Density functional study of the second row transition metal dimers

Equilibrium geometries, vibrational frequencies and dissociation energies of the second row transition metal dimers (from Y-2 to Cd-2 except Tc-2) ere studied by use of density functional methods B3LYP, BLYP, B3PW91, BHLYP, BP86, B3P86, SVWN, MPW1PW91 and PBE1PBE. The accuracy DFT methods is found to be highly dependent on the functional employed, in particular for vibrational frequency and dissociation energy. In most cases, the predicted bond distance is in general agreement with experiment and previous theoretical results. For van der Waals dimer Cd-2, B3LYP and BLYP have excellent performance in predicting the bond distance. For Ag-2, all density functional methods used in this study perform well in producing the bond distance, vibrational frequency and dissociation energy.

Electronic structures of hafnium dimer and trimer by density functional theory

Equilibrium geometries, vibrational frequencies and dissociation energies of hafnium dimer and trimer were studied by density functional methods B3LYP, BLYP, B3PW91, BHLYP, BP86, B3P86, mPW1PW91 and PBE1PBE. The results indicate that singlet is the ground state both for hafnium dimer and for trimer. For hafnium dimer, the calculated bond distance is less sensitive to the methods used. Except at BHLYP level, the calculated vibrational frequency is comparable to the experimental value. For hafnium trimer, equilateral triangle with D-3h symmetry is slightly favored compared with isosceles triangle with C-2v, symmetry except at BHLYP level. This conclusion is in agreement with experiment in which the ground state of Hf-3 is fluxional and low-spin or closed shell is preferred.

Ground state of lutetium dimer by density functional methods

Bond distances, vibrational frequencies and dissociation energies for the ground state of Lu-2 were studied by density functional methods B3LYP, B3PW91, BLYP, BHLYP, BP86, B3P86, MPW1PW91, PBE1PBE and SVWN with CEP-121G and SDD basis sets. Singlet state is predicted to be the most stable. CEP-121G has a better overall performance than SDD. At CEP-121G basis set, all density functional methods used in this study perform well in reproducing the spectroscopic constants.

Electronic structures of 3d-metal mononitrides

Bond distances, vibrational frequencies, electron affinities, ionization potentials, and dissociation energies of the title molecules in neutral, positively, and negatively charged ions were studied by use of density functional methods B3LYP, BLYP, BHLYP, BPW91, and B3PW91. The calculated results are compared with experiments and previous theoretical studies. It was found that the calculated properties are highly dependent on the functionals employed, in particular for the dissociation energy and vibrational frequency. For neutral species, pure density functional methods BLYP and BPW91 have relatively good performance in reproducing the experimental bond distance and vibrational frequency. For cations, hybrid exchange functional methods B3LYP and B3PW91 are good in predicting the dissociation energy. For both neutral and charged species, BHLYP tends to give smaller dissociation energy.

Electronic structures and chemical bonding in transition metal monosilicides MSi (M=3d, 4d, 5d elements)

Bond distances, vibrational frequencies, electron affinities, ionization potentials, dissociation energies, and dipole moments of the title molecules in neutral, positively, and negatively charged ions were studied using the density functional method. Ground state was assigned for each species. The bonding patterns were analyzed and compared with both the available data and across the series. It was found that besides an ionic component, covalent bonds are formed between the metal s, d orbitals and the silicon 3p orbital. The covalent character increases from ScSi (YSi) to NiSi (PdSi) for 3d (4d) metal monosilicides, then decreases. For 5d metal monosilicides, the covalent character increases from LaSi to OsSi, then decreases. For the dissociation of cations, the dissociation channel depends on the magnitude of the ionization potential between metal and silicon. If the ionization potential of the metal is smaller than that of silicon, channel MSi+-> M++Si is favored. Otherwise, MSi+-> M+Si+ will be favored. A similar behavior was observed for anions, in which the dissociation channel depends on the magnitude of electron affinity.

Chemical bonding and electronic structure of 4d-metal monocarbides

Bond distances, vibrational frequencies, dissociation energies, electron affinities, ionization potentials and dipole moments of the title molecules in neutral and charged ions were studied by use of density functional method. Ground states for each molecule were assigned. For neutral and cationic molecules, the bond distance decreases from YC (YC+) to RhC (RhC+), then increases, while for anionic molecules, the bond distance decreases from YC- to RuC-, then increases. Opposite trend was observed for vibrational frequency. The bond ionic character decreases from ZrC to PdC for neutral molecules. The bonding patterns are discussed and compared with the available studies.

Geometries and electronic properties of Ta-n, TanO and TaOn (n=1-3) clusters

Geometries, vibrational frequencies, electron affinities, ionization potentials and dissociation energies of the title clusters in both neutral and positively and negatively charged states were studied by use of density functional theory. For both neutral and charged species, different initial isomers were studied in order to determine the structure with the lowest energy. Vibrational analysis was also performed in order to characterize these isomers. For Ta-2, Ta-Ta metallic bond is strengthened by adding or removing an electron, i.e. the charged species are much more stable than the neutral counterpart. For Ta-3, equilateral triangle with D-3h symmetry has the lowest energy for both neutral and charged species (near equilateral triangle for cation). TaO and its charged species have much larger dissociation energy compared with other tantalum oxides. For Ta2O and TaO2. structure with C-2v symmetry is much more stable than linear chains. For Ta3O, planar structure with doubly bridging oxygen atoms of C-2v, symmetry is the global minimum for both neutral and charged species. While for TaO3, three-dimensional structures are favored for both neutral (C-1 symmetry) and charged species (C-3v symmetry).

Studies on beta-cyclodextrin amino acids inclusion complexes by electrospray ionization mass spectrometry

The positive- and negative-ion electrospray ionization mass spectra of beta-cyclodextrin-amino acids complexes in NH4Ac buffer have been reported in this paper. Compared with positive-ion ESI mass spectra of beta-cyclodextrin-amino acids complexes under the same condition, negative-ion mass spectra obtained for inclusion complexes of beta-cyclodextrin (CD) with tyrosine, phenylalanine and tryptophan, respectively, were completely dominated by deprotonated complex ions and [CD-H](-) ion which is the only daughter ion in collision-induced dissociation (CID) experiment of deprotonated complexes, The results indicated that the charged position for protonated and deprotonated complexes is different from each other. In addition, two complex ions for the same complex have similarly relative dissociation energies, which are higher than that of [CD+NH4](+), indicating that complexes observed in gasphase are not electrostatic adducts at all but complexes formed by hydrogen bonds.

Mechano-Chemical Coupling at Molecular Level: Forced Dissociation of Selectin/Ligand Binding

Mechano-chemical coupling is a common phenomenon that exists in various biological processes at different physiological levels. Bone tissue remodeling strongly depends on the local mechanical load. Leukocytes are sheared to form the transient aggregates with platelets or other leukocytes in the circulation. Flow pattern affects the signal transduction pathways in endothelial cells. Receptor/ligand interactions are important to cell adhesion since they supply the physical linkages...

Forced Dissociation of Selectin-ligand Complexes Using Steered Molecular Dynamics Simulation

Selectin-ligand interactions are crucial to such biological processes as inflammatory cascade or tumor metastasis. How transient formation and dissociation of selectin-ligand bonds in blood flow are coupled to molecular conformation at atomic level, however, has not been well understood. In this study, steered molecular dynamics (SMD) simulations were used to elucidate the intramolecular and intermolecular conformational evolutions involved in forced dissociation of three selectin-ligand systems: the construct consisting of P-selectin lectin (Lec) and epidermal growth factor (EGF)-like domains (P-LE) interacting with synthesized sulfoglycopeptide or SGP-3, P-LE with sialyl Lewis X (sLeX), and E-LE with sLeX. SMD simulations were based on newly built-up force field parameters including carbohydrate units and sulfated tyrosine(s) using an analogy approach. The simulations demonstrated that the complex dissociation was coupled to the molecular extension. While the intramolecular unraveling in P-LESGP-3 system mainly resulted from the destroy of the two anti-parallel sheets of EGF domain and the breakage of hydrogen-bond cluster at the Lec-EGF interface, the intermolecular dissociation was mainly determined by separation of fucose (FUC) from Ca2+ ion in all three systems. Conformational changes during forced dissociations depended on pulling velocities and forces, as well as on how the force was applied. This work provides an insight into better understanding of conformational changes and adhesive functionality of selectin-ligand interactions under external forces.

2D Kinetics and Forced Dissociation of Selectin-ligand Bindings

Cell adhesion is crucial to many pathophysiological processes, such as inflammatory reaction and tumor metastasis. It is mediated by specific interactions between receptors and ligands, and provides the physical linkages among cells. For example, interactions between selectins and glycoconjugate ligands mediate leukocyte initially tethering to and subsequently rolling on vascular surfaces in sites of inflammation or injury, which is determined by their fast kinetic rates. To mediate cell adhesion, the interacting receptors and ligands must anchor to apposing surfaces of two cells or a cell and the substratum, i.e. , the so-called two-dimensional (2D) binding, which differs from interactions in the fluid phase, i.e. , the three-dimensional (3D) binding. How structural variations and surface environments of interacting molecules affect their 2D kinetics, and how external forces manipulate their dissociation has little been known quantitatively, and nowadays attracts more and more attentions.

Dissociation of egocentric and allocentric spatial processing in prefrontal cortex

Monkeys with lesions of areas 9 and 46 performed three variants of the spatial delayed response (SDR) task. There were no impairments in allocentric spatial memory in which geometrical relationships between environmental cues were used to identify spatial location; thus, memory of a 3D environmental map is intact. In contrast, there were severe impairments in egocentric spatial memory guided by visual or tactile cues that monkeys can relate to their viewing perspective during testing. These results strongly suggest that dorsolateral prefrontal cortex selectively mediates spatial memory tasks that are solved by referencing the location of targets to the body's orientation. (C) 2003 Lippincott Williams Wilkins.

Analysis of the energies of the triple base triplets

Sixty-four sets of three-dimensional models of DNA triplex base triplets (TBT) were built up based on codons by homologous modeling method and their energies were minimized. According to sequence of TBT and orientation of the third ODN strand third, the energies of monomers and water-K+-TBT ternary complexes of TBT were analyzed. The results showed: (i) The energies of the symmetric parallel monomers are generally lower than those of the symmetric anti-parallel monomers of TBT, but the energies of the symmetric parallel ternary complexes are higher than those of the symmetric anti-parallel ternary complexes of TBT. (ii) No matter TBTs are monomers or ternary complexes, the energies of asymmetric parallel TBTs are generally lower than those of the asymmetric anti-parallel ones. (iii) Although the energies of the parallel TBTs are correlated with those of the anti-parallel ones, the energy differences are significant between them. The results here suggest the sequences of TBTs and the orientations of the third ODN strands are two of the key factors that can influence the formation and stability of TBT. (C) 2002 Elsevier Science B.V. All rights reserved.