Mimicking the two-dimensional spectrochemical series using density functional computations

With tetragonal distortions of tetrahedral d2 complexes as examples, nonadditive and additive ligand fields are compared computationally, using Kohn-Sham density functional theory (KS-DFT) and ligand-field theory to obtain 45 linear, parametrical equations. For each complex, a "data" reduction from three nonadditive-field parameters to two parameters of the additive field occurs. The complexes V and CrX4- (where X=F, Cl, Br, I) provide the two-dimensional spectrochemical series of the sigma and pi AOM parameters, which are known semiempirically for the halide ligands. The same parametrical results can be obtained from the Kohn-Sham orbital energies of the "average of configuration" computation.     

Synthesis of 5,6-dihydro-4H-thiopyran-4-ones

The anions of 1,4-diaryl-3-buten-2-ones 1 reacts with arylisothiocyanates, yielding intermediates 4 which can ring close to 5,6-dihydro-4H-thiopyran-4-ones 5 . Under similar reaction conditions ethyl 3-oxo-4-pentenoates 7 gives the 6-spiropyrans 9 . Methylation of 3 gives the S-methylated open form 6 .     

Using model complexes to augment and advance metalloproteinase inhibitor design

The tetrahedral zinc complex [(Tp(Ph,Me))ZnOH] (Tp(Ph,Me) = hydrotris(3,5-phenylmethylpyrazolyl)borate) was combined with 2-thenylmercaptan, ethyl 4,4,4-trifluoroacetoacetate, salicylic acid, salicylamide, thiosalicylic acid, thiosalicylamide, methyl salicylate, methyl thiosalicyliate, and 2-hydroxyacetophenone to form the corresponding [(Tp(Ph,Me))Zn(ZBG)] complexes (ZBG = zinc-binding group). X-ray crystal structures of these complexes were obtained to determine the mode of binding for each ZBG, several of which had been previously studied with SAR by NMR (structure-activity relationship by nuclear magnetic resonance) as potential ligands for use in matrix metalloproteinase inhibitors. The [(Tp(Ph,Me))Zn(ZBG)] complexes show that hydrogen bonding and donor atom acidity have a pronounced effect on the mode of binding for this series of ligands. The results of these studies give valuable insight into how ligand protonation state and intramolecular hydrogen bonds can influence the coordination mode of metal-binding proteinase inhibitors. The findings here suggest that model-based approaches can be used to augment drug discovery methods applied to metalloproteins and can aid second-generation drug design.     

Asymmetric catalytic Mannich reactions catalyzed by urea derivatives: enantioselective synthesis of beta-aryl-beta-amino acids

Highly enantioselective addition reactions between silyl ketene acetals and N-Boc aldimines are catalyzed by the thiourea-based catalyst 1c. Extraordinary scope is observed in this methodology with regard to the imine substrate, with aryl and heteroaromatic derivatives generally affording nearly quantitative yields of beta-amino ester product in up to 98% enantioselectivity.     

Ruthenium Complexes Containing "Noninnocent" o-Benzoquinone Diimine/o-Phenylenediamide(2-) Ligands. Synthesis and Crystal Structure of the Nitrido-Bridged Complex [{LRu(o-C(6)H(4)(NH)(2))}(2)(&mgr;-N)](PF(6))(2).3CH(3)CN.C(6)H(5)CH(3)

Reaction of LRu(III)Cl(3) (L = 1,4,7-trimethyl-1,4,7-triazacyclononane) with 1,2-phenylenediamine (opdaH(2)) in H(2)O in the presence of air affords [LRu(II)(bqdi)(OH(2))](PF(6)) (1), where (bqdi) represents the neutral ligand o-benzoquinone diimine. From an alkaline methanol/water mixture of 1 was obtained the dinuclear species [{LRu(II)(bqdi)}(2)(&mgr;-H(3)O(2))](PF(6))(3) (1a). The coordinated water molecule in 1 is labile and can be readily substituted under appropriate reaction conditions by acetonitrile, yielding [LRu(II)(bqdi)(CH(3)CN)](PF(6))(2) (2), and by iodide and azide anions, affording [LRu(II)(bqdi)I](PF(6)).0.5H(2)O (3) and [LRu(bqdi)(N(3))](PF(6)).H(2)O (4), respectively. Heating of solid 4 in vacuum at 160 degrees C generates N(2) and the dinuclear, nitrido-bridged complex [{LRu(o-C(6)H(4)(NH)(2))}(2)(&mgr;-N)](PF(6))(2) (5). Complex 5 is a mixed-valent, paramagnetic species containing one unpaired electron per dinuclear unit whereas complexes 1-4 are diamagnetic. The crystal structures of 1, 1a.3CH(3)CN, 3, 4.H(2)O, and 5.3CH(3)CN.0.5(toluene) have been determined by X-ray crystallography: 1 crystallizes in the monoclinic space group P2(1)/m, Z = 2, with a = 8.412(2) ?, b = 15.562(3) ?, c = 10.025 ?, and beta = 109.89(2) degrees; 1a.3CH(3)CN, in the monoclinic space group C2/c, Z = 4, with a = 19.858(3) ?, b = 15.483(2) ?, c = 18.192(3) ?, and beta = 95.95(2) degrees; 3, in the orthorhombic space group Pnma, Z = 4, with a = 18.399(4) ?, b = 9.287(2) ?, and c = 12.052(2) ?, 4.H(2)O, in the monoclinic space group P2(1)/c, Z = 4, with a = 8.586(1) ?, b = 15.617(3) ?, c = 16.388(5) ?, and beta = 90.84(2) degrees; and 5.3CH(3)CN.0.5(toluene), in the monoclinic space group P2(1)/c, Z = 4, with a = 15.003(3) ?, b = 16.253(3) ?, c = 21.196(4) ?, and beta = 96.78(3) degrees. The structural data indicate that in complexes 1-4 the neutral o-benzoquinone diimine ligand prevails. In contrast, in 5 this ligand has predominantly o-phenylenediamide character, which would render 5 formally a mixed-valent Ru(IV)Ru(V) species. On the other hand, the Ru-N bond lengths of the Ru-N-Ru moiety at 1.805(5) and 1.767(5) ? are significantly longer than those in other crystallographically characterized Ru(IV)=N=Ru(IV) units (1.72-1.74 ?). It appears that the C(6)H(4)(NH)(2) ligand in 5 is noninnocent and that formal oxidation state assignments to the ligands or metal centers are not possible.     

Beta-sheet preferences from first principles

The natural amino acids have different preferences of occurring in specific types of secondary protein structure. Simulations are performed on periodic model beta-sheets of 14 different amino acids, at the level of density functional theory, employing the generalized gradient approximation. We find that the statistically observed beta-sheet propensities correlate very well with the calculated binding energies. Analysis of the calculations shows that the beta-sheet propensities are determined by the local flexibility of the individual polypeptide strands.     

Linear programs with an additional reverse convex constraint

A constraintg(x)0 is said to be a reverse convex constraint if the functiong is continuous and strictly quasi-convex. The feasible regions for linear programs with an additional reverse convex constraint are generally non-convex and disconnected. It is shown that the convex hull of the feasible region is a convex polytope and, as a result, there is an optimal solution on an edge of the polytope defined by only the linear constraints. The only possible edges which can contain such an optimal solution are characterized in relation to the best feasible vertex of the polytope defined by only the linear constraints. This characterization then provides a finite algorithm for finding a globally optimal solution.Research supported by NSF Grant ENG76-12250 and ONR Contract N00014-78-C-0428.     

An average-of-configuration method for using Kohn-Sham density functional theory in modeling ligand-field theory

The Amsterdam Density Functional (ADF) package has been used to constrain Kohn-Sham DFT in such a fashion that a transition from KS-DFT to ligand-field theory in the form of the parametrical d(q)() model is completely well-defined. A relationship is established between the strong-field approximation of the parametrical d(2) model for the tetrahedral complexes VCl(4)(-) and VBr(4)(-) and certain fixed-orbital ADF-computed energies. In this way values for all the parameters of the d(2)() model may be computed, thus allowing the ADF results to be expressed in terms of a KS-DFT energy matrix that can be diagonalized. This means that the KS-DFT deficiency with regard to computation of nondiagonal elements has been overcome and the KS-DFT eigenenergies have become available through the KS-DFT mimicking of the ligand-field plus repulsion model. By using mutually orthogonal strong-field energy matrices, the mimicking has been further elucidated. The computed values for the empirical parameters of VCl(4)(-) and VBr(4)(-) are in good agreement with experimental data. The spectrochemical and the nephelauxetic series have been computed by including the remaining halide complexes and the quantitatively special position of F(-)() among the halides corroborated for both series.     

Explorative data analysis of two-dimensional electrophoresis gels

Methods for classification of two-dimensional (2-DE) electrophoresis gels based on multivariate data analysis are demonstrated. Two-dimensional gels of ten wheat varieties are analyzed and it is demonstrated how to classify the wheat varieties in two qualities and a method for initial screening of gels is presented. First, an approach is demonstrated in which no prior knowledge of the separated proteins is used. Alignment of the gels followed by a simple transformation of data makes it possible to analyze the gels in an automated explorative manner by principal component analysis, to determine if the gels should be further analyzed. A more detailed approach is done by analyzing spot volume lists by principal components analysis and partial least square regression. The use of spot volume data offers a mean to investigate the spot pattern and link the classified protein patterns to distinct spots on the gels for further investigation. The explorative approach in analysis of 2-D gels makes it possible, in a fast and convenient way, to screen many gels in order to determine the protein patterns that form clusters and could be selected for further examination.     

UV absorption spectra of HO2, CH3O2, C2H5O2, and CH3C(O)CH2O2 radicals and mechanism of the reactions of F and Cl atoms with CH3C(O)CH3

Pulse radiolysis techniques were used to measure the gas phase UV absorption spectra of the title peroxy radicals over the range 215–340 nm. By scaling to σ(CH₃O₂)_{240 nm} = (4.24 ± 0.27) × 10^?18, the following absorption cross sections were determined: σ(HO₂)_{240 nm} = 1.29 ± 0.16, σ(C₂H₅O₂)_{240 nm} = 4.71 ± 0.45, σ(CH₃C(O)CH₂O₂)_{240 nm} = 2.03 ± 0.22, σ(CH₃C(O)CH₂O₂)_{230 nm} = 2.94 ± 0.29, and σ(CH₃C(O)CH₂O₂)_{310 nm} = 1.31 ± 0.15 (base e, units of 10^?18 cm² molecule^?1). To support the UV measurements, FTIR‐smog chamber techniques were employed to investigate the reaction of F and Cl atoms with acetone. The F atom reaction proceeds via two channels: the major channel (92% ± 3%) gives CH₃C(O)CH₂ radicals and HF, while the minor channel (8% ± 1%) gives CH₃ radicals and CH₃C(O)F. The majority (>97%) of the Cl atom reaction proceeds via H atom abstraction to give CH₃C(O)CH₂ radicals. The results are discussed with respect to the literature data concerning the UV absorption spectra of CH₃C(O)CH₂O₂ and other peroxy radicals. © 2002 Wiley Periodicals, Inc. Int J Chem Kinet 34: 283–291, 2002