A New Systematization of the Conformational Behavior of Seven-Membered Rings. Isoclinal Anomeric and Related Orientations(1)

Origin of High Diastereoselectivity in Reactions of Seven-Membered-Ring Enolates

Unlike many reactions of their six-membered-ring counterparts, the reactions of chiral seven-membered-ring enolates are highly diastereoselective. Diastereoselectivity was observed for a range of substrates, including lactam, lactone, and cyclic ketone derivatives. The stereoselectivity arises from torsional and steric interactions that develop when electrophiles approach the diastereotopic π-faces of the enolates, which are distinguished by subtle differences in the orientation of nearby atoms of the ring.

Nucleoside Analogues with a Seven-Membered Sugar Ring: Synthesis and Structural Compatibility in DNA-RNA Hybrids

Herein we describe results on the pairing properties of synthetic DNA and RNA oligonucleotides that contain nucleotide analogues with a 7-membered sugar ring (oxepane nucleotides). Specifically, we describe the stereoselective synthesis of a set of three oxepane thymine nucleosides (OxT), their conversion to phosphoramidite derivatives, and their use in solid-phase synthesis to yield chimeric OxT-DNA and OxT-RNA strands. The different regioisomeric OxT phosphoramidites allowed for positional variations of the phosphate bridge and assessment of duplex stability when the oxepane nucleotides were incorporated in dsDNA, dsRNA, and DNA-RNA hybrids. Little to no destabilization was observed when two of the three regioisomeric OxT units were incorporated in the DNA strand of DNA-RNA hybrids, a remarkable result considering the dramatically different structure of oxepanes in comparison to 2'-deoxynucleosides. Extensive molecular modeling and dynamics studies further revealed the various structural features responsible for the tolerance of both OxT modifications in DNA-RNA duplexes, such as base-base stacking and sugar-phosphate H-bond interactions. These studies suggest that oxepane nucleotide analogues may find applications in synthetic biology, where synthetic oligonucleotides can be used to create new tools for biotechnology and medicine.

Binding of Gold(III) from Solutions by the [Ag6{S2CN(CH2)6}6] Cluster: Synthesis, Thermal Behavior, and Self-Organization of the Supramolecular Structure of the Double Complex [Au{S2CN(CH2)6}2]2[AgCl2]Cl·2CHCl3 (Role of Secondary Au⋅⋅⋅Cl, Ag⋅⋅⋅S, and Cl⋅⋅⋅Cl Interactions)

Abstract

The capability of silver(I) cyclo-hexamethylenedithiocarbamate to concentrate gold(III) from solutions characterized by a high level of salinity (5.15 M NaCl) into the solid phase has been established. The double chloroform-solvated Au(III)–Ag(I) complex [Au{S2CN(CH2)6}2]2[AgCl2]Cl·2CHCl3 (I) was preparatively isolated as an individual form of binding of [AuCl4]– anions. The composition of the ionic structural units of compound I indicates that gold(III) binding from a solution to the solid phase is accompanied by the complete redistribution of the HmDtc ligands between the coordination spheres of Ag(I) and Au(III). Complex I characterized by IR spectroscopy, simultaneous thermal analysis, and X-ray structure analysis (CIF file CCDC no. 2051654) exhibits the supramolecular structure containing two oppositely charged pseudo-polymeric subsystems. Complex cations [Au{S2CN(CH2)6}2]+ and anions [AgCl2]– (in a ratio of 2 : 1) form a complicatedly organized cation-anionic pseudo-polymeric ribbon ({[Au(HmDtc)2]⋅⋅⋅[AgCl2]⋅⋅⋅[Au(HmDtc)2]}+)n due to secondary interactions Ag⋅⋅⋅S (3.2613 Å) and Au⋅⋅⋅Cl (3.2765 Å). The pseudo-polymeric ribbon consists of two rows of cations and a row of anions. The outer-sphere chloride ions combine the solvate chloroform molecules by two equivalent hydrogen bonds Cl⋅⋅⋅H–C yielding anion-molecular triads [Cl3CH⋅⋅⋅Cl⋅⋅⋅HCCl3]–, which are involved in the formation of the supramolecular ribbon due to the secondary Cl⋅⋅⋅Cl interactions (3.4058 Å) between the nonequivalent chlorine atoms of the nearest solvate molecules. The study of the thermal behavior of complex I makes it possible to determine the character of thermolysis and conditions for the quantitative regeneration of bound gold.

Following Ramachandran 2: exit vector plot (EVP) analysis of disubstituted saturated rings

EVP analysis of common saturated rings revealed five regions (α–ε); only part of them corresponds to 3D molecular structures.

C-H Activation in Primary 3-Phenylpropylamines: Synthesis of Seven-Membered Palladacycles through Orthometalation. Stoichiometric Preparation of Benzazepinones and Catalytic Synthesis of Ureas

The dimeric cyclometalated complexes [Pd2{κ(2)C,N-C6H4CH2CH2C(R)(Me)NH2-2}2(μ-Cl)2] (R = Me (1a), H (1b)) are prepared by reacting 1,1-dimethyl-3-phenylpropylammonium or 1-methyl-3-phenylpropylammonium triflate with Pd(OAc)2 in a 1:1 molar ratio and subsequent treatment with excess NaCl. The mononuclear derivatives [Pd{κ(2)C,N-C6H4CH2CH2C(R)(Me)NH2-2}Cl(L)] (L = PPh3, R = Me (3a), H (3b); L = 4-picoline (4-pic), R = Me (4a), H (4b)) were prepared from 1a,b by splitting the chloro bridges with the neutral ligands L. A conformational analysis of the mononuclear palladacycles in solution has been carried out. Insertion of CO takes place into the Pd-C bond of complexes 1a,b, affording Pd(0) and the tetrahydro-benzazepinone 5a or 5b, which possesses potential pharmacological interest. Additionally, the triflate salt A or B undergoes catalytic carbonylation with CO to afford the corresponding N,N'-dialkylurea, using Pd(OAc)2/Cu(OAc)2, in boiling acetonitrile. The crystal structures of 3a·(1)/2H2O, 3b, 4b·CHCl3, and 5a were determined by X-ray diffraction studies.

Three closely related dibenzazepine carboxylic acids: hydrogen-bonded aggregation in one, two and three dimensions

In the structure of (6R*,11R*)-5-acetyl-11-ethyl-6,11-dihydro-5H-dibenzo[b,e]azepine-6-carboxylic acid, C19H19NO3, (I), the molecules are linked into sheets by a combination of O-H...O and C-H...O hydrogen bonds; in the structure of the monomethyl analogue (6RS,11SR)-5-acetyl-11-ethyl-2-methyl-6,11-dihydro-5H-dibenzo[b,e]azepine-6-carboxylic acid, C20H21NO3, (II), the molecules are linked into simple C(7) chains by O-H...O hydrogen bonds; and in the structure of the dimethyl analogue (6RS,11SR)-5-acetyl-11-ethyl-1,3-dimethyl-6,11-dihydro-5H-dibenzo[b,e]azepine-6-carboxylic acid, C21H23NO3, (III), a combination of O-H...O, C-H...O and C-H...π(arene) hydrogen bonds links the molecules into a three-dimensional framework structure. None of these structures exhibits the R2(2)(8) dimer motif characteristic of simple carboxylic acids.

Formation and base hydrolysis of oxidimethaneamine bridges in CoIII-amine complexes

cis-[CoL2](3+) (1a(3+)), trans-[CoL2](3+) (2a(3+)), cis-[Co(MeL)2](3+) (1b(3+)), and trans-[Co(MeL)2](3+) (2b(3+)), L = 1,4-diazepan-6-amine (daza) and MeL = 6-methyl-1,4-diazepan-6-amine (Medaza), were allowed to react as templates in acetonitrile with paraformaldehyde and triethylamine. Several Co(III) complexes, where two adjacent amino groups of two ligand moieties are interlinked by an oxidimethaneamine bridge, were obtained. Connection of a primary with a secondary amino group (prim-sec bridging) was found to be predominant. The singly and doubly bridged daza- and Medaza-derivatives 7a(3+), 9a(3+) and 7b(3+), 9b(3+) were characterized by crystal-structure analysis. The bridging process resulted in a slight lengthening of the mean Co-N distance, a red shift of the A1g-T1g transition, and an increase of the Co(III)/Co(II) reduction potential. Several minor components, which could be only partially separated by chromatographic methods, were also formed. The daza-derivatives 6a(3+) (prim-prim bridged) and 10a(3+) (bidentate coordination of one daza frame) formed in small quantities. The Medaza derivatives 3b(3+) and 4b(3+) (trans configuration of the Medaza frames, with additional pending carbinolamino groups), and 8b(3+) (with a methylideneimino group) represent intermediates of the condensation process. Their structure was again corroborated by X-ray diffraction. All bridged species (6a(3+), 7a(3+), 7b(3+), 8b(3+), 9a(3+), 9b(3+), and 10a(3+)) exhibited exclusively a cis orientation of the two diazepane frames, even if the trans configured 2a(3+) or 2b(3+) were used as starting materials. Molecular mechanics calculations indicate that in the bridged species with a trans configuration steric strain is substantially more pronounced. In alkaline aqueous media, 9a(3+) and 9b(3+) revealed a complete degradation of the bridges whereby the original 1a(3+) and 1b(3+) reformed. The pseudo-first-order rate constant k(obs) of the degradation reaction was found to depend linearly on OH(-) concentration. The degradation of the first bridge is about 100 times faster than the degradation of the second. The mechanism of formation and degradation of such oxidimethaneamine bridges is discussed.

Molecular dynamics of 6-methyl-2-phenyl-2,3-dihydro-4H-chromen-4-one and 6-methyl-2-(4-nitrophenyl)-2,3-dihydro-4H-chromen-4-one (flavanone) derivatives in a solution studied by NMR spectroscopy

Molecular dynamics of benzoxazepin, oxime, pyrazole, and thiosemicarbazone derivatives of some flavanones have been investigated in a solution using NMR. The results confirm the formation of different O-H···O, O-H···N, N···H-N type intramolecular hydrogen bonds in the pyrazole and oxime molecules. The rotational barrier energy and energy of intramolecular hydrogen bonds have been determined.

Synthesis and properties of septanose carbohydrates

Seven-atom ring sugars, called septanoses, are increasingly the focus of scientific inquiries because of their potential biological activities. This article details the synthesis, conformational analysis, and protein-binding properties of septanose carbohydrates. A distinction is drawn between septanoses that are substituted in the 6-position of the ring and those that are not. When a C-6 substituent is absent, the structure is essentially that of an aldohexose in its septanose, rather than furanose or pyranose, ring form; they may play as-of-yet unexplored roles in glycobiology. Septanoses having a hydroxymethyl group at C-6, on the other hand, are ring-expanded analogues of pyranoses. Syntheses have moved beyond the preparation of seven-membered ring monosaccharides to the development of septanosyl donors. These donors have been used in the synthesis of novel di- and trisaccharides that contain septanoses as well as a variety of glycoconjugates. Low-energy conformations adopted by septanoses have been organized based on ring substitution and stereochemistry. Instances where septanoses have been demonstrated to bind to natural proteins are presented and analyzed. The major conclusion drawn in the chapter is that advances in the synthesis of septanose carbohydrates now enable a detailed investigation of their activity in a number of biological contexts.

Conformational analysis of methyl 5-O-methyl septanosides: effect of glycosylation on conformer populations

Methyl 5-O-methyl-alpha-d-glycero-d-idoseptanoside (3) and methyl 5-O-methyl-beta-d-glycero-d-guloseptanoside (4) were investigated as (1-->5)-linked di-/oligoseptanoside mimetics. Here we report the synthesis of 3 and 4 and describe their preferred solution conformations through a combination of ab initio/DFT calculations and (1)H (3)J(H,H) NMR coupling constant analysis. The conformations of 3 and 4 observed in this study are discussed in comparison to those of the parent (C5 hydroxy) compounds 1 and 2. The results indicate that methyl 5-O-methyl-alpha-septanoside 3 is relatively rigid and adopts the same (3,4)TC(5,6) conformation as 1. Methyl 5-O-methyl-beta-septanoside 4 is somewhat less rigid than its parent septanoside (2). In addition to the (6,O)TC(4,5) conformation adopted by 2, beta-septanoside 4 also populates the adjacent (3,4)TC(5,6) conformation. Glycosylation at C5 on beta-septanoside 4 therefore increases its overall flexibility and allows access to alternative ring conformations.

Sequential Cyclization−Elimination Route to Carbohydrate-Based Oxepines

A five-step preparation of carbohydrate-based oxepines from hept-1-enitols is presented. The hept-1-enitols were subjected to silyl protection and hydroboration/oxidation to give the protected heptan-1-itols. Swern oxidation of the homologated alcohols followed by sequential acetal formation/cyclization provided methyl 2-deoxyseptanosides that underwent elimination reactions to give the carbohydrate-based oxepines. The new sequence is an alternative to the ring-closing metathesis for the synthesis of carbohydrate-based oxepines from protected pyranose sugars. The product oxepines can serve as glycosyl donors in the synthesis of novel septanose carbohydrates. In addition, C-methylenealdehydo arabinofuranoside 16 was formed from 2-deoxyseptanoside 10 as the only product during protic acid mediated elimination reactions. This novel ring contraction complements other reported preparations of C-methylenaldehydo furanosides and underscores the acid-mediated reactivity introduced by competing eliminations between the C-1/C-2 and C-2/C-3 bonds.

Septanose Carbohydrates: Synthesis and Conformational Studies of Methyl α-d-glycero-d-Idoseptanoside and Methyl β-d-glycero-d-Guloseptanoside

We report the synthesis of methyl alpha-D-glycero-D-idoseptanoside (1) and methyl beta-D-glycero-D-guloseptanoside (2) and the characterization of their preferred solution conformations by computational chemistry and (1)H NMR (3)J(H,H) coupling constant analysis. Central to the synthetic approach was the epoxidation of glucose-derived oxepine 3 using DMDO. Nucleophilic attack on the resulting 1,2-anhydroseptanose using NaOCH(3) in CH(3)OH followed by deprotection provided the 1,2-trans diastereomers 1 and 2. The computational approach for determining the preferred low energy septanose conformations began with a pseudo Monte Carlo search for each isomer using minimization with the AMBER force field. Single-point energy calculations (HF/6-31G *and B3LYP/6-31+G**) as well as full geometry optimizations in a model for aqueous solvent were then conducted using the conformers within 5 kcal/mol of the AMBER global minimum. Calculated (3)J(H,H) values, based on a Boltzmann distribution of the computed low energy conformers, were compared to experimental (3)J(H,H) values from (1)H NMR coupling constant analyses. The correlation between calculated and observed values suggest that septanose carbohydrates are not so flexible and should generally prefer one twist-chair (TC) conformation.