PubMed Health⌕ Search

Biomedical subjects

Christian Ochsenfeld

Publications and source records attributed to Christian Ochsenfeld.

9 recordsLinked to original sources
PubMed2006

The "azido gauche effect"-implications for the conformation of azidoprolines.

The "azido gauche effect" was examined both experimentally and theoretically and was found to determine the conformation of, for example, (4R)- and (4S)-azidoproline (Azp) derivatives. For (4R)Azp derivatives, the azido gauche effect induces a preferred C(4)-exo conformation of the pyrrolidine ring, which leads to stabilization of the s-trans amide conformer of, e.g., Ac-(4R)Azp-OCH(3) (5R) via an n-->pi interaction between the nonbonding electrons of the oxygen of the acetyl group and the carbonyl group of the ester. For (4S)Azp derivatives, the azido gauche effect results in a C(4)-endo conformation of the pyrrolidine ring that does not allow for this stabilizing n-->pi interaction of the s-trans conformer. Consequently, a significantly higher s-trans:s-cis amide conformer ratio is observed for (4R)Azp compared to (4S)Azp derivatives (e.g., 6.1:1 versus 2.6:1 in D(2)O for Ac-(4R)Azp-OCH(3) (5R) compared to Ac-(4S)Azp-OCH(3) (5S)). These conformational preferences are reflected in the higher tendency of (4S)Azp-containing peptides to form cyclic peptides with all-cis amide bonds compared to (4R)Azp derivatives. Ab initio calculations demonstrate that the strength of the azido gauche effect is comparable to that of the well-known "fluorine gauche effect". For azidoethane derivatives N(3)-CH(2)CH(2)-X (X = N(3), NHCOH, NHAc, or N(CH(3))Ac), the ab initio calculations revealed energy differences of 5-13 kJ mol(-)(1) between the anti and gauche conformations in favor of the gauche conformer. Calculations were also performed for the (4R)Azp and (4S)Azp derivatives 5R and 5S, supporting the experimentally observed data.

Journal Article↗
PubMed2006

Advances in methods and algorithms in a modern quantum chemistry program package.

Advances in theory and algorithms for electronic structure calculations must be incorporated into program packages to enable them to become routinely used by the broader chemical community. This work reviews advances made over the past five years or so that constitute the major improvements contained in a new release of the Q-Chem quantum chemistry package, together with illustrative timings and applications. Specific developments discussed include fast methods for density functional theory calculations, linear scaling evaluation of energies, NMR chemical shifts and electric properties, fast auxiliary basis function methods for correlated energies and gradients, equation-of-motion coupled cluster methods for ground and excited states, geminal wavefunctions, embedding methods and techniques for exploring potential energy surfaces.

Algorithms↗
PubMed2006

Molecular tweezer and clip in aqueous solution: unexpected self-assembly, powerful host-guest complex formation, quantum chemical 1H NMR shift calculation.

The newly prepared water-soluble naphthalene tweezer 2a and anthracene clip 4a (substituted both with lithium methanephosphonate groups in the central spacer unit) undergo an unexpected self-assembly in aqueous solution. The highly ordered intertwined structures of the self-assembled dimers [2a]2 and [4a]2 were elucidated by quantum chemical 1H NMR shift calculations. 2a and 4a form extremely stable host-guest complexes with N-methylnicotinamide 8 in methanol and water as well. According to the thermodynamic parameters determined by 1H NMR titration experiments at various temperatures the self-assembly of 2a and 4a and their strong binding to NMNA 8 observed in aqueous solution are enthalpy driven (DeltaH << 0); the enthalpic driving force is partially compensated by an unfavorable entropy (TDeltaS < 0). Self-assembly and the host-guest binding are therefore beautiful examples of the nonclassical hydrophobic effect.

Journal Article↗
PubMed2005

Multipole-based integral estimates for the rigorous description of distance dependence in two-electron integrals.

We derive multipole-based integral estimates (MBIE) as rigorous and tight upper bounds to four-center two-electron integrals in order to account for the 1/R distance decay between the charge distributions, which is missing in the Schwarz screening commonly used in ab initio methods. Our screening criteria are valid for all angular momenta and can be formulated for any order of multipoles. We have found the expansion limited to dipoles to be sufficiently tight for estimating the integrals in Hartree-Fock and density-functional theories, while the screening effort is negligible. For, e.g., a DNA fragment with 1052 atoms and 10,674 basis functions (6-31G*) the exchange part is faster by a factor of 2.1 as compared to the Schwarz screening both within our linear exchange scheme, whereas a smaller factor of 1.3 is gained for the Coulomb part within the continuous fast multipole method. Most importantly, our new MBIE screening is perfectly suited to exploit the strong distance decay of electron-correlation effects of at least 1/R4 in atomic-orbital-based formulations of correlation methods.

Journal Article↗
PubMed2005

Rigorous integral screening for electron correlation methods.

We derive rigorous multipole-based integral estimates (MBIE) in order to account for the distance dependence occurring in atomic-orbital (AO) formulations of electron correlation theory, where our focus is on AO-MP2 theory within a Laplace scheme. We find for the exact transformed integral products an extremely early onset of a linear-scaling behavior and a very small number of significant products. To preselect the significant integral products we adapt our MBIE method as rigorous upper bound. In this way it is possible to exploit the favorable scaling behavior observed and to reduce the scaling of estimated products asymptotically to linear, without sacrificing accuracy or reliability. By separating Coulomb- and exchange-type contractions only half-transformed integrals need to be computed. Furthermore, our scheme of rigorously preselecting transformed integral products via MBIE seems to offer particularly interesting perspectives for a direct formation of half- or fully transformed integrals by using multipole expansions and auxiliary basis sets.

Journal Article↗
PubMed2005

Selective complexation of N-alkylpyridinium salts: binding of NAD+ in water.

A new class of receptor molecules is presented that is highly selective for N-alkylpyridinium ions and electron-poor aromatics. Its key feature is the combination of a well-preorganized molecular clip with an electron-rich inner cavity and strategically placed, flanking bis-phosphonate monoester anions. This shape and arrangement of binding sites attracts predominantly flat electron-poor aromatics in water, binds them mainly by pi-cation, pi-pi, CH-pi, and hydrophobic interactions, and leads to their highly efficient desolvation. NAD(+) and NADP, the important cofactors of many redox enzymes, are recognized by the new receptor molecule, which embraces the catalytically active nicotinamide site and the adenine unit. Even nucleosides such as adenosine are likewise drawn into the clip's cavity. Complex formation and structures were examined by one- and two-dimensional NMR spectroscopy, Job plot analyses, and isothermal titration microcalorimetric (ITC) measurements, as well as quantum chemical calculations of (1)H NMR shifts. The new receptor molecule is a promising tool for controlling enzymatic oxidation processes and for DNA chemistry.

Calorimetry↗
PubMed2001

Structure and Dynamics of the Host-Guest Complex of a Molecular Tweezer: Coupling Synthesis, Solid-State NMR, and Quantum-Chemical Calculations S.P.B. thanks the Alexander von Humboldt Foundation for a research fellowship. C.O. acknowledges financial support by a Liebig "Habilitation" fellowship from the Fonds der Chemischen Industrie (FCI). This work was supported by the Deutsche Forschungsgemeinschaft (SFB 452) and the FCI. We thank Dr. Ingo Schnell for his involvement in the early part of this project, Dr. Kay Saalwächter for advice concerning the heteronuclear experiment, and Dr. Ulrich Burkert for his help during the synthesis of the complex.

Explore the source record for details and available documents.

Journal Article↗
PubMedDate not supplied

A study of a moleculartweezer host-guest system by a combination of quantum-chemical calculations and solid-state NMR experiments.

A study of a host-guest system consisting of a naphthalene-spaced tweezer with a 1,4 dicyanobenzene guest molecule is presented. The complex is investigated using a combination of quantum-chemical calculations and solid-state NMR experiments. The advantages of such an approach are illustrated. The focus is on the calculation of (1) 1H NMR and (2) 13C NMR chemical shifts for model fragments of the solid-state structure, (3) the analysis of host-guest interactions important for molecular recognition, and (4) the investigation of the process of a guest molecule rotation. For modeling the solid-state structure, up to three host-guest units are considered and the convergence with respect to the size of the solid-state fragment is investigated.

Carbon Isotopes↗