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Bond Angles (bond + angle)
Kinds of Bond Angles Selected AbstractsDesign of a G-Quadruplex Topology through Glycosidic Bond Angles,ANGEWANDTE CHEMIE, Issue 48 2009Mateus Webba, Silva Dr. Baugenehmigung: Bisher wurden neuartige DNA-Quadruplextopologien durch Zufall entdeckt. Mit dem hier vorgestellten System lassen sich nun auf der Grundlage des Winkels der Glycosidbindung von Guanosinen einige Regeln ableiten, um Quadruplextopologien vorherzusagen. Die Methode wurde auf bekannte Strukturen angewendet und genutzt, um neue selbstorganisierte DNA-Quadruplexe zu erhalten. [source] The Room-Temperature Superstructure of ZrP2O7 Is Orthorhombic: There Are no Unusual 180° P,O,P Bond Angles.CHEMINFORM, Issue 33 2006Henrik Birkedal Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF. [source] Sodium Hydro(isothiocyanato)borates: Synthesis and StructuresEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 5 2004Heinrich Nöth Abstract Sodium thiocyanate reacts in THF solution with 18-crown-6 to give the molecular compound Na(18-crown-6)(THF)NCS (3) with the N atom of the NCS anion oriented towards Na+. The same reaction with 15-crown-5 yields the ion pair Na(15-crown-5)NCS (4). In contrast, Na(NCS)(py)4, obtained by treating a solution of Na(H3BNCS) in THF with pyridine, yields Na(py)4(NCS) (5), which has a chain structure with hexacoordinate Na atoms coordinated to five N atoms and an S atom. Na(NCS) in THF adds 1 equiv. of BH3 to give Na(H3BNCS)·nTHF. Addition of 18-crown-6 to this solution yields crystals of the salt [Na(18-crown-6)(THF)2][H3BNCS] (1), as shown by X-ray crystallography. Both the cation and the anion show site disorder. However, when 15-crown-5 is used for complexation, the salt [Na(15-crown-5)(THF)][H3BNCS] (2) can be isolated. Its anion shows an almost linear B,N,C,S unit. Only a mixture of (catecholato)(isothiocyanato)borates results on treating Na(NCS) in THF with catecholborane. However, the borate Na[catB(NCS)2] is readily formed by adding Na(NCS) to B -(isothiocyanato)catecholborane. Single crystals of this compound were obtained as the salt [Na(18-crown-6)(THF)2][catB(NCS)2] (6). On the other hand, the reaction of Na(NCS) with 9-borabicyclo[3.3.1]nonane (9-BBN) in THF yields Na[(9-BBN)NCS)]·nTHF, and, on addition of 18-crown-6, the complex [Na(18-crown-6)(THF)2][(9-BBN)NCS] was isolated. Suitable crystals for X-ray structure determination were, however, only obtained by crystallization from tetrahydropyran. This solvate has the rather unusual structure [Na(18-crown-6)(thp)2][{(9-BBN)NCS}2Na(thp)4] (8). The sodiate anion has an Na atom coordinated by two S and four O atoms. DFT calculations support these experimental results: The (isothiocyanato)borates are more stable than the thiocyanato isomers. For the latter a bent structure of the B,S,C,N unit with a B,S,C bond angle of 105.7° is predicted. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004) [source] Substituent effects on the physical properties and pKa of phenolINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 4-5 2001Kevin C. Gross Abstract Substituent effects on the physical properties and pKa of phenol were studied using density functional theory [B3LYP/6-311G(d,p)] calculations. Substituents alter the physical properties of phenol such as the hydroxyl-group CO and OH bond lengths, the C OH bond angle, and the energy barrier to rotation about the C O bond, and also influence the hydroxyl-group pKa. Except for the rotational barrier, Hammett , constants showed strong correlation with these property changes. Several quantum chemical parameters, including the natural charge on the phenolic hydrogen Qn(H) and the natural charge on the phenoxide oxygen Qn(O,), the HF/6-311G(d,p) HOMO energy Ehomo, and the proton-transfer energy ,Eprot, outperformed the empirical Hammett constants in modeling changes in the pKa. All of these latter parameters yielded correlation coefficients ,r,>0.94 for the pKa. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001 [source] 27 ps DFT molecular dynamics simulation of ,-maltose: A reduced basis set study,JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 11 2010Udo Schnupf Abstract DFT molecular dynamics simulations are time intensive when carried out on carbohydrates such as ,-maltose. In a recent publication (Momany et al., J. Mol. Struct. THEOCHEM, submitted) forces for dynamics were generated from B3LYP/6-31+G* electronic structure calculations. The implicit solvent method COSMO was applied to simulate the solution environment. Here we present a modification of the DFT method that keeps the critical aspects of the larger basis set (B3LYP/6-31+G*) while allowing the less-essential atom interactions to be calculated using a smaller basis set, thus allowing for faster completion without sacrificing the interactions dictating the hydrogen bonding networks in ,-maltose. In previous studies, the gg,-gg-c solvated form quickly converged to the "r" form during a 5 ps dynamics run. This important conformational transition is tested by carrying out a long 27 ps simulation. The trend for the "r" conformer to be most stable during dynamics when fully solvated, is confirmed, resulting in ,20/80% c/r population. Further, the study shows that considerable molecular end effects are important, the reducing end being fairly stable, the O6H pointing at the O5, while the nonreducing end moves freely to take on different conformations. Some "kink" and transition state forms are populated during the simulation. The average H1,···H4 distance of 2.28 Å confirms that the syn form is the primary glycosidic conformation, while the average C1,O1,C4 bond angle was 118.8°, in excellent agreement with experimental values. The length of this simulation allowed the evaluation of vibrational frequencies by Fourier transform of the velocity correlation function, taken from different time segments along the simulation path. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Modeling of loops in protein structuresPROTEIN SCIENCE, Issue 9 2000András Fiser Abstract Comparative protein structure prediction is limited mostly by the errors in alignment and loop modeling. We describe here a new automated modeling technique that significantly improves the accuracy of loop predictions in protein structures. The positions of all nonhydrogen atoms of the loop are optimized in a fixed environment with respect to a pseudo energy function. The energy is a sum of many spatial restraints that include the bond length, bond angle, and improper dihedral angle terms from the CHARMM-22 force field, statistical preferences for the main-chain and side-chain dihedral angles, and statistical preferences for nonbonded atomic contacts that depend on the two atom types, their distance through space, and separation in sequence. The energy function is optimized with the method of conjugate gradients combined with molecular dynamics and simulated annealing. Typically, the predicted loop conformation corresponds to the lowest energy conformation among 500 independent optimizations. Predictions were made for 40 loops of known structure at each length from 1 to 14 residues. The accuracy of loop predictions is evaluated as a function of thoroughness of conformational sampling, loop length, and structural properties of native loops. When accuracy is measured by local superposition of the model on the native loop, 100, 90, and 30% of 4,, 8,, and 12,residue loop predictions, respectively, had <2 Å RMSD error for the mainchain N, Ca, C, and O atoms; the average accuracies were 0.59 6 0.05, 1.16 6 0.10, and 2.61 6 0.16 Å, respectively. To simulate real comparative modeling problems, the method was also evaluated by predicting loops of known structure in only approximately correct environments with errors typical of comparative modeling without misalignment. When the RMSD distortion of the main-chain stem atoms is 2.5 Å, the average loop prediction error increased by 180, 25, and 3% for 4,, 8,, and 12,residue loops, respectively. The accuracy of the lowest energy prediction for a given loop can be estimated from the structural variability among a number of low energy predictions. The relative value of the present method is gauged by (1) comparing it with one of the most successful previously described methods, and (2) describing its accuracy in recent blind predictions of protein structure. Finally, it is shown that the average accuracy of prediction is limited primarily by the accuracy of the energy function rather than by the extent of conformational sampling. [source] Diaquatetrakis(tert -butyl isocyanide)cobalt(II) bis(perchlorate): an example of cobalt(II) coordinated by only four alkyl isocyanide ligandsACTA CRYSTALLOGRAPHICA SECTION C, Issue 8 2009Clifford A. L. Becker The title compound, [Co(C5H9N)4(H2O)2](ClO4)2, crystallizes in the monoclinic space group C2/m. The cation has space-group-imposed 2/m symmetry, while the perchlorate ion is disordered about a mirror plane. The two slightly non-equivalent Co,C bonds [1.900,(3) and 1.911,(3),Å] form a rectangular plane, with a C,Co,C bond angle of 86.83,(11)°, and the linear O,Co,O C2 axis is perpendicular to this plane. The C[triple-bond]N bond lengths are 1.141,(4),Å and the Co,C[triple-bond]N and C[triple-bond]N,C angles average 175.5,(4)°. The perchlorate counter-ions are hydrogen bonded to the water molecules. The title compound is the first example of four alkyl isocyanide ligands coordinating CoII upon initial reaction of Co(ClO4)2·6H2O/EtOH with alkyl isocyanide. In all other known examples, five alkyl isocyanide molecules are coordinated, as in [(RNC)5Co,Co(CNR)5](ClO4)4 (R = Me, Et, CHMe2, CH2Ph, C4H9 - n or C6H11) or [Co(CNC8H17 - t)5](ClO4)2. This complex, therefore, is unique and somewhat unexpected. [source] Structural comparisons between methylated and unmethylated nitrophenyl lophinesACTA CRYSTALLOGRAPHICA SECTION C, Issue 8 2009Diana Yanover The lophine derivative 2-(2-nitrophenyl)-4,5-diphenyl-1H -imidazole, C21H15N3O2, (I), crystallized from ethanol as a solvent-free crystal and from acetonitrile as the monosolvate, C21H15N3O2·C2H3N, (II). Crystallization of 2-(4-nitrophenyl)-4,5-diphenyl-1H -imidazole from methanol yielded the methanol monosolvate, C21H15N3O2·CH4O, (III). Three lophine derivatives of methylated imidazole, namely, 1-methyl-2-(2-nitrophenyl)-4,5-diphenyl-1H -imidazole methanol solvate, C22H17N3O2·CH4O, (IV), 1-methyl-2-(3-nitrophenyl)-4,5-diphenyl-1H -imidazole, C22H17N3O2, (V), and 1-methyl-2-(4-nitrophenyl)-4,5-diphenyl-1H -imidazole, C22H17N3O2, (VI), were recrystallized from methanol, acetonitrile and ethanol, respectively, but only (IV) produced a solvate. Compounds (III) and (IV) each crystallize with two independent molecules in the asymmetric unit. Five imidazole molecules in the six crystals differ in their molecular conformations by rotation of the aromatic rings with respect to the central imidazole ring. In the absence of a methyl group on the imidazole [compounds (I),(III)], the rotation angles are not strongly affected by the position of the nitro group [44.8,(2) and 45.5,(1)° in (I) and (II), respectively, and 15.7,(2) and 31.5,(1)° in the two molecules of (III)]. However, the rotation angle is strongly affected by the presence of a methyl group on the imidazole [compounds (IV),(VI)], and the position of the nitro group (ortho, meta or para) on a neighbouring benzene ring; values of the rotation angle range from 26.0,(1) [in (VI)] to 85.2,(1)° [in (IV)]. This group repulsion also affects the outer N,C,N bond angle. The packing of the molecules in (I), (II) and (III) is determined by hydrogen bonding. In (I) and (II), molecules form extended chains through N,H...N hydrogen bonds [with an N...N distance of 2.944,(5),Å in (I) and 2.920,(3),Å in (II)], while in (III) the chain is formed with a methanol solvent molecule as the mediator between two imidazole rings, with O...N distances of 2.788,(4),2.819,(4),Å. In the absence of the imidazole N,H H-atom donor, the packing of molecules (IV),(VI) is determined by weaker intermolecular interactions. The methanol solvent molecule in (IV) is hydrogen bonded to imidazole [O...N = 2.823,(4),Å] but has no effect on the packing of molecules in the unit cell. [source] Low temperature powder diffraction and DFT solid state computational study of hydrogen bonding in NH4VO3CRYSTAL RESEARCH AND TECHNOLOGY, Issue 9 2009. Smr Abstract The crystal structure of NH4VO3 was refined by the geometry optimization done by total energy minimization in solid state using DFT/plane waves approach. The lattice parameters were derived by the Le Bail technique from the low temperature X-ray (40-293 K) and synchrotron (100-293 K) powder diffraction data. The structure is formed by the infinite chains of irregular VO4 tetrahedra running approximately parallel to the c -axis, which are interlinked by the ammonium ions placed between them. The ammonium ions link to the [VO4], chains through one linear, one bifurcated and two trifurcated N-H,O hydrogen bonds. Considering their stability there are six distinct N-H,O hydrogen bonds: two strong with the N-H,O bond angles close to the straight, two medium with the bond angles of 123° and 148° and two very bent (105° and 107°) and hence weak hydrogen bonds. There is a reasonable agreement between the energies of the stretching ,(NH) modes estimated using the optimised N,O contact distances and those obtained experimentally. (© 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Development of polyphosphate parameters for use with the AMBER force fieldJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 9 2003Kristin L. Meagher Abstract Accurate force fields are essential for reproducing the conformational and dynamic behavior of condensed-phase systems. The popular AMBER force field has parameters for monophosphates, but they do not extend well to polyphorylated molecules such as ADP and ATP. This work presents parameters for the partial charges, atom types, bond angles, and torsions in simple polyphosphorylated compounds. The parameters are based on molecular orbital calculations of methyldiphosphate and methyltriphosphate at the RHF/6-31+G* level. The new parameters were fit to the entire potential energy surface (not just minima) with an RMSD of 0.62 kcal/mol. This is exceptional agreement and a significant improvement over the current parameters that produce a potential surface with an RMSD of 7.8 kcal/mol to that of the ab initio calculations. Testing has shown that the parameters are transferable and capable of reproducing the gas-phase conformations of inorganic diphosphate and triphosphate. Also, the parameters are an improvement over existing parameters in the condensed phase as shown by minimizations of ATP bound in several proteins. These parameters are intended for use with the existing AMBER 94/99 force field, and they will permit users to apply AMBER to a wider variety of important enzymatic systems. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1016,1025, 2003 [source] Conformational analysis of thiopeptides: derivation of sp2 sulfur parameters for the CFF91 force fieldJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 10 2001Tran Trung Tran Abstract When a sulfur atom is used to substitute for the oxygen in peptide bonds, its bulkiness should restrict the conformational space available to an amino acid. This conformational restriction as well as the ability to confer resistance to enzymatic degradation in the body means that thio-substituted amino acids are potentially useful building blocks for drug design. To simulate the effects of thio substitution, force field parameters for sp2 sulfur are required. In this article, parameters for the thioamide group have been derived for the molecular mechanics CFF91 force field (available at http://www.ludwig.edu.au/archive/tran). The bond increment charges were obtained by fitting to ab initio charges and dipoles. The van der Waals parameters were obtained by fitting to high-resolution crystallographic data, and the nonbonded parameters were verified by comparing with experimentally derived lattice energy. The bonded parameters were derived by least-square fits to the ab initio calculated energy surfaces, i.e., conformational energy as well as their first and second derivatives of seven model thioamide molecules. When the sp2 sulfur parameters were tested on a set of seven X-ray crystallographic structures from the Cambridge Structural Database, they satisfactorily reproduced the bond lengths, bond angles, torsional angles, and nonbonded distances of all the crystal structures. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1010,1025, 2001 [source] A comparison of crystallographic and NMR data for thieno[2,3- b:4,5- b,]dipyridine and its monohydroperchlorate saltJOURNAL OF HETEROCYCLIC CHEMISTRY, Issue 4 2000Leroy H. Klemm X-ray crystallographic studies of thieno[2,3- b:4,5- b,]dipyridine (1) and its monohydroperchlorate salt (1a) show that 1 is protonated at N1 in ring A and not at N6 in ring C. In each compound individual rings are planar, but there is a small dihedral angle-of-twist between the A and C rings. On going from 1 to 1a the largest changes in bond angles and bond lengths occur in ring A. 1H and l3C nmr spectra of 1 plus the 13C nmr spectrum of 1a are reported. [source] Crystal topologies , the achievable and inevitable symmetriesACTA CRYSTALLOGRAPHICA SECTION A, Issue 3 2009Georg Thimm The link between the crystal topology and symmetry is examined, focusing on the conditions under which a structure with a given topology can exhibit a certain symmetry. By defining embeddings for quotient graphs (finite representations of crystal topologies) and the corresponding nets (the graph-theoretical equivalents of structures), a strong relationship between the automorphisms of the quotient graphs and the symmetry of the embedded net is established. This allows one to constrain the relative node positions under the premise that an embedding of a net has a certain symmetry, and allows one to assign nodes to equivalents of Wyckoff positions. Two-dimensional examples as well as known crystal structures are used to illustrate the findings. A comparison with a related publication and a discussion on whether constraints on distances between atoms and on bond angles result in restrictions on symmetry without causing confusion conclude the work. [source] Evaluation at atomic resolution of the role of strain in destabilizing the temperature-sensitive T4 lysozyme mutant Arg 96 , HisPROTEIN SCIENCE, Issue 5 2009Blaine H. M. Mooers Abstract Mutant R96H is a classic temperature-sensitive mutant of bacteriophage T4 lysozyme. It was in fact the first variant of the protein to be characterized structurally. Subsequently, it has been studied extensively by a variety of experimental and computational techniques, but the reasons for the loss of stability of the mutant protein remain controversial. In the crystallographic refinement of the mutant structure at 1.9 Å resolution one of the bond angles at the site of substitution appeared to be distorted by about 11°, and it was suggested that this steric strain was one of the major factors in destabilizing the mutant. Different computationally-derived models of the mutant structure, however, did not show such distortion. To determine the geometry at the site of mutation more reliably, we have extended the resolution of the data and refined the wildtype (WT) and mutant structures to be better than 1.1 Å resolution. The high-resolution refinement of the structure of R96H does not support the bond angle distortion seen in the 1.9 Å structure determination. At the same time, it does confirm other manifestations of strain seen previously including an unusual rotameric state for His96 with distorted hydrogen bonding. The rotamer strain has been estimated as about 0.8 kcal/mol, which is about 25% of the overall reduction in stability of the mutant. Because of concern that contacts from a neighboring molecule in the crystal might influence the geometry at the site of mutation we also constructed and analyzed supplemental mutant structures in which this crystal contact was eliminated. High-resolution refinement shows that the crystal contacts have essentially no effect on the conformation of Arg96 in WT or on His96 in the R96H mutant. [source] Studies of electric field induced structural and electron-density modifications by X-ray diffractionACTA CRYSTALLOGRAPHICA SECTION A, Issue 5 2004Niels K. Hansen During the last two decades, a number of X-ray diffraction studies on the response of a crystal to an applied electric field have been carried out. In a few cases, the electron-density polarizations could be determined. The analysis of the induced variations of the structural properties on an atomic scale are of prime importance in order to acquire a better understanding of physical properties like the piezoelectric and dielectric properties of crystals. This article reviews the experimental technique used and the modelling methods of the Bragg scattering variations induced by the field. Some noteworthy results are presented that illustrate the possibility of detecting subtle structural changes, for example as small as 0.1° in bond angles arising from applying a strong field, 10,40,kV,cm,1, as well as the pitfalls of such an approach for clarifying the relevance of the structural properties in physical mechanisms. [source] Ab initio structure determination of phase II of racemic ibuprofen by X-ray powder diffractionACTA CRYSTALLOGRAPHICA SECTION B, Issue 1 2010Patrick Derollez Annealing of the quenched ibuprofen at 258,K yielded a new crystalline form, called phase II. Powder X-ray diffraction patterns of this phase II were recorded with a laboratory diffractometer equipped with an INEL G3000 goniometer and a curved position-sensitive detector CPS120. The starting structural model was found by a Monte-Carlo simulated annealing method. The final structure was obtained through Rietveld refinements with rigid-body constraints for the phenyl group and soft restraints on the other interatomic bond lengths and bond angles. The cell volume is 5% larger than that of the conventional phase I at 258,K. It is also shown that the orientation of the propanoic acid group is drastically changed with respect to phase I, leading to strong modifications of the orientation of the O,H...O hydrogen bonds with respect to the chains of dimers. These structural considerations could explain the metastable character of this phase II. [source] Quantitative description of the tilt of distorted octahedra in ABX3 structuresACTA CRYSTALLOGRAPHICA SECTION B, Issue 2 2007Rafael Tamazyan A description of the tilt of octahedra in ABX3 perovskite-related structures is proposed that can be used to extract the unique values for the tilt parameters ,, , and , of ABX3 structures with regular and distorted octahedra up to the point symmetry , from atomic coordinates and lattice parameters. The geometry of the BX6 octahedron is described by three B,X bond lengths (r1, r2, r3) and three X,B,X bond angles (,12, ,13 and ,23) or alternatively by a local strain tensor together with an average B,X bond length. Connections between the proposed method and Glazer's tilt system are discussed. The method is used to analyze structural transformations of I2/c, Pbnm and Immm structures. The proposed description allows the analysis of group,subgroup relations for the ABX3 structures with distorted octahedra, in terms of octahedral deformations and tilting. The method might also be of interest in the study of the phase transitions in the family of ABX3 structures. [source] 4,6-Dimethyl-2-(3-pyridyl)quinolin-5-amineACTA CRYSTALLOGRAPHICA SECTION C, Issue 4 2007José Antonio Henao The title compound, C16H15N3, shows a hindrance effect between adjacent amino and methyl groups that leads to a structural distortion, which is reflected in the non-planarity of the quinoline entity and in the bond angles and distances. The crystal packing consists of chains along the b axis sustained by an intermolecular hydrogen bond between the amino group and the N atom of the pyridyl ring. [source] Crystallographic report: Ethyltriphenyltin(IV), Et(Ph)3SnAPPLIED ORGANOMETALLIC CHEMISTRY, Issue 2 2004José S. Casas Abstract The crystal lattice of the title compound comprises isolated molecules. The coordination polyhedron is a slightly distorted tetrahedron with C,Sn,C bond angles ranging from 106.62(17)° to 113.9(3)°. Copyright © 2004 John Wiley & Sons, Ltd. [source] 2-Bromo-6-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)pyridine, a new unexpected bifunctional building block for combinatorial chemistryACTA CRYSTALLOGRAPHICA SECTION C, Issue 10 2003Jana Sopková-de Oliveira Santos The first reported structure of a pyridin-2-ylboron derivative, viz. the title compound, C11H15BBrNO2, (I), is compared with its regioisomer 2-bromo-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)pyridine, (II) [Sopková-de Oliveira Santos, Lancelot, Bouillon & Rault (2003). Acta Cryst. C59, o111o113]. Structural differences are observed, firstly in the orientation of the dioxaborolane ring with respect to the pyridine ring and secondly in the bond angles of the BO2 group. These differences do not explain the experimentally observed differences in chemical reactivity between (I) and (II) but do confirm the relatively lower stability of (I). However, ab initio calculations of the HOMO (highest occupied molecular orbital) and LUMO (lowest unoccupied molecular orbital), based on the known crystal structures of the two compounds, show different distributions, which correspond to the differences observed during chemical reactions. [source] Alkaline metal oxoantimonates(III), A3[SbO3] (A = K or Cs)ACTA CRYSTALLOGRAPHICA SECTION C, Issue 10 2001Franziska Emmerling The two title trialkaline trioxoantimonates(III), tripotassium trioxoantimonate(III), K3[SbO3], (I), and tricaesium trioxoantimonate(III), Cs3[SbO3], (II), crystallize in the cubic Na3[AsS3] structure type in space group P213. The structures show discrete ,-tetrahedral [SbO3]3, anions with C3v point-group symmetry. The Sb,O distances are 1.923,(4),Å in (I) and 1.928,(2),Å in (II), and the O,Sb,O bond angles are 99.5,(2)° in (I) and 100.4,(1)° in (II). [source] A comparison of 2,7-dihydro-2,2,7,7-tetramethyl-3,6-diphenyl-1,4,5-thiadiazepine and the corresponding 1,1-dioxideACTA CRYSTALLOGRAPHICA SECTION C, Issue 4 2001Eric Cuthbertson The structures of the highly substituted title heterocycles, C20H22N2S and C20H22N2O2S, have been determined at 123,(1),K. Both molecules possess exact C2 symmetry and the seven-membered rings have very similar twist-boat conformations. The magnitudes of the C,S,C bond angles, 107.13,(6) and 108.27,(7)°, respectively, are influenced significantly by the four substituent methyl groups on the seven-membered rings. [source] Using a conformation-dependent stereochemical library improves crystallographic refinement of proteinsACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2010Dale E. Tronrud The major macromolecular crystallographic refinement packages restrain models to ideal geometry targets defined as single values that are independent of molecular conformation. However, ultrahigh-resolution X-ray models of proteins are not consistent with this concept of ideality and have been used to develop a library of ideal main-chain bond lengths and angles that are parameterized by the ,/, angle of the residue [Berkholz et al. (2009), Structure, 17, 1316,1325]. Here, it is first shown that the new conformation-dependent library does not suffer from poor agreement with ultrahigh-resolution structures, whereas current libraries have this problem. Using the TNT refinement package, it is then shown that protein structure refinement using this conformation-dependent library results in models that have much better agreement with library values of bond angles with little change in the R values. These tests support the value of revising refinement software to account for this new paradigm. [source] Refinement of protein crystal structures using energy restraints derived from linear-scaling quantum mechanicsACTA CRYSTALLOGRAPHICA SECTION D, Issue 3 2005Ning Yu A novel method is proposed in which combined restraints derived from linear-scaling semiempirical quantum-mechanical (QM) calculations and X-ray diffraction data are combined to refine crystal structures of proteins. Its performance has been tested on a small protein molecule, bovine pancreatic trypsin inhibitor (BPTI). The refinement involves minimization of the sum of a geometric energy function and an X-ray target function based on either the least-squares residual or the maximum-likelihood formalism. For comparison, similar refinement runs have also been performed using energy restraints derived from the force field available in the Crystallography & NMR System (CNS) program. The QM refinements were carried out with weights that were varied by several orders of magnitude and the optimal weights were identified by observing the trend in the final free R values, QM heats of formation and coordinate root-mean-square deviations (r.m.s.d.s) from the crystal structure. It is found that the QM weights are typically smaller but generally on the same scale as the molecular-mechanics (MM) weights for the respective X-ray target functions. The crystallographic R, free R, real-space R values and correlation coefficients based on the structures refined with the energy restraints derived from our QM calculations and Engh and Huber parameters are comparable, suggesting that the QM restraints are capable of maintaining reasonable stereochemistry to a similar degree as the force-field parameters. A detailed inspection of the structures refined with the QM and MM energy restraints reveals that one of the common differences between them and the crystal structure is that the strained bond angles in the crystal structure are corrected after energetically restrained refinements. Systematic differences in certain bond lengths between the QM-refined structures and the statistical averages of experimental structures have also been observed and discussed. [source] Synthesis and Characterization of Hydroxy-Functionalized Models for the Active Site in Fe-Only-HydrogenasesCHEMISTRY & BIODIVERSITY, Issue 9 2007Ulf-Peter Apfel Abstract The reactions of dl -1,4-disulfanylbutane-2,3-diol and 1,3-disulfanylpropan-2-ol with dodecacarbonyltriiron have been investigated. As main products, the iron complexes 1 and 2 were isolated and characterized by spectroscopic methods, as well as single crystal X-ray analysis. Additionally, the unusually large bond angles in the dithiolato bridge was investigated via density-functional theory (DFT) calculations. Moreover, the electrochemical features have been studied by cyclic voltammetry. [source] Oriented Ensembles in Ultrafast Electron DiffractionCHEMPHYSCHEM, Issue 7 2006J. Spencer Baskin Abstract Electron scattering expressions are presented which are applicable to very general conditions of implementation of anisotropic ultrafast electron diffraction (UED) experiments on the femto- and picosecond time scale. "Magic angle" methods for extracting from the experimental diffraction patterns both the isotropic scalar contribution (population dynamics) and the angular (orientation-dependent) contribution are described. To achieve this result, the molecular scattering intensity is given as an expansion in terms of the moments of the transition-dipole distribution created by the linearly polarized excitation laser pulse. The isotropic component (n=0 moment) depends only on population and scalar internuclear separations, and the higher moments reflect bond angles and evolve in time due to rotational motion of the molecules. This clear analytical separation facilitates assessment of the role of experimental variables in determining the influence of anisotropic orientational distributions of the molecular ensembles on the measured diffraction patterns. Practical procedures to separate the isotropic and anisotropic components of experimental data are evaluated and demonstrated with application to reactions. The influence of vectorial properties (bond angles and rotational dynamics) on the anisotropic component adds a new dimension to UED, arising through the imposition of spatial order on otherwise randomly oriented ensembles. [source] | |||||||||||||||||||||||||