A proposed bioactive conformation of Peptide T

The conformational profiles of Peptide T, (5–8)Peptide T, [Abu⁵](4–8)Peptide T and (4–8)Peptide T were computed independently to assess the geometrical characteristics of the bioactive conformation of Peptide T. The conformational profiles of the peptides were computed within the molecular mechanics framework using an effective dielectric constant of 80. The conformational space was thoroughly sampled using an iterative simulated annealing protocol. The bioactive conformation was assessed by pairwise cross comparisons of each of the unique low energy conformations found for each of the different analogs studied. After a putative bioactive conformation was selected, in order to further validate our hypothesis the conformational profile of the potent compound cyclo(Thr-Thr-Asn-Tyr-Thr-Asp) was computed and the putative bioactive conformation was found. The conformation exhibits a pseudo -turn involving the side chain of Thr⁵ and the carbonyl oxygen of Tyr⁷ forming a C12 ring.     

X-ray structures and pharmacological activities of lidocaine derivatives

The molecular and crystal structures of the lidocaine analogs 2-(pyrazol-1-yl)-2′-methylacetanilide (1), 2-(3,5-dimethyl-4-iodo-pyrazol-1-yl)-2′-methylacetanilide (2), 2-(3,5-dimethyl-4-iodo-pyrazol-1-yl)-3′-methylacetanilide (3), and 2-(pyrazol-1-yl)-4′-methylacetanilide (4), are reported, with a summary of their pharmacological activities. In this series, the moiety comprising the heterocyclic ring and the amide alkyl linker displays a common conformation. Molecules of 1–4 form identical hydrogen bonded motifs in their crystals, namely linear chains via intermolecular N–H···O=C hydrogen bonding. Moderate anesthetic and anti-arrhythmic potencies recorded for 1–4 relative to lidocaine are countered by their significantly lower toxicities.     

2,3:4,6‐Di‐O‐isopropylidene‐α‐l‐sorbofuranose and 2,3‐O‐isopropylidene‐α‐l‐sorbofuranose

In the title compounds, C₁₂H₂₀O₆, (I), and C₉H₁₆O₆, (II), the five‐membered furanose ring adopts a ⁴T₃ conformation and the five‐membered 1,3‐dioxolane ring adopts an E₃ conformation. The six‐membered 1,3‐dioxane ring in (I) adopts an almost ideal ^OC₃ conformation. The hydrogen‐bonding patterns for these compounds differ substantially: (I) features just one intramolecular O—H...O hydrogen bond [O...O = 2.933 (3) Å], whereas (II) exhibits, apart from the corresponding intramolecular O—H...O hydrogen bond [O...O = 2.7638 (13) Å], two intermolecular bonds of this type [O...O = 2.7708 (13) and 2.7730 (12) Å]. This study illustrates both the similarity between the conformations of furanose, 1,3‐dioxolane and 1,3‐dioxane rings in analogous isopropylidene‐substituted carbohydrate structures and the only negligible influence of the presence of a 1,3‐dioxane ring on the conformations of furanose and 1,3‐dioxolane rings. In addition, in comparison with reported analogs, replacement of the –CH₂OH group at the C1‐furanose position by another group can considerably affect the conformation of the 1,3‐dioxolane ring.     

Synthesis,spectral and RAHB studies on some arylhydrazones of β-diketones: crystal and molecular structures of 2-(2-(3-pyridyl)hydrazono)-5,5-dimethylcyclohexane-1,3-dione and 2-(2-(2-methoxyphenyl)hydrazono)-5,5-dimethylcyclohexane-1,3-dione

The present study describes the synthesis and spectral analysis of a series of arylhydrazones of β-diketones (1–6) along with the single crystal X-ray structural studies of 2-(2-(3-pyridyl)hydrazono)-5,5-dimethylcyclohexane-1,3-dione (3) and 2-(2-(2-methoxyphenyl)hydrazono)-5,5-dimethylcyclohexane-1,3-dione (6). Spectral and structural studies clearly exemplify the effective intramolecular hydrogen bonding and as a result the NH proton signals and carbonyl carbon signals are shifted to higher frequency region in NMR spectra. Structural implications imposed by the formation of pseudo six-membered ring after hydrogen bonding is well observed in XRD analysis. XRD analysis also evidences the envelop conformation of the dimedone ring in both the cases and resonance assisted hydrogen bonding (RAHB) studies were also performed.     

Synthesis and anticancer activities of proline-containing cyclic peptides and their linear analogs and congeners

A solution phase method was adopted for the synthesis of proline-containing cyclic pentapeptide 2 and total synthesis of naturally occurring cyclic heptapeptide Reniochalistatin B 3. For the synthesis of 3, both divergent and convergent strategies were used to improve the overall yield from 12 to 25%. Different N and C terminal modified linear analogs and congeners of 2 and 3 were synthesized. Both cyclic peptides 2 and 3 and their linear analogs/congeners were evaluated for anti-cancer activity against HeLa cell line, among which pentapeptide 2?h and hexapeptide 3n with N-terminal protected hexafluoroisopropyl carbamates (HFIPC) interestingly showed higher cytotoxicity with an IC₅₀ of 2.73 and 4.3?µM, respectively compared to their Boc-protected analogs 2a (IC₅₀ 20?µM) and 3c (IC₅₀ 38.51?µM) and cyclic peptides 2 (>100?µM) and 3 (47?µM). These results were further validated by biological experiments such as colony formation and wound healing assays.     

Synthesis of tetrahydroisoquinoline-based pseudopeptides and their characterization as suitable reverse turn mimetics

New peptidomimetics containing the Tic moiety were synthesized in enantiomerically pure form and their conformational features were studied by NMR, IR, and molecular modeling techniques. The presence of a reverse turn conformation was observed in all the structures, suggesting the key role of the scaffold as reverse turn inducer. In particular, all the analyses led to the conclusion that a β-turn conformation is mostly stabilized in tetrapeptide mimetic 4b and in hexapeptide mimetics 5a,b. In the case of 5a,b, the C1 stereochemistry plays a central role in determining stable conformations, supporting the formation of a β-hairpin arrangement with a 14-membered intramolecular hydrogen bond ring only in 5b.     

Synthesis and conformational analysis of 18-membered Aib-containing cyclohexapeptides

The synthesis and conformational analysis of two Aib-containing cyclic hexapeptides, cyclo(Gly-Aib-Leu-Aib-Phe-Aib) 1 and cyclo(Leu-Aib-Phe-Gly-Aib-Aib) 2, is described. The linear precursors of 1 and 2 were prepared using solution phase techniques, and the cyclization efficiency of three different coupling reagents (HATU, PyAOP, DEPC) was examined. The success of the cyclization was found to be reagent dependent. Solid-state conformational analysis of 1 and 2 was performed by X-ray crystallography and has revealed some unusual features as all three Aib residues of 1 assume nonhelical conformations. Furthermore, the residue Aib⁴ adopts an extended conformation (?=−175.9(3)°, ψ=+178.6(2)°), which is, to the best of our knowledge, the first observation of an Aib residue adopting an extended conformation in a cyclopeptide. The structure of 1 is also a rare example in which an Aib residue occupies the (i+1) position of a type II′ β-turn, stabilized by a bifurcated hydrogen bond. The cyclic peptide 2 adopts a more regular conformation in the solid state, consisting of two fused β-turns of type I/I′, stabilized by a pair of intramolecular hydrogen bonds. In addition, the conformational study of the cyclic peptide 1 in DMSO-d₆ by NMR spectroscopy and molecular dynamics simulations revealed a structure, which is very similar to its structure in the crystalline state.     

The crystal and molecular structures of the diastereomeric (4Z)- and (4E)-3-oxo-2,3-dihydrobilatrienes-abc

The molecular and crystal structures of two diastereomeric 3-oxo-2,3-dihydrobilatrienes-abc1 and2 are determined at low (1, 2) and room temperature (2). The configurations at the exocyclic double bond in position 4 are found to be (Z) for1 and (E) for2. Tautomerism, conformation and crystal packing of1 and2 can be understood on the basis of the pattern of intra- and intermolecular hydrogen bonds. Compared to1, a more open helix conformation is found for the (E) diastereomer2. An analysis of crystallographically observed temperature factors of2 yields the result that the highest flexibility is found for the saturated lactam ring.Herrn Prof.Josef Schurz zum 60. Geburtstag gewidmet.     

Theoretical Study Of β2,3‐Peptide Models

Conformational features of α,β‐disubstituted β^2,3‐dipeptide models have been studied with quantum mechanics method. Geometries were optimized with the HF/6‐31G** method, and energies were evaluated with the B3LYP/6‐31G** method. Solvent effect was evaluated with the SCIPCM method. For (2S,3S)‐β^2,3‐dipeptide model 1 , a six‐membered‐ring hydrogen bonded structure is most stable. However, the conformation corresponding to the formation of the 14‐helix is only about 1.7 kcal/mol less stable in methanol solution, indicating that the 14‐helix is favored if a (2S,3S)‐β^2,3‐polypeptide contains more than 5 residues. On the other hand, the conformation corresponding to the formation of β‐sheet is most stable for (2R,3S)‐β^2,3‐dipeptide model 2 , suggesting that this type of β‐peptides is intrinsically favored for the formation of β‐sheet secondary structure.     

Conformational Behaviour of Substituted 2-Methoxy-2-Oxo-1,2-Oxaphospholan-3-Ols

Abstract

Conformational behaviour of about 30 2-methoxy-2-oxo-1,2- oxaphospho l an-3-0 1 s containing various substituents was examined by ¹H and ¹³C NMR. Vicinal coupling constants J(HCCH), J(HCCP), J(HCOP), J(CCOP) and J(CCCP) were employed in this study. Conformation of the 1,2-oxaphospholane ring is governed almost exclusively by substituents at C-3, C-4 and C-5, as we l l as by their orientation. The configuration of the P atom has little or no influence on conformation of the ring in diastsreomeric pairs. Strong preference of phenyl, methyl and substituted methyl groups to occupy the equatorial or pseudoequatoria l positions was observed for all but one compounds studied. In the cis-fused bicyclic syst ems conformat ionally rigid 6-membered rings forced the 1,2-oxaphospholane rings to adopt an enve l ope-l ike (E₄) conformation. No influence of the p=o……HO-C-3 hydrogen bond on conformation of the 1,2-oxaphospholane ring was found. Preferred conformations for (2R, 3R, 4R)-3-(hydroxymethyI)-2-methoxy-2-oxo-1,2-oxaphospho lane-3,4-diol and its triacetate are shown below.     

CYCLIC OXYPHOSPHORANES

Abstract

A review on pertinent information on cyclic oxyphosphoranes is presented. Recent X-ray structures and variable temperature ¹H NMR investigations of cyclic pentaoxyphosphoranes reveals a preference for a boat conformation for saturated six-membered rings in apical-equatorial orientations of trigonal bipyramids. These studies include five-, six-, and seven-membered rings and show that the solid state structures are retained in solution. Apical-equatorial ring pseudorotations are more facile for five-membered rings, whereas ligand exchange via diequatorial ring placement is more facile for the larger rings. The importance of the apical-equatorial ring orientation for phosphorinanes appearing as trigonal bipyramidal intermediates in enzymatic reactions of cyclic AMP analogs is emphasized.     

Unusual Conformational Behavior of 3,7-Dihetera(N,N-;N,O-;N,S-) Bicyclo[3.3.1]Nonan-9-Ols Via Nmr Analysis

Abstract

Based upon the analysis of ¹H NMR data, along with molecular modeling, it was shown that the reduction of 3,7-dihetera(N,N-; N,O-; N,S-)bicyclo[3.3.1]nonan-9-ones by LiAlH₄ led to a mixture of two stereoisomeric secondary alcohols with different orientations of the hydroxyl groups in one of the ring systems. Diaza derivatives in deuterochloroform exist in predominant chair-boat conformations. However, the replacement of nitrogen in one of the heterocycles by oxygen or sulfur led to stereoisomers one of which existed in chair-boat conformation and another in a chair–chair conformation. In all cases the boat conformation is stabilized by formation of an intramolecular hydrogen bond (IMHB) between a lone electron pair of the nitrogen atom and a proton on the pseudo axial hydroxyl group of the other ring.     

Structure of D-Fructosamine Hydrochloride and D-Fructosamine Hydroacetate

D-Fructosamine derivatives are key intermediates of the early Maillard reaction and have been a subject of numerous studies in food and health sciences due to their implication in the nutritional and organoleptic quality of foods, as well as to complications in diabetes and renal disease. We report the crystal structure analyses of 1-deoxy-β -D-fructopyranos-1-ylamine hydrochloride (1) and -hydroacetate (2) salts. The carbohydrate rings adopt the normal ²C₅ pyranose chair conformation in 1 and 2. Bond lengths and valence angles in 1 and 2 compare well with the average values from related pyranose structures. There are two conformationally nonequivalent molecules in the asymmetric unit in 1. All hydroxyl and ring oxygen atoms, ammonium groups, and chloride ions in 1 are involved in an extensive three-dimensional hydrogen bonding network. The hydrogen bonding network in 2 is formed by one type of infinite chain with attached antidromic cycles.     

cis‐[(4R,5R)‐4,5‐Bis­(amino­methyl)‐2,2‐di­methyl‐1,3‐dioxolane‐N,N′](malonato‐O,O′)­platinum(II), an anticancer agent

In the title compound, [Pt(C₃H₂O₄)(C₇H₁₆N₂O₂)], the Pt atom is coordinated to two O and two N atoms in a square‐planar arrangement. The two independent mol­ecules, which have very similar structures, are approximately related by pseudo‐twofold screw‐axis symmetry. The six‐membered chelate ring in the leaving ligand assumes a conformation intermediate between the half‐chair and boat forms. The seven‐membered ring in the carrier ligand assumes a twist‐chair conformation and the oxolane ring assumes an envelope conformation. The crystal packing consists of extensive hydrogen‐bonding networks which form two‐dimensional molecular layers, and there are weak van der Waals interactions between these layers.     

Monovalent cation-promoted ordering of a glycine-rich cyclic peptide

This report describes an accelerated self-assembly of a synthetic cyclic hexapeptide in the presence of alkali metal ions. Time-dependent aggregation of hexapeptide was considerably influenced upon co-incubation with monovalent metal ions, of which K⁺ afforded the most significant effect both on the time-scale required for self-assembly and on the morphology of aged structures. Metal ion adducts formation ability of the hexapeptide was confirmed by electrospray ionization mass spectrometry measurements and ¹³C NMR spectrometry. The effect of metal ion binding on peptide structure was also probed by circular dichroism, optical microscopy, and scanning electron microscopy. K⁺ ions not only interacted more efficiently with the hexapeptide enabling it to reach conformational state(s) conducive for self-assembly, but also altered the morphologies of the aged peptide fibers, when compared to the unmetalated peptide.     

Amidoximes α-Hydroxylées Dérivées de Sucres

The two epimeric α-hydroxyamidoximes 5 and 6 - and some derivatives thereof, particularly oxadiazoles 16 and 17 - have been stereospecifically prepared from the keto sugar 1. Compound 5 was found to exist in two polymorphous crystalline forms (α and β) depending on the crystallization solvent. Both forms are orthorhombic, space group P2₁2₁2₁ (α-form : a = 10.408(3), b = 10.559(2), c = 14.144(2) Å; β-form : a = 7.890(1), b = 10.305(2), c = 19.064(4) Å). The calculation of pseudorotation parameters showed that each polymorph is associated with a slightly different conformation of the dioxolane rings. The Oacetyl derivative 11 of 6 adopts a different conformation of the furanose ring. In the three structures, a network of hydrogen bonds exists. The amidoxime 5 forms a cupric complex [Cu(5)₂] whose ESR spectrum proved its square structure.     

Hydrogen-Bonded Double Strands: Crystal Structure and Spectroscopic Propertiesof a 2,2′-Dipyrryl Ketone

 The synthesis, crystal structure determination, conformational analysis, and spectroscopic properties of 3,3′-diethyl-4,4′-dimethyl-2,2′-dipyrryl ketone (1) are reported. The dipyrryl ketone is a model for the dipyrrole core of 10-oxobilirubin, a presumed metabolite in alternate pathways of excretion of the yellow pigment of jaundice, bilirubin. In the crystal, 1 adopts a helical conformation, with a molecule of one helicity being hydrogen-bonded to two molecules of the opposite helicity. Thus, 1 self-assembles via hydrogen bonding into supramolecular double-stranded arrays, where molecules of the same helicity comprise one strand and are paired through hydrogen bonding to molecules of opposite helicity in the second strand. In the observed molecular conformation each pyrrole ring and adjacent carbonyl group are rotated into an sc conformation (torsion angle ∼29 °), with each N-H pointing in the same direction as the C*O. Molecular mechanics/dynamics calculations predict the sc,sc conformation, absent hydrogen bonding, to be the most stable, but only by a few tenths of a kj/mol. In CHCl₃, 1 is monomeric according to vapor pressure osmometry studies (). ¹H NMR NH chemical shifts in CDCl₃ suggest a predominantly anti orientation of the C=O and pyrrole NHs, which is opposite to the orientation observed in the crystal.     

Hydrogen-Bonded Double Strands: Crystal Structure and Spectroscopic Propertiesof a 2,2′-Dipyrryl Ketone

Summary.  The synthesis, crystal structure determination, conformational analysis, and spectroscopic properties of 3,3′-diethyl-4,4′-dimethyl-2,2′-dipyrryl ketone (1) are reported. The dipyrryl ketone is a model for the dipyrrole core of 10-oxobilirubin, a presumed metabolite in alternate pathways of excretion of the yellow pigment of jaundice, bilirubin. In the crystal, 1 adopts a helical conformation, with a molecule of one helicity being hydrogen-bonded to two molecules of the opposite helicity. Thus, 1 self-assembles via hydrogen bonding into supramolecular double-stranded arrays, where molecules of the same helicity comprise one strand and are paired through hydrogen bonding to molecules of opposite helicity in the second strand. In the observed molecular conformation each pyrrole ring and adjacent carbonyl group are rotated into an sc conformation (torsion angle ∼29 °), with each N-H pointing in the same direction as the C*O. Molecular mechanics/dynamics calculations predict the sc,sc conformation, absent hydrogen bonding, to be the most stable, but only by a few tenths of a kj/mol. In CHCl₃, 1 is monomeric according to vapor pressure osmometry studies (). ¹H NMR NH chemical shifts in CDCl₃ suggest a predominantly anti orientation of the C=O and pyrrole NHs, which is opposite to the orientation observed in the crystal. Received February 4, 2000. Accepted February 14, 2000     

Effect of benzannelation on the conformational flexibility of the rings in oxo, imino, and methylene derivatives of cyclohexa-1,4-diene

The effect of benzannelation on the equilibrium conformation and flexibility of the dihydrocycle in cyclohexa-1,4-dienone,para-quinone, and their imino and methylene analogs was studied by the semiempirical quantum-chemical AM1 method. The equilibrium conformations of the carbonyl derivatives are planar. In the imino- and methylene-substituted analogs, the dihydrocycle adopts a boat conformation due to repulsions between substituted analogs, the dihydrocycle adopts a boat conformation due to repulsions between the hydrogen atoms at the exocyclic double bond and in theperi positions of the benzene rings. Annelation of cyclohexa-2,5-dien-1-one andpara-quinone with benzene rings at the C=C double bonds causes an increase in the conformational flexibility of the partially hydrogenated ring owing to an increase in the bending strain in the first compound and a decrease in the conjugation between the carbonyl groups and the remaining part of the molecule in the second compound. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 388–390, March, 1998.