Quantum Mechanical Study of the Syn and Anti Conformations of Solvated Cyclic GMP

Self-consistent Reaction Field (SCRF) computational methods have been applied to guanosine 3:5-cyclic monophosphate (cGMP) to determine the geometries and energetics of the syn and anti conformations of this cyclic nucleotide in aqueous solution. The syn conformation of cGMP has been predicted to be more stable in the gas phase due to an internal hydrogen bond. The syn conformation is observed in the crystal structure of the sodium tetrahydrate salt, although a bridging water molecule is present in lieu of the internal hydrogen bond. In the gas phase, we find from Hartree–Fock/6-31+G(d) optimizations that the syn conformation is more stable than the anti by about 4 kcal/mol. However, we report here that the anti conformation is more stable in aqueous solution, according to estimates based upon results from both the Onsager model and the Isodensity Polarized Continuum Method (IPCM). Our best estimate from single-point IPCM B3LYP/6-31+G(d) calculations has the anti conformation 19 kcal/mol lower in energy. For comparison purposes, we also present SCRF results for syn and anti adenosine 3:5-cyclic monophosphate (cAMP). For cAMP, we estimate the anti conformation to be more stable than the syn by about 6 kcal/mol. We suggest that the relative stability of the anti conformation of cGMP be considered in studies, such as, enzyme docking.     

syn- and anti-(1-Alkyl-π-Allyl)palladium chlorides

π-Allylpalladium chlorides with bulky substituents on the terminal carbon atoms are often formed with these substituents in the less stable anti configuration. The activation energy of the π-σ-π rearrangement to the syn configuration increases with the bulkiness of the substituent. The difference in energy between the anti and syn configurations decreases with increasing size of the substituents on the terminal and meso carbon atoms. The phenomena can best be explained by assuming that there is steric interaction between the substituents on the terminal carbons of the π-allyl ligand and either other ligands on the metal or the substituent on the mso carbon of the π-allyl ligand.     

Stereochemical Prins cyclization: electronic versus steric effects on the synthesis of 2,4,6-trisubstituted tetrahydropyran rings

A convenient approach towards the synthesis of both syn- and anti-2,4,6-chlorotetrahydropyrans has been developed. The electronic and steric influences on the stereochemistry of the Prins cyclized products were investigated based on the substituents of the homoallylic alcohol.     

Dipyridyl/pyridinium thieno[2,3-b]thiophenes as new atropisomeric systems. Synthesis, conformational analysis and energy minimization

Synthesis of a new class of cofacially oriented dipyridyl(pyridinium)lthieno[2,3-b]thiophenes with or without -CO₂Et and -COMe substituents at C2, and C5 positions of thieno[2,3-b]thiophene ring was readily accomplished using a double Dieckman cyclization protocol as the key step. While C2/C5 substituted dipyridylthieno[2,3-b]thiophenes exhibited syn/anti atropisomerism at least up to 70 °C with Arrhenius energy of activation (ΔG^≠) in the range of 17-18 kcal/mol, on the other hand unsubstituted dipyridylthieno[2,3-b]thiophene and its bis-N-quaternized salt were found to show free conformational rotation with an estimated ΔG^≠ of lower than 10 kcal/mol. Conformational energy minimization using AM1 protocol revealed a slight preference for the anti over syn isomers. Compared to the unsubstituted dipyridylthieno[2,3-b]thiophenes, higher energy barriers to rotation (3.7-5.1 kcal/mol) in substituted dipyridylthieno[2,3-b]thiophenes can be attributed to steric encumbrance resulting from -CO₂Et and -COMe substituents located on the non-rotating thienothiophene platform.     

Synthesis and separation of the atropisomers of 2-(5-benzo[b]fluorenyl)-2′-hydroxy-1,1′-binaphthyl and related compounds

Several syn and anti atropisomers of 2-(5-benzo[b]fluorenyl)-2′-hydroxy-1,1′-binaphthyl and related compounds were synthesized from 1,1′-binaphthyl-2,2′-diol (BINOL). It was possible to separate the syn and anti atropisomers by silica gel column chromatography. The syn atropisomers are potential hetero-bidentate ligands for complex formation with metals. By starting from enantiomerically pure (R)-(+)-BINOL and (S)-(−)-BINOL, four optically active syn atropisomers and two anti atropisomers with high enantiomeric purity were obtained. The structures of two syn atropisomers and one anti atropisomer were established by X-ray structure analyses.     

Synthesis and Comparative Analysis of Molecular and Supramolecular Structures of 4,8-Disubstituted 1,5-Dichloro-2,6-dioxotricyclo[5.1.0.0 3,5]octanes

Summary. A series of 4,8-disubstituted 1,5-dichloro-2,6-dioxotricyclo-[5.1.0.0^3,5]octanes, synthesized by various methods, were studied by X-ray single crystal diffraction. The conformation (syn/anti) of the molecules does not depend on the method of preparation and nature of substituents. All the compounds crystallize in centrosymmetric space groups with half of the molecules in the asymmetric part of the unit cell. The main influence which the substituents render is on the packing of molecules in crystals and on the types of intermolecular interactions and supramolecular structures.Received November 7, 2002; accepted (revised) December 16, 2002 Published online June 23, 2003     

Acid-induced conformational alteration of cis-preferential aromatic amides bearing N-methyl-N-(2-pyridyl) moiety

A series of cis-preferential aromatic N-methyl amides was designed and synthesized, and acid-induced conformational alteration of these compounds was investigated by means of NMR measurements in solution and X-ray crystal structure analysis. Compounds with a terminal N-methyl-N-(2-pyridyl) amide unit showed acid-induced conformational change from cis to trans, while those with a terminal N-methyl-2-pyridinecarboxamide unit showed a change of the carbonyl orientation from anti to syn with retention of cis conformation.     

Factors that regulate the conformation of m-benziporphodimethene complexes: agostic metal-arene interaction, hydrogen bonding, and η2,π coordination

Group 12 and silver(I) tetramethyl‐m‐benziporphodimethene (TMBPDM) complexes with phenyl, methylbenzoate, or nitrophenyl groups as meso substituents were synthesized and fully characterized. The dimeric silver(I) complex displays an unusual η²,π coordination from the β‐pyrrolic C?C bond to the silver ion. All of the complexes displayed a close contact between the metal ion and the inner C(22)? H(22) on the m‐phenylene ring. The downfield chemical shifts of H(22) and large coupling constants between Cd^II and H(22) strongly support the presence of an agostic interaction between the metal ion and inner C(22)–H(22). Crystal structures revealed that the syn form is the predominant conformation for TMBPDM complexes. This is distinctively different from the exclusive anti conformation observed in m‐benziporphyrin and tetraphenyl‐m‐benziporphodimethene (TPBPDM) complexes. Evidently, intramolecular hydrogen‐bonding interactions between axial chloride and methyl groups stabilize syn conformations. Unlike the merely syn conformation observed in the solid‐state structures of TMBPDM complexes that contain an axial chloride, in solution these complexes display highly solvent‐ and temperature‐dependent syn/anti ratio changes. The observation of dynamic ¹H NMR spectroscopic scrambling between syn and anti conformations from the titration of chloride ion into the solution of the TMBPDM complex suggests that axial ligand exchange is a likely pathway for the conversion between syn and anti forms. Theoretical calculations revealed that intermolecular hydrogen‐bonding interactions between the axial chloride and CHCl₃ stabilizes the anti conformation, which explains the increased ratio for the anti form when dichloromethane or chloroform was used as the solvent.     

Facile synthesis of various substituted taurines,especially syn- and anti-1,2-disubstituted taurines,from nitroolefins

Taurine and substituted taurines present a group of important structural elements in many natural products. Various substituted taurines, including 1- and 2-substituted, 1,1-, syn-1,2-, and anti-1,2-disubstituted taurines, were synthesized from the corresponding nitroolefins via Michael addition with thioacetic acid, oxidation with peroxyformic acid, and the catalytic hydrogenation under the catalysis of palladium on carbon or platinum dioxide. It is a general, versatile, and salt-free method for the preparation of substituted taurines, especially for syn- and anti-1,2-disubstituted taurines and some taurines with more bulky substituents. The stereostructures of both syn- and anti-1,2-disubstituted taurines were deduced from the nitroalkyl thioacetates in the Michael addition, which were identified via the Karplus equation analysis and computational analysis, and finally confirmed by the XRD single crystal analysis. The diastereoselectivity in the Michael addition was rationalized with the Cram rule.     

Stereoselective synthesis of anti-2-oxazolidinones by Ph3P-CCl4-Et3N mediated SN2 cyclization of N-Boc-β-amino alcohols

Ethyl anti-4-substituted phenyl-2-oxo-1,3-oxazolidine-5-carboxylates were synthesized stereoselectively in excellent yields using the Ph₃P-CCl₄-Et₃N system by S_N2 cyclization of N-Boc-β-amino alcohols. syn to anti conversion of ethyl 4-substituted phenyl-2-oxo-1,3-oxazolidine-5-carboxylates using DBU as base is also described.     

Stereoselective total synthesis of 4-((3S,5R)-3,5-dihydroxynonadecyl)phenol

A stereoselective total synthesis of 4-((3S,5R)-3,5-dihydroxynonadecyl)phenol has been accomplished in two different synthetic approaches. In the first approach, Prins cyclization has been successfully utilized to produce the anti-1,3-diol unit, which was further converted into a required syn-1,3-diol through Mitsunobu reaction. The side chain was constructed through cross metathesis and hydrogenation sequence. In the second approach, the chiral syn-1,3-diol was prepared by a sequence of reactions such as alkylation of 1,3-dithane with (R)-epichlorohydrin, ring opening of the epoxide with vinylmagnesium bromide, and 1,3-syn-reduction of the β-hydroxyketone with NaBH₄ in the presence of diethylmethoxyborane.     

Synthesis and Comparative Analysis of Molecular and Supramolecular Structures of 4,8-Disubstituted 1,5-Dichloro-2,6-dioxotricyclo[5.1.0.0 3,5]octanes

A series of 4,8-disubstituted 1,5-dichloro-2,6-dioxotricyclo-[5.1.0.0^3,5]octanes, synthesized by various methods, were studied by X-ray single crystal diffraction. The conformation (syn/anti) of the molecules does not depend on the method of preparation and nature of substituents. All the compounds crystallize in centrosymmetric space groups with half of the molecules in the asymmetric part of the unit cell. The main influence which the substituents render is on the packing of molecules in crystals and on the types of intermolecular interactions and supramolecular structures.     

First report of syn isomers in the diastereoselective synthesis of highly functionalized piperidines catalysed by wet picric acid: factors influencing the syn-anti ratios

This is the first report of the formation of a syn-diastereoisomer in the diastereoselective synthesis of highly functionalized piperidines catalysed by wet picric acid via a one-pot, step-economic condensation of aromatic aldehydes, 1,3-dicarbonyl compounds and aromatic amines. DFT calculation shows that anti isomers are more stable compared to the syn. The syn-anti ratio of the products depends on the temperature and the nature of substitution on both the aromatic aldehydes and aromatic amines. Conditions for getting pure anti and pure syn compounds have been studied.     

Condensation products of formylcamphor with diamines : Structures in alcoholic solutions as derived from uv absorption and circular dichroism spectroscopy

The condensation products of optically active diamines with two molecules of formylcamphor have been investigated in methanolic solutions, where the formylcamphor chromophore is known to exist in the anti or (E) configuration. UV absorption and circular dichroism spectra are rationalised within an exciton formalism to give information about the absolute configuration.As with chloroform solutions, where the chromophore exists in the syn configuration, it is demonstrated that the title compounds may achieve the low energy conformation in seemingly different ways depending on substituents. Because of the different structure of the molecule when the chromophore is in the anti configuration as compared with the syn configuration, rotational conformations with respect to the substituted ethylene bridge in the same compound may be different in CH₃OH and CHCl₃.Finally “chelating solvation” in hydrogen bonding media is demonstrated through dissolution of the compounds in various alcohols.     

Synthesis and NMR spectra of the syn and anti isomers of substituted cyclobutanes—evidence for steric and spatial hyperconjugative interactions

The syn and anti isomers of cis,cis-tricyclo[5.3.0.0^2,6]dec-3-ene derivatives have been synthesized and their ¹H and ¹³C NMR spectra unequivocally analyzed. Both their structures and their ¹H and ¹³C NMR chemical shifts were calculated by DFT, the latter two calculations employing the GIAO perturbation method. Additionally, calculated NMR shielding values were partitioned into Lewis and non-Lewis contributions from the bonds and lone pairs involved in the molecules by accompanying NBO and NCS analyses. The differences between the syn and anti isomers were evaluated with respect to steric and spatial hyperconjugation interactions.     

Asymmetric O-methylhalohydrin reaction of chiral N-enoyl-2-oxazolidinones: synthesis of N-protected syn-β-methoxyphenylalanine, an unusual amino acid component of cyclomarins

Asymmetric O-methylhalohydrin reactions of chiral N-enoyl-2-oxazolidinones were performed with halogens (Br₂/I₂) promoted by silver(I) in methanol with high regio- and anti-selectivity and moderate to good diastereoselectivity. Reagent-controlled opposite diastereoselectivity was observed especially for cinnamoyl and electron-deficient cinnamoyl substrates. This method was applied to the short enantioselective synthesis of N-protected syn-β-methoxyphenylalanine, an unusual amino acid component of cyclomarins.     

Centrosymmetric and Non-centrosymmetric Packing of Aligned Molecular Fibers in the Solid State Self Assemblies of Cyclodextrin-based Rotaxanes

Two [2]-rotaxanes each comprising α-cyclodextrin as the rotor, and with either 3,3′-difluoro- or 3,3′-dichloro-stilbene as the axle and trinitrophenylamino substituents as the blocking groups at the 4- and 4′-positions, were prepared and their structures analyzed in solution and the solid state using ¹H NMR spectroscopy and X-ray crystallography, respectively. With each rotaxane, in solution the stilbene rotates freely within the cyclodextrin annulus. In the solid state the 3,3′-dichlorostilbene-based rotaxane adopts two very similar conformations, each having the chlorines in the anti,anti-orientation. By comparison, the 3,3′-difluorostilbene-based rotaxane adopts anti,anti-, anti,syn- and syn,syn-orientations of the substituents. The crystal packing of each rotaxane displays aligned molecular fibers, which are centrosymmetrically orientated in the case of the difluoride due to the head-to-head/tail-to-tail alignment of the cyclodextrins. By contrast, all of the cyclodextrins in the dichloride are aligned head-to-tail along a single axis to give a polar, non-centrosymmetric crystal.     

A microwave and quantum chemical study of allyltrifluorosilane

The structural and conformational properties of allytrifluorsilane, H₂CCH-CH₂-SiF₃, have been explored by microwave (MW) spectroscopy and high-level ab initio and density functional theory quantum chemical calculations. The microwave spectrum was investigated in the 18-62 GHz spectral regions. The a-type R-branch transitions of one conformer were assigned for the ground as well as for 10 vibrationally excited states. The CC-C-Si chain of atoms in this rotamer takes an anti-clinal (‘skew’) conformation, with a dihedral angle calculated to be 111.6° from the syn-periplanar (0°) conformation. The question whether a CC-C-Si syn-periplanar conformer exists as a high-energy form in the gas phase remains open. In most of the quantum chemical calculations this conformation is predicted to be a transition state. However, in the most advanced calculations (B3LYP/aug-cc-pVTZ level of theory) the syn-periplanar conformer is predicted to be a stable rotamer that is calculated to be 6.5 kJ/mol higher in energy than the anti-clinal form. Since there is no indication in the MW spectrum for the presence of high-energy form(s), it is concluded that the anti-clinal conformer is at least 4 kJ/mol more stable than any other hypothetical rotamer.     

anti-Markovnikov addition of tellurium tetrachloride to trimethyl ethynyl silane

An investigation of the TeCl₄ interaction with trimethyl ethynyl silane 1 in CHCl₃ has shown that anti-Markovnikov adduct [Z-1-(trimethylsilyl)-2-chlorovinyl]tellurium trichloride is formed as the only product. In time, it is hydrolyzed to give [Z-1-(trimethylsilyl)-2-chlorovinyl]tellurium (hydroxy) dichloride which, in turn, is dehydrated to afford bis[(2-chloro-1-trimethyl-silylvinyl)dichlorotellurium]oxide. These data revealed that the reaction studied was the first example of anti-Markovnikov syn-addition of TeCl₄ to terminal acetylenes. A computed simulation of the TeCl₄ interaction with ethynyl silane 1 in a gas state using PES method did not reveal dominating orientation of the addition but showed the conditions at which anti-Markovnikov addition can occur and which were probably met in carrying out the reaction in CHCl₃.     

Asymmetric synthesis of syn and anti methyl 2,3-diamino-3-phenylpropanoate derivatives from N-substituted imines and Schöllkopf's bislactim ether

The reaction between differently N-substituted benzaldimines and (2R)-Schöllkopf's bislactim ether was studied: the azaenolate addition to imines followed by hydrolysis of the resulting adducts gave syn-(2S,3R) and anti-(2S,3S)-methyl 2,3-diamino-3-phenylpropanoate derivatives in good yields. The configurations of the newly formed stereocenters of α,β-diamino acids were assigned on the basis of the ¹H NMR analysis and by comparison with known products. The diastereoisomeric ratios were explained taking into account the effect of the substituent present on the imine nitrogen on the transition state stability. This method represents a new approach for stereoselective synthesis of α,β-diamino acids.