The precise structure of the isolated molecule 4,4-difluoro-8-phenyl-4-bora-3a,4a-diaza-s-indacene (Ph-BODIPY) was determined by simultaneous gas-phase electron diffraction/mass spectrometry (GED/MS) in combination with quantum chemical calculations. It was found that Ph-BODIPY in the gas phase possesses an almost planar dipyrromethene skeleton with certain twist of the phenyl group with respect to the frame of the molecule. Since this is the first example of GED study of molecular structure of free BODIPY derivative, a choice of an appropriate approach of GED structural analysis in such cases was methodologically considered. The experimental equilibrium structure of Ph-BODIPY obtained in the work and the results of DLPNO-CCSD(T0) calculations were employed to evaluate the accuracy of various quantum chemical computations. The highest concordance with experimental data was achieved using calculations with the CAM-B3LYP functional, which, along with PBE0 and mPW1PW91, is recommended for a dependable description of the molecular geometry in similar systems.
The composition of the saturated vapors of two platinum complexes with the macrocyclic ligands 5,10,15,20-tetraphenylporphyrin (PtTPP) and 5,10,15,20-tetrakis(pentafluorophenyl)porphyrin (PtTF5PP) and their structures were determined by synchronous gas-phase electron diffraction/mass spectrometry (GED/MS). These porphyrin complexes are those with the heaviest metal atom in the coordination cavity that have been structurally investigated in the gas phase. The mass spectra confirm the presence of a single molecular form of each, PtTPP (T=629 K) and PtTF5PP (T=597 K). Their structures can serve as references for related complexes in the crystalline state or solutions. Differences between the geometries of PtTPP and PtTF5PP in the crystalline and gaseous states include a significant deformation of the tetrapyrrole macrocycle in solid PtTPP. The experimental Pt-N bond lengths of both complexes are in agreement with quantum chemical calculations (DFT/B97D/ECP(Pt)) taking into account relativistic effects. The effect of lanthanide contraction is evident from the similarity of the Pd-N and Pt-N internuclear distances of analogous compounds. The strong electron density transfer from the porphyrin backbone to the metal ion and the resulting low effective positive charge on the platinum atom, studied by NBO and QTAIM methods, helps to rationalize the high catalytic activity of such platinum compounds.
The study of the electronic and geometric structure of cobalt etioporphyrin-II (CoEP-II) and parent cobalt porphyrin (CoP) molecules was carried out using density functional theory (DFT) and complete active space selfconsistent field (CASSCF) calculations. Calculations at different levels of theory give contradictory and ambiguous results regarding the ground state of these compounds. The ground state according to various calculations can be quartet and doublet. These states are characterized by changes in the geometry of the molecule, in particular the distance between the cobalt and nitrogen atoms. It has been shown that these differences are sufficient to be recorded in a gas electron diffraction (GED) experiment. The found Co-N distance of 1.977(5) & Aring; indicates that at the GED experiment temperature of 584(8) K the CoEP-II complex exists in a low-spin electronic state. The re-molecular structure of CoEP-II was determined for the first time by the GED method.
The dialectic of the development of science is expressed in the fact that today’s experiments must give way to tomorrow’s theory, which makes these experiments unnecessary, but which, in turn, must give way to a new, more accurate experiment the day after tomorrow, and so on along the path of progress [...]
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.
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.
The equilibrium structure of free 4-(4-hydroxyphenylazo)phthalonitrile (p-HPhAPN, C14N4H8O) molecules was investigated for the first time by combined gas-phase electron diffraction and mass spectrometry (GED/MS) experiment, as well as through quantum chemical (QC) calculations. It was determined that p-HPhAPN in the vapor is represented by planar azo forms. & Scy;is-trans isomerism, azo-hydrazone tautomerism and rotations of different moieties in p-HPhAPN were studied in B3LYP-D3/pcseg-2 and DLPNO-CCSD(T0) levels of theory. Electron impact mass spectra of p-HPhAPN are typical for azobenzenes and are interpreted using the results of QCxMS calculations at the GFN2-xTB level of theory. Due to the exciting possibility of p-HPhAPN in the preparation of phthalocyanines with macrocyclic and azo chromophores, the structures of corresponding isomers of zinc phthalocyanines were investigated.
A comprehensive study of the structural, spectral and energetic properties of chloroboron(III) complexes of subphthalocyanine (H(12)SubPc, for the first time) and dodecafluorosubphthalocyanine (F(12)SubPc, reinvestigation) was performed by mass-spectroscopy (MS), gas-phase electron diffraction (GED), IR spectroscopy and quantum-chemical (QC) calculations. A synchronous GED/MS method showed that at T = 630 K and T = 540 K, thermally stable H(12)SubPc and F(12)SubPc molecular forms are present in the gas phase. The geometric structure of free molecules has been determined, in which the N-3-B-Cl fragment has the structure of a distorted tetrahedron, and the phthalocyanine skeleton has a dome shape. QC calculations of the geometry agree well with the GED results. The similarities and differences of the molecular structure in the gas and solid phases were discussed. It is shown, that despite the similarity of most geometric parameters, the H(12)SubPc and F(12)SubPc have significant differences in electronic characteristics, which determines the differences in their physicochemical properties. The interpretation of the experimental IR spectra was carried out. The distribution of potential energy of normal vibrations over the internal vibrational coordinates has been analyzed. The sublimation enthalpies of H(12)SubPc (Delta H-s(589 K) = 135(5) kJ & sdot; mol(-1)) and F(12)SubPc (Delta H-s(516 K) = 189(3) kJ & sdot; mol(-1)) were determined by the mass spectrometric Knudsen effusion method. The obtained data is important for designing processes employed in fabricating optoelectronic devices based on subphthalocyanines by PVD. Experimental geometric parameters for free molecules and vibrational frequencies can be used to calculate the thermodynamic functions of gaseous H(12)SubPc and F(12)SubPc.
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 D-3h symmetry with a Hg-C distance of 2.075(5) & Aring; and a Hg-Hg distance of 3.614(7) & Aring; (both r(h1)). 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 & sdot;& sdot;& sdot;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.
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.
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 electron diffraction and quantum chemical study of the isolated H2TPP molecule was carried out, which can be considered as a reference point for tetraphenylporphyrin metal complexes. Using Knudsen effusion mass spectrometry, the enthalpy of sublimation of the H2TPP was determined to be 212(4) kJ/mol (535 K). Using DFT/B97D/cc-pVTZ in combination with gas electron diffraction it is shown that the saturated vapor of H2TPP consists of a mixture of conformers. The conformers differ in the mutual orientation of the four phenyl fragments relative to each other and have close energies. Bond lengths and bond angles in conformers were determined. NBO analysis showed a change in the delocalization of the electron density between the phenyl substituents and the macroheterocyclic (MHC) skeleton with a change in the torsion angle. This delocalization is the reason for the non- orthogonal position of phenyl meso-substituents in the conformers of H2TPP and other tetraphenyl substituted porphyrins. Non-covalent interactions between the MHC skeleton and phenyl substituents have been described using the FI-SAPT0 method. The change in geometric and electronic characteristics in the series of molecules H2P, H2TPP, H2FTPP, ZnTPP and PdTPP is considered. Based on Valence Shell Electron Pair Repulsion (VSEPR) theory, an explanation is given for the influence of the substituent on the parameters of the MHC skeleton. Analysis of changes in the energy of frontier orbitals in the indicated series of molecules makes it possible to predict the direction of changes in the red-ox properties of compounds with various modifications ofH2TPP.
Structural, spectroscopic and thermodynamic studies carried out in the scientific labora-tories of the Physics Department of the Ivanovo State University of Chemistry and Technology in the last 5-10 years are briefly reviewed.
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.
The structural and dynamic non-rigidity of two types of hydrogen-bonded complexes was investigated: cyclic dimers A∙∙∙A of 4-n-alkyloxy and 4-n-alkyl-substituted aromatic acids (A) and complexes A∙∙∙B∙∙∙A with hydrogen bonds O-H∙∙∙N, where B1 – 4,4′-bipyridine and B2 – 4,4′-azopyridine. Dynamic non-rigidity depends on temperature and is determined by the values of the intramolecular vibrational amplitudes (VibAmp) of various structural groups of the complexes. VibAmp were calculated using the force field obtained by the method DFT/CAM-B3LYP/6-311++G**. It was shown that the core of acid dimers, including intermolecular hydrogen bonds, can be considered rigid over a wide temperature range. The dynamic non-rigidity of the A∙∙∙A dimers is mainly determined by the vibrations of the alkyl substituents. A correlation has been established between the VibAmp of the terminal methyl groups l((H3)C···C(H3)) of acid dimers and the temperatures of phase transitions TLC→I in homologous series of 4-n-alkyloxycinnamic, 4-n-alkyloxybenzoic and 4-n-alkylbenzoic acids, which exhibit an odd–even effect. The higher the vibrational amplitude l((H3)C∙∙∙C(H3)), the lower the temperature of the phase transition TLC→I, since the increased vibrational amplitudes prevent ordered intermolecular interactions that stabilize the structure of the liquid crystal. The structural and dynamic non-rigidity of A∙∙∙A dimers and A∙∙∙B∙∙∙A complexes was compared. The non-rigid core of the A∙∙∙B∙∙∙A complex contributes to a significant increase in both the VibAmp of the core and the terminal groups of substituents and a decrease in the TC→LC temperature of the phase transition “crystal-liquid crystal” in comparison with that for acid dimers. The concept of the structural and dynamic non-rigidity of possible hydrogen-bonded complexes can serve as a basis for understanding the influence of various factors and types of hydrogen bonds on the stability of complexes and the manifestation of mesomorphic properties of systems consisting of supramolecules.
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.
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.
Mass spectrometric and gas-phase electron diffraction (GED/MS) studies of overheated Sc(acac)3 vapor at temperature 812(5) K were performed. Experimental data indicate that overheated vapor contains, along with tris-form Sc(acac)3, bis-complex Sc(acac)2, which is the result of partial thermal dissociation of tris form. Testing of three models D2h(2Ag), D2h(2B3g) and D2d(2B1) of bis-complex geometric and electronic structure showed that the planar model D2h(2B3g) best fits GED/MS data. Reinterpretation of GED/MS data for saturated vapor of Sc(acac)3 at T = 428 K was carried out. Temperature dependence of rg(Sc-O) parameters of effective temperature-averaged geometric configuration Sc(acac)3 is noted.
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.
Conformational manifold of 1,3,5,7-tetraphenyl-aza-BODIPY and 1,3,5,7-tetra(2-thiophenyl)-aza-BODIPY was studied by B3LYP calculations. The addition of four cyclic groups to the aza-BODIPY core defines the non-planarity of the molecule and movement of the substitu-ents from the heterocycle plane. The rotation angles of the phenyl and thiophenyl groups in the molecules are about 30?? and 17??, respectively. For phenyl-substituted aza-BODIPY four con-formers were found using quantum chemical calculations (B3LYP/6-31G* and B3LYP/cc-pVTZ), for thiophenyl-substituted aza-BODIPY ??? 30 conformers. Relative energies of some conformers are quite low, therefore they should be taken into account in the treatment of the gas electron dif-fraction (GED) experimental data. In current work the sensitivity of the GED method to the structural changes induced by different positions of phenyl and thiophenyl substituents relative to the aza-BODIPY core and each other was examined. Model radial distribution curves f(r) for all conformers were compared. It demonstrates that the bond distances can be reliably determined from experimental data, while the refinement of mutual orientations of neighboring groups relat-ing to each other is at the limit of the possibilities of the GED method. Based on experimental da-ta, it is possible to distinguish 1,3,5,7-tetra(2-thiophenyl)-aza-BODIPY conformers, which differ in the mutual arrangement of sulfur atoms. The use of the results of various quantum chemical calculations leads to the same conclusions about the possibility of the gas electron diffraction method to determine the conformational composition.