Lubomír Rulíšek

Coordination geometries of selected transition metal ions (Co2+, Ni2+, Cu2+, Zn2+, Cd2+, and Hg2+) in metalloproteins.

In order to determine preferred coordination geometries of six divalent cations (Co2+, Ni2+, Cu2+, Zn2+, Cd2+, and Hg2+), two sources of experimental data were exploited: Protein Data Bank and Cambridge Structural Database. Metal-binding sites of approximately 100 metalloproteins and 3000 smaller transition metal complexes were analyzed and classified. The correlation between the geometries of small-molecule crystal structures and the metal-binding sites in metalloproteins was investigated. The abundance of amino acid residues participating in coordination metal-protein bonds of metalloproteins was evaluated. From the performed analysis it follows that the octahedral arrangement is preferred by Co2+ and Ni2+, tetrahedral by Zn2+, square planar by Cu2+, and linear by Hg2+. Cadmium (II) cation tends to bind in both tetrahedral and octahedral arrangements and single coordination geometry cannot be unambiguously ascribed to it.

An organometallic route to long helicenes

Along with the recent progress in the development of advanced synthetic methods, the chemical community has witnessed an increasing interest in promising carbon-rich materials. Among them, helicenes are unique 3D aromatic systems that are inherently chiral and attractive for asymmetric catalysis, chiral recognition and material science. However, there have been only limited attempts at synthesizing long helicenes, which represent challenging targets. Here, we report on an organometallic approach to the derivatives of undecacyclic helicene, which is based on intramolecular [2 + 2 + 2] cycloisomerization of aromatic hexaynes under metal catalysis closing 6 new cycles of a helicene backbone in a single operation. The preparation of nonracemic compounds relied on racemate resolution or diastereoselective synthesis supported by quantum chemical (density functional theory) calculations. The fully aromatic [11]helicene was studied in detail including the measurement and theoretical calculation of its racemization barrier and its organization on the InSb (001) surface by STM. This research provides a strategy for the synthesis of long helical aromatics that inherently comprise 2 possible channels for charge transport: Along a π-conjugated pathway and across an intramolecularly π-π stacked aromatic scaffold.

On the Mechanism of Asymmetric Allylation of Aldehydes with Allyltrichlorosilanes Catalyzed by QUINOX, a Chiral Isoquinoline N-Oxide

Allylation of aromatic aldehydes 1a-m with allyl- and crotyl-trichlorosilanes 2- 4, catalyzed by the chiral N-oxide QUINOX (9), has been found to exhibit a significant dependence on the electronics of the aldehyde, with p-(trifluoromethyl)benzaldehyde 1g and its p-methoxy counterpart 1h affording the corresponding homoallylic alcohols 6g, h in 96 and 16% ee, respectively, at -40 degrees C. The kinetic and computational data indicate that the reaction is likely to proceed via an associative pathway involving neutral, octahedral silicon complex 22 with only one molecule of the catalyst involved in the rate- and selectivity-determining step. The crotylation with (E) and (Z)-crotyltrichlorosilanes 3 and 4 is highly diastereoselective, suggesting the chairlike transition state 5, which is supported by computational data. High-level quantum chemical calculations further suggest that attractive aromatic interactions between the catalyst 9 and the aldehyde 1 contribute to the enantiodifferentiation and that the dramatic drop in enantioselectivity, observed with the electron-rich aldehyde 1h, originates from narrowing the energy gap between the (R)- and (S)-reaction channels in the associative mechanism (22). Overall, a good agreement between the theoretically predicted enantioselectivities for 1a and 1h and the experimental data allowed to understand the specific aspects of the reaction mechanism.

Synthesis and Photophysical Properties of Biaryl-Substituted Nucleos(t)ides. Polymerase Synthesis of DNA Probes Bearing Solvatochromic and pH-Sensitive Dual Fluorescent and 19F NMR Labels

The design of four new fluorinated biaryl fluorescent labels and their attachment to nucleosides and nucleoside triphosphates (dNTPs) by the aqueous cross-coupling reactions of biarylboronates is reported. The modified dNTPs were good substrates for KOD XL polymerase and were enzymatically incorporated into DNA probes. The photophysical properties of the biaryl-modified nucleosides, dNTPs, and DNA were studied systematically. The different substitution pattern of the biaryls was used for tuning of emission maxima in the broad range of 366-565 nm. Using methods of computational chemistry the emission maxima were reproduced with a satisfactory degree of accuracy, and it was shown that the large solvatochromic shifts observed for the studied probes are proportional to the differences in dipole moments of the ground (S(0)) and excited (S(1)) states that add on top of smaller shifts predicted already for these systems in vacuo. Thus, we present a set of compounds that may serve as multipurpose base-discriminating fluorophores for sensing of hairpins, deletions, and mismatches by the change of emission maxima and intensities of fluorescence and that can be also conviently studied by (19)F NMR spectroscopy. In addition, aminobenzoxazolyl-fluorophenyl-labeled nucleotides and DNA also exert dual pH-sensitive and solvatochromic fluorescence, which may imply diverse applications.

On the origin of diastereoselectivity in [2 + 2 + 2] cycloisomerization of chiral triynes: controlling helicity of helicene-like compounds by thermodynamic factors.

Diastereoselective CoI-mediated [2 + 2 + 2] cycloisomerization of CH(3)O-substituted optically pure aromatic triynes to obtain nonracemic functionalized helicene-like compounds (comprising a penta-, hexa-, and heptacyclic helical scaffold) was studied. The stereochemical outcome of the reaction at 140 degrees C using CpCo(CO)(2) was controlled by thermodynamic factors yielding diastereomeric ratios up to 91:9. Using CpCo(ethylene)(2) at room temperature, a kinetic control took place leading to the loss of stereoselectivity. Barriers to epimerization for selected helicene-like compounds were measured indicating their lower configurational stability in comparison to the parent carbohelicenes. Free energy differences between corresponding pairs of diastereomers (calculated at the DFT B3LYP/TZV+P level) were in excellent agreement with the experimental data and allowed for the prediction of the stereochemical outcome of the reaction. An optically pure hexacyclic helicene-like alcohol was prepared on a multigram scale. Its X-ray structure confirmed the previous helicity assignments being based on (1)H-(1)H correlations in ROESY (1)H NMR spectra.

Evaluation of the intramolecular basis set superposition error in the calculations of larger molecules: [n]helicenes and Phe-Gly-Phe tripeptide

Correlated ab initio calculations on large systems, such as the popular MP2 (or RI‐MP2) method, suffer from the intramolecular basis set superposition error (BSSE). This error is typically manifested in molecules with folded structures, characterized by intramolecular dispersion interactions. It can dramatically affect the energy differences between various conformers as well as intramolecular stabilities, and it can even impair the accuracy of the predictions of the equilibrium molecular structures. In this study, we will present two extreme cases of intramolecular BSSE, the internal stability of [n]helicene molecules and the relative energies of various conformers of phenylalanyl‐glycyl‐phenylalanine tripeptide (Phe‐Gly‐Phe), and compare the calculated data with benchmark values (experimental or high‐level theoretical data). As a practical and cheap solution to the accurate treatment of the systems with large anticipated value of intramolecular BSSE, the recently developed density functional method augmented with an empirical dispersion term (DFT‐D) is proposed and shown to provide very good results in both of the above described representative cases.

Sexual attraction in the silkworm moth: Nature of binding of bombykol in pheromone binding protein - An ab initio study

An analysis of the crystal structure of [BmPBP...bombykol] complex identified nine amino acid residues involved in a variety of intermolecular interactions binding the ligand. Using simple model fragments as the representatives of the residues, the interaction energies of their complexes with bombykol were calculated using high-level ab initio methods. The results were discussed in terms of the method and basis set dependence and were further corrected to account for their pair nonadditivities. This enabled us to describe quantitatively the nature and origin of the binding forces in terms of contribution of the individual amino acids and individual types of interaction to the overall stability. All of these interactions are well defined and cannot be considered as nonspecific hydrophobic interactions, one of the major conclusions of this work.

Theoretical Description of the Structure and Magnetic Properties of Nitroxide-Cu(II)-Nitroxide Spin Triads by Means of Multiconfigurational Ab Initio Calculations

The structural, electronic and magnetic properties of two different models of the heterospin polymer chain complexes of Cu2+ hexafluoroacetylacetonate with two pyrazole-substituted nitronyl nitroxides Cu(hfac)2L(R) have been studied by means of multiconfigurational perturbation theory based on a CASSCF (complete active space self-consistent field) wave function, i.e. the CASPT2 method. Our calculations reveal the presence of two minima in the electronic energy curve along the Cu-O(L) bond, separated by only 6 kcal/mol, and corresponding to the X-ray structures of the CuO6 centers in Cu(hfac)2L(Pr) at 115 and 293 K, respectively. The two energetic minima are characterized by a different electronic structure, thus giving rise to a different three-spin exchange coupling and explaining the thermally induced spin transitions in this family of compounds. The concomitant variations in the magnetic properties, i.e. g factors and magnetic moments mu(eff)(T) were calculated and compared with the experimental data of Cu(hfac)2L(Pr). Even if the correspondence is only qualitative, our calculations provide a convincing explanation of the observed magnetic peculiarities. In particular, at low temperatures, the predicted ground-state is 2A(u), well separated from the 2A(g), 4A(u) states and therefore exclusively populated. Its calculated g factors, g(parallel) = 1.848, g(perpendicular) = 1.965, 1.974, qualitatively correspond to the observed g < 2 signals in the low-temperature EPR spectra. The previously assumed formal spin assignment >N-O*-Cu-*O-N < for these linear spin triads is challenged by our calculations, pointing instead to a more important role of the end-standing NO in the exchange interactions with Cu(II).

Effect of spin-orbit coupling on reduction potentials of octahedral ruthenium(II/III) and osmium(II/III) complexes.

Reduction potentials of several M(2+/3+) (M = Ru, Os) octahedral complexes, namely, [M(H2O)6](2+/3+), [MCl6](4-/3-), [M(NH3)6](2+/3+), [M(en)3](2+/3+) [M(bipy)3](2+/3+), and [M(CN)6](4-/3-), were calculated using the CASSCF/CASPT2/CASSI and MRCI methods including spin-orbit coupling (SOC) by means of first-order quasi-degenerate perturbation theory. It was shown that the effect of SOC accounts for a systematic shift of approximately -70 mV in the reduction potentials of the studied ruthenium (II/III) complexes and an approximately -300 mV shift for the osmium(II/III) complexes. SOC splits the sixfold-degenerate (2)T(2g) ground electronic state (in ideal octahedral symmetry) of the M(3+) ions into the E((5/2)g) Kramers doublet and G((3/2)g) quartet, which were calculated to split by 1354-1573 cm(-1) in the Ru(3+) complexes and 4155-5061 cm(-1) in the Os(3+) complexes. It was demonstrated that this splitting represents the main contribution to the stabilization of the M(3+) ground state with respect to the closed-shell (1)A(1g) ground state in M(2+) systems. Moreover, it was shown that the accuracy of the calculated reduction potentials depends on the calculated solvation energies of both the oxidized and reduced forms. For smaller ligands, it involves explicit inclusion of the second solvation sphere into the calculations, whereas implicit solvation models yield results of sufficient accuracy for complexes with larger ligands. In such cases (e.g., [M(bipy)3](2+/3+) and its derivatives), very good agreement between the calculated (SOC-corrected) values of the reduction potentials and the available experimental values was obtained. These results led us to the conclusion that especially for Os(2+/3+) complexes, inclusion of SOC is necessary to avoid systematic errors of approximately 300 mV in the calculated reduction potentials.

Biochemical characterization of human glutamate carboxypeptidase III

Human glutamate carboxypeptidase II (GCPII) is a transmembrane metallopeptidase found mainly in the brain, small intestine, and prostate. In the brain, it cleaves N‐acetyl‐l‐aspartyl‐glutamate, liberating free glutamate. Inhibition of GCPII has been shown to be neuroprotective in models of stroke and other neurodegenerations. In prostate, it is known as prostate‐specific membrane antigen, a cancer marker. Recently, human glutamate carboxypeptidase III (GCPIII), a GCPII homolog with 67% amino acid identity, was cloned. While GCPII is recognized as an important pharmaceutical target, no biochemical study of human GCPIII is available at present. Here, we report the cloning, expression, and characterization of recombinant human GCPIII. We show that GCPIII lacks dipeptidylpeptidase IV‐like activity, its activity is dependent on N‐glycosylation, and it is effectively inhibited by several known inhibitors of GCPII. In comparison to GCPII, GCPIII has lower N‐acetyl‐l‐aspartyl‐glutamate‐hydrolyzing activity, different pH and salt concentration dependence, and distinct substrate specificity, indicating that these homologs might play different biological roles. Based on a molecular model, we provide interpretation of the distinct substrate specificity of both enzymes, and examine the amino acid residues responsible for the differences by site‐directed mutagenesis. These results may help to design potent and selective inhibitors of both enzymes.