Structures and conformations of 1-aryl-1,4-dihydro-3(2H)-isoquinolinones

The X-ray crystal structures of series of 1-aryl-1,4-dihydro-3(2H)-isoquinolinones (1-7) have been determined. Lactame heterocyclic ring possesses more or less deformed boat conformation in all examined structures. The aryl substituent adopts the equatorial position in the structures 1-3 and the axial one in 5-7. In the structure of 4, due to extremely flattened heterocyclic ring, aryl substituent location can be named as bisectional. In all solved structures the molecules are joined into the dimers via two N-H?O hydrogen bonds. At the same time, ¹H NMR studies in DMSO-d₆ solutions were accomplished and profound analysis of ²J, ³J, and ⁵J coupling constants have shown that in isoquinolinone system the heterocyclic ring adopts the boat conformation in all investigated compounds. The stereochemical orientations of the phenyl ring at C1 do not depend on the nature of the substituent but, exclusively, on the mode of substitution. However, three forms of undulated laktam heterocyclic ring conformation in respect of 1-aryl substituent positions were confirmed by calculation (conformational analysis).     

DFT,solution, and crystal conformation of eremophilanolides

The minimum energy conformation of five eremophilanolides (1–5) from the tubercles of Psacalium paucicapitatum was calculated using density functional theory (DFT) at the B3LYP/6-31G¹ level. Comparison of the experimental ¹H–¹H coupling constant values of 1–5 with those generated employing a generalized Karplus-type relationship using dihedral angles extracted from the DFT calculation and from the crystal structures for 1 and 3–5 shows good agreement. The A ring of 1–5 adopts an almost perfect chair conformation with the Me-14 group in an axial position and the Me-15 in an equatorial position.     

The configuration and conformation of isogermacrone. The significance of crossed conformations in olefinic cyclisations

The 9,10-double bond of isogermacrone was assigned the Z configuration based on¹HNMR nOe measurements and the ¹³CNMR shifts of the methyl groups. An X-ray crystal structure determination verified this conclusion and the structure of isogermacrone was shown to be (2Z, 7E)-3,7-dimethyl-10(1-methylethyl-idene)-2,7-cyclodecadien-1-one (1). The molecule crystallised in an anti conformation, which according to ¹HNMR is the predominant conformation in solution at room temperature.¹H NMR spectroscopy revealed the presence of syn and anti conformers in the ratio 1:2 at about -60°. The stereochemistry of the base-induced formation of isogermacrone 1 from germacrone 2 and that of the transannular cyclisation of isogermacrone are discussed.     

(4R)-4-Hydroxy-1-nitroso-l-proline: synthesis, X-ray structure, ab initio and conformational calculations

4-Hydroxy-l-proline, an amino acid, an important component of collagen, was transformed into its N-nitroso-derivative, (4R)-4-hydroxy-1-nitroso-l-proline, 1 by butylnitrite in the acidic medium. The structure is a cyclic hydroxy-N-nitrosoacid with the carboxyl and hydroxyl groups trans to each other. The carboxyl group is in the syn-conformation. In the structure, the neutral molecules are connected via classical intermolecular O-H?O hydrogen bonds involving the hydroxyl and carboxyl groups [O?O=2.6251(14) Å], and form chains along the a-axis direction. The chains are linked into sheets via O-H?O hydrogen bond, [O?O=2.6813(15) Å] with participation of oxygen atom of nitroso group. Ab initio calculations based on density functional theory at the B3LYP/6-311++G(d, p) level of theory were performed to analyze the influence of 4-hydroxy-l-proline (Hyp) nitrosation on the conformation of the synthesized N-nitroso-compound. The geometry optimization of 1 and initial 4-hydroxy-l-proline was carried out in the gas phase and in solution using the polarizable continuum model. The single-point calculation was performed for the crystal structure of 1. The most stable conformer of 1 is observed in an aqueous solution. In this state, the pyrrolidine ring adopts an envelope conformation, which is also maintained in the gas phase. The twisted conformation of the pyrrolidine ring is present in all states of Hyp and in the crystal structure of 1. In 1 the interchange of five-membered ring conformation in solution and in the gas phase in comparison with the crystal is accompanied by an increase of the dipole moment of the molecule, which is maximal in solution.     

Conformational analysis—XIII: Syn and anti [3.2]-, [3.3]-, [4.2]-, and [4.3]-metacyclophanes

While in [3.3]metacyclophane (19) the aromatic rings preferentially adopt the syn arrangement, its lower and higher homologues, i.e. [2,2]-, [3.2]-, [4.2], and [4.3]-metacyclophane (1, 6, 26 and 30), adopt the anti conformation. Substituted [m,n]metacyclophanes do not necessarily behave similarly to the parent hydrocarbons. Substituted compounds exhibiting a different conformation are [3.2]metacyclophane-1,11-dione (7) (syn), [3.3]metacyclophane-2,11-dione (24) and the corresponding bis[propylene thioacetal] (25) (anti), [4.2]metacyclophane-2,12-dione (27) (syn), and [4.3]metacyclophane-2,13-dione (31) (syn). Thus, the solution conformation of an [m.n]metacyclophane is sensitive both to chain length [m.n.] of the bridges and substitution. The ring inversion barriers determined by variable temperature ¹H NMR decrease with increasing length of the bridges and qualitatively correlate with the transanular strain present in the pertinent system.     

Conformational study on some β-phenyl-α,β-unsaturated ketones

The conformation of three (E)-β-phenyl-α,β-unsaturated ketones and their corresponding (Z)-isomers 1, 2, and 3 was established by IR and ASIS. (Z)-1 and (E)-1 have exclusively the s-trans conformation. The two isomers of 2 occur in both conformations but there is a higher s-cis to s -trans ratio with the (Z) than with the (E)-isomer. (Z)-3 appears to exist exclusively in the s-cis conformation, the (E)-isomer has a small content of the s-trans conformation. It was concluded that the ASIS for H_b, is a measure of the s-cis content of the conformational equilibrium.     

DBU induced formation of 8-bromoguanosine dimer with three hydrogen bonds between the GG− base pairs

Upon hemideprotonation of 8-bromoguanosine (8-BrG) at the N1 position, induced by DBU, the adduct [8-BrG][8-BrG]^?[DBU–H]⁺ was formed. Slow evaporation of the 8-BrG methanol solution, in the presence of 0.5 equiv of DBU, yielded two polymorphic structures (1 and 2), where a neutral [8-BrG] (A) and N1 deprotonated, anionic 8-bromoguanosine [8-BrG]^? (B) were joined together through three intermolecular hydrogen bonds involving O6, N1 and C2–NH₂ sites. Such pairing gave planar GG^? dimers as the basic motif of crystal packing in both polymorphs. Both neutral and deprotonated guanosine molecules in the structure of 1 had the ribose units in a syn conformation. In the structure of polymorph 2, the N1 deprotonated guanosine molecule (B) retained the syn glycosidic conformation, while the non-deprotonated guanosine molecule (A) adopted the natural anti conformation of the ribose unit with respect to the nucleobase. Ribose rings revealed different puckering; only those of deprotonated molecules 1B and 2B possessed the usual C2′-endo envelope conformation. Crystal packing in both structures was guided by the highly complex H-bonded pattern. The CSD was searched for related structures, which are discussed with reference to polymorphs 1 and 2. ¹H and ¹³C NMR spectroscopic evidence is provided showing that the three H-bonded adduct [8-BrG][8-BrG]^?[DBU–H]⁺ was also formed in the highly H-bond competitive DMSO solution.     

Synthesis,structure, and conformation of terphenylene-derived azacalix[4]aromatics

Several novel azacalix[4]aromatics constituting terphenylene units have been synthesized via sequential nucleophilic aromatic substitution reactions of 5′-t-butyl-(1,1′:3′,1″-terphenyl)-3,3″-diamine 9 and 5′-t-butyl-(1,1′:3′,1″-terphenyl)– 4,4″-diamine 11 with 1,5-difluoro-2,4-dinitrobenzene and cyanuric chloride, respectively. The bridging –NH– functions of the tetra-nitro substituted azacalix[2]arene[2]terphenylenes 1 and 2 have been transformed to the corresponding –N(CH₃)– bridged azacalix[2]arene[2]terphenylenes 3 and 4 via N-alkylation. Single crystal X-ray analysis revealed that the terphenyl-3,3″-diamine derived azacalix[2]terphenylene[2]triazine 5 adopts a distorted chair conformation in the solid state, and the terphenyl-4,4″-diamine derived azacalix[2]terphenylene[2]triazine 6 was found to adopt a 1,3-alternate conformation.     

Synthesis and conformational analysis of exo-and endo-7-substituted-3-azabicyclo[3.3.1]nonanes

The synthesis of some 7-substituted-3-azabicyclo[3.3.1]nonanes is described. Routes followed were the debenzoylation of the 7-benzoyl derivative 7 and the decarboxylation of the 7-carboxy compounds 21 and 27. The so-obtained 7-oxo-N-tosyl-3-azabicyclo[3.3.1]nonanes 8and 11 show an extremely low reactivity towards a series of nucleophilic reagents. From analysis of the ¹H NMR spectral data of a series of derivatives, the twin-chain conformation for the 7-exo compounds and the chair-boat conformation for the 7-endo compounds is indicated.     

Synthesis,crystal structure and 3D-QSAR studies of antifungal (bis-)1,2,4-triazole Mannich bases containing furyl and substituted piperazine moieties

This article exhibited the synthesis, crystal structure and 3D-QSAR studies of antifungal furyl- and piperazine- containing (bis-)1,2,4-triazole Mannich bases.     

Synthesis, characterization, and coordination chemistry of two new tartaric acid-derived bis(phosphite) ligands

The syntheses of two chiral bis(phosphite) ligands with tartaric acid-derived backbones: 1 (from dimethyl tartrate) and 2 (from dipyrollidene tartramide), three complexes of 1: cis-Mo(CO)₄(1), cis-PtCl₂(1), and cis-PdCl₂(1) and two complexes of 2: cis-Mo(CO)₄(2) and cis-PdCl₂(2) are described. Each ligand and complex has been fully characterized by ¹H, ¹³C, and ³¹P NMR spectroscopy, and the coordination ³¹P NMR chemical shifts have been compared to those observed for complexes of related ligands. The X-ray crystal structures of each of the metal complexes have also been determined. The X-ray crystal structures indicate that the conformation of the seven-membered chelate ring varies depending on the substituents on the tartrate backbone. However, the conformations of the seven-membered rings do not change when the metal center is changed or when the coordination environment around the metal center is changed.     

Synthese,Kristallstruktur und Konformation vontrans-[2.2](1,2)Ferrocenophan und seinen 1-Hydroxyderivaten

Starting from1-(dimethylaminomethyl)-2-iodo-ferrocene (3) [2.2](1,2)ferrocenophane (2) was prepared in an 8-step synthesis with 17% overall yield. Both from the oxoderivative12 and the ferrocenophane2 puretrans-isomers (12b and2b, resp.) were obtained; the former (12b) was reduced to a separable mixture ofexo andendo 1-hydroxy-ferrocenophanes13a andb, resp. (～ 3:7), the configurations of which were assigned by the LIS-method. X-ray crystal structure analysis of2b revealed a centrosymmetrical chair conformation. From¹H- and¹³C-NMR spectra both for2b and for the hydroxyderivatives13 a rigidexo-exo chair conformation was deduced.     

Molecular geometry and optical activity of N-nitroso-2,2,6,6-tetramethylpiperidines generated by spontaneous crystallization and inclusion complexation with optically active diols

Three sterically strained N-nitrosamines and their inclusion complexes with optically active diols (TADDOLs) were obtained and their solid state crystal structures are described. Owing to the formation of N-nitroso-4-hydroxy-2,2,6,6-tetramethylpiperidine 2 as spontaneously resolvable conglomerate crystals (space group P3₂) its solid state CD was measured. The crystal structures of the inclusion complexes revealed that in all cases the guest nitrosamines assume chiral conformations as seen by their chiroptical spectra. The optically active nitrosamines are configurationally labile and rapidly racemize in solution. The solid state structures revealed that in order to avoid an allylic 1,3-strain [A^(1,3)], caused by an interaction of the nitrosamino group with the methyl substituents, the piperidine ring in 1 and 2 assumes a chair conformation significantly flattened at the amino nitrogen whereas in the 4-oxo derivative 3 the piperidine ring assumes a twist-boat conformation.     

Circular dichroism of some cyclopropane ring containing 1,3-cyclo-5,10-seco-steroidal ketones

Circular dichroism of the rearranged keto steroids 3 and 4, containing a condensed three and nine-membered ring system, shows that the conformation of the nine-membered ring is the same in solution as in the crystal; reduction of the kto group does not change this situation. CD also indicates that epimerization at C(5) in the pair $\text{7}\text{8}$ and the pair $\text{11}\text{12}$ leaves the cyclononanone ring conformation unchanged.     

The structure and absolute configuration of verticillol,a macrocyclic diterpene alcohol from the wood of sciadopitys verticillata sieb. et zucc. (taxodiaceae)

The structure of verticillol diepoxide 4 has been established by direct single crystal X-ray analysis. The structure of verticillol 5 follows from the chemical correlation to the diepoxide 4 as well as from NMR-LIS studies on verticillol which also provide evidence for the conformation of this alcohol. The absolute configuration of verticillol 5 has been assigned on the basis of CD data for the verticillol norketodiepoxide 6a.     

Synthesis and structure characterization of unsymmetrical oxacalix[2]benzene[2]pyrazines

The synthesis of two unsymmetrically linked oxacalix[2]benzene[2]pyrazines (1 and 2) is described. X-ray single crystal structure analysis revealed a highly distorted 1,3-alternate conformation of compound 1 (containing ortho- and meta-diphenol components) and a distorted boat conformation of compound 2 (containing meta- and para-diphenol components). Oxacalix[2]benzene[2]pyrazine containing both ortho- and para-diphenol components was not obtained via similar synthetic strategy.     

Stereochemical analysis of d-glucopyranosyl-sulfoxides via a combined NMR,molecular modeling and X-ray crystallographic approach

(S)-α-Methoxyphenylacetic acid (MPAA) was used as an NMR shift reagent in combination with molecular modeling to predict the absolute configuration of a representative epimeric pair of glucopyranosyl sulfoxides. The correctness of this assignment was confirmed by X-ray crystallographic examination of one of the epimers, 3a1. The crystal structure of ethyl 2,3-di-O-acetyl-4,6-O-benzylidene-1-thio-β-d-glucopyranoside S-oxide monohydrate 3a1 was solved by direct methods and was shown to bear the (R)-configuration at the sulfinyl center in accordance with our prediction. Furthermore, the conformation of 3a1 in the solid state was found to be remarkably similar to that predicted by molecular mechanics calculations.     

Synthesis of enantiomerically pure inherently chiral calix[4]arenes using the meta-substitution strategy

A meta-substituted aminocalix[4]arene 4 immobilized in the cone conformation was prepared via mercuration of the starting tetra-propoxy derivative, followed by nitrosation and reduction reactions. Acylation of the amino group by chiral amino acid residues ((S)-N-trifluoroacetyl-Ala or (S)-N-trifluoroacetyl-Phe) allowed for the preparation of diastereomeric amides that were separated by preparative TLC on silica gel. Subsequent cyclization under Bischler-Napieralski reaction conditions yielded calixarenes 7b and 7c bearing an oxazole moiety in the meta position instead of the expected upper rim-bridged compounds. The reaction sequence represents a straightforward approach towards enantiomerically pure inherently chiral calix[4]arene derivatives (without HPLC separation steps). The absolute configuration of the enantiomers were confirmed by single crystal structure determination (X-ray).     

Synthesis,structural characterization and properties of one-dimensional coordination polymers of cobalt(II)- and nickel(II)-phosphonate complexes with 2,2′-bipyridine as a secondary ligand component: Observation of both cis and trans conformations of a diphosphonic acid

Two new isomorphous cobalt and nickel phosphonates [M^II(2,2′-bipy)₂LH₄]_n[LH₂]_n, M = Co (compound 1), M = Ni (compound 2) were hydrothermally synthesized from p-xylylenediphosphonic acid (LH₄) and the corresponding metal salts with 2,2′-bipyridine as secondary ligand component. Both the compounds 1 and 2 are characterized by routine elemental analyses, IR-, electronic-spectral analyses, thermogravimetric studies and unambiguously characterized by single crystal X-ray crystallography. The structures were refined in monoclinic space group C2/c. The crystal structure consists of 1D [M(2,2′-bipy)₂LH₄]²⁺ chains and [LH₂]²⁻ anions. The flexibility of non-rigid ligand p-xylylenediphosphonic acid (LH₄) tends to adopt a rare cis conformation in the crystal structure to meet the coordination requirement of the metal center from the usual trans conformation. The hydrogen bonding in the crystal structure leads to cylindrical tubes that extend via p-xylylenediphosphonic acid resulting in a 2D supramolecular sheet throughout the crystal. Compounds 1 and 2 are additionally characterized by thermogravimetric studies.     

Sequence and three-dimensional structure of cycloreticulins A and B, new cyclooctapeptides from the seeds of Annona reticulata

Two cyclooctapeptides, cycloreticulin A, cyclo(Pro¹-Gly²-Asp³-Ile⁴-Ser⁵-Ile⁶-Tyr⁷-Tyr⁸) (1) and cycloreticulin B, cyclo(Pro¹-Mso²-Tyr³-Gly⁴-Thr⁵-Val⁶-Ala⁷-Val⁸) (2), have been isolated from the methanol extract of the seeds of Annona reticulata L. The sequences were elucidated on the basis of the MS/MS fragmentation using a QTOF mass spectrometer equipped with an ESI source, chemical degradation and extensive 2D-NMR. The solid state conformation of cycloreticulin A, carried out by X-ray study, is characterised by the presence of two β-turns (types II and III) and an inversed γ-turn. Its solution structure appeared quite similar to the crystal one. The cyclic backbone solution structure of cycloreticulin B, close to that of the cyclooctapeptide squamin A, from which its sequence only differs by a Val⁸/Ile⁸ substitution, involves three β-turns, two of type I and one of type III, being similar to the crystal structure of squamin A.