The Perfluoro-o-phenylene-mercury Trimer [Hg(o-C6F4)]3 - a Textbook Example of Phase-Dependent Structural Differences.

The geometric and electronic structure of [Hg(o-C6F4)]3 (1) in the gas phase, i. e. free of intermolecular interactions, was determined by a synchronous gas-phase electron diffraction/mass spectrometry experiment (GED/MS), complemented by quantum chemical calculations. 1 is stable up to 498 K and the gas phase contains a single molecular form: the trimer [Hg(o-C6F4)]3. It has a planar structure of D3h symmetry with a Hg-C distance of 2.075(5) Šand a Hg-Hg distance of 3.614(7) Š(both rh1). Structural differences between the crystalline and gaseous state have been analyzed. Different DFT functional-basis combinations were tested, demonstrating the importance to consider the relativistic effects of the mercury atoms. The combination PBE0/MWB(Hg),cc-pVTZ(C,F) turned out to be the most appropriate for the geometry optimization of such organomercurials. The electronic structure of 1, the nature of the chemical bonding in C-Hg-C fragments and the nature of the Hg⋅⋅⋅Hg interactions have been analyzed in terms of the Natural Bond Orbital (NBO) and Quantum Theory of Atoms in Molecules (QTAIM) approaches. The influence of the nature of halogen substitution on the structure of the molecules in the series [Hg(o-C6H4)]3, [Hg(o-C6F4)]3, [Hg(o-C6Cl4)]3, [Hg(o-C6Br4)]3 was also analyzed.

Is There an Adduct of Pyridine N-Oxide and Boron Trifluoride in the Gaseous State? Gas Electron Diffraction vs Mass Spectrometry.

A study of saturated vapor over the pyridine N-oxide-boron trifluoride (PyO-BF3) adduct was carried out at T = 448(5) K by a synchronous gas electron diffraction/mass spectrometry (GED/MS) experiment. Due to the absence of ions in the mass spectrum, indicating the presence of a structure with an O-B dative bond, several models of vapor composition were tested by the GED method. It was found that the dominant molecular form (up to 100%) in vapor is the PyO-BF3 adduct. Using the DFT/M06-2X/aug-cc-pVTZ method, geometric optimization of the molecular ion [PyO-BF3]+ was carried out, which showed its intrinsic instability and dissociation into a [PyO]+ cation and a BF3 molecule. This study certainly demonstrates the significant advantage of the GED method to determine the qualitative and quantitative gas-phase composition of dative-bonded adducts and other noncovalent complexes as well, whereas the interpretation of mass spectra may be ambiguous due to the possible intrinsic instability of ions containing a dative bond. The nature of the O-B bond is discussed in terms of the natural bond orbitals (NBOs) and the quantum theory of atoms in molecules (QTAIM). A comparison of structural and energetic parameters for PyO-BF3 and the previously studied BF3 adducts allows the theoretical comprehension of the nature of the O-B bond to be extended and to explain the different thermal stabilities of these compounds.

First Examples of s-Metal Complexes with Subporphyrazine and Its Phenylene-Annulated Derivatives: DFT Calculations.

Using quantum chemical calculation data obtained by the DFT method with the B3PW91/TZVP and M062X/def2TZVP theory levels, the possibility of the existence of four Be(II) coordination compounds, each of which contains in the inner coordination sphere and the double deprotonated forms of subporphyrazine (H2SP), mono[benzo]subporphyrazine (H2MBSP), di[benzo]subporphyrazine (H2DBSP), and tri[benzo]subporphyrazine (subphthalocyanine) (H2TBSP) with a ratio Be(II) ion/ligand = 1:1, were examined Selected geometric parameters of the molecular structures of these (666)macrotricyclic complexes with closed contours are given; it was noted that BeN3 chelate nodes have a trigonal-pyramidal structure and exhibit a very significant (almost 30°) deviation from coplanarity; however, all three 6-membered metal-chelate and three 5-membered non-chelate rings in each of these compounds are practically planar and deviate from coplanarity by no more than 2.5°. The bond angles between two nitrogen atoms and a Be atom are equal to 60° (in the [BeSP] and [BeTBSP]) or less by no more than 0.5° (in the [BeMBSP] and [BeDBSP]). The presence of annulated benzo groups has little effect on the parameters of the molecular structures of these complexes. Good agreement between the structural data obtained using the above two versions of the DFT method was noticed. NBO analysis data for these complexes are presented; it was noted that, according to both DFT methods used, the ground state of the each of complexes under study is a spin singlet. Standard thermodynamic parameters of formation (standard enthalpy ΔfH0, entropy S0, and Gibbs free energy ΔfG0) for the above-mentioned macrocyclic compounds were calculated.

Accurate single crystal and gas-phase molecular structures of acenaphthene: a starting point in the search for the longest C-C bond.

The molecular structure of acenaphthene has been determined experimentally in the gas phase using gas electron diffraction intensities and literature-available rotational constants. Supplementary high-level quantum-chemical calculations were utilized in refinements of the semi-empirical equilibrium structure. In this work we investigate on how different schemes of GED data averaging and weighting can be used for obtaining the most accurate and precise structural parameters. Single-crystal X-ray diffraction experiments at different temperatures have been performed and the solid-state structure of acenaphthene has been determined. Both gas and solid-state acenaphthene molecules are planar and possess a non-twisted ethylene bridge. The aliphatic C-C bond in the ethylene fragment is elongated to 1.560(4) Å in the gas phase and 1.5640(4) Å in the solid phase. Based on the experimental data several theoretical approximations have been calibrated and predictions for other molecules were made, taking into account dispersion and electrostatic interactions. Particular derivatives of acenaphthene may potentially have significantly elongated C-C bonds up to 1.725 Å. However, among the experimental gas-phase structures available to date probably the longest C-C bond (re,(av) = 1.750(28) Å at w = 0.93) was determined in a carbaborane derivative 1,2-(SeH)2-closo-1,2-C2B10H10.

Molecular Structure of Gaseous Oxopivalate Co(II): Electronic States of Various Multiplicities.

Synchronous electron diffraction/mass spectrometry was used to study the composition and structure of molecular forms existing in a saturated vapor of cobalt(II) oxopivalate at T = 410 K. It was found that monomeric complexes Co4O(piv)6 dominate in the vapor. The complex geometry possesses the C3 symmetry with bond lengths Co-Oc = 1.975(5) Å and Co-O = 1.963(5) Å, as well as bond angles Oc-Co-O = 111.8(3)°, Co-Oc-Co = 110.4(6)°, O-Co-O = 107.1(3)° in the central OcCo4 fragment and four OcCoO3 fragments. The presence of an open 3d shell for each Co atom leads to the possibility of the existence of electronic states of the Co4O(piv)6 complex with Multiplicities 1, 3, 5, 7, 9, 11, and 13. For them, the CASSCF and XMCQDPT2 calculations predict similar energies, identical shapes of active orbitals, and geometric parameters, the difference between which is comparable with the error of determination by the electron diffraction experiment. QTAIM and NBO analysis show that the Co-Oc and Co-O bonds can be attributed to ionic (or coordination) bonds with a significant contribution of the covalent component. The high volatility and simple vapor composition make it possible to recommend cobalt (II) oxopivalate as precursors in the preparation of oxide films or coatings in the CVD technologies. The features of the electronic and geometric structure of the Co4O(piv)6 complex allows for the conclude that only a very small change in energy is required for the transition from antiferromagnetically to ferromagnetically coupled Co atoms.

Dimer Rhenium Tetrafluoride with a Triple Bond Re-Re: Structure, Bond Strength.

Based on the data of the gas electron diffraction/mass spectrometry (GED/MS) experiment, the composition of the vapor over rhenium tetrafluoride at T = 471 K was established, and it was found that species of the Re2F8 is present in the gas phase. The geometric structure of the Re2F8 molecule corresponding to D4h symmetry was found, and the following geometric parameters of the rh1 configuration were determined: rh1(Re-Re) = 2.264(5) Å, rh1(Re-F) = 1.846(4) Å, α(Re-Re-F) = 99.7(0.2)°, φ(F-Re-Re-F) = 2.4 (3.6)°. Calculations by the self-consistent field in full active space approximation showed that for Re2F8, the wave function of the 1A1g ground electronic state can be described by the single closed-shell determinant. For that reason, the DFT method was used for a structural study of Re2X8 molecules. The description of the nature of the Re-Re bond was performed in the framework of Atom in Molecules and Natural Bond Orbital analysis. The difference in the experimental values of r(Re-Re) in the free Re2F8 molecule and the [Re2F8]2- dianion in the crystal corresponds to the concept of a triple σ2π4 (ReIV-ReIV) bond and a quadruple σ2π4δ2 (ReIII-ReIII) bond, respectively, which are formed between rhenium atoms due to the interaction of d-atomic orbitals. The enthalpy of dissociation of the Re2F8 molecular form in two monomers ReF4 (ΔdissH°(298) = 109.9 kcal/mol) and the bond energies E(Re-Re) and E(Re-X) in the series Re2F8→Re2Cl8→Re2Br8 molecules were estimated. It is shown that the Re-Re bond energy weakly depends on the nature of the halogen, while the symmetry of the Re2Br8 (D4d) geometric configuration differs from the symmetry of the Re2F8 and Re2Cl8 (D4h) molecules.

Gas-phase equilibrium molecular structures and ab initio thermochemistry of anthracene and rubrene.

Semi-experimental gas-phase structures of anthracene and rubrene (5,6,11,12-tetraphenyltetracene) were determined by means of gas electron diffraction (GED). The use of the flexible restraints in the refinement of the GED data successfully resolves non-equivalent C-C bond lengths. The tetracene core of an isolated rubrene molecule was found to exhibit a twist distortion of about 18°; this is less than DFT calculations predict (30-40°). The modified Feller-Peterson-Dixon method in conjunction with high-level DLPNO-CCSD(T) calculations was employed to resolve the discrepancy between the available experimental gas-phase enthalpies of formation for rubrene. The theoretical value of meets its recent experimental counterpart (765.6 ± 8.4 kJ mol-1) and is in strong disagreement with the previous estimation (882 kJ mol-1).

Cyclic Dimers of 4-n-Propyloxybenzoic Acid with Hydrogen Bonds in the Gaseous State.

A comprehensive study of saturated vapors of 4-n-propyloxybenzoic acid (POBA) by gas electron diffraction (GED) and mass spectrometric (MS) methods supplemented by quantum chemical (QC) calculations was carried out for the first time. An attempt was made to detect dimeric forms of the acid in the gaseous state. It has been established that at the temperature of GED experiment, vapor over a solid sample contains up to 20 mol.% of cyclic dimers with two O-H...O hydrogen bonds. The main geometrical parameters of gaseous monomers and dimers of POBA are obtained. The distance r(O…O) = 2.574(12) Å in the cyclic fragment of the gaseous dimer is close to that in the crystal structure (2.611 Å). In the mass spectrum of the POBA recorded the ions of low intensity with a mass exceeding the molecular mass of the monomer were detected. The presence of ions, whose elemental composition corresponds to the dissociative ionization of the dimer, confirms the results of the GED experiment on the presence of POBA dimers in the gas state. The results of GED studies of acetic acid, benzoic acid, and POBA were compared. It is shown that the COOH fragment saves its geometric structure in monomers, as well as the COOH...HOOC fragment with two hydrogen bonds in dimers of different acids. The intermolecular interaction energy in considered acid dimers was estimated using QC calculations (B97D/6-311++G **). The significant value of last (>84 kJ/mol) is the reason for the noticeable presence of dimers in the gas phase.

Molecular Structure, Vibrational Spectrum and Conformational Properties of 4-(4-Tritylphenoxy)phthalonitrile-Precursor for Synthesis of Phthalocyanines with Bulky Substituent.

By DFT method with B3LYP, PBE, CAM-B3LYP, and B97D functionals, it was found that the molecule 4-(4-tritylphenoxy)phthalonitrile (TPPN) has four conformers. The geometric structure, vibrational frequencies, electronic characteristics, and thermodynamic functions of conformers, as well as the structure and energy of transition states, were determined. IR spectrum of TPPN film contains vibrational bands belonging to different conformers. The assignment of bands was performed basing the distribution of normal vibration energy on internal coordinates. A synchronous electron diffraction/mass spectrometric experiment was performed to determine the structure of conformers in a saturated TPPN vapor. The elemental composition of the ions recorded in the mass spectrum indicates the thermal stability of TPPN at least up to T = 200 °C. The difference in the structure of tetrasubstituted metal phthalocyanines, which can be synthesized from different TPPN conformers, has been shown.

Gas-Phase Structures of Potassium Tetrakis(hexafluoro- acetylacetonato) Lanthanide(III) Complexes [KLn(C5 HF6 O2 )4 ] (Ln=La, Gd, Lu).

The molecular structures of potassium tetrakis(hexafluoroacetylacetonato)lanthanide(III) complexes [KLn(hfa)4 ] (Ln=La, Gd, Lu; hfa=C5 HF6 O2 ,) were studied by synchronous gas-phase electron diffraction/mass spectrometry (GED/MS) supported by quantum-chemical (DFT/PBE0) calculations. The compounds sublime congruently and the vapors contain a single molecular species: the heterobinuclear complex [KLn(hfa)4 ]. All molecules are of C1 symmetry with the lanthanide atom in the center of an LnO8 coordination polyhedron, while the potassium atom is coordinated by three ligands with formation of three K-O and three K-F bonds. One hfa ligand is not bonded to the potassium atom. Topological analysis of the electron-density distributions confirmed the existence of ionic-type K-O and K-F bonding. The structures of the free [KLn(hfa)4 ] molecules are compared with those of the related compounds [KDy(hfa)4 ] and [KEr(hfa)4 ] in their crystalline state. The complex nature of the chemical bonding is discussed on the basis of electron-density topology analyses.

Molecular Structure of Nickel Octamethylporphyrin-Rare Experimental Evidence of a Ruffling Effect in Gas Phase.

The structure of a free nickel (II) octamethylporphyrin (NiOMP) molecule was determined for the first time through a combined gas-phase electron diffraction (GED) and mass spectrometry (MS) experiment, as well as through quantum chemical (QC) calculations. Density functional theory (DFT) calculations do not provide an unambiguous answer about the planarity or non-planar distortion of the NiOMP skeleton. The GED refinement in such cases is non-trivial. Several approaches to the inverse problem solution were used. The obtained results allow us to argue that the ruffling effect is manifested in the NiOMP molecule. The minimal critical distance between the central atom of the metal and nitrogen atoms of the coordination cavity that provokes ruffling distortion in metal porphyrins is about 1.96 Å.

Accurate equilibrium structure of 3-aminophthalimide from gas electron diffraction and coupled-cluster computations and diverse structural effects due to electron density transfer.

For the first time, the molecular structure of 3-aminophthalimide has been determined by the gas electron diffraction (GED) method supported by a mass-spectrometric analysis of the gas phase and results of quantum-chemical computations up to coupled-cluster level of theory, CCSD(T). The semiexperimental equilibrium structure, rsee, has been derived from the GED data by taking into account harmonic and anharmonic vibrational corrections estimated from the quantum-chemical force field (up to cubic terms). High accuracy structures have been exploited for the observation of fine structural effects arising due the presence of the electron-donating amino group and the formation of a hydrogen bond. Natural bond orbital (NBO) analysis and quantum theory of atoms in molecules (QTAIM) have been applied to explain these effects.

Molecular Structure of Pyrazinamide: A Critical Assessment of Modern Gas Electron Diffraction Data from Three Laboratories.

Accuracy and precision of molecular parameters determined by modern gas electron diffraction have been investigated. Diffraction patterns of gaseous pyrazinamide have been measured independently in three laboratories, in Bielefeld (Germany), Ivanovo (Russia), and Moscow (Russia). All data sets have been analyzed in equal manner using a highly controlled background elimination procedure and flexible restraints in molecular structure refinement. In detailed examination and comparison of the obtained results we have determined the average experimental precision of 0.004 Å for bond lengths and 0.2° for angles. The corresponding average deviations of the refined parameters from the ae-CCSD(T)/cc-pwCVTZ theoretical values were 0.003 Å and 0.2°. The average precision for refined amplitudes of interatomic vibrations was determined to be 0.005 Å. It is recommended to take into account these values in calculations of total errors for refined parameters of other molecules with comparable complexity.

Molecular structure and electron distribution of 4-nitropyridine N-oxide: Experimental and theoretical study of substituent effects.

The molecular structure of 4-nitropyridine N-oxide, 4-NO2-PyO, has been determined by gas-phase electron diffraction monitored by mass spectrometry (GED/MS) and by quantum chemical calculations (DFT and MP2). Comparison of these results with those for non-substituted pyridine N-oxide and 4-methylpyridine N-oxide CH3-PyO, demonstrate strong substitution effects on structural parameters and electron density distribution. The presence of the electron-withdrawing -NO2 group in para-position of 4-NO2-PyO results in an increase of the ipso-angle and a decrease of the semipolar bond length r(N→O) in comparison to the non-substituted PyO. The presence of the electron-donating -CH3 group in 4-CH3-PyO leads to opposite structural changes. Electron density distribution in pyridine-N-oxide and its two substituted compounds are discussed in terms of natural bond orbitals (NBO) and quantum theory atoms in molecule (QTAIM).

The Effect of Intramolecular Hydrogen Bond Type on the Gas-Phase Deprotonation of ortho-Substituted Benzenesulfonic Acids. A Density Functional Theory Study.

Structural factors have been identified that determine the gas-phase acidity of ortho-substituted benzenesulfonic acid, 2-XC6H4-SO3H, (X = -SO3H, -COOH, -NO2, -SO2F, -C≡N, -NH2, -CH3, -OCH3, -N(CH3)2, -OH). The DFT/B3LYP/cc-pVTZ method was used to perform conformational analysis and study the structural features of the molecular and deprotonated forms of these compounds. It has been shown that many of the conformers may contain anintramolecular hydrogen bond (IHB) between the sulfonic group and the substituent, and the sulfonic group can be an IHB donor or an acceptor. The Gibbs energies of gas-phase deprotonation ΔrG0298 (kJ mol-1) were calculated for all compounds. It has been set that in ortho-substituted benzenesulfonic acids, the formation of various types of IHB is possible, having a significant effect on the ΔrG0298 values of gas-phase deprotonation. If the -SO3H group is the IHB donor, then an ion without an IHB is formed upon deprotonation, and the deprotonation energy increases. If this group is an IHB acceptor, then a significant decrease in ΔrG0298 of gas-phase deprotonation is observed due to an increase in IHB strength and the A- anion additional stabilization. A proton donor ability comparative characteristic of the -SO3H group in the studied ortho-substituted benzenesulfonic acids is given, and the ΔrG0298 energies are compared with the corresponding values of ortho-substituted benzoic acids.

Ligand Coordination in Bis(ß-diketonato) d Metals: The Mn(II) Case of D2 h versus D2 d Symmetry.

The structure of free manganese(II) bis-acetylacetonate [Mn(acac)2] was determined experimentally by gas-phase electron diffraction. The vapor at 197(5) °C is composed of a single conformer of Mn(acac)2 in D2 d symmetry with a central structural motif of an elongated MnO4 tetrahedron with a Mn-O distance ( re) of 2.035(5) Å and a bond angle in chelate rings (∠O-Mn-O) of 89.4(6)°. This result contradicts the predicted planar structure of the MO4 moiety ( D2 h) with a short Mn-O distance ( re) of 1.771 Å from a MC(5i5)QDPT2 calculation. From these findings and by comparison with data from the literature, we conclude that in general in bis(ß-diketonato) coordination compounds of d metals there is a perpendicular arrangement of the two ligands for d0, d5, and d10 coordination centers and a planar arrangement ( D2 h) for others.

The molecular structure of 4-methylpyridine-N-oxide: Gas-phase electron diffraction and quantum chemical calculations.

The molecular structure of 4-methylpiridine-N-oxide, 4-MePyO, has been studied by gas-phase electron diffraction monitored by mass spectrometry (GED/MS) and quantum chemical (DFT) calculations. Both, quantum chemistry and GED analyses resulted in C S molecular symmetry with the planar pyridine ring. Obtained molecular parameters confirm the hyperconjugation in the pyridine ring and the sp2 hybridization concept of the nitrogen and carbon atoms in the ring. The experimental geometric parameters are in a good agreement with the parameters for non-substituted N-oxide and reproduced very closely by DFT calculations. The presence of the electron-donating CH3 substituent in 4-MePyO leads to a decrease of the ipso-angle and to an increase of r(N→O) in comparison with the non-substituted PyO. Electron density distribution analysis has been performed in terms of natural bond orbitals (NBO) scheme. The nature of the semipolar N→O bond is discussed.

Gas-phase structure of 1,8-bis[(trimethylsilyl)ethynyl]anthracene: cog-wheel-type vs. independent internal rotation and influence of dispersion interactions.

The gas-phase structure of 1,8-bis[(trimethylsilyl)ethynyl]anthracene (1,8-BTMSA) was determined by a combined gas electron diffraction (GED)/mass spectrometry (MS) experiment as well as by quantum-chemical calculations (QC). DFT and dispersion corrected DFT calculations (DFT-D3) predicted two slightly different structures for 1,8-BTMSA concerning the mutual orientation of the two -C-C[triple bond, length as m-dash]C-SiMe3 units: away from one another or both bent to the same side. An attempt was made to distinguish these structures by GED structural analysis. To probe the structural rigidity, a set of Born-Oppenheimer molecular dynamics (BOMD) calculations has been performed at the DFT-D level. Vibrational corrections Δr = ra - re were calculated by two BOMD approaches: a microcanonically (NVE) sampled ensemble of 20 trajectories (BOMD(NVE)) and a canonical (NVT) trajectory thermostated by the Noose-Hoover algorithm (BOMD(NVT)). In addition, the conventional approach with both, rectilinear and curvilinear approximations (SHRINK program), was also applied. Radial distribution curves obtained with models using both MD approaches provide a better description of the experimental data than those obtained using the rectilinear (SHRINK) approximation, while the curvilinear approach turned out to lead to physically inacceptable results. The electronic structure of 1,8-BTMSA was investigated in terms of an NBO analysis and was compared with that of the earlier studied 1,8-bis(phenylethynyl)anthracene. Theoretical and experimental results lead to the conclusion that the (trimethylsilyl)ethynyl (TMSE) groups in 1,8-BTMSA are neither restricted in rotation nor in bending at the temperature of the GED experiment.

The Structure of Mn(acac)3 -Experimental Evidence of a Static Jahn-Teller Effect in the Gas Phase.

The structure of free manganese(III) tris(acetylacetonate) [Mn(acac)3 ] was determined by mass-spectrometrically controlled gas-phase electron diffraction. The vapor of Mn(acac)3 at 125(5) °C is composed of a single conformer of Mn(acac)3 in C2 symmetry with the central structural motif of a tetragonal elongated MnO6 octahedron and 47(2) mol % of acetylacetone (Hacac) formed by partial thermal decomposition of Mn(acac)3 . Three types of Mn-O separations have been refined (rh1 =2.157(16), 1.946(5), and 1.932(5) Å. We have found no indication for a significant deviation of the -C-C-C-O-Mn-O- six-membered rings from planarity, which is observed in the solid state.

Accurate Determination of Equilibrium Structure of 3-Aminophthalonitrile by Gas Electron Diffraction and Coupled-Cluster Computations: Structural Effects Due to Intramolecular Charge Transfer.

For the first time, the molecular structure of 3-aminophthalonitrile with unique electronic properties has been determined by the gas electron diffraction (GED) method supported by a mass spectrometric analysis of the gas phase. Moreover, it has been optimized at the high-level quantum-chemical coupled-cluster theory, CCSD(T), in conjunction with the triple-ζ basis set. The equilibrium structure has been determined from the GED data taking into account harmonic and anharmonic vibrational corrections estimated from the quantum-chemical force field (up to cubic terms). The computed CCSD(T) structure has been corrected for the core-core and core-valence electron-correlation effects estimated at the MP2 level and extrapolated to the basis set of quadruple-ζ quality. A remarkable agreement between the experimental and theoretical equilibrium structural parameters (bond lengths and angles) points to a high accuracy of both the molecular structure and applied theories. The high accuracy of structure computations and experimental determination allows the observation of structural changes due to the intramolecular charge transfer predicted by natural bond orbital (NBO) calculations. According to the NBO analysis, the amino group is the electron-donating substituent, whereas the nitrile groups are able to withdraw the π electrons from the benzene ring. Noticeable variations in the structural parameters are also explained by the interaction of σ → π* orbitals of the nearest C≡N and N-H bonds.