Unusual ribose conformation in a ternary copper(II) 2?deoxyribonucleotide complex

The ternary metal deoxyribonucleotide complex [Cu(bzim)(5?-dGMP)(H2O)3](bzim = benzimidazole, 5?-dGMP = 2?-deoxyguanosine 5?-monophosphate) has been prepared and the structure analysed by X-ray diffraction. The compound crystallizes in the space group P1 with a= 7.069(6), b= 13.959(10), c= 14.204(12)Å, ?= 75.12(6), ?= 94.15(6), ?= 97.98(6)° and Z= 2. The structure was solved by the heavy-atom method and refined by full-matrix least-squares procedures on the basis of 2813 observed [I[gt-or-equal] 3?(I)] reflections to final R and R? values of 0.050 and 0.052 respectively. There are two independent molecules in the asymmetric unit and both copper(II) centres have square-pyramidal co-ordination geometry. An unusual feature of the structure is the co-ordination of the metal by N(7) of the base, in the presence of a ?-aromatic amine, bzim. The structure is stabilized by intermolecular base�bzim stacking. The nucleotides of both the molecules have an anti conformation about the glycosyl bond, and a gauche-gauche conformation about the C(4?)�C(5?) bond. A feature of particular interest is the unusual sugar conformation. The base furanose rings of the two nucleotide molecules adopt C(3?)-exo/C(2?)-endo pucker and C(3?)-exo pucker respectively.

Monte Carlo and molecular dynamics simulation of argon clusters andn-alkanes in the confined regions of zeolites

Geometry and energy of argon clusters confined in zeolite NaCaA are compared with those of free clusters. Results indicate the possible existence of magic numbers among the confined clusters. Spectra obtained from instantaneous normal mode analysis of free and confined clusters give a larger percentage of imaginary frequencies for the latter indicating that the confined cluster atoms populate the saddle points of the potential energy surface significantly. The variation of the percentage of imaginary frequencies with temperature during melting is akin to the variation of other properties. It is shown that confined clusters might exhibit inverse surface melting, unlike medium-to-large-sized free clusters that exhibit surface melting. Configurational-bias Monte Carte (CBMC) simulations of n-alkanes in zeolites Y and A are reported. CBMC method gives reliable estimates of the properties relating to the conformation of molecules. Changes in the conformational properties of n-butane and other longer n-alkanes such as n-hexane and n-heptane when they are confined in different zeolites are presented. The changes in the conformational properties of n-butane and n-hexane with temperature and concentration is discussed. In general, in zeolite Y as well as A, there is significant enhancement of the gauche population as compared to the pure unconfined fluid.

Modulation of lifetimes and diastereomeric discrimination in triplet-excited substituted butane-1,4-diones through intramolecular charge-transfer quenching

Triplet lifetimes have been determined for the diastereomers of a broad set of butane-l,4-dione derivatives (1-3). A remarkable dependence of lifetimes on conformational preferences is revealed in that the lifetimes are shorter for the meso diastereomers of 1-3 than those for the racemic ones. The intramolecular beta-phenyl quenching is promoted in the case of meso diastereomers by virtue of the gauche relationship between the excited carbonyl group and the beta-aryl ring, while a distal arrangement in the lowest energy conformation (H-anti) in racemic diastereomers prevents such a deactivation. The involvement of charge transfer in the intramolecular beta-phenyl quenching is suggested by the correlation of the triplet lifetimes of the meso diastereomers of compounds 2 with the nature of the substituent on the beta-phenyl rings. In the case of racemic diastereomers, beta-methoxy substitution on the beta-phenyl ring (2-OCH3, 3-OCH3) also led to a decrease of the triplet lifetimes when compared to those of the nonsubstituted compounds (2-H, 3-H). This shortening is accounted for by the deactivation of a small proportion of the excited molecules through beta-phenyl quenching. In addition to the above factors, the lifetimes in the case of meso diastereomers can further be controlled by increasing the energy spacing between the T-1 and T-2 states, since beta-phenyl quenching occurs from the latter for compounds 2 and 3. Through a rational conformational control, a surprisingly long triplet lifetime (300 ns) has been measured for the first time for a purely n,pi* triplet-excited beta-phenylpropiophenone dimer (1-rac).

N-3-benzoyl-2 ',3 '-di-O-benzoyluridine

The structure of N-3-benzoyl-2',3'-di-O-benzoyluridine, C30H24N2O9, has two molecules in the asymmetric unit. The uracil bases of both the molecules are in the anti conformation with respect to the ribose moiety and the furanosyl rings adopt a C3'-endo conformation. The orientation about the C4'-C5' bond is gauche-gauche. The two crystallographically independent molecules are linked through several C-H ... O hydrogen bonds. The nucleoside molecules pack as columns along the a axis and these columns repeat along the c axis.

N-4-anisoylcytidine dihydrate

The title compound, C17H19N3O7. 2H(2)O, has C2'-endo, C3'-exo puckering, The orientation of the base with respect to the sugar is anti and the geometry about C4'-C5' is gauche,trans. The angle between the cytidine base and the phenyl ring of the anisoyl group is 15.5(2)degrees.

N-6-anisoyladenosine monohydrate

The title compound, C18H19N5O6. H2O, has a syn conformation about the glycosidic bond. Its furanose ring shows a C2'-endo-C3'-exo twist conformation and trans-gauche geometry about the C4'-C5' bond. The angle between the adenine base and the phenyl ring of the anisoyl group is 22.9 degrees. Adenine and anisoyl groups stack along the b axis at a separation of 3.4 Angstrom.

Oxidative addition of tetrachloro-1,2-benzoquinone to lambda(3)-cyclotriphosphazanes. An unusual ring contraction-rearrangement

The lambda(3)-cyclotriphosphazanes, [EtNP(OR)](3) [R = 2,6-Me2C6H3 (1), 4-BrC6H4 (2), or CH2CF3(3)], on treatment with tetrachloro-1,2-benzoquinone (TCB) give the lambda(5)-cyclodiphosphazanes, [EtNP(O2C6Cl4)(OR)][EtNP(O2C6Cl4){N(Et)P(OR)(2)}] (5-7) by an unusual ring contraction-rearrangement. The reaction of the mixed substituent lambda(3)-cyclotriphosphazane, [(EtN)(3)P-3(OR)(2)(OR')] [R = 2,6-Me2C6H3, R' = 4-BrC6H4] (4), with TCB gives the lambda(5)-cyclodiphosphazane, [EtNP(O2C6Cl4)(OR')][EtNP(O2C6Cl4){N(Et)P(OR)(2)}] (8), in which 4-bromophenoxide resides on one of the ring phosphorus atoms. The lambda(3)-bicyclic tetraphosphapentazane, (EtN)(5)P-4(OPh)(2), on treatment with TCB undergoes a double ring contraction-rearrangement to give the lambda(5)-cyclodiphosphazane, (EtN)[(EtN)(2)P-2(O2C6Cl4)(2)(OPh)](2) (9). Variable-temperature and high-field P-31 NMR studies indicate the presence of more than one isomer in solution for the rearranged products 5-9. The solid state structure of 8 reveals a trans arrangement of the substituents with respect to the P2N2 ring in contrast to the gauche arrangement observed for 5.

Characterization of alkyl chain conformation in an intercalated cationic lipid bilayer by IR spectroscopy

A structural analysis of alkyl chain conformation of an intercalated cationic lipid bilayer is described. Dialkyl dimethylammonium ions (di-C(n)DA) were ion exchanged into the galleries of layered cadmium thiophosphate to give Cd0.83PS3(di-C(n)DA)(0.34). The grafting density and interlayer expansions were identical to those for the intercalated single chain alkyl trimethylammonium (C(n)TA) bilayers. The increased methylene chain density in the galleries, however, forces the intercalated lipid to adopt a more trans ordered structure. Progression bands arising from the coupling of vibrational modes of trans methylene units are used to establish the extent of trans registry. Two types of ordered structures of the intercalated cationic lipid may be distinguished. One in which both alkyl chains adopt an all-trans geometry, and one in which the methylene bond adjacent to the headgroup on one of the alkyl chains is gauche. The latter structure is typically found in the crystalline state of these cationic lipids. The concentrations of the two structures were determined from the ratio of the intensities of the progression bands and were found to remain unchanged with temperature.

Stress induced phase transition in a monomolecular perfluroalkylsilane film self assembled on aluminium surface

We control the stiffnesses of two dual double cantelevers placed in series to control penetration into a perflurooctyltrichlorosilane monolayer self assembled on aluminium and silicon substrates. The top cantilever which carries the probe is displaced with respect to the bottom cantilever which carries the substrate, the difference in displacement recorded using capacitors gives penetration. We further modulate the input displacement sinusoidally to deconvolute the viscoelastic properties of the monolayer. When the intervention is limited to the terminal end of the molecule there is a strong viscous response in consonance with the ability of the molecule to dissipate energy by the generation of gauche defects freely. When the intervention reaches the backbone, at a contact mean pressure of 0.2GPa the damping disappears abruptly and the molecule registers a steep rise in elastic modulus and relaxation time constant, with increasing contact pressure. We offer a physical explanation of the process and describe this change as due to a phase transition from a liquid like to a solid like state.

Revisiting the Mechanism of the Triosephosphate Isomerase Reaction: The Role of the Fully Conserved Glutamic Acid 97 Residue

An analysis of 503 available triosephosphate isomerase sequences revealed nine fully conserved residues. Of these, four residues-K12, H95, E97 and E165-are capable of proton transfer and are all arrayed around the dihydroxyacetone phosphate substrate in the three-dimensional structure. Specific roles have been assigned to the residues K12, H95 and E165, but the nature of the involvement of E97 has not been established. Kinetic and structural characterization is reported for the E97Q and E97D mutants of Plasmodium falciparum triosephosphate isomerase (Pf TIM). A 4000-fold reduction in k(cat) is observed for E97Q, whereas the E97D mutant shows a 100-fold reduction. The control mutant, E165A, which lacks the key catalytic base, shows an approximately 9000-fold drop in activity. The integrity of the overall fold and stability of the dimeric structure have been demonstrated by biophysical studies. Crystal structures of E97Q and E97D mutants have been determined at 2.0 angstrom resolution. In the case of the isosteric replacement of glutamic acid by glutamine in the E97Q mutant a large conformational change for the critical K12 side chain is observed, corresponding to a trans-to-gauche transition about the C gamma-C delta (chi(3)) bond. In the E97D mutant, the K12 side chain maintains the wild-type orientation, but the hydrogen bond between K12 and D97 is lost. The results are interpreted as a direct role for E97 in the catalytic proton transfer cycle. The proposed mechanism eliminates the need to invoke the formation of the energetically unfavourable imidazolate anion at H95, a key feature of the classical mechanism.

Brillouin Scattering Investigation of Solvation Dynamics in Succinonitrile-Lithium Salt Plastic Crystalline Electrolytes

Temperature dependent Brillouin scattering studies have been performed to ascertain the influence of solvent dynamics on ion-transport in succinonitrile-lithium salt plastic crystalline electrolytes. Though very rarely employed, we observe that Brillouin spectroscopy is an invaluable tool for investigation of solvent dynamics. Analysis of various acoustic (long wavelength) phonon modes observed in the Brillouin scattering spectra reveal the influence of trans-gauche isomerism and as well as ion-association effects on ion transport. Although pristine SN and dilute SN-LiClO(4) samples show only the bulk longitudinal-acoustic (LA) mode, concentrated SN-LiClO(4) (similar to 0.3-1 M) electrolytes display both the bulk LA mode as well as salt induced brillouin modes at ambient temperature. The appearance of more than one brillouin mode is attributed to the scattering of light from regions with different compressibilities (''compactness''). Correspondingly, these modes show a large decrease in the full width at half-maximum (abbreviated as nu(f)) as the temperature decreases. Anomalous temperature dependent behavior of nu(f) with addition of salt could be attributed to the presence of disorder or strong coupling with a neighbor. The shape of the spectrum was evaluated using a Lorentzian and Fano line shape function depending on the nature and behavior of the Brillouin modes.

The Structural Characterization of Folded Peptides Containing the Conformationally Constrained beta-Amino Acid Residue beta(2,2)Ac(6)c

Backbone alkylation has been shown to result in a dramatic reduction in the conformational space that is sterically accessible to a-amino acid residues in peptides. By extension, the presence of geminal dialkyl substituents at backbone atoms also restricts available conformational space for beta and ? residues. Five peptides containing the achiral beta 2,2-disubstituted beta-amino acid residue, 1-(aminomethyl)cyclohexanecarboxylic acid (beta 2,2Ac6c), have been structurally characterized in crystals by X-ray diffraction. The tripeptide Boc-Aib-beta 2,2Ac6c-Aib-OMe (1) adopts a novel fold stabilized by two intramolecular H-bonds (C11 and C9) of opposite directionality. The tetrapeptide Boc-Aib-beta 2,2Ac6c]2-OMe (2) and pentapeptide Boc-Aib-beta 2,2Ac6c]2-Aib-OMe (3) form short stretches of a hybrid a beta C11 helix stabilized by two and three intramolecular H-bonds, respectively. The structure of the dipeptide Boc-Aib-beta 2,2Ac6c-OMe (5) does not reveal any intramolecular H-bond. The aggregation pattern in the crystal provides an example of an extended conformation of the beta 2,2Ac6c residue, forming a polar sheet like H-bond. The protected derivative Ac-beta 2,2Ac6c-NHMe (4) adopts a locally folded gauche conformation about the C beta?Ca bonds (?=-55.7 degrees). Of the seven examples of beta 2,2Ac6c residues reported here, six adopt gauche conformations, a feature which promotes local folding when incorporated into peptides. A comparison between the conformational properties of beta 2,2Ac6c and beta 3,3Ac6c residues, in peptides, is presented. Backbone torsional parameters of H-bonded a beta/beta a turns are derived from the structures presented in this study and earlier reports.

Electrophile-Induced C-C Bond Activation of Vinylcyclopropanes for the Synthesis of Z-Alkylidenetetrahydrofurans

We present a detailed study on the behavior of vinylcyclopropanes as masked donor acceptor system toward the stereoselective synthesis of Z-alkylidenetetrahydrofurans. Results of bromenium catalyzed indirect activation of C-C bond of vinylcyclopropanes and concomitant cyclization to alkylidenetetrahydrofuran and other heterocycles have been discussed. The stereoselective formation of the Z-isomer is strongly controlled by the extent of destabilization of one of the gauche conformers of the vinylcyclopropane. The ring-opening/cyclization step was found to be stereospecific as in the case of DA cyclopropanes. The activation of the C-C bond leads to a tight-carbocation intermediate, which is evident from the complete retention of the stereochemistry. The retention of configuration has been established by a necessary control experiment that rules out the possibility of a double inversion pathway. The present results serve as direct stereochemical evidence in support of a tight ion-pair intermediate versus the controversial S(N)2 pathway. A 2D potential energy scan has been carried out at B3LYP/6-31G(d) level theory to obtain the relative energies of the conformers. The Z-selectivity observed has been explained on the basis of the relative population of the conformers and modeling the intermediate and transition state involved in the reaction at M06-2x/6-31+G(d) level. Energy profile for the cyclization step was modeled considering various possible pathways through which cyclization can happen. The methodology has been successfully demonstrated on vinylcyclobutanes as well.

Microwave Spectroscopic and Atoms in Molecules Theoretical Investigations on the ArPropargyl Alcohol Complex: ArHO, Ar, and ArC Interactions

The structure of the Arpropargyl alcohol (ArPA) complex is determined from the rotational spectra of the parent complex and its two deuterated isotopologues, namely ArPA-D(OD) and ArPA-D(CD). The spectra confirm a geometry in which PA exists in the gauche form with Ar located in between OH and CCH groups. All a, b and c types of transitions show small splitting due to some large-amplitude motion dominated by COH torsion, as in the monomer. Splittings in a- and b-type transitions are of the order of a few kilohertz, whereas splitting in the c-type transitions is relatively larger (0.92.6 MHz) and decreases in the order ArPA>ArPA-D(CD)>ArPA-D(OD). The assignments are well supported by ab initio calculations. Atoms in molecules (AIM) and electrostatic potential calculations are used to explore the nature of the interactions in this complex. AIM calculations not only reveal the expected OHAr and Ar interactions in the Argauche-PA complex, but also novel CAr (of CH2OH group) and OHAr interactions in the Artrans-PA complex. Similar interactions are also present in the Armethanol complex.

H/F isosteric substitution to attest different equi-energetic molecular conformations in crystals

The sequential replacement of aromatic H-atoms by F-atoms in 1,6-bis(phenylcarbonate) hexa-2,4-diyne allows access to its possible iso-energetic ``syn'', ``gauche'' and ``anti'' conformations.