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Michael W Schmidt

Publications and source records attributed to Michael W Schmidt.

10 recordsLinked to original sources
PubMed2007

Why does electron sharing lead to covalent bonding? A variational analysis.

Ground state energy differences between related systems can be elucidated by a comparative variational analysis of the energy functional, in which the concepts of variational kinetic pressure and variational electrostatic potential pull are found useful. This approach is applied to the formation of the bond in the hydrogen molecule ion. A highly accurate wavefunction is shown to be the superposition of two quasiatomic orbitals, each of which consists to 94% of the respective atomic 1s orbital, the remaining 6% deformation being 73% spherical and 27% nonspherical in character. The spherical deformation can be recovered to 99.9% by scaling the 1s orbital. These results quantify the conceptual metamorphosis of the free-atom wavefunction into the molecular wavefunction by orbital sharing, orbital contraction, and orbital polarization. Starting with the 1s orbital on one atom as the initial trial function, the value of the energy functional of the molecule at the equilibrium distance is stepwise lowered along several sequences of wavefunction modifications, whose energies monotonically decrease to the ground state energy of H2+. The contributions of sharing, contraction and polarization to the overall lowering of the energy functional and their kinetic and potential components exhibit a consistent pattern that can be related to the wavefunction changes on the basis of physical reasoning, including the virial theorem. It is found that orbital sharing lowers the variational kinetic energy pressure and that this is the essential cause of covalent bonding in this molecule.

Journal Article↗
PubMed2006

Reactivity of 1-hydro-5-carbaphosphatrane based on tautomerization between pentavalent phosphorane and trivalent cyclic phosphonite.

The reaction behavior of 1-hydro-5-carbaphosphatrane (1 a) was examined. Treatment of 1 a with oxidants such as 3-chloroperoxybenzoic acid (mCPBA) and tBuOCl gave cyclic phosphonate 2 and 1-chloro-5-carbaphosphatrane (4), respectively, via cyclic phosphonite 3, a tautomer of 1 a. Compound 4 was readily hydrolyzed to afford 2. Compound 1 a was also sulfurized via 3 by elemental sulfur to afford cyclic thioxophosphonate 5, which was also obtained by reactions in the presence of bases. Treatment of 1 a with bases also proceeded through 3 to give an equilibrium mixture of the corresponding phenoxide anion 10 and the phosphoranide anion 9, which was quenched with MeI to afford a mixture of 11 and 1-methyl-5-carbaphosphatrane (1 b). Such reactivities are typical for neutral phosphoranes. Theoretical investigations of these reactivities were also performed.

Journal Article↗
PubMed2006

Scalable implementation of analytic gradients for second-order Z-averaged perturbation theory using the distributed data interface.

The analytic gradient expression for second-order Z-averaged perturbation theory is revised and its parallel implementation is described in detail. The distributed data interface is used to access molecular-orbital integral arrays stored in distributed memory. The algorithm is designed to maximize the use of local data and reduce communication costs. The iterative solution and the preconditioner used to induce the convergence of the coupled-perturbed Hartree-Fock equations are presented. Several illustrative timing examples are discussed.

Journal Article↗
PubMed2006

Parallel coupled perturbed CASSCF equations and analytic CASSCF second derivatives.

A parallel algorithm for solving the coupled-perturbed MCSCF (CPMCSCF) equations and analytic nuclear second derivatives of CASSCF wave functions is presented. A parallel scheme for evaluating derivative integrals and their subsequent use in constructing other derivative quantities is described. The task of solving the CPMCSCF equations is approached using a parallelization scheme that partitions the electronic hessian matrix over all processors as opposed to simple partitioning of the 3 N solution vectors among the processors. The scalability of the current algorithm, up to 128 processors, is demonstrated. Using three test cases, results indicate that the parallelization of derivative integral evaluation through a simple scheme is highly effective regardless of the size of the basis set employed in the CASSCF energy calculation. Parallelization of the construction of the MCSCF electronic hessian during solution of the CPMCSCF equations varies quantitatively depending on the nature of the hessian itself, but is highly scalable in all cases.

Journal Article↗
PubMed2005

Solvent-dependent crystallization of 1-hydro-6-carbaphosphatrane and its tautomer.

1-Hydro-6-carbaphosphatrane 2 was obtained as a mixture with its tautomer, 3. Tautomers 2 and 3 were isolated by the recrystallization from different solvents, respectively, and each structure was determined by X-ray crystallographic analysis. Variable-temperature NMR experiments revealed that pentacoordinate 2 and tricoordinate 3 are under the equilibrium, showing that 3 is more stable. The theoretical calculations found a weaker transannular PC bond in 2 than in 1-hydro-5-carbaphosphatrane, 1, which can be considered to be the reason 1-hydro-6-carba-phosphatrane 2 is less stable than its tautomer 3.

Journal Article↗
PubMed2005

Triazolium-based energetic ionic liquids.

The energetic ionic liquids formed by the 1,2,4-triazolium cation family and dinitramide anion are investigated by ab initio quantum chemistry calculations, to address the following questions: How does substitution at the triazolium ring's nitrogen atoms affect its heat of formation, and its charge delocalization? What kind of ion dimer structures might exist? And, do deprotonation reactions occur, as a possible first step in the decomposition of these materials?

Journal Article↗
PubMed2004

Ab initio vibrational state calculations with a quartic force field: applications to H2CO, C2H4, CH3OH, CH3CCH, and C6H6.

For polyatomic molecules, n-mode coupling representations of the quartic force field (nMR-QFF) are presented, which include terms up to n normal coordinate couplings in a fourth-order polynomial potential energy function. The computational scheme to evaluate third-and fourth-order derivatives by finite differentiations of the energy is fully described. The code to generate the nMR-QFF has been implemented into GAMESS program package and interfaced with the vibrational self-consistent field (VSCF) and correlation corrected VSCF (cc-VSCF) methods. As a demonstration, fundamental frequencies have been calculated by the cc-VSCF method based on 2MR-QFF for formaldehyde, ethylene, methanol, propyne, and benzene. The applications show that 2MR-QFF is a highly accurate potential energy function, with errors of 1.0-1.9% relative to the experimental value in fundamental frequencies. This approach will help quantitative evaluations of vibrational energies of a general molecule with a reasonable computational cost.

Journal Article↗
PubMed2004

Rapid prefractionation of complex protein lysates with centrifugal membrane adsorber units improves the resolving power of 2D-PAGE-based proteome analysis.

BACKGROUND: Two-dimensional gel electrophoresis (2D-PAGE) has proven over the years to be a reliable and efficient method for separation of hundreds of proteins based on charge and mass. Nevertheless, the complexity of even the simplest proteomes limits the resolving power of 2D-PAGE. This limitation can be partially alleviated by sample prefractionation using a variety of techniques. RESULTS: Here, we have used Vivapure Ion Exchange centrifugal adsorber units to rapidly prefractionate total fission yeast protein lysate based on protein charge. Three fractions were prepared by stepwise elution with increasing sodium chloride concentrations. Each of the fractions, as well as the total lysate, were analyzed by 2D-PAGE. This simple prefractionation procedure considerably increased the resolving power of 2D-PAGE. Whereas 308 spots could be detected by analysing total protein lysate, 910 spots were observed upon prefractionation. Thorough gel image analysis demonstrated that prefractionation visualizes an additional set of 458 unique fission yeast proteins not detected in whole cell lysate. CONCLUSIONS: Prefractionation with Vivapure Q spin columns proved to be a simple, fast, reproducible, and cost-effective means of increasing the resolving power of 2D-PAGE using standard laboratory equipment.

Centrifugation↗
PubMed2002

Synthesis, structure, and bonding properties of 5-carbaphosphatranes: a new class of main group atrane.

1-Hydro-5-carbaphosphatrane (1) and 1-methyl-5-carbaphosphatrane (2), the first 5-carbon analogues of phosphatranes, were synthesized by a demethylation reaction of cyclic phosphinate 3. X-ray analysis revealed that 1 has a typical trigonal bipyramidal structure with hydrogen and carbon atoms at the apical position and three oxygen atoms at the equatorial positions, indicating that 1 is a phosphorane in the perfectly "anti-apicophilic" arrangement. Apical P-C and P-H bond lengths were 1.921(2) and 1.38(2) A, respectively. The (1)J(PH) value of 1 and the (1)J(PC)(P-CH(3)) value of 2 were 852 and 215 Hz, respectively, which are extraordinarily large for the apical coupling constants of phosphoranes, but close to those of the reported phosphatranes with a 5-nitrogen atom. IR and Raman spectra are also reported. Force constant calculations indicate the transannular bond in carbaphosphatrane is 3 times stronger than in silatrane, due to its covalent character.

Bridged Bicyclo Compounds, Heterocyclic↗