Hydrogen bond CH…O in a methanolic solution of hydrogen chloride

The existence of a hydrogen bond in which a methyl group of the (MeOH)₂H⁺ ion acts as a proton donor is examined. The fundamental vibration frequencies of this ion were calculated for different numbers and strengths of CH…O bonds. The atomic charges in neutral ((MeOH) _n ,n=1–4) and protonated ((MeOH) _m H⁺,m=2–6) associates of methanol molecules were also calculated. The experimentally observed decrease in the v(CH) vibration frequencies of the (MeOH)₂H⁺ ion to 2890 cm⁻¹ and 2760 cm⁻¹ is attributable to the fact that each methyl group of the ion is involved in formation of two CH…O bonds with strength of −12.5 kJ mol⁻¹. The proton-donating ability of the CH bond depends on the charge on its H atom; however, it does not correlate with the dipole moment of this bond. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 2, pp. 306–312, February, 1999.     

Ab initio calculations of methionines and their protonated forms

Ab initio calculations of molecular and electronic structures of neutral molecules and protonated forms of methionine and its derivatives in the gaseous phase were carried out by the Hartree-Fock method using the 6–31G^* basis set with full geometry optimization. Proton affinities of methionine (1), methionine sulfoxide (2), and methionine sulfone (3) were calculated for different modes of coordination of the proton. The results of calculations demonstrated that in protonated forms of 1 and 3, bonding between the proton and the N atom is most favorable, while in protonated form of 2, bonding between the proton and the O atom of the SO group is most favorable. The proton affinities of the amino acids are as follows: 223.2 (1), 241.2 (2), and 221.5 (3) kcal mol⁻¹,i.e., methionine sulfoxide 2 exhibits the highest proton affinity in the series of the amino acids under consideration. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 8, pp. 1487–1490, August, 1998.     

Protonation of the acyclic tetraaza metallocomplex of gold(III) [Au(C9H19N4)]2+ in aqueous solution. Synthesis and crystal and molecular structure of [Au(C9H20N4)](H5O2)(ClO4)4

Protonation equilibrium has been studied for the acyclic gold(III) tetraaza metallocomplex [AuB]²⁺ [B = N, N′-bis(2-aminoethyl)-2,4-pentanediiminato(1−)] in aqueous solution. The synthetic procedure is described. The crystal and molecular structure of the protonated form of the [AuHB](H₅O₂)(ClO₄)₄ complex has been determined. Monoclinic crystals with unit cell dimensions a = 11.964(2) Å, b = 13.789(3) Å, c = 15.496(3) Å, β = 109.00(3)°, V = 2417.1(8) ų, Z = 4, ρcalc = 2.243 g/cm³, space group P2₁/n. The structure is built of nearly planar [Au(C₉H₂₀N₄)]³⁺ complex cations, (H₅O₂)⁺ cations, and [ClO₄]⁻ anions. The gold atom coordinates four nitrogen atoms of the ligand, forming a square plane. The six-membered chelate ring of the ligand is protonated at the central β-carbon atom and contains imine C=N bonds. The oxygen atoms of the perchlorate ions are hydrogen bonded to the (H₅O₂)⁺ dihydroxonium ion and to the nitrogen atoms of the NH₂ groups of the [AuHB]³⁺ cation. Original Russian Text Copyright ? 2005 by V. A. Afanasieva, L. A. Glinskaya, R. F. Klevtsova, and I. V. Mironov __________ Translated from Zhurnal Strukturnoi Khimii, Vol. 46, No. 5, pp. 909–915, September–October, 2005.     

Microhydration of protonated nucleic acid bases and protonated nucleosides in the gas phase

Thermochemical data, ΔH _n ^o , ΔS _n ^o , and ΔG _n ^o , for the hydration of protonated nucleic acid bases and protonated nucleosides have been experimentally studied by equilibrium measurements using an electrospray high-pressure mass spectrometer equipped with a pulsed ion-beam reaction chamber. For protonated nucleobases the hydration enthalpies were found to be similar for all studied systems and varied between 12.4–13.1 kcal/mol for the first and 11.2–11.5 kcal/mol for the second water molecule. While for protonated nucleosides the water binding enthalpies (11.7–13.3 kcal/mol) are very close to those for protonated nucleobases, the entropy values are “more negative.” The structural and energetic aspects of hydrated ions are discussed in conjunction with the available theoretical data.     

Structure of molecular complexes in liquid CO2 solutions of water

The calculated anharmonic frequencies and intensities of simultaneous vibrational transitions in CO₂−H₂O and (CO₂)₂−H₂O hydrogen-bonded complexes are compared with known experimental data. Hydrogen-bonded complexes form in liquid CO₂ solutions of water under normal conditions, unlike the gas phase in which the CO₂ and H₂O molecules are coupled by van der Waals bonds. The majority of these complexes are 2∶1 complexes. N. S. Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences. Translated fromZhurnal Strukturnoi Khimii, Vol. 36, No. 2, pp. 375–379, March–April, 1995. Translated from E. Taskaeva     

Electrochemical behavior and parameters of hydrofullerene C60H36

Electrochemistry of hydrofullerene C₆₀H₃₆ was studied by cyclic voltammetry in THF and CH₂Cl₂ in the −47–14 °C temperature range. Hydrofullerene undergoes reversible one-electron reduction to form a radical anion in THF (E ⁰=−3.18 V (Fc⁰/Fc⁺), Fc=ferrocene) and irreversible one-electron oxidation in CH₂Cl₂ (E _p ^a =1.22 V (Fc⁰/Fc⁺)). The reduction potential was used to estimate electron affinity of hydrofullerene as EA=−0.33 eV. It was suggested that C₆₀H₃₆ is an isomer withT-symmetry in which 12 double bonds form four isolated benzenoid rings located in vertices of an imaginary inscribed tetrahedron on the molecular surface. For hydrofullerene, the “electrochemical gap” is an analog of the energy gap (HOMO−LUMO), equal to (E ^Ox−E ^Red)=4.4 V, and indicates that C₆₀H₃₆ is a sufficiently “hard” molecule with a low reactivity in redox reactions. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 11, pp. 2083–2087, November, 1999.     

Molecular structures of acetylene derivatives of tin

The geometry and force fields of the bis(trimethylstannyl)acetylene molecule (a conformer withD _3d symmetry corresponding to a minimum of the total energy of the molecule) were calculated by the RHF and MP2(fc) methods. The effective core potential in SBK form with the optimized 31G^* valence basis set was employed in the case of Sn atoms. The 6–31G^** and 6–311G^** basis sets were used for carbon and hydrogen atoms. Vibrational spectra of the light and perdeuterated isotopomers of bis(trimethylstannyl)acetylene were interpreted using the procedure of scaling the quantum-chemical force fields. For Part 5, see Ref. 1. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 616–626, April, 2000.     

Spectral studies of the mechanism of oxidation of Cp2Fe by ozone

The mechanism of oxidation of Cp₂Fe by ozone in CCl₄ was studied by chemiluminescence (CL), photoluminescence, IR, UV, and NMR spectral techniques, Ozone attacks Cp₂Fe at the Fe−C and C=C bonds to form peroxides CpOOFe, CpFeOOH, triplet (3 nπ^*) ketones (CL emitters), and organic acids. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 794–797, April, 1999.     

Thermodynamic characteristics of the acid dissociation of dopamine hydrochloride in water-ethanol solutions

Enthalpies of the interaction of protonated dopamine with a hydroxide ion in water-ethanol mixtures in the concentration range of 0–0.8 EtOH mole fractions are measured calorimetrically. The neutralization process of dopamine hydrochloride is shown to occur endothermally in solvents with an ethanol concentration of ≥0.5 mole fractions. Standard thermodynamic characteristics (Δ_r H ^○, Δ_r G ^○, and Δ_r S ^○) of the first-step acid dissociation of dopamine hydrochloride in solutions are calculated with regard to the autoprotolysis enthalpy of binary solvents. It is found that dissociation enthalpies vary within 9.1–64.8 kJ/mol, depending on the water-ethanol solvent composition.     

Calculation of diatomic van der Waals systems inert gas Atom-Halogen type inert gas ion in the ground state

Interatomic potentials are calculated for the systems inert gas ion in the ground state-inert gas atom Ne⁺, Xe⁺ -Ne, Ar, Kr, Xe, Fr. The calculation is performed by the effective pseudopotential method using the new form of the polarization interaction potential obtained by calculating the most important polarization diagrams of perturbation theory in the Thomas-Fermi approximation. The quasimolecular states of these van der Waals systems are calculated to refine the available data; some data are obtained for the first time. Translated fromZhumal Strukturnoi Khimii, Vol. 39, No. 4, pp. 591–595, July–August, 1998.     

Interpenetrating inclusion lattices: Comparison of the Β-hydroquinone and ellipsoidal clathrate structures

Crystallization of 2,7-dimethyltricyclo[43.1.1^3,8]undecane-syn-2,syn-7-diol 2 from acetonitrile or dichloro-methane yields the compounds (2)₄-(guest) in space group 14₁/acd which are further examples of the ellipsoidal clathrate structure. Both enantiomers of 2 are linked through (O-H)₄ cycles of hydrogen bonds to form a three-dimensional sublattice. Two inversion related sublattices interpenetrate thereby generating a superlattice with guest-occupied voids situated between the two individual sublattices. The two X-ray structures are compared and contrasted with that of Powell’s (hydroquinone)₃ (SO₂) clathrate compound. Translated fromZhurnal Strukturnoi Khimii, Vol. 40, No. 5, pp. 822–831, September–October, 1999.     

X-ray emission and X-ray photoelectron study of the electronic structure of polymeric cubanocluster compounds Re4−x Mo x S4Te4

The electronic structure of cubanocluster compounds of the series Re_4−xMo_xS₄Te₄ was studied by X-ray emission and X-ray photoelectron spectroscopy. The electronic structure of the (Re₄S₄)⁸⁺ cluster was calculated by the EHT method. It is shown that replacement of rhenium atoms by molybdenum atoms leads to changes both in the chemical bonds of the Re₄S₄ cubanocluster fragment and in the bond of the latter with the Te₄ fragment. Institute of Inorganic Chemistry, Siberian Branch, Russian Academy of Sciences. Translated fromZhurnal Strukturnoi Khimii, Vol. 37, No. 5, pp. 901–906, September–October, 1996. Translated by L. Smolina     

Rearrangement Pathways of the <Emphasis Type="BoldItalic">a</Emphasis><Subscript><Emphasis Type="BoldItalic">4</Emphasis></Subscript> Ion of Protonated YGGFL Characterized by IR Spectroscopy and Modeling

The structure of the a ₄ ion from protonated YGGFL was studied in a quadrupole ion trap mass spectrometer by ‘action’ infrared spectroscopy in the 1000–2000 cm^–1 (‘fingerprint’) range using the CLIO Free Electron Laser. The potential energy surface (PES) of this ion was characterized by detailed molecular dynamics scans and density functional theory calculations exploring a large number of isomers and protonation sites. IR and theory indicate the a ₄ ion population is primarily populated by the rearranged, linear structure proposed recently (Bythell et al., J. Am. Chem. Soc. 2010, 132, 14766). This structure contains an imine group at the N- terminus and an amide group –CO–NH₂ at the C-terminus. Our data also indicate that the originally proposed N-terminally protonated linear structure and macrocyclic structures (Polfer et al., J. Am. Chem. Soc. 2007, 129, 5887) are also present as minor populations. The clear differences between the present and previous IR spectra are discussed in detail. This mixture of gas-phase structures is also in agreement with the ion mobility spectrum published by Clemmer and co-workers recently (J. Phys. Chem. A 2008, 112, 1286). Additionally, the calculated cross-sections for the rearranged structures indicate these correspond to the most abundant (and previously unassigned) feature in Clemmer’s work.     

The role of the negatively charged (Si3−Si−F2)− complexes in interactions of fluorine with the (111) surface of silicon

We used the AM1 quantum chemical and cluster models to study the mechanism of formation of a SiF₂-like layer and dissociation of the Si−Si bond during the interaction of atomic fluorine with the (111) surface of silicon. It is shown that the negatively charged (Si₃−Si−F₂)⁻ complex with the five-coordinated centered silicon atom plays an important part in these processes. The above complex participates in the interaction of atomic fluorine with silicon to form a SiF₂-like layer and break the subsurface Si−Si bonds without penetration of fluorine atoms into the subsurface silicon layers. Institute of Semiconductor Physics, Siberian Branch, Russian Academy of Sciences. Translated fromZhurnal Strukturnoi Khimii, Vol. 37, No. 1, pp. 14–21, January–February, 1996. Translated by I. Izvekova     

Theoretical studies of electron and hydrogen transfer reactions between semiquinone radicals and oxygen

 To explore the interactions between ubiquinones and oxygen in living organisms, the thermodynamics of a series of electron and hydrogen transfer reactions between semiquinone radicals, as well as their corresponding protonated forms, and oxygen, singlet or triplet, were studied using the hybrid Hartree–Fock–density functional theory method Becke's three parameter hybrid method with the Lee, Yang, and Parr correlation functional. Effects of the solvent and of the isoprenyl tail on the electron and hydrogen transfer reactions were also investigated. It is found that semiquinone radicals (semiquinone anion radicals or protonated semiquinone radicals) cannot react with triplet oxygen to form the superoxide anion radical O₂ ⁻. In contrast, neutral quinones can scavenge O₂ ⁻ efficiently. In the gas phase, only protonated semiquinone radicals can react spontaneously with singlet oxygen to produce peroxyl radical (HO₂). However, both semiquinone anion radicals and protonated semiquinone radicals can react with singlet oxygen to produce harmful oxygen radicals (O₂ ^{− a l l b u l l} and HO₂, respectively) in aqueous and protein environments. The free-energy changes of the corresponding reactions obtained for different ubiquinone systems are very similar. It clearly shows that the isoprenyl tail does not influence the electron and hydrogen transfer reactions between semiquinone radicals and oxygen significantly. Results of electron affinities, vertical ionization potentials, and proton affinities also show that the isoprenyl tail has no substantial effect on the electronic properties of ubiquinones. Received: 3 July 2000 / Accepted: 6 September 2000 / Published online: 21 December 2000     

Problems of unusual hydrogen bonds between proton donors and transition metal hydrides and borohydrides

The results of experimental and theoretical studies of intermolecular MH...HX and BH...HX hydrogen bonds with the hydride hydrogen atom acting as a proton accepting site are analyzed. Spectral (IR and NMR) criteria for their formation are presented. The spectral, structural, and thermodynamic characteristics of these unusual hydrogen bonds obey the regularities found for classical hydrogen bonds. It was shown that the MH...HX bonds participate in the proton transfer with the formation of nonclassical cationic hydrides and the |M(η²-H₂|⁺ hydrogen bonds are formed in low-polarity media. Problems arising in this new line of investigations are discussed. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 5, pp. 846–851, May, 1998.     

Selectivity of vibronic coupling in complex molecules with benzene fragments

This paper deals with the mechanisms of localization of Franck-Condon vibronic coupling of πσ^*- or πlπ^*-orbital type in a few vibrational modes, (LVM) in excited electronic states of polyatomic molecules. The analysis of vibronic coupling uses highly symmetric basis sets (for representing MO structures and normal coordinates ξ_R) as well as simplified models that relate the shift Δ_R of the electron potential minima along the normal coordinates to the MO structure and to ξ_R in the form of analytical expressions. The modes that are active in LVM are determined from the experimental luminescence spectra. These ideas about approximately high local symmetry of vibronic coupling in benzene fragments as well as the estimates of Δ_R depending on variations in the MO structure explain the experimental results. L. Ya. Karpov Physicochemical Scientific Research Institute. Translated fromZhurnal Strukturnoi Khimii, Vol. 36, No. 2, pp. 286–291, March–April, 1995. Translated by L. Smolina     

Electronic structure and chemical bonding of δ-Bi2O3

The band structure of the fluorite-type δ-Bi₂O₃ was calculated by the linear LMTO methods in the approximation of overlapping atomic spheres using the basis set of orthogonal orbitals (LMTO-ASA) and by the full-potential LMTO method (LMTO-FP) for two vacancy orientations over a wide range of oxygen concentrations. The calculated parameters of chemical bonds—the binding energy E_bin and the pressure of the electron-nuclear system—show that the most stable compound is that with two vacancies per unit cell, oriented predominantly along the (111) direction. The hybrid Bi−O bonds are weak, and mostly the Bi−Bi bonds are responsible for the structural stabilization of δ-Bi₂O₃. The mechanism of the formation of a semiconductor gap in the band structure of δ-Bi₂O₃ is discussed. Institute of Solid State Chemistry, Ural Branch, Russian Academy of Sciences. Translated fromZhurnal Strukturnoi Khimii, Vol. 37, No. 1, pp. 48–58, January–February, 1996. Translated by I. Izvekova     

Electronics structures of amidine and its complex with platinum(IV). Orotonation of coordinated amidine

The electronic structures of amidine CH₃C(NH)NH₂ and its complex [Pt(NH₃)₅{CH₃C(NH)NH₂}]⁴⁺ are studied by the semiempirical CNDO method and by the ab initio Hartree-Fock-Roothaan method using the effective core potential for the platinum atom by the GAUSSIAN-92 program. It is shown that in free amidine the protonation of the NH group is energetically more profitable than the protonation of the NH₂ group. Formation of the amidine-platinum(IV) ion complex is accompanied by a considerable redistribution of electron density in amidine atoms and bonds. In the above complex, the amidine NH₂ group exhibits enhanced protophilic properties. St. Petersburg State Technological Institute (Technical University). Translated fromZhurnal Strukturnoi Khimii, Vol. 37, No. 2, pp. 220–224, March–April, 1996. Translated by I. Izvekova     

Ab initio study of molecular structure and internal rotation in methyldicyanophosphine and methyldiisocyanophosphine. The Raman spectrum of methyldicyanophosphine and its interpretation with the use of scaling ofab initio force fields

The equilibrium geometric parameters and structures of transition states of internal rotation for the molecules of methyldicyanophospine MeP(CN)₂ and its isocyano analog MeP(NC)₂ were calculated by the RHF and MP2 methods with the 6–31G^* and 6–31G^** basis sets. At the MP2 level, the total energy of cyanide is −35 kcal mol⁻¹ lower than that of isocyanide and the barriers to internal rotation of methyl group for MeP(CN)₂ and MeP(NC)₂ are 2.2 and 2.7 kcal mol⁻¹, respectively. For both molecules, the one-dimensionalab initio potential functions of internal rotation approximated by a truncated Fourier series were used to determine the frequencies of torsional transitions by solving direct vibrational problems for a non-rigid model. The Raman spectrum of crystalline MeP(CN)₂ was recorded in the range 3500–50 cm⁻¹. The vibrational spectra of this compound were interpreted by scalingab initio force fields calculated by the RHF and MP2 method. The vibrational spectrum of methyldiisocyanophosphine was predicted with the use of the obtained scale factors. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 9, pp. 1703–1714, September, 1998.