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At least 469 records · Page 26Linked to original sources
PubMed1980

[Molecular structure of hybrid phage phi80hy43].

The phage hybrid phi80hy43 derived from a vegetative cross phi80cIhlambda x lambdacIc17 was constructed for discrimination phi80mono- and polylysogens. Molecular structure of this hybrid was established using heteroduplex analysis and restriction endonuclease EcoRI. It is found that the hybrid phi80hy43 represents a phage phi80 containing a foreign piece of DNA between genes cI and 0. The length of this piece of DNA comprises 0.7%, corresponding to the length of cy-cII region of th phage lambda. So it is believed that the hybrid phi80hy43 was formed due to insertion of the lambdacy region with the mutation c17 into phi80hlambda phage genome.

Bacteriophage lambda↗
PubMed1975

Structural studies of metabolic products of dopamine. IV. Crystal and molecular structure of (-)-noradrenaline.

The crystal structure of (-)-noradrenaline has been determined by X-ray methods, using 1000 observed reflections collected by counter diffractometer techniques. The crystals are orthorhombic, space group P212121, with a=8.611(2), B=6.138(2), And c=14.912(4) A. Least-squares refinements yielded a conventional R-factor of 0.036. Standard deviations in bond lengths are 0.003 A and in bond angles 0.2 degrees. The crystal structure of (-)-noradrenaline corresponds closely to that of (-)-adrenaline in molecular geometry, conformation, and arrangement in the crystals. The results of the structure investigations are discussed in relation to the biological activity of these biogenic amines.

Chemical Phenomena↗
PubMedDate not supplied

Prediction of aqueous solubility of heteroatom-containing organic compounds from molecular structure.

The use of quantitative structure-property relationships (QSPRs) to predict aqueous solubilities (log S) of heteroatom-containing organic compounds from their molecular structure is presented. Three data sets are examined. Data set 1 contains 176 compounds having one or more nitrogen atoms with some oxygen (log S[mol/L] range is -7.41 to 0.96). Data set 2 contains 223 compounds having one or more oxygen atoms, with no nitrogen (log S[mol/L] range is -8.77 to 1.57). Data set 3 contains all 399 compounds from sets 1 and 2 (log S/mol/L] range is -8.77 to 1.57). After descriptor generation and feature selection, multiple linear regression (MLR) and computational neural network (CNN) models are developed for aqueous solubility prediction. The best results were obtained with nonlinear CNN models. Root-mean-square (rms) errors for training with the three data sets ranged from 0.3 to 0.6 log units. All models were validated with external prediction sets, with the rms errors ranging from 0.6 log units to 1.5 log units.

Journal Article↗
PubMed2006

The molecular structure and vibrational spectra of 3-acetyl-4-[N-(2'-aminopyridinyl)-3-amino]-3-buten-2-one by Hartree-Fock and density functional theory calculations.

The molecular structure and vibrational spectra of 3-acetyl-4-[N-(2'-aminopyridinyl)-3-amino]-3-buten-2-one (C(11)H(13)N(3)O(2)) in the ground state have been investigated by Hartree-Fock and density functional method (B3LYP and BLYP) with 6-31G(d) basis set. The optimized geometric bond lengths and bond angles obtained by using HF and DFT show the best agreement with the experimental data. Comparison of the observed fundamental vibrational frequencies of title compound and calculated results by HF and DFT methods indicate that B3LYP is superior to the scaled HF approach for molecular problems.

Butanones↗
PubMed2005

Dative sigma- and pi-bonding in boron-nitrogen compounds: molecular structures of (CH3)2NB(CH3)N(CH3)B(CH3)2 and [(CH3)2B]2NN(CH3)2 determined by gas electron diffraction and quantum chemical calculations.

The molecular structures of dimethylamino[(dimethylboryl)methylamino]methylborane, Me2NBMeNMeBMe2 (1) and 1,1-bis(dimethylboryl)-2,2-dimethylhydrazine, (Me2B)2NNMe2 (2) have been determined by gas electron diffraction (GED), density functional theory calculations at the B3PW91/6-311++G** level and ab initio calculations at the MP2/6-311++G** level. 1 adopts an open structure similar to that of the isoelectronic hydrocarbon molecule permethylbutadiene; the central B-N bond distance at 148.0/149.3(7) pm (MP2/GED) corresponds to a single covalent N--B bond distance, the two terminal distances, 140.9/140.5(4) pm and 141.8/141.3(4) pm, correspond to the distance between N and B atoms joined by a covalent sigma-bond and a dative pi-bond. A closed form where the establishment of a dative bond between the terminal N and B atoms has led to the formation of a four-membered ring also corresponds to a minimum on the potential energy surface, but the energy is calculated to be 14.3 kJ mol(-1) higher at the MP2 level. This structure is also incompatible with the GED data. 2 adopts a structure in which a dative sigma-bond between the dimethylamino N atom and one of the boron atoms has led to the formation of a three-membered N(2)B ring. The dative sigma-bond distance is 165.5/164.0(13) pm, the two other bond distances in the ring are N-B=150.6/148.9(9) pm corresponding to a covalent sigma-bond and N-N=145.1/145.4(3) pm. The terminal B--N distance 139.6/138.9(9) pm is consistent with a covalent sigma-bond augmented by a dative pi-bond. An open Y-shaped structure also corresponds to a minimum on the potential energy surface, but the energy is 18.7 kJ mol(-1) higher (MP2) and it is incompatible with the GED data.

Journal Article↗
PubMed2006

Theoretical studies of molecular structure and vibrational spectra of melaminium citrate.

The molecular geometry and vibrational frequencies of melaminium citrate in the ground state have been calculated using the Hartree-Fock (HF) and density functional method (B3LYP) with 6-31G(d) basis set. The optimized geometric bond lengths and bond angles obtained by using HF and density functional theory (DFT, B3LYP) show the best agreement with the experimental data. Comparison of the observed fundamental vibrational frequencies of melaminium citrate 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.

Citrates↗
PubMed2002

Molecular structures of two metal tetrakis(tetrahydroborates), Zr(BH4)(4) and U(BH4)(4): equilibrium conformations and barriers to internal rotation of the triply bridging BH4 groups.

The molecular structures of Zr[(mu-H)(3)BH](4) and U[(mu-H)(3)BH](4) have been investigated by density functional theory (DFT) calculations and gas electron diffraction (GED). The triply bridged bonding mode of the tetrahydroborate groups in the former is confirmed, but both DFT calculations and GED structure refinements indicate that the BH(4) groups are rotated some 12 degrees away from the orientation in which the three bridging B-H bonds are staggered with respect to the opposing ZrB(3) fragment. As a result the symmetry of the equilibrium conformation is reduced from T(d) to T. Bond distances and valence angles are as follows (DFT/GED): Zr-B = 232.2/232.4(5) pm; Zr-H(b) = 214.8/214.4(6) pm; B-H(b) = 125.3/127.8(8) pm; B-H(t) = 119.4/118.8(17) pm; angle ZrBH(b) = 66.2/65.6(3) degrees; the smallest dihedral angle of type tau(BZrBH(b)) = 48/45(2) degrees. DFT calculations on Hf(BH(4))(4) indicate that the structure of this molecule is very similar to that of the Zr analogue. Matrix-isolation IR spectroscopy and DFT calculations on U(BH(4))(4) show that while the polymeric solid-state structure is characterized by terminal triply bridging and metal-metal bridging bidentate BH(4) groups, all BH(4) groups are triply bridging in the gaseous monomer. Calculations with one of the two nonbonding 5f electrons on U occupying an a(1) and the other distributed equally among the three t(2) orbitals indicate that the equilibrium conformation has T(d) symmetry, i.e. that the three B-H(b) bonds of each tetrahydroborate group are exactly staggered with respect to the opposing UB(3) fragment with tau(BUBH(b)) = 60 degrees. Calculations including spin-orbit interactions indicate that Jahn-Teller distortions from T(d) symmetry are either absent or very small. The best agreement between observed and calculated GED intensity data was obtained for a model of T(d) symmetry, but models of T symmetry with dihedral angles tau(BUBH(b)) > 42 degrees cannot be ruled out. Bond distances and valence angles are as follows (DFT/GED): U-B = 248.8/251.2(4) pm; U-H(b) = 227.7/231.5(6) pm; B-H(b) = 126.0/131.6(5) pm, B-H(t) = 119.5/117.8(11) pm; angle UBH(b) = 65.6/63.1(3) degrees. It is suggested that the different equilibrium conformations of the three molecules are determined primarily by repulsion between bridging H atoms in different tetrahydroborate groups.

Journal Article↗
PubMed2006

Molecular structures of arachno-decaborane derivatives 6,9-X2B8H10 (X = CH2, NH, Se) including a gas-phase electron-diffraction study of 6,9-C2B8H14.

The molecular structures of the three heterodecaboranes arachno-6,9-C2B8H14, arachno-6,9-N2B8H12, and arachno-6,9-Se2B8H10 have been determined by ab initio MO theory. In addition, the structure of arachno-6,9-C2B8H14 was experimentally determined using gas-phase electron diffraction (GED). The accuracy of all four of these structures has been confirmed by the good agreement of the (11)B chemical shifts calculated at the GIAO-MP2 level with the experimental values. A comparison of the GIAO-HF and GIAO-MP2 methods shows that for these heteroborane clusters, electron correlation effects on the computed delta((11)B) values are quite substantial and that it is necessary to go beyond the HF level in the NMR computation.

Journal Article↗
PubMed2006

Synthesis, molecular structure, and reactivity of the isolable silylenoid with a tricoordinate silicon.

The first tricoordinate fluorosilylenoid, (t-Bu2MeSi)2SiFLi.3THF (1), was synthesized, and its X-ray molecular structure was determined. 1 was synthesized in 40% yield by a bromine-lithium exchange reaction in THF of the corresponding fluorobromosilane with t-Bu2MeSiLi. 1 is best described as an R2SiF- anion attracted to a (Li.3THF)+ cation with a small contribution of resonance structure that consists of a silylene fragment and FLi.3THF. 1 reacts as a nucleophile with MeCl, PhH2SiCl, H2O, and MeOH, as an electrophile with MeLi, and as a silylene with Li (or t-BuLi) and Na, yielding alpha-lithium and alpha-sodium silyl radicals, respectively. Either photolysis or thermolysis of 1 yields the corresponding disilene R2Si=SiR2 (R = t-Bu2MeSi), probably via dimerization of R2Si:.

Journal Article↗
PubMed1997

Molecular Structure of 3,4-Dimethylenehexa-1,5-diene ([4]Dendralene), C(8)H(10), in the Gas Phase As Determined by Electron Diffraction and ab Initio Calculations.

The molecular structure of 3,4-dimethylenehexa-1,5-diene ([4]dendralene), C(8)H(10), has been determined in the gas phase. A single conformer with C(2) symmetry, having two almost planar, anti butadiene groups orientated with a dihedral angle C(2)C(3)C(4)C(5) of 71.7(19) degrees, is detected by electron diffraction employing flexible restraints derived from ab initio computations. Other experimental structural parameters (r(alpha)/pm, angle(alpha)/ degrees ) are: C(1)=C(2) 133.4(1), C(3)=C(7) (not in main chain) 134.0(1), C(2)-C(3) 147.4(2), C(3)-C(4) 149.6(3), C(1)C(2)C(3) 124.4(3), C(2)C(3)C(4) 119.2(5), C(4)C(3)C(7) 117.6(7), and C(7)C(3)C(2)C(1) -174.8(28). Ab initio computations at the MP2/6-311G level predict that the vapor consists of ca. 90% of the conformer found experimentally, the other 10% comprising four other conformers.

Journal Article↗
PubMed2006

Molecular structure of a supported VO4 cluster and its interfacial geometry as a function of the SiO2, Nb2O5, and ZrO2 support.

The influence of the support oxide on the molecular structure of a VO(4) cluster and its interfacial geometry has been determined for SiO(2), Nb(2)O(5), and ZrO(2) as supports. Raman, IR, UV-vis-NIR diffuse reflectance, electron spin resonance, and extended X-ray absorption fine structure (EXAFS) spectroscopies were used to characterize the supported vanadium oxide clusters after dehydration. It has been found that for all supports under investigation the vanadium ion is tetrahedral coordinated and consists of one V=O and three V-O bonds. For a VO(4)/SiO(2) catalyst it has been established that only one O neighbor is shared with the SiO(2) support via a V-O(b)-Si(support) bond with an angle of approximately 101 degrees (+/-0.5 degrees ) and a V...Si distance of 2.61 A. The absence of a second vanadium atom in the vicinity of the vanadium oxide cluster further subverts the classical assignment of the 920 cm(-1) Raman band to a V-O-V related vibration. The EXAFS results combined with structural modeling using Cerius(2) software lead to structural constraints, which imply a similar V-O(b)-M(support) interaction for Nb(2)O(5) and ZrO(2) as well. The V-O(b) and the V...M(support) distances depend on the geometry of each support surface. The results show that the classical model with three V-O(b)-M(support) bonds could not be experimentally observed with EXAFS under the applied measuring conditions. Additional experiments with IR and Raman spectroscopy under experimental conditions mimicking those of the EXAFS measurements reveal the presence of V-OH groups, giving further support for the presence of a O=V(OH)(2)-O(b)-M moiety at the support surface.

Journal Article↗
PubMed2004

Molecular structure of tris(dipivaloylmethanato)lutetium(iii) studied by gas electron diffraction and ab initio and DFT calculations.

Combined gas electron diffraction/mass spectrometry (GED/MS) was used to determine the molecular structure of tris(dipivaloylmethanato)lutetium(III), Lu(dpm)(3)(dpm = 2,2,6,6-tetramethyl-heptane-3,5-dionato). Up to about 520-570 K the vapour consisted only of molecules Lu(dpm)(3). The experimental data recorded at 408(5) K indicate that the molecules have D(3) symmetry. The bond distances (r(h1)) in the chelate ring are Lu-O 2.197(6) Angstrom, C-O 1.270(4) Angstrom and C-C 1.390(6) Angstrom . Theoretical computations at the HF and DFT levels with basis sets up to 6-311G* afford structures similar to those found experimentally, with a distorted LuO(6) antiprism.

Journal Article↗
PubMed1996

The molecular structure of reptilian keratin.

X-ray diffraction and electron microscope studies of hard keratins (e.g. claws, scales, feathers and hair) have shown that they all have a filamentous texture but that the molecular structure of the filaments in mammalian keratins is quite different from that in avian keratins. The framework of the filaments in mammalian keratin consists of two-strand coiled coils of alpha-helices whereas the framework in avian keratins is composed of beta-sheets. Reptilian hard keratins have not been studied in detail but the X-ray diffraction pattern is very similar to that obtained from avian hard keratins leading to the supposition that the framework of the filaments is also composed of beta-sheets. The present contribution describes an analysis of the sequence of a lizard claw protein using structural probes which reveal the origins of the common structural features of the filaments in avian and reptilian keratin.

Animals↗
PubMed1974

The Crystal and Molecular Structure of Ethyl Chlorophyllide a.2H(2)O and Its Relationship to the Structure and Aggregation of Chlorophyll a.

Determination of the crystal structure of ethyl chlorophyllide a.2H(2)O by single crystal x-ray diffraction techniques has provided the first detailed molecular structural data available for a magnesium-containing derivative of chlorophyll. At the same time the aggregation observed in this structure serves as the basis for a model of chlorophyll aggregation in vitro and in vivo. The magnesium atom in ethyl chlorophyllide is displaced 0.4 A from the plane of the chlorin ring in the same direction as the methyl ester substituent. A water molecule occupies the fifth coordination site. A second water molecule is hydrogen bonded to the coordinated water molecule and also to the carbonyl oxygen atom of the methyl ester. Hydrogen bonds between the water molecules and carbonyl oxygen atoms link the chlorophyllide molecules into a two-dimensional aggregate of crosslinked one-dimensional polymers. The relationship of this aggregate to aggregates of chlorophyll both in vitro and in vivo is discussed, as is the efficiency of exciton transport within the polymer.

Journal Article↗
PubMed1989

The molecular structure of Okazaki fragment r(CGCA)d(AAAAAGCG):d(CGCTTTTTTGCG) in solution.

The hetero duplex molecule, r(CGCA)d(AAAAAGCG):d(CGCTTTTTTGCG) which corresponds to Okazaki fragment was synthesized and its molecular structure has been analyzed by NMR study. The RNA strand of RNA-DNA hybrid region adopts A-form and DNA strand of the same region deviates from the standard B-form. The conformation of DNA-DNA duplex segment belongs to B-form. The hybrid-DNA duplex junction shows a structural discontinuities, A-B junction. The same conformational characteristic of oligo(dA): oligo(dT) tract as that of DNA oligomer which has same base sequence has been observed.

Base Sequence↗
PubMed2000

Molecular structure of polystyrene at Air/Polymer and Solid/Polymer interfaces

IR-visible sum-frequency generation (SFG) spectroscopy has been used in a total internal reflection geometry to study the molecular structure of polystyrene (PS) at PS/sapphire and PS/air interfaces, simultaneously. The symmetric vibrational modes of the phenyl rings dominate the SFG spectra at the PS/air interface as compared to the antisymmetric vibrational modes at the PS/sapphire interface. This indicates approximately parallel orientation of the phenyl rings at the PS/air interface while nearly perpendicular orientation at the PS/sapphire interface, with respect to the surface normal.

Journal Article↗
PubMed1985

Synthesis and molecular structure of prolame, N-(3-hydroxy-1,3,5(10)-estratrien-17 beta-yl)-3-hydroxypropylamine; an amino-estrogen with prolonged anticoagulant and brief estrogenic effects.

The synthesis and molecular structure of prolame, N-(3-hydroxy-1,3,5(10)-estratrien-17 beta-yl)-3-hydroxypropylamine, is described. It was characterized by ir, nmr, mass spectrometry and chemical analysis. The crystal structure of this compound was determined by single-crystal x-ray diffraction. Prolame belongs to space group P212121. Cell dimensions are: a = 8.356(2), b = 13.343(4) and c = 16.119(4) A. Z = 4; R = 4.1%.

Anticoagulants↗