Biomedical subjects

Peter Pulay

Publications and source records attributed to Peter Pulay.

9 recordsLinked to original sources

PubMed2005

Accuracy and efficiency of atomic basis set methods versus plane wave calculations with ultrasoft pseudopotentials for DNA base molecules.

Recent results from Preuss et al. (J Comput Chem 2004, 25, 112) on DNA base molecules, obtained by plane wave density functional calculations using ultrasoft pseudopotentials, are compared with calculations using Gaussian basis sets. Bond lengths and angles agree closely, but dihedral angles and vibrational frequencies show significant differences. The Gaussian basis calculations are at least an order of magnitude more efficient than the plane wave/ultrasoft pseudopotential calculations at a similar level of accuracy; the advantage is even larger if the Fourier Transform Coulomb method is used. To obtain definite benchmark values, the geometries of the four DNA bases were optimized at the MP2 level with large basis sets, up to cc-pVQZ and aug-cc-pVTZ.

DNA↗

PubMed2004

An efficient atomic orbital based second-order Møller-Plesset gradient program.

Based on the orbital-invariant atomic orbital formulation of the MP2 (Møller-Plesset second-order perturbation theory) energy and gradient [P. Pulay and S. Saebø, Theor. Chim. Acta 69, 357 (1986)], we have derived and programmed detailed working equations for closed-shell MP2 gradients. The orbital-invariant form avoids the difficulties of other formulations with frozen orbitals, and allows the use of arbitrary occupied orbitals, an important consideration for local correlation theories, although the present program uses canonical molecular orbitals. The atomic orbital formulation offers savings both in storage and computer time. Test calculations on systems containing up to approximately 100 atoms and approximately 1000 basis functions, performed on a single personal computer, are reported. Parallelization of the code is underway.

Journal Article↗

PubMed2003

Combined experimental/theoretical refinement of indole ring geometry using deuterium magnetic resonance and ab initio calculations.

We have used experimental deuterium NMR spectra from labeled tryptophans in membrane-spanning gramicidin A (gA)(1) channels to refine the geometry of the indole ring and, specifically, the C2-(2)H bond direction. By using partial exchange in a cold organic acid, we were able to selectively deuterate ring positions C2 and C5 and, thereby, define unambiguous spectral assignments. In a backbone-independent analysis, the assigned spectra from four distinct labeled tryptophans were used to assess the geometry of the planar indole ring. We found that the C2-(2)H bond makes an angle of about 6 degrees with respect to the normal to the indole ring bridge, and the experimental geometry was confirmed by density functional calculations using a 6-311G** basis set. The precisely determined ring geometry and the experimental spectra in turn are the foundation for calculations of the orientation of each tryptophan indole ring, with respect to the bilayer membrane normal, and of a principal order parameter S(zz) for each ring. The results have general significance for revising the tryptophan ring geometry that is used in protein molecular modeling, as well as for the analysis of tryptophan ring orientations in membrane-spanning proteins. The experimental precision in the definition of the indole ring geometry demonstrates yet another practical application emanating from fundamental research on the robust gramicidin channel.

Deuterium↗

PubMed2003

Assessment of the OLYP and O3LYP density functionals for first-row transition metals.

We have investigated the performance of the OLYP and O3LYP density functionals for predicting atomic excitation energies and ionization potentials, and bond dissociation energies, geometries, and vibrational frequencies for selected first-row transition metal compounds, including hydrides (MH) and singly charged methylene and methyl cations. The OLYP and O3LYP functionals are similar to the well-known BLYP and B3LYP functionals, respectively, but use a new optimized exchange functional (OPTX) developed by Handy and Cohen (Mol Phys 2001, 99, 403) in place of the standard B88 exchange. A previous study by us on organic reactions (J Chem Phys 2002, 117, 1331) indicated that both OLYP and O3LYP gave results for heats of reaction and barrier heights that were overall superior to those using the popular B3LYP functional. For transition metals, however, although OLYP is overall superior to BLYP for molecular calculations, it is inferior to B3LYP. O3LYP provides results for molecules of about the same quality as B3LYP. For atomic excitation and 4s ionization energies, unless relativistic effects are included, OLYP and O3LYP are clearly worse than both BLYP and B3LYP. There is thus no real incentive to use either OLYP or O3LYP in place of B3LYP for calculations involving first-row transition metals.

Journal Article↗

PubMed2003

Parallel stored-integral and semidirect Hartree-Fock and DFT methods with data compression.

Recent developments in magnetic disk technology have made stored-integral techniques competitive with the currently more widely used direct methods, which involve the recalculation of the basic two-electron integrals. We present efficient conventional (all integrals stored) and semidirect Hartree-Fock and DFT algorithms with data compression for single-processor and distributed memory parallel computers, and compare them with the corresponding direct algorithms. On inexpensive modern personal computer-based hardware, the stored integral method is up to three times more efficient than the direct method in terms of total elapsed job time.

Journal Article↗

PubMed2003

Calculated and experimental geometries and infrared spectra of metal tris-acetylacetonates: vibrational spectroscopy as a probe of molecular structure for ionic complexes. Part II.

Following on from our previous work on Sc, Fe, Cr, and Al (Part I; see J. Phys. Chem. A, 105 (2001) 238), the geometries and infrared spectra of the trivalent metal tris-acetylacetonate complexes (M[O2C5H7]3; M = Ti, V, Mn, Co) have been studied both experimentally and theoretically using nonlocal hybrid density functional theory with a split-valence plus polarization basis for the ligand and valence triple-zeta for the metal. Unlike the D3 complexes studied in Part I, those of Ti, V and Mn are candidates for Jahn-Teller distortion due to fractional d-shell occupancy. Using scale factors transferred from Part I, our calculated frequencies are in very good agreement with experimentally observed fundamentals. Our investigation shows that the V and Mn complexes distort to C2 ground states, but D3 Ti tris-acetylacetonate is stable. Further investigation of the weak band observed around 800 cm(-1) in the Fe complex (and present in almost all studied first-row transition metal tris-acetylacetonates), which we were unable to assign theoretically in Part I, supports the argument that this band is not a fundamental but is due to Fermi resonance.

Ions↗

PubMed2002

Accurate prediction of proton chemical shifts. II. Peptide analogues.

Proton chemical shifts of eight cyclic amide molecules were measured in DMSO and D2O solutions. The magnetic shieldings of the corresponding aliphatic, aromatic, and amide protons were calculated by Hartree-Fock and DFT, using the 6-311G**, 6-311++G**, and TZVP basis sets. For aliphatic protons, all of these methods reproduce the experimental values in DMSO solutions excellently after linear regression. The Hartree-Fock method tends to give slightly better agreement than DFT. The best performance is given by the HF/6-311G** method, with an rms deviation of 0.068 ppm. The deviations from experimental chemical shifts in D2O solutions are only slightly larger than those in DMSO solutions. This suggests that we can use the calculated gas phase proton chemical shifts directly to predict experimental data in various solvents, including water. For amide protons, which exchange with water and form hydrogen bonds with DMSO, only modest agreement is obtained, as expected. The present studies confirm that the GIAO approach can reach high accuracy for the relative chemical shifts of aliphatic and aromatic protons at a low cost. Such calculations may provide constraints for the conformational analysis of proteins and other macromolecules.

Amides↗

PubMed2002

An efficient parallel algorithm for the calculation of canonical MP2 energies.

We present the parallel version of a previous serial algorithm for the efficient calculation of canonical MP2 energies (Pulay, P.; Saebo, S.; Wolinski, K. Chem Phys Lett 2001, 344, 543). It is based on the Saebo-Almlöf direct-integral transformation, coupled with an efficient prescreening of the AO integrals. The parallel algorithm avoids synchronization delays by spawning a second set of slaves during the bin-sort prior to the second half-transformation. Results are presented for systems with up to 2000 basis functions. MP2 energies for molecules with 400-500 basis functions can be routinely calculated to microhartree accuracy on a small number of processors (6-8) in a matter of minutes with modern PC-based parallel computers.

Journal Article↗

PubMed2002

Backbone structure confirmation and side chain conformation refinement of a bradykinin mimic BKM-824 by comparing calculated (1)H, (13)C and (19)F chemical shifts with experiment.

Calculated and experimental (1)H, (13)C and (19)F chemical shifts were compared in BKM-824, a cyclic bradykinin antagonist mimic, c[Ava(1)-Igl(2)-Ser(3)-DF5F(4)-Oic(5)-Arg(6)] (Ava=5-aminovaleric acid, Igl=alpha-(2-indanyl)glycine, DF5F=pentafluorophenylalanine, Oic=(2S,3aS,7aS)-octahydroindole-2-carboxylic acid). The conformation of BKM-824 has been studied earlier by NMR spectroscopy (M. Miskolzie et al., J. Biomolec. Struct. Dyn. 17, 947-955 (2000)). All NMR structures have qualitatively the same backbone structure but there is considerable variation in the side chain conformations. We have carried out quantum mechanical optimization for three representative NMR structures at the B3LYP/6-31G* level, constraining the backbone dihedral angles at their NMR structure values, followed by NMR chemical shift calculations at the optimized structures with the 6-311G** basis set. There is an intramolecular hydrogen bond at Ser(3) in the optimized structures. The experimental (13)C chemical shifts at five C(alpha) positions as well as at the Cbeta, Cgamma and Cdelta position of Ava(1), which forms part of the backbone, are well reproduced by the calculations, confirming the NMR backbone structure. A comparison between the calculated and experimental H(beta) chemical shifts in Igl(2) shows that the dominant conformation at this residue is gauche. Changes of proton chemical shifts with the scan of the chi(1) angle in DF5F(4) suggest that chi(1)180 degrees. The calculated (1)H and (13)C chemical shifts are in good agreement with experiment at the rigid residue Oic(5). None of the models gives accurate results for Arg(6), presumably because of its positive charge. Our study indicates that calculated NMR shifts can be used as additional constraints in conjunction with NMR data to determine protein conformations. However, to be computationally effective, a database of chemical shifts in small peptide fragments should be precalculated.

Bradykinin↗