What to Learn from a Comparative Genomic Sequence Analysis of <Emphasis Type="Italic">L</Emphasis>-Carnitine Dehydrogenase

Summary. In contrast to eukaryotic cells certain eubacterial strains have acquired the ability to utilize L-carnitine (R-(–)-3-hydroxy-4-(trimethylamino)butyrate) as sole source of energy, carbon and nitrogen. The first step of the L-carnitine degradation to glycine betaine is catalysed by L-carnitine dehydrogenase (L-CDH, EC 1.1.1.108) and results in the formation of the dehydrocarnitine. During the oxidation of L-carnitine a simultaneous conversion of the cofactor NAD⁺ to NADH takes place. This catabolic reaction has always been of keen interest, because it can be exploited for spectroscopic L-carnitine determination in biological fluids – a quantification method, which is developed in our lab – as well as L-carnitine production.Based on a cloned L-CDH sequence an expedition through the currently available prokaryotic genomic sequence space began to mine relevant information about bacterial L-carnitine metabolism hidden in the enormous amount of data stored in public sequence databases. Thus by means of homology-based and context-based protein function prediction is revealed that L-CDH exists in certain eubacterial genomes either as a protein of approximately 35 kDa or as a homologous fusion protein of approximately 54 kDa with an additional putative domain, which is predicted to possess a thioesterase activity. These two variants of the enzyme are found on one hand in the genome sequence of bacterial species, which were previously reported to decompose L-carnitine, and on the other hand in gram-positive bacteria, which were not known to express L-CDH. Furthermore we could not only discover that L-CDH is located in a conserved genetic entity, which genes are very likely involved in this L-carnitine catabolic pathway, but also pinpoint the exact genomic sequence position of several other enzymes, which play an essential role in the bacterial metabolism of L-carnitine precursors.     

Energetic and topological analysis of the reaction of Mo and Mo2 with NH3, C2H2, and C2H4 molecules

The Density functional theory has been applied to characterize the structural features of Mo(1,2)-NH(3),-C(2)H(4), and -C(2)H(2) compounds. Coordination modes, geometrical structures, and binding energies have been calculated for several spin multiplets. It has been shown that in contrast to the conserved spin cases (Mo(1,2)-NH(3)), the interaction between Mo (or Mo(2)) and C(2)H(4) (or C(2)H(2)) are the low-spin (Mo-C(2)H(4) and -C(2)H(2)) and high-spin (Mo(2)-C(2)H(4) and -C(2)H(2)) complexes. In the ground state of Mo(1,2)-C(2)H(4) and -C(2)H(2), the metal-center always reacts with the C-C center. The spontaneous formation of the global minima is found to be possible due to the crossing between the potential energy surfaces (ground and excited states with respect to the metallic center). The bonding characterization has been performed using the topological analysis of the Electron Localization Function. It has been shown that the most stable electronic structure for a pi-acceptor ligand correlates with a maximum charge transfer from the metal center to the C-C bond of the unsaturated hydrocarbons, resulting in the formation of two new basins located on the carbon atoms (away from hydrogen atoms) and the reduction of the number of attractors of the C-C basin. The interaction between Mo(1,2) and C(2)H(4) (or C(2)H(2)) should be considered as a chemical reaction, which causes the multiplicity change. Contrarily, there is no charge transfer between Mo(1,2) and NH(3), and the partners are bound by an electrostatic interaction.     

On Mercury(I) Oxo Compounds — Quasi‐Relativistic Computational and Experimental Studies

About 60 molecular species composed of up to 10 mercury atoms and of oxygen atoms and/or of some other elements or groups (such as halogen, OH₂, OH, H, alkali, NO₃) have been investigated quantum chemically. Different density functional approaches and the ab initio SCF‐MP2 method were applied, comparing different basis sets and different atomic core sizes. It is important not to treat the Hg 5s, p, d as inactive core shells, and to use sufficiently many polarization functions. The shape of the 〉O‐Hg‐Hg‐O〈 units is not favorable concerning the formation of lattices composed of Hg^I, O and OH only. Despite its bulkiness, the OHgHgO units can easily come into contact with each other and then disproportionate. This is prevented in the so‐called ternary M‐Hg^I oxides by the embedded oxometallate (oxoacidic) anions. Furthermore, the Hg^I and Hg^II oxide bond energies are less favorable towards the stability of Hg^I oxo compounds, as compared to Hg halidic or oxoacidic compounds. Both points are not promising concerning the search for Hg^I oxides/hydroxides, although the preparation of such compounds, including spacer groups, by topochemical reactions can still not be excluded. So far, experimental efforts towards the synthesis of such a new class of compounds have only demonstrated that Hg^II is strictly preferred over Hg^I in the formation of solids of binary Hg‐O or ternary A‐Hg‐O composition (A = electropositive metal such as alkali, in contrast to M = transition or semi‐metal). This is so even if compounds containing ‘electron rich Hg^δ— atoms’ (i.e. A‐Hg amalgams) are oxidized under mild conditions.     

First‐order correlation‐kinetic contribution to Kohn–Sham exchange charge density function in atoms,using quantal density functional theory approach

Using the static exchange‐correlation charge density concept, the total integrated exchange‐charge density function is calculated within the nonrelativistic spin‐restricted exchange‐only (i) optimized effective potential model, and (ii) nonvariational local potential derived from the exchange‐only work potential within the quantal density functional theory, for the ground‐state isoelectronic series: Ga⁺, Zn, Cu^?; In⁺, Cd, Ag^?; and Tl⁺, Hg, Au^?. The difference between the exchange charge density function derived from these potentials is employed to evaluate the first‐order correlation‐kinetic contribution to the integrated exchange charge density. This contribution is found to be important for both the intra‐ and inter‐shell regions. Screening effects on the contribution due to the nd¹⁰ (n = 3–5) subshells are discussed through comparisons with similar calculations on Ca, Sr, and Ba, wherein nd¹⁰ electrons are absent. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Probing the hydride transfer process in the lumiflavine-1-methylnicotinamide model system using group softness

The hydride transfer process between the isoalloxazine moiety of flavins and the nicotinamide moiety of NAD(P)H has been explored by using density functional theory based reactivity index in the 1-methylnicotinamide-lumiflavine model system. Based on crystallographic data available, we have found that the group softness index helps to locate and orientate reactive regions in these interacting molecules while the electrophilicity index successfully describes the reactivity pattern of this system.     

Silica-Based and Transition Metal-Based Inorganic-Organic Hybrid Materials—A Comparison

Organically substituted metal alkoxides can be prepared by reaction of the parent alkoxides with complexing organic compounds. The chemical and structural consequences of such substitutions are discussed in this article. Examples are given showing how functional organic moieties, such as polymerizable groups, can be incorporated into sol-gel materials via the complexing ligands. Major structural differences between silica-based and metal-based hybrid materials originate from the different charge/coordination number ratios of silicon and most metals. This results in a high tendency for the molecular building blocks to aggregate. In many cases, metal oxide clusters are formed which are capped by the organic ligands. Such surface-modified clusters are themselves very valuable condensed matter units for materials syntheses.     

Accurate pKa determination for a heterogeneous group of organic molecules.

Single-molecule studies that allow to compute pKa values, proton affinities (gas-phase acidity/basicity) and the electrostatic energy of solvation have been performed for a heterogeneous set of 26 organic compounds. Quantum mechanical density functional theory (DFT) using the Becke-half&half and B3LYP functionals on optimized molecular geometries have been carried out to investigate the energetics of gas-phase protonation. The electrostatic contribution to the solvation energies of protonated and deprotonated compounds were calculated by solving the Poisson equation using atomic charges generated by fitting the electrostatic potential derived from the molecular wave functions in vacuum. The combination of gas-phase and electrostatic solvation energies by means of the thermodynamic cycle enabled us to compute pKa values for the 26 compounds, which cover six distinct chemical groups (carboxylic acids, benzoic acids, phenols, imides, pyridines and imidazoles). The computational procedure for determining pKa values is accurate and transferable with a root-mean-square deviation of 0.53 and 0.57 pKa units and a maximum error of 1.0 pKa and 1.3 pKa units for Becke-half&half and B3LYP DFT functionals, respectively.     

Design and Theoretical Study of Nickel Catalysts for Syndiotactic Polyolefins

A nickel catalyst was nodeled with ligand L^2,[NH=CH-CH=CH-0]^-,which should have potential use as a syndiotactic plyolefin catalyst,and the reaction mechanism was studied by theoretical calculations using the density functinal method at the B3LYP/LANL2MB level.The mechanism involves the formation of the intermediate [NiL^2Me]^ ,in which the metal occupies a T-shaped geometry.This intermediate has two possible structures with the methyl group trans either to the oxygen or to the nitrogen atom of L^2.The results show that both structures can lead to the desired product via similar reaction paths,A and B.Thus,the polymerization could be considered as taking place either with the alkyl group occupying the position trans to the Ni-0 or trans to the Ni-N bond in the catalyst.The polymerization process thus favors the catalysis of syndiotactic polyolefins.The syndiotactic synthesis effects could also be enhanced by varations in the ligand substituents.From energy considerations,we can conclude that it is more favorable for the methyl ttrans-O position to form a complex than to occupy the trans-N position.From bond length considerations,it is also more favoured for ethene to occupy the trans-O position than to occupy the trans-N position.     

Optimization of auxiliary basis sets for the LEDO expansion and a projection technique for LEDO-DFT

We present a systematic procedure for the optimization of the expansion basis for the limited expansion of diatomic overlap density functional theory (LEDO-DFT) and report on optimized auxiliary orbitals for the Ahlrichs split valence plus polarization basis set (SVP) for the elements H, Li--F, and Na--Cl. A new method to deal with near-linear dependences in the LEDO expansion basis is introduced, which greatly reduces the computational effort of LEDO-DFT calculations. Numerical results for a test set of small molecules demonstrate the accuracy of electronic energies, structural parameters, dipole moments, and harmonic frequencies. For larger molecular systems the numerical errors introduced by the LEDO approximation can lead to an uncontrollable behavior of the self-consistent field (SCF) process. A projection technique suggested by L?wdin is presented in the framework of LEDO-DFT, which guarantees for SCF convergence. Numerical results on some critical test molecules suggest the general applicability of the auxiliary orbitals presented in combination with this projection technique. Timing results indicate that LEDO-DFT is competitive with conventional density fitting methods.     

trans-Bis-[(−)ephedrinate]-palladium complex: synthesis, molecular modeling and use as catalyst

The reaction between palladium acetate, (−)-ephedrine and potassium acetate led to bis-chelate complex Pd[OCH(Ph)NH(Me)]₂ whose the trans-structure is obtained from calculations. The use of this complex to catalyze either the 1,4-hydrogenation of (E)-2-benzyliden-1-tetralone or Heck reaction of phenyl iodide with 3-methyl-3-buten-2-ol led to a low enantiomeric excess.