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.     

Antihydrophobic solvent effects: an experimental probe for the hydrophobic contribution to enzyme-inhibitor binding

The hydrophobic component to the binding affinities of one acyclic phosphinate (4) and three macrocyclic phosphonamidate inhibitors (1-3) to the zinc peptidase thermolysin was probed by varying the solvent composition. Increasing the percentage of ethanol in the buffer solution over the range 0-9% increases the inhibition constants, K(i), by up to an order of magnitude. This approach represents an experimental method for distinguishing solvation from conformational or other effects on protein-ligand binding. The size of the "antihydrophobic effect" is correlated with the amount of hydrophobic surface area sequestered from solvent on association of the inhibitor and enzyme, although it is attenuated from that calculated from the surface tension of ethanol-water mixtures. The results are consistent with the Lum-Chandler-Weeks explanation for the size dependence of the hydrophobic effect.     

Challenges in the structural characterization of thin organic films

This review addresses the special problems associated with the micro-structural characterization of thin and ultrathin organic films, primarily by optical spectroscopies. Films which are deposited by Langmuir-Blodgett techniques, self-assembly chemistry, and bulk film deposition techniques are considered. The use of enhanced optical excitation using surface phasma resonances and integrated optical structures is discussed extensively, as is the use of ellipsometry. Discussion of the spectroscopies used is broken into a section on electronic spectroscopies and an extensive discussion of vibrational spectroscopies. Vibrational information may be obtained with photons (absorption or scattering) or electrons (loss spectra), and the types of experimental systems amenable to each, along with the advantages and disadvantages of each are explored.     

Conformational preferences of 34 valence electron A2X4 molecules: An ab initio Study of B2F4, B2Cl4, N2O4, and C2O

Ab initio molecular orbital structures and energies of B₂F₄, B₂Cl₄, N₂O₄, and C₂O have been calculated for both perpendicular D_2d and planar D_2h rotamers. The experimental trend toward greater preference for the D_2d forms in going from B₂F₄ to B₂Cl₄ is reproduced. N₂O₄ favors the planar conformation, although the rotation barrier is overestimated at the theoretical levels used. The oxalate dianion is calculated to be more stable in the D_2d conformation; the experimental planar arrangement in the solid may be due to crystal packing forces. The preferences for one conformation over another are small; analysis indicates that different effects may predominate in each case: π stabilization for B₂F₄, hyperconjugation for B₂Cl₄, lone-pair interactions for N₂O₄, and electrostatic repulsions for C₂O.     

Reactions of tetrahydro-as-triazine-3(2H)-thiories with α, β-difunctional compounds

The results of allowing tetrahydro-as-triazine-3(2H)-thiones to react with various α,β-diiunctional compounds, such as, α-bromoethyl p-toluenesulfonate, chloroacetaldehyde, α-bromophenylacet-uldehyde, phenaeyl bromide, chloroacetonitrile, α-bromophenylaeelonitrile, and α-cyanobenzyl p-toluenesulfonate are discussed. These condensations give either a 5H-thiazolo[3,2-b]-as-triazine or a 2H-thiazolo[2,3-c]-as-triazine.     

Addition reactions of cyclooctatetraene with 1,3-diphenylisobenzofuran the benzene ring as dienophile in a [4+2] cycloaddition reaction

Addition reactions of cyclooctatetraene with 1,3-diphenylisobenzofuran resulted in the formation of three 1:1 cycloadducts, 1, 2, and 3, and a 1:2 cycloadduct, 4. Single crystal x-ray analysis established 3 to be a cage compound formed by an unprecedented [4+2] cycloaddition reaction of 1 in which the double bond of the benzene moiety acted as the dienophile.     

Template synthesis in the nickel(II)–thiocarbohydrazide–propanone triple system

The complexing process proceeding in the Ni^II–thiocarbohydrazide (H₂N–H–NC(=S)–NH–NH₂)–propanone triple system in EtOH solution and nickel(II)hexacyanoferrate(II) gelatin-immobilized matrix has been studied. It has been found that in the first case, template synthesis leading, as a minimum, to formation of three coordination compounds of Ni^II with (N,N,S,S)-donor tetradentate ligands having NiL¹, NiL² and NiL³compositions where L¹ is 4,6,6-trimethyl-2,3,7,8-tetraazanonen-3-di(thiohydrazide)-1,9, L² is 4,6,6,12-tetrametyl-1,9-dithio-2,3,7,8,10,11-hexaazatridekadien-3,11-hydrazide-1 and L³ is 2,8,10,10,16-pentamethyl-5,13-dithio-3,4,6,7,11,12,14,15-octaazaheptadekatrien-2,7,15 is observed, whereas in the gelatin-immobilized matrix, a complexing process in the system considered does not occur.     

Calculation of the frequencies and intensities in the infrared and raman spectra of cyclopropenone

By using the values of the vibrational frequencies of normal and deuterated cyclopropenone (II-d₀ , II-d₂ ) and ¹⁶ O-and ¹⁸ O-substituted dimethylcyclopropenone (III) as -well as the infrared and Raman intensities of II a consistent set of force constants has been derived for the cyclopropenone skeleton. The derived values show that the zwitterionic form makes a substantial contribution to the electronic ground state of the molecule. The combined frequency and intensity calculation - simulation of the infrared and the Raman spectrum - is shown to be a good method for making a proper assignment of calculated and observed vibrations and deriving realistic sets of force constants.     

An NMR study of the rotational barriers in cobalt-stabilized carbocations: X-ray crystal structures of (η-C4Ph4)Co-(η-C5H4R), where R is CH3CO, CHO, CH(Bu)OH

Treatment of the aldehyde (η⁴-C₄Ph₄)Co(η⁵-C₅H₄-CHO) (4b) with tert-butyllithium or phenyllithium yields the secondary alcohols (η⁴-C₄Ph₄)Co(η⁵-C₅H₄-CH(R)OH), where R=tert-butyl (5) or phenyl (6). Protonation of 5 and 6 at −80 °C furnishes the deep purple, cobalt-stabilized cations, 7 and 8, respectively, both of which exhibit restricted rotation about the external C₅H₄-CHR⁺ linkage on the NMR time-scale. These data indicate a minimum value for the barrier to rotation of 15 kcal mol⁻¹, but it is certainly much higher, indicating a considerable degree of C-C double bond character. X-ray crystal structures of 4b, 5 and also of the ketone (η⁴-C₄Ph₄)Co(η⁵-C₅H₄-C(O)CH₃ (4a) are reported. The secondary alcohol 5 exhibits disorder in the solid state because of the presence of diastereomers as a consequence of the stereogenic center at the α-carbon and the clockwise or anticlockwise propeller orientations of the tetraphenylcyclobutadiene ligand.