Cisoid Conformation Research Articles

Theoretical study of stereoselective reduction controlled by NADH analogs

The potential energy surfaces (PES) of 2-methyl-4-( R)-methyl-1,4-dihydropyridine-3-carboxamide (4 R-DM, 1), 2-methyl-4-( S)-methyl-1,4-dihydropyridine-3-carboxamide (4 S-DM, 2) and 2-methyl-1,4-dihydropyridine-3-carboxamide (MM, 3) have been explored with ab initio calculations at the RHF/6-311G ** and MP2/6-311G ** levels of theory. In agreement with previous experimental and computational results, the PES provides three minima for each of the above molecules. The calculations reported herein indicate that the cisoid conformation is most favorable in gas phase and hydrophobic environments. Nevertheless, the preference of the cis conformation can be controlled by different solvents. The most favorable conformation in methanol, water, and probably in the polar (or water medicated) enzyme active sites, however, would be the one in which the carbonyl group is in a transoid position and is syn to H syn. In addition, our calculations suggest that the carbonyl group in the syn, rather than anti, position relative to H syn is preferred. These observations are in very good agreement with previous computational and experimental results. Our computational studies have provided an explanation as to why the transoid conformation is preferred in enzyme active sites as well as in many other NADH mimics. Furthermore, these new data imply that the stereoselectivity of NADH analogs can be controlled by means of changing solvents in which the reaction is carried out.

Preparation of α‐Substituted γ‐Alkoxyallylstannanes from β‐Tributylstannyl Acrolein Acetals: Scope of the Method and Primary Rationalization of the Obtained Results.

AbstractFor Abstract see ChemInform Abstract in Full Text.

Self-assembly and third-order optical properties of HgI 2 with linear and angular bipyridine ligands

Two bis(pyridyl) ligands: N, N′-bis(4-pyridyl)-1,4-benzenedicarboxamide (bpba) and N, N′-bis(3-pyridylformyl)imidazolidine-2-thione (bpit) have been designed and synthesized. Self-assembly of the linear ligand bpba and angular ligand bpit with HgI 2 results in a one-dimensional zigzag polymer {[HgI 2(bpba)] · 1.5CH 3OH} n ( 1) and a binuclear metallamacrocycle [HgI 2(bpit)] 2 · 3H 2O ( 2), respectively. Single crystal X-ray diffraction analyses reveal that in the crystal structure of 1 the linear ligand bpba is in transoid conformation, while in the crystal structure of 2 the angular ligand bpit coordinates with HgI 2 in cisoid conformation, the different geometries of the two ligands attribute to forming the dissimilar frameworks of two HgI 2 adducts. The determination of third-order nonlinear optical (NLO) properties of 1 and 2 in DMF solution shows that adducts 1 and 2 possess strong NLO self-focusing effect. The hyperpolarizability γ values of 1 and 2 are calculated to be 2.10 × 10 −29 and 3.24 × 10 −29 esu, respectively, which are comparable to those of some NLO materials. And the result indicates that the heavier atoms Hg and I together with the polymeric aggregation play an important role in determining their NLO properties.

Amino-functionalized DNA: the properties of C5-amino-alkyl substituted 2'-deoxyuridines and their application in DNA triplex formation

The incorporation of C5-amino-modified 2′-deoxyuridine analogues into DNA have found application in nucleic acid labelling, the stabilization of nucleic acid structures, functionalization of nucleic acid aptamers and catalysts, and the investigation of sequence-specific DNA bending. In this study, we describe the physicochemical properties of four different C5-amino-modified 2′-deoxyuridines in which the amino group is tethered to the base via a 3-carbon alkyl, Z- or E-alkenyl or alkynyl linker. Conformational parameters of the nucleosides and their pKa values were deduced using 1H NMR. All of them display the expected anti-conformation of the nucleoside with 2′-endo sugar puckers for the deoxyribose ring. A preference for the cisoid conformation for the Z-alkenyl analogue is found, while the E-alkenyl analogue exists exclusively as its transoid conformation. The pKa values range from 10.0 for the analogue with an aliphatic propyl linker to 8.5 for the propargylamino analogue. The analogues have been used for the synthesis of triple-helix forming oligonucleotides (TFOs) in which they replace thymidine in the natural sequence. Oligonucleotides containing the propargylamino analogue display the highest stability especially at low pH, while those containing analogues with propyl and especially Z-alkenyl linkers are destabilized to a great extent. TFOs containing the analogue with the E-alkenyl linker have stability similar to the unmodified structures. The chemical synthesis of TFOs containing the analogue, 5-(3-hydroxyprop-1-ynyl)-2′-deoxyuridine that possesses a neutral but polar side chain show a remarkable stability, which is higher than that of all TFOs containing the alkylamino or alkenylamino analogues and only slightly lower than that of TFOs containing the propargylamino analogue. Both the hydroxyl and propargylamino substitutions impart enhanced triple-helix stability relative to the analogous sequences containing C5-propynyl-2′-deoxyuridine. Furthermore, a similar dependence of stability on pH is found between TFOs containing the hydroxypropynyl modifications and those containing the propargylamino side chains. This suggests that the major factor responsible for stabilizing such triple helices is due to the presence of the alkyne with an attached electronegative group.

Synthesis and structures of alkaline earth metal salts of bis[(trifluoromethyl)sulfonyl]imide

A series of alkaline earth metal salts of the bis[(trifluoromethyl)sulfonyl]imide anion have been prepared and structurally characterized. The magnesium cation is fully hydrated with no direct interaction with the anion, although there is extensive hydrogen bonding involving coordinated and lattice water molecules and the anion. The calcium cation is heavily hydrated, but also directly interacts with two anions. As with the magnesium salt, hydrogen bonding plays a major role in determining the crystal packing. The strontium salt is anhydrous, and the eight-coordinate cation interacts directly with several anions to form a two-dimensional layered structure. The barium salt is a monohydrate, with a nine-coordinate cation. As with strontium, it also forms a layered structure. Despite the differences, all of the structures exhibit extensive fluorine segregation which results in the formation of hydrophilic and hydrophobic domains. In all but the magnesium salt, the anion is chelated to the metal and has a cisoid conformation with the trifluoroalkyl groups lying to the same side of the S N S plane. This is in keeping with our previous observations that the cisoid conformation is preferred when the anion is coordinated to a metal ion, while the transoid is preferred for noncoordinating cations.

A latent photoreaction predominates within water-soluble calixarenes: photochemistry of benzoin alkyl ethers

Benzoin alkyl ethers encapsulated in a cisoid conformation within water-soluble p-sulfonatocalix[8]arenes preferentially yield the Norrish Type II reaction product deoxybenzoin.

Preparation of α-substituted γ-alkoxyallylstannanes from β-tributylstannyl acrolein acetals: scope of the method and primary rationalization of the obtained results

α-Substituted γ-alkoxyallylstannanes were obtained from β-tributylstannyl acrolein acetals when reacted with lower order magnesium cyanocuprates in the presence of boron trifluoride at low temperature. In the case of n-alkylcyanocuprates an anti S N2′ substitution on a cisoid conformation appears to be the main reaction pathway. However, subtle competitions with other mechanisms may occur depending on the experimental conditions, on the reagents or on the substrates. These drawbacks constitute limitations for the use of the method especially when enantioenriched α-substituted γ-alkoxyallylstannanes are desired.

Torsional profiles of protonated and metal-coordinated 2,2′-bipyridine

The rotational profiles of both the mono and di-protonated 2,2′-bipyridinium cations were calculated with ab initio Hartree Fock and density functional theoretical methods. The most stable form of the singly protonated bipyridine is the planar cisoid conformation with a weak, bent and strongly asymmetric NHN hydrogen brigde. The transoid conformer is predicted to exhibit the maximal charge delocalization in the coplanar arrangement, however, it is twisted due to sterical hindrance. The di-protonated species is most stable in a twisted (about 40°) transoid conformation with a very shallow potential minimum of the twisted cisoid form. Rotational profiles of transition metal complexes [bipyZn(H 2O) n] 2+ with n=2–4 and [bipyRu(CO) 4] 2+ leading from the monodentate transoid to the stable bidentate bipy complex are also calculated with density functional theory methods. There is no potential energy barrier between the coordinated cisoid and transoid bipy complexes with [bipyZn(H 2O) n ] 2+ and a small barrier is found for [bipyRu(CO) 4] 2+.

A B3LYP study of the effects of phenyl substituents on 1,5-hydrogen shifts in 3-(Z)-1,3-pentadiene provides evidence against a chameleonic transition structure.

The effects of one or two phenyl substituents on the activation enthalpy for a 1,5-hydrogen shift in 3-(Z)-1,3-pentadiene (1) and on the geometry of the transition structure (TS) have been investigated by B3LYP/6-31G calculations. The phenyl-substituent effects on the experimentally measured activation enthalpies are predicted to be sizable, spanning a range of nearly 10 kcal/mol. However, if differences between steric effects in the transoid isomers of the reactants are factored out by comparing the activation enthalpies in the cisoid conformers, the electronic components of the phenyl-substituent effects on both the barrier heights and the TS geometries are found to be quite modest in size. Unlike the TS in the Cope rearrangement, the TS for a 1,5-hydrogen shift in 1 is not highly variable in nature, and the reason the 1,5-hydrogen shift TS is not chameleonic is discussed.

Properties of two multifunctional plant fatty acid acetylenase/desaturase enzymes.

The properties of the Delta6 desaturase/acetylenase from the moss Ceratodon purpureus and the Delta12 acetylenase from the dicot Crepis alpina were studied by expressing the encoding genes in Arabidopsis thaliana and Saccharomyces cerevisiae. The acetylenase from C. alpinaDelta12 desaturated both oleate and linoleate with about equal efficiency. The desaturation of oleate gave rise to 9(Z),12(E)- and 9(Z),12(Z)-octadecadienoates in a ratio of approximately 3 : 1. Experiments using stereospecifically deuterated oleates showed that the pro-R hydrogen atoms were removed from C-12 and C-13 in the introduction of the 12(Z) double bond, whereas the pro-R and pro-S hydrogen atoms were removed from these carbons during the formation of the 12(E) double bond. The results suggested that the Delta12 acetylenase could accommodate oleate having either a cisoid or transoid conformation of the C(12)-C(13) single bond, and that these conformers served as precursors of the 12(Z) and 12(E) double bonds, respectively. However, only the 9(Z),12(Z)-octadecadienoate isomer could be further desaturated to 9(Z)-octadecen-12-ynoate (crepenynate) by the enzyme. The evolutionarily closely related Delta12 epoxygenase from Crepis palaestina had only weak desaturase activity but could also produce 9(Z),12(E)-octadecadienoate from oleate. The Delta6 acetylenase/desaturase from C. purpureus, on the other hand, produced only the 6(Z) isomers using C16 and C18 acyl groups possessing a Delta9 double bond as substrates. The Delta6 double bond was efficiently further converted to an acetylenic bond by a second round of desaturation but only if the acyl substrate had a Delta12 double bond and that this was in the Z configuration.

Magneto-structural characterization of metallocene-bridged nitronyl nitroxide diradicals by X-Ray, magnetic measurements, solid-state NMR spectroscopy, and ab initio calculations.

Crystallization of ferrocene and ruthenocene substituted in the 1- and 1'-positions by two nitronyl nitroxide radicals gave the new crystal phases beta-1 (besides the known phase alpha-1), alpha-2, and beta-2 whose structures were determined by X-ray analysis. In beta-1 the radical moieties adopt transoid positions, whereas two different cisoid conformations are adopted by alpha-2 and beta-2. These conformations result from inter- and intramolecular hydrogen bonds, respectively. All compounds experience antiferromagnetic interactions, and J/k(B) values up to -7 K have been found by fitting the experimental magnetic susceptibilities to a modified Bleaney-Bowers equation. The solid diradicals alpha-1, beta-1, alpha-2, and beta-2 as well as the ferrocene 3, which was substituted by a unique nitronyl nitroxide, were investigated by (13)C and (1)H NMR spectroscopy with magic angle spinning. The carbon signals cover a range of 2000 ppm, and are well resolved such that the structure could be confirmed. Conversion of the signal shifts into spin densities disclosed the mechanisms by which spin delocalization from the nitronyl nitroxide substituents to the metallocene core occurs. The spin density distribution in alpha-1, beta-1, and 3 was also predicted by DFT calculations. There is good agreement between the experimental and theoretical trends of the spin delocalization. The magnetic interactions were discussed in the light of intramolecular spin transfer and its dependence on geometric constraints, demonstrating that the 1,1'-metallocenylene bridge is not a robust magnetic coupler.

2,2'-Bipyridinium(1+) bromide monohydrate.

In the crystal structure of 2,2'-bipyridinium(1+) bromide monohydrate, C(10)H(9)N(2)(+).Br(-).H(2)O, the cation has a cisoid conformation with an intramolecular N-H.N hydrogen bond. The cation also forms an N-H.O hydrogen bond to an adjacent water molecule, which in turn forms O-H.Br(-) hydrogen bonds to adjacent Br(-) anions. In this way, a chain is formed extending along the b axis. Additional interactions (C-H.Br(-) and pi-pi) serve to stabilize the structure further.

Metal Chelations in Asymmetric Diels—Alder Reaction.

AbstractFor Abstract see ChemInform Abstract in Full Text.

Heterodimetallic compounds assembled from ferrocenedicarboxylato and ferrocenecarboxylato ligands.

Heteropolynuclear organometallic compounds have been constructed by using two kinds of ferrocene-based ligands, 1,1'-ferrocenedicarboxylic acid (H(2)L(1)) and ferrocenecarboxylic acid (HL(2)). Reactions the ligand H(2)L(1) with copper(II) and nickel(II) salts, in the presence of pyridine, give a tetranuclear Cu(2)Fe(2) mixed-metallic box Cu(2)L(1)(2)(Py)(2)(DMF)(2)(H(2)O)(2) (1) and a tetranuclear heterobimetallic helix Ni(2)L(1)(2)(Py)(4)(H(2)O) (2), respectively. In these complexes, the ferrocene moieties show cisoid conformations which lead to the formation of the finite coordination geometry, i.e. to molecular complexes. Interactions of the ligand H(2)L(1) with lanthanide ions afford two-dimensional networks [La(2)L(1)(3)(CH(3)OH)(4)]( infinity ) (3), [Eu(2)L(1)(3)(H(2)O)(5)]( infinity ) (4), and [Gd(2)L(1)(3)(CH(3)OH)(2)(H(2)O)(3)]( infinity ) (5), respectively, in which transoid conformations of the ferrocene moiety provide opportunities to form infinite 2-D networks. It is suggested that the conformational freedom of the ferrocene moiety makes the ligand L(1) display different conformations and coordination modes in these complexes. In addition, the pi.pi interactions related to the ferrocene moieties were also found to stabilize the supramolecular architectures in the solid state. As a comparison, reaction of lanthanide ions with the ligand HL(2) resulted in three isostructural heterodinuclear windmill-shaped compounds Ln(2)L(2)(6)(CH(3)OH)(2)(H(2)O)(5) [Ln = La (6), Eu (7), and Gd (8)] by simply diffusing the solutions of lanthanide ions into the mixture of HL(2) and NaOH, respectively. Electrochemical properties of the ferrocene-containing complexes 1-8 are also investigated in the solution or solid state.

Triphenylphosphine oxide-3-chlorobenzoic acid (1/1).

In the title compound, C(18)H(15)OP.C(7)H(5)ClO(2), the triphenylphosphine oxide molecule forms a single directed hydrogen bond with the 3-chlorobenzoic acid molecule, with an O.O=P distance of 2.607 (2) A. The C-Cl and C=O bonds adopt a cisoid conformation in the 3-chlorobenzoic acid molecule.

Tetra- and octalactam macrocycles and catenanes with exocyclic metal coordination sites: versatile building blocks for supramolecular chemistry.

The synthesis of a new tetralactam macrocycle and the simultaneous formation of catenanes and larger octalactam macrocycles is reported. These species bear 2,2'-biquinoline moieties suitably positioned to bind a metal center at the outer periphery of the macrocycles. (1)H NMR chemical shifts permit the unambiguous distinction of transoid and cisoid conformations of the biquinoline moiety, thereby allowing an unequivocal identification of the catenane and octalactam structures, despite the fact that both have the same elemental composition and bear identical structural subunits. With the aid of an anion template effect, rotaxanes can be prepared from the smaller tetralactam macrocycle. These reveal significantly altered requirements in terms of the stopper size as compared to previously reported tetralactam wheels. Several copper(I)-mediated dimers and a (bpy)(2)Ru(II) complex (bpy=2,2'-bipyridine) have been synthesized from the tetralactam macrocycle and the rotaxanes. The anion binding abilities of the tetralactam macrocycle and its (bpy)(2)Ru(II) complex in DMSO have been compared by (1)H NMR titration experiments, which revealed significantly enhanced binding by the metal complex. Mass spectrometry has been used to study the potential formation of larger assemblies of copper(I) and the catenane built-up from two tetralactam macrocycles. Indeed, a 2:2 complex was identified. In contrast, the octalactam macrocycle of the same elemental composition yields only 1:1 complexes, with the Cu(I) ion connecting its two biquinoline moieties in the center of a figure-eight-shaped molecule. Molecular modeling studies support the structural assignments made.

Crystal Structure of N,N,N’,N’-tetra-[(3,5-dimethyl-1-pyrazolyl) methyl]-para-phenylenediamine

The title compound, molecular formula C30H40N10, crystallizes and exhibits a cisoidal conformation around a central p-phenylenediamine ring suggesting that this bis-tripodal ligand is highly flexible and could be accommodated by many and original metal coordinations. All four five-membered pyrazole rings are identical. The molecule presents an inversion centre that coincides with the phenyl ring centre: pyrazole rings are two-by-two equivalent. The electrostatic spatial intramolecular repulsion between N4 and N5 is probably responsible for this general arrangement. These data emphasize the basic character of nitrogens N4 and N5.

Optical Rotatory Feature of (R or S)‐1, 1′‐Binaphthalene‐2, 2′‐diol (BINOL) in Various Solvents

AbstractThe changes of the specific rotation and sign of optically active BINOL have been studied in polar/non‐polar solvents and at the different pH values of solvent. It is considered that these changes are determined by the equilibrium studies between cisoid and transoid conformations of BINOL with the same configuration (R or S) which related to the change of the dihedral angle between two naphthalene ring planes of BINOL.

Metal Chelations in Asymmetric Diels-Alder Reaction

In the presence of chiral catalysts, Diels-Alder reaction of a N-acryloyl chiral dienophile with cyclopentadiene gave the corresponding endo norbornenecarboxamide with high diastereoselectivity. In the reaction, 8-membered chelation was effective enough to distinguish transoid and cisoid conformation in the presence of divalent Lewis acid catalysts, such as TiCl 4 .

THE CRYSTAL STRUCTURES OF 1:1 MOLECULAR COMPLEXES OF MONOALKYLAMMONIUM HALIDES WITH RAC-1,1′-BI-2-NAPHTHOL

The monoalkyltrimethylammonium halides CH 3 (CH 2 ) n m 1 N + (CH 3 ) 3 X m (X=Br or Cl, when n=12, and X=Br, when n=16) and rac-1,1'-bi-2-naphthol (C 20 H 14 O 2 ) have been found to form 1:1 crystalline complexes. In all the complexes, the host molecules are sandwiched between the BNP molecules in a similar manner. The bent tail region of the alkyl chains in all the host molecules are arranged in a uniquely interdigitated fashion. The bent conformation of the alkyl chains could be attributed to the effect of placing a naphthol plane almost normal to the long alkyl chain axis. The change of the counter anion in the host molecule does not show any significant variation in the packing arrangement observed in the complexes of 12TAB/BNP and 12TAC/BNP or 16TAB/BNP and 16TAC/BNP. The nonplanar shape of the BNP molecule affects the molecular packing of the alkyl chains. The BNP molecule adopts a cisoid conformation in all the complexes. Hydrogen bonds and C-H… ~ interactions stabilize these crystal structures.