Noncovalent interactions in paired DNA nucleobases investigated by terahertz spectroscopy and solid-state density functional theory.

Cocrystallized adenine and thymine derivatives, along with the pure monomeric crystals, were investigated by terahertz spectroscopy and solid-state density functional theory (DFT). The methylated nucleobase derivatives crystallize in planar hydrogen-bonded adenine-thymine pairs similar to the manner found in DNA. The spectra obtained for 1-methylthymine, 9-methyladenine, and the 1:1 cocrystal in the range of 10-100 cm(-1) clearly demonstrate that absorptions in this spectral range originate from the uniquely ordered assembly and the intermolecular interactions found in each individual crystal system. The quality of spectral reproduction for the DFT simulations of each system was clearly improved by the inclusion of an empirical correction term for London-type dispersion forces to the calculations. Notably, it was found that these weak dispersion forces in the adenine-thymine cocrystal were necessary to produce a properly converged crystal structure and meaningful simulation of the terahertz vibrational spectrum.

Terahertz spectroscopic investigation of S-(+)-ketamine hydrochloride and vibrational assignment by density functional theory.

The terahertz (THz) spectrum of (S)-(+)-ketamine hydrochloride has been investigated from 10 to 100 cm(-1) (0.3-3.0 THz) at both liquid-nitrogen (78 K) and room (294 K) temperatures. Complete solid-state density functional theory structural analyses and normal-mode analyses are performed using a single hybrid density functional (B3LYP) and three generalized gradient approximation density functionals (BLYP, PBE, PW91). An assignment of the eight features present in the well-resolved cryogenic spectrum is provided based upon solid-state predictions at a PW91/6-31G(d,p) level of theory. The simulations predict that a total of 13 infrared-active vibrational modes contribute to the THz spectrum with 26.4% of the spectral intensity originating from external lattice vibrations.

Investigation of (1R,2S)-(-)-ephedrine by cryogenic terahertz spectroscopy and solid-state density functional theory.

The terahertz (THz) spectrum of the pharmaceutical (1R,2S)-(-)-ephedrine from 8.0 to 100.0 cm(-1) is investigated at liquid-nitrogen (78.4 K) temperature. The spectrum exhibits several distinct features in this range that are characteristic of the crystal form of the compound. A complete structural analysis and vibrational assignment of the experimental spectrum is performed using solid-state density functional theory (DFT) and cryogenic single-crystal X-ray diffraction. Theoretical modeling of the compound includes an array of density functionals and basis sets with the final assignment of the THz spectrum performed at a PW91/6-311G(d,p) level of theory, which provides excellent solid-state simulation agreement with experiment. The solid-state analysis indicates that the seven experimental spectral features observed at low temperature consist of 13 IR-active vibrational modes. Of these modes, nine are external crystal vibrations and provide approximately 57% of the predicted spectral intensity. This study demonstrates that the THz spectra of complex pharmaceuticals may be well reproduced by solid-state DFT calculations and that inclusion of the crystalline environment is necessary for realistic and accurate simulations.

Solid-state coordination chemistry of copper(II) tetrazolates: anion control of frameworks constructed from trinuclear copper(II) building blocks.

The products of the reactions of copper(II) starting materials with 4-pyridyltetrazole (4-Hpt) in N,N-dimethylformamide (DMF)/methanol solutions are determined by the anion identity and concentration. In the absence of chloride, the 3-D open-framework material [Cu(3)(OH)(3)(4-pt)(3)(DMF)(4)].5DMF.3MeOH (1.5DMF.3MeOH) is isolated, while variations in the chloride concentration yield the 2-D and 3-D materials, 2 and 3, respectively. All three structures exhibit trinuclear copper(II) building blocks: the triangular {Cu(3)(mu(3)-OH)}(5+) core in 1 and {Cu(3)Cl(4)(4-pt)(4)(4-Hpt)(2)}(2-) and {Cu(3)Cl(2)(4-pt)(8)}(4-) chains in 2 and 3, respectively. All three materials display microporosity, which is highly dependent on the method of sample preparation.

The hydrothermal and structural chemistry of oxovanadium-arylphosphonate networks and frameworks.

The hydrothermal reactions of NH4VO3 with the aromatic phosphonate ligands 1,4-, 1,3-, and 1,2-phenylenediphosphonic acids (H4L1, H4L3, H4L4, respectively); biphenyl-4,4'-diyldiphosphonic acid (H4L2); and 1,3,5-tris(phenyl)-4,4'-triphosphonic acid (H6L5) yielded materials of the V(x)O(y)/organophosphonate family [VO(H2L1)] (1), [VO(H2L2)] (2), [V2O2(H2O)2(L3)] x 1.5 H2O (3 x 1.5 H2O), [V2O2(H2O)2(L4)] x 2 H2O (4 x 2 H2O), and [V3O3(OH)(H3L5)2] x 7.5 H2O (6 x 7.5 H2O). The reactions were carried out in the presence of HF, and in one case, fluoride was incorporated to provide [V2F(OH)(H2O)3(L4)] x 2.25 H2O (5 x 2.25 H2O). The materials exhibit diverse structural chemistry, including the prototypical buttressed layer architecture for 1 and 2, a complex three-dimensional structure for 3, and unique two-dimensional structures for 4, 5, and 6. The structures of this oxovanadium-arylphosphonate family are quite distinct from those previously described for the V(x)O(y)/alkyldiphosphonate series.

Construction of metal-organic oxides from molybdophosphonate clusters and copper-bipyrimidine building blocks.

A series of organic-inorganic hybrid materials of the copper(II)-molybdophosphonate family have been prepared using conventional hydrothermal conditions. The reactions of MoO(3), copper(II) acetate, bipyrimidine (bpyr), a phosphonic acid, and water at temperatures below 160 degrees C and in the presence of a mineralizer such as acetic acid or HF provided crystalline samples of materials of the general class {Cu(2)(bpyr)}(4+)/Mo(x)O(y)-phosphonate. The recurrent themes of the structures are the presence of the binuclear {Cu(2)(bpyr)}(4+) and pentanuclear {Mo(5)O(15)(O(3)PR)(2)}(4-) building blocks. For the alkylphosphonate-containing materials, [{Cu(2)(bpyr)(2)}Mo(5)O(15)(O(3)PCH(3))(2)].2.5H(2)O (1.2.5H(2)O) is two-dimensional and exhibits {Cu(bpyr)}(n)(2n+) chains, while [{Cu(2)(bpyr)(H(2)O)}Mo(5)O(15)(O(3)PCH(2)CH(3))(2)] (2) is three-dimensional. The diphosphonate series of materials {{Cu(2)(bpyr)}(4+)[Mo(5)O(15){O(3)P(CH(2))(n)PO(3)}](4-) with n = 2-6 (4, 5, 7-9) in all cases contain the characteristic [Mo(5)O(15){O(3)P(CH(2))(n)PO(3)}](n)(2n+) chains, linked through {Cu(2)(bpyr)}(4+) rods into three-dimensional frameworks. When n = 1, the three-dimensional phase [{Cu(2)(bpyr)}MoO(2)(HO(3)PCH(2)PO(3))(2)].2H(2)O (3.2H(2)O) is obtained, the exclusive example of a structure constructed from isolated {MoO(6)} polyhedra rather than pentamolybdate clusters. The Ni(II)-containing phase [{Ni(2)(bpyr)(H(2)O)(4)}Mo(5)O(15){O(3)P(CH(2))(3)PO(3)}].9H(2)O (6.9H(2)O) was also prepared and compared to the structure of the Cu(II) analogue, [{Cu(2)(bpyr)(H(2)O)(4)}Mo(5)O(15){O(3)P(CH(2))(3)PO(3)}].3H(2)O (5.3H(2)O). Magnetic susceptibility studies of the compounds revealed that the magnetic behavior was consistent in all cases with antiferromagnetically coupled dimers. However, the magnitude of the exchange coupling was clearly dependent on the orientation of the M(II) mean equatorial or basal planes relative to the bipyrimidine plane. Thus, when the metal and bipyrimidine planes are nearly coplanar, the J values are in the -77 to -87 cm(-1) range, while J values of -2 to -5 cm(-1) are observed for the compounds with out-of-plane orientations.

Inelastic neutron scattering and Raman spectroscopic investigation of L-alanine alaninium nitrate, a homologue of a ferroelectric material.

The 2 : 1 amino acid salt of L-alanine with nitric acid was crystallized and the vibrational spectrum measured at 25 K by incoherent inelastic neutron scattering (INS) spectroscopy. The spectrum was simulated using solid-state density functional theory based on a new 90 K structure determination. A feature observed at approximately 450 cm(-1) in the INS spectrum of L-alanine alaninium nitrate is noticeably absent in the calculation. Raman spectroscopy reveals spectral differences between the spectra at 77 and 293 K with a 450 cm(-1) feature appearing at low temperature. The nature of these spectral changes and the disagreement between the INS spectrum and its simulation are discussed in relation to an apparent structural change involving motion of a proton at low (<90 K) temperature.

Examination of phencyclidine hydrochloride via cryogenic terahertz spectroscopy, solid-state density functional theory, and X-ray diffraction.

The terahertz (THz) spectrum of phencyclidine hydrochloride from 7.0 to 100.0 cm(-1) has been measured at cryogenic (78.4 K) temperature. The complete structural analysis and vibrational assignment of the compound have been performed employing solid-state density functional theory utilizing eight generalized gradient approximation density functionals and both solid-state and isolated-molecule methods. The structural results and the simulated spectra display the substantial improvement obtained by using solid-state simulations to accurately assign and interpret solid-state THz spectra. A complete assignment of the spectral features in the measured THz spectrum has been completed at a VWN-BP/DNP level of theory, with the VWN-BP density functional providing the best-fit solid-state simulation of the experimentally observed spectrum. The cryogenic THz spectrum contains eight spectral features that, at the VWN-BP/DNP level, consist of 15 infrared-active vibrational modes. Of the calculated modes, external crystal vibrations are predicted to account for 42% of the total spectral intensity.

Cryogenic terahertz spectrum of (+)-methamphetamine hydrochloride and assignment using solid-state density functional theory.

The cryogenic terahertz spectrum of (+)-methamphetamine hydrochloride from 10.0 to 100.0 cm(-1) is presented, as is the complete structural analysis and vibrational assignment of the compound using solid-state density functional theory. This cryogenic investigation reveals multiple spectral features that were not previously reported in room-temperature terahertz studies of the title compound. Modeling of the compound employed eight density functionals utilizing both solid-state and isolated-molecule methods. The results clearly indicate the necessity of solid-state simulations for the accurate assignment of solid-state THz spectra. Assignment of the observed spectral features to specific atomic motions is based on the BP density functional, which provided the best-fit solid-state simulation of the experimental spectrum. The seven experimental spectral features are the result of thirteen infrared-active vibrational modes predicted at a BP/DNP level of theory with more than 90% of the total spectral intensity associated with external crystal vibrations.

2-({3-[(2R,4S,5R)-4-Hydr-oxy-5-hydroxy-methyl-2,3,4,5-tetra-hydro-furan-2-yl]-5-methyl-2,6-dioxo-1,2,3,6-tetra-hydro-pyrimidin-1-yl}meth-yl)isoindoline-1,3-dione.

The title compound, C(19)H(19)N(3)O(7), is a thymidine derivative and serves as an inter-mediate in the synthesis of a (99m)Tc radiolabeled nucleoside analog. Inter-molecular O-H⋯O hydrogen bonding is observed between the hydr-oxy functionalities of the ribose unit themselves as well as between a hydr-oxy group and an O atom of the phthalimide group of an adjacent mol-ecule. The mol-ecules are stacked on top of each other in the direction of the a axis. The crystal packing is further stabilized by weak intra- and inter-molecular C-H⋯O hydrogen bonds. The absolute configuration of the compound is known from the synthesis.

A thermally and hydrolytically stable microporous framework exhibiting single-chain magnetism: structure and properties of [Co2(H0.67bdt)3] x 20 H2O.

Fixing a hole: Hydrothermal chemistry has been exploited in the preparation of a 3D framework material exhibiting 48% accessible void volume and 1.5% hydrogen uptake by weight at 120 kPa (see picture). The title compound also exhibits single-chain magnetic behavior and reversible changes in magnetic properties upon solvation and desolvation.

Toward efficient nanoporous catalysts: controlling site-isolation and concentration of grafted catalytic sites on nanoporous materials with solvents and colorimetric elucidation of their site-isolation.

We report that the polarity and dielectric constants of solvents used for grafting organosilanes on mesoporous materials strongly affect the concentration of grafted organic groups, the degree of their site-isolation, and the catalytic properties of the resulting materials. Polar and nonpolar organosilanes as well as polar-protic, dipolar-aprotic, and nonpolar solvents were investigated. Polar-protic solvents, which have high dielectric constants, resulted in smaller concentrations ( approximately 1-2 mmol/g) of polar organic groups such as 3-aminopropyl groups, higher surface area materials, site-isolated organic groups, and more efficient catalytic properties toward the Henry reaction of p-hydroxybenzaldehyde with nitromethane. On the other hand, dipolar-aprotic and nonpolar solvents resulted in larger concentrations ( approximately 2-3 mmol/g) of grafted polar functional groups, lower-to-higher surface area materials, more densely populated catalytic groups, and poor-to-efficient catalytic properties toward the Henry reaction. Both the polar-protic and dipolar-aprotic solvents resulted in significantly lower concentration of grafted groups for nonpolar organosilanes such as (3-mercaptopropyl)trimethoxysilane compared to corresponding grafting of the polar amino-organosilanes. The relationship between the solvent properties and the percentage and degree of site-isolation of the grafted functional groups was attributed to differences in solvation of the organosilanes and silanols in various solvents and possible hydrogen-bonding between the organsilanes and the solvents. The degree of site-isolation of the amine groups, which affect the material's catalytic properties, was elucidated by a new colorimetric method involving probing of the absorption maxima (lambdamax) on the d-d electronic spectrum of Cu2+ complexes with the amine-functionalized materials and the colors of the samples. The absorption lambdamax and the colors of the materials were found to be uniquely dependent on the type of solvents used for grafting the organoamines. For instance, the monoamine- and diamine-functionalized samples grafted in methanol resulted in pale blue and light purple colors with lambdamax at approximately 720 and 650 nm, respectively. These correspond to CuNO5 and CuN2O4 structures, respectively, which are indicative of the presence of site-isolated organoamines in samples grafted in methanol. The monoamine and diamine samples grafted in toluene resulted in purple and deep purple colors with lambdamax at approximately 590 and 630 nm, respectively. These correspond to CuN2O4 and CuN4O2, which are indicative of the presence of closely spaced organoamines in samples grafted in toluene. The samples grafted in isopropanol gave colors and lambdamax intermediate between those of samples grafted in toluene and methanol.

2-(1,3-Dioxoisoindolin-2-yl)ethyl 4-methyl-benzene-sulfonate.

In the title mol-ecule, C(17)H(15)NO(5)S, the dihedral angle between the essentially planar atoms of the tosyl moiety (the S atom and the seven tolyl C atoms) and the phthalimide moiety is 6.089 (3)°. The mol-ecule is folded about the ethyl-ene bridge, adopting a staggered conformation such that the benzene ring of the tosyl group and the five-membered ring of the phthalimide moiety have a face-to-face orientation with a centroid-to-centroid separation of 3.7454 (12) Å. The crystal structure is stabilized by weak inter-molecular π-π inter-actions between symmetry-related five-membered rings of the phthalimide groups, with a centroid-to-centroid distance of 3.3867 (11) Å. The compound is used for the attachment of a suitable chelate functionality for radiolabeling purposes.

1-(Phthalimidometh-yl)pyridinium p-toluene-sulfonate.

In the crystal of the title compound, C(14)H(11)N(2)O(2) (+)·C(7)H(7)O(3)S(-), the cation and anion inter-act by way of an aromatic π-π inter-action [centroid-centroid separation = 3.5783 (2) Å] and a T-stacking (C-H⋯π) inter-action between cations. The dihedral angle between the aromatic rings in the cation is 61.73 (8)°. The ionic units are aligned in a zigzag fashion in the b-axis direction.

Redetermination of (+)-methamphetamine hydro-chloride at 90 K.

THE TITLE CRYSTAL STRUCTURE (SYSTEMATIC NAME: N-methyl-1-phenyl-propan-2-aminium chloride), C(10)H(16)N(+)·Cl(-), was orginally determined by Simon, Bocskei & Torok [Acta Pharm. Hung. (1992). 62, 225-230] and Yao, Kan & Wang [Huaxue Shijie (1999). 40, 568-570] at room temperature but no atomic coordinates are available for these determinations. The mol-ecule has inter-est with respect to biological activity. In the crystal structure, inter-molecular N-H⋯Cl hydrogen bonds form one-dimensional chains.

Redetermination of cyclo-trimethyl-ene-trinitramine.

The redetermined structure of 1,3,5-trinitro-1,3,5-triaza-cyclo-hexane, C(3)H(6)N(6)O(6), at 90 (2) K has ortho-rhom-bic (Pbca) symmetry. It is of inter-est with respect to energetic compounds. The structure was originally investigated through X-ray diffraction by Hultgren [(1936). J. Chem. Phys.4, 84]. Later X-ray investigations were completed by McCrone [(1950). Anal. Chem.22, 954-955] and Harris, Reed & Gluyas [(1959). AFOSR-TR-59-165 Ohio State University Research Foundation, Columbus, Ohio, USA]. A single-crystal neutron diffraction study was performed by Choi & Prince [(1972). Acta Cryst. B28, 2857-2862] to ascertain the H-atom positions, which had not been defined by the earlier X-ray diffraction studies. All previous studies were performed at or near room temperature. The structure provided is the α polymorph of the title compound. The ring atoms are arranged in the chair conformation with two nitro groups occupying pseudo-equatorial positions and the remaining nitro group is axial. The crystal packing is stabilized by close intramolecular interactions from one H atom in each methylene group to O atoms of adjacent nitro groups, ranging from 2.251 to 2.593 Å.

(S)-(+)-Ketamine hydro-chloride.

The crystal structure of the title compound {systematic name: (S)-(+)-N-[1-(2-chloro-phen-yl)-2-oxocyclo-hexyl]meth-anam-in-ium chloride}, C(13)H(17)ClNO(+)·Cl(-), was determined at 90 (2) K. The (S)-(+)-ketamine hydro-chloride salt is a well known anesthetic compound and is dramatically more potent than its R isomer. In the title compound, the cyclo-hexa-none ring adopts a chair conformation with the oxo group in the equatorial orientation. The methyl-amino and 2-chloro-phenyl groups at the 2-position have an equatorial and an axial orientation, respectively. The packing of ions is stabilized by an infinite one-dimensional ⋯Cl⋯H-N-H⋯Cl⋯ hydrogen-bonding network, involving NH(2) (+) groups as donors and chloride anions as acceptors.

Syntheses, structural characterization and properties of transition metal complexes of 5,5'-(1,4-phenylene)bis(1H-tetrazole) (H(2)bdt), 5',5''-(1,1'-biphenyl)-4,4'-diylbis(1H-tetrazole) (H(2)dbdt) and 5,5',5''-(1,3,5-phenylene)tris(1H-tetrazole) (H(3)btt).

The hydrothermal chemistry of a variety of M(II)SO(4) salts with the tetrazole (Ht) ligands 5,5'-(1,4-phenylene)bis(1H-tetrazole) (H(2)bdt), 5',5''-(1,1'-biphenyl)4,4'-diylbis(1H-tetrazole) (H(2)dbdt) and 5,5',5''-(1,3,5-phenylene)tris(1H-tetrazole) (H(3)btt) was investigated. In the case of Co(II), three phases were isolated, two of which incorporated sulfate: [Co(5)F(2)(dbdt)(4)(H(2)O)(6)]·2H(2)O (1·2H(2)O), [Co(4)(OH)(2)(SO(4))(bdt)(2)(H(2)O)(4)] (2) and [Co(3)(OH)(SO(4))(btt)(H(2)O)(4)]·3H(2)O (3·3H(2)O). The structures are three-dimensional and consist of cluster-based secondary building units: the pentanuclear {Co(5)F(2)(tetrazolate)(8)(H(2)O)(6)}, the tetranuclear {Co(4)(OH)(2)(SO(4))(2)(tetrazolate)(6)}(4-), and the trinuclear {Co(3)(µ(3)-OH)(SO(4))(2) (tetrazolate)(3)}(2-) for 1, 2, and 3, respectively. The Ni(II) analogue [Ni(2)(H(0.67)bdt)(3)]·10.5H(2)O (4·10.5H(2)O) is isomorphous with a fourth cobalt phase, the previously reported [Co(2)(H(0.67)bat)(3)]·20H(2)O and exhibits a {M(tetrazolate)(3/2)}(∞) chain as the fundamental building block. The dense three-dimensional structure of [Zn(bdt)] (5) consists of {ZnN(4)}tetrahedra linked through bdt ligands bonding through N1,N3 donors at either tetrazolate terminus. In contrast to the hydrothermal synthesis of 1-5, the Cd(II) material (Me(2)NH(2))(3)[Cd(12)Cl(3)(btt)(8)(DMF)(12)]·xDMF·yMeOH (DMF = dimethylformamide; x = ca. 12, y = ca. 5) was prepared in DMF/methanol. The structure is constructed from the linking of {Cd(4)Cl(tetrazolate)(8)(DMF)(4)}(1-) secondary building units to produce an open-framework material exhibiting 66.5% void volume. The magnetic properties of the Co(II) series are reflective of the structural building units.

Solid state coordination chemistry of microporous metal-organic frameworks of the cadmium(ii)-4-pyridyltetrazolate family: the structural influences of chloride incorporation.

While the metal-organic framework [Cd(4)(OH)(2)(4-pt)(6)(DMF)(4)].12DMF (.12DMF) (4-pt = 4-pyridyltetrazolate) is constructed from binuclear metal subunits, linked into porous {Cd(2)(OH)(DMF)(2)(4-pt)(3)}(6) cages, introduction of increasing concentrations of chloride yields the 3-D framework materials, [Cd(4)Cl(3)(4-pt)(4)(OH)(DMF)(3)].8DMF.14MeOH (.8DMF.14MeOH) and [Cd(5)Cl(6)(4-pt)(DMF)(2)(H(2)O)(2)].10DMF (.10DMF), constructed from tetranuclear and chain building blocks, respectively.