Biomedical subjects

Thomas Bondo Pedersen

Publications and source records attributed to Thomas Bondo Pedersen.

5 recordsLinked to original sources

PubMed2006

Fast noniterative orbital localization for large molecules.

We use Cholesky decomposition of the density matrix in atomic orbital basis to define a new set of occupied molecular orbital coefficients. Analysis of the resulting orbitals ("Cholesky molecular orbitals") demonstrates their localized character inherited from the sparsity of the density matrix. Comparison with the results of traditional iterative localization schemes shows minor differences with respect to a number of suitable measures of locality, particularly the scaling with system size of orbital pair domains used in local correlation methods. The Cholesky procedure for generating orthonormal localized orbitals is noniterative and may be made linear scaling. Although our present implementation scales cubically, the algorithm is significantly faster than any of the conventional localization schemes. In addition, since this approach does not require starting orbitals, it will be useful in local correlation treatments on top of diagonalization-free Hartree-Fock optimization algorithms.

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PubMed2006

Origin invariant approaches to the calculation of two-photon circular dichroism.

The origin dependence of the expression of two-photon circular dichroism in the length formulation employed by the authors in a recent computational study [B. Jansik et al., Chem. Phys. Lett. 414, 461 (2005)] is discussed in detail, and some inherently origin invariant alternative formulations are introduced. Extensive computational tests on a small reference chiral system, namely, a chiral form of H(2)O(2), are performed at the density functional theory (DFT)/B3LYP level of theory with large diffuse correlation consistent basis sets. The results indicate that the velocity formulation originally proposed by Tinoco, Jr. [J. Chem. Phys. 62, 1006 (1975)] provides the most convenient approach for an origin invariant calculation of two-photon circular dichroism.

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PubMed2006

Ab initio potential-energy surface and rovibrational states of the HCN-HCl complex.

A four-dimensional intermolecular potential-energy surface has been calculated for the HCN-HCl complex, with the use of the coupled cluster method with single and double excitations and noniterative inclusion of triples. Data for more than 13,000 geometries were represented by an angular expansion in terms of coupled spherical harmonics; the dependence of the expansion coefficients on the intermolecular distance R was described by the reproducing kernel Hilbert space method. The global minimum with De=1565 cm(-1) and Re=7.47a0 has a linear HCN-HCl hydrogen-bonded structure with HCl as the donor. A secondary hydrogen-bonded equilibrium structure with De=564 cm(-1) and Re=8.21a0 has a T-shaped geometry with HCN as the donor and the acceptor HCl molecule nearly perpendicular to the intermolecular axis. This potential surface was used in a variational approach to compute a series of bound states of the isotopomers HCN-H35Cl, DCN-H35Cl, and HCN-H37Cl for total angular momentum J=0,1,2 and spectroscopic parities e, f. The results could be analyzed in terms of the approximate quantum numbers of a linear polyatomic molecule with two coupled bend modes, plus a quantum number for the intermolecular stretch vibration. They are in good agreement with the recent high resolution spectrum of Larsen et al. [Phys. Chem. Chem. Phys. 7, 1953 (2005)] in the region of 330 cm(-1) corresponding to the HCl libration. The (partly anomalous) effects of isotopic substitutions on the properties of the complex were explained with the aid of the calculations.

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PubMed2006

Coupled cluster and density functional theory studies of the vibrational contribution to the optical rotation of (S)-propylene oxide.

In a previous study (Chemical Physics Letters 2005, 401 , 385) we computed the optical rotatory dispersion of (S)-propylene oxide in gas phase and solution using the hierarchy of coupled cluster models CCS, CC2, CCSD, and CC3. Even for the highly correlated CC3 model combined with a flexible basis set, the theoretical gas-phase specific rotation at 355 nm was found to be negative in contrast to the experimental result. We argued that vibrational contributions could be crucial for obtaining a complete understanding of the experimental result. Here, we show that this indeed is the case by using coupled cluster models and density functional theory methods to calculate the vibrational contributions to the gas-phase specific rotation at 355, 589.3, and 633 nm. While density functional theory (B3LYP and SAOP functionals) overestimates the specific rotation at 355 nm by approximately 1 order of magnitude and yields an incorrect sign at 589.3 and 633 nm, the coupled cluster results are in excellent agreement with the experimentally measured optical rotations. We find that all vibrational modes contribute significantly to the optical rotation and that temperature effects must be taken into account.

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PubMed2004

Polarizability and optical rotation calculated from the approximate coupled cluster singles and doubles CC2 linear response theory using Cholesky decompositions.

A new implementation of the approximate coupled cluster singles and doubles CC2 linear response model using Cholesky decomposition of the two-electron integrals is presented. Significantly reducing storage demands and computational effort without sacrificing accuracy compared to the conventional model, the algorithm is well suited for large-scale applications. Extensive basis set convergence studies are presented for the static and frequency-dependent electric dipole polarizability of benzene and C60, and for the optical rotation of CNOFH2 and (-)-trans-cyclooctene (TCO). The origin-dependence of the optical rotation is calculated and shown to persist for CC2 even at basis set convergence.

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