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Structures of oligoprolines

Description / Information

HF/6-31G** optimized capped oligoprolines AcN−[Pro]₁₅−CONH₂ and AcN−[Pro]₁₅−CO₂CH₃ for PP1 and PP2 helical arrangement of the backbone. The initial structures were generated using the program package Maestro assuming idealized dihedral angles for the respective helix backbone
(for PPI: φ = -75°, ψ = 160°, ω = 0° and
for PPII: φ = -75°, ψ = 145°, ω = 180° ).

If used for publication, please cite the following reference:
M. Kuemin, S. Schweizer, C. Ochsenfeld, and H. Wennemers, J. Am. Chem. Soc. , 131, 15474 (2009).

Download pp_structures.tgz

Structures of amylose chains

Description / Information

Structures of amylose chains containing n=1,2,4,8,16,32,48,64 -D-glucose units. The original structures have been obtained by the SWEET tool [A. Bohne, E. Lang, and. C. W. von der Lieth, J. Mol. Model. 4, 33 (1998); A. Bohne, E. Lang, and. C. W. von der Lieth, Bioinformatics 15, 767 (1999)].
The sequence has been reordered by applying the reverse Cuthill-McKee algorithm onto the connectivity matrix.

If used for publication, please cite the following reference:
J. Kussmann and C. Ochsenfeld, J. Chem. Phys. 127, 054103 (2007).

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Complete directory as tar-ball

SparseCholesky

Description / Information

SparseCholesky provides a set of routines for decomposing and inverting sparse, symmetric positive-definite matrices in a linear scaling fashion. In addition, a linear equation solver is supplied. In the sparse algebra routines the compressed sparse row (CSR) storage format is employed. The code is written in C/C++, but can easily embedded in Fortran code.

If used for publication, please cite the following reference:
S. Schweizer, J. Kussmann, B. Doser, and C. Ochsenfeld, J. Comp. Chem. 29, 1004 (2008).

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SparseCholesky.tgz

DNA adenine-thymine fragments
	Description / Information Structures of DNA_n fragments containing n=1,2,4,8,16 adenine-thymine base pairs. The original structures have been obtained by the Spartan package. If used for publication, please cite the following reference: B. Doser, D. S. Lambrecht, J. Kussmann, and C. Ochsenfeld, J. Chem. Phys. 130, 064107 (2009). Download dna_fragments.tgz

Modified Polyalanine Helices
	Description / Information Structures of model peptides consisting of a modified polyalanine helix in different protonation states. The original structures have been obtained by the Maestro package . If used for publication, please cite the following reference: C. V. Sumowski and C. Ochsenfeld, J. Phys. Chem. A 113 , 11734 (2009). Download peptides_qmmm.tgz