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.     

Allyl complexes of dicyclopentadienyl-niobium(III) and -tantalum(III)

The synthesis and the properties of the complexes Cp₂TaCl₂, Cp₂M(allyl), Cp₂M(1-methylallyl) and Cp₂M(2-methylallyl) with M  Nb, Ta are described. The complex Cp₂TaCl₂ has one unpaired electron per tantalum atom, while the allyl complexes are diamagnetic. The IR and PMR spectra indicate that the allyl group is π-bonded to the metal. The mass spectra of the complexes are discussed; the thermal stability of the Cp₂Nb- and Cp₂Ta-(allyl) complexes was investigated by differential thermal analysis. The properties of the niobium and tantalum complexes are compared with those of the corresponding titanium complexes.     

Dipole moments of compounds containing a cobalttin bond

The molecular electric dipole moments are reported for the series of tin-substituted tetracarbonyl cobalt compounds R_nY_m?nSn{Co(CO)₄}_4?m (m = 1–3; n ? m; R = alkyl, phenyl; Y = halogen). The effect of the substituents at the tin atom on the nature of the CoSn bond is established on calculating the (CO)₄CoSn group dipole moments. It is shown that the charge transfer in the CoSn bond is mainly determined by the inductive properties of the ligands attached to tin.     

Effect of electric field strength and exposure time on epoxy and high density polyethylene measured by positron annihilation lifetime

Using the positron annihilation lifetime technique, the annihilation parameters have been measured for epoxy and high density polyethylene (HDPE) as a function of AC electric field strength and the exposure time. The lifetime spectra have been resolved into three components, the longest component (I₃₃) is attributed to the pick-off annihilation of o-Ps in the amorphous regions. The intermediate one (I₂₂) is due to the annihilation of free positrons, while the shorter component (I₁₁) stems from self annihilation of p-Ps. In HDPE, the o-Ps parameters ₃ andI ₃ are measured as a function of electric field strengths in the range from 10 to 100 kV/cm exposed for 24 hours. A decrease inI ₃ of 8% is observed from zero to 50 kV/cm followed by an increase of the same order from 50 to 100 kV/cm. By investigating the effect of the exposure time from 2 to 24 hours at 16 and 50 kV/cm, the effect is confirmed and is attributed to the inhibition of o-Ps formation at lower field strength. In epoxy, the effect or exposure time onI ₃ at 166 and 133 kV/cm shows a similar behavior as in HDPE. At 133 kV/cmI ₃ decreases by only 2.5%. On the other hand, the changes in ₃ occur at short exposure times. Again at large times the saturation is obtained. These effects are attributed to the expansion of free volume (increase of ₃) competing at longer exposure times with other phenomena, such as liberation of free radicals, which reduce the o-Ps intensityI ₃ through the conversion to p-Ps. The reactions between o-Ps and free radicals might also lead to free positrons, which could explain the increase ofI ₂ and the decrease of ₃ at longer exposure times.     

Determination of reducing end sugar residues in oligo- and polysaccharides by gas-liquid chromatography

Reducing end sugar residues in maltodextrins and arabinoxylans are determined as alditol acetates by gas-liquid chromatography following reduction, acid hydrolysis and acetylation of the samples. After this conversion to alditol acetates, the reducing end sugars are thus separated from their acetylated aldose counterparts. The method allows to identify individual reducing end sugars quantitatively and is a good alternative for colorimetric reducing sugar assays and 1H-NMR analysis. To demonstrate the advantages of the method, an application in a study of enzymic solubilisation and degradation of water unextractable arabinoxylan from a flour squeegee fraction is described.     

Elimination of methane from protonated acetaldehyde: The Ab initio transition state

The transition state (TS) for loss of CH₄ from protonated acetaldehyde has been located at the second-order Moller-Plesset (MP2)/6-31G(d,p) level of theory. The activation energy is predicted to be 263.9 kJ/mol starting from the more stable form (methyl and hydrogen E) and 261.6 kJ/mol starting from the less stable form (methyl and hydrogen Z) that is required for reaction. The products (methane and the formyl ion) are predicted to lie 136.6 kJ/mol below the TS for their formation. MP2 methods underestimate the heats of formation of both the TS and the reaction products by about 40 kJ/mol when compared with experiment. Restricted Hartree-Fock (RHF) calculations give much more accurate relative energies. The MP2 TS leads directly to fragmentation and is described as a protonation of the methyl group by the acidic proton on oxygen. Under RHF theory the reaction is stepwise. An RHF TS similar to the MP2 TS leads to a nonclassical intermediate (which is stable at this level of theory) that has one of the C---H bonds protonated. This mechanism (protonation of an alkyl group) appears to be a general one for high energy 1,2 eliminations from organic cations. (J Am Soc Mass Spectrom 1994, 5, 1102-1106)     

Amidinoethylation—a new reaction—IV : The amidinoethylation of alcohols: a facile synthesis of 3-alkoxy-N,N'-substituted-propanamidines

The amidinoethylation of alcohols takes place by the addition of sodium alkoxides 2 (R¹ = Me, Et) to the CC double bond of a variety of N,N'-substituted-propenamidines 1 (Method A). This illustrates the activation of the CC double bond by the conjugated amidine function and provides a new class of Michael acceptors for alcohols. However, this activation is poorer than with other nucleophiles or Michael acceptors. The amidinoethylation makes available 3-alkoxy-N,N'-substituted-amidines not easily accessible by other classical methods. However, it is demonstrated that the general N,N'-substituted-amidine synthesis via the nitrilium salts can also apply to nitrile compounds having an alkoxygroup present on the molecule (method B). Since the cyanoethylation of alcohols (4) is a very fast and facile reaction the method B is the preferred strategy for the synthesis of 3-alkoxy-N,N'-substituted-propanamidines 3.     

Thermal decompositions of N-methylpyridinium,quinolinium, isoquinolinium and phenanthridinium salts in a mass spectrometer. Evidence for a specific HI elimination and for an oxidation to amides

The mass spectra of some N-methylpyridinium, quinolinium, isoquinolinium and phenanthridinium salts (R⁺X^?)

1 The salt will be represented by R⁺X^? or RX, R⁺ being the organic moiety, with its associated mass and X- the inorganic anion.

are analyzed (X^? = I^? or ClO₄^?). For X^? = I^?, thermal decomposition gives rise mainly to the superimposed spectra of CH₃I and the free base. Hence, iodide salts cannot be determined specifically by their mass spectra. When an α-methyl group is present, e.g. 2-methylpyridinium methiodide, elimination of HI becomes an important thermal process. For X^? = ClO₄^?, the same pattern is observed, but in addition a generally important peak at [R + 15] is present. This peak is due to the oxidation, mainly α to the nitrogen of the organic moiety by the ClO₄^? ion, giving rise to the corresponding amide. In some cases, chlorination of the organic moiety has been observed as well as double oxidation. The thermal processes for the perchlorate salts are characteristic and are useful in the elucidation of the quaternary structure.     

Dispersion phenomena in reactors for flow analysis

Both coiled open tubular reactors and packed-bed reactors can be used in flow analysis. Band broadening and pressure drop in these reactors are discussed. Theoretical analysis shows that packed-bed reactors are to be preferred. It is shown that for a given residence time and equal band-broadening values the pressure drop over a packed-bed reactor is lower than over a coiled open tubular reactor. Rules for optimal design are given for coiled tubular reactors and packed-bed reactors. The application of both reactors is shown for the spectrophotometric determination of phosphate with a vanadomolybdate reagent yielding a yellow colour.