N. m. r. and infrared spectroscopic studies of hydrogen bonding in hindered alcohols. An instance of a true hydrogen bonded dimer in an alcohol

Hydrogen bonding in the highly hindered alcohol 2,4-dimethyl-3-ethyl-3-pentanol has been studied by proton n.m.r. and infrared spectroscopy. This alcohol associates to form a dimer but no higher hydrogen bonded species; hence the monomer–dimer equilibrium can be studied without interference from competing processes. Spectral and thermodynamic properties for the hydrogen bonding are reported.

Crystal and molecular structure of the ammonium salt of the dinucleoside monophosphate d(CpG)

The crystal and molecular structure of the ammonium salt of deoxycytidylyl-(3'-5')-deoxyguanosine has been determined from 0.85 A resolution single crystal X-ray diffraction data. The crystals obtained by acetone diffusion technique at -20 degrees C, are orthorhombic, P212121, a = 12.880(2), b = 17444(2) and c = 27.642(2) A. The structure was solved by high resolution Patterson and Fourier methods and refined to R = 0.136. There are two d(CpG) molecules in the asymmetric unit forming a mini left handed Z-DNA helix. This is in contrast to the earlier reported forms of d(CpG) where the molecules form self base paired duplexes. There are two ammonium ions in the asymmetric unit. The major groove NH+4 ion interacts with N7 of guanines through water bridges besides making H-bonded interactions directly with the phosphate oxygen atoms. A second NH+4 ion is found in the minor groove interacting directly with the phosphate oxygen atoms. Symmetry related molecules pack in such a way that the cytosine base stacks on cytosine and guanine base on guanine. Our structure demonstrates that alternating d(CpG) sequences have the ability to adopt the left handed Z-DNA structure even at the dimer level i.e., in a sequence which is only two base pairs long.

Modelling studies on neurodegenerative disease causing triplet repeat sequences d(CGG/GCC) and d(CAG/CTG): Duplexes vs Quadruplexes

Model building and molecular mechanics studies have been carried out to examine the potential structures for d(GGC/GCC)5 and d(CAG/CTG)5 that might relate to their biological function and association with triplet repeat expansion diseases. Model building studies suggested that hairpin and quadruplex structures could be formed with these repeat sequences. Molecular mechanics studies have demonstrated that the hairpin and hairpin dimmer structures of triplet repeat sequences formed by looping out of the two strands are as favourable as the corresponding B-DNA type hetero duplex structures. Further, at high salt condition, Greek key type quadruplex structures are energetically comparable with hairpin dimer and B-DNA type duplex structures. All tetrads in the quadruplex structures are well stacked and provide favourable stacking energy values. Interestingly, in the energy minimized hairpin dimer and Greek key type quadruplex structures, all the bases even in the non-G tetrads are cyclically hydrogen bonded, even though the A, C and T-tetrads were not hydrogen bonded in the starting structures.

Conformational Polymorphism in Telomeric Structures: Loop Orientation and Interloop Pairing in d(G4TnG4),

Sequence repeats constituting the telomeric regions of chromosomes are known to adopt a variety of unusual structures, consisting of a G tetraplex stem and short stretches of thymines or thymines and adenines forming loops over the stem. Detailed model building and molecular mechanics studies have been carried out for these telomeric sequences to elucidate different types of loop orientations and possible conformations of thymines in the loop. The model building studies indicate that a minimum of two thymines have to be interspersed between guanine stretches to form folded-back structures with loops across adjacent strands in a G tetraplex (both over the small as well as large groove), while the minimum number of thymines required to build a loop across the diagonal strands in a G tetraplex is three. For two repeat sequences, these hairpins, resulting from different types of folding, can dimerize in three distinct ways-i.e., with loops across adjacent strands and on same side, with loops across adjacent strands and on opposite sides, and with loops across diagonal strands and on opposite sides-to form hairpin dimer structures. Energy minimization studies indicate that all possible hairpin dimers have very similar total energy values, though different structures are stabilized by different types of interactions. When the two loops are on the same side, in the hairpin dimer structures of d(G(4)T(n)G(4)), the thymines form favorably stacked tetrads in the loop region and there is interloop hydrogen bonding involving two hydrogen bonds for each thymine-thymine pair. Our molecular mechanics calculations on various folded-back as well as parallel tetraplex structures of these telomeric sequences provide a theoretical rationale for the experimentally observed feature that the presence of intervening thymine stretches stabilizes folded-back structures, while isolated stretches of guanines adopt a parallel tetraplex structure

Comprehensive investigations on DNa center dot center dot center dot A (D = H/F) complexes show why `sodium bonding' is not commonly observed

A comprehensive study of D-Na center dot center dot center dot A (D = H/F) complexes has been done using advanced ab initio and atoms in molecule (AIM) theoretical analyses. The correlation between electron density at bond critical point and binding energy gives a distinguishing feature for hydrogen bonding, different from the `electrostatic complexes' formed by LiD and NaD. Moreover, the LiD/NaD dimers have both linear and anti-parallel minima, as expected for electrostatic dipole-dipole interactions. The HF dimer has a quasi-linear minimum and the anti-parallel structure is a saddle point. Clearly, characterizing hydrogen bonding as `nothing but electrostatic interaction between two dipoles' is grossly in error.

Insights into stabilizing interactions in the distorted domain-swapped dimer of Salmonella typhimurium survival protein

The survival protein SurE from Salmonella typhimurium (StSurE) is a dimeric protein that functions as a phosphatase. SurE dimers are formed by the swapping of a loop with a pair of beta-strands and a C-terminal helix between two protomers. In a previous study, the Asp230 and His234 residues were mutated to Ala to abolish a hydrogen bond that was thought to be crucial for C-terminal helix swapping. These mutations led to functionally inactive and distorted dimers in which the two protomers were related by a rotation of 167 degrees. New salt bridges involving Glu112 were observed in the dimeric interface of the H234A and D230A/H234A mutants. To explore the role of these salt bridges in the stability of the distorted structure, E112A, E112A/D230A, E112A/H234A, E112A/D230A/H234A, R179L/H180A/H234A and E112A/R179L/H180A/H234A mutants were constructed. X-ray crystal structures of the E112A, E112A/H234A and E112A/D230A mutants could be determined. The dimeric structures of the E112A and E112A/H234A mutants were similar to that of native SurE, while the E112A/D230A mutant had a residual rotation of 11 degrees between the B chains upon superposition of the A chains of the mutant and native dimers. The native dimeric structure was nearly restored in the E112A/H234A mutant, suggesting that the new salt bridge observed in the H234A and D230A/H234A mutants was indeed responsible for the stability of their distorted structures. Catalytic activity was also restored in these mutants, implying that appropriate dimeric organization is necessary for the activity of SurE.

I. The crystal structure of a new dimer of triphenylfluorocyclobutadiene. II. A low temperature refinement of the cyanuric triazide structure

I. THE CRYSTAL STRUCTURE OF A NEW DIMER OF TRIPHENYLFLUOROCYCLOBUTADIENE

The crystal structure of thermal isomer of the “head-to-head” dimer of triphenylfluorocyclobutadiene was determined by the direct method. The Σ₂ relationship involving the low angle reflections with the largest E’s were found and solved for the signs by the symbolic method of Zachariasen. The structure was seen in the electron density map and the E-map, and was refined antisotropically by the method of least squares. The residual R was 0.065.

The structure is a gem-difluorohexaphenyldihydropentalene. All of the phenyl groups are planar as it is the cyclopentadiene ring of the dihydropentalene skeleton. Overcrowding at the position of the flourines causes some deviations from the normal bond angles in the cyclopentene ring.

The list of observed and calculated structure factors on pages 32-34 will not be legible on the microfilm. Photographic copies may be obtained from the California Institute of Technology.

II. A LOW TEMPERATURE REFINEMENT OF THE CYANURIC TRIAZIDE STRUCTURE

The structure of cyanuric triazide was refined anisotropically by the method of least squares. Three-dimensional intensity data, which has been collected photographically with MoK_α radiation at -110˚C, were used in the refinement. The residual R was reduced to 0.081.

The structure is completely planar, and there is no significant bond alternation in the cyanuric ring. The packing of the molecules causes the azide groups to deviate from linearity by 8 degrees.

Electronic structures of hafnium dimer and trimer by density functional theory

Equilibrium geometries, vibrational frequencies and dissociation energies of hafnium dimer and trimer were studied by density functional methods B3LYP, BLYP, B3PW91, BHLYP, BP86, B3P86, mPW1PW91 and PBE1PBE. The results indicate that singlet is the ground state both for hafnium dimer and for trimer. For hafnium dimer, the calculated bond distance is less sensitive to the methods used. Except at BHLYP level, the calculated vibrational frequency is comparable to the experimental value. For hafnium trimer, equilateral triangle with D-3h symmetry is slightly favored compared with isosceles triangle with C-2v, symmetry except at BHLYP level. This conclusion is in agreement with experiment in which the ground state of Hf-3 is fluxional and low-spin or closed shell is preferred.

Novel polyoxometalate-templated, 3-D supramolecular networks based on lanthanide dimers: Synthesis, structure, and fluorescent properties of [Ln(2)(DNBA)(4)(DMF)(8)][Mo6O19] (DNBA=3,5-dinitrobenzoate)

The spherical Lindquist type polyoxometalate, Mo6O192-, has been used as a noncoordinating anionic template for the construction of novel three-dimensional lanthanide-aromatic monocarboxylate dimer supramolecular networks [Ln(2)(DNBA)(4)(DMF)(8)][Mo6O19] (Ln = La 1, Ce 2, and Eu 3, DNBA = 3,5-dinitrobenzoate, DMF = dimethylformamide). The title compounds are characterized by elemental analyses, IR, and single-crystal X-ray diffractions. X-ray diffraction experiments reveal that two Ln(III) ions are bridged by four 3,5-dinitrobenzoate anions as asymmetrically bridging ligands, leading to dimeric cores, [Ln(2)(DNBA)(4)(DMF)(8)](2+); [Ln(2)(DNBA)(4)(DMF)(8)](2+) groups are joined together by pi-pi stacking interactions between the aromatic groups to form a two-dimensional grid-like network; the 2-D supramolecular layers are further extended into 3-D supramolecular networks with 1-D box-like channels by hydrogen-bonding interactions, in which hexamolybdate polyanions reside. The compounds represent the first examples of 3-D carboxylate-bridged lanthanide dimer supramolecular "host" networks formed by pi-pi stacking and hydrogen-bonding interactions encapsulating noncoordinating "guest" polyoxoanion species. The fluorescent activity of compound 3 is reported.

A novel dimer - Heteropolytungstate with a vanadium atom as the centre - Synthesis and structural characterization of (H3O)(4)[VW12O40Na (H2O)(4)](2)

A novel dimer-tungstovanadate, (H3O)(4)[VW12O40Na (H2O)(4)](2), was hydrothermally synthesized and structurally characterized by single crystal X-ray diffraction, IR spectra, TGA-DSC thermal analysis and polarograpy. The yellowish crystal crystallized in the triclinic system, space group P1, a = 1.464 5(3) nm, b = 1.468 6(3) nm, c = 1.411 1(3) nm, alpha = 111.82(2)degrees, beta = 93.17(3)degrees, gamma = 117.47(3)degrees, V = 2.210 6(8) nm(3), Z = 1, D-c = 4.552 g . cm(-3), lambda (Mo K alpha) = 0.071 073 nm, mu = 31.402 mm(-1) F(000) = 2 6481 R = 0.078 0. The title compound consists of two Keggin structure units linked together with two hydrated sodium cations to form a dimer with a porous structure with the pore dimension of 0.766 nm X 0.778 5 nm.

A NOVEL METAL THIAMINE COMPLEX WITH A CYCLIC DIMER FORMED BY METAL-BRIDGED 2 THIAMINE LIGANDS - CRYSTAL-STRUCTURE OF [MN(THIAMINE)CL2(H2O)]2[THIAMINE]2CL4.2H2O

The crystal structure of [Mn(thiamine)Cl2(H2O)]2[thiamine]2Cl4.2H2O has been determined by X-ray diffraction methods. The compound contains a cyclic dimer of a complex cation with two thiamine ligands bridged by two Mn(II) ions across a crystallographic center of symmetry. Each Mn(II) is coordinated by two chloride atoms, a water molecule, a N(1') atom of the pyrimidine from a thiamine and an O(53) atom of the hydroxyethyl side chain from another thiamine. There are two free-base thiamine molecules related by a center of symmetry in the unit cell, which form a base-pair through the hydrogen bonds. Both the independent thiamine molecules in the asymmetric unit assume the common F conformation with phi-T = 10.0(9) and 3.6(10) and phi-P = 85.6(7) and 79.6(7), respectively. The compound provides a possible model for a metal-bridged enzyme-coenzyme complex in thiamine catalysis. Crystallographic data: triclinic, space group P1BAR, a = 12.441(4), b = 13.572(4), c = 11.267(3) angstrom, alpha = 103.15(2), beta 89.03(3), gamma = 115.64(2)-degrees, Z = 1, D(calc) = 1.524 g cm-3, and R = 0.050 for 3019 observed reflections with I > 3-sigma(I).

Concertedness and solvent effects in multiple proton transfer reactions: The formic acid dimer in solution

The issue of multiple proton transfer (PT) reactions in solution is addressed by performing molecular dynamics simulations for a formic acid dimer embedded in a water cluster. The reactant species is treated quantum mechanically, within a density functional approach, while the solvent is represented by a classical model. By constraining different distances within the dimer we analyze the PT process in a variety of situations representative of more complex environments. Free energy profiles are presented, and analyzed in terms of typical solvated configurations extracted from the simulations. A decrease in the PT barrier height upon solvation is rationalized in terms of a transition state which is more polarized than the stable states. The dynamics of the double PT process is studied in a low-barrier case and correlated with solvent polarization fluctuations. Cooperative effects in the motion of the two protons are observed in two different situations: when the solvent polarization does not favor the transfer of one of the two protons and when the motion of the two protons is not synchronized. This body of observations is correlated with local structural and dynamical properties of the solvent in the vicinity of the reactant. (C) 2000 American Institute of Physics. [S0021-9606(00)51121-0].

New families of enantiopure cyclohexenone cis-diol, o-quinol dimer and hydrate metabolites from dioxygenase-catalysed dihydroxylation of phenols

Toluene dioxygenase-catalysed cis-dihydroxylation of phenols has led to the discovery of new enantiopure cyclohexenone cis-diol, o-quinol dimer and phenol hydrate metabolites having synthetic potential.

Isoprenylation of the G protein gamma subunit is both necessary and sufficient for beta gamma dimer-mediated stimulation of phospholipase C

We have previously shown that isoprenylation and/or additional pest-translational processing of the G protein gamma(1) subunit carboxyl terminus is required for beta(1) gamma(1) subunit stimulation of phospholipase C-beta(2) (PLC beta(2)) [Dietrich, A., Meister, M., Brazil, D., Camps, M., & Gierschik, P. (1994) Eur. J. Biochem. 219, 171-178]. To examine whether isoprenylation of the gamma(1) subunit alone is sufficient for beta(1) gamma(1)-mediated PLC beta(2) stimulation or whether any of the two subsequent modifications, proteolytic removal of the carboxyl-terminal tripeptide and/or carboxylmethylation, is required for this effect, nonisoprenylated recombinant beta(1) gamma(1) dimers were produced in baculovirus-infected insect cells, purified to near homogeneity, and then isoprenylated in vitro using purified recombinant protein farnesyltransferase. Analysis of the beta(1) gamma(1) dimer after in vitro farnesylation by reversed phase high-performance liquid chromatography followed by delayed extraction matrix-assisted laser desorption/ionization mass spectrometry confirmed that the gamma(1) subunit was carboxyl-terminally farnesylated but not proteolyzed and carboxylmethylated. Functional reconstitution of in vitro-farnesylated beta(1) gamma(1) dimers with a recombinant PLC beta(2) isozyme revealed that farnesylation rendered recombinant nonisoprenylated beta(1) gamma(1) dimers capable of stimulating PLC beta(2) and that the degree of this stimulation was only approximately 45% lower for in vitro-farnesylated beta(1) gamma(1) dimers than for fully modified native beta(1) gamma(1) purified from bovine retinal rod outer segments. Taken together, these results suggest that isoprenylation of the gamma subunit is both necessary and sufficient for beta gamma dimer-mediated stimulation of phospholipase C.