Partial Retention Of Diatomic Differential Overlap Research Articles

Molecular orbital study of polypeptides. Conformational and electronic structure of polyglycine

Approximate ab initio molecular orbital calculations are presented for the di-, tri-, tetra-, and pentapeptides of glycine. Six key conformations of polyglycine were considered: fully extended, parallel chain-pleated sheet, antiparallel chain-pleated sheet, α helix, 3-10 helix, and polyglycine II. Beyond the pentapeptide level the α-helix and 3-10-helix conformations were predicted to be the most stable. The stability of the latter pair of conformations is attributed to hydrogen bonding, an effect which is confirmed by a detailed population analysis of the wave function. Additional evidence for hydrogen bond formation is provided by the localized molecular orbitals which are reported for several conformations studied here. An analysis of the eigenvalue spectrum of these molecules reveals a band structure that is characteristic of periodic systems. All calculations were performed using the partial retention of diatomic differential overlap (PRDDO) approximation. Comparisons of the PRDDO results with experiment and with other molecular orbital techniques are also made.

Strained Configurations in Three-Dimensional Analogues of Kekulé-Type Structures for Deltahedral Boranes

Localized structures analogous to the Kekulé structures for benzenoid hydrocarbons can be constructed for the deltahedral boranes BnHn2-. These localized structures contain exactly three two-center two-electron (2c-2e) B-B bonds and n - 2 three-center two-electron (3c-2e) B-B-B bonds. The number of equivalent such Kekulé-type structures corresponds to the index of the symmetry group of the Kekulé structure, K, in the symmetry group, D, of the deltahedron. Three-dimensional Kekulé-type structures with the following configurations exhibit excessive strain and are therefore unfavorable: (i) structures having one or more pairs of boron atoms connected simultaneously by a 2c-2e B-B bond and a 3c-2e B-B-B bond (violation of the O'Neill-Wade restrictions); (ii) structures in which the three 2c-2e B-B bonds are excessively concentrated occupying only three or four vertices (the undesirable ∆, U, and Y configurations). Computations by Lipscomb and coworkers with partial retention of diatomic differential overlap (PRDDO) suggest that wide distribution of the three 2c-2e B-B bonds throughout the deltahedron and a minimum number of empty faces are more important than maximum symmetry in leading to the most favorable Kekulé-type structure.

Nonempirical wave functions for very large molecules. II. The PRDDO/M/FCP method

The authors describe enhancements to the method of partial retention of diatomic differential overlap (PRDDO). The new method, denoted PRDDO/M, employs a basis set of not quite orthogonal atomic orbitals (NQOAOS) and utilizes sparse matrix techniques to greatly increase the computational efficiency for large molecules. Other modifications, including a complete reparametrization of the method against ab initio STO-3G calculations and implementation of integral screening/damping algorithms, are described. The method is an order of magnitude or more faster than are STO 3G single-point calculations using modern ab initio codes, with little loss in accuracy. 15 refs., 5 figs., 6 tabs.

Theoretical estimates of the η 6 bonding capability of buckminsterfullerene in transition metal complexes

In order to provide a quantitative description of the relative ability of C 60 to bond as an η 6 ligand, arene exchange energies for tricarbonyl(arene)chromium systems were calculated using the method of partial retention of diatomic differential overlap (PRDDO). This represents the first theoretical estimate of the relative affinity of C 60 as an η 6 ligand, and results indicate that C 60 is an inferior ligand compared to benzene. The arenes considered included benzene, chlorobenzene, p-difluorobenzene, and buckminsterfullerene. The exchange of benzene for C 60 as an arene ligand is calculated to require 19 kcal/mol, but this can be reduced by modifying the exchanging ligand. Reduced overlap from C 60 hybrid orbitals is found to be partly responsible for less favorable η 6 bonding, which suggests that larger metals such as tungsten may be better able to bond in an η 6 fashion to C 60.

Titanium and copper in Si: Barriers for diffusion and interactions with hydrogen.

We present the results of a theoretical study of the diffusion barriers of titanium and copper in crystalline silicon, and of the interactions between titanium and hydrogen, and between copper and hydrogen. The calculations were performed using various molecular clusters and the Hartree-Fock method. The method of partial retention of diatomic differential overlap (PRDDO) predicts diffusion barriers of 3.29 eV for ${\mathrm{Ti}}^{+}$, 2.25 eV for ${\mathrm{Ti}}^{0}$, and 0.24 eV for ${\mathrm{Cu}}^{+}$. PRDDO also predicts that substitutional ${\mathrm{Ti}}^{0}$ is a deep trap for interstitial H, with a gain in energy of 1.84 eV relative to atomic H far outside the cluster. AB initio Hartree-Fock calculations show that a ${\mathrm{Ti}}^{+}$ ion at a tetrahedral interstitial site also forms a bond with interstitial H, with a dissociation energy of 2.31 eV. On the other hand, interstitial ${\mathrm{Cu}}^{+}$ does not form a bond with H. Several issues relevant to H passivation of interstitial 3d transition-metal impurities in Si are discussed.

Hydrogen passivation of shallow acceptors and donors in c-Si: Comparisons and trends.

The equilibrium geometries and electronic structures of hydrogen-passivated acceptors (B, Al, and Ga) and donors (P and As) in crystalline silicon are calculated in two clusters: X${\mathrm{HSi}}_{7}$${\mathrm{H}}_{18}$ and X${\mathrm{HSi}}_{34}$${\mathrm{H}}_{36}$, where X is the acceptor or donor. The results, obtained using the method of partial retention of diatomic differential overlap (PRDDO) and ab initio Hartree-Fock with various basis sets, show that all these complexes are metastable. In the case of passivated acceptors, the stable configuration corresponds to H close to the bond-centered site and the metastable one to H at the antibonding site of one of the Si atoms nearest to the acceptor. The configuration where H is antibonding to the acceptor is a saddle point of the energy. The effects of 〈111〉 uniaxial stress on the position of the H passivator are qualitatively analyzed. In the case of donors, the lowest-energy site for H is at the antibonding site to one of the Si atoms nearest to the donor. The configurations where H is at the bond-centered site or is antibonding to the donor are nearly energetically equivalent. The similarities and differences between the various complexes are discussed.

Hydration of CO2 by carbonic anhydrase: intramolecular proton transfer between Zn2+-bound H2O and histidine 64 in human carbonic anhydrase II.

The energy barrier for the intramolecular proton transfer between zinc-bound water and His 64 in the active site of human carbonic anhydrase II (HCA II) has been studied at the partial retention of diatomic differential overlap (PRDDO) level. The most important stabilizing factor for the intramolecular proton transfer is the zinc ion, which lowers the pKa of zinc-bound water and electrostatically repels the proton. The energy barrier of 127.5 kcal/mol for proton transfer between a water dimer is completely removed in the presence of the zinc ion. The zinc ligands, which donate electrons to the zinc ion, raise the barrier slightly to 34 kcal/mol for a 4-coordinated zinc complex including three imidazole ligands from His 94, His 96, and His 119 and to 54 kcal/mol for the 5-coordinated zinc complex including the fifth water ligand. A few model calculations indicate that these energy barriers are expected to be reduced to within experimental range (approximately 10 kcal/mol) when large basis set, correlation energies, and molecular dynamics are considered. The proton-transfer group, which functions as proton receiver in the intramolecular proton transfer, helps to attract the proton; and the partially ordered active site water molecules are important for proton relay function.

Lattice relaxation for normal muonium in diamond

The effects of symmetric lattice relaxation around the tetrahedral (T) and the hexagonal (H) interstitial sites are calculated for normal muonium (Mu) in diamond using the non-semiempirical method of Partial Retention of Diatomic Differential Overlap (PRDDO). We use clusters containing 3 and 4 host atom shells around the T and the H sites (C20H32 and C30H40). The only significant relaxations are the outward displacement of the 6 nearest neighbors (NN) to the H site and, when the muon is at the T site, the simultaneous outward displacement of the first and second NN to the T site. In the case of diamond, the effects of these relaxations on the energy profiles and spin densities are small.

Molecular mechanics studies of enthalpies of formation and strain energies of azoxyalkanes

AbstractA force field has been developed, on the basis of available experimental and partial retention of diatomic differential overlap (PRDDO) data, to permit molecular mechanics calculations on azoxyalkanes. The calculated structures and enthalpies of formation are in fair agreement with experimental results. The calculated enthalpies of formation and strain energies are compared with the corresponding quantities for analogous azoalkanes.

Extension of the method of partial retention of diatomic differential overlap to second row atoms and transition metals

The method of partial retention of diatomic differential overlap (PRDDO) has been extended to the elements through the first transition series. A minimum basis set of Slatertype orbitals is employed, with optional 3d functions on atoms in the second major row. The 3d shell for transition metal atoms is a fixed-contracted double-zeta combination of Slater orbitals. The method retains the basic n(3) dependency inherent in PRDDO. Limited one-center parameterization and empirical two-center exchange integrals are included. The overall accuracy of the approach is comparable to that of the PRDDO method as previously applied to molecules containing first-row atoms only.

Conformations and electronic structures of oxidized and reduced isoalloxazine.

The conformations of oxidized and reduced isoalloxazine have been examined by a molecular orbital method, PRDDO (partial retention of diatomic differential overlap). The angle theta of fold about the N...N line of the central ring is zero for the planar oxidized form, but a bend of theta = 10 degrees requires only 2 kcal/mol. On the other hand, the reduced form is nonplanar (theta approximately 15 degrees), and the barrier for reversal of this bend is 4 kcal/mol, comparable with that in simple amines. Molecular properties and reactivity are interpreted in terms of charge and orbital distributions, and localized molecular orbitals have been derived by the method of Boys.

Localized molecular orbitals for polyatomic molecules: Part VII. The tetracyanoquinodimethan molecule and its anions

Wavefunctions for TCNQ, TCNQ −1 and TCNQ −2 have been obtained in the approximation of partial retention of diatomic differential overlap (PRDDO). For TCNQ and TCNQ −2 the geometries were partially optimized. Localized molecular orbitais (LMO's) have been obtained for TCNQ and TCNQ −2 using the Boys' criterion. For TCNQ these LMO's give the usual description of the bonding in the molecule. However, for TCNQ −2 the LMO's show an unexpected bonding pattern of a benzenoid ring and lone pairs on C7 and C8. The rotation barrier about the C1–C7 bond in TCNQ −2 is calculated to be 12 kcal mole −1, the maximum value for the conjugative effect in this bond.

Molecular orbital studies of enzyme activity: I: Charge relay system and tetrahedral intermediate in acylation of serine proteinases.

The charge relay ststem and its role in the acylation of serine proteinases is studied using the partial retention of diatomic differential overlap (PRDDO) technique to perform approximate ab initio molecular orbital calculations on a model of the enzyme-substrate complex. The aspartate in the charge relay system is seen to act as the ultimate proton acceptor during the charging of the serine nucleophile. A projection of the potential energy surface is obtained in a subspace corresponding to this charge transfer and to the coupled motions of active site residues and the substrate. These results together with extended basis set results for cruder models suggest that a concerted transfer of protons from Ser-195 to His-57 and from His-57 to Asp-102 occurs with an energy barrier of 20-25 kcal/mole (84-105 kJ/mole). The subsequent nucleophilic attack on the scissile peptide linkage by the charged serine is then seen to proceed energetically downhill to the tetrahedral intermediate. The formation of the tetrahedral intermediate from the Michaelis complex is calculated to be nearly thermoneutral.

Localized molecular orbitals for polyatomic molecules

Molecular wavefunctions have been generated by the PRDDO (Partial Retention of Diatomic Differential Overlap) method for the monocyclic aromatic rings containing six π-electrons (C4H 4 −2 , C5H 5 − , C6H6, C7H 7 + , and C8H 8 +2 ) and ten π-electron species (C8H 8 −2 , C9H 9 − , C10H10). The eigenvalue spectra of the canonical molecular orbitals are presented. Localized molecular orbitals (LMO's) generated using the Boys criterion are reported for localizations involving all occupied molecular orbitals (complete localizations) and localizations of the π orbitals only. We find evidence for σ-π separation in the complete localizations for some of these molecules even though the Boys criterion is often biased against such results. We demonstrate for C6H6 and find for the other molecules that the π-orbital localizations are indeterminate (i.e. there are an infinite number of equally satisfactory LMO structures between two limiting extremes). This result may be viewed as a corollary of Huckel's (4n+2) rule for aromaticity.