Ab Initio Determination of a New Complex Structure (55 Non-Hydrogen Atoms) from Synchrotron Powder Data: An Uncommon Nickel Succinate, Ni7(C4H4O4)4(OH)6(H2O)3•7H2O

2004 ◽  
Vol 443-444 ◽  
pp. 333-336
Author(s):  
N. Guillou ◽  
C. Livage ◽  
W. van Beek ◽  
G. Férey
Keyword(s):  
Ab Initio ◽  
Complex Structure ◽  
Three Dimensional ◽  
Free Water ◽  
Hydrogen Atoms ◽  
Monoclinic System ◽  
Synchrotron Powder Diffraction ◽  
Chloride Hexahydrate ◽  
Autogenous Pressure

Ni7(C4H4O4)4(OH)6(H2O)3. 7H2O, a new layered nickel(II) succinate, was prepared hydrothermally (180°C, 48 h, autogenous pressure) from a 1:1.5:4.1:120 mixture of nickel (II) chloride hexahydrate, succinic acid, potassium hydroxide and water. It crystallizes in the monoclinic system (space group P21/c, Z = 4) with the following parameters a = 7.8597(1) Å, b = 18.8154(3)Å, c = 23.4377(4) Å,ϐ = 92.0288(9)°, and V = 3463.9(2) Å3. Its structure, which contains 55 non-hydrogen atoms, was solved ab initio from synchrotron powder diffraction data. It can be described from hybrid organic-inorganic layers, constructed from nickel oxide corrugated chains. These chains are built up from NiO6hexameric units connected via a seventh octahedron. Half of the succinates decorate the chains, and the others connect them to form the layers. The three dimensional arrangement is ensured by hydrogen bonds directly between two adjacent layers and via free water molecules.

AB INITIO CALCULATIONS OF THE ELECTRONIC STRUCTURES AND BIOLOGICAL FUNCTIONS OF PROTEIN MOLECULES

2002 ◽  
Vol 16 (30) ◽  
pp. 1151-1162 ◽  
Author(s):  
HAOPING ZHENG
Keyword(s):  
Ab Initio ◽  
Trypsin Inhibitor ◽  
Electronic Structures ◽  
Biological Function ◽  
Three Dimensional ◽  
Protein Molecule ◽  
Computational Effort ◽  
Biological Functions ◽  
Protein Molecules

The self-consistent cluster-embedding (SCCE) calculation method reduces the computational effort from M3 to about M1 (M is the number of atoms in the system) with precise calculations. Thus the ab initio, all-electron calculation of the electronic structure and biological function of protein molecule has become a reality, which will promote new proteomics considerably. The calculated results of two real protein molecules, the trypsin inhibitor from the seeds of squash Cucurbita maxima (CMTI-I, 436 atoms) and the ascaris trypsin inhibitor (912 atoms, two three-dimensional structures), will be presented in this paper. The reactive sites of the inhibitors are determined and explained. The accuracy of structure determination of the inhibitors are tested theoretically.

Determination of the structure of p-methylbenzamidinium formate monohydrate

1988 ◽  
Vol 53 (12) ◽  
pp. 3131-3137
Author(s):  
Bohumil Kratochvíl ◽  
Jan Ondráček ◽  
Jindřich Hašek ◽  
László Csordás
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Three Dimensional ◽  
Direct Methods ◽  
Monoclinic Space Group ◽  
Hydrogen Atoms ◽  
Intermolecular Hydrogen Bonds ◽  
Dimensional Network ◽  
Intramolecular Hydrogen

The molecular and crystal structure of p-methylbenzamidinium formate monohydrate, C9H14N2O3, was solved by direct methods. The positions of all the atoms were localized and the structure was refined anisotropically. The final value of the R factor equalled 0·043 for 1 150 observed reflections (I > 1·96σ(I)). The substance crystallizes in the P21/c monoclinic space group with lattice parameters a = 1 038·9(4), b = 1 146·1(5), c = 912·4(3) pm, β = 94·77(3)0, Z = 4. The molecule contains an amidinium-carboxylate bond, formed by two intramolecular hydrogen bridges of the N-H···O type. Intermolecular hydrogen bonds are formed by the side hydrogen atoms of the amidine and the hydrogen atoms of the water molecule and are of the N-H···O and O-H···O types; they form a three-dimensional network in the crystal structure. In this, the structure of p-methylbenzamidinium formate monohydrate differs from the related structures of benzamidinium pyruvate and benzamidinium bromoacetate, characterized by infinite intermolecular chains formed through hydrogen bonding.

On Potential Energy Models for EA-based Ab Initio Protein Structure Prediction

2010 ◽  
Vol 18 (2) ◽  
pp. 255-275 ◽  
Author(s):  
Milan Mijajlovic ◽  
Mark J. Biggs ◽  
Dusan P. Djurdjevic
Keyword(s):  
Protein Structure ◽  
Potential Energy ◽  
Ab Initio ◽  
Protein Structure Prediction ◽  
Structure Prediction ◽  
Three Dimensional ◽  
Free Energy Surface ◽  
Energy Models ◽  
Parameter Values

Ab initio protein structure prediction involves determination of the three-dimensional (3D) conformation of proteins on the basis of their amino acid sequence, a potential energy (PE) model that captures the physics of the interatomic interactions, and a method to search for and identify the global minimum in the PE (or free energy) surface such as an evolutionary algorithm (EA). Many PE models have been proposed over the past three decades and more. There is currently no understanding of how the behavior of an EA is affected by the PE model used. The study reported here shows that the EA behavior can be profoundly affected: the EA performance obtained when using the ECEPP PE model is significantly worse than that obtained when using the Amber, OPLS, and CVFF PE models, and the optimal EA control parameter values for the ECEPP model also differ significantly from those associated with the other models.

An accurate determination of the structure of ammonium oxamate

1963 ◽  
Vol 275 (1363) ◽  
pp. 469-491 ◽  
Keyword(s):  
Crystal Structure ◽  
Hydrogen Atom ◽  
Accurate Determination ◽  
Three Dimensional ◽  
Ammonium Ion ◽  
Intensity Data ◽  
Single Bond ◽  
Hydrogen Atoms ◽  
Librational Motion

The crystal structure of ammonium oxamate (CONH 2 .COONH 4 ) has been studied using Cu Ka X-radiation, by means of a three-circle diffractometer incorporating a xenon-filled proportional counter. Accurate three-dimensional intensity data were collected and a least-squares refinement was carried out. The positions of the hydrogen atoms were obtained and refined. A peak of electron density, about half as high as a hydrogen atom, was observed at the centre of the C—C bond and a correction applied for it increased the length of the bond by 0.003 Å. The bond lengths were corrected for librational motion, and the values obtained are C—C =1.564 ±0.002 Å; C—N = 1.324± 0.002 Å; C—O (amidic) = 1.248± 0.002 A; C— O (carboxylate) = 1.257 + 0.003 Å and 1.256 ± 0.003 Å. The oxamate ion is found to be planar, and the ammonium ion tetrahedral. The length of the C—C bond is greater than any theoretical value yet suggested for the length of a single bond between trigonally hybridized carbons atoms.

Modelling Porosity in Quasi-Brittle Reactor Core Graphite

2013 ◽  
Vol 577-578 ◽  
pp. 337-340
Author(s):  
G.E. Smith ◽  
Peter E.J. Flewitt ◽  
A. Hodgkins
Keyword(s):  
Nuclear Reactors ◽  
Complex Structure ◽  
Three Dimensional ◽  
Reactor Core ◽  
Virgin Material ◽  
Element Determination ◽  
Mechanical And Physical Properties ◽  
The Uk ◽  
Graphite Moderator

Some designs of nuclear reactors involve a graphite moderator within their core. Different forms of graphite have been adopted in the UK gas-cooled reactors but all have a complex structure of filler particles, matrix and pores. Changes occur in the graphite during service and in particular, porosity increases from that found in the virgin material. As part of a structural assessment, it is important to analyse the effects of this change in porosity. Software has been developed to represent the microstructure of pile grade A (PGA) and Gilsocarbon graphite with a range of porosities, to support finite element determination of material properties. The models are three dimensional geometric and voxel models based on the observed microstructures of these different graphites. Creating a sequence of model specimens with increasing porosities while holding other parameters constant, provides a representative microstructure to test the effect of increasing porosity on mechanical and physical properties.

Ab initio crystal structure determination of two chain functionalized pyrroles from synchrotron X-ray powder diffraction data

2012 ◽  
Vol 27 (3) ◽  
pp. 172-178
Author(s):  
Iván da Silva ◽  
Sara López-Tosco ◽  
David Tejedor ◽  
Fernando García-Tellado ◽  
Javier González-Platas
Keyword(s):  
Crystal Structure ◽  
Monte Carlo ◽  
Ab Initio ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Powder Diffraction Data ◽  
Monoclinic System ◽  
X Ray ◽  
Space Approach

The crystal structure of two chain functionalized pyrroles, methyl 1-benzyl-5-(1-(4-chlorobenzoyloxy)-2-methoxy-2-oxoethyl)-4-(4-chlorophenyl)-1H-pyrrole-2-carboxylate and methyl 1-benzyl-4-(biphenyl-4-yl)-5-(1-(4-biphenylcarbonyloxy)-2-methoxy-2-oxoethyl)-1H-pyrrole-2-carboxylate, which are both important active candidates as antitumoral agents, have been obtained ab initio from synchrotron X-ray powder diffraction data. Both compounds crystallize in the monoclinic system (space group P21/c), with a = 20.2544(3) Å, b = 6.80442(9) Å, c = 21.1981(3) Å, β = 111.6388(9)° and a = 29.7747(6) Å, b = 6.27495(14) Å, c = 18.8525(3) Å, β = 107.053(2)°, respectively. These structures were determined using a direct space approach, by means of Monte Carlo technique, followed by Rietveld refinement.

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