On single-crystal neutron-diffraction in DACs: quantitative structure refinement of light elements on SNAP and TOPAZ

ABSTRACT

Quantitative single crystal neutron-diffraction in diamond anvil cells has so far been limited by the neutron flux available at the various neutron sources. As a result, highly precise measurements of the exact position of light elements have not been possible preventing, for example, structural studies of hydrogen and hydrogen bonds under pressure. Here we report experiments carried out on SNAP at the Spallation Neutron Source (ORNL, TN, USA) to explore the possibility and current limits of such studies. Furthermore, we benchmarked the obtained data quality with reference experiments carried out on TOPAZ, a dedicated single-crystal instrument.

We show that measuring single-crystal diffraction intensities on SNAP is possible to such a precision that we are able to resolve the hydrogen bonds in potassium dideuterium phosphate (DKDP) as well as in ice VI.     

GEOM: A new tool for molecular modelling based on distance geometry calculations with NMR data

Summary GEOM is a new graphics tool which allows the use of distance geometry to compute linear and cyclic structures typically arising in drug design situations. Modified amino acids or monomeric organic entities can be easily constructed in an interactive way and deposited in the library of the distance geometry program together with geometric information required for structure calculation in dihedral angle space. In addition, GEOM is able to produce all files needed to calculate a structure based on NMR data (NOE and J-coupling constraints) and it permits the graphic analysis and comparison of computed structures. The application of GEOM is demonstrated in three examples: modelling of cyclosporin A structures with and without a limited set of H-bond constraints and modelling of a cyclic hexapeptide with a full NMR data set.     

A Water Rich Crystalline Hydrate Formed by 1,4,7,10-Tetraazacyclododecane, Siliconhydrofluoric Acid and Water: Structure and Properties

Novel complementary associations have been found in a crystalline ternarycomplex of the macrocyclic tetramine, [12]aneN₄ (e.g. =1,4,7,10-tetraazacyclododecane, cyclen, L), hexafluorosilicate ions andwater (I). The final compound belongs to the host—guest type with themacrocycle as the host (H), the inorganic entity as a guest (G) and watermolecules. It was characterized by X-ray techniques, IR spectroscopy andthermogravimetric study. X-ray crystal analysis revealed that the structureis built of the charged entities, with a 3D-network uniting thequadriprotonated form of the macrocycle, hexafluorosilicate as counterionsand lattice water molecules viaN—H⁺...F^-,N—H⁺...O(w),OH...F^- and O—-H(w)...O(w)hydrogen bonds. The overall complex stoichiometry comprises fourSiF₆ ^2- anions and seven water molecules per two[LH₄]⁴⁺ cations. Crystals of (I) are monoclinic,space group P2₁/n with a = 14.585(3), b = 16.384(2), c =16.500(3) Å, = 92.84(3)°, V = 3938(1)ų and Z = 8 forC₈H₃₁F₁₂N₄O_3.5Si₂.     

The structure of adsorbed water in cellulose acetate membranes

 The structure of water adsorbed in cellulose acetate membranes is determined by the fundamental and overtone IR spectra. Water is weakly H-bonded to ester and ether groups of the membrane, at low water contents. With increasing water content, more and more liquid-like water is observed. In addition, a small amount of a third type of water is present. The amounts of these three species are estimated from the spectra. At high water contents, the amount of liquid-like water increases strongly. The H-bond cooperativity of such water may be the cause for this increase and for the common anomalous water adsorption isotherms. The H-bond energy of the first hydration shell is relatively small, contrary to the anomalous large adsorption heats ΔH _ad. This could be described by larger van der Waals interactions between this type of water and the membrane groups as a result of a higher coordination number compared with Z=4.4 of liquid-like water. This model is in agreement with the decrease of ΔH _ad with increasing water sorption reaching the evaporization enthalpy of pure water at high water contents. Received: 24 May 1997 Accepted: 1 July 1997     

Synthesis and structure of tricyclic quinazoline alkaloid oxalates

Oxalates of the alkaloids deoxyvasicinone, 2,3-tetra-, and their seven-membered analog 2,3-pentamethylen-3,4-dihydroquinazol-4-one and the complex of 2,3-pentamethylen-3,4-dihydroquinazol-4-one hydrochloride with oxalic acid were synthesized. It was found that 2:1, 2:1, and 1:1 alkaloid:oxalic acid complexes, respectively, were formed. The last complex had 2,3-pentamethylen-3,4-dihydroquinazol-4-one, oxalic acid, and HCl in a 2:1:2 ratio, respectively. X-ray crystal structures of single crystals were performed. The oxalate of 2,3-pentamethylen-3,4-dihydroquinazol-4-one and its hydrochloride formed salts with a protonated N1 atom and involvement of only one hydroxyl. The other alkaloids formed a complex with oxalic acid through N1…H-O H-bonds involving both acid hydroxyls. __________ Translated from Khimiya Prirodnykh Soedinenii, No. 2, pp. 152–156, March–April, 2007.     

(C6H16N2)Zn3(HPO3)4H2O: a new layered zinc phosphite templated by diprotonated trans-1,4-diaminocyclohexane

Employing trans-1,4-diaminocyclohexane (trans-1,4-DACH) as a template, a new two-dimensional layered zinc phosphite (C₆H₁₆N₂)Zn₃(HPO₃)₄H₂O (1) has been prepared hydrothermally. Single-crystal X-ray diffraction analysis shows that it crystallizes in the monoclinic space group P2₁/n with a=10.458(2) Å, b=14.720(3) Å, c=13.079(3) Å, β=97.93(3)°, V=1994.1(7) ų, Z=4, R₁=0.0349 (I>2σ(I)) and wR₂=0.0605 (all data). The inorganic layer is built up by alternation of ZnO₄ tetrahedra and HPO₃ pseudo pyramids forming a 4.6.8-net. The sheet is featured by a series of capped six-membered rings. The diprotonated trans-1,4-DACH molecules reside in the interlayer region and interact with the inorganic network through H-bonds.     

Investigation of structures and properties of cyclic peptide nanotubes by experiment and molecular dynamics

In order to investigate the structures and properties of cyclic peptide nanotubes of cyclo[(-D: -Phe-L: -Ala)( n = 3,4,5,6)-], cyclo[(-D: -Phe-L: -Ala)( n = 4)-] was synthesized and self-assembled to nanotubes, and its structure and morphology of the nanotube were characterized by mass spectrometry (MS), fourier transform infrared spectroscopy (FT-IR) and scanning electron microscopy (SEM). On the basis of these experimental results, the structures of cyclo[(-D: -Phe-L: -Ala)( n = 3,4,5,6)-] were characterized by molecular dynamics. In addition, the motion behaviors of H(2)O molecules in nanotubes were investigated by molecular dynamics using a COMPASS force field. Experimental results show that cyclo[(-D: -Phe-L: -Ala)( n = 4)-] peptides self-assemble into nanotube bundles. Molecular modeling results indicate that cyclic peptide nanotubes with n = 3, 4, 5 and 6 are very stable; these nanotubes have internal diameters of 5.9 A, 8.1 A, 10.8 A and 13.1 A and outer diameters of 18.2 A, 21.7 A, 23.4 A and 25.9 A respectively. Modeling results demonstrate that H(2)O molecules move in cooperation in single nanotube and they diffuse in one dimension, but they did not diffuse unilaterally due to the antiparallel ring stacking arrangement.     

Ab initio investigation of the simultaneous motion of protons in the hydrogen bonds in the cyclic dimer of formamide

The simultaneous motion of protons in interacting H-bonds plays an important role in biochemistry. By means of the simple example of the cyclic dimer of formamide some significant properties of the simultaneous motion of protons are discussed.Starting from the calculations of Dreyfus, Maigret, and A. Pullman [9] an energy surface as well as a surface of dipole moment for the linear motion of the two protons is calculated point by point using a selfwritten program of the SCF-MO-LC (LCGO)-method and using a Gaussian basis set of intermediate size.The resulting surface of total energy is further used to determine the states of vibration of the simultaneous motion of the protons. Whereas the surface of dipole moment is used to compute the relative transition intensities. These spectroscopic properties are finally used to find a criterion for estimating the kind of motion - mainly correlated or mainly independent.Held at the 6^th Jerusalem Symposium, April 9–13, 1973.     

Stabilization of germanium(IV) aquafluorocompounds in host-guest type complexes with crown ethers. synthesis,crystal structure and ir spectra of the complexes [(GeF5-H2O)2-(H2-1,10-Diaza-l 8-Crown-6)] and [(trans-GeF4 · 2H2O) · 18-Crown-6·2H2O]

Stable products have been obtained from the interaction of GeO₂-HF solution with 18-membered crown ethers, 1,10-diaza-l8-crown-6 and 18-crown 6. Complexes were characterized by X-ray analysis and IR spectroscopy. Both Ge(IV) aquafluorocompounds are isostructural with their Si analogues. It was established that in the host-guest type complexes the germanium moiety as a central atom has been stabilized in the form of octahedral complexes. The host-guest interaction occurs by means of O-H(W)...O_cr, OH...F and N-H...F hydrogen bonds.     

Anti-cooperativity of the two water OH groups

This paper presents the results concerning anti-cooperativity effects between two H-bonds of a water molecule. The IR OH stretching band shifts Δν—as a measure of the H-bond energy—are compared for HOD with different bases B of 1:1 complexes B…HOD…Cl₄ (Δν₁₁) and 1:2 complexes B…HOD…B (Δν₁₂). We found that Δν₁₂ of the 1:2 complexes for different bases B are 25% smaller than Δν₁₁ for the 1:1 complexes. Corrections for the solvent shifts are introduced. This effect is in line with different observations concerning cooperativity effects of OH H-bonds by polarization with neighbouring molecules. The reduction of Δν₁₂ in 1:2 complexes can be understood on the assumption of a negative polarization by the first H-bond to the second OH or OD group and is called anti-cooperativity. This anti-effect has been already detected by NMR observation on NH₂.

We already observe a decrease of the CCl₄ solvent shift by van der Waals forces OH…CCl₄ of 1:1 complexes, induced by the H-bond of the other OH or OD group. This decrease is measured by the CCl₄ solvent effect for monomers. This indicates a real negative polarization by the H-bond in 1:1 complexes on the second OH/OD. This experiment establishes the real polarization and excludes the importance of repulsions of the bases as the cause. The dependence of intermolecular forces is known on the polarizability. Our method demonstrates directly the polarization by interactions.

The anti-cooperativity of symmetric complexes B₁…HOD…B₁ by a strong base B₁ can be reduced in unsymmetric 1:2 complexes B₁…HOD…B₂ by weaker bases B₂. This weakening of the anti-cooperativity of the stronger base could be predicted quantitatively. Similarly, the anti-cooperativity of the weaker base B₂ is strengthened in unsymmetric 1:2 complexes by stronger bases B₁.

It is known that H-bonds XH…B can be strengthened by cooperativity with a second H-bond XH…XH…B. They can be weakened for water by anti-cooperativity of two H-bonds B…HOH…B. The H-bond B₁…HO of 1:2 complexes B₁…HOH…B₂ can be weakened if the base strength of B₂ is stronger than of B₁ or strengthened if B₂ is weaker than B₁. Nature may use these possibilities in biochemistry.