Energetic and stereochemical effects of the protein environment on substrate: a theoretical study of methylmalonyl-CoA mutase

QM/MM methods were used to study the isomerization step from (2R)-methylmalonyl-CoA to succinyl-CoA. A pathway via a "fragmentation-recombination" mechanism is ruled out on energetic grounds. For the other radicalic pathway, involving an addition recombination step, geometries and vibrational contributions have been determined, and a barrier height of 11.70 kcal/mol was found. The effect of adjacent hydrogen-donating groups was found to reduce the energy barrier by 1-2 kcal/mol each and thus to provide a significant catalytic effect for this reaction. By means of molecular dynamics studies, the stereochemistry of the methylmalonyl-CoA mutase catalyzed reaction was examined. It is shown that TYR89 is essential for maintaining stereoselectivity of the abstraction of a hydrogen in the backreaction. The subsequent selective formation of one isomer of methylmalonyl-CoA is probably due to the presence of a bulky side chain.     

Double proton transfer in the isolated and DNA-embedded guanine-cytosine base pair

The energetics and dynamics of double proton transfer (DPT) is investigated theoretically for the Watson-Crick conformation of the guanine-cytosine (GC) base pair. Using semiempirical density functional theory the isolated and DNA-embedded GC pair is considered. Differences in the energetics and dynamics of DPT thus addresses the question of how relevant studies of isolated base pairs are for the understanding of processes occurring in DNA. Two-dimensional potential energy surfaces involving the transferring hydrogen atoms and the proton donors and acceptors are presented for both systems. The DPT reaction is accompanied by a contraction of the distance between the two bases with virtually identical energetic barriers being 18.8 and 18.7 kcal/mol for the isolated and DNA-embedded system, respectively. However, the transition state for DPT in the DNA-embedded GC pair is offset by 0.1 A to larger N-H separation compared to the isolated GC pair. Using activated ab initio molecular dynamics, DPT is readily observed for the isolated base pair with a minimal amount of 21.4 kcal/mol of initial average kinetic energy along the DPT normal mode vector. On a time scale of approximately 100 fs DPT has occurred and the excess energy is redistributed. For the DNA-embedded GC pair considerably more kinetic energy is required (30.0 kcal/mol) for DPT and the process is completed within one hydrogen vibration. The relevance of studies of isolated base pairs and base pair analogs in regard of reactions or properties involving DNA is discussed.     

Conformational analysis of self-organized monolayers with scanning tunneling microscopy at near-atomic resolution

We describe the synthesis and a novel approach to the conformational analysis of 2,2'-bipyridines (bpy) bearing aromatic rich Frechet-type dendritic wedges of the first and second generation as substituents. The evaporation of solutions of these new ligands on graphite surfaces under ambient conditions results in the formation of self-organized monolayers. Scanning tunneling microscopy (STM) investigations of the monolayers under ambient conditions (air, 298 K) gave images at submolecular and near-atomic resolution. The analysis of the STM images includes the following processes: (i) identification and reproduction of potential homoconformational domains, (ii) exclusion of improper data using quality criteria for drift and feedback artifacts, (iii) compilation of running averages and checking for averaging artifacts, (iv) analysis of three-dimensional and contour plots, (v) calculation of the HOMO properties of the free molecules, and (vi) final conformational assignment based on all accessible information. Following this procedure, two different conformations could be assigned to domains observed in the monolayers of the first-generation (G1) and second-generation (G2) dendritic compounds. Homoconformational domains are observed side-by-side. The different conformations arise from syn or anti arrangements at the ether substituents. An additional conformational effect is found upon treating the G1 domains with HCl gas, when a partial rearrangement of the bpy from trans to cis occurs, concomitant with protonation.     

Structure and properties of the dendron-encapsulated polyoxometalate (C(52)H(60)NO(12))(12)[(Mn(H(2)O))(3)(SbW(9)O(33))(2)], a first generation dendrizyme

Combining analytical and theoretical methods, we present a detailed study of a heteropolytungstate cluster encapsulated in a shell of dendritically branching surfactants, namely (C(52)H(60)NO(12))(12)[(Mn(H(2)O))(3)(SbW(9)O(33))(2)], 3. This novel surfactant-encapsulated cluster (SEC) self-assembles spontaneously from polyoxometalate-containing solutions treated with a stoichiometric amount of dendrons. Compound 3 exhibits a discrete supramolecular architecture in which a single polyoxometalate anion resides in a compact shell of dendrons. Our approach attempts to combine the catalytic activity of polyoxometalates with the steric properties of tailored dendritic surfactants into size-selective catalytic systems. The structural characterization of the SEC is based on analytical ultracentrifugation (AUC) and small-angle neutron scattering (SANS). The packing arrangement of dendrons at the cluster surface is gleaned from molecular dynamics (MD) simulations, which suggests a highly porous shell structure due to the dynamic formation of internal clefts and cavities. From analysis of the MD trajectory of 3, a theoretical neutron-scattering function is derived that is in good agreement with experimental SANS data. Force field parameters used in MD simulations are partially derived from a quantum mechanical geometry optimization of [(Zn(H(2)O))(3)(SbW(9)O(33))(2)](12)(-), 2b, at the density functional theory (DFT) level. DFT calculations are corroborated by X-ray structure analysis of Na(6)K(6)[(Zn(H(2)O))(3)(SbW(9)O(33))(2)].23H(2)O, which is isostructural with the catalytically active Mn derivative 2a. The combined use of theoretical and analytical methods aims at rapidly prototyping smart catalysts ("dendrizymes"), which are structurally related to naturally occurring metalloproteins.     

Oxydation von Allylalkoholen mit Blei(IV)-acetat

Lead tetraacetate (LTA) oxidation of the allylic alcohols 1, 10, 14 and 19 leads to the formation of the epoxides 2, 11, 15 and 20 , products of a novel internal addition reaction of the electron deficient alcohol oxygen to the allylic double bond. In some cases ( 10, 14 ) the formation of a new type of acetoxylated enolethers ( 12, 16 ) is observed. The LTA oxidation of the allylic dienols 21 and 29 gives rise to the formation of the epoxyacetates 25 and 33 , products of a similar internal addition reaction. Furthermore, a variety of cyclization products ( 22, 23, 24, 26, 30, 31, 32 and 34 ) has been isolated whose formation requires an isomerisation of the allylic trans double bond to a cis one.     

Biosynthesis of flavocoenzymes

The biosynthesis of one riboflavin molecule requires one molecule of GTP and two molecules of ribulose 5-phosphate. The imidazole ring of GTP is hydrolytically opened, yielding a 2,5-diaminopyrimidine that is converted to 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione by a sequence of deamination, side chain reduction, and dephosphorylation. Condensation of 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione with 3,4-dihydroxy-2-butanone 4-phosphate obtained from ribulose 5-phosphate affords 6,7-dimethyl-8-ribityllumazine. Dismutation of the lumazine derivative yields riboflavin and 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione, which is recycled in the biosynthetic pathway. The enzymes of the riboflavin pathway are potential targets for antibacterial agents.     

Impact of Transition Metal Substituents on Polysilane Properties: Iron versus Ruthenium

Summary. The previously unknown ruthenio disilanes Rp–Si₂Me₄–C₆H₄X (Rp = η⁵-C₅H₅Ru(CO)₂; X = H, Br, –CHO, CH=C(CN)₂) were synthesized from ClSi₂Me₄C₆H₄X (X = H, Br) and Rp⁻ using conventional chemical methods. Trends in the UV/Vis absorption spectra indicate strong electronic coupling within the Rp–Si–Si–C_aryl fragment and, therefore, closely resemble the ones observed for the corresponding iron complexes. The four compounds however, were shown to be less sensitive towards UV irradiation. The crystal structure of Rp–Si₂Me₄–C₆H₄CH=C(CN)₂ was determined by X-ray diffraction and exhibits an all-trans-array of the Ru–Si–Si–C_aryl moiety, what is a basic requirement for optimal through-bond interaction.     

Total synthesis of the marine alkaloid halitulin

The structure of the strongly cytotoxic marine alkaloid halitulin (1) has been confirmed by total synthesis and its absolute configuration determined as (15S). The synthesis follows a strategy previously reported by one of us and uses an efficient preparation of the quinoline-7,8-diol unit by modified Baeyer-Villiger and Skraup reactions. The O-benzyl protecting groups were removed in the last step of the synthesis by transfer hydrogenolysis without concomitant reduction of the quinoline ring. The method can be applied for the synthesis of halitulin analogues.