragments were two hydroxyphenyl derivatives reported previously in lignins and a novel aliphatic-aromatic ester trimer that is identified provisionally. Together these protocols help to characterize the carbohydrate types that are bound covalently to the suberin polyester and to identify the interunit covalent linkages among the aliphatic ester, phenolic, and carbohydrate moieties in suberized potato tissue. The strategies described herein may also advance molecular-level investigations of lignocellulosic materials or vegetable tissues that exhibit strengthened intercellular adhesion.

Indicators and Reagents↗
PubMed1983

First observation of a beta-turn conformation fused with the oxy-analogue of an alpha-turn: the molecular structure of a model peptide of the C-terminal part of gramicidin A.

The molecular structure of N-tert-butyloxycarbonyl-D-leucyl-L-phenylalanyl ethanolamide (t-Boc-D-Leu-L-Phe-EA), a protected analogue of the C-terminal dipeptide of the membrane-active linear antibiotic gramicidin A, has been determined by X-ray diffraction. One of the two independent molecules in the asymmetric unit is characterized by a chain reversal stabilized by an intramolecular, three-centre, double hydrogen bonding. It represents the first experimental evidence for a beta-turn conformation fused with the oxy-analogue of an alpha-turn.

Chemical Phenomena↗
PubMed1994

Application of machine learning to structural molecular biology.

A technique of machine learning, inductive logic programming implemented in the program GOLEM, has been applied to three problems in structural molecular biology. These problems are: the prediction of protein secondary structure; the identification of rules governing the arrangement of beta-sheets strands in the tertiary folding of proteins; and the modelling of a quantitative structure activity relationship (QSAR) of a series of drugs. For secondary structure prediction and the QSAR, GOLEM yielded predictions comparable with contemporary approaches including neural networks. Rules for beta-strand arrangement are derived and it is planned to contrast their accuracy with those obtained by human inspection. In all three studies GOLEM discovered rules that provided insight into the stereochemistry of the system. We conclude machine learning used together with human intervention will provide a powerful tool to discover patterns in biological sequences and structures.

Amino Acid Sequence↗
PubMed1984

The molecular structure of 11-methylbenz[a]anthracene: an almost planar substituted benz[a]anthracene.

The molecular structure of the almost inactive 11-methylbenz[a]anthracene has been determined by single-crystal X-ray diffraction analysis and refined to a final discrepancy index R of 0.036 over 955 independent reflections. With the benzo-ring A inclined at only 1.8 degrees to the furthest anthracene ring D, the benz[a]anthracene nucleus is much more nearly planar than in other (and carcinogenically more active) benz[a]anthracenes with bay-methyl substituents. Several carbon atoms in rings D and A deviate by approximately 0.05 A from the mean plane through the ring-carbon atoms of the bay-ring B. The shortest carbon-carbon bonds are C5-C6 = 1.341(5) A (at the K-region), C3-C4 = 1.355(5) and C8-C9 = 1.360(5) A, while C10-C11 next to the substituent is also quite short at 1.367(5) A.

Benz(a)Anthracenes↗