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Zhi-Xiang Wang

Publications and source records attributed to Zhi-Xiang Wang.

11 recordsLinked to original sources
PubMed2006

Strike a balance: optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides.

Based on the AMBER polarizable model (ff02), we have re-optimized the parameters related to the main-chain (Phi, Psi) torsion angles by fitting to the Boltzmann-weighted average quantum mechanical (QM) energies of the important regions (i.e., beta, P(II), alpha(R), and alpha(L) regions). Following the naming convention of the AMBER force field series, this release will be called ff02pol.rl The force field has been assessed both by energetic comparison against the QM data and by the replica exchange molecular dynamics simulations of short alanine peptides in water. For Ace-Ala-Nme, the simulated populations in the beta, P(II) and alpha(R) regions were approximately 30, 43, and 26%, respectively. For Ace-(Ala)(7)-Nme, the populations in these three regions were approximately 24, 49, and 26%. Both were in qualitative agreement with the NMR and CD experimental conclusions. In comparison with the previous force field, ff02pol.rl demonstrated good balance among these three important regions. The optimized torsion parameters, together with those in ff02, allow us to carry out simulations on proteins and peptides with the consideration of polarization.

Computer Simulation↗
PubMed2005

Evidence for d orbital aromaticity in square planar coinage metal clusters.

Quantitative evidence for the existence of aromaticity involving the d orbitals of transition metals is provided for the first time. The doubly bridged square planar (D(4)(h)()) coinage metal clusters (M(4)Li(2), M = Cu (1), Ag (2), and Au (3)) are characterized as aromatic by their substantial nucleus independent chemical shifts (NICS) values in the centers (-14.5, -14.1, and -18.6, respectively). Nevertheless, the participation of p orbitals in the bonding (and cyclic electron delocalization) of 1-3 is negligible. Instead, these clusters benefit strongly from the delocalization of d and to some extent s orbitals. The same conclusion applies to Tsipis and Tsipis' H-bridged D(4)(h)() Cu(4)H(4) ring (4). Canonical MO-NICS analysis of structures 1-3 shows the total diatropic d orbital contributions to the total NICS to be substantial, although the individual contributions of the five sets of filled d orbitals vary. The d orbital aromaticity of Cu(4)Li(2) also is indicated by its atomization energy, 243.2 kcal/mol, which is larger than Boldyrev's doubly (sigma and pi) aromatic Al(4)Li(2) (215.9 kcal/mol).

Journal Article↗
PubMed2004

Solvation effects on alanine dipeptide: A MP2/cc-pVTZ//MP2/6-31G** study of (Phi, Psi) energy maps and conformers in the gas phase, ether, and water.

The effects of solvation on the conformations and energies of alanine dipeptide (AD) have been studied by ab initio calculations up to MP2/cc-pVTZ//MP2/6-31G**, utilizing the polarizable continuum model (PCM) to mimic solvation effects. The energy surfaces in the gas phase, ether, and water bear similar topological features carved by the steric hindrance, but the details differ significantly due to the solvent effects. The gas-phase energy map is qualitatively consistent with the Ramachandran plot showing seven energy minima. With respect to the gas-phase map, the significant changes of the aqueous map include (1) the expanded low-energy regions, (2) the emergence of an energy barrier between C5-beta and alpha(R)-beta(2) regions, (3) a clearly pronounced alpha(R) minimum, a new beta-conformer, and the disappearance of the gas-phase global minimum, and (4) the shift of the dominant region in LEII from the gas-phase C7(ax) region to the alpha(L) region. These changes bring the map in water to be much closer to the Ramachandran plot than the gas-phase map. The solvent effects on the geometries include the elongation of the exposed N-H and C=O bonds, the shortening of the buried HN--CO peptide bonds, and the enhanced planarity of the peptide bonds. The energy surface in ether has features similar to those both in the gas phase and in water. The free energy order computed in the gas phase and in ether is in good agreement with experimental studies that concluded that C5 and C7(eq) are the dominant species in both the gas phase and nonpolar solvents. The free energy order in water is consistent with the experimental observation that the dominant C7(eq) in the nonpolar solvent was largely replaced by P(II)-like (i.e., beta) and alpha(R) in the strong polar solvents. Based on calculations on AD + 4H(2)O and other AD-water clusters, we suggest that explicit water-AD interactions may distort C5 and beta (or alpha(R) and beta) to an intermediate conformation. Our analysis also shows that the PCM calculations at the MP2/cc-pVTZ//MP2/6-31G** level give good descriptions to the bulk solvent polarization effect. The results presented in this article should be of sufficient quality to characterize the peptide bonds in the gas phase and solvents. The energy surfaces may serve as the basis for developing of strategies enabling the inclusion of solvent polarization in the force field.

Alanine↗
PubMed2003

Experimental and theoretical characterization of H(2)OOO(+).

This report presents the preparation and characterization of H2OOO+, an important intermediate in water-oxygen chemistry. The H2OOO+ cation was produced by co-deposition of H2O/Ar with radio frequency discharged O2/Ar at 4 K and was identified by four fundamental infrared absorptions. Quantum chemical calculations indicate a doublet ground state with a H2O-O2 hemi-bonded Cs structure.

Models, Molecular↗
PubMed2003

A "sea urchin" family of boranes and carboranes: the 6m + 2n electron rule.

A new family of related borane and carborane cages has been designed computationally. These compounds obey a new electron counting rule (6m + 2n rule) rather than Wade's rule. The structures of these cages can be conceived by combining m aromatic pyramidal and n aromatic triangular units. The interstitial electrons from the m pyramids (six electrons for each unit) and the n triangles (two electrons for each unit) constitute the total 6m + 2n skeletal electrons. The greater number of skeletal electron pairs in large closo-borane cages (e.g., B32H328- or C8B24H32) achieves stabilization through the optimal occupancy of all bonding orbitals. The favorable electronic structure, the large HOMO-LUMO gaps, the large lowest positive frequencies, and the local aromaticity of the pyramidal and triangular units (as demonstrated by the large negative NICS values) of the new large closo-cages auger well for their eventual experimental realization.

Journal Article↗
PubMed2003

Neutral bishomoaromatic semibullvalenes.

Isolobal substitution of CH units by boron carbonyl groups (BCO) at C2,6 and C2,8,4,6 in semibullvalene favors the delocalized neutral bishomoaromatic systems substantially. The homoaromaticity is documented by the computed diatropic nucleus independent chemical shifts (NICS). In addition, BCO substitution can result in low-lying triplet and open-shell singlet states. In contrast, substitution at C1,5 more than doubles the related Cope rearrangement barrier. The C2,6 and C2,8,4,6 BCO-substituted barbaralanes, barbaralones, and bullvalenes have substantially reduced barriers.

Journal Article↗
PubMed2003

Monocyclic boron carbonyls: novel aromatic compounds.

Monocyclic boron carbonyls, (BCO)nm, with 4n + 2 delocalized electrons are highly aromatic, as indicated by the computed nucleus independent chemical shift (NICS) and the computed energies for benzene analogue.

Journal Article↗
PubMed2002

B4CO2: a new, observable sigma-pi diradical.

A new sigma-pi diradical, B4(CO)2, prepared in matrix isolation, was characterized unambiguously by isotopic-substitution infrared spectroscopy and by theoretical computations. Both open-shell singlet and triplet states have three pi electrons but are aromatic with moderately large NICS values. Quantum chemical calculations at various levels indicate that the open-shell singlet is slightly more stable than the triplet state. However, the singlet and triplet are computed to have very similar IR features which do not allow experimental differentiation.

Journal Article↗
PubMed2002

The theoretical design of neutral planar tetracoordinate carbon molecules with C(C)(4) substructures.

Using a new charge-compensation strategy, we designed neutral molecules with perfectly planar C(C)(4)-type tetracoordinate carbon arrangements (ptC) employing DFT computations. These designs, based on the planar preference of methane dications, replace two remote carbons in spiroalkaplanes by borons or two remote hydrogens by BH(3) groups; the two formally anionic boron units which result compensate the formal double positive charge on the central ptC's. The LUMOs correspond to the "wasted" lone pair HOMOs of the alkaplanes. As compared to the latter, pi occupancies on the central carbon are much smaller (less than 0.7e), and the IPs are much larger. The newly predicted compounds utilize all of the electrons more effectively. There are no lone pairs, and the ptC-C bond lengths are ca. 1.50 A. The Wiberg bond index sums of the ptC's are near 3.2, and the boron sums are close to 4.

Journal Article↗