Individual Atoms (individual + atom)

Distribution by Scientific Domains

Selected Abstracts

13C and 1H nuclear magnetic resonance of methyl-substituted acetophenones and methyl benzoates: steric hindrance and inhibited conjugation

Abstract The 1H and 13C NMR spectra of 14 methyl-substituted acetophenones and 14 methyl-substituted methyl benzoates were assigned and interpreted with respect to the conformation of the Car,C(O) bond. The substituent effects are proportional in the two series and can be divided into polar and steric: each has different effects on the 13C SCS of the individual atoms. In the case of C atoms C(O), C(1) and CH3(CO), the steric effects were quantitatively separated by comparing SCS in the ortho and para positions. The steric effects are proportional for the individual C atoms and also to steric effects estimated from other physical quantities. However, they do not depend simply on the angle of torsion , of the functional group as anticipated hitherto. A better description distinguishes two classes of compounds: sterically not hindered or slightly hindered planar molecules and strongly sterically hindered, markedly non-planar. In order to confirm this reasoning without empirical correlations, the J(C,C) coupling constants were measured for three acetophenone derivatives labeled with 13C in the acetyl methyl group. The constants confirm unambiguously the conformation of 2-methylacetophenone; their zero values are in accord with the conformation of 2,6-dimethylacetophenone. The zero values in the unsubstituted acetophenone are at variance with previous erroneous report but all J(C,C) values are in accord with calculations at the B3LYP/6-311++G(2d,2p)//B3LYP/6,311+G(d,p) level. Copyright 2004 John Wiley & Sons, Ltd. [source]

Investigations of the bond-selective response in a piezoelectric Li2SO4H2O crystal to an applied external electric field

O. Schmidt
Piezoelectric lithium sulfate monohydrate, Li2SO4H2O, was analyzed with respect to the relationship between the static structural properties of the crystal and its response to an external electric field. The static electron density was determined via standard low-temperature X-ray data collection at 90,(5) K using an Enraf,Nonius CAD-4 diffractometer, Mo K, radiation and multipole model refinement. Then a synchrotron-radiation experiment using the D3 beamline at HASYLAB was conducted in order to investigate the structural deformations in Li2SO4H2O caused by an applied external electric field. In particular, the shifts of Bragg-peak positions induced by the electric field were measured and the piezoelectric constants d211, d222, d233 and d213 of Li2SO4H2O were obtained from the shifts. With the same experimental setup the variations of more than 100 Bragg intensities were measured under an applied electric field. The data were used to refine the corresponding displacements of individual atoms within the unit cell. The distortions of the cation,anion bond lengths in the LiO4, LiO3(H2O) and SO4 tetrahedra were evaluated and then analyzed in terms of the electron-density-related properties of the Li,O and S,O bonds. The two lithium structural units were found to be strongly deformed by the applied electric field, while the SO4 tetrahedron changed less. This is in agreement with the low bond strength of the Li,O bonds. [source]

CIRSE: A solvation energy estimator compatible with flexible protein docking and design applications

David S. Cerutti
Abstract We present the Coordinate Internal Representation of Solvation Energy (CIRSE) for computing the solvation energy of protein configurations in terms of pairwise interactions between their atoms with analytic derivatives. Currently, CIRSE is trained to a Poisson/surface-area benchmark, but CIRSE is not meant to fit this benchmark exclusively. CIRSE predicts the overall solvation energy of protein structures from 331 NMR ensembles with 0.951 0.047 correlation and predicts relative solvation energy changes between members of individual ensembles with an accuracy of 15.8 9.6 kcal/mol. The energy of individual atoms in any of CIRSE's 17 types is predicted with at least 0.98 correlation. We apply the model in energy minimization, rotamer optimization, protein design, and protein docking applications. The CIRSE model shows some propensity to accumulate errors in energy minimization as well as rotamer optimization, but these errors are consistent enough that CIRSE correctly identifies the relative solvation energies of designed sequences as well as putative docked complexes. We analyze the errors accumulated by the CIRSE model during each type of simulation and suggest means of improving the model to be generally useful for all-atom simulations. [source]

Application of graph theory to detect disconnected structures in a crystallographic database: copper oxide perovskites as a case study

Yuri Kotliarov
Every crystal structure can be described as a graph with atoms as vertices and bonds as edges. Although such a graph loses the space arrangement of atoms and symmetry elements, it can mathematically represent the connectivity between atoms. This topological approach was used to develop a new method for detecting disconnected structures, in which individual atoms or structural fragments are located too far from each other, forming impossibly large gaps. Approximately 2300 perovskite-related crystal structures have been extracted from the Inorganic Crystal Structure Database (in 1999) and the maximum disconnecting distances, and the relations between them and the ionic radii of elements, have been analysed. Several disconnected structures, which are erroneous by our definition, have been revealed. Conventional tests for crystallographic data checking did not detect those entries. [source]

A genetic algorithm for the identification of conformationally invariant regions in protein molecules

Thomas R. Schneider
Understanding macromolecular function often relies on the comparison of different structural models of a molecule. In such a comparative analysis, the identification of the part of the molecule that is conformationally invariant with respect to a set of conformers is a critical step, as the corresponding subset of atoms constitutes the reference for subsequent analysis for example by least-squares superposition. A method is presented that categorizes atoms in a molecule as either conformationally invariant or flexible by automatic analysis of an ensemble of conformers (e.g. crystal structures from different crystal forms or molecules related by non-crystallographic symmetry). Different levels of coordinate precision, both for different models and for individual atoms, are taken explicitly into account via a modified form of Cruickshank's DPI [Cruickshank (1999), Acta Cryst. D55, 583,601] and are propagated into error-scaled difference distance matrices [Schneider (2000), Acta Cryst. D56, 715,721]. All pairwise error-scaled difference distance matrices are then analysed simultaneously using a genetic algorithm. The algorithm has been tested on several well known examples and has been found to converge rapidly to reasonable results using a standard set of parameters. In addition to the description of the algorithm, a criterion is suggested for testing the identity of two three-dimensional models within experimental error without any explicit superposition. [source]