Ab initio study of the binding of Trichostatin A (TSA) in the active site of histone deacetylase like protein (HDLP)

Histone deacetylase (HDAC) inhibitors have recently attracted considerable interest because of their therapeutic potential for the treatment of cell proliferative diseases. An X-ray structure of a very potent inhibitor, Trichostatin A (TSA), bound to HDLP (an HDAC analogue isolated from Aquifex aeolicus), is available. From this structure, an active site model (322 atoms), relevant for the binding of TSA and structural analogues, has been derived, and TSA has been minimized in this active site at HF 3-21G* level. The resulting conformation is in excellent accordance with the X-ray structure, and indicates a deprotonation of the hydroxamic acid in TSA by His 131. Also, a water molecule was minimized in the active site. In addition to a similar deprotonation, in accordance with a possible catalytic mechanism of HDAC as proposed by Finnin et al. (M. S. Finnin, J. R. Donigian, A. Cohen, V. M. Richon, R. A. Rifkind and P. A. Marks, Nature, 1999, 401, 188-193), a displacement of the resulting OH- ion in the active site was observed. Based on these results, the difference in energy of binding between TSA and water was calculated. The resulting value is realistic in respect to experimental binding affinities. Furthermore, the mechanism of action of the His 131-Asp 166 charge relay system was investigated. Although the Asp residue in this motif is known to substantially increase the basicity of the His residue, no proton transfer from His 131 to Asp 166 was observed on binding of TSA or water. However, in the empty protonated active site, this proton transfer does occur.     

COSMO-RS: A novel view to physiological solvation and partition questions

Both, dielectric continuum solvation models as well as surface or group based methods using polarity and lipophilicity parameters have been proven to be useful tools for the analysis of solvation and partition questions. For the first time, COSMO-RS provides an integrated theory, which combines the aspects of continuum solvation and surface interactions, and which ends up with chemical potentials of molecules in almost arbitrary solvents and mixtures. Due to its sound theoretical basis, COSMO-RS does not only provide a new quantitative access to solvation and partition properties in well defined solvents, but it also opens a novel view and gives a better understanding of the general problem of solvation. Finally, this allows for a generalisation of COSMO-RS to sophisticatedphysiological partition problems involving as complex phases as blood, brain, or cell membranes. The use of COSMO-RS for drug discovery and design is demonstrated by applications to blood-brain partition coefficients, and water solubility.     

Integral approximations for molecular orbital theory

The electron repulsion integrals arising in LCAO-MO theory are approximated by replacement of the product of two orbitals on different centers by linear combinations of one-center products. The approximation differs from those previously proposed in that the coefficients of the various terms are determined by requiring agreement for certain integrals, and in the emphasis of the role of symmetry in selecting the one-center products. For two-center integrals, the new approximation is significantly better than older approximate methods. Reasons are given for expecting this improvement to extend also to multi-center integrals.

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Zusammenfassung Es wird ein Verfahren zur näherungsweisen Berechnung von Elektronenwechselwirkungsintegralen der LCAO-MO-Theorie beschrieben, bei welchem das Produkt zweier Zustandsfunktionen an verschiedenen Zentren durch eine Linearkombination von Produkten am gleichen Zentrum ersetzt wird. Der Unterschied zu ähnlichen Ansätzen liegt in der Justierung der Koeffizienten. Für Zweizentrenintegrale liefert die hier vorgeschlagene Methode bedeutend bessere Ergebnisse als das Mulliken-Verfahren.

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Résumé Les intégrales de répulsion électroniques intervenant dans la théorie LCAO MO sont calculées d'une manière approchée en remplaçant le produit de deux orbitales sur des centres différents par des combinaisons linéaires de produits à un centre. Cette approximation diffère de celles proposées auparavant par la détermination des coefficients des différents termes au moyen de l'ajustement de certaines intégrales et par l'importance du rôle de la symétrie dans le choix des produits monocentriques. Cette nouvelle approximation est bien meilleure que les anciennes en ce qui concerne les intégrales bi-centriques. Nous donnons des raisons d'espérer que cette amélioration s'étendra aux intégrales polycentriques.

     

π-Olefin—iridium -komplexe : III. Über (η4-cyclodien)(η5-cyclodienyl)iridium-verbindungen,einen neuartigen hydridoiridium-komplex und das (η4-cyclooctadien)(η6-cyclooctatrien)iridium-kation

The complexes [Ir(COD)(η⁵-C₇H₉)] and [Ir(COD)(η⁵-C₈H₁₁)] are obtained by the isoprophyl Grignard synthesis of [Ir(COD)Cl]₂ (COD = η⁴-1,5-cyclooctadiene) in the presence of cycloheptatriene, and cyclooctatriene, respectively. The later reaction yields [IrH(COD)(δ⁴-1,3,6-C₈H₁₀)] as a by-product which, in contrast to other [IrH(η⁴-cyclodiene)₂] complexes, does not show H-addition-elimination equilibria. Reduction of [Ir(1,3-C₇H₁₀)₂Cl] with C₂H₅OH/Na₂CO₃ yields [Ir(η⁴-1,3-C₇H₁₀)](η⁵-C₇H₉)] which was characterized by X-ray analysis. [Ir(COD)Cl]₂ reacts with Na₂C₈H₈, and after hydrolysis unstable [Ir(COD)(η⁵-C₈H₉)] is formed which by protonation with HPF₆ is converted into the [Ir(COD)(η⁶-1,3,5-C₈H₁₀)]⁺ cation. All these compounds are fluxional in solution.     

Thermodynamic and kinetic data for adduct formation, cis-trans isomerization and redox reactions of ML4 complexes: a case study with rhodium- and iridium-tropp complexes in d8, d9 and d10 valence electron configurations (tropp=dibenzotropylidene phosphanes)

The formation of adducts of the square-planar 16-electron complexes trans-[M(tropp(ph))(2)](+) and cis-[M(tropp(ph))(2)](+) (M=Rh, Ir; tropp(Ph)=5-diphenylphosphanyldibenzo[a,d]cycloheptene) with acetonitrile (acn) and Cl(-), and the redox chemistry of these complexes was investigated by various physical methods (NMR and UV-visible spectroscopy, square-wave voltammetry), in order to obtain some fundamental thermodynamic and kinetic data for these systems. A trans/cis isomerization cannot be detected for [M(tropp(ph))(2)](+) in non-coordinating solvents. However, both isomers are connected through equilibria of the type trans-[M(tropp(ph))(2)](+)+L<==>[ML(tropp(ph))(2)](n)<==>cis-[M(tropp(ph))(2)](+)+L, involving five-coordinate intermediates [ML(tropp(ph))(2)](n) (L=acn, n=+1; L=Cl(-), n=0). Values for K(d) (K(f)), that is, the dissociation (formation) equilibrium constant, and k(d) (k(f)), that is, the dissociation (formation) rate constant, were obtained. The formation reactions are fast, especially with the trans isomers (k(f)>1x10(5) m(-1) s(-1)). The reaction with the sterically more hindered cis isomers is at least one order of magnitude slower. The stability of the five-coordinate complexes [ML(tropp(ph))(2)](n) increases with Ir>Rh and Cl(-)>acn. The dissociation reaction has a pronounced influence on the square-wave (SW) voltammograms of trans/cis-[Ir(tropp(ph))(2)](+). With the help of the thermodynamic and kinetic data independently determined by other physical means, these reactions could be simulated and allowed the setting up of a reaction sequence. Examination of the data obtained showed that the trans/cis isomerization is a process with a low activation barrier for the four-coordinate 17-electron complexes [M(tropp(ph))(2)](0) and especially that a disproportionation reaction 2 trans/cis-[M(tropp(ph))(2)](0)-->[M(tropp(ph))(2)](+)+[M(tropp(ph))(2)](-) may be sufficiently fast to mask the true reactivity of the paramagnetic species, which are probably less reactive than their diamagnetic equilibrium partners.     

Hard-soft acid-base interactions of silylenes and germylenes

A detailed investigation of the electrophilic and nucleophilic character of singlet silylenes and germylenes, divalent compounds of silicon and germanium, respectively, substituted by first- and second-row elements is presented. In a first part, the Lewis acid properties of these compounds were studied through their complexation reaction with the Lewis bases NH3, PH3, and AsH3. The results indicate that this complexation is most favorable with the hardest base NH3, classifying these compounds as hard Lewis acids. This is confirmed by the linear correlation between the interaction energies and the value of the electrostatic potential, used as an approximation to the local hardness, near the empty p orbital of these compounds, indicating a charge-controlled interaction in the complex. Also the electrophilicity index, proposed by Parr et al., computed both at the global and the local level, correlates linearly with the complexation energies of the compounds with NH3. The Lewis base character of these silylenes has been investigated, through their interaction with the acids BH3 and AlH3. Also in this case, the electrostatic potential can be used to probe the reactivity of the compounds. It will finally be demonstrated that an increasing stability of the silylenes and germylenes is accompanied by an increase in their nucleophilicity and a decrease of the electrophilicity.     

Synthesis,purification and spectroscopic characterization of potential impurities of hexamethylmelamine

The syntheses and spectroscopic properties (ir, ¹H nmr, ¹³C nmr, uv and ms) of pure samples of 2-chloro-4,6-bis(dimethylamino)-s-triazine 1 , 4,6-dichloro-2-dimethylamino-s-triazine 2 , 4,6-bis(dimethylamino)-s-triazin-2(lH)-one 3 , 4-chloro-6-dimethylamino-s-triazin-2(1H)-one 4 , 6-dimethylamino-s-triazine-2,4(1H,3H)-dione 5 , and 2,4,6-tris(dimethylamino)-s-triazine (altretamine, HMM) are reported. Evidence for enol-keto equilibria are also presented for 3 , in which the enol form exhibits as an H-bonded dimer structure similar to the dimer of organic carboxylic acids.     

Synthesis of 2′-Deoxyribofuranosides of 8-Aza-7-deazaguanine and Related Pyrazolo[3,4-d]pyrimidines

The N(1)- and N(2)-(2′-deoxyribofuranosides) 1 and 2 , respectively, of 8-aza-7-deazaguanine were prepared via phase-transfer glycosylation in the presence or absence of Bu₄NHSO₄ as catalyst of 6-amino-4-methoxy-lH-pyrazolo[3,4-d]pyrimidine ( 7c ) with 2-deoxy-3,5-di-O-(p-toluoyl)-α-D -erythro-pentofuranosyl chloride ( 10 ). On a similar route, but without catalyst and employing THF as organic phase, the 6-amino-4-chloronucleosides 11b and 12b were synthesized from 7a and converted into the N(1)-and N(2)-substituted 4-thioxo analogues 17a and 18a , respectively. The ratio of N(1)- to N(2)-glycosylation was 2:1 for 7c and 1:1 for 7a , viz. depending on the nucleobase structure. The rate of the H⁺-catalyzed N-glycosyl hydrolysis was strongly decreased for the N(2)-(β-D -2′-deoxyribofuranosides) as compared to the N(1)-compounds. However, the N(1)-nucleoside 1 , which is an isostere of 2′-deoxyguanosine, is sufficiently stable to be employed later in solid-phase oligonucleotide synthesis.     

Synthesis and Structure of Mixed Ba12F19ClδBr5–δ Crystals

In the structure Ba₁₂F₁₉Cl₅ [hexagonal space group P6 2m] the two chlorides on the sites Cl(1) and Cl(2) can partially be replaced by bromide ions. Single crystals of the type Ba₁₂F₁₉Cl_δBr_5–δ with a chloride to bromide ratio up to 2 : 3 could be obtained by cooling a flux of 75 mol% BaF₂ and 25 mol% BaX₂ with X = Cl, Br. The crystal quality decreases with increasing bromide concentration. Structural parameters of five selected single crystals with different chloride/bromide ratio were studied by single crystal X-ray diffraction methods. The refined total Cl^?/Br^? population ratio in the crystals is close to the one of the flux. The lattice parameters and interatomic distances change in various ways, when the smaller chloride ion is replaced by the bigger bromide ion. The refinements show a statistical disorder on the halide sites with preferential bromide substitution on site Cl(1).     

A reinvestigation of asymmetric induction in diels-alder reactions to chiral acrylates.

The chiral induction in the Diels-Alder addition $\text{1}$ → $\text{2}$, assessed reliably by ¹⁹F-NMR-spectroscopy of the endo-esters $\text{4}$, varied between 47 - 93% in favor of the 2-(R)-adducts $\text{2}$ depending on the auxiliary chiral group and the Lewis-acid catalyst.