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Molecular Symmetry (molecular + symmetry)
Selected AbstractsUnderstanding chemical shielding tensors using group theory, MO analysis, and modern density-functional theoryCONCEPTS IN MAGNETIC RESONANCE, Issue 2 2009Cory M. Widdifield Abstract In this article, the relationships between molecular symmetry, molecular electronic structure, and chemical shielding (CS) tensors are discussed. First, a brief background on the CS interaction and CS tensors is given. Then, the visualization of the three-dimensional nature of CS is described. A simple method for examining the relationship between molecular orbitals (MOs) and CS tensors, using point groups and direct products of irreducible representations of MOs and rotational operators, is outlined. A number of specific examples are discussed, involving CS tensors of different nuclei in molecules of different symmetries, including ethene (D2h), hydrogen fluoride (C,v), trifluorophosphine (C3v), and water (C2v). Finally, we review the application of this method to CS tensors in several interesting cases previously discussed in the literature, including acetylene (D,h), the PtX42, series of compounds (D4h) and the decamethylaluminocenium cation (D5d). © 2009 Wiley Periodicals, Inc. Concepts Magn Reson Part A 34A: 91,123, 2009. [source] Symmetric Versus Unsymmetric Platinum(II) Bis(aryleneethynylene)s with Distinct Electronic Structures for Optical Power Limiting/Optical Transparency Trade-off OptimizationADVANCED FUNCTIONAL MATERIALS, Issue 4 2009Guijiang Zhou Abstract A new series of symmetric and unsymmetric Pt(II) bis(acetylide) complexes of the type DC,CPt(PBu3)2C,CD (DPtD), AC,CPt(PBu3)2C,CA (APtA) and DC,CPt(PBu3)2C,CA (DPtA) (D, donor groups; A, acceptor groups) are synthesized, and show superior optical power limiting (OPL)/optical transparency trade-offs. By tailoring the electronic properties of the aryleneethynylene group, distinct electronic structures for these metalated complexes can be obtained, which significantly affect their photophysical behavior and OPL properties for a nanosecond laser pulse at 532,nm. Electronic influence of the ligand type and the molecular symmetry of metal group on the optical transparency/nonlinearity optimization is thoroughly elucidated. Generally, aryleneethynylene ligands with , electron-accepting nature will effectively enhance the harvesting efficiency of the triplet excited states. The ligand variation to the OPL strength of these Pt(II) compounds follows the order: DPtD,>,DPtA,>,APtA. These results could be attributed to the distinctive excited state character induced by their different electronic structures, on the basis of the data from both photophysical studies and theoretical calculations. All of the complexes show very good optical transparencies in the visible-light region and exhibit excellent OPL responses with very impressive figure of merit ,ex/,o values (up to 17), which remarkably outweigh those of state-of-the-art reverse saturable absorption dyes such as C60 and metallophthalocyanines with very poor transparencies. Their lower optical-limiting thresholds (0.05,J,cm,2 at 92% linear transmittance) compared with that of the best materials (ca. 0.07,J,cm,2 for InPc and PbPc dyes) currently in use will render these highly transparent materials promising candidates for practical OPL devices for the protection of human eyes and other delicate electro-optic sensors. [source] Practical modeling of molecular systems with symmetriesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 9 2010Sergei Grudinin Abstract A new method for efficient modeling of macromolecular systems with symmetries is presented. The method is based on a hierarchical representation of the molecular system and a novel fast binary tree-based neighbor list construction algorithm. The method supports all types of molecular symmetry, including crystallographic symmetry. Testing the proposed neighbor list construction algorithm on a number of different macromolecular systems containing up to about 200,000 of atoms shows that (1) the current binary tree-based neighbor list construction algorithm scales linearly in the number of atoms for the central subunit, and sublinearly for its replicas, (2) the overall computational overhead of the method for a system with symmetry with respect to the same system without symmetry scales linearly with the cutoff value and does not exceed 50% for all but one tested macromolecules at the cutoff distance of 12 Å. (3) the method may help produce optimized molecular structures that are much closer to experimentally determined structures when compared with the optimization without symmetry, (4) the method can be applied to models of macromolecules with still unknown detailed structure. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Bond-based 3D-chiral linear indices: Theory and QSAR applications to central chirality codificationJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 15 2008Juan A. Castillo-Garit Abstract The recently introduced non-stochastic and stochastic bond-based linear indices are been generalized to codify chemical structure information for chiral drugs, making use of a trigonometric 3D-chirality correction factor. These improved modified descriptors are applied to several well-known data sets to validate each one of them. Particularly, Cramer's steroid data set has become a benchmark for the assessment of novel quantitative structure activity relationship methods. This data set has been used by several researchers using 3D-QSAR approaches such as Comparative Molecular Field Analysis, Molecular Quantum Similarity Measures, Comparative Molecular Moment Analysis, E-state, Mapping Property Distributions of Molecular Surfaces, and so on. For that reason, it is selected by us for the sake of comparability. In addition, to evaluate the effectiveness of this novel approach in drug design we model the angiotensin-converting enzyme inhibitory activity of perindoprilate's ,-stereoisomers combinatorial library, as well as codify information related to a pharmacological property highly dependent on the molecular symmetry of a set of seven pairs of chiral N -alkylated 3-(3-hydroxyphenyl)-piperidines that bind ,-receptors. The validation of this method is achieved by comparison with earlier publications applied to the same data sets. The non-stochastic and stochastic bond-based 3D-chiral linear indices appear to provide a very interesting alternative to other more common 3D-QSAR descriptors. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008 [source] Adsorption Behavior of Asymmetrical Triblock Copolymers at the Solid-Liquid Interface by Monte Carlo SimulationMACROMOLECULAR THEORY AND SIMULATIONS, Issue 8 2004Changjun Peng Abstract Summary: Monte Carlo simulation on a simple lattice model has been used to study the adsorption of asymmetrical triblock copolymers from a non-selective solvent at the solid-liquid interface. The size distributions of train, loop and tail configurations for those copolymers are obtained as well as other details of the adsorption layer microstructure. Also the influence of adsorption energy and the role of molecular symmetry are investigated. A segment-density profile, the adsorption amount, the surface coverage, and the adsorption layer thickness have been determined. Finally, it is shown that the adsorption behavior of an asymmetrical copolymer can be predicted from the symmetrical copolymer. Size distributions of the tail configuration for A8,kB20Ak. [source] An aza-cyclophane stacked in racemic columnar assemblies: whole-molecule disorder in a two-dimensional solid solutionACTA CRYSTALLOGRAPHICA SECTION B, Issue 2 2009Matthias Zeller The oxime derivative of [1.1.1]cyclophane cyclotriveratrylene (CTV) was ring expanded utilizing a Beckmann rearrangement to provide a ten-membered N -acetyl macrocyclic amide that crystallizes as a chloroform monosolvate in columnar assemblies manifesting an unusual disorder within the crystal. Columns made up of this structure consist of infinite columnar assemblies of alternating d and l enantiomers and therefore necessarily are made up of a racemate, yet the chiralities of individual molecules in adjacent columns are independent of one another, leading to the overall formation of a two-dimensional solid solution. The random arrangement of the columns within the structure leads to the emergence of a crystallographic mirror plane not reflected by the molecular symmetry, to a change of symmetry from Pna21 to Pnma and to whole-molecule disorder of the bowl-shaped molecules within the columns. [source] Rotationally disordered phase of 1,3-dibromo-5-iodo-2,4,6-trimethylbenzene at 293 KACTA CRYSTALLOGRAPHICA SECTION C, Issue 10 2009Soumia Ghanemi In the crystal state at room temperature, the molecule of dibromoiodomesitylene (1,3-dibromo-5-iodo-2,4,6-trimethylbenzene), C9H9Br2I, is prone to strong disorder, apparently involving only the three halogen sites (occupied identically by 66.7% Br and 33.3% I). This disorder, of the rotational type according to previously published NMR measurements, corresponds to fast 2,/3 stochastic in-plane reorientations of the whole molecule between three discernable locations. This kind of rotational disorder can be revealed for the first time by diffractometry thanks to the C2v idealized molecular symmetry of the title compound, although it has been indirectly suspected at room temperature in other trihalogenomesitylenes of similar crystal packing but of D3h molecular symmetry. The average endocyclic angles facing the Br/I sites and the methyl groups are 124.14,(6) and 115.85,(2)°, respectively. The angle between the normal to the aromatic ring and the normal to the (100) plane is 4.1°. TLS analysis indicates that only the aromatic ring and the methyl groups behave as a rigid body with respect to the thermal librations. [source] Conformational enantiomeric disorder in tripivaloylmethaneACTA CRYSTALLOGRAPHICA SECTION C, Issue 6 2007Branko Kaitner Tripivaloylmethane [systematic name: 4-(2,2-dimethylpropanoyl)-2,2,6,6-tetramethylheptane-3,5-dione], C16H28O3, is a 1,3,3,-triketone with C3 molecular symmetry, prepared by ,-acylation of 2,2,6,6-tetramethylheptane-3,5-dione with 2,2-dimethylpropanoyl anhydride in the presence of barium metal. The molecules are conformationally chiral and pack so that each molecular site is occupied with equal probability by the two enantiomers. The carbonyl groups of the two superimposed enantiomeric molecules are at an angle of 75.4,(16)°. [source] The lack of C2 molecular symmetry in (1R,2R,3S,6S)-3,6-dibenzyloxycyclohex-4-ene-1,2-diolACTA CRYSTALLOGRAPHICA SECTION C, Issue 7 2001Robert W. Clark The results of a single-crystal X-ray experiment and density functional theory calculations performed for the title compound, C20H22O4, demonstrate that the lowest energy conformation of this molecule does not contain C2 molecular symmetry. [source] Purification, crystallization and molecular symmetry of CDP- d -glucose 4,6-dehydratase from Yersinia pseudotuberculosisACTA CRYSTALLOGRAPHICA SECTION D, Issue 2 2002Erik M. Vogan The enzyme CDP- d -glucose 4,6-dehydratase (EC 4.2.1.45) is an NAD+ -dependent oxidoreductase which catalyzes the irreversible conversion of CDP- d -glucose to CDP-4-keto-6-deoxy- d -glucose. The product of this reaction is an intermediate in the synthesis of all CDP-linked 3,6-dideoxyhexoses, an important class of antigenic determinants found in the lipopolysaccharide layer of Gram-negative bacteria. Crystals of a recombinant form of this enzyme from Yersinia pseudotuberculosis have been grown in two crystal forms, both possessing pseudo-translational non-crystallographic symmetry, with dramatically different diffraction characteristics. A complete 1.8,Å data set has been collected from the primitive orthorhombic crystal form, for which the non-crystallographic symmetry is described in detail. [source] Understanding High-Resolution Spectra of Nonrigid Molecules Using Group TheoryCHEMPHYSCHEM, Issue 4 2010Melanie Schnell Dr. Abstract Permutation-inversion group theory has developed to become an important tool in the high-resolution spectroscopy of nonrigid molecules. This large class of molecules is very intriguing to study. Small molecules such as ammonia or Na3 are known to be nonrigid. With increasing size, however, several large-amplitude motions are possible in a molecule, and can even interact with each other. The high-resolution spectra of nonrigid molecules are known to be quite complicated and very rich in information. Details about the molecule and its internal dynamics can be extracted, such as the molecular structure, the character of the chemical bonds, and the barrier heights to internal rotation and their dependence on the chemical bonds. However, due to the nonrigidity of the molecule and the complexity of such spectra, their analysis is usually quite challenging. Theoretical methods are needed for their prediction and analysis. This Review concentrates on permutation-inversion group theory and its usefulness for the analysis of high-resolution spectra of nonrigid molecules, which is examined in more detail using different examples. In a separate section, a special aspect of molecular symmetry is discussed: the breakdown of symmetry principles. Special emphasis is placed on the breakdown of space inversion symmetry (parity violation) in chiral molecules and its possible implications in high-resolution spectroscopy. [source] Asymmetry Induction by Cooperative Intermolecular Hydrogen Bonds in Surface-Anchored Layers of Achiral Molecules,CHEMPHYSCHEM, Issue 10 2006Alexandre Dmitriev Dr. Abstract The mesoscale induction of two-dimensional supramolecular chirality (formation of 2D organic domains with a single handedness) was achieved by self-assembly of 1,2,4-benzenetricarboxylic (trimellitic) acid on a Cu(100) surface at elevated temperatures. The combination of spectroscopic [X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine structure (NEXAFS)], real-space-probe [scanning tunneling microscopy (STM)], and computational [density functional theory (DFT)] methods allows a comprehensive characterization of the obtained organic adlayers, where details of molecular adsorption geometry, intermolecular coupling, and surface chemical bonding are elucidated. The trimellitic acid species, comprising three functional carboxylic groups, form distinct stable mirror-symmetric hydrogen-bonded domains. The chiral ordering is associated with conformational restriction in the domains: molecules anchor to the substrate with an ortho carboxylate group, providing two para carboxylic acid moieties for collective lateral interweaving through H bonding, which induces a specific tilt of the molecular plane. The ease of molecular symmetry switching in domain formation makes homochiral-signature propagation solely limited by the terrace width. The molecular layer modifies the morphology of the underlying copper substrate and induces ,m-sized strictly homochiral terraces. [source] | |||||||||||||