Alpha-carbon Atom Research Articles

One‐Step Ethynylation of Silyl Enol Ether with Chlorosilylethyne.

AbstractFor Abstract see ChemInform Abstract in Full Text.

Tripyrrolylphosphine as a unique bridging ligand in the Rh6CO14(mu2-P(NC4H4)3) cluster: structure, bonding, fluxionality, thermodynamics, and kinetics studies.

Tripyrrolylphosphine reacts with the cluster Rh6CO15(NCMe) to afford the disubstituted Rh6CO14(mu2)-P(NC4H4)3) derivative (2) via the Rh6CO15P(NC4H4)3 intermediate (1) with eta(1)-P coordination. In the solid state, 2 has the phosphine occupying a bridging position where it is bonded to two neighboring Rh atoms in the Rh(6) octahedron through the P-atom and an approximately tetrahedral alpha-carbon atom of one of the pyrrolyl rings. This can be described by the interaction of an electron pair, associated with a negative charge on one of the canonical forms of the NC(4)H(4) ring, with the adjacent Rh center. (1)H NMR spectra show that the solid-state structure is retained in solution, but the phosphine is not rigid, and three distinctive dynamic processes are observed. Each of these represents independent hindered rotation of inequivalent pyrrolyl rings about P-N bonds, the ring involved in the interaction with the Rh(6) skeleton displaying the highest activation barrier with deltaH = 15.8 +/- 0.1 kcal mol(-1) and deltaS = 1.4 +/- 0.3 cal K(-1) mol(-1). The assignment has been confirmed by 1H TOCSY and EXSY experiments, and a mechanism is proposed. The formation of 2 from 1 is reversible in the presence of CO, which is highly unusual for bridged clusters. The kinetics of the forward and reverse reactions have been studied, and the values of DeltaH degrees and DeltaS degrees for formation of 2 (+1.3 +/- 0.5 kcal mol(-1) and -9 +/- 2 cal K(-1) mol (-1), respectively) show that the Rh-C bond in the bridge is comparable in strength with the Rh-CO bond it replaces. The intrinsic entropy of 2 is exceptionally unfavorable, overcoming the favorable entropy caused by CO release, and this allows the reversibility of bridge formation. The reactions proceed via a reactive intermediate that may involve agostic bonding of the ring. The reverse reaction has an exceedingly unfavorable activation entropy that emphasizes the unique nature of 2.

One-step ethynylation of silyl enol ether with chlorosilylethyne.

[reaction: see text] In the presence of GaCl(3), silyl enol ethers are ethynylated at the alpha-carbon atom with chlorotrimethylsilylethyne. This reaction can provide alpha-ethynylated aryl ketones possessing acidic alpha-protons without isomerization to conjugated allenyl ketones.

A sphere-based descriptor for matching protein structures.

This paper describes the use of a descriptor based on the number of alpha-carbon atoms within a sphere centered on the alpha-carbon in each amino acid residue in a protein. The descriptor can be used instead of the residue types in a dynamic programming algorithm, thus providing an efficient way of aligning protein structures. The method is applied to the alignment of protein families and to database searching. The results indicate that the method can quickly align protein sequences considering the 3D structure and can find proteins that are 3D structurally similar and dissimilar to the target protein.

Protein--protein docking of electron transfer complexes: cytochrome c oxidase and cytochrome c.

Electron transferring protein complexes form only transiently and the crystal structures of electron transfer protein--protein complexes involving cytochrome c could so far be determined only for the pairs of yeast cytochrome c peroxidase (CcP) with iso-1-cytochrome c (iso-1-cyt c) and with horse heart cytochrome c (cyt c). This article presents models from computational docking for complexes of cytochrome c oxidase (COX) from Paracoccus denitrificans with horse heart cytochrome c, and with its physiological counterpart cytochrome c552 (c552). Initial docking is performed with the FTDOCK program, which permits an exhaustive search of translational and rotational space. A filtering procedure is then applied to reduce the number of complexes to a manageable number. In a final step of structural and energetic refinement, the complexes are optimized by rigid-body energy minimization with the molecular mechanics package CHARMM. This methodology was first tested on the CcP:iso-1-cyt c complex, in which the complex with the lowest CHARMM energy has an RMSD from the crystal structure of only 1.8 A (C(alpha) carbon atoms). Notably, the crystal conformation has an even lower energy. The same procedure was then applied to COX:cyt c and COX:c552. The lowest-energy COX:cyt c complex is very similar to a docking model previously described for the complex of bovine cytochrome c oxidase with horse heart cytochrome c. For the COX:c552 complex, cytochrome c552 is found in two different orientations, depending on whether it is docked against COX from a two-subunit or from a four-subunit crystal structure, respectively. Both conformations are discussed critically in the light of the available experimental data.

Ab initio and experimental study on thermally degradable polycarbonates: the effect of substituents on the reaction rates.

Thermal elimination reactions on polycarbonates are investigated from both theoretical and experimental points of view, to obtain insight into the microscopic aspects that influence the reaction mechanism and rates. In particular, attention is focused on the influence of the type of substituents in the polymer chain on the reaction rates. Ab initio density functional theory calculations are performed on a series of model compound systems for the polycarbonates under study, in particular carbonates differing by the groups attached at the alpha and beta carbon atoms. Reactants, products, and transition states are optimized at the B3LYP/6-311g level of theory. The structures of the activated complex give insight into the mechanistic details of this type of E(i) elimination reactions. The C(alpha)-O bond dissociates before the C(beta)-H bond, developing some carbocation character in the transition state on the C(alpha) atom. The kinematics of the thermal decomposition reactions have been studied by means of transition state theory by construction of the microscopic partition functions. It turns out that the rates of the E(i) elimination reactions are increased by the presence of those substituents on the C(alpha) and C(beta) carbon atoms which are stabilizing the carbocation character in the transition state. In a second part, degradation temperatures have been experimentally measured for some polycarbonates through thermogravimetric analysis. It is investigated whether the relative rates of the model compound carbonate systems are representative of the behavior of the thermal degradation temperatures in polycarbonates. The study as presented here proves that ab initio calculations on small model systems, which are representative for the active area of the degradation process in polycarbonates, can provide insight into the principal ingredients that govern the reaction rates.

Visualizing protein conformational changes on a personal computer – alpha carbon pseudo bonding as a constraint for interpolation in internal coordinate space

A Java program has been developed to produce animations and movies of protein conformation changes. The animations, primarily intended for teaching purposes, are produced by visualizing a series of aligned structures interpolated between two forms of the same protein. To produce plausible intermediate structures, the interpolation is performed in internal coordinate space and uses a simple constraint to avoid the production of artifactual movements of the protein backbone. This constraint involves the introduction of ‘pseudo’ bonds linking the protein alpha carbon atoms. All of the steps from alignment of initial structures to the production of AVI movies can be performed on readily available personal computers.

Elucidating protein secondary structures using alpha-carbon recurrence quantifications.

Secondary structures of proteins were studied by recurrence quantification analysis (RQA). High-resolution, 3-dimensional coordinates of alpha-carbon atoms comprising a set of 68 proteins were downloaded from the Protein Data Bank. By fine-tuning four recurrence parameters (radius, line, residue, separation), it was possible to establish excellent agreement between percent contribution of alpha-helix and beta-sheet structures determined independently by RQA and that of the DSSP algorithm (Define Secondary Structure of Proteins). These results indicate that there is an equivalency between these two techniques, which are based upon totally different pattern recognition strategies. RQA enhances qualitative contact maps by quantifying the arrangements of recurrent points of alpha carbons close in 3-dimensional space. For example, the radius was systematically increased, moving the analysis beyond local alpha-carbon neighborhoods in order to capture super-secondary and tertiary structures. However, differences between proteins could only be detected within distances up to about 6-11 A, but not higher. This result underscores the complexity of alpha-carbon spacing when super-secondary structures appear at larger distances. Finally, RQA-defined secondary structures were found to be robust against random displacement of alpha carbons upwards of 1 A. This finding has potential import for the dynamic functions of proteins in motion.

Selective inhibition of human inducible nitric oxide synthase by S-alkyl-L-isothiocitrulline-containing dipeptides.

The aim of this study was to investigate the structure-activity relationship of S-alkyl-L-isothiocitrulline-containing dipeptides towards three partially purified recombinant human nitric oxide synthase (NOS) isozymes, as well as the effects of these compounds on cytokine-induced NO production by human DLD-1 cells. In an in vitro assay, S-methyl-L-isothiocitrulline (L-MIT) was slightly selective for human neuronal NOS (nNOS) over the inducible (iNOS) or endothelial (eNOS) isozyme, but the combination of a hydrophobic L-amino acid (L-Phe, L-Leu or L-Trp) with L-MIT dramatically altered the inhibition pattern to give selective iNOS inhibitors. Introduction of a hydroxy, nitro, amino or methoxy group at the para position of the aromatic ring of L-MIT-L-Phe (MILF) decreased the selectivity and inhibitory potency. A longer or larger S-alkyl group also decreased the selectivity and potency. Dixon analysis showed that all of the dipeptides were competitive inhibitors of the three isoforms of human NOS. The enzymatic time course curves indicated that MILF was a slow binding inhibitor of human iNOS. These results suggest that the human NOS isozymes have different-sized cavities in the binding site near the position to which the C-terminal of L-arginine binds, and the cavity of iNOS is hydrophobic. Interestingly, L-MIT-D-Phe (MIDF) showed little inhibitory activity or selectivity, suggesting that the cavity of human iNOS is located in a well-defined direction from the alpha carbon atom. NO production in cytokine-stimulated human DLD-1 cells was measured with a fluorescent indicator, DAF-FM. MILF, L-MIT-L-Trp(-CHO) (MILW) and L-MIT-L-Tyr (MILY) showed more potent activity than L-MIT in this whole-cell assay. Thus, S-alkyl-L-isothiocitrulline-containing dipeptides are selective inhibitors of human iNOS, and work efficiently in cell-based assay.

A new class of dianionic sulfur-ylides: alkylenediazasulfites.

The compounds [[(thf)Li2-[H2CS(NtBu)2]]2] (1) and [((thf)Li2[(Et)-(Me)CS(NtBu)2])2] (2) can be synthesized in a two-step reaction. Firstly addition of an alkyllithium to sulfur diimide gives the diazaalkylsulfinate [RS(NtBu)2] (R =Me, sBu). In a second step the alpha-carbon atom in R is metalated with one equivalent of methyllithium to give the S-ylides. This new class of compounds can be rationalized as sulfite analogues, in which two oxygen atoms are each isoelectronically replaced by a NtBu group and the remaining oxygen atom is replaced by a CR2 group. Similar to Corey's S-ylides (R2(O)S+-CR2) and Wittig's phosphonium ylides (R3P+ - -CR2), these molecules contain a positively charged sulfur atom next to a carbanionic center. Therefore nucleophilic addition reactions of the carbon atom are feasible. The reaction of a sulfur diimide with the anionic carbon center in [H2CS-(NtBu)2]2- gives the intermediate alkylbis(diazasulfinate) [(tBuN)2SCH2S(NtBu)2]2-. The acidity of the hydrogen atoms at the bridging CH2 group is high enough to give, upon deprotonation, the [(tBuN)2SCHS(NtBu)2]3- trianion in [[(thf)Li3[(tBuN)2SCHS(NtBu)2]]2] (3). In [(Et)(Me)CS(NtBu)2]2 the nucleophilic carbon atom is sterically hindered and transimidation instead of deprotonation is observed. In a complex redox process [(thf)6Li6S((NtBu)3S]2] is recovered. The two new classes of compounds broaden the rich coordination chemistry of the triazasulfites by the introduction of a hard carbon center.

Peptoid - peptide hybrids that bind Syk SH2 domains involved in signal transduction.

Peptoid-peptide hybrids are oligomeric peptidomimetics that contain one or more N-substituted glycine residues. In these hybrids, the side chains of one or several amino acids are "shifted" from the alpha-carbon atom to the amide nitrogen atom. A library of phosphorylated peptoid-peptide hybrids derived from the sequence pTyr-Glu-Thr-Leu was synthesized and tested for binding to the tandem SH2 domain of the protein tyrosine kinase Syk. A considerable influence of the side chain position was observed. Compounds 19-21, 24, and 25 comprising a peptoid NpTyr and/or NGlu residue did not show any binding. Compounds 22, 23, and 26 containing an NhThr (hThr=homothreonine) and/or NLeu peptoid residue showed binding with IC(50) values that were only five to eight times higher than that of the tetrapeptide lead compound 18. These data show that side chain shifting is possible with retention of binding capacity, but only at the two C-terminal residues of the tetramer. This method of a peptoid scan using peptoid-peptide hybrids appears to be very useful to explore to what extent a peptide sequence can be transformed into a peptoid while retaining its affinity.

GaCl3-promoted ethenylation of silylated beta-dicarbonyl compound with silylethyne. Synthesis of ethenylmalonate.

[reaction: see text]. In the presence of GaCl3, silyl enol ethers derived from alpha-substituted beta-ketoesters or malonates are ethenylated at the alpha-carbon atom with trimethylsilylethyne in high yields. Ethenylmalonates can also be synthesized by this method.

Control of peptide conformation by the Thorpe-Ingold effect (C alpha-tetrasubstitution).

The preferred conformations of peptides heavily based on the currently extensively exploited achiral and chiral alpha-amino acids with a quaternary alpha-carbon atom, as determined by conformational energy computations, crystal-state (x-ray diffraction) analyses, and solution ((1)H-NMR and spectroscopic) investigations, are reviewed. It is concluded that 3(10)/alpha-helical structures and the fully extended (C(5)) conformation are preferentially adopted by peptide sequences characterized by this family of amino acids, depending upon overall bulkiness and nature (e.g., whether acyclic or C(alpha) (i) <--> C(alpha) (i) cyclized) of their side chains. The intriguing relationship between alpha-carbon chirality and bend/helix handedness is also illustrated. gamma-Bends and semiextended conformations are rarely observed. Formation of beta-sheet structures is prevented.

RETRO ABRAMOV VS. REARRANGEMENT PATH COMPETITION IN HYDROXYPHOSPHONATE DECOMPOSITION

1-hydoxyphosphonates in the presence of aliphatic amine undergo two competitive processes: retro Abramov reaction and intramolecular hydroxyphosphonate-phosphate rearrangement. Both reaction rates and their ratio strongly depend on the nature of the substituent on a alpha carbon atom. Kinetic experiments indicate that two reactions proceed via common transition state.

Solid-phase synthesis and structural characterization of highly substituted hydroxyproline-based 2,5-diketopiperazines

Two general solid-phase methods for the synthesis of a new class of 2,5-diketopiperazines (DKPs) containing the trans-4-hydroxy-L-proline amino acid residue (Hyp) have been developed. An N-protected hydroxyproline methyl ester was linked through the hydroxyl function to the Ellman resin. The synthesis procedures were conceived to enable a sequence of Hyp alkylation, Hyp N-acylation, cyclization, and amide bond alkylation. Up to three different centers of molecular diversity were introduced around the DKP scaffold. Highly functionalized bicyclic compounds were obtained in good yield and purity. The alkylation of hydroxyproline alpha CH was performed without control of the diastereoselectivity. During the final alkylation of the backbone, amide bond epimerization at the alpha-carbon atoms of the two amino acid residues was observed. The structures of representative DKPs were elucidated with multidimensional NMR experiments. The described reaction pathways can be applied to the identification of heterocyclic molecule inhibitors to diverse enzyme targets.

A copper(I) oxygenation precursor in the entatic state: two isomers of a copper(I) compound of a rigid tetradentate ligand

Oxygenation of [CuI(L1)(NC-CH3)]+ (L1 = dimethyl 2,4-bis(2-pyridinyl)-3,7-diazabicyclo-[3.3.1]-nonane-9-on-1,5-dicarboxylate) leads to a relatively stable mu-peroxo-dicopper(II) product. The stability of this type of oxygenation product has been shown before to be the result of the square pyramidal geometry of L1; preorganization by a dinucleating ligand has been shown to increase the stability of the mu-peroxo-dicopper(II) compound. The structural data presented here indicate that destabilization of the copper(I) precursor is another important factor. There are two isomers of [CuI(L1)(NCCH3)]+; one is yellow, and the other is red. X-ray crystallography indicates that one pyridinyl donor is not coordinated in the yellow compound and that the red compound is 5-coordinate. In the light of the X-ray structure of the metal-free ligand and that of the corresponding copper(II) compound, it emerges that the ligand cavity is well suited for copper(II), whereas the copper(I) compounds are highly strained. This is supported by 1H NMR spectra of the copper(I) species where a fast dynamic process leads to line broadening and by electrochemical data, which indicate that the copper(II) products are exceptionally stable. Also presented are structural (copper(II)), electrochemical, and spectroscopic data (1H NMR, copper(I)) of the derivative [Cu(L2)(X)]n+ with a methyl substituent at the alpha-carbon atom of the two coordinated pyridinyl groups (L2 = dimethyl 2,4-bis(2-pyridinyl-6-methyl)-3,7-diazabicyclo-[3.3.1]-nonane-9-on-1,5-dicarboxylate). There are two structural forms of [CuII(L2)(X)]n+ (X = NCCH3, Cl), which depend on the steric demand of the fifth donor X. For both, van der Waals repulsion leads to a destabilization of the copper(II) products, and this is also evident from an increase in the reduction potential (-110 mV vs. -477 mV, Ag/AgNO3).

(alphaMe)Aun: a highly lipophilic, chiral, Calpha-tetrasubstituted alpha-amino acid. Incorporation into model peptides and preferred conformation.

Using a chemo-enzymatic approach we prepared the highly lipophilic, chiral, Calpha-methylated alpha-amino acid (alphaMe)Aun. Two series of terminally protected model peptides containing either D-(alphaMe)Aun in combination with Aib or L-(alphaMe)Aun in combination with Gly were synthesized using solution methods and fully characterized. A detailed solution conformational analysis, based on FT-IR absorption, 1H NMR and CD techniques, allowed us to determine the preferred conformation of this amino acid and the relationship between chirality at its alpha-carbon atom and screw sense of the helix that is formed. The results obtained strongly support the view that D-(alphaMe)Aun favors the formation of the left-handed 3(10)-helical conformation.

Preferred solution conformation of peptides rich in the lipophilic, chiral, C(alpha)-methylated alpha-amino acid (alpha Me)Aoc.

The lipophilic, chiral, C(alpha)-methylated alpha-amino acid L-(alphaMe)Aoc (2-methyl-2-amino-octanoic acid) was prepared using a chemo-enzymatic approach. Two series of terminally protected model peptides, from dimer through to hexamer, containing L-(alphaMe)Aoc in combination with either Gly or Aib, were synthesized by solution methods and were fully characterized. A solution conformational analysis, based on FT-IR absorption, 1H-NMR and circular dichroism (CD) techniques, was performed with the aim at determining the preferred conformation of this novel amino acid and the relationship between chirality at its alpha-carbon atom and screw sense of the helix that is formed. The results obtained strongly support the view that L-(alphaMe)Aoc favours the formation of the right-handed 3(10)-helical conformation.

Algorithmic approach to quantifying the hydrophobic force contribution in protein folding.

Though the electrostatic, ionic, van der Waals, Lennard-Jones, hydrogen bonding, and other forces play an important role in the energy function minimized at a protein's native state, it is widely believed that the hydrophobic force is the dominant term in protein folding. Here we attempt to quantify the extent to which the hydrophobic force determines the positions of the backbone alpha-carbon atoms in PDB data, by applying Monte-Carlo and genetic algorithms to determine the predicted conformation with minimum energy, where only the hydrophobic force is considered (i.e. Dill's HP-model, and refinements using Woese's polar requirement). This is done by computing the root mean square deviation between the normalized distance matrix D = (di,j) (di,j is normalized Euclidean distance between residues ri and rj) for PDB data with that obtained from the output of our algorithms. Our program was run on the database of ancient conserved regions drawn from GenBank 101 generously supplied by W. Gilbert's lab, as well as medium-sized proteins (E. Coli RecA, 2reb, Erythrocruorin, 1eca, and Actinidin 2act). The root mean square deviation (RMSD) between distance matrices derived from the PDB data and from our program output is quite small, and by comparison with RMSD between PDB data and random coils, allows a quantification of the hydrophobic force contribution. A preliminary version of this paper appeared at GCB'99 (http:¿bibiserv.techfak.uni-bielefeld.de/gcb9 9/).

Electrochemical behaviour of amino acids on Pt(hkl). A voltammetric and in situ FTIR study

The electrochemical oxidation of serine and alanine was performed at Pt(100) and Pt(110) electrodes and analysed by means of FTIR spectroscopy and cyclic voltammetry. The open circuit adsorption of both amino acids was also investigated. The oxidation of serine gives rise to the formation of two types of strongly adsorbed species, COads coming from the CH2OH group and CNads, which appears as a consequence of the dehydrogenation of the amino group. These species can be isolated at the surface of both electrodes during open-circuit adsorption experiments. The oxidation of alanine also yields adsorbed cyanide adlayers on Pt(100) and Pt(110) electrodes. However, the amount of adsorbed cyanide formed from this amino acid is much lower than that formed in the case of serine. Thus, the presence of the methyl group bonded to the alpha carbon atom seems to stabilise the amino acid against its oxidation on both Pt(100) and Pt(110) electrodes.