Two-dimensional dynamics of molecules and structure of fluorographite intercalated with acetone

Institute of Inorganic Chemistry, Siberian Branch, Academy of Sciences of the USSR Translated from Zhurnal Strukturnoi Khimii, Vol. 30, No. 1, pp. 66–71, January–February, 1989.     

Fullerite with intercalated freon Ch2F2

Fullerite C₆₀ with intercalated CH₂F₂ (Freon-32) was prepared for the first time. The sample was studied by elemental analysis, X-ray powder diffraction, mass spectrometry, and IR spectroscopy. The composition of the sample was found to be (CH₂F₂)C₆₀. The sample had a face-centered cubic lattice with the lattice parameter (1.4284 nm) much larger than that of pure fullerite (1.416 nm). The gas released from the sample during heating in a vacuum to 450°C largely consisted of initial Freon (mass spectrometry data); no Freon destruction products were observed at this temperature. The C-F stretching vibration frequency (1058 cm^?1) was shifted in (CH₂F₂)C₆₀ by 30 cm^?1 toward lower wave numbers compared with the gas phase. The absorption bands at 1182 and 1428 cm^?1 (IR active modes (F _1u ) of high-symmetry (I _h ) C₆₀ molecules) did not change their positions in the intercalate.     

Transport properties of CO2-expanded acetonitrile from molecular dynamics simulations

Carbon-dioxide-expanded liquids, which are mixtures of organic liquids and compressed CO2, are novel media used in chemical processing. The authors present a molecular simulation study of the transport properties of liquid mixtures formed by acetonitrile and carbon dioxide, in which the CO2 mole fraction is adjusted by changing the pressure, at a constant temperature of 298 K. They report values of translational diffusion coefficients, rotational correlation times, and shear viscosities of the liquids as function of CO2 mole fraction. The simulation results are in good agreement with the available experimental data for the pure components and provide interesting insights into the largely unknown properties of the mixtures, which are being recognized as important novel materials in chemical operations. We find that the calculated quantities exhibit smooth variation with composition that may be represented by simple model equations. The translational and rotational diffusion rates increase with CO2 mole fraction for both the acetonitrile and carbon dioxide components. The shear viscosity decreases with increasing amount of CO2, varying smoothly between the values of pure acetonitrile and pure carbon dioxide. Our results show that adjusting the amount of CO2 in the mixture allows the variation of transport rates by a factor of 3-4 and liquid viscosity by a factor of 8. Thus, the physical properties of the mixture may be tailored to the desired range by changes in the operating conditions of temperature and pressure.     

The crystal and molecular structure of octafluorobiphenylene,C12F8

Octafluorobiphenylene was made by heating 1,2-diiodotetrafluorobenzene in a sealed, evacuated tube with either copper, lead or bismuth. The crystal used for the diffraction studies was grown from hexane. Crystal data: C₁₂F₈, M_r = 296.116, monoclinic, A2/a, a = 21.140(2), b = 6.430(6), c = 36.340(3) ÅA, β = 123.76(3)°, U = 4106.73 ÅA³, Z = 16, D_m = 1.884 g cm⁻³, D_x = 1.907 g cm⁻³, λ(Cuka) = 1.5418 ÅA, μ = 1.810 mm⁻¹, F(000) = 2304, measurement temperature = 293K, R = 0.059 for 2230 reflections with I > 3σ(I).     

X-ray spectroscopic study of graphite fluoride (C2F) n intercalated with benzene

Samples of intercalated graphite fluoride of the C₂F·zR type (R is C₆H₆) before and after heating to 150 °C in a spectrometer vacuum chamber were studied by X-ray fluorescence spectroscopy. The C-Kα differential spectra of the samples mainly characterizes the electron state of carbon atoms in the benzene molecule inside the C₂F matrix. The differential spectrum is distinct from the spectrum of solid benzene by additional maxima, which indicate the interaction between the benzene molecules and the graphite fluoride matrix. Comparative analysis of the spectrum of the heated sample and those of graphite and graphite fluoride (CF) _n suggests that the layers of the C₂F matrix contain considerable regions of both completely fluorinated and graphite-like regions. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 705–708, April, 2000.     

Reaction of (C6F5)2HGeGeH(C6F5)2 with triethylbismuth: molecular structure of [(C6F5)2Ge]4Bi2

The reaction of (C₆F₅)₂HGeGeH(C₆F₅)₂ with triethylbismuth affords a new polynuclear germylbismuth derivative, [(C₆F₅Ge]₄Bi₂ (1). The metal framework of molecule1 has the form of a gable roof built by two central Bi atoms and four peripheral Ge atoms with covalent Bi-Bi bonds [3.045(3) Å], Bi-Ge [2.724(5)-2.755(4) Å] and Ge-Ge [2.444(6), 2.465(6) Å].Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 5, pp. 921–924, May, 1994.     

Squaraine [2]catenanes: synthesis, structure and molecular dynamics

Three squaraine [2]catenanes are synthesized and found to have bright, deep-red fluorescence and high chemical stability. The interlocked molecules undergo two large-amplitude dynamic processes, twisting of the squaraine macrocycle and skipping over the partner tetralactam.     

Structural change from homogenous structure to staging in benzoic acid intercalated LDH: experimental and molecular dynamics simulation insights

The intercalation the of 4,4'-oxybis(benzoic acid) anion (OBA(2-)) into MgAl-layered double hydroxide (LDH) was carried out in formamide, and the structural change of the nanocomposites from homogenous to staging was investigated through in situ XRD, FT-IR, TG-DSC, SEM and molecular dynamics (MD) simulations. In both formamide and water, the nanocomposites had a homogenous structure with a basal spacing of ～1.7 nm, showing the configuration of OBA(2-) was vertical to the LDH layers; however, with a decrease in water content after drying, the structure changed to a staging with a basal spacing of 2.62 nm. This resulted from the 1.72 nm phase and another one of 0.85 nm, which was produced by the configuration of OBA(2-) horizontal to the LDH layers. MD simulations revealed that the LDH layers distorted surrounding OBA(2-), and the deformation became more severe with decreasing water content in the interlayer, leading to the staging formation. The simulated XRD pattern confirmed that the staging observed in the experimental pattern was of the Daumas-Hérold type.     

The crystal and molecular structure of 5,5-diphenyloctafluorogermanthrene, (C6H5)2GeC12F8

F---F steric interaction between the two 6,6′-fluorines of the C₆F₄ rings in C₁₂F₈Ge(C₆H₅)₂ cause quite distortions in the molecule as these two fluorine atoms are forced to within 2.419 Å of each other (Van der Waals distance ⋍ 2.7 Å). Crystal data: C₁₂F₈Ge(C₆H₅)₂, M_r 522.89, C2/c, a 29.065(2), b 8.066(2), c 23.000(3) Å, β 129.85°, U 4139.63 ų, Z = 8, D_x 1.678 Mg m⁻³, Mo-K_α, λ 0.7107 Å, μ 15.58 cm⁻¹, F(000) = 2064, T 293 K, R = 0.044 for 2264 reflections with I > 3σ(I); Δϱ ± 0.5 e⁻     

The NMR structure of [Xd(C2)]4 investigated by molecular dynamics simulations

The i‐motif tetrameric structure is built up from two parallel duplexes intercalated in a head‐to‐tail orientation, and held together by hemiprotonated cytosine pairs. Two topologies exist for the i‐motif structure, one with outermost 3′ extremities and the other with outermost 5′ extremities, called the 3′E and 5′E topology, respectively. Since the comparison of sugar and phosphate group interactions between the two topologies is independent of the length of the intercalation motif, the relative stability of the 3′E and 5′E topologies therefore should not depend on this length. Nevertheless, it has been shown that the 3′E topology of the [d(C2)]4 is much more stable than the 5′E topology, and that the former is the only species observed in solution. In order to understand the reason for this atypical behavior, the NMR structure of the [Xd(C2)]4 was determined and analyzed by molecular dynamics simulations. In the NMR structure, the width of the narrow groove is slightly smaller than in previously determined i‐motif structures, which supports the importance of phosphodiester backbone interactions in the structure stability. The simulations show that the stacking of cytosines, essential for the i‐motif stability, is produced by a similar and non‐negative twisting of the phosphodiester backbones. The twisting is induced by an interaction between the backbones; the [Xd(C2)]4 in 5′E topology, exhibiting very limited interaction between the phosphodiester backbones, is thus unstable. Copyright © 2002 John Wiley & Sons, Ltd.     

Rates of reaction of atomic oxygen with C2H3F,C2H3Cl,C2H3Br, 1,1-C2H2F2, and 1,2-C2H2F2

Rate constants for the reactions of atomic oxygen (O³P) with C₂H₃F, C₂H₃Cl, C₂H₃Br, 1,1-C₂H₂F₂, and 1,2-C₂H₂F₂ have been measured at 307°K using a discharge-flow system coupled to a mass spectrometer. The rate constants for these reactions are (in units of 10¹¹ cm³ mole^?1 s^?1) 2.63 ± 0.38, 5.22 ± 0.24, 4.90 ± 0.34, 2.19 ± 0.18, and 2.70 ± 0.34, respectively. For some of these reactions, the product carbonyl halides were identified.     

Crystal and molecular structures of trifluoroacrylonitrile, F2C=CF-CN, and trifluorovinyl isocyanide, F2C=CF-NC, by low-temperature X-ray crystallography and ab initio calculations

The structures of trifluoroacrylonitrile, F2C=CF-CN, monoclinic, P2(1/n) (no. 14), a = 8.595(4), b = 8.748(1), c = 5.421(1) A, beta = 102.83(2) degrees, Z = 4, and its thermally unstable isomer trifluorovinyl isocyanide, F2C=CF-NC, monoclinic, P2(1/n), a = 8.501(2), b = 8.828(2), c = 5.599(2) A, beta = 101.11(2) degrees, Z = 4 were determined by X-ray crystal structure analysis at 113 and 128 K, respectively, from single crystals grown by partial melting and gradient cooling in small glass capillaries. Selected experimental bond lengths of F2C=CF-CN/F2C=CF-NC are as follows: C=C 1.326(1)/1.304(2), C...N 1.158(1)/1.167(2) A. The C-F bond lengths of the CF2 group are significantly shorter than those of the CF(NC) and CF(CN) units, respectively. The vibrational frequencies and molecular geometries of this cyanide/isocyanide pair were also calculated by ab initio methods for comparison with the experimental results, which were found to be in general agreement.     

Photodissociation of diiodomethane in acetonitrile solution and fragment recombination into iso-diiodomethane studied with ab initio molecular dynamics simulations

Series of hydrates of the most stable glycine-H+/2H2+ in the gas phase are presented at the B3LYP level. The results show that only the amino hydrogens and hydroxyl hydrogens can be monohydrated for the glycine-H+, and the amino hydrogens are preferred. The H6(O4) of glycine-2H2+ is the best site for a water molecule to attach, i.e., the corresponding hydrate is the most stable one among its isomers. Calculations reveal that the binding energies of hydrated hydrogens decrease relative to their counterparts in the isolated glycine-H+/2H2+ complexes and they are positive values and without proton transfer except those of monohydrated glycine-2H2+ complexes with the combination modes of H3O+...(glycine-H+). The complex H3O+...(glycine-H+) is formed by the combination of a H2O molecule and one hydroxyl-site proton of glycine-2H2+, and with the proton transfer to H2O. Here the interaction between the proton of H3O+ and the glycine-H+ mainly depends on an electronic one instead of an initial covalent one of the isolated glycine-2H2+. The generation of the bond between the H3O+ and the glycine-H+ makes the energy of the complex higher than the energy sum of its two separated species (or two reactants of the complex), just like the case of M+...(glycine-H+) bond (M = Li,Na). The observation can explain satisfactorily why the combinations of both a proton and an alkali ion or two alkali ions to a glycine molecule can make the corresponding complex hold reservation energy bond(s), while the combination of two protons and a glycine in our previous work cannot [H. Ai et al., J. Chem. Phys. 117, 7593 (2002)]. For the glycine-2H2+, monohydration at the any site of its amino hydrogens can make the binding strength of any other neighboring proton (hydrogens) stronger relative to its counterpart in the isolated glycine-2H2+. Further hydration, especially at the site of either of hydroxyl hydrogens, would disfavor the reservation energy of the system.     

Energy-flow dynamics in the molecular channel of propanal photodissociation, C2H5CHO --> C2H6 + CO: direct ab initio molecular dynamics study

Direct ab initio molecular dynamics calculations have been carried out for the molecular channel of the photodissociation of propanal, C2H5CHO --> C2H6 + CO, at the RMP2(full)/cc-pVDZ level of ab initio molecular orbital theory. The initial conditions were generated using the microcanonical sampling to put the excess energy randomly into all vibrational modes of the TS. Starting from the TS, a total of approximately 700 trajectories were numerically integrated for 100 fs. The obtained final energy distributions for the C2H6 and CO fragments and their relative translational motion were found to be quite similar to those obtained for the acetaldehyde reaction, CH3CHO --> CH4 + CO, in our previous study (Chem. Phys. Lett. 2006, 421, 549) despite the fact that the number of degree of freedom for C2H6 is larger than that for CH4. The coupling between the intrinsic reaction coordinate and one of the generalized normal modes orthogonal to it was predicted substantially strong around s = 1.4 amu(1/2) bohr, and it is expected that the energy flow out of C2H6 proceeds through this coupling. However, the obtained energy distributions strongly suggest that the coupling among the modes in C2H6 is quite small and the intramolecular energy redistribution does not occur efficiently in this molecule.     

Electron diffraction study of the molecular structure of WO2F2

The saturated vapor over solid W ₂ O ₄ F has been studied by electron diffractometry. Structure analysis was fulfilled assuming complex composition of the vapor. It has been established that at T=1043±30 K the vapor consists of WO ₂ F ₂ and WOF ₄ molecules in amounts of 90 and 10 more % respectively. There are two alternative models describing the geometrical structure of the WO ₂ F ₂ molecule (C _2v symmetry) which fit experimental data equally well. In one model, the valence OWO angle is greater than the FWF angle, while in the other, the inverse relation is observed.Ivanovo State University. Moscow Mendeleev Chemical Engineering Institute. Ivanovo Chemical Engineering Institute. Translated fromZhurnal Strukturnoi Khimii, Vol. 34, No. 3, pp. 41–46, May–June 1993.Translated by L. Smolina     

Simulation of molecular and electronic structure of polyhydrogenated (n,0)-tubulenes and their analogs intercalated with lithium

Molecular and electronic structure of four polyhydrogenated (n,0)-tubulenes, namely, [−C₂₄H₄−] _m (1), two isomers of composition [−C₂₈H₄−] _m (2 and3), and [−C₃₂H₄−] _m (4) withn benzene rings in the cross section (n=6, 7, 7, and 8, respectively), was simulated atm>1 (m is the number of repeating fragemnts). It was assumed that hydrogen atoms are attached to all carbon atoms lying on the two most distant elements of the cylinders of the corresponding tubulenes. The energy band structures of macromolecules1–4 and their Li-intercalated analogs [−C₂₄H₄Li−] _m (5) [−C₂₈H₄Li−] _m (two isomers,6 and7), and [−C₃₂H₄Li−] _m (8), containing one Li atom per repeating unit at each center, were obtained in the EHT approximation by the crystal orbital method. Geometric parameters of repeating units of structures1–8 were found after MNDO/PM3 optimization of the energies of hydrocarbon molecules C₇₂H₂₄, C₈₄H₂₆ (two geometric isomers), and C₉₆H₂₈, containing three repeating units of corresponding tubulenes1–4 each. The conductivity types of polyhydrogenated tubulenes1–4 are the same as those of their precursors, (6,0)-, (7,0)-, and (8,0)-tubulenes. Dispersion curves of systems5–8 are much the same as those of macromolecules1–4; however, electron energy spectra of5–8 possess metallic conductivity type and the positions of Fermi levels for these systems are higher than for compounds1–4. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 11, pp. 2061–2067, November, 1999.