Conformational flexibility in 2,2'-Dioxybiphenyl-chloro-cyclotetraphosphazenes and its relevance to polyphosphazene analogues

The reaction of the cyclotetraphosphazene, [N4P4Cl8], with the difunctional reagent, 2,2'-biphenol, in the presence of potassium carbonate in acetone produced the spiro-substituted derivatives, 2,2'-dioxybiphenylhexachlorocyclotetraphosphazene, bis(2,2'-dioxybiphenyl)tetrachloro-cyclotetraphosphazene, and tris(2,2'-dioxybiphenyl)dichlorocyclotetraphosphazene. Both cis and trans geometrical isomers of the bis compound are observed. Although chromatographic separation of these was unsuccessful, a sample of the trans isomer was obtained by fractional crystallization. The compounds all show non-first-order 31P NMR spectra which were simulated to extract the spectral parameters. Single-crystal X-ray structures of both the trans bis and the tris compounds show that the cyclophosphazene rings exhibit conformational flexibility which gives rise to different crystalline forms being obtained from the same solvent systems. Crystals of trans-bis(2,2'-dioxybiphenyl)tetrachloro-cyclotetraphosphazene were obtained in two different space groups: Pnna (orthorhombic) and P21/n (monoclinic). In the orthorhombic structure, the dominant (72%) conformation of one phosphazene ring is a chair form, and the other (28%) resembles a boat. While for the monoclinic structure, the ring is virtually flat with an oval shape. In both cases the dioxybiphenyl groups are found in R and S configurations in the same molecule and are pi stacked in columns (Pnna) or involved in pi-pi or pi-H interactions (P21/n), thus anchoring the phosphorus atoms of the cyclotetraphosphazenes but still allowing flexibility in the ring conformations. Three crystalline modifications of tris(2,2'-dioxybiphenyl)dichloro-cyclotetraphosphazene were obtained: two in space group P (triclinic), which contained two molecules of dichloromethane in the unit cell, and one solvent-free form in space group P21/n (monoclinic). The cyclophosphazene rings exhibit puckered conformations with the trans-dioxybiphenyl moieties having opposing RS or SR conformations. DFT calculations were carried out on each of the phosphazene ring conformations in trans-bis(2,2'-dioxybiphenyl)tetrachlorocyclotetraphosphazene identified from the X-ray diffraction analysis. It is concluded that intermolecular interactions (i.e., pi-pi or pi-H) between the dioxybiphenyl groups is a factor that modifies the nature of the potential energy surface between the different conformers. The flexibility of the phosphazene ring is supported computationally through the calculated low-energy barriers and experimentally through the highly disordered phosphazene ring conformations observed in the solid state. The results on 2,2'-dioxybiphenyl-substituted cyclotetraphosphazenes provide evidence that microcrystalline domains in their 2,2'-dioxybiphenyl-substituted polyphosphazene analogues will be generated by similar pi-pi and pi-H interactions.     

Synthesis and solid-state structures of dimethyl 2,2'-bithiophenedicarboxylates

The syntheses of dimethyl 2,2'-bithiophene-4,4'-dicarboxylate (3), dimethyl 2,2'-bithiophene-3,4'-dicarboxylate (4), and dimethyl 2,2'-bithiophene-3,3'-dicarboxylate (5) are described. Single-crystal X-ray structural analysis of these compounds shows that the thiophene rings in 3 and 4 are nearly coplanar (dihedral angle close to 0 degrees ) and they adopt the anti sulfur conformation in the solid state. Further, the structure of 4 is in agreement with our previous suggestion that there is an electrostatic stabilization of the planar structure due to attraction of the 3-carbonyl oxygen to the sulfur of the distal ring. In 5, however, the thiophene rings are nearly perpendicular (dihedral angle 75 degrees ), indicating considerable steric hindrance between the two large ester groups at the 3- and 3'-positions. Unlike compounds 3 and 4, where the thiophene rings have the sulfur atoms anti, the sulfur atoms in 5 are completely syn. This is the first instance where a bithiophene has been shown to adopt a conformation where the sulfur atoms are completely syn. The solid-state conformations of 3, 4, and 5 are in agreement with ab initio theoretical calculations on these compounds; particularly, the planar conformations of 3 and 4 reflect the previously calculated low rotation barriers of these molecules.     

Dissociative and associative mechanisms of cope rearrangements of fluorinated 1,5-hexadienes and 2,2'-bis-methylenecyclopentanes

The effects of fluorine substitution on the Cope rearrangements of 1,5-hexadiene and 2,2'-bis-methylenecyclopentane have been examined computationally using (U)B3LYP/6-31+G(d,p) and CASPT2/6-31G(d) methodology. The calculations indicate that fluorine substituents at the hexadiene termini generally stabilize the transition states relative to the ground states of the chair conformations and destabilize pathways that occur via boat conformations, in accord with the experimental observations of Dolbier. With meso-2,2'-bis(difluoromethylene)cyclopentane, this destabilization is sufficient to favor a relatively dissociative concerted transition state resembling weakly interacting allyl radicals over a normal aromatic concerted boat transition state. This preference is due partly to an increase in the activation enthalpy for the concerted rearrangement coupled with the more favorable entropy for dissociation. In octafluoro- and decafluorohexadienes, the situation is reversed, and reaction through a cyclohexane-1,4-diyl is favored. Even in the octafluoro system with no radical stabilizing substituents at C(2) and C(5), the preference of fluorine for sp(3) centers causes reaction via the cyclohexane-1,4-diyl. In establishing methodology for this study, the conformations of 1,2-difluoroethane and 1,1,2,2-tetrafluoroethane were also examined thoroughly by the B3LYP method using three basis sets.     

Conformational analysis of a cyclopropane analogue of phenylalanine with two geminal phenyl substituents

Quantum mechanical methods have been used to investigate the intrinsic conformational preferences of 1-amino-2,2-diphenylcyclopropanecarboxylic acid (c(3)Dip), a cyclopropane analogue of phenylalanine bearing two phenyl substituents on the same beta-carbon. Geometries, energies, and frequencies were calculated on the N-acetyl-N'-methylamide derivative at the HF and B3LYP levels using the 6-31G(d), 6-311G(d), and 6-31+G(d,p) basis sets. Four minimum energy conformations were characterized: axial C(7), equatorial C(7), right-handed helix, and polyproline II. Analysis of the whole results, which are fully consistent with available experimental data, indicates that c(3)Dip tends to promote gamma-turn conformations.     

Cyclic water clusters in tape-like and cage-like structures

Controlling the ratio of 2,2'-bpy to benzene-1,3,5-tricarboxylic acid produces two interesting complexes, namely [Co(2,2'-bpy)?]?(SO?)?8.5H?O (1) and [Cu?(BTCA) (2,2'-bpy)?] (OH)?(2,2'-bpy)?.??14H?O (2) (H?BTCA = benzene-1,3,5-tricarboxylic acid, 2,2'-bpy = 2,2'-bipyridine). We report the structural evidence in the solid state of discrete lamellar water cluster conformations. These units are found to act as supramolecular glue in the aggregation of cobalt (II) or copper (II) complexes to give three dimensional cage-like networks through hydrogen-bonding. It is interesting that the structure of complex 1 contains a 3D negatively charged cage.     

Vibrational spectra of 2,2-dichlorobutane

IR and Raman spectra were obtained for 2,2-dichlorobutane, which was found to exist in two molecular conformations. Normal coordinate calculations were made for 2,2-dichloropropane and both conformers of 2,2-dichlorobutane.     

Ab initio calculations and mass spectrometric determination of the gas-phase proton affinities of 4,4'-disubstituted 2,2'-bipyridines

The gas-phase proton affinities of 4,4'-di(R)-2,2'-bipyridines (R: H, Br, Cl, NO(2), Me) were determined by mass spectrometric measurements and by ab initio calculations at the HF/6-31G and MP2/6-31G levels of theory. The energy barriers for rotation about the central C-C bond were also studied computationally. Two minima were found for both unprotonated and protonated species, the global minima being at the trans planar and cis planar conformations, respectively. Local minima for the unprotonated compounds were at the cis nonplanar conformation and for the protonated compounds at the trans nonplanar. Two different proton affinity values were calculated for each compound by employing different conformations for the protonated species. The computational values were in good agreement with the experimental proton affinities. Substituents affect the proton affinity according to their ability to withdraw or to donate electrons, halogen and nitro-substituted bipyridines having a lower proton affinity and methyl-substituted bipyridine having a higher proton affinity than 2,2'-bipyridine itself.     

Effect of side chains on turns and helices in peptides of beta3-aminoxy acids

We have investigated, using NMR, IR, and CD spectroscopy and X-ray crystallography, the conformational properties of peptides 1-10 of beta(3)-aminoxy acids (NH(2)OCHRCH(2)COOH) having different side chains on the beta carbon atom (e.g., R = Me, Et, COOBn, CH(2)CH(2)CH=CH(2), i-Bu, i-Pr). The beta N-O turns and beta N-O helices that involve a nine-membered-ring intramolecular hydrogen bond between NH(i)(+2) and CO(i), which have been found previously in peptides of beta(2,2)-aminoxy acids (NH(2)OCH(2)CMe(2)COOH), are also present in those beta(3)-aminoxy peptides. X-ray crystal structures and NMR spectral analysis reveal that, in the beta N-O turns and beta N-O helices induced by beta(3)-aminoxy acids, the N-O bond could be either anti or gauche to the C(alpha)-C(beta) bond depending on the size of the side chain; in contrast, only the anti conformation was found in beta(2,2)-aminoxy peptides. Both diamide 1 and triamide 9 exist in different conformations in solution and in the solid state: parallel sheet structures in the solid state and predominantly beta N-O turn and beta N-O helix conformations in nonpolar solvents. Theoretical studies on a series of model diamides rationalize very well the experimentally observed conformational features of these beta(3)-aminoxy peptides.     

2,2'-联吡啶同自旋双自由基的量子化学研究

采用量子化学abinitio方法,讨论了2,2'-联吡啶同自旋双自由基体系构象变化对铁磁耦合的影响。结果表明,在各种构象下,体系的磁性耦合符合自旋极化规则;对于·CH2,·MH2^+两种自由基磁性耦合性质是机同的,只影响到体系磁性耦合的强度,这一结论为有机磁性材料的分子设计提供了有益的信息。     

Determination of molecular structure in solution using vibrational circular dichroism spectroscopy: the supramolecular tetramer of S-2,2'-dimethyl-biphenyl-6,6'-dicarboxylic acid

The infrared (IR) and vibrational circular dichroism (VCD) spectra of S-2,2'-dimethyl-biphenyl-6,6'-dicarboxylic acid, S-1, in CDCl(3) solution are concentration-dependent, showing that oligomerization occurs with increasing concentration. DFT calculations support the conclusion that the oligomer formed is the cyclic tetramer (S-1)(4), in which S-1 monomers are linked by hydrogen(H)-bonded (COOH)(2) moieties. Due to the existence of two inequivalent tautomeric conformations of each (COOH)(2) moiety, six inequivalent conformations of (S-1)(4) are possible. B3LYP/6-31G* DFT calculations predict that the conformation "aaab", possessing three equivalent (COOH)(2) conformations, a, and one tautomeric conformation, b, has the lowest free energy. B3LYP/6-31G* IR and VCD spectra vary substantially with conformation. The B3LYP/6-31G* IR and VCD spectra of the C=O stretch modes of "aaab" are in excellent agreement with the experimental spectra, while those of all other conformations exhibit poor agreement, confirming the prediction that the "aaab" conformation is the predominant conformation. Comparison of the calculated IR and VCD spectra of the six conformations to the experimental spectra in the range 1100-1600 cm(-1) further supports this conclusion. The study is the first to use VCD spectroscopy to determine the structure of a supramolecular species.     

Conformational Stability of 2,2′-Dialkoxybenzpinacols in Solid State

Abstract

X-ray analyses of the 2,2′-dialkoxybenzpinacols have established that the previously tentative assignment of configuration is incorrect. For example, the dl-and meso-isomer of 2,2′-dimethoxy-, 2,2′-diethoxy-, and 2,2′-dibutoxybenzpinacols proved to have a rigid conformation (1aα, 1bα, 1eα) and (1aβ, 1bβ, 1cα) where hydroxy groups are always in an anti fashion, in the solid state, respectively. MM2 and semi-empirical molecular orbital calculations for possible conformations were performed, suggesting that the conformational stability of the present pinacols is controlled by repulsive gauche interactions between aryl groups associated with intramolecular hydrogen bondings.     

Conformation of heterocycles controlled by the existence of unusual C-H...X hydrogen bonds: syntheses and structure determination of aluminum aryloxides

The reactions of AlMe3 in diethyl ether with 1 molar equiv of 2,2'-methylenebis(4-methyl-6-tert-butylphenol) (MMBP-H2), 2,2'-methylenebis(4,6-di-tert-butylphenol) (MDBP-H2), and 2,2'-ethylidenebis(4,6-di-tert-butylphenol) (EDBP-H2) afford series of four-coordinate monomeric aluminum aryloxides, MeAl(O-O)(OEt2), 1-3 (1, (O-O) = MMBP; 2, (O-O) = MDBP; 3, (O-O) = EDBP). In THF, 1 molar equiv of EDBP-H2 reacts with AlMe3 to provide the THF-coordinated complex MeAl(EDBP)(THF) 4. However, in the absence of a coordinating solvent, the reaction of EDBP-H2 with AlMe3 yields the dimeric complex [MeAl(mu-EDBP)]2 (5). Complex 5 further reacts with Et4NCl, Et4NBr, and Ph3PO to afford the corresponding monomeric ionic complex [Et4N][MeAl(EDBP)(X)] (6, X = Cl; 7, X = Br) and the neutral complex [MeAl(EDBP)(O=PPh3)] (8), respectively. Complexes 1, 2, 4 and 6-8 are subjected to X-ray structure analyses, and the solid state structures reveal that the conformations of the eight-membered heterocycles are governed by the formation of the unusual C-H...X hydrogen bonds.     

Synthesis and structure of spirocyclic tetraethers derived from [1,1'-binaphthalene]-2,2'-diol and pentaerythritol

Molecular scaffolds that have well-defined geometries, are easy to synthesize and functionalize, and can hold attached sites of molecular recognition in suitable orientations are useful tools in various areas of science and technology. The utility of the tetraphenyl ether of pentaerythritol (4) as a scaffold in crystal engineering led us to study rigidified analogue SBINOX (5), the spirocyclic tetraether derived from pentaerythritol and [1,1'-binaphthalene]-2,2'-diol (BINOL). We have found that SBINOX (5) and derivatives can be prepared conveniently in acceptable yields and in stereoisomerically pure (S,S), (R,S), and (R,R) forms. X-ray crystallographic studies have revealed that the benzannulated 9-membered dioxonane rings in these structures adopt characteristic conformations of C1 symmetry. Intraannular C-H...O interactions help maintain the conformations of the individual rings, and the geometry of the spirocyclic SBINOX core is also controlled in part by distinctive short interannular C-H...O and C-H...pi interactions. Despite the inherent flexibility of the dioxonane rings, derivatives of SBINOX (5) can be expected to orient peripheral substituents in preferred ways, making SBINOX a potentially useful scaffold for applications in drug discovery, crystal engineering, and other fields.     

Threshold dissociation and molecular modeling of transition metal complexes of flavonoids

The relative threshold dissociation energies of a series of flavonoid/transition metal/auxiliary ligand complexes of the type [MII (flavonoid - H) auxiliary ligand]+ formed by electrospray ionization (ESI) were measured by energy-variable collisionally activated dissociation (CAD) in a quadrupole ion trap (QIT). For each of the isomeric flavonoid diglycoside pairs, the rutinoside (with a 1-6 inter-saccharide linkage) requires a greater CAD energy and thus has a higher dissociation threshold than its neohesperidoside (with a 1-2 inter-saccharide linkage) isomer. Likewise, the threshold energies of complexes containing flavones are higher than those containing flavanones. The monoglycoside isomers also have characteristic threshold energies. The flavonoids that are glycosylated at the 3-O- position tend to have lower threshold energies than those glycosylated at the 7-O- or 4'-O- position, and those that are C- bonded have lower threshold energies than the O- bonded isomers. The structural features that substantially influence the threshold energies include the aglycon type (flavanone versus flavone), the type of disaccharide (rutinose versus neohesperidose), and the linkage type (O- bonded versus C- bonded). Various computational means were applied to probe the structures and conformations of the complexes and to rationalize the differences in threshold energies of isomeric flavonoids. The most favorable coordination geometry of the complexes has a plane-angle of about 62 degrees , which means that the deprotonated flavonoid and 2,2'-bipyridine within a complex do not reside on the same plane. Stable conformations of five cobalt complexes and five deprotonated flavonoids were identified. The conformations were combined with the point charges and helium accessible surface areas to explain qualitatively the differences in threshold energies for isomeric flavonoids.     

Synthesis and Conformational Analysis of Pentapeptides Containing Enantiomerically Pure 2,2‐Disubstituted Glycines

The synthesis and conformational analysis of model pentapeptides with the sequence Z‐Leu‐Aib‐Xaa‐Gln‐Valol is described. These peptides contain two 2,2‐disubstituted glycines (α,α‐disubstituted α‐amino acids), i.e., Aib (aminoisobutyric acid), and a series of unsymmetrically substituted, enantiomerically pure amino acids Xaa. These disubstituted amino acids were incorporated into the model peptides via the ‘azirine/oxazolone method’. Conformational analysis was performed in solution by means of NMR techniques and, in the solid state, by X‐ray crystallography. Both methods show that the backbones of these model peptides adopt helical conformations, as expected for 2,2‐disubstitued glycine‐containing peptides.     

Surface Trapping and STM Observation of Conformational Isomers of a Bis(Terpyridine) Ligand from Metallosupramolecular Grids

Tetranuclear Co‐grid complexes incorporating bis‐tridentate ligands, namely 4,6‐bis(2,2′‐bipyrid‐6‐yl)‐2‐phenylpyrimidine, were electrosprayed onto a Au(111) substrate under an ultrahigh vacuum. Fragmentation occurs leaving the ligands in four different conformations. Most ligands are found to form H‐bonded dimers. The most abundant conformer of the ligand on the Au surface is an asymmetric form, which has not been observed before. The present results indicate that the fragmentation of coordination compounds during the deposition process, in principle, allows for surface trapping, identification, and investigation of high energy, out‐of‐equilibrium conformations of the ligand molecules at low temperatures, which otherwise would not be observable.     

Aromatic Amide Polymers that Form Two Helical Conformations with Twist Sense Bias in Water

Two benzene/2,2′‐bipyridine‐alternately incorporated amide polymers have been prepared, which are driven by hydrophobicity to form two different helical conformations. Both helices exhibit twist sense bias in water induced by chiral valine side chains and the coordination of the 2,2′‐bipyridine unit to the Ni²⁺ ions.     

A new route for the synthesis of phosphate esters: 2,2′‐[benzene‐1,2‐diylbis(oxy)]bis(5,5‐dimethyl‐1,3,2‐dioxaphosphinane) 2,2′‐dioxide

Podand‐type ligands are an interesting class of acyclic ligands which can form host–guest complexes with many transition metals and can undergo conformational changes. Organic phosphates are components of many biological molecules. A new route for the synthesis of phosphate esters with a retained six‐membered ring has been used to prepare 2,2′‐[benzene‐1,2‐diylbis(oxy)]bis(5,5‐dimethyl‐1,3,2‐dioxaphosphinane) 2,2′‐dioxide, C₆H₄{O[cyclo‐P(O)OCH₂CMe₂CH₂O]}₂ or C₁₆H₂₄O₈P₂, (1), 2‐[(2′‐hydroxybiphenyl‐2‐yl)oxy]‐5,5‐dimethyl‐1,3,2‐dioxaphosphinane 2‐oxide, [cyclo‐P(O)OCH₂CMe₂CH₂O](2,2′‐OC₆H₄–C₆H₄OH), (2), and oxybis(5,5‐dimethyl‐1,3,2‐dioxaphosphinane) 2,2′‐dioxide, O[cyclo‐P(O)OCH₂CMe₂CH₂O]₂, (3). Compound (1) is novel, whereas the results for compounds (2) and (3) have been reported previously, but we record here our results for compound (3), which we find are more precise and accurate than those currently reported in the literature. In (1), two cyclo‐P(O)OCH₂CMe₂CH₂O groups are linked through a catechol group. The conformations about the two catechol O atoms are quite different, viz. one C—C—O—P torsion angle is −169.11 (11)° and indicates a trans arrangement, whereas the other C—C—O—P torsion angle is 92.48 (16)°, showing a gauche conformation. Both six‐membered POCCCO rings have good chair‐shape conformations. In both the trans and gauche conformations, the catechol O atoms are in the axial sites and the short P=O bonds are equatorially bound.     

Temperature Dependence of Chain Conformation and Local Rigidity of Isomerized Polyimides in Dimethyl Formamide

Temperature dependence of chain conformation and local rigidity of two soluble isomerized polyimides (PIs), poly(hexafluorodianhydride/3,3'-dimethylbenzidine)[poly(6FDA/3,3'-DMB)] and poly(hexafluorodianhy-dride/2,2'-dimethylbenzidine)[poly(6FDA/2,2'-DMB)] were investigated by dilute solution viscosity, size exclusion chromatography(SEC) coupled with multi-angle laser light scattering, viscometer, and refractive index detector in dimethylformamide(DMF) with either 0.1 mol/L LiBr or 3.1 mmol/L tetrabutylammonium bromide(TBAB) in the temperature range of 30 to 50 ℃. The scaling relationships of[η]=K_ηM^α and R_g=K_gM^v obtained are employed to investigate the temperature dependence of chain conformation for the two polyimides. The values of α and v are in the range of 0.66―0.69 and 0.53―0.56, respectively, for poly(6FDA/3,3'-DMB), meanwhile they are in the range of 0.64―0.68 and 0.53―0.56, respectively, for poly(6FDA/2,2'-DMB). These results reveal that random coil conformations for both PIs are not affected visibly with increasing temperature from 30 ℃ to 50 ℃. However, values of more exact intrinsic viscosity from dilute solution measurement indicate there is only tiny coil extension or shrinkage for both PIs with temperature rising. Parameters related to chain flexibility of polymer, including persistence length l_p, shift factor M_L(relative molecular weight per unit contour length) and backbone diameter d are estimated from the relationship between intrinsic viscosity and molecular weight for the continuous wormlike cylinder model, which indicates that two samples are flexible chains, only the chain of poly(6FDA/3,3'-DMB) is stiffer than that of poly(6FDA/2,2'-DMB) slightly.     

An IR Study of the Structure of New Thiocarboxylic Acid N-(1-Arenesulfonamido-2-phenyl-2,2-dichloroethyl- and -2,2,2-trichloroethyl)amides

An IR study of thiocarboxylic acid N-(1-arenesulfonamido-2-phenyl-2,2-dichloroethyl- and -2,2,2-trichloroethyl)amides revealed intramolecular hydrogen bonds whose formation is accompanied by electron density delocalization and stabilization of conformations with quasiaromatic rings. Formation of chelate species was confirmed by AM1 calculations.