Covalent Bond Length Research Articles

Preparation of Asymmetric Spiro Orthocarbonates via Cyclic Thionocarbonates

The development of monomers that show no shrinkage in volume upon polymerization is highly desirable in the field of materials such as dental fillings, high-strength composites, precision castings, and adhesives. 1 Volume shrinkage during polymerization results from the conversion of van der Waals distances between monomers to covalent bond lengths. Since the van der Waals distance separates monomer molecules approximately three times greater than a covalent bond does, the formation of new covalent bonds upon polymerization is destined to produce the substantial amount of volume contraction. A hopeful approach to prevent this shrinkage could be attained by using monomers that polymerize via the double ring-opening process, which results in two bonds breaking for each new bond formation. Since the double ring-opening polymerization was reported in 1972, 2 various monomers based on spiro orthoester (SOE), 3 bicyclo orthoester (BOE), 4 polycyclic ketal lactone (PKL), 5 cyclic ether, 6 spiroketal, 7 and spiro orthocarbonate (SOC) skeletons 8 have been developed to show the expansion in volume upon polymerization. Among them, spiro orthocarbonates (SOCs) are the most widely investigated monomers because they show the biggest volume expansion. Moreover SOCs containing exo-methylene groups undergo the ring-opening polymerization not only with cationic initiators 9 but also with radical initiators. 10 Asymmetric SOCs possessing one exo-methylene group are more favorable than symmetric SOCs, because the extra exomethylene group remained in the polymer from symmetric monomers affords the crosslinking reaction that causes the volume shrinkage. 11 Recently, N,S- 12 and S,S-analogs 13 of

ATOMIC STRUCTURE OF THE Ge(112)-(4×1)-In RECONSTRUCTION

We have studied the Ge(112)-(4×1)-In reconstruction with scanning tunneling microscopy (STM). Based on our bias dependent STM images and the characteristic electronic structure of stable submonolayer group Ⅲ-metal/group-Ⅳ-semiconductor interfaces, we propose an atomic model of this reconstruction for further investigation. The adsorption sites of In atoms are the same as In atoms' adsorption sites in the Si(112)-(7×1)-In reconstruction, but are different from the adsorption sites of Al and Ga atoms on the Si(112) surface. We suggest that this difference in adsorption sites is mainly due to the longer covalent bond length of In atoms. We further propose that, due to the smaller misfit, Al and Ga atoms may form longer nano wires along the step edges on the Ge(112) surface.

Pex, analytical tools for PDB files. I. GF-Pex: Basic file to describe a protein

Pex are created to extract numeric and string descriptions of protein structures from PDB files. This concerns covalent bond lengths and angles, secondary structures, residues in interaction, H-bond lengths and geometry, etc. Several kinds of Pex are generated: (1) general feature (GF-Pex); (2) H-bond (H-Pex); and (3) accessible surface (AS-Pex) and force potential (FP-Pex). We describe the general principles of Pex and detail the GF-Pex files. Using the GF-Pex of 131 proteins, we analyze the mean residue frequencies, the straight phi/psi distribution and the major kinds of secondary structures in proteins. Thomas et al. (this issue) analyzes the main chain H-bonds in those proteins. The GF-Pex and H-Pex files of the 131 proteins can be downloaded from the CBMN site (http://www.fsagx.ac.be/bp/). Proteins 2001;43:28-36.

Atomic refinement using orientational restraints from solid-state NMR.

We describe a procedure for using orientational restraints from solid-state NMR in the atomic refinement of molecular structures. Minimization of an energy function can be performed through either (or both) least-squares minimization or molecular dynamics employing simulated annealing. The energy, or penalty, function consists of terms penalizing deviation from "ideal" parameters such as covalent bond lengths and terms penalizing deviation from orientational data. Thus, the refinement strives to produce a good fit to orientational data while maintaining good stereochemistry. The software is in the form of a module for the popular refinement package CNS and is several orders of magnitude faster than previous software for refinement with orientational data. The short computer time required for refinement removes one of the difficulties in protein structure determination with solid-state NMR.

Structural characteristics of areneselenenyl bromide and areneselenenyl chloride stabilized by hypervalent coordination with a halide anion in the solid state

Solid-state molecular structures of 2-[( N-cyclohexyl- N-methylamino)methyl]benzeneselenenyl bromide (ArSeBr) and chloride (ArSeCl), stabilized by hypervalent coordination with a halide anion (Br − or Cl −, respectively), were determined by X-ray diffraction method. By comparing bond parameters of the observed hypervalent BrSe⋯Br fragment with those reported previously for other organoselenium compounds, which have a similar T-shaped selenium fragment, it was revealed that there is decent hyperbolic relationship between the two linear SeBr atomic distances in the solid state, reflecting the possibility of a pathway for the addition reaction of benzeneselenenyl bromide (PhSeBr) in solution. In addition, the existence of significant bond-shortening (∼0.1 Å) due to intermolecular weak packing interactions was strongly suggested by comparison of the extrapolated SeBr covalent bond length (2.220 Å) in the solid state with that reported for PhSeBr (2.325 Å) in the gas phase. Ab initio molecular orbital calculations at the RHF/6-31G(d,p) level using Ahlrichs pVDZ basis sets for Se and Br estimated the perturbation energy in the solid state to be roughly 1.5 kcal mol −1 independent of the packing structure.

Crystal structures of the metal-dependent 2-dehydro-3-deoxy-galactarate aldolase suggest a novel reaction mechanism.

Carbon-carbon bond formation is an essential reaction in organic chemistry and the use of aldolase enzymes for the stereochemical control of such reactions is an attractive alternative to conventional chemical methods. Here we describe the crystal structures of a novel class II enzyme, 2-dehydro-3-deoxy-galactarate (DDG) aldolase from Escherichia coli, in the presence and absence of substrate. The crystal structure was determined by locating only four Se sites to obtain phases for 506 protein residues. The protomer displays a modified (alpha/beta)(8) barrel fold, in which the eighth alpha-helix points away from the beta-barrel instead of packing against it. Analysis of the DDG aldolase crystal structures suggests a novel aldolase mechanism in which a phosphate anion accepts the proton from the methyl group of pyruvate.

Intrinsic Distribution and Atomic Level Stress in Polymeric Melts

The relationship between stress production and relaxation on one hand and the local structure on the other is studied in model polymeric melts by the use of equilibrium and nonequilibrium molecular dynamics. The analysis is performed in the intrinsic coordinate systema mobile frame tied to the generic bond. The variation of the intrinsic distribution of interacting neighbors about a representative atom, g̃, with density and temperature is investigated above and below the glass transition. It is shown that g̃ captures close packing effects and the buildup of structure upon transition, similar to the radial distribution function g(r). When computed from the nearest nonbonded neighbors, the intrinsic distribution is nonuniform due to steric shielding. Neighbors at distances larger than a covalent bond length from the representative atom, however, lead to a uniform distribution g̃. Thus, the steric shielding effect generates a nonzero intrinsic deviatoric stress in both equilibrium and nonequilibrium systems, while longer range interactions do not contribute to deviatoric stress production. Consequently, each intrinsic frame carries a nonhydrostatic stress (induced by both bonded and nonbonded interactions) which, upon rotation in the global coordinate system, contributes to the global stress in the melt. A preferential orientation of intrinsic frames (induced, for instance, by the deformation of the fluid) generates therefore a deviatoric global stress. In nonequilibrium simulations, the intrinsic distribution is seen to be independent of the deformation of the fluid. Furthermore, when computed from chain inner atoms, the intrinsic distribution is also chain length independent. This implies, in turn, that intrinsic stresses are deformation and chain length independent. The relevance of these observations to stress relaxation in polymeric melts is discussed.

Atomic mutations at the single tryptophan residue of human recombinant annexin V: effects on structure, stability, and activity.

The single tryptophan residue (Trp187) of human recombinant annexin V, containing 320 residues and 5328 atoms, was replaced with three different isosteric analogues where hydrogen atoms at positions 4, 5, and 6 in the indole ring were exchanged with fluorine. Such single atom exchanges of H --> F represent atomic mutations that result in slightly increased covalent bond lengths and inverted polarities in the residue side-chain structure. These minimal changes in the local geometry do not affect the secondary and tertiary structures of the mutants, which were identical to those of wild-type protein in the crystal form. But the mutants exhibit significant differences in stability, folding cooperativity, biological activity, and fluorescence properties if compared to the wild-type protein. These rather large global effects, resulting from the minimal local changes, have to be attributed either to the relatively strong changes in polar interactions of the indole ring or to differences in the van der Waals radii or to a combination of both facts. The changes in local geometry that are below resolution of protein X-ray crystallographic studies are probably of secondary importance in comparison to the strong electronegativity introduced by the fluorine atom. Correspondingly, these types of mutations provide an interesting approach to study cooperative functions of integrated residues and modulation of particular physicochemical properties, in the present case of electronegativity, in a uniquely structured and hierarchically organized protein molecule.

Solution Structure of Porcine Delta Sleep-inducing Peptide Immunoreactive Peptide A Homolog of the ShortsightedGene Product

The 77-residue delta sleep-inducing peptide immunoreactive peptide (DIP) is a close homolog of the Drosophila melanogaster shortsighted gene product. Porcine DIP (pDIP) and a peptide containing a leucine zipper-related partial sequence of pDIP, pDIP(9-46), was synthesized and studied by circular dichroism and nuclear magnetic resonance spectroscopy in combination with molecular dynamics calculations. Ultracentrifugation, size exclusion chromatography, and model calculations indicated that pDIP forms a dimer. This was confirmed by the observation of concentration-dependent thermal folding-unfolding transitions. From CD spectroscopy and thermal folding-unfolding transitions of pDIP(9-46), it was concluded that the dimerization of pDIP is a result of interaction between helical structures localized in the leucine zipper motif. The three-dimensional structure of the protein was determined with a modified simulated annealing protocol using experimental data derived from nuclear magnetic resonance spectra and a modeling approach based on an established strategy for coiled coil structures. The left-handed super helical structure of the leucine zipper type sequence resulting from the modeling approach is in agreement with known leucine zipper structures. In addition to the hydrophobic interactions between the amino acids at the heptade positions a and d, the structure of pDIP is stabilized by the formation of interhelical i to i' + 5 salt bridges. This result was confirmed by the pH dependence of the thermal-folding transitions. In addition to the amphipatic helix of the leucine zipper, a second helix is formed in the NH2-terminal part of pDIP. This helix exhibits more 310-helix character and is less stable than the leucine zipper helix. For the COOH-terminal region of pDIP no elements of regular secondary structure were observed.

A comparative study of the thermal stability of the (103) surface of group-III-metal/group-IV-semiconductor systems

To investigate and understand the thermal stability of the (103) surface of the Al Si , Ga Si , In Si , Al Ge , Ga Ge , and In Ge systems, in the present article we study well-annealed surfaces of the systems as well as those of the Ga Si , Al Ge , and Ga Ge(001) systems by means of LEED and AES. The results show that the (103) surfaces of the Al Ge and Ga Ge systems are unstable while those of the other four III IV(103) systems are very stable. On the basis of the atomic structure of the III IV(103) 1 × 1 surface and the covalent bond length of the involved elements, we suggest that this is because group-III atoms would induce significant tensile stresses to the surface of the Al Ge and Ga Ge systems, while tensile stresses around group-III atoms are not favored by the III IV systems.

Systematic search in conformational analysis

The coupling of conformation to activity and reactivity is a widely accepted concept, and as such has driven the development of tools which execute conformational searches in rapid and robust fashion [T.F. Havel, Prog. Biophys. Molec. Biol., 56 (1991) 43–78; A.R. Leach, In Rev. Comput. Chem.; K.B. Lipkowitz and D.B. Boyd, Ed.; VCH Publishers, Inc.: New York, N.Y., 1991, Vol. II, pp. 1–55]. Among the aims of these methods are the determination of a complete set of local minima from which the global energy minimum can be identified, or the generation of conformations consistent with constraints derived from SAR or structural studies. Most methods fall into two broad categories: those which are random or stochastic, and those which are systematic. Yet another group consists of those which are based on heuristics and artificial intelligence [A.R. Leach, K. Prout, D.P. Dolata, J. Comput. Chem. 11 (1990) 680–693]. The first category is typified by molecular dynamics [W.F. van Gunsteren and H.J.C. Berendsen, Angew. Chem. Int. Ed. Eng., 29 (1990) 992–1023], Monte Carlo [M.P. Alien and D.J. Tildesley, Computer Simulation of Liquids, Oxford Science Publications, 1989], distance geometry [J.M. Blaney and J.S. Dixon, in K.B. Lipkowitz and D.B. Boyd (Eds.), Reviews in Computational Chemistry, VCH, New York, Vol. 5, pp. 299–335, 1994], and other approaches [M. Saunders, J. Comput. Chem., 10 (1989) 203–208] in which the path by which conformational space is examined is ideally completely random, but bounded by the geometries of covalent bond lengths and angles. In traditional systematic searches, the variable to be examined, e.g. torsion angles, is divided into a regular grid. Each and every grid point is evaluated in a systematic fashion to determine its validity. The path through the grid points is regular and defined. In principle, systematic search can, within the resolution of the grid, identify all sterically allowed conformations of a molecule. Consequently, systematic search is an ideal tool for conformational analysis because it is not path dependent and cannot become entrapped in local minima. In this article we review some of the basics of systematic search, algorithmic improvements that have enhanced its speed, and new developments that have increased its accuracy by moving away from the limitations of a fixed torsional grid.

EXAFS study of amorphous selenium under pressure

Extended X-ray absorption fine structures (EXAFS) of amorphous solids selenium (a-Se) under pressures from 0 to 10 GPa and liquid Se at 10 GPa were studied. Structure of a-Se changed gradually with pressure until crystallization was induced at 10 GPa. In spite of the compression, the covalent bond length of a-Se increased slightly with pressure and rapidly just before the crystallization. The correlation between interchain atoms in a-Se was much weaker than that in crystalline Se at low pressures. It became prominent under higher pressure before the crystallization. EXAFS spectrum of liquid selenium at 10 GPa was successfully measured. The weakening of covalent bond upon melting under high pressure was observed.

Experimental determination of covalent radii of elements

The results of direct experimental determination of covalent bond lengths in molecular structures are presented. This made it possible to establish the values of normal covalent radii. The recommended values of covalent radii for 56 elements are tabulated.

Empirical relation between inverse covalent bond length and force constant, and its consequences for potential energy curves

It is well known that short covalent bonds have high force constants k. Here this is expressed through the empirical relation k = A exp(sRe), where Re is the equilibrium bond length. The value of s depends on the period in the Periodic Table, but is approximately constant throughout a period. Force constants are reproduced from bond lengths to within 20% in the second period groups III to VI (B2 to F2) with two constants A and s, and more accurately for groups III to VII in the third and fourth periods. Knowledge of k then permits predictions of Re, for example in the metal dimers Ga2 (300pm) and Rb2 (410pm). Finally, the implications of this empirical relation between k and Re are considered for analytical representation of potential energy curves.

Weak hydrogen bonding. Part 1. Neutron diffraction data of amino acid Cα–H suggest lengthening of the covalent C–H bond in C–H ⋯ O interactions

In C–H ⋯ O contacts observed in 16 high-precision neutron crystal-structure determinations of α-amino acids, there is good evidence for a correlation between the covalent bond length of Cα–H and the Hα⋯ O separation. For the shortest H ⋯ O contacts, ∼2.3 A, the lengthening of C–H is 0.008 A compared with the longest contacts of ∼2.7 A. This supports the view that C–H ⋯ O interactions have the nature of hydrogen bonds. The experimental results are in excellent agreement with calculations from the valence model of the hydrogen bond.

Luminescence and relaxation of the excited states in covalent-linked tetratolylporphyrin-phthalocyanine

The feature of the charge transfer in the binary molecules of the covalently bound porphyrin-phthalocyanine has been investigated by using a technique of the nondegenerate four-wave mixing. The energy transfer from porphyrin to phthalocyanine is spectrally found. The relation between the charge transfer and the covalent-bond length is also discussed.

Second‐order Jahn–Teller instability and the activation energy for Al+(1S) + H2 → AlH+(2∑+) + H

AbstractThe interaction of Al+ (1S) ions with H2 on the lowest electronic energy surface is studied using ab initio electronic structure methods. A Cs symmetry transition state is located and found to have the geometry of a product AlH+ ion loosely bound to a H atom, consistent with the Hammond postulate for this endothermic reaction. Locating this transition state, beginning at geometries that characterize vibrationally cold H2 and translationally hot Al+, posed special challenges to the commonly used “hill‐climbing” algorithm because of regions of geometrical instability along the path thus generated. This instability was found to be a result of second‐order Jahn–Teller coupling with a low‐lying 1B2 electronic state. In addition to these primary findings, a weakly bound T‐shaped Al+ ——— H2 C2v van der Waals complex is found that lies only 242 cm−1 below the Al+ and H2 asymptote, with HH internuclear separation only slightly distorted from the equilibrium bond distance of H2 and AlH distance (3.5 Å) much longer than the covalent bond length in AlH+ (1.6 Å). The locally stable but thermodynamically unstable linear HAlH+ (1∑) species and, of course, the H + AlH+(2∑+) reaction products have also been identified as critical points on the ground‐state surface. Where known, the geometries and energies that we calculte agree well with experimental data. © 1993 John Wiley & Sons, Inc.

Loop closure via bond scaling and relaxation

AbstractWe describe, test, and apply a new computational algorithm for generating protein loop conformations subject to distance and secondary structure constraints. The algorithm is based upon initial scaling and subsequent relaxation of covalent bond lengths. The scaling‐relaxation procedure needs no additional energy terms and can be readily incorporated into existing molecular modeling packages. The algorithm uses an all‐atom energy function from the outset in a straightforward way so that about 60% of the generated loop conformations are free of severe distortions of covalent bond lengths and angles. An extensive application to the major loop conformations of TFIIIA‐type zinc fingers (Zif268 and ADR1) is presented, as well as preliminary calculations on hypervariable loops of two immunoglobulins (MCPC603 and Bence‐Jones). © 1993 John Wiley & Sons, Inc.

Structure of Selenium under High Pressure

The high-pressure X-ray structural analysis of rhombohedral selenium has revealed that with increasing pressure, an intermolecular distance decreases rapidly, while an intramolecular covalent bond length increases gradually. On the other hand, the pressure-induced softening of the bond stretching mode, especially A1 mode, has been observed in the Raman spectra of both rhombohedral and α-monoclinic selenium. These findings suggest that the intramolecular covalent bonding in selenium crystal decreases with pressure.

Metal-insulator phase transition of phosphorus treated through a magnetic approach.

This paper first discusses the possibility of treating half-filled band problems on spin-nonfrustrated lattices from the single-determinant approach in the strongly correlated domain (4\ensuremath{\Vert}t\ensuremath{\Vert}U) or from a Heisenberg effective Hamiltonian in the strongly delocalized domain (4\ensuremath{\Vert}t\ensuremath{\Vert}gU). The second approach is used to treat metallic and covalent phases of phosphorus using an r-dependent Heisenberg Hamiltonian extracted from the spectroscopy of P and ${\mathrm{P}}_{2}$. The cubic phase of phosphorus and its distortion toward a rhombohedral (A7) lattice are treated by perturbing a N\'eel state to the second order. The cubic phase presents a minimum energy for a 2.35-\AA{} bond length (experiment: 2.377 \AA{}). For a slightly larger interatomic distance (r=2.47 \AA{}) the cubic phase becomes unstable and undergoes a distortion toward an A7 lattice; a saddle point (${\mathit{r}}_{1}$=2.22 \AA{}; ${\mathit{r}}_{2}$=2.71 \AA{}) leads to the strongly distorted valley. In agreement with experiment, the metal-insulator transition is of first order. Although the use of the Heisenberg Hamiltonian becomes questionable when the angles between bonds significantly deviate from 90\ifmmode^\circ\else\textdegree\fi{} (as occurs in black phosphorus), we have attempted to determine the conformation and cohesive energy of strongly distorted structures by perturbing a product of bond singlets along the short covalent bonds under the effect of (singlet\ensuremath{\rightarrow}triplet${)}^{2}$ double excitations. The interatomic distances between layers is too large (4.1 \AA{} instead of 3.56 \AA{}), but the covalent bond lengths (2.18 \AA{}) and cohesive energy (75 kcal ${\mathrm{mol}}^{\mathrm{\ensuremath{-}}1}$) compare favorably with the experimental values (2.22--2.28 \AA{} and 79 kcal ${\mathrm{mol}}^{\mathrm{\ensuremath{-}}1}$) for black phosphorus.