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At least 271 records · Page 15Linked to original sources
PubMed1990

Molecular structure of nicked DNA: a substrate for DNA repair enzymes.

The molecular structure of a nicked dodecamer DNA double helix, made of a ternary system containing d(CGCGAAAACGCG) + d(CGCGTT) + d(TTCGCG) oligonucleotides, has been determined by x-ray diffraction analysis at 3 A resolution. The molecule adopts a B-DNA conformation, not unlike those found in intact dodecamer DNA molecules crystallized in a somewhat different crystal lattice, despite a gap due to the absence of a phosphate group in the molecule. The helix has a distinct narrow minor groove near the center of the molecule at the AAAA region. This suggests that the internal stabilizing forces due to base stacking and hydrogen-bonding interactions are sufficient to overcome the loss of connectivity associated with the disruption of the covalent backbone of DNA.

Base Sequence↗
PubMed2004

Molecular structure, spectroscopy and matrix photochemistry of fluorocarbonyl iodide, FC(O)I.

The molecular structure of FC(O)I has been determined by gas electron diffraction. High-level ab initio methods, including coupled-cluster and the new correlation-consistent basis sets for fourth row elements, have been used to calculate the structure of FC(O)I. A comprehensive vibrational spectroscopic study (both IR and Raman) complemented by high-level calculations has also been performed. Furthermore, UV, mass, and NMR spectra have been recorded for FC(O)I. The matrix photochemistry of FC(O)I has been studied with a low-pressure mercury lamp and with a high-pressure xenon lamp in combination with interference and cut-off filters. UV photolysis revealed the formation of the OC. IF and OC.FI complexes and further photolysis of these complexes at lambda>320 nm resulted in a re-formation of FC(O)I. The structural conformation of the complexes has been characterized by comparing shifts in their CO and IF vibrational modes with respect to those of the free species. The structures, vibrational properties, and stability of the complexes were analyzed with the aid of coupled-cluster ab initio calculations.

Journal Article↗
PubMed2006

An intricate molecule: aluminum triiodide. Molecular structure of AlI3 and Al2I6 from electron diffraction and computation.

The molecular structure of aluminum triiodide was investigated in the gas phase by high-temperature gas-phase electron diffraction and high-level computations. The geometries of monomeric, AlI3, and dimeric, Al2I6, molecules were determined from two separate experiments carried out under carefully controlled conditions to prevent decomposition. This is the first experimental determination of the dimer structure by modern techniques. The computed geometrical parameters strongly depend on the applied methods and basis sets as well as on core-valence correlation effects. The electron diffraction thermal average bond length, r(g), of AlI3 at 700 K is 2.448(6) A; while those of Al2I6 at 430 K are 2.456(6) A (terminal) and 2.670(8) A (bridging). The equilibrium geometry of the monomer molecule is planar with D(3h) symmetry. The dimer molecule is extremely floppy, and it is difficult to determine the symmetry of its equilibrium geometry by computation, as it is sensitive to the applied methods. MP2 and CCSD calculations find the Al2I6 molecule puckered with C(2v) symmetry (although with a very small barrier at planarity), while density functional methods give a structure with a planar central ring of D(2h) symmetry. Comparison of the computed vibrational frequencies with the gas-phase experimental ones favors the D(2h) symmetry structure.

Journal Article↗
PubMed1994

Molecular structure of a heme-copper redox center of the Escherichia coli ubiquinol oxidase: evidence and model.

Biochemical, spectroscopic, and molecular biological studies on bacterial respiratory oxidases in the last decade have greatly increased our understanding of a molecular structure of the metal centers which catalyze the dioxygen reduction chemistry. Based upon the latest physicochemical and molecular biological evidence and theoretical consideration of a folding mechanics of membrane proteins, we propose here the tertiary structure of the heme-copper metal center of the Escherichia coli bo-type ubiquinol oxidase, the cytochrome bo complex. The molecular mechanism of electron transfer-coupled proton pumping in the heme-copper respiratory oxidases is reviewed on the basis of this predicted model.

Amino Acid Sequence↗
PubMed2005

Molecular structure, vibrational spectra and photochemistry of 2-methyl-2H-tetrazol-5-amine in solid argon.

In this work, the molecular structure, infrared spectrum and UV photochemistry of 2-methyl-2H-tetrazol-5-amine (2MTA) isolated in solid argon (10 K) were investigated. The experimental studies were supported by extensive DFT(B3LYP)/6-311++G(d,p) calculations. The infrared spectrum of matrix-isolated 2MTA was fully assigned and correlated with structural properties. Taking into consideration the observed frequency of the NH2 wagging mode, it is suggested that, in the matrixes, the amine group becomes slightly more planar than in the gas phase, due to matrix-packing effects. In situ UV irradiation (lambda > 235 nm) of the matrix-isolated 2MTA monomer is shown to induce three main primary photochemical processes: (1) tautomerization to mesoionic 3-methyl-1H-tetrazol-3-ium-5-aminide; (2) nitrogen elimination, with production of 1-methyl-1H-diazirene-3-amine; (3) ring cleavage leading to production of methyl azide and cyanamide. Following the primary photoproducts, secondary reactions were observed, leading to spectroscopic observation of methylenimine and isocyanidric acid.

Argon↗
PubMed2006

On the emergence of molecular structure from atomic shape in the 1/r2 harmonium model.

The formal similarity of the three-body Hamiltonians for helium and the hydrogen molecule ion is used to demonstrate the unfolding of a rotating dumbbell-like proton distribution from a (1s)2-type electron distribution by smooth variation of the particles' masses in the 1/r2 harmonium model. The 1/r2 harmonium is an exactly solvable modification of the harmonium model (also known as Hooke's law atom) where the attraction between different particles is harmonic and the repulsion between the two equal particles is given by a 1/r2 potential. The dumbbell-like molecular structure appears as an expression of increasing spatial correlation due to increasing mass. It gradually appears in the one-density distribution of the two equal particles if their mass exceeds a critical value depending on the mass of the third particle. For large mass of the equal particles, their one-density distribution approaches an asymptotic form derived from the Born-Oppenheimer treatment of H2+ in the 1/r2 harmonium model. Below the critical value, the one density is a spherical, Gaussian-type atomic density distribution with a maximum at the center of mass. The topological transition at the critical value separates molecular structure and atomic shape as two qualitatively different manifestations of spatial structure.

Journal Article↗
PubMed1990

Molecular structure of F-actin and location of surface binding sites.

Comparisons of three-dimensional maps of vertebrate muscle thin filaments obtained by cryo-electron microscopy and image analysis, reveal the molecular structure of F-actin, the location of the C terminus of the monomer and the positions of the binding sites of tropomyosin, the myosin head and the N-terminal portion of the myosin A1 light chain on the filament. These data provide strong constraints for evaluating models built from the atomic structure of the monomer and the subsequent identification of molecular contacts.

Actins↗
PubMed1986

Relationships of the molecular structure of aldosterone derivatives with their binding affinity for mineralocorticoid receptor.

The molecular structures of 19-nor-11-deoxycorticosterone (III) and 21-hydroxypregna-4,11-diene-3,20-dione (IV) were determined by X-ray crystallographic analysis and the factors affecting the binding affinities for the mineralocorticoid receptor were examined with six aldosterone derivatives (I-VI) containing these two compounds. The most important factor was found to be the steric one; affinity increased with increasing flatness of the structure. The electronic factor may be a minor influence although a good relationship was found between the affinity and the 13C-NMR chemical shift of the C(5) atom. The factor playing no role in the binding is the hydrophobic one.

Aldosterone↗
PubMed1999

The molecular structure of 2alpha-hydroxyneoanisatin and structure-activity relationships among convulsant sesquiterpenes of the seco-prezizaane and picrotoxane types.

The molecular structure of 2alpha-hydroxyneoanisatin, a positional isomer of the potent neurotoxin anisatin, was determined by X-ray crystallographic analysis. This compound and four further seco-prezizaane type sesquiterpene lactones previously isolated from Illicium floridanum, which represent different structural types with respect to the mode of cyclisation, did not induce anisatin/picrotoxinin-like convulsions in mice. Based on these results and literature data for other seco-prezizaanes, structural requirements for convulsant activity are discussed. Comparison of the three dimensional molecular shape and electrostatic properties of active and inactive seco-prezizaane type lactones with compounds of the picrotoxane type resulted in the identification of a common pharmacophore structure for these different skeletal classes of convulsant natural products.

Animals↗
PubMed1990

Crystal and molecular structure of Boc-D-Ala-delta Phe-Gly-delta Phe- D-Ala-OMe: a 3 10-helical dehydropeptide.

The crystal and molecular structure of the pentapeptide Boc-D-Ala-delta Phe-Gly-delta Phe-D-Ala-OMe, containing two dehydrophenylalanine residues, was determined by x-ray diffraction. The molecule crystallizes in the orthorombic P2(1)2(1)2(1) space group, with a = 10.439(3), b = 15.319(3) and c = 21.099(4) A. In the solid state, the conformation of the pentapeptide is characterized by the presence of two type III' beta-turns. Thus the peptide assumes a left-handed 3(10-helical conformation, the left sense being due to the D configuration of the alanine residues. The two unsaturated residues are located in the (i + 1) position of the first beta-turn and in the (i + 2) position of the second beta-turn, respectively. In the crystal, the helical molecules are linked head to tail by hydrogen bonds. Lateral hydrogen bonds are also formed between molecules related by a twofold screw symmetry. This gives rise to a typical mode of packing characterized by infinite helical "chains,' similar to the packing found in other oligopeptides that adopt a 3(10)-helical structure.

Amino Acid Sequence↗
PubMed1964

THE CRYSTAL AND MOLECULAR STRUCTURE OF 5-FLURO-2'-DEOXY-BETA-URIDINE.

The crystal structure of 5-fluoro-2'-deoxy-beta-uridine (FUDR) has been solved and the details of the molecular structure determined by x-ray analysis. The bond lengths and angles have been measured and are compared with the dimensions found for calcium thymidylate and adenylic acid. In all three compounds the bonds formed by the nitrogen atom involved in the glycosidic bond are not coplanar. Furthermore, it is found that in FUDR the C2' carbon atom is out of the plane of the ribose ring. The possible effect of these observations on nucleic acid structures is discussed.

Chemical Phenomena↗
PubMed1989

Molecular structure of DNA by scanning tunneling microscopy.

Uncoated DNA molecules marked with an activated tris(l-aziridinyl) phosphine oxide (TAPO) solution were deposited on gold substrates and imaged in air with the use of a high-resolution scanning tunneling microscope (STM). Constant-current and gap-modulated STM images show clear evidence of the helicity of the DNA structure: pitch periodicity ranges from 25 to 35 angstroms, whereas the average diameter is 20 angstroms. Molecular structure within a single helix turn was also observed.

DNA↗
PubMed2006

The molecular structure and vibrational spectra of 1-amino-5-benzoyl-4-phenylpyrimidin-2(1H) by Hartree-Fock and density functional methods.

The molecular structure and vibrational spectra of 1-amino-5-benzoyl-4-phenylpyrimidin-2(1H) (C(17)H(13)N(3)O(2)) have been investigated by Hartree-Fock and density functional method using standard B3LYP with 6-31G(d) basis set. The calculated results of the geometric bond lengths and bond angles obtained by using HF and DFT (B3LYP) are in very good agreement with the experimental values. Comparison of the observed fundamental vibrational frequencies of 1-amino-5-benzoyl-4-phenylpyrimidin-2(1H) (C(17)H(13)N(3)O(2)) and calculated results by density functional B3LYP and Hartree-Fock methods indicate that B3LYP is superior to the scaled Hartree-Fock approach for molecular vibrational problems.

Algorithms↗
PubMed1997

Selective release of human adipocyte fatty acids according to molecular structure.

The objective of the present study was to investigate the mobilization of individual fatty acids from human white fat cells. Mammary adipose tissue from eight healthy non-obese women in their normal dietary state was collected, and isolated adipocytes were incubated with lipolytic agents. The mobilization of 34 individual fatty acids was measured by comparing the composition of non-esterified fatty acids (NEFA) with that of the triacylglycerols (TAG) from which they originated through lipolysis. Compared with TAG, NEFA were enriched in some polyunsaturated fatty acids with 18-20 carbon atoms. Conversely, the percentage of very-long-chain (20-22 carbon atoms) saturated and monounsaturated fatty acids was approx. 2 times lower in NEFA than in TAG. The relative mobilization (% in NEFA/% in TAG) of the most readily mobilized fatty acid (C20:5, n-3; 2.25) was more than 6-fold higher than that of the least readily mobilized (C22:1,n-11; 0.37). Relationships were found between the molecular structure of fatty acids and their mobilization rate. For a given chain length, the relative mobilization rate increased with increasing unsaturation, whereas for a given unsaturation, it decreased with increasing chain length. The relative mobilization rate for essential fatty acids decreased in the following order: C20:5,n-3>C20:4,n-6>C18:3,n-3>C18:2, n-6>C22:6,n-3. Interestingly, C20:5,n-3 and C20:4,n-6, which are respectively precursors of the 3- and 2-series of prostaglandins, were preferentially mobilized. It is concluded that fatty acids are selectively mobilized from human fat cells according to molecular structure, in full agreement with animal studies. By modulating the qualitative fatty acid supply to organs and by remodelling the fatty acid composition of adipose tissue, this selectivity would be relevant for consideration in physiology, health and epidemiology.

Adipocytes↗
PubMed1989

The crystal and molecular structure of the alpha-helical nonapeptide antibiotic leucinostatin A.

The crystal and molecular structure of the nonapeptide antibiotic leucinostatin A, containing some uncommon amino acids and three Aib residues, has been determined by x-ray diffraction analysis. The molecule crystallizes in the orthorhombic space group P2(1)2(1)2(1), a = 10.924, b = 17.810, c = 40.50 A, C62H111N11O13, HCl.H2O, Z = 4. The peptide backbone folds in a regular right-handed alpha-helix conformation, with six intramolecular i----(i + 4) hydrogen bonds, forming C13 rings. The nonapeptide chain includes at the C end an unusual beta-Ala residue, which also adopts the helical structure of the other eight residues. In the crystal the helices are linked head to tail by electrostatic and hydrogen-bond interactions, forming continuous helical rods. The crystal packing is formed by adjacent parallel and antiparallel helical rods. Between adjacent parallel helical columns there are only van der Waals contacts, while between adjacent antiparallel helical columns hydrogen-bond interactions are formed.

Amino Acid Sequence↗
PubMed1999

[The relationship between the thin-layer chromatographic retention values and the molecular structures of a group of amino acids by using back-propagation artificial neural networks].

The relationship between the thin-layer chromatographic retention values and the molecular structures of fifteen amino acids was studied by using back-propagation artificial neural networks (ANNs). In this paper, firstly, lots of parameters of amino acids have been determined, accumulated and computed. Then, correlation coefficients of all parameters were computed by taking advantage of correlation analysis. Taking the correlation coefficient approaching one as the criteria in the correlation analysis, all parameters were classified into three kinds. Three parameters were selected from each kind, respectively, to consist of one group. Then, the optimized groups of parameters, which have clearer physicochemical meanings, were used as the inputting parameters of artificial neural networks. Correlation coefficients of experimental retardation values and those calculated by using ANNs were computed and showed good agreement. The present work shows that the ANNs method may take an important role in the study of the relationship between TLC behavior and compound structure.

Amino Acids↗
PubMed1997

[Crystal and molecular structure of the antimalarial agent alpha-(dibutylaminomethyl)-2, 7-dichloro-9-(p-chlorobenzylidene)-4- fluorenemethanol(benflumetol)].

The three-dimensional crystal and molecular structure of benflumetol(I), alpha-(dibutylaminomethyl)-2, 7-dichloro-9-(p-chlorobenzylidene)-4-fluorenemethanol, was determined by X-ray crystallography and compared with the crystal structures of the cinchona alkaloids. The aromatic rings of fluorene-phenyl system of benflumetol are twisted from each other by 52.8 degrees. The torsion angle of N-C-C-O of benflumetol is 47.6 degrees. The intramolecular aliphatic N-O distance in benflumetol is 2.709A, which is close to the N-O distance found in antimalarial cinchona alkaloids. Benflumetol contains an intramolecular hydrogen bond between the aliphatic nitrogen and oxygen atoms, no intermolecular hydrogen bond was found, which is different from the known amino alcohol antimalarials.

Antimalarials↗