Conformational analysis of carbonic anhydrase inhibitors using ab initio molecular orbital methods. 1. Rotational isomerism in methane sulfonamide anion, CH3-SO2-NH−

Ab initio calculations have been performed on methane sulfonamide anion. Geometries have been optimized using Hartree-Fock basis sets up to 6-31+G*, and single-point calculations employing those Hartree-Fock geometries have been performed at levels up to MP2/6-311++G**. In addition, geometry optimizations for the 0°, 90°, 150°, and 180° conformers have been carried out at the MP2/6-31G*, MP2/6-31+G*, and MP2/6-311++G** levels. Vibrational frequencies have been calculated using the HF/4-31G*, MP2/6-31G*, and MP2/6-31+G* geometries. All calculations at or above the 4-31G* level agree that H—N—S—C ˜90° is the global minimum. The H—N—S—C = 180° conformer is clearly higher in energy although the relative energy of this conformer varies from 0.36 to 1.03 kcal/mol for the post-HF calculations depending on basis set. The H—N—S—C = 180° conformer appears to be a very shallow local minimum. However, the potential energy surface is quite flat in this region, and the highest-level calculations, including MP2 optimizations and vibrational frequency analysis, are ambiguous on this point. The conformer with an H—N—S—C torsion of 0° is a transition state with a relative energy ˜8 kcal/mol. Received: 3 December 1996 / Accepted: 2 January 1997     

Molecular Structure and Conformational Composition of 1-[(Methylthio)methyl]-2-nitrobenzene (MTMNB): A Theoretical and Experimental Study

The conformational composition of gaseous MTMNB and the molecular structures of the rotational forms have been studied by electron diffraction at 130^∘C aided by results from ab initio and density functional theory calculations. The conformational potential energy surface has been investigated by using the B3LYP/6-31G(d,p) method. As a result, six minimum-energy conformers have been identified. Geometries of all conformers were optimized using MP2/6-31G(d,p), B3LYP/6-31G(d,p), and B3LYP/cc-pVTZ methods. These calculations resulted in accurate geometries, relative energies, and harmonic vibrational frequencies for all conformers. The B3LYP/cc-pVTZ energies were then used to calculate the Boltzmann distribution of conformers. The best fit of the electron diffraction data to calculated values was obtained for the six conformer model, in agreement with the theoretical predictions. Average parameter values (r_a in angstroms, angle α in degrees, and estimated total errors given in parentheses) weighted for the mixture of six conformers are r(C–C) = 1.507(5), r(C–C)_{ring, av} = 1.397(3), r(C–S)_av = 1.814(4), r(C–N) = 1.495(4), r(N–O)_av = 1.223(3), ∠(C–C–C)_ring = 116.0–122.5, ∠ C6–C4–C7 = 118.2(4), ∠ C–C–S = 113.6(6), ∠ C–S–C = 98.5(12), ∠ N–C–C4 = 121.9(3), ∠(O–N–C)_av = 116.8(3), ∠ O–N–O = 127.0(4). Torsional angles could not be refined. Theoretical B3LYP/cc-pVTZ torsional angles for the rotation about C–N bond, φ_C−N, were found to be 30.5–36.5^∘ for different conformers. As to internal rotation about C–C and C–S bonds, values of φ_C−C = 68–118^∘ and φ_C−S = 66–71^∘ were obtained for the three most stable conformers with gauche orientation with respect to these bonds. Some conclusions of this work were presented in a short communication in Russ. J. Phys. Chem. 2005, 79, 1701.     

Synthesis and crystal structure of β-hexanitrohexaazaisowurtzitane

A polycyclic caged compound with high strain—hexanitrohexaazaisowurtzitane (HNIW)—has been synthesized via a three-step reaction: condensation, hydrogenolysis debenzylation and nitrolysis, starting with benzylamine and glyoxal. HNIW is the most powerful high energy density compound (HEDC) ever tested. β-HNIW possesses a caged structure consisting of two five-membered rings and one six-membered ring with a nitro group attached to each of the six bridging nitrogens. The nitro group lies basically within a plane. The lengths of C—C bonds of β-HNIW range from 0. 156 nm to 0.159 nm, 0.002–0.005 nm longer than the sp³ C-C bond. The β-HNIW’s crystal belongs to orthorhombic system and space groupPca2₁ with parameters:a = 0.9670 (2),b = 1.1616 (2),c = 1.3032 (3) nm;V = 1.4638(5) nm³,Z = 4; D_c = 1.989 g/cm³ and D_m = 1.982 g/cm³. Project supported by the Advanced Research Funds (12060451867) from the Commission of Science and Technology for National Defence.     

A novel rearrangement in the system 3-[aryl(chloro)methyl]quinoxalin-2(1H)-one— α-picoline as a simple and efficient route to indolizin-2-ylbenzimidazoles

A reaction of 3-(α-chlorobenzyl)quinoxalin-2(1 H)-one with α-picoline gives 2-(3-phenyl-indolizin-2-yl)benzimidazole as a result of a ring-contracting rearrangement involving the fragment C(2)—C(3)—C(Cl)Ph of the quinoxaline system and the fragment N=CH—Me of the α-picoline system. Possible pathways of this reaction are discussed.     

Cyclopalladated 2-phenyldihydrooxazole complexes with ethylenediamine, 2,2′-bipyridine,and bridging acetate ligands

The ¹H NMR, electronic absorption, and luminescence spectra, as well as voltammograms of the reduction and oxidation of the complexes [Pd(C∧N)(N∧N)]ClO₄ and [Pd(C∧N)(μ-OOCCH₃)]₂ [where (C∧N)⁻ is deprotonated 2-phenyl-4,5-dihydro-1,3-oxazole, and N∧N is ethylenediamine or 2,2′-bipyridine (bpy)] were compared. Magnetic nonequivalence of protons in the dihydrooxazole ring and upfield shift of the corresponding signals were observed as a result of anisotropic effect of the ring current in palladated phenyl substituents in the [Pd(C∧N)(μ-OOCCH₃)]₂ complex having a C ₂ symmetry. One-electron reduction wave of [Pd(C∧N)bpy]⁺ was assigned to ligand-centered electron transfer to the π* orbital of 2,2′-bipyridine, and two oxidation waves of [Pd(C∧N)(μ-OOCCH₃)]₂ were attributed to successive one-electron oxidations of the palladium centers. Low-temperature (77 K) phosphorescence of [Pd(C∧N)En]⁺ and [Pd(C∧N)bpy]⁺ was ascribed to optical transition localized on the metal-complex fragment {Pd(C∧N)} and to interligand charge transfer between the chelating and cyclopalladated ligands. The formation of metal-metal bond in the complex [Pd(C∧N)(μ-OOCCH3₎]₂ gives rise to radiative decay of photoexcitation energy from two electronically excited states, one of which is localized on the {Pd(C∧N)} fragment, and the second corresponds to the charge transfer metal-metal-cyclopalladated ligand.     

C–H...O and C–H...N interactions in RNA structures

Small molecule studies indicate that C–H...X interactions (X: O,N) constitute weak H-bonds. We have performed a comprehensive analysis of their occurrence and geometry in RNA structures. Here, we report on statistical properties of the total set of interactions identified and discuss selected motifs. The distance/angle distribution of all interactions exhibits an excluded region where the allowed C–H...X angle range increases with an increasing H...X distance. The preferred short C–H...X interactions in RNA are backbone-backbone contacts between neighbour nucleotides. Distance/angle distributions generated for various interaction types can be used for error recognition and modelling. The axial C2′(H)...O4′ and C5′(H)...O2′ interactions connect two backbone segments and form a seven-membered ring that is specific for RNA. An AA base pair with one standard H-bond and one C–H...N interaction has been identified in various structures. Despite the occurrence of short C–H...X contacts their free energy contribution to RNA stability remains to be assessed. Received: 17 May 1998 / Accepted: 4 August 1998 / Published online: 2 November 1998     

Composition and structure refinement of superconducting crystals Y1? x Tb x Ba2Cu3O6+δ ( x = 0.10; δ = 0.75)

Crystals of Y_0.90Tb_0.10Ba₂Cu₃O_6.75 have been prepared by spontaneous crystallization from slowly cooled non-stoichiometric melt of the system Y-Tb-Ba-Cu-O. Average size of platelet crystals having mirror surface is 2×2, the largest — 8×9 mm with thickness 0.1–0.2 mm. The crystals have been characterized by powder X-ray diffraction and electron microprobe analysis. Tetragonal symmetry of the crystals has been determined by X-ray diffraction. Magnetic susceptibility measurements have revealed that the crystals manifest transition to superconducting state without additional annealing (T _c = 60 K). Structures and compositions — Y/Tb ratio (σ = 0.01) and oxygen content (σ = 0.04) — have been refined for two single crystals. Possibility of rhombic distortion of the tetragonal symmetry is discussed. __________ Translated from Zhurnal Strukturnoi Khimii, Vol. 49, No. 6, pp. 1101–1107, November–December, 2008. Original Russian Text Copyright ? 2008 by L. P. Kozeeva, N. V. Podberezskaya, N. V. Kuratieva, M. Yu. Kamaneva, and A. G. Blinov     

Ag clusters electrochemically reduced in stearic acid Langmuir-Blodgett films and their structural characterizations

Silver ions confined in the silver stearate Langmuir-Blodgett (L-B) films of 8-14 layers were elec-trochernically reduced into Ag clusters,which made the observation of well-ordered scanning tunneling microscope (STM) images of the films with molecular resolution.A hexagonal packing of the hydrophobic chains was obtained,which was superimposed on the two-dimensional Ag clusters of 2-3 nm m diameter.Furthermore,a (2×1) struc-time of the hexagonal packing was observed.It was attributed to a self-assembled structure of the hydrophilic surface of the L-B films through hydrogen bonding.The strong surface enhanced Raman scattering (SERS) effect of Ag clusters made it possible to record Raman spectra of two-layer steanc acid L-B films in the region of C-C stretching vibration frequencies The appearance of the bands at 1 128 0 and 1 100.7 cm-1,which correspond to the antisymmetric C-C stretching model of the acyl chains m the all-trans conformation and the C-C stretching model of the acyl chains in the gauche     

Reaction of 1,2-dialkyldiaziridines with ketenes as a new approach to cyclic and linear systems containing the N— C—N fragment

The reaction of 1,2-dialkyldiaziridines with ketenes proceeds through the N—N bond cleavage to form three types of structures containing the N—C—N fragment, viz., 1,3-dialkylimidazolidin-4-ones, 3,5-diacyl-3,5-diazahept-1-enes, and β-lactams. The reaction pathway depends on the reaction conditions and the structures of the starting compounds. Dedicated to Corresponding Member of the Russian Academy of Sciences E. P. Serebryakov on the occasion of his 70th birthday. __________ Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 997–1006, April, 2005.     

Theoretical analysis of bonding properties in 1,1-dicyanocyclopentane and 1,1-dichlorocyclopentane by applying the AIM and NBO approaches

Using Bader’s quantum-topological theory of atoms in molecules (AIM) and Weinhold’s Natural Bond Orbital (NBO) analysis we could rationalize the impact of the geminal substitution by C≡N and Cl on the geometry and electronic structure of the cyclopentane ring in 1,1-dicyanocyclopentane (DCCP) and 1,1-dichlorocyclopentane (DClCP). Among the crucial results we obtained are: 1. The topological quantities, particularly the bond ellipticity of 0.035 for the C–CN bond, indicate that this bond possesses higher bond order than a single bond. This conclusion is clearly supported by the NBO results. 2. The AIM theory as well as the NBO analysis confirm uniformly the non-linearity of the C–C≡N moiety. 3. Regardless the quantum mechanical method that has been employed for a variety of nitriles the sign of the Laplacian of the charge density, ∇²ρ(r), of the C≡N group changes its sign from negative to positive upon moving from the triple zeta to the double zeta basis set. A possible explanation for this striking behavior has been provided. By invoking the AIM and NBO approaches the different endocyclic C–C bond lengths in DCCP and DClCP as a consequence of the geminal substitution could be explained. Also the variations of these bond lengths upon moving from the more stable C _s to the energetically less favorable C ₂ conformer of both compounds could be rationalized. For the purpose of comparison and verification of some findings of this work, we also carried out AIM and NBO calculations on various related cyclic and non-cyclic compounds.     

Kinetics of carbon deposition from ethylene on Pt(110) surface

The formation of carbonaceous deposits on Pt(110) surface due to ethylene decomposition in the temperature range of 770–970 K has been studied. Both kinetic and XPS data show that chemisorbed carbon (with no C−C bonds, but only C−Pt bonds) forms at T=770–870 K, the saturation coverage θ_s being about 1 ML. At higher temperatures, θ_s increases by a factor of 1.5, indicating the formation of more densely packed carbon species (DPC) due to C−C bonding. A kinetic model has been proposed to describe the process of carbon conversion.     

Photochemical generation of triplet—triplet nitrene pairs in aromatic diazide crystals

The molecular and crystal structures of 4-amino-2,6-diazido-3,5-dichloropyridine and 6-amino-2,4-diazido-1,3,5-triazine, as well as the paramagnetic photolysis products of their crystals at 77 K, were studied using X-ray diffraction analysis and ESR spectroscopy. Triplet nitrenes generated during the photolysis of diazidopyridine form triplet—triplet nitrene pairs, whose ESR spectrum corresponds to the quintet spin state. The high-spin state (S = 2) results from the exchange interaction between two triplet molecules with the zero-field splitting parameters |D| = 1.0280 cm⁻¹ and |E| = 0.0038 cm⁻¹ and the γ angle between two C—N nitrene bonds equal to 133°. This angle is close to an angle of 136.2° between the C-N bonds of two adjacent molecules in the crystal structure. No formation of the triplet—triplet nitrene pairs is observed during the photolysis of crystalline diazidotriazine, whose molecules lie in the parallel planes. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 513–520, March, 2008.     

Intermolecular interactions in 2,4-dinitrophenylhydrazine hydrochloride hydrate: X-ray structural and quantum mechanical study

2,4-dinitrophenylhydrazine hydrochloride hydrate (I) was determined by X-ray crystallography, and the intermolecular interaction energies were calculated in terms of Natural Bond Orbital analysis. The asymmetric unit of (I) consists of a dinitrophenylhydrazinium cation, a chloride anion and a water molecule. The interatomic distances and angles in (I) show no unusual values. In the structure there are intermolecular N—H⊎⊎⊎O, N—H⊎⊎⊎Cl, O—H⊎⊎⊎Cl, C—H⊎⊎⊎O hydrogen bonds with bonding energy ranging form 16.03 to 0.76 kcal mol⁻¹. These hydrogen bonds create the following N1 motifs: 6D, S(5), S(6), C(6), C(9). N₁D motifs become infinite at the third level and are 2C₃²(6), C₃²(7).      

Peculiarities of the mechanism of chlorotropic and conformational isomerism in a series of chloromethyl isocyanates

The thermodynamic and kinetic stability of chlorotropic isomers in a series of chloromethyl isocyanates Cl_3−nH_nC−N=C=O, where n=0, 1, 2, has been shown by quantum chemical calculations, using the MNDO method, and by³⁵Cl NQR spectroscopy. The phase transformations of two polymorphic modifications of N-chlorocarbonyl dichloride, which is a stable iminocarbonyl form of trichloromethyl isocyanate with small conformational activation barriers, have been studied. Institute of Bioorganic and Petrochemistry, National Academy of Sciences of Ukraine, 1 Murmansk ul., Kiev-94 252660, Ukraine. Translated from Teoreticheskaya i éksperimental’naya Khimiya, Vol. 34, No. 3, pp. 164–169, May–June, 1998.     

Redox induced reactions of transition metal π- and σ,π-complexes

In this review, redox-induced reactions of π- and σ,π-complexes leading to the selective formation (or cleavage) of C–H, C–C, and C–O bonds have been summarized. To illustrate the synthetic potential of such methodology, the following representative reactions studied in our group are discussed: (1) oxidatively induced hydrogen elimination from “open” cyclic diene and dienyl complexes resulting in formation of “closed” dienyl and arene complexes, respectively; (2) reductive activation of C–H bonds in diene, vinylidene, and carbyne complexes forming new multiple C–C bonds; (3) oxidative dehydrodimerization of vinylidene complexes into binuclear μ-divinylidene species; and (4) oxidatively induced addition of oxygen nucleophiles to μ-divinylidene complexes affording cyclic μ-dicarbene derivatives. Oleg V. Gusev, deceased on October 31.     

Reactions of Co2(CO)6(RC≡CR′) (RC2R′—hydroxy- or alkoxysilyl-alkynes) with tetraethyl-orthosilicate

Co₂(CO)₈ has been reacted with but-2-yn-1,4-diol (BUD) and the reactivity of the resulting complex Co₂(CO)₆(HOCH₂C≡CCH₂OH) (complex 1) is discussed. Complex 1 has been reacted with all the components used in the synthesis of sol-gel materials based on tetraethyl-orthosilicate (TEOS) with the aim at obtaining evidences for the processes occurring during the formation of inorganic-organometallic sol-gel materials containing BUD. Reaction pathways are discussed. BUD and complex 1 have also been reacted with 3-(triethoxysilyl)propyl isocyanate (TSI); the new ligand [(EtO)₃Si(CH₂)₃NHC(— O)OCH₂C≡CCH₂OC(—O)NH(C H₂)₃Si(OEt)₃] (TB) and the complex Co₂(CO)₆[(EtO)₃Si(CH₂)₃NHC(—O)OCH₂C≡CCH₂OC(—O)NH(CH₂)₃Si(OEt)₃] (11) have been obtained; these were characterized by means of spectroscopic techniques and mass spectrometry. Reactions of ligand TB and of complex 11 with TEOS have been performed. “Condensation” reactions of ligand TB (with TB) and of complex 11 (with complex 11) have also been attempted. Solid, amorphous materials were obtained: these were characterized by means of IR-Raman, SEM microscopy and XRD on powders.     

Radical addition reactions: factors determining the transition-state geometry

Interatomic distances in the reaction centers of the addition reactions of (i) H^· to the C=C, C=O, N≡C, and C≡C bonds, (ii) ^·CH₃ radical to the C=C, C=O, and C≡C bonds, and (iii) alkyl, aminyl, and alkoxyl radicals to olefin C=C bonds were determined using a new semiempirical method for calculating transition-state geometries of radical reactions. For all reactions of the type X^· + Y=Z → X— Y—Z^· the r ^# _X...Y distance in the transition state is a linear function of the enthalpy of reaction. Parameters of this dependence were determined for seventeen classes of radical addition reactions. The bond elongation, Δr ^# _X...Y, in the transition state decreases as the triplet repulsion, electronegativity difference between the atoms X and Y in the reaction center, and the force constant of the attacked multiple bond increase. __________ Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 894–902, April, 2005.     

Distillation, on-line RP C18 preconcentration and HPLC-UV-PCO-CVAAS as a new combination for the determination of methylmercury in sediments and fish tissue

Distillation as a way of sample digestion has been combined with on-line RP C18 preconcentration and HPLC-UV-PCO-CVAAS (high performance liquid chromatography — ultra violet — post column oxidation — cold vapour atomic absorption spectrometry) for the determination of methylmercury at back-ground levels in sediments, soils and fish tissue. To prove the accuracy of this method, it was applied to sediment and fish tissue reference materials. The results correspond with the reference values within their error ranges. Excellent recoveries (92–95%) were obtained for the sediment samples by means of the standard addition method. The standard deviations of the sediment samples were within an acceptable range (7.2–12.5%), those of the fish samples were substantially lower (3.4–5.0%). The detection limit is 0.04 ng/g for 1 g sample weight.     

Synthesis and photophysical properties of luminescent mononuclear and dinuclear gold(I) complexes with ethynyl-substituted phenanthrolines

A novel asymmetric dinuclear gold(I) complex with 3,6-diethynylphenanthroline, 3,6-bis{(PPh₃)–Au–C≡C}₂-phen, has been synthesized from Au(PPh₃)Cl (PPh₃ = triphenylphosphine) and 3,6-diethynyl-1,10-phenanthroline. The asymmetrical dinuclear gold(I) complex, 3,6-bis{(PPh₃)–Au–C≡C}₂-phen, demonstrated a weak phosphorescence assignable to the metal-perturbed ³ π–π* transition in the long wavelength region compared to an intense emission of the symmetrical dinuclear complex with 3,8-diethynylphenanthroline, 3,8-bis{(PPh₃)–Au–C≡C}₂-phen. A similar tendency of phosphorescent bands for the mononuclear gold(I) complexes with 5-ethynylphenanthroline, 5-{(PPh₃)–Au–C≡C}-phen, and 3-ethynylphenanthroline, 3-{(PPh₃)–Au–C≡C}-phen was observed. The absorption bands assignable to the π–π*(C≡Cphen) transition and phosphorescent emission assignable to the metal-perturbed ³ π–π* transition for these four gold(I) complexes were reasonably consistent with the results calculated by DFT and TD-DFT.     

Thermal, spectral and AFM studies of calcium silicate hydrate-polymer nanocomposite material

A non-ionic polymer (poly(vinyl alcohol) (PVA)) has been incorporated into the inorganic layers of calcium silicate hydrate (C–S–H) during precipitation of quasicrystalline C–S–H from aqueous solution. C–S–H and a C–S–H-polymer nanocomposite (C–S–HPN) material were synthesized and characterized by X-ray fluorescence (XRF), energy dispersive spectroscopy (EDS), ²⁹Si magic angle spinning nuclear magnetic resonance (²⁹Si MAS NMR) and ¹³C cross-polarization nuclear magnetic resonance (¹³C CP NMR) spectroscopy, atomic force microscopy (AFM), thermal conductivity, thermogravimetric analysis (TG) and differential thermal analysis (DTA). Thermal conductivity of PVA, C–S–H and C–S–HPN material was studied in the temperature range 25–50°C. C–S–HPN materials exhibited the highest thermal conductivity at 25 and 50°C. The thermal conductivity increases from 25 to 50°C are 7.03, 17.46 and 14.85% for PVA, C–S–H and C–S–HPN material, respectively. Three significant decomposition temperature ranges were observed on the TG curve of C–S–HPN material.