Changes In Bond Angles Research Articles

An ab initio and force field study on the conformation and chain flexibility of the dichlorophosphazene trimer

AbstractAb initio molecular orbital calculations have been used to study the conformation, valence electron charge density, and chain flexibility of a dichlorophosphazene trimer (CH3[NP(Cl2)]3CH3). The calculations were carried out at the restricted Hartree‐Fock level with the 6–31 G* basis set. The dichlorophosphazene trimer adopts a planar transcis conformation. The valence electron charge distribution indicates strong charge separations along the backbone of the molecule, and is in agreement with Dewar's island delocalization model for bonding in linear and cyclic phosphazenes. In order to determine the height of the torsional barrier (2,5 kcal/mol), the torsional potential of a central PN bond of the trimer was studied with a rigid rotor scan and geometry optimizations of selected rotamers. The flexibility of the PNP bond angle contributes significantly to the chain flexibility. Based on the results of the ab initio calculations, an empirical force field for the dichlorophosphazene trimer was developed. The energy expression includes bond stretch, angle bend, electrostatic, van der Waals, and torsional potential terms. A relaxed scan with the force field achieves good agreement with the ab initio results for the torsional potential in the vicinity of the stable conformation, and an excellent agreement with the ab initio results on changes in the P2N2P3 bond angle and the N1P2  N2P3 dihedral angle during a full rotation around the N2  P3 bond.

Synthesis and structural characterization of a tungstophosphate heteropoly blue

A single crystal of heteropoly blue, NaH 6PW 12O 40 ∗d 4H 2O, has been prepared by electrochemical reduction and isolated by evaporation under nitrogen. The crystal structure of the compound was determined by X-ray crystallography and refined to R = 0.0552 based on 4047 observed reflections. The heteropoly blue anion has an α-Keggin structure as in the unreduced heteropoly anion, but the structure is distorted and the expected changes in bond lengths and angles are observed. The compound has also been characterized by IR, UV-vis, X-band, ESR and XPS techniques.

On the Space Group of BaV3O8

The crystal structure of BaV3O8, recently described in space groupP21, is better described inP21/m. Refinement inP21/mleads to small but highly significant changes in bond lengths and angles; the general description of the structure is unchanged.

The isomerization of nitrobenzene to phenylnitrite

We report ab initio calculations on nitrobenzene (C 6H 5NO 2) and phenylnitrite (C 6H 5ONO) performed at the MP2(FC) 6-31G ∗ level. The results paint a detailed picture of the isomerization pathway between the two species on the ground electronic surface. They show that phenylnitrite is stable with respect to dissociation into phenoxy and nitric radicals by 80.6 kJ mol −1 and lies only 20.2 kJ mol −1 higher in energy than the nitrobenzene global minimum. We estimate the barrier between the two isomers to be less than 108.9 kJ mol −1 (1.13 eV), but we are unable to locate a fully converged transition state. Calculation of the isomerization pathway shows that there is an early barrier close to the initial nitrobenzene geometry. It also provides a clear picture of the extensive rearrangement involving a CN bond being broken, a new CO bond being formed, and further changes in bond lengths, bond angles, and dihedral angles in the C NO 2 moiety of the nitrobenzene molecule. The harmonic frequencies of the two isomers and those for the phenoxy and nitric oxide radicals calculated at the same level of theory compare well with previous experimental and theoretical studies. These calculations also bear on our experimental study of the kinetic and internal energy disposal in the photodissociation of nitrobenzene.

Conductivity in polyacetylene. I. Ab initio calculation of charge localization, bond distances, and reorganization energy in model molecules

The electronic structure and geometry of neutral or charged molecules of the type trans-H(CH)nH is calculated using ab initio methods. The reorganization energy λ for adding or subtracting electrons is obtained for the cases with n=10, 11, and 12 using (U)MP2 with a 6-31G basis set. We find contributions to λ not only from C–C bond distance changes but also from C–C–C bond angle changes, whereas the contribution from C–H bond length and C–C–H bond angle changes are unimportant. The change of bond length when electrons are added to or subtracted from a neutral molecule with an even number of carbon atoms is typically 0.05–0.08 Å and occurs over a large part of the molecule, even if the donated charge is concentrated near the positive alkali ion. λ for one-electron reduction or oxidation is large in an even C chain but small in an odd C chain. The introduction of electronic correlation at (at least) the level of second-order Mo/ller–Plesset perturbation theory is important in the calculation of bond lengths and reorganization energies.

Mössbauer, magnetic susceptibility, EPR, and EXAFS investigations of the vibrationally-induced low-spin/high-spin transition in a biomimetic Fe(III) complex

Magnetic susceptibility measurements from 2 to 520 K, Mossbauer measurements from 1.2 to 450 K, and EPR measurements at 10 K have been performed on the monomeric FeIII complex (1,4,7-tris(4-tert-butyl-2-mercaptobenzyl)-1,4,7-triaza-cyclononan)Fe. The complex exhibits a low-spin/high-spin transition at temperatures above 250 K. This behavior is quantitatively explained on the basis of a crystal-field model, which explicitly includes the vibrational properties of iron ligands. The EPR spectrum at 10 K yields a pure FeIII low-spin signal withg values 2.58(5), 2.12(5), 1.45(5). The values are consistently described by a crystal-field model, which explicitly includes spin-orbit coupling within the t2g subspace. The temperature dependence of the quadrupole splitting indicates a phase transition at approximately 100 K. The existence of the phase transition is corroborated by the temperature dependence of the effective thickness. The observation of only one quadrupole doublet up to 450 K indicates that the relaxation time between the high-spin and the low-spin configurations is shorter than the quadrupole precession time. X-ray structure analysis on single crystals at RT and temperature-dependent EXAFS investigation of powder material between 30 and 200 K indicate that the observed phase transition induces only changes of bond angles, while the low-spin/high-spin transition most likely induces changes of metal-ligand bond distances.

Structural changes of sarcoplasmic reticulum Ca 2+-ATPase upon Ca 2+ binding studied by simultaneous measurement of infrared absorbance changes and changes of intrinsic protein fluorescence

Ca 2+ binding to sacoplasmic reticulum Ca 2+-ATPase was investigated by Fourier transform infrared (FTIR) spectroscopy using the photolytic release of Ca 2+ from the photolabile Ca 2+ chelator 1-(2-nitro-4,5-dimethoxy)- N, N, N′, N′,-tetrakis[(oxy-carbonyl)]methyl-1,2-ethandiamine (DM-nitrophen). IR absorbance changes in 1H 2O and 2H 2O were detected in the spectral region from 1800 cm −1 to 1200 cm −1, reflecting photolysis of DM-nitrophen and Ca 2+ binding to the Ca 2+-ATPase. As an independent probe for protein conformational changes, intrinsic fluorescence changes upon Ca 2+ release were monitored simultaneously to the FTIR measurements. Both the IR absorbance changes and the fluorescence intensity changes correlated well with the Ca 2+ binding activity of the ATPase in this specific step. Ca 2+ binding caused IR difference bands mainly in the region of amide I absorption of the polypeptide backbone, reflecting conformational changes of the protein. The small amplitude of the signals indicates that only a few residues perform local structural changes such as changes of bond angles or hydrogen bonding. Other absorbance changes appearing above 1700 cm −1 can be assigned to Ca 2+ binding to Glu or Asp side chain carboxyl groups and concomitant deprotonation of these residues. This assignment is strengthened by downshifts of these bands by 4 cm −1 to 6 cm −1 upon 1H 2O/ 2H 2O exchange. This is in line with results of mutagenesis studies where such residues containing carboxyl groups were associated with the high affinity Ca 2+ binding site (Clarke, D.M., Loo, T.W. and MacLennan, D.H. (1990) J. Biol. Chem. 265, 6262–6267).

Estimation of changes in side chain configurational entropy in binding and folding: General methods and application to helix formation

Theoretical estimations of changes in side chain configurational entropy are essential for understanding the different contributions to the overall thermodynamic behavior of important biological processes like folding and binding. The configurational entropy of any given side chain in any particular protein can be evaluated from the complete energy profile of the side chain. Calculations of the energy profiles can be performed using the side chain single bond dihedrals as the only independent variables as long as the structures at each value of the dihedrals are allowed to relax through small changes in the valence bond angles. The probabilities of different side chain conformers obtained from these energy profiles are very similar to the conformer populations obtained by analysis of side chain preferences in the proteins of the Protein Data Bank. Also, side chain conformational entropies obtained from the energy profiles agree extremely well with those obtained from the Protein Data Bank conformer populations. Changes in side chain configurational entropy in binding and folding can be computed as differences in conformational entropy because, in most cases, the frequency of the rotational oscillation around the energy minimum of any given conformer does not appear to change significantly in the reactions. Changes of side chain conformational entropy calculated in this way were compared with experimental values. The only available experimental data--the effect of side chain substitution on the stability of alpha-helices--were used for this comparison. The experimental values were corrected to subtract the solvent contributions. This comparison yields an excellent agreement between calculated and experimental values, validating not only the theoretical estimates but also the separability of the entropic contributions into configurational terms and solvation related terms.

Structural transformation in densified silica glass: A molecular-dynamics study.

Pressure-induced structural transformation and the concomitant loss of intermediate-range order (IRO) in high-density ${\mathrm{SiO}}_{2}$ glass are investigated with the molecular-dynamics (MD) approach. The MD simulations cover a wide range of mass densities---from normal density (2.20 g/${\mathrm{cm}}^{3}$) to the density corresponding to stishovite (4.28 g/${\mathrm{cm}}^{3}$). This twofold increase in the density produces significant changes in the short-range order and intermediate-range order. As the density increases from 2.20 to 4.28 g/${\mathrm{cm}}^{3}$, the Si-O bond length increases from 1.61 to 1.67 \AA{}, the Si-O and O-O coordinations change from 4 to 5.8 and from 6 to 12, respectively, and the O-Si-O bond angle changes from 109\ifmmode^\circ\else\textdegree\fi{} to 90\ifmmode^\circ\else\textdegree\fi{}. These results provide firm evidence of structural transition from a corner-sharing Si(${\mathrm{O}}_{1/2}$${)}_{4}$ tetrahedral network to a network of Si(${\mathrm{O}}_{1/3}$${)}_{6}$ octahedra jointed at corners and edges. At normal density, the first sharp diffraction peak (FSDP) in the static structure factor S(q) is at 1.6 A${\mathrm{\r{}}}^{\mathrm{\ensuremath{-}}1}$ whereas under pressure the height of the FSDP is considerably diminished and its position shifts to larger q values. At a density of 2.64 g/${\mathrm{cm}}^{3}$, a peak in S(q) appears at 2.85 A${\mathrm{\r{}}}^{\mathrm{\ensuremath{-}}1}$. The height of this peak grows as the density increases. All of these results are in agreement with the recent high-pressure x-ray measurements on ${\mathrm{SiO}}_{2}$ glass.

New extended point defect structure in diamond cubic crystals.

In the course of atomistic simulations of the dislocation array at the Ge/Si(001) interface, we have generated a new closed symmetric defect structure comprising eighteen atoms that may be found in a variety of circumstances including dislocation intersections and grain boundaries. The structure maintains tetrahedral bonding with reasonable changes in bond lengths and angles, and may have interesting electronic properties. At the Ge/Si interface, these extended point defects may reach a very high planar concentration of \ensuremath{\sim}${10}^{12}$/${\mathrm{cm}}^{2}$.

The treatment of weak intensities in diffractometer data; the effect of truncating data

Abstract It appears to be normal practice to exclude weak data from the least squares refinement, even when this data has already been collected on a diffractometer. What is more, there is no standard criterion for what is or is not a weak intensity. By means of a computing exercise based on two recently determined structures, it is pointed out that the effect of excluding weak data will improve the residual but this is cosmetic as it is accompanied by changes in coordinates, temperature factors, bond lengths and angles which are not only detectable but may exceed the e.s.d. in particular parameters thus leading to unquantifiable errors. In some cases changes in bond lengths and angles are apparently systematic with the degree of truncation. In addition truncating the data may lead to an increase in the computed e.s.d. in the parameters. This confirms previous work that data should not be truncated and all available data should be used for crystal structure determination.

The Synthesis and Structure of Encapsulating Ligands: Properties of Bicyclic Hexamines

Template syntheses based on tris (ethane-1,2-diamine)cobalt(III) lead to cobalt(III) complexes of cage hexamines of the ' sarcophagine ' type ( sarcophagine = sar = 3,6,10,13,16,19- hexaazabicyclo [6.6.6] icosane ) rapidly and in high yield. Reduction of these species to their cobalt(II) forms enables the ligands to be removed in concentrated acids at elevated temperatures, and in hot aqueous solutions containing excess cyanide ion. The free sarcophagine and 1,8-diaminosarcophagine [(NH2)2sar or diamsar] ligands are strong bases, accepting up to four and five protons, respectively, in aqueous solution. In chloride medium, I = 1.0, at 298 K, pK1 = 11.95, pK2 = 10.33, pK3 = 7.17, pK4 ≈ 0 for sarcophagine , and pK1 = 11.44, pK2 = 9.64, pK3 = 6.49, pK4 = 5.48, pK5 ≈ 0 for diaminosarcophagine , with very similar values being found for triflate medium. Crystal structure determinations for both free bases, the chloride, sulfate, perchlorate and nitrate salts of diamsar , the complex of zinc chloride with sar, and the magnesium nitrate complex with diamsar show remarkably small variations in the cavity defined by the bicyclic ligands, though relatively subtle bond length and bond angle changes can be rationalized in terms of the effects of proton and metal ion binding. Exhaustive methylation of sarcophagine produces the highly lipophilic, hexatertiary base hexamethylsarcophagine , which, in the solid state, adopts quite different conformations and nitrogen-atom configurations to those of sar itself. All the ligands rapidly form metal ion complexes of generally exceptional kinetic and thermodynamic stability.

Computer simulation of materials using parallel architectures

Algorithms are designed to implement molecular dynamics (MD) and quantum molecular dynamics (QMD) simulations on emerging concurrent architectures. For systems with finite-range interactions, a domain-decomposition algorithm is used to implement the multiple-time-step (MTS) approach to MD simulations on distributed-memory multiple instruction multiple data (MIMD) machines. Parallel algorithms are also designed for MD simulations of bulk Coulombic systems. The performances of these algorithms are tested on the Intel iPSC/860 system. The computational complexities of these algorithms are O( N) and parallel efficiencies close to 0.9. The core computational kernel of the QMD approach consists of solutions of parabolic partial differential equations (PDE) such as the time-dependent Schrödinger equation or time-dependent Kohn-Sham equation. This problem is coupled with another computationally intensive problem, i.e., solution of elliptic PDEs (the Poisson equation) for the long-range electron-electron interaction. We have designed parallel algorithms for both problems on SIMD (single instruction multiple data) machines. In the past two years, we have used the parallel computer architectures in our Concurrent Computing Laboratory for Materials Simulations (CCLMS) to carry out MD and QMD simulations on network glasses, ceramic composites, nanophase materials, solid C 60 and graphitic tubules, and quantum transport in nanoscale devices. Structural transformation, intermediate-range order and dynamic behavior of SiO 2 glass at high pressures are investigated with molecular dynamics. At high densities, the height of the first sharp diffraction peak is considerably diminished, its position changes from 1.6 to 2.2 Å −1, and a new peak appears at 2.85 Å -1. At twice the normal density, SiO bond length increases, SiO coordination changes from 4 to 6 and OSiO bond-angle changes from 109° to 90°. This is a tetrahedral to octahedral transformation, which was reported recently by Meade, Hem1ey, and Mao. Molecular dynamics simulations of porous silica, in the density range 2.2-0.1 g/cm 3, are carried out on a 41 472 particle system using a MIMD computer. The internal surface area, pore surface-to-volume ratio, pore-size distribution, fractal dimension, correlation length and mean-particle size are determined as a function of the density. Structural transition between a condensed amorphous phase and a low-density porous phase is characterized by these quantities. Various dissimilar porous structures with different fractal dimensions are obtained by controlling the preparation schedule and temperature.

Inverse bond length/bond angle relationships Part 5. An ab initio study of molecules with multiple bonds

Abstract A theoretical study at the Hartree—Fock 6-31G * level has been made of geometrical relaxation as a response to forced bond angle changes in CH 3 CH 3 , CH 2 CH 2 , CHCH, CO 2 , SO 2 , and cis - and trans -FNNF. In each case, bond angles were fixed at different values and the remaining geometry was optimized to show structural trends. Over wide angle ranges, changes in the central bond lengths are nearly linear with changes in the adjacent angles, the “inverse bond length/bond angle” relationship. At more extreme angular ranges and for the heteroatom compounds, more complicated behavior was found.

Determination of structural substituent effects in nitrobenzene by NMR spectroscopy of partially oriented molecules in liquid crystals

It is demonstrated that NMR spectroscopy of oriented molecules can be used to measure structural substituent effects (changes in bond lengths and angles) in benzene derivatives, and the results agree with other methods and with theoretical predictions. Discrepancies in earlier results are shown to originate from a missing correction for the molecular deformation which is caused by the anisotropic interaction with the liquid-crystal solvent.

Ion beam modification of Gd 2Ti 2O 7

Irradiation of Gd 2Ti 2O 7 with 3 MeV Ar + ions results in expansion of the unit cell volume and irradiation-induced amorphization. The damage cross section for amorphization determined from X-ray diffraction data is 0.023 nm 2. Transmission electron microscopy and electron diffraction confirm the irradiation-induced amorhous character at high fluences. Raman spectroscopy indicates a decrease in scattered intensity and an increase in linewidth with fluence for the principal vibrational modes, consistent with increasing-induced disorder. The wave number of the most intense Raman peak at ≈310 cm −1 (attributed to the O-Gd-O bending mode) decreases with fluence, indicating a change in bond angle. The increase with fluence in the wave number of the Raman peak at ≈ 515 cm −1 (attributed to the Gd-O stretching mode) suggests a decrease in this bond length. At intermediate fluences, a forbidden peak at ≈ 765 cm −1 becomes slightly activated by irradiation-induced disorder on the cation sites.

Supplementary d and f functions in molecular wave functions at large and small internuclear separations

AbstractThe CO, CO2, CS, CIF, and SO2 molecules were used to test the dependence of supplementary d and f function exponents to changes in bond lengths and bond angles in MO calculations utilizing Gaussian basis sets in Hartree–Fock and Moller–Plesset calculations. Using Dunning–Hay double zeta basis sets, optimizations were performed at internuclear separations from 100–200 pm and beyond. The energy cost of not reoptimizing d function exponents when bonds are stretched or compressed is much smaller for correlated calculations than for those at the Hartree–Fock level and is greatest at the lower end of the range of internuclear distances. The problem is much less serious at all levels when multiple sets of d functions are used. © 1993 John Wiley & Sons, Inc.

Metal dependence of the nonplanar distortion of octaalkyltetraphenylporphyrins

The biological activity of porphyrins and related tetrapyrroles in proteins may be modulated by nonplanar conformational distortions; consequently, two aspects of nonplanarity have been investigated in the highly nonplanar octaalkyltetraphenylporphyrins (OATPPs). In the first part, the effect of the central metal ion (M = Ni(II), Co(II), Cu(II), Zn(II), Co(III), Fe(III)) on the conformation of the OATPP macrocycle has been determined. Crystallographic studies reveal that the sterically encumbered, nonplanar porphyrin 2,3,7,8,12,13,17,18-octaethyl-5,10,15,20-tetraphenylporphyrin (OETPP) remains sufficiently flexible to show a small decrease in nonplanarity for large metal ions. This decrease in nonplanarity for the OETPP metal complexes is predicted by using a molecular mechanics force field derived from structural and vibrational data for planar metalloporphyrins. A detailed analysis of the crystal structures of the Co(II) and Cu(II) complexes of OETPP reveals that the metal-dependent changes in bond lengths and bond angles are qualitatively similar to the changes observed for the OEP complexes. As the metal size increases, both OEPs and OETPPs exhibit expansion of the meso bridges (increases in the C[sub [alpha]]-C[sub m] bond length and the C[sub [alpha]]-C[sub m]-C[sub [alpha]] bond angle) and a movement of the coordinating nitrogen atoms away from the metal atom (increases in the M-N bond length andmore » the C[sub [alpha]]-N-C[sub [alpha]] bond angle and a decrease in the N-C[sub [alpha]] bond length). In the second part, a combination of molecular mechanics and INDO/CI molecular orbital calculations successfully predicts the optical spectra of a series of highly substituted OATPPs with increasing nonplanar distortion. The successes of these calculations indicates the importance of including both the macrocycle conformation and the peripheral substituents in the INDO calculations. 62 refs., 10 figs., 6 tabs.« less

Synthesis, structure and properties of the cluster anions [(Mo 6Cl 8i)X 6a] 2− with X aF, Cl, Br, I

The tetrabutylammonium (TBA) salts of the octa- μ 3-chloro-hexahalogeno-octahedrohexamolybdate(2−) ions [(Mo 6Cl 8 1)X 6 a;] 2− with X aF, Cl, Br, I were synthesized from the appropriate free acid of the type H 2[(Mo 6Cl 8 1)X 6 a] with X a(BF 4) −, Cl −, Br −, I − and the corresponding TBA halide. The crystal structures determined from single crystals show systematic changes in bond distances and angles with the F a a ̊ I a ligand exchange (increasing Mo 6 octahedron; slight compression of the Cl 8 1 cube). Infrared and Raman spectra were measured in solution and in the solid state (80 K). The vibrational modes of the cluster kernel Mo 6Cl 8 1 are approximately site constant, but all vibrations with contributions of the X a ligands show characteristic shifts. The most important bands are assigned by use of normal coordinate analyses.

Potential energy surfaces for OsH2

We compute the potential energy surfaces of 12 electronic states of OsH2 (four quintet, four triplet, and four singlet) arising from5D ground state of the Os atom as well as triplet and singlet excited states using the complete active space multiconfiguration self-consistent field (CAS-MCSCF) followed by multireference configuration interaction (MRCI) and relativistic CI (RCI) calculation which include up to 430,000 configurations. We find that the5D ground state of Os atom does not insert into H2 while the excited3F state of Os does. The3B1 ground state of OsH2 (there are two other nearly degenerate states) in the absence of spin-orbit coupling was found to be 22 kcal/mol more stable than Os(5D)+H2. The spin-orbit mixing of3B1,3B2,3A2, and1A1 states was so strong that it induces significant change in bond angles (up to 10°) for OsH2.