Biomedical subjects

Mark R Hoffmann

Publications and source records attributed to Mark R Hoffmann.

4 recordsLinked to original sources

PubMed2006

Theoretical UV circular dichroism of cyclo(L-Proline-L-Proline).

MP2, DFT, and molecular mechanics (AMBER, CVFF, and CFF91) geometry optimizations were performed on the cyclic dipeptide cyclo(L-Pro-L-Pro) starting from crystal structure data. Three stable conformations were identified as energy minima by all methods, but assignment of relative energy varied between the methods. The pi-pi transition feature of the UV circular dichroic (CD) spectrum was predicted for each minimized structure using the classical physics method of the dipole interaction model. The model was sensitive to the different conformations. The UV-CD predictions were compared individually and as a Boltzmann-weighted composite with published experimental CD spectra [Bowman, R. L.; Kellerman, M.; Johnson, W. C., Jr. Biopolymers 1983, 22, 1045]. For all structures, the original parameters of Applequist [Applequist, J. J. Chem. Phys. 1979, 71, 4324] with a bandwidth of 3000 cm(-1) most accurately replicated experiment, except for the CFF91 structures, which matched experiment best with a bandwidth of 4000 cm(-1). The inclusion of solvent by a continuum model did not significantly alter the minimized geometries obtained by molecular or quantum mechanics, but it did have an effect on the relative predicted energies of CFF91 and B3LYP conformations. The overall effect of solvent inclusion was negligible when Boltzmann-weighted spectra were considered. Gas-phase CFF91 structures were also reasonably good for prediction of CD spectra, and when water was included via a continuum model for energy calculations, the weighting scheme resembled that of the higher-level weightings. The CD calculated using the MP2/6-311G structures and energies for weighting were most descriptive of the 180 nm negative band in the experimental CD, but red-shifted the location of the 205 nm band. DFT structures were comparably, though not identically, as descriptive of the first pi-pi band, and did a better job with placement of the second (positive) pi-pi band. DFT calculations were less sensitive to basis set effect than the MP2 calculations, with 6-31G results in close agreement with 6-311G. The results suggest that it is possible to use geometries obtained from a variety of different methods (molecular mechanical or quantum mechanical) with the classical physics dipole interaction model to qualitatively reproduce the UV CD of model amides.

Circular Dichroism↗

PubMed2005

Theoretical UV circular dichroism of aliphatic cyclic dipeptides.

Four cyclic dipeptides (piperazine-2,5-diones), cyclo(L-Pro-Gly), cyclo(L-Pro-L-Leu), cyclo(L-Ala-L-Ala), and cyclo(L-Pro-L-Ala), were modeled from crystal structure data. Conformations resulting from energy minimization using molecular mechanics were compared with traditional ab initio and density functional theory geometric optimizations for each dipeptide. In all computational cases, the gas phase was assumed. The pi-pi transition feature of the UV circular dichroic (CD) spectra was predicted for each peptide structure via the classical dipole interaction model. The dipole interaction model predicted CD spectra that qualitatively agreed with experiment when MP2 or DFT geometries were used. By coupling MP2 or DFT geometric optimizations with the classical physics method of the dipole interaction model, significantly better CD spectra were calculated than those using geometries obtained by molecular mechanics. Thus, one can couple quantum mechanical geometries with a classical physics model for calculation of circular dichroism.

Circular Dichroism↗

PubMed2005

Multireference configuration interaction based electronic Floquet states for molecules in an intense radiation field: theory and application to Li(2)+.

A multireference configuration interaction (CI) method which includes single and double excitations based description of adiabatic Floquet states for the electronic structure of a molecule in an intense laser field is introduced. Using a variant of a recently introduced configuration state function (CSF) based Table-CI methodology, it is shown that the multiple states of several irreducible representations required for a good description of low-lying Floquet states can be obtained using modifications of computational molecular electronic structure techniques. In particular, formulas for all components of the transition dipole moment matrix elements within the CSF-based Table-CI method are derived and presented. Moreover, the flexibility of the recently introduced macroconfiguration description of model and external configuration spaces is shown to lead to multiple potential energy surfaces of sufficiently uniform quality to allow construction of useful Floquet states. The formalism and computer programs developed are demonstrated on Li(2) (+) in a 0.9 x 10(12) W/cm(2) field. In analogy with Na(2) (+), the 1,2 (2)Sigma(g) (+), 1,2 (2)Sigma(u) (+), 1 (2)Pi(g), and 1 (2)Pi(u) states are of relevance, although the pattern of couplings is shown to be more complex. A hitherto unnoticed metastable state, which correlates asymptotically with 2 (2)Sigma(u) (+), is described.

Journal Article↗

PubMed2004

Multireference spin-adapted variant of density functional theory.

A new Kohn-Sham formalism is developed for studying the lowest molecular electronic states of given space and spin symmetry whose densities are represented by weighted sums of several reference configurations. Unlike standard spin-density functional theory, the new formalism uses total spin conserving spin-density operators and spin-invariant density matrices so that the method is fully spin-adapted and solves the so-called spin-symmetry dilemma. The formalism permits the use of an arbitrary set of reference (noninteracting) configurations with any number of open shells. It is shown that the requirement of degeneracy of the total noninteracting energies of the reference configurations (or configuration state functions) is equivalent to the stationary condition of the exact energy relative to the weights of the configurations (or configuration state functions). Consequently, at any molecular geometry, the weights can be determined by minimization of the energy, and, for given reference weights, the Kohn-Sham orbitals can be determined. From this viewpoint, the developed theory can be interpreted as an analog of the multiconfiguration self-consistent field approach within density functional theory.

Journal Article↗