Nature of weak inter- and intramolecular interactions in crystals. 1. The F...O and F...H contacts in the crystal of 2-trifluoroacetyl-5-trifluoromethylpyrrole

The topological analysis of the electron density distribution in the crystal of 2-trifluoroacetyl-5-trifluoromethylpyrrole revealed that the F...H and F...O intermolecular contacts correspond to attractive interactions. The energies of these interactions were estimated from the experimental data and it was shown that these contacts are similar to the C—H...O contacts. Analysis of the deformation electron density revealed that the F...O contacts correspond to transfer of the lone electron pair of a fluorine atom to the antibonding -orbital of the C=O bond.     

Photoelectron spectra and electronic structure of derivatives of imidazoline

We have obtained for the first time the photoelectron spectra (PES) of 20 diamagnetic and paramagnetic derivatives of imidazole. On the basis of calculations in the MNDO approximation, analysis of the vibrational structure, and comparisons in a series we have interpreted the bands in the range 7–11 eV. In the nitroxyl radicals of 3-imidazoline the highest occupied molecular orbital is the _NO ^* orbital, having also a contribution on the C⁴ atom. On introducing N-oxide groups there is a considerable rearrangement of the electronic structure of the radicals. In the PES of the nitroxyl radicals of 3-imidazoline-3-oxide there is multiplet splitting of the ionization band of the n_o·MO, amounting to 0.3–0.4 eV. Replacement of the methyl groups on the C² atom by methoxyl groups leads to an increase in the interactions of the unshared pairs of the O atoms of the nitronium and nitroxyl groups, while the same replacement on the C⁵ atoms leads to a considerable decrease in this interaction. When the substituent on the N¹ atom in derivatives of 3-imidazoline-3-oxide is varied the energy of ionization of the _C-NO MO decreases in the series: CH₃ < H OH < O < NO.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 8, pp. 1769–1777, August, 1990.     

The formation of three-center bonds in chemisorption

Summary It is proposed that molecular adsorption may be brought about by the formation of three-center bonds. In this two donor-acceptor bonds are formed between the molecule to be adsorbed and an atom in the adsorbent surface. The molecule to be adsorbed, for instance, ethylene, acts as a donor because of its -electron pair and the adsorbent atom because of its p-orbital. At the same time the adsorbent atom is a donor on account of its electron pair in a d_XZ-orbital and the molecule an acceptor on account of its antibonding ¹-²- orbital; by this a dative bond is formed. In the case of a metal without d-electrons (for instance, Al) a dative bond is impossible, but the metal can give an acceptor bond because of its empty p-orbital.Such a three-center chemisorption must proceed with a small activation energy, that is, be reversible, unactivated and rapid. Most often chemisorption at low temperature has these properties. The heat of such a chemisorption may vary between a few times ten or a few kcal.Three-center chemisorption may be of considerable importance in catalytic reactions and also in exchange processes on the surface.Only a considerable activation energy and a very high heat of adsorption is a reliable proof that the adsorbed substance occurs on the surface as atoms or in a state in which one adsorbent atom forms a stable chemical bond with only one adsorbate atom.Translated from Zhurnal Strukturnoi Khimii, Vol. 1. No. 2, pp. 189–199, July–August, 1960     

Quantum-Chemical Study of Structural and Energy Characteristics of Benzonitrile Dimers

Ab initio MP2 calculations with several basis sets proved the existence of a stable benzonitrile dimer with a planar structure and a short contact between the H atom of one molecule and the N atom of another. The structure is greatly stabilized by attraction between the neighboring oppositely directed dipoles and donor-acceptor interaction between the orbital of the lone electron pair of the N′ atom and the vacant antibonding orbital localized on the C-H bond.Original Russian Text Copyright © 2004 by O. V. Sizova, E. P. Sokolova, V. I. Baranovskii, D. A. Rozmanov, and O. A. Tomashenko__________Translated from Zhurnal Strukturnoi Khimii, Vol. 45, No. 5, pp. 807–815, September–October, 2004.     

Crystal structure of ether solvate of octanuclear lutetium aluminohydride complex {[(Bu 2 t C5H3)LuH]4[Et2O·AlH4]2[AlH4]2}·Et2O

Overall X-ray structural analysis (XSA) of ether solvate crystals of the unusual octanuclear lutetium aluminohydride complex [(CpLuH)₄(Et₂O·AlH₄)₂(AlH₄)₂]·Et₂O (I) (Cp = 1.3–Bu₂ ¹C₅H₃) is reported. In complex I, four Lu atoms are located in vertices of an elongated tetrahedron; over each face of the tetrahedron there is one Al atom. Th'e octanuclear metal core of I is a very distorted cube with an approximate point symmeby D_2d formed by the bridging hydrogen bonds (covalent metal-metal bonds are absent in I). Each Lu atom in I (neglecting individual H and C atoms) has the same distorted square-pyramidal coordination with the -Cp ring in the apical position and three Al atoms and the nearest Lu atom in the base of the pyramid.Institute of Physiologically Active Substances, Russian Academy of Sciences. Translated fromZhurnal Strukturnoi Khimii, Vol. 34, No. 5, pp. 167–174, September–October, 1993.Translated by T. Yudanova     

New method for qualitative quantum chemical deductions on organic or inorganic molecules or clusters directly from structural formulas or ORTEP diagrams

A pictorial blackboard mnemonic type method presented allows the molecular orbital level patterns, the numbers of non-bonding, bonding, and anti-bonding orbitals to be figured out from the actual or tentative structural formulas (or ORTEP diagrams) of saturated or unsaturated molecules or intermediates regardless of symmetry. The simple pictorial rules are illustrated on: bicyclo[p.q.0] hydrocarbons, pyridine, alkyl groups, quaternium ions, some amines, ethers, water and alcohols, and on some fluorohydrocarbons. The readily obtained MO level patterns, e.g. during rearrangements, give a handle on the qualitative behaviour of various structures or species. The method applies also to metal atom and other clusters.List of abbreviations AO Atomic orbital - ECI Electron count index - H.F. Hartree-Fock - LPI Level pattern indices - MO Molecular orbital - SC Structurally covariant - SCF Self-consistent field - SEF Structural-electronic formula - SF Structural formula - VB Valence-bond - VIF Valency points interaction formula - VP Valency point - VL VP-VP' interaction line - VSEPR Valence shell electron pair repulsion     

Physical studies in the field of unsaturated aryl ethers and their derivatives

Conclusions Consideration of the foregoing results leads us to the following generalizations. The molecular wave functions of the mobile electrons are not localized on individual groups of atoms in the compounds under consideration, but belong to the molecule as a whole. The fact that the oxygen atom is linked to two unsaturated radicals leads to a considerable additional change in the density of the mobile electrons of this atom. The interaction of the p electrons of oxygen with each of these radicals, as expressed in the density distribution of the mobile electrons, is primarily determined by the nature of the particular radical, and apparently to a lesser extent by the nature of the second radical.An increase in the acceptor properties of one of the radicals leads to an increase in the calculated positive charge on the oxygen atom and in the order of the corresponding C–O bond. Changes in the order of the second C–O bond and the density distribution of the mobile electrons neighboring this bond are determined by weak composition for the p electron of the oxygen between the unsaturated groups to which this atom is attached.We may suppose that the change in the integral Raman-line intensity associated with the valence vibrations of the double bond and, possibly, the oscillations of the benzene-ring framework (1600 cm^–1) in vinylaryl ethers is connected with the existence of a common system of mobile electrons and with variations in the polarizability of this system.The author finds it his pleasant duty to express sincere thanks to Professor N. A. Prilezhaeva of Tomsk University for help and valuable discussions.Translated from Zhurnal Strukturnoi Khimii, Vol. 7, No. 3, pp. 417–427, May–June, 1966     

Nonempirical calculations of dipole moments of molecules in semifloating gaussian basis sets

For the example of the calculation of the dipole moments of the HF, HCl, H₂O, NH₃, CO, H₂CO, CH₃F molecules in two-exponent and three-exponent Gaussian basis sets, we have studied the effect of including floating functions in the basis, directly giving the effect of polarization of the electron shell of the atom in the molecule. We have established a weak dependence of the calculated dipole moment on the dimensionality of the basis, the number of floating functions, and also the orbital exponents of the hydrogen atoms. The correction introduced by the floating functions in molecules with polar bonds is considerably greater than the correlation correction. The proposed approach allows us to decrease the dimensionality of the orbital basis by a factor of 1.5–2 without making the agreement with experiment worse.Translated from Teoreticheskaya i Éksperimental'naya Khimiya, Vol. 26, No. 4, pp. 481–485, July–August, 1990.     

Theoretical study of the interaction of a proton with the O, F and Cl atoms of enflurane (CHFCl–CF2–O–CHF2)

Ab initio MP2 and density functional B3LYP calculations were performed to investigate the interaction of a proton with the O, F and Cl atoms of enflurane (CHFCl–CF₂–O–CHF₂) in the gas phase. The study included the optimized structures, proton affinities, interactions energies and thermodynamic properties of protonated enflurane. The proton affinities (PAs) of the O and Cl atoms are 154.5 and 139.8 kcal mol⁻¹, respectively, whereas PAs of five of the fluorine atoms are between 143.6 and 165.5 kcal mol⁻¹ (MP2 results). In contrast to protonation at the O and Cl atoms, protonation at each of the F atoms of enflurane reveals a striking result, it leads to a cleavage of the C–F bond and formation of an ion–dipole complex between the enfluranyl cation and neutral hydrogen fluoride. The [(enfluranyl)⁺FH] complexes are weakly bound, the SAPT-calculated interaction energy varies between −12.5 and −11.7 kcal mol⁻¹. The long range attraction in these complexes is dominated by the electrostatic term (70%), whereas the induction and dispersion components contribute by about 15% each. Protonation at the chlorine atom of enflurane does not lead to a cleavage of the C–Cl bond. For the O-protonated enflurane the results from the natural bond orbital analysis (NBO) are discussed in details.     

Stereochemical and structural features of N-methoxyaziridines. structures of cis- and trans-amides of the monoethyl ester of 1-methoxyaziridine-2,2-dicarboxylic acid

Features of the structures of N-methoxyaziridines have been considered on the basis of the results of x-ray structural analysis, ¹³C NMR spectroscopy, qualitative MO theory, and the secondary orbital rehybridization method. The causes of the configurational and chemical stability of the N-methoxyaziridines, the orientation of the unshared electron pairs of the N and O atoms relative to the O-N bond and the O-C bond of the methoxy group, the structural and conformational manifestation of the interaction of a -acceptor with the aziridine ring, the laws of the change in the exocyclic valence angles at the carbon atoms of the aziridine ring, and the close values of the SSCCs of the carbonyl carbon atoms with the protons of the ring are discussed.Communication 33 of the series Asymmetric Nitrogen. For communication 32, see [1].Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 1. pp. 48–55, January, 1984.     

Theoretical study of the SN2 reaction of Cl−(H2O)+CH3Cl using our own N-layered integrated molecular orbital and molecular mechanics polarizable continuum model method (ONIOM, PCM)

The effects of solvation in the S_N2 reaction Cl^–(H₂O)+CH₃Cl were investigated using our own N-layered integrated molecular orbital and molecular mechanics (ONIOM) polarizable continuum model (PCM) method [Vreven T, Mennucci B, da Silva CO, Morokuma K, Tomasi J (2001) J Chem Phys 115:62–72], which surrounds the microsolvated ONIOM system with a polarizable continuum. The microsolvating water molecule tends to stay in the vicinity of the original chloride ion. In the ONIOM calculations, Cl^–+CH₃Cl was considered as the model system and was handled with the high-level method, while the explicit water molecule in the microsolvated complex was treated at the low-level. The molecular orbital (MO) and ONIOM(MO:MO) calculations allow us to assess the errors introduced by the ONIOM extrapolation, as well as the effects of microsolvation on the potential-energy surfaces. We find that ONIOM[B3LYP/6-31+G(d,p):HF/6-31+G(d,p)] and ONIOM[B3LYP/6-31+G(d,p):HF/6-31+G(d,p)]-PCM methods are good approximations to the target B3LYP/6-31+G(d,p) and B3LYP/6-31+G(d,p)-PCM methods. In addition, several approximate (computationally less expensive) schemes in the ONIOM-PCM method have been compared to the exact scheme, and all are shown to perform well.Contribution to the Jacopo Tomasi Honorary Issue     

The single-electron hydrogen, lithium, and halogen bonds with HBe, H2B, and H3C radicals as the electron donor: an ab initio study

Quantum chemical calculations have been performed for the complexes with HBe, H₂B, and H₃C radicals as the electron donors and with HF, LiF, and ClF as the electron acceptors. For HBe, H₂B, and H₃C radicals, the ability of donating electrons is dependent on the nature of the electron donor atom. In addition, it is also affected by the nature of the electron acceptor atom. A partially covalent bond is formed in HBe–Cl···F and H₂B–Cl···F complexes, which exhibits a large interaction energy, short binding distance, large bond elongation, and big frequency shift. The complexes have also been analyzed with natural bond orbital and atoms in molecules.     

Study of the magnetic state of transition element atoms in compounds and alloys usingKα 1 spectra

A review is given for investigations of the magnetic state of transition element atoms in compounds and alloys using K₁ spectra. The shift and width of the K₁ line are used for determining changes in the spin and charge density on the emitting atom depending on the type and concentration of the components. This method permits us to determine the local magnetic moment at an atom with precision of 0.1–0.2 _B . The electron state density in the conductance band affects the spin density formed on the resonance 3d level of an atom in the field of a 2p vacancy. Localization of 3d states was observed upon the transition of an atom to an impurity state. The contribution to the spin state on the emitting atom in Pauli paramagnetics is proportional to the state density on the Fermi level. The width of the K₁ line of transition element atoms was found to depend on the magnetic moment on the atoms of the immediate environment and on the magnitude and sign of the exchange interaction between them, which permits us to study magnetic phase transitions.Institute of the Mineralogy, Geochemistry, and Crystal Chemistry of Rare Elements. Translated from Zhurnal Strukturnoi Khimii, Vol. 30, No. 6, pp. 122–137, November–December, 1989.     

Photoelectron spectroscopy of phenyldihalophosphites

In order to explain the reactivity of aryldihalophosphites towards halophosphomum salts, photoelectron spectra of PhOPX₂ (X=F, Cl) were studied. Electron densities of boundary molecular orbitals (MO) for these compounds were calculated using the MNDO method and analyzed. Replacement of F by Cl was shown to substantially affect the orbital. When X= Cl, this MO embraces the whole of the OPX₂ moiety whereas for X=F it is localized on the P-O bond.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 2, pp. 323–324, February, 1993.     

A study of the transfer of the electronic influence of substituents in o-carboranes by nuclear quadrupole resonance

The ³⁵Cl NQR spectra of 2-substituted 1-chloromethyl-o-carboranes and of 1-chloromethyl-9,12-dihalogeno-o-carboranes have been investigated. The anomalous influence of two halogen atoms present in positions 9 and 12 of the carborane nucleus on the electron density of the chlorine atom in the CH₂Cl group is explained by the combined action of their –I and +M effects, and also by the effect of p d conjugation. The comparatively high ³⁵Cl NQR frequency for o-ClCH₂CB₁₀H₁₀CH is due to the large –I effect of the carboranyl group. The induction constants of a number of groups attached to the carborane ring have been evaluated. In the molecules of the 2-substituted 1-chloromethyl-o-carboranes spatial interaction between X and Cl clearly appears. The substituents X in compounds of this series can be divided into three types according to their electronic influence: 1) electron-donating substituents, 2) substituents containing a mobile hydrogen atom (capable of forming a hydrogen bond), and 3) substituents possessing an unshared pair of electrons capable of passing into the vacant 3d orbital of a chlorine atom.     

Heteroorganic derivatives of furan. 69. Analysis of electron structures of 2-furyltriethoxysilane and 1′-(2-furyl)-silatrane by the MO LCAO CNDO/2 method

The electron structures (charges on the atoms, additive populations of the atomic orbitals, and multiplicities of the chemical bonds) of 2-furyltriethoxysilane, 1-(2-furyl)silatrane, and the starting triethanolamine were analyzed by the MO LCAO CNDO/2 method taking into account the d orbitals. The localized molecular orbitals and the hybrid atomic orbitals that form them were constructed by the Polak projection method.see [1–3] for Communications 66–68.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 10, pp. 1314–1321, October, 1989.     

Photoelectron spectra and orbital structures of silatranes: Organic derivatives of pentacoordinate silicon

The photoelectron (PE) spectra of silatranes (1), 2,8,9-trioxa-5-aza-1-silabicyclo [3.3.3] undecanes, have been analyzed and partially reinvestigated. In the PE spectra of 1 the bands in the 8.2–8.9 eV region, which were previously ascribed to the lone electron pair (LEP) orbital of the nitrogen atom or the SiN bond, are due to the presence of impurities, the products of incomplete hydrolysis. Interpretation of the bands in the PE spectra of pure compounds was carried out by analysis of orbital-correlation diagrams and results of MNDO and AM1 calculations. The first ionization potential of1 is associated with a MO localized to a great extent on the axial X-Si-N fragment. The increase with shortening of the Si-N distance is related to the corresponding increase in the degree of noncoplanarity of the nitrogen atom when its LEP is involved in the hypervalent X-Si-N bond.     

Abilities of different electron donors (D) to engage in a P···D noncovalent interaction

Previous work has documented the ability of the P atom to form a direct attractive noncovalent interaction with a N atom, based in large measure on the charge transfer from the N lone pair into the σ* antibonding orbital of the P-H that is turned away from the N atom. The present work considers whether other atoms, namely, O and S, can also participate as electron donors, and in which bonding environments. Also considered are the π-systems of multiply bonded C atoms. Unlike an earlier observation that the interaction is unaffected by the nature of the electron-acceptor atom, there is strong sensitivity to the donor. The P···D binding energy diminishes in the order D = NH(3) > H(2)CO > H(2)CS > H(2)O > H(2)S, different from the patterns observed in both H and halogen bonds. The P···D interactions are comparable to, and in some cases stronger than, the analogous H-bonds formed by HOH as proton donor. The carbon π systems form surprisingly strong P···D complexes, augmented by the back-donation from the P lone pair to the C-C π* antibond, which surpass the strengths of H-bonds, even some with HF as proton donor.     

Synthesis,crystal structure and magnetism of a 1-D polymeric manganese(II) complex with pyrazine-2-carboxylate as bridging ligand

A one-dimensional chain complex {[Mn(pyz)(SCN)(H₂O)₂] · H₂O} (pyz = pyrazine-2-carboxylic anion) has been synthesized and its crystal structure determined by X-ray crystallography. In the complex each Mn ion is located in a distorted octahedral environment with two oxygen atoms O(3), O(4) from terminal ligands of two water molecules, another oxygen atom O(1) from the carboxylate group of pyz, and three nitrogen atoms N(1), N(2A) from two different pyz units and N(3) from the terminal ligand thiocyanate anion, in which a chelated five-membered ring is formed by coordination of O(1) and N(1) to the Mn(1) atom. Thus, an infinite zigzag chain consisting of Mn and pyz is constructed and the chains are linked together by hydrogen bonding from coordinated and uncoordinated water molecules, the sulfur atom of thiocyanate and the carboxylate oxygen of pyz. The variable-temperature magnetic susceptibility of the complex was measured in the 4–300 K range. The magnetic coupling parameter is consistent with an antiferromagnetic exchange between the two manganese(II) centers and the data fit a binuclear magnetic exchange model based on the Hamiltonian operator (H = –2JS ₁ S ₂, S ₁ = S ₂ = 5/2), giving the antiferromagnetic coupling parameter of 2J = –0.17 cm^–1. This is the first pyrazine-2-carboxylic anion bridging complex dealing with the magnetic interaction study.     

Synthesis,crystal structure and magnetic properties of triaquahexakis(μ2-betaine)(μ3-oxo)triiron(III) perchlorate heptahydrate

The synthesis and characterization of the oxo-centered carboxylato-bridged trinuclear iron(III) complex, triaquahexakis(₂-betaine)(₃-oxo)triiron(III) perchlorate heptahydrate are described. X-ray crystallography shows that the Fe^III atom in the complex has a slightly distorted octahedral geometry, coordinated by four oxygen atoms from different betaine ligands [Fe—;O = 2.009(3) 2.034(3) Å], one aqua ligand [Fe—O = 2.028(4) and 2.031(3) Å] and the central ₃-oxo atom [Fe—O = 1.917(2) and 1.917(3) Å]. The central oxygen is ideally coplanar with the plane of the three metal atoms. Magnetic susceptibility data (4–320 K) show the presence of an antiferromagnetic exchange interaction with a coupling constant of J = –20.2 cm^–1.