Relative stability of major types of beta-turns as a function of amino acid composition: a study based on Ab initio energetic and natural abundance data

Folding properties of small globular proteins are determined by their amino acid sequence (primary structure). This holds both for local (secondary structure) and for global conformational features of linear polypeptides and proteins composed from natural amino acid derivatives. It thus provides the rational basis of structure prediction algorithms. The shortest secondary structure element, the beta-turn, most typically adopts either a type I or a type II form, depending on the amino acid composition. Herein we investigate the sequence-dependent folding stability of both major types of beta-turns using simple dipeptide models (-Xxx-Yyy-). Gas-phase ab initio properties of 16 carefully selected and suitably protected dipeptide models (for example Val-Ser, Ala-Gly, Ser-Ser) were studied. For each backbone fold most probable side-chain conformers were considered. Fully optimized 321G RHF molecular structures were employed in medium level [B3LYP/6-311++G(d,p)//RHF/3-21G] energy calculations to estimate relative populations of the different backbone conformers. Our results show that the preference for beta-turn forms as calculated by quantum mechanics and observed in Xray determined proteins correlates significantly.     

Molecular orbital studies on the conformation of GABA (γ-aminobutyric acid)

In distinction to Extended Hückel Theory which predicts as the most stable conformation of free zwitterionic GABA a totally extended form, PCILO and SCF ab initio studies show that the intrinsically preferred conformation of the isolated molecule is a highly folded one, resulting from strong interactions between the two charged ends. Computations are also carried out for hydrated GABA in the supermolecule approach allowing moreover for the flexibility of binding of some of the water molecules of the first hydration shell. They predict the coexistence in solution of a large number of conformations showing different degrees of folding (or extension), a result confirmed by recent NMR studies. This and a number of similar results show that we have to adapt our thinking on the role of conformations in pharmacological activity to this situation, which was frequently obscured by the more abundant results of X-ray crystallography yielding a single conformation.     

Molecular conformation search by distance matrix perturbations

Three-dimensional molecular structure is fundamental in chemical function identification and computer-aided drug design. The enumeration of a small number of feasible conformations provides a rigorous way to determine the optimal or a few acceptable conformations. Our contribution concerns a heuristic enhancement of a method based on distance geometry, typically in relation with experiments of the NMR type. Distance geometry has been approached by different viewpoints; ours is expected to help in several subtasks arising in the process that determines 3D structure from distance information. More precisely, the input to our algorithm consists of a set of approximate distances of varying precision; some are specified by the covalent structure and others by Nuclear Magnetic Resonance (NMR) experiments (or X-ray crystallography which, however, requires crystallization). The output is a valid tertiary structure in a specified neighborhood of the input. Our approach should help in detecting outliers of the NMR experiments, and handles inputs with partial information. Moreover, our technique is able to bound the number of degrees of freedom of the conformation manifold. We have used numerical linear algebra algorithms for reasons of speed, and because they are well-implemented, fully documented and widely available. Our main tools include, besides distance matrices, structure-preserving matrix perturbations for minimizing singular values. Our MATLAB (or SCILAB) implementation is described and illustrated.AMS subject Classification: 92E10 Molecular structure, 92C40 Biochemistry, molecular biology, 65F15 Eigenvalues, eigenvectors, 15A18 Eigenvalues, singular values, and eigenvectors     

New synthetic pathways into dithiazolyl radicals: Preparation and characterisation of 3′-methyl-benzo-1,3,2-dithiazolyl, M’BDTA

A general three-step synthesis to a range of benzo-fused-1,3,2-dithiazolylium salts bearing both electron-withdrawing (CN) and electron-donating (Me) groups is described. This methodology has also been extended to pyridyl derivatives and offers a potential route to a diversity of 1,3,2-dithiazolylium rings and their corresponding 1,3,2-dithiazolyl free radicals. The key steps in the reaction are treatment of a substituted 1,2,-dichlorobenzene with two equivalents of [^tBuS]Na, followed by chlorination to yield the corresponding bis(sulfenyl chloride). Subsequent ring closure with Me₃SiN₃ yields the target 1,3,2-dithiazolylium ring system in good yield. The preparation and crystal structures of 3′-methyl-benzo-1,3,2-dithiazolylium chloride and 3′-methyl-benzo-1,3,2-dithiazolyl are described and the electronic properties of the radical examined through EPR spectroscopy, DFT calculations and variable temperature magnetic susceptibility measurements.     

Symmetry or asymmetry in cheletropic additions forming cyclopropanes

Cheletropic additions forming cyclopropane rings were studied theoretically. Ten addition paths were traced by means of density-functional-theory calculations. Two 1,4-dienes, 1,4-pentadiene, and tricyclo[5.3.1.0^4,9]undeca-2,5-diene were adopted as substrates. CO, SO₂, C₂H₅PCl₂, CCl₂ and SiCl₂ were employed as cheletropic reagents (Xs). An orbital correlation diagram of the Woodward–Hoffmann (W–H) rule and frontier molecular orbital (FMO) interactions between them were investigated in detail. The FMO interactions, HOMO (1,4-diene)lumo (X) and homo (X)LUMO (diene), work reasonably for the progress of the reactions. Those cause the formation of two C–X bonds and a cyclopropane ring, and alternation of double bonds to single bonds. All the additions are concerted. The easiness of the ring formation depends upon the energy gap between HOMO and lumo and that between homo and LUMO, and the spatial directions of HOMO and LUMO extensions. Symmetry conservation of the W–H rule does not hold necessarily for those addition paths. The symmetry-breaking was discussed in terms of FMO interactions.Acknowledgement This work was supported by a Grant-in-Aid for Scientific Research from the Ministry of Education, Science and Culture, Japan and by Nishida Memorial Foundation for Fundamental Chemical Research.     

Synthesis, structure and conformation of partially-modified retro- and retro-inverso psi[NHCH(CF3)]Gly peptides

Partially modified retro- (PMR) and retro-inverso (PMRI) psi[NHCH(CF(3))]Gly peptides, a conceptually new class of peptidomimetics, have been synthesized in wide structural diversity and variable length by aza-Michael reaction of enantiomerically pure alpha-amino esters and peptides with enantiomerically and geometrically pure N-4,4,4-trifluorocrotonoyl-oxazolidin-2-ones. The factors underlying the observed moderate to good diastereocontrol have been investigated. The conformations of model PMR-psi[NHCH(CF(3))]Gly tripeptides have been studied in solution by (1)H NMR spectroscopy supported by MD calculations, as well as in the solid-state by X-ray diffraction. Remarkable stability of turn-like conformations, comparable to that of parent malonyl-based retropeptides, was evidenced, as a likely consequence of two main factors: 1) severe torsional restrictions about sp(3) bonds in the [CO-CH(2)-CH(CF(3))-NH-CH(R)-CO] module, which is biased by the stereoelectronically demanding CF(3) group and the R side chain; 2) formation of nine-membered intramolecularly hydrogen-bonded rings, which have been clearly detected both in CHCl(3) solution and in some crystal structures. The former factor seems to be more important, as turn-like conformations were found in the solid-state even in the absence of intramolecular hydrogen bonding. The relative configuration of the -C*H(CF(3))NHC*H(R)- stereogenic centers has a major effect on the stability of the turn-like conformation, which seems to require a syn stereochemistry. X-ray diffraction and ab initio computational studies showed that the [-CH(CF(3))NH-] group can be seen as a sort of hybrid between a peptide bond mimic and a proteolytic transition state analogue, as it combines some of the properties of a peptidyl -CONH- group (low NH basicity, CH(CF(3))-NH-CH backbone angle close to 120 degrees, C-CF(3) bond substantially isopolar with the C=O) with some others of the tetrahedral intermediate [-C(OX)(O(-))NH-] involved in the protease-mediated hydrolysis reaction of a peptide bond (high electron density on the CF(3) group, tetrahedral backbone carbon).     

Stereoselective synthesis of the ABCD ring framework of azaspiracids

A stereoselective synthesis of the ABCD ring framework of azaspiracid-1 and azaspiracid-3 has been achieved using a tandem bis-spiroketalization protocol in the presence of a mild proton source from 1,4-diketone precursor. A tetrahydrofuran intermediate with the correct stereochemistry for the D ring of azaspiracids-1 and 3 was then taken through a linear sequence of reactions to afford the desired diketone precursor. The D-ring of azaspiracid-1 was then constructed by employing a Sharpless asymmetric dihydroxylation followed by etherification using a homoallyl derivative. The structure of the ABCD ring framework with four contiguous rings was established by extensive NMR analysis.     

Ring‐Rearrangement Metathesis

Ring‐rearrangement metathesis (RRM) refers to the combination of several metathesis transformations into a domino process, in which an endocyclic double bond of a cycloolefin reacts with an exocyclic alkene. RRM has proven to be a powerful method for the rapid construction of complex structures. The extension of the basic ring‐opening–ring‐closing metathesis process by further metathesis steps as well as an examination of the driving forces, limits, scope, recent advantages, and future perspectives of these domino sequences is presented with various examples, thus reflecting the high efficiency and utility of RRM in organic synthesis.     

Chemical reactivity of [1,2,3]triazolo[1,5-a]- and [1,5-c]-pyrimidinium salts

The chemical reactivity of the [1,2,3]triazolo[1,5-a]- and [1,5-c]-pyrimidinium salts towards morpholine, water and sodium methoxide have been studied. Among others, new 1-aza and 2-azabutadienes substituted by a [1,2,3]-triazole ring were obtained in the course of the opening of the positively charged pyrimidine ring.     

Solvothermal synthesis of an open-framework zinc chlorophosphate, [C8N4H26][Zn3Cl(HPO4)3(PO4)], with a layer structure

A solvothermal reaction of ZnO, HCl, H₃PO₄, and N,N′(3-bisaminopropyl)-1,2-ethylenediamine (BAPEN) in diethyleneglycol at 160°C yields a new zinc chlorophosphate, [C₈N₄H₂₆][Zn₃Cl(HPO₄)₃(PO₄)], I. The structure comprises ZnO₄, ZnO₃Cl, HPO₄ and PO₄ tetrahedral units connected through their vertices giving rise to a layered structure with 10-membered apertures. The position of the Zn and P atoms gives rise to double-four ring like building unit with one Zn missing. The fully protonated amine molecules occupy the inter-lamellar region and interacts with the framework through N-H?O hydrogen bonds. Crystal data: M=792.85, orthorhombic, space group=Pca2₁ (no. 29), a=9.8410(2), b=15.0912(2), c=16.1220(4) Å, V=2394.32(8) Å³, Z=4, ρ_calc=2.199 g cm⁻³, μ(MoKα)=3.443 mm⁻¹, R₁=0.0520, wR₂=0.1256 and S=1.054.