Search results for "Bent molecular geometry"
showing 10 items of 38 documents
An Improved Force Field for O2, CO and CN Binding to Metalloporphyrins
2004
Parametrization of a molecular-mechanics program to include terms specific for five- and six-coordinate transition metal complexes is applied to heme complexes. The principal new feature peculiar to five and six coordination is a term that represents the effect of electron-pair repulsion modified by the ligand electronegativity and takes into account the different possible structures of complexes. The model system takes into account the structural differences of the fixing centre in the haemoglobin subunits. The customary proximal histidine is added. The macrocycle heme IX is wholly considered in our model. The calculations show clearly that certain conformations of heme IX–histidine models…
Halogen bond directionality translates tecton geometry into self-assembled architecture geometry
2013
The structures of halogen-bonded infinite chains involving two diiodoperfluoroalkanes and a bent bis(pyrid-4′-yl)oxadiazole show that the geometry of the pyridyl pendant rings is translated into the angle between the formed halogen bonds.
Nature of O2, CO, and CN binding to hemoprotein models
2004
Parametrization of a molecular-mechanics program to include terms specific for five- and six-coordinate transition metal complexes results in computer-simulated structures of hemo complexes. The principal new feature peculiar to five- and six-coordination is a term that measures the effect of electron-pair repulsion modified by the ligand electronegativity and takes into account the different structural possibilities. The work consists in the modification of program molecular mechanics for penta and hexacoordination. The model system takes into account the structural differences of the fixing center in the hemoglobin subunits. The customary proximal histidine is added. The macrocycle hemo I…
Nature of FeIII–O2, FeII–CO and FeIII–CN complexes of hemoprotein models
2003
Abstract Parametrization of a molecular-mechanics program to include terms specific for 5- and 6-coordinate transition metal complexes results in computer-simulated structures of hemo complexes. The principal new feature peculiar to 5- and 6-coordination is a term that measures the effect of electron-pair repulsion modified by the ligand electronegativity and takes into account the different structural possibilities. The work consists in the modification of program molecular mechanics for 5- and 6-coordination. The model system takes into account the structural differences of the fixing centre in the haemoglobin (Hb) subunits. The customary proximal histidine is added. The macrocycle hemo I…
Effects of Bending on Raman-active Vibration Modes of Carbon Nanotubes
2008
We investigate vibration modes and their Raman activity of single-walled carbon nanotubes that are bent within their intrinsic elastic limits. By implementing novel boundary conditions for density-functional based tight-binding, and using non-resonant bond polarization theory, we discover that Raman activity can be induced by bending. Depending on the degree of bending, high-energy Raman peaks change their positions and intensities significantly. These effects can be explained by migration of nodes and antinodes along tube circumference. We discuss the challenge of associating the predicted spectral changes with experimental observations.
The Engineering of Hot Carbon Nanotubes with a Focused Electron Beam
2004
Single-wall and multiwall carbon nanotubes at high temperature are irradiated with the focused electron beam in an electron microscope. Nanotubes can be tailored with monolayer precision, and new morphologies of nanotubes are created. Atoms from layers of multiwall tubes can be removed and the tubes can be bent by a predefined angle. Bundles of single-wall tubes are transformed locally to multiwall tubes with coherent transition between the two modifications.
Densely packed semiflexible macromolecules in a rigid spherical capsule
2018
The ordering of semiflexible polymers with persistence length lp and contour length L confined in a sphere of radius R is studied by molecular dynamics simulations of a coarse-grained model. Monomer densities are chosen where the corresponding bulk lyotropic solution or melt is a well-ordered nematic, and purely repulsive walls of the rigid confining sphere are considered. It is found that polymers close to the walls are bent according to the curvature of the confining spheres with all their monomers in a few layers parallel to the sphere surface, whereas the remaining macromolecules closer to the sphere center have one chain end and their center of mass far from the surface. The latter cha…
Analysis of static friction and elastic forces in a nanowire bent on a flat surface: A comparative study
2014
ZnO nanowires bent to a complex shape and held in place by static friction force from supporting flat surface are investigated experimentally and theoretically. The complex shapes are obtained by bending the nanowires inside a scanning electron microscope with a sharp tip attached to a nanopositioner. Several methods previously described in the literature are applied along with author's original method to calculate the distributed friction force and stored elastic energy in the nanowires from the bending profile. This comparative study evidences the importance of the usage of appropriate models for accurate analysis of the nanowires profile. It is demonstrated that incomplete models can lea…
Di-chlorido-[N-(N,N-di-methyl-carbamimido-yl)-N',N',4-tri-methyl-benzohydrazonamide]-platinum(II) nitro-methane hemisolvate.
2014
In the title compound, [PtCl2(C13H21N5)]·0.5CH3NO2, the PtIIatom is coordinated in a slightly distorted square-planar geometry by two Cl atoms and two N atoms of the bidentate ligand. The (1,3,5-triazapentadiene)PtIImetalla ring is slightly bent and does not conjugate with the aromatic ring. In the crystal, N—H...Cl hydrogen bonds link the complex molecules, forming chains along [001]. The nitromethane solvent molecule shows half-occupancy and is disordered over two sets of sites about an inversion centre.
Electron capture activation of the disulfide bond. The role of the asymmetry and electronegativity.
2010
The effects of electron capture on the structure of XSSX' disulfide derivatives in which the substituents attached to the sulfur atoms have different electronegativites have been investigated at different levels of theory, namely DFT, MP2, QCISD and CASSCF/CASPT2. Although it has been generally assumed that electron attachment to disulfide derivatives leads to a systematic and significant activation of the S-S bond, our results show that this is the case only when the substituents X or X' have low electronegativity. Otherwise, the S-S bond in the anion remains practically unperturbed and only the S-X bond is largely activated or even broken, because the extra electron occupies the sigma*(S-…