Ring Torsion Angles Research Articles

The indenyl effect on d0 organotransition metal complex LMCT luminescence: Synthesis, structural characterization, cyclic voltammetry, spectroscopic studies, and TD-DFT computations on (η5-permethylindenyl)tetrachlorotantalum(V), and comparison to (η5-pentamethylcyclopentadienyl)tetrachlorotantalum(V)

The new organotantalum(V) chloride (η5-permethylindenyl)tetrachlorotantalum, Ind*TaCl4, was prepared by addition of previously-unreported Ind*SnBu3 to TaCl5 in toluene at 70° in 53 % isolated yield. The solid-state four-legged piano-stool structure, consistent with solution multinuclear NMR spectroscopies, demonstrated that tantalum is bonded to all carbons of the five-membered ring of the permethylindenyl ligand, with little deviation in the Ta-C distances. The permethylindenyl ring torsional angles for the three independent molecules in the unit cell vary from 2.46(17)° to 5.10(17)°. The cyclic voltammogram of Ind*TaCl4 in tetrahydrofuran showed one reversible reduction feature at −1.24 V [Ta(V)/Ta(IV)] and one quasi-reversible reduction feature at −1.65 V [Ta(IV)/Ta(III)] vs. Fc/Fc+. The UV/vis LMCT absorption λmax at 593 nm (ε = 2000 M−1 cm−1) in toluene is remarkably red-shifted from that of the known η5-pentamethylcyclopentadienyl analog, luminescent-yellow Cp*TaCl4. TD-DFT calculations were used to explain the comparative UV/vis absorption spectra.

Solid-state structure of cyclic dipeptides: an X-ray and computational study of cis- and trans-diketopiperazines of N-methyl-phenylalanine with the thia-pipecolic acids and thia-prolines

Ten new crystal structures of cis and trans bicyclic diketopiperazines (DKPs) of thia-pipecolic acid (with sulfur in the β, γ or δ position) or thia-proline (with sulfur in the β or γ position) and N-methyl phenylalanine [(NMe)Phe]: cyclo[(β-S)Pip-(NMe)Phe], cyclo[(γ-S)Pip-(NMe)Phe], cyclo[(δ-S)Pip-(NMe)Phe], cyclo[(β-S)Pro-(NMe)Phe] and cyclo[(γ-S)Pro-(NMe)Phe] were determined with X-ray crystallography. Density functional theory calculations of these molecules in the gas phase succeed in reproducing the observed molecular conformations in the crystal remarkably well. This illustrates the weak to moderate impact of intermolecular packing forces in the absence of classical N—H...O hydrogen bonds. The effect of sulfur on the geometry of the DKP ring and details of amide bond non-planarity are discussed. Molecular flexibility of the DKP ring, as estimated from the calculated deformation energies of its endocyclic ring torsion angles, is not in general the decisive factor for the occurrence of multiple symmetry independent molecules in the unit cell (Z′ > 1), though in some cases a correlation is observed.

Naphthylaminoborane: from structural switches to frustrated Lewis pair reactivity.

A series of naphthyl-bridged amino-borane derivatives, namely 1-(dimethylamino)-8-naphthylboranes (1, 3, 5, 7) and 5-(dimethylamino)-6-acenaphthylboranes (2, 4, 6, 8, 10, 11), differing in the steric and electronic properties of the boryl moiety, have been synthesized and fully characterized by spectroscopic and crystallographic means. Structural X-ray analysis of the peri-atom displacement and ring torsion angles served to experimentally assess the presence and magnitude of the B-N interactions. The reversible quaternarization of nitrogen has been explored and was found to provide an efficient switch corresponding to different molecular organizations. The electronic characteristics of the nature of B-N interactions were further studied by Natural Bonding Orbital analysis derived from the theoretically calculated electron densities. This real-space bonding indicator discriminates the bonding B-N contact in 5 from the nonbonding in 8, which correlates with the flexibility of the naphthyl scaffold to respond to the Lewis acidity of boron allowing shorter peri interactions. Whereas, the steric shielding imposed by the two mesityl groups, and/or the rigidity of the acenaphthene framework disrupt B-N interaction. Thus, this communication reports on the modulation of the B-N bonding continuum by means of structural tuning leading to a molecular switch, as well as its implications towards revealing FLP reactivities through the isolation of intermediates of a stepwise mechanism.

Investigating proline puckering states in diproline segments in proteins

In the current study, the puckering states of the Proline ring occurring in diproline segments ((L) Pro-(L) Pro) in proteins has been investigated with a segregation made on the basis of cis and trans states for the Pro-Pro peptide bond and the conformational states for the diproline segment to investigate the effects of conformation of the diproline segment on the corresponding puckering state of the Proline ring in the segment if any. The value of the endocyclic ring torsional angles of the pyrrolidine ring has been used for calculating and visualizing various puckering states using a proposed new sign convention (+/-) nomenclature. The results have been compared to that obtained in a previous study on peptides from this group. In this study, quite interestingly, the Planar (G) conformation that was present in 14.3% of the cases in peptides, appears to be nearly a rare conformation in the case of proteins (1.9%). The present study indicates that the (C(γ)-exo/C(γ)-exo), (C(γ)-exo/Twisted C(γ)-exo-C(β)-endo) and (Twisted C(γ)-endo-C(β)-exo/Twisted C(γ)-endo-C(β)-exo) categories are the most preferred combinations. For Proline rings in proteins, the states C(γ)-exo, Twisted C(γ)-exo-C(β)-endo and Twisted C(γ)-endo-C(β)-exo are the most preferred states. Within diproline segments, the pyrrolidine ring conformations do not show a strong co-relation to the backbone conformation in which they are observed. It is likely that five-membered rings have a considerable plasticity of structure and are readily deformed to accommodate a variety of energetically preferred backbone conformations.

Platinum Complexes of 5,6‐Dihydroacenaphtho[5,6‐cd]‐1,2‐dichalcogenoles

AbstractSix bis(phosphane)platinum complexes bearing dichalcogen acenaphthene ligands have been prepared by metathesis from cis‐[PtCl2(PR3)2] (R3 = Ph3, Ph2Me, PhMe2) and the dilithium salts of the parent 5,6‐dihydroacenaphtho[5,6‐cd]‐1,2‐dichalcogenoles (AcenapE2, L1 E = S, L2 E = Se). For their synthesis, the appropriate disulfide or diselenide species was treated with super hydride [LiBEt3H] to afford the dilithium salt by in situ reduction of the AcenapE2 E–E bond. Further reaction, by metathetical addition to the cis‐platinum precursor afforded the respective platinum(II) complexes [Pt(5,6‐AcenapE2)(PR3)2] (R3 = Ph3: E = S 1, Se 2; R3 = Ph2Me: E = S 3, Se 4; R3 = PhMe2: E = S 5, Se 6). All six complexes have been fully characterised, principally by multinuclear magnetic resonance spectroscopy, IR spectroscopy and MS. The selenium complexes 4 and 6 provide examples of AA′X spin systems, as displayed by their 31P{1H} NMR spectra. The X‐ray structures of L1, L2, 1, 2, 5 and 6 were determined and, where appropriate, the platinum metal geometry, peri‐atom displacement, splay angle magnitude, acenaphthene ring torsion angles and E···E interactions were analysed. The platinum atoms were found to adopt a distorted square‐planar geometry in all four complexes, and the nature of the AcenapE2 ligand plays little part in the conformation of the substituents bound to the trivalent phosphorus atoms.

3β,5α,6β-Trihy-droxy-androstan-17-one.

The title compound, C19H30O4, is an androstan-17-one derivative synthesized from the dehydro­epiandrosterone through a sequential addition of an oxidant, followed by a trans-diaxial opening of the epoxide generated, with Bi(OTf)3 (OTf is trifluoro­methane­sulfonate). The six-membered rings have a slightly flattened chair conformation, while the five-membered ring adopts a 14-α envelope conformation. All rings are trans fused. In the crystal, the mol­ecules are connected by O—H⋯O hydrogen bonds involving the hydroxyl and carbonyl groups, forming a three-dimensional network. A quantum mechanical ab initio Roothan Hartree–Fock calculation of the free mol­ecule gives bond lengths, valency angles and ring torsion angles of the free molecule at equilibrium geometry (energy minimum) close to the experimental values.

ChemInform Abstract: Conformation of an Eleven-Membered Lactone: Structure of (E,13R,14S)- 13-Hydroxy-17-nor-8,9-secolabd-9(11)-en-8,14-olide.

C19H3203, Mr=308.49, orthorhombic, P212121, a = 7-072 (3), b = 9389 (3), c = 27-888(11)A, v=1852(2)A 3, z=4, Ox = I. 11 Mg m - 3, ,t(Mo Ka) = 0.71069 )k, /z = 0.08 mm-1, F(000) = 680, T = 293 K, R = 0.050 for 1475 independent reflections with I> 2-5o'(/). The conformation of the l l-membered lactone ring is essentially the same as the calculated minimum- energy conformation of trans, trans-cycloundeca- 1,6-diene with differences between corresponding ring torsion angles of only 1-15 ° (mean 6°). This conformation is found in several cytochalasans and dolabellane diterpenoids but not in the pyrrolizidine alkaloids with l l-membered dilactone rings. The cyclohexane ring is distorted to alleviate 1,3-diaxial repulsion between methyl substituents (C(18)-C(20) = 3.291 (7) A); the smallest torsion angles (-47.4 (5), 48.1 (5) °) are at ring bonds between the methyl groups, the largest torsion angles (-55-6 (6), 56.4 (6) °) at bonds remote from these substituents. Introduction. Eleven-membered rings are features of several classes of natural products, e.g. the cyto- chalasans (Tamm, 1980), dolabellane diterpenoids (Matsuo, Kamio, Uohama, Yoshida, Connolly & Sim, 1988) and pyrrolizidine alkaloids (Robins, 1982). Examination of crystallographic results reveals two conformations for the trans, trans- cycloundeca-l,5-diene system in humulene deriva- tives (Khan, MacAlpine, Porte & Sim, 1983) and a number of dolabellane diterpenoids (Matsuo, Uohama, Yoshida, Nakayama, Hayashi, Connolly &

Heparin/Heparan Sulfate N-Sulfamidase from Flavobacterium heparinum

Sulfated polysaccharides such as heparin and heparan sulfate glycosaminoglycans (HSGAGs) are chemically and structurally heterogeneous biopolymers that that function as key regulators of numerous biological functions. The elucidation of HSGAG fine structure is fundamental to understanding their functional diversity, and this is facilitated by the use of select degrading enzymes of defined substrate specificity. Our previous studies have reported the cloning, characterization, recombinant expression, and structure-function analysis in Escherichia coli of the Flavobacterium heparinum 2-O-sulfatase and 6-O-sulfatase enzymes that cleave O-sulfate groups from specific locations of the HSGAG polymer. Building on these preceding studies, we report here the molecular cloning and recombinant expression in Escherichia coli of an N-sulfamidase, specific for HSGAGs. In addition, we examine the basic enzymology of this enzyme through molecular modeling studies and structure-function analysis of substrate specificity and basic biochemistry. We use the results from these studies to propose a novel mechanism for nitrogen-sulfur bond cleavage by the N-sulfamidase. Taken together, our structural and biochemical studies indicate that N-sulfamidase is a predominantly exolytic enzyme that specifically acts on N-sulfated and 6-O-desulfated glucosamines present as monosaccharides or at the nonreducing end of odd-numbered oligosaccharide substrates. In conjunction with the previously reported specificities for the F. heparinum 2-O-sulfatase, 6-O-sulfatase, and unsaturated glucuronyl hydrolase, we are able to now reconstruct in vitro the defined exolytic sequence for the heparin and heparan sulfate degradation pathway of F. heparinum and apply these enzymes in tandem toward the exo-sequencing of heparin-derived oligosaccharides.

Reduction of ring-torsion angles and band gap of polyaniline under high pressure

Variation ground states of pernigraniline-base polymer were investigated with various values of potential parameter V 2,0 in an extended Ginder–Epstein model. The results showed that ring-torsion angles and the energy gap reduced with decreasing V 2,0. We estimated pressure perpendicular to nitrogen plane of a chain in the polymer by the ring-torsion angles. While V 2,0 decreased from 2.0 to 0.8 eV, our estimated pressure increased from 0 to 9.03 GPa. The results agree with the experimental observations that electrical conductivity is increasing with applied pressure until a saturated value.

The molecular structure of a curl-shaped retinal isomer

Computational studies of retinal protonated Schiff base (PSB) isomers show that a twisted curl-shaped conformation of the retinyl chain is a new low-lying minimum on the ground-state potential energy surface. The curl-shaped isomer has a twisted structure in the vicinity of the C(11)=C(12) double bond where the 11-cis retinal PSB isomerizes in the rhodopsin photoreaction. The twisted configuration is a trapped structure between the 11-cis and all-trans isomers. Rotation around the C(10)-C(11) single bond towards the 11-cis structure is prevented by steric interactions of the two methyl groups on the retinyl chain and by the torsion barrier of the C(10)-C(11) bond in the other direction. Calculations of spectroscopic properties of the 11-cis, all-trans, and curl-shaped isomers provide useful data for future identification of the new retinal PSB isomer. Circular dichroism (CD) spectroscopy might be used to distinguish between the retinal PSB isomers. The potential energy surface for the orientation of the beta-ionone ring of the 11-cis retinal PSB reveals three minima depending on the torsion angle of the beta-ionone ring. Two of the minima correspond to 6-s-cis configurations and one has the beta-ionone ring in 6-s-trans position. The calculated CD spectra for the two 6-s-cis configurations differ significantly indicating that the sign of the beta-ionone ring torsion angle could be determined using CD spectroscopy. Calculations of the CD spectra suggest that a flip of the beta-ionone ring might occur during the first 1 ps of the photoreaction. Rhodopsin has a negative torsion angle for the beta-ionone ring, whereas the change in the sign of the first peak in the experimental CD spectrum for bathorhodopsin could suggest that it has a positive torsion angle for the beta-ionone ring. Calculated nuclear magnetic resonance (NMR) shielding constants and infrared (IR) spectra are also reported for the retinal PSB isomers.

High-resolution FTIR study of the para-terphenyl phase transition at high pressure

High-resolution infrared (IR) spectroscopy has been used to investigate the pressure-induced (0–11 kbar) polymorphic phase transition of crystalline para-terphenyl at low temperature (25 K). A number of doublet bands observed in low-pressure triclinic p-terphenyl were observed to coalesce in the high-pressure monoclinic phase. The coalescing of doublet bands was attributed to changes in factor group (Davydov) splittings associated with the transition from a low-pressure triclinic phase to a high-pressure monoclinic phase. The bands that ‘disappear’ also do not correlate with frequency changes associated with changes in molecular symmetry. Molecular dynamics (MD) simulations at low temperature (20 K) yield a non-planar average molecular structure for the high-pressure monoclinic phase, in contrast to the high-temperature monoclinic phase. The MD simulations also reveal a broadening of the distribution of ring torsion angles near the triclinic–monoclinic phase transition pressure.

Intrachain confinement of excitons and radiative recombination in polyaniline grains

Abstract Suppression of the benzenoid-to-quinoid excitonic transition (BQET) and enhancement of the quantum yield of photoluminescence (PL) at ∼390 nm has been observed in grained films of the emeraldine base (EB) of polyaniline. The major PL band from the EB films with the grained morphology was relatively narrow, with FWHM of about 1020 cm−1, followed by vibronic overtones the intensity of which was dependent on the mode of the PL excitation. The change of the film morphology, where instead of grains large aggregates were formed, leaded to the recovery of the absorption band corresponding to the BQET and quenching of the emission, respectively. It is suggested that the origin of PL in EB films is due to the distorted polymer chains in EB grains where the ring torsion angle of benzenoid group in respect to the adjacent quinoid group increases, thus resulting in the suppressed BQET and enhanced emission.

Normal Modes of Redox-Active Tyrosine: Conformation Dependence and Comparison to Experiment

Redox-active tyrosine residues play important roles in long-distance electron reactions in enzymes such as prostaglandin H synthase, ribonucleotide reductase, and photosystem II (PSII). Spectroscopic characterization of tyrosyl radicals in these systems provides a powerful experimental probe into the role of the enzyme in mediation of long-range electron transfer processes. Interpretation of such data, however, relies critically on first establishing a spectroscopic fingerprint of isotopically labeled tyrosinate and tyrosyl radicals in nonenzymatic environments. In this report, FT-IR results obtained from tyrosinate, tyrosyl radical (produced by ultraviolet photolysis of polycrystalline tyrosinate), and their isotopologues at 77 K are presented. Assignment of peaks and isotope shifts is aided by density-functional B3LYP/6-311++G(3df,2p)//B3LYP/6-31++G(d,p) calculations of tyrosine and tyrosyl radical in several different charge and protonation states. In addition, characterization of the potential energy surfaces of tyrosinate and tyrosyl radical as a function of the backbone and ring torsion angles provides detailed insight into the sensitivity of the vibrational frequencies to conformational changes. These results provide a detailed spectroscopic interpretation, which will elucidate the structures of redox-active tyrosine residues in complex protein environments. Specific application of these data is made to enzymatic systems.

Synthesis and Hybridization Studies of 2‘-Amino-α-L-LNA and Tetracyclic “Locked LNA”

A convergent route to a new class of locked nucleic acids, i.e., 2'-amino-alpha-L-LNA, has been developed. The optimized synthetic route to the corresponding phosphoramidite building block of thymine proceeds in 4% overall yield over 15 steps from the starting diol. Crucial synthetic steps include (a) introduction of a C2-azido group prior to nucleobase coupling, (b) Vorbrüggen glycosylation primarily affording the desired alpha-anomer, (c) separation of alpha-L-ribo- and beta-L-ribo-configured bicyclic nucleosides, and (d) selection of a suitable protecting group to avoid intramolecular Michael addition of the C2'-amino group onto the C6-position. Incorporation of a 2'-amino-alpha-L-LNA monomer into oligodeoxyribonucleotides results in modest changes in thermal stability with complementary DNA, whereas significant increases in thermal stability are observed with RNA complements along with excellent Watson-Crick discrimination. These results, along with the flexibility of the synthetic strategy allowing chemoselective N2'-functionalization at a late stage, render 2'-amino-alpha-L-LNA a promising building block for nucleic acid based nanobiotechnology and therapeutics. A slight modification in strategy facilitated the synthesis of the corresponding phosphoramidite building blocks of Michael adducts, which due to their tetracyclic skeletons exhibit a conformationally restricted furanose ring and glycosidic torsion angle (anti-range). Incorporation of such a "locked LNA" monomer into oligodeoxyribonucleotides results in large decreases in thermal affinity toward DNA/RNA complements.

Interaction of Torsional Oscillations with Polarons and Bipolarons in Conjugated Polymer

We propose a model for the electronic interaction associated with torsional and bond length vibrations in quasi one dimensional chains of conjugated polymers. The model admits conformational bond length objects like polarons and bipolarons and torsional modes of vibration. It is shown that the dynamics of these objects can be studied by numerically integrating the corresponding time-dependent equations of motion for the bond length, ring torsion angle and pi-electrons. An extension of the PPP and SSH models is numerically solved using the Time-Dependent Hartree-Fock approximation. An wide range of conducting polymers is simulated by varying the moment of inertia of the monomers (ranging from polypyrrole to poly(3-hexyl)thiophene). The stereometric interactions between chains are parametrically considered with different torsional potentials. The results show that polarons and bipolarons are trapped between the antinodes of torsional vibration modes with wave length larger than their width. This effect damps down their mobility. It is also found that torsional vibration modes with very long wave lengths or wave lengths shorter than the width of polarons and bipolarons produces almost no effect on their propagation.

Intermolecular Forces and Functional Group Effects in the Packing Structure of Thiophene Derivatives

Thiophene was derivatized at the β-carbon with isophthalic, dipicolinic, and four nitrobenzoic acids to yield 4-thiophen-3-yl-pyridine-2,6-dicarboxylic acid diethyl ester, I; 5-thiophen-3-yl-isophthalic acid diethyl ester, II; 2-nitro-4-thiophen-3-yl benzoic acid ethyl ester, III; 3-nitro-4-thiophen-3-yl benzoic acid ethyl ester, IV; 3-nitro-2-thiophen-3-yl benzoic acid ethyl ester, V; and 2-nitro-5-thiophen-3-yl benzoic acid ethyl ester, VI. These resulting compounds have been isolated and characterized by X-ray single-crystal diffraction. The solid-state structures of these substances are discussed as a function of the position and nature of the functional groups and the intermolecular forces. Modeling of the thiophene−aromatic ring torsion angle allowed us to attribute large differences in torsion angles to packing effects in the structures, due to π−π interactions between the aromatic rings.

Dynamic interaction between polarons and torsional vibrations in conjugated polymers

AbstractWe propose a model for the electronic interaction associated with torsional and bond length vibrations in quasi‐one‐dimensional chains of conjugated polymers. The model admits conformational bond length objects like polarons and bipolarons and torsional modes of vibration. It is shown that the dynamics of these objects can be studied by numerically integrating the corresponding time‐dependent equations of motion for the bond length; ring torsion angle, and π‐electrons. An extension of the PPP and SSH models is numerically solved using the time‐dependent Hartree–Fock approximation. A wide range of conducting polymers is simulated by varying the moment of inertia of the monomers [ranging from polypyrrole to poly(3‐hexyl)thiophene]. The stereometric interactions between chains are parametrically considered with different torsional potentials. The results show that polarons and bipolarons are trapped between the antinodes of torsional vibration modes with wavelengths larger than their widths. This effect damps down their mobility. We also found that torsional vibration modes with very long wavelengths or wavelengths shorter than the width of polarons and bipolarons produce almost no effect on their propagation. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005

3,7‐Dibromohinokitiol: A Redetermination.

AbstractFor Abstract see ChemInform Abstract in Full Text.

Trends in exchange coupling for trimethylenemethane-type Bis(semiquinone) biradicals and correlation of magnetic exchange with mixed valency for cross-conjugated systems.

A magnetostructural correlation (conformational electron spin exchange modulation) within an isostructural series of biradical complexes is presented. X-ray crystal structures, variable-temperature electron paramagnetic resonance spectroscopy, zero-field splitting parameters, and variable-temperature magnetic susceptibility measurements were used to evaluate molecular conformation and electron spin exchange coupling in this series of molecules. Our combined results indicate that the ferromagnetic portion of the exchange couplings occurs via the cross-conjugated pi-systems, while the antiferromagnetic portion occurs through space and is equivalent to incipient bond formation. Thus, molecular conformation controls the relative amounts of ferro- and antiferromagnetic contributions to exchange coupling. In fact, the exchange parameter correlates with average semiquinone ring torsion angles via a Karplus-Conroy-type relation. Because of the natural connection between electron spin exchange coupling and electronic coupling related to electron transfer, we also correlate the exchange parameters in the biradical complexes to mixed valency in the corresponding quinone-semiquinone radical anions. Our results suggest that delocalization in the cross-conjugated, mixed-valent radical anions is proportional to the ferromagnetic contribution to the exchange coupling in the biradical oxidation states.

3,7-dibromohinokitiol: a redetermination.

The structure of the title compound (systematic name: 3,7-dibromo-2-hydroxy-6-isopropylcyclohepta-2,4,6-trien-1-one), C(10)H(10)Br(2)O(2), previously described by Ito, Fukazawa & Iitaka [Tetrahedron Lett. (1972), 13, 745-749], has been redetermined. Strong inter- and intramolecular hydrogen bonds, with H.O distances of 2.17 (9) and 2.06 (6) A, respectively, are observed. There are also two short Br...Br and two short Br.(ring centroid) interactions. Important dimensions include C--O(carbonyl) = 1.252 (5) A, C--O(hydroxyl) = 1.355 (5) A, C-Br(3-position) = 1.904 (4) A and C--Br(7-position) = 1.905 (4) A, and an O--C--C--O ring torsion angle of -6.7 (6) degrees.