Effects of fused benzene rings on tautomerizations and inversions of benzo, azabenzo, and oxabenzocycloheptatrienes at theoretical levels

Biologically important bicyclic species, including 6H-, 6H-6-aza-, and 6-oxabenzocycloheptatrienes (in which the benzene moiety is fused meta with respect to the tetrahedral constituents: –CH₂–, –NH–, and –O–, respectively), show strong shifts of tautomerizations in favor of the corresponding tricyclic benzonorcaradienes (with ΔH values of −11.49, −14.55, and −19.20 kcal mol⁻¹, respectively), at B3LYP/6-311++G**//B3LYP/6-31G*, and MP2/6-311++G**//MP2/6-31G* levels, and at 298 K. In contrast, such shifts are strongly disfavored by the isomeric bicyclic species in which the benzene moieties are fused ortho or para with respect to –CH₂–, –NH–, and –O–, respectively. Hence for species with ortho benzene rings including 5H-, 5H-5-aza- and 5-oxabenzocycloheptatrienes, tautomerization ΔH values are 30.76, 31.89, and 25.27 kcal mol⁻¹, respectively, while for species with para fused benzene moieties including 7H-, 7H-7-aza-, and 7-oxabenzocycloheptatrienes, tautomerization ΔH values are 24.12, 26.00, and 19.55 kcal mol⁻¹, respectively. NICS calculations are successfully used to rationalize these results. The calculated energy barriers for inversion of the seven-membered rings of bicyclic species predict a dynamic nature for all the structures except for the virtually planar 6H-6-aza- and 6-oxabenzocycloheptatrienes. Finally, our theoretical data are compared to the experimental results where available. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Crystallographic and theoretical studies of 4,4′-dimethyl-7,7′-bi([1,2,5]thiadiazolo[3,4-b]pyridylidene)–chloranilic acid (1/1) with intermolecular O–H···N hydrogen bonds and S···O heteroatom interactions

Abstract  The molecular and crystal structure of a 1:1 co-crystal of 4,4′-dimethyl-7,7′-bi([1,2,5]thiadiazolo[3,4-b]pyridylidene)–chloranilic acid, (1), has been determined by X-ray diffraction at the monoclinic space group P2₁/c with cell parameters of a = 8.422(6), b = 7.343(4), c = 16.112(7) ?, β = 104.988(8)°, V = 962.5(10) ?³ and Z = 2. In the crystal structure, two components connect via the intermolecular O–H···N hydrogen bonds [2.804(4) ?] and S···O heteroatom interaction [2.945(3) ?] with R ₂ ²(7) couplings to form a unique and infinite one-dimensional supramolecular tape structure. The calculations of (1) at the HF/6-31G(d), MP2/6-31G(d), and B3LYP/6-31G(d) levels can almost reproduce X-ray geometry. In addition, the distances of the intermolecular O–H···N and S···O interactions by MP2/6-31G(d) and B3LYP/6-31G(d) levels agree well with those in the crystal. The calculated binding energies corrected BSSE and ZPE are −4.487 (HF), −7.473 (MP2), and −5.640 (B3LYP) kcal/mol. The results suggest that the complex (1) is very stable and the dispersion interaction is significantly important for the attractive intermolecular interaction in (1). The NBO analysis has revealed that the n(N) → σ*(O–H) interaction gives the strongest stabilization to the system and the major interaction for the intermolecular S···O contact is n(O) → σ*(S–N). Index Abstract  In the crystal structure of the title compound, the molecules are linked by intermolecular O–H···N hydrogen bonds and short S···O heteroatom interactions with R ₂ ²(7) couplings to construct a unique and infinite one-dimensional supramolecular tape structure.      

Experimental and computational studies on (<Emphasis Type="Italic">Z</Emphasis>)-1-((4-phenylamino)phenylamino)-methylene)naphthalen-2(1<Emphasis Type="Italic">H</Emphasis>)-one

The Schiff base compound (Z)-1-((4-phenylamino)phenylamino)methylene)naphthalen-2(1H)-one has been synthesized and characterized by IR, UV–Vis, and X-ray single-crystal determination. Molecular geometry from X-ray experiment of the title compound in the ground state have been compared using the Hartree–Fock (HF) and density functional method (B3LYP) with 6−31G(d,p) basis set. Calculated results show that density functional theory DFT and HF can well reproduce the structure of the title compound. Using the time-dependent density functional theory (TD-DFT) and Hartree–Fock (TD-HF) methods, electronic absorption spectra of the title compound have been predicted and a good agreement with the TD-DFT method and experimental ones is determined. The energetic behavior of the title compound in solvent media has been examined using B3LYP method with the 6−31G(d,p) basis set by applying the polarizable continuum model (PCM). The total energy of the title compound decreases with increasing polarity of the solvent. In addition, DFT calculations of the title compound, molecular electrostatic potential (MEP), natural bond orbital analysis (NBO), and non-linear optical (NLO) properties were performed at B3LYP/6−31G(d,p) level of theory.     

Comparative quantum chemical investigation of structures and properties of diazocyclopropane and other diazoalkanes

The electronic structures and dissociation energies of diazocyclopropane (1), diazomethane (2), 2-diazopropane (3), and diazocyclobutane (4) were calculated at the density functional B3LYP and the ab initio MP2 levels using the 6-31G(d) basis set and at the G2(MP2,SVP)//B3LYP/6-31G(d) level. Distinctive features of diazocyclopropane 1 are the low energy of dissociation with loss of the nitrogen molecule; ΔE = 18.7 kcal mol⁻¹, B3LYP; 9.2 kcal mol⁻¹, G2 at 0 K) and a nonplanar structure, in which the C=N bond forms an angle of 115.7° with the plane of the cyclopropane ring. The behavior of molecules 1 and 2 in the 1,3-dipolar cycloaddition to ethylene (5), acrylonitrile (6), and methyl acrylate (7) was studied. The reactions of 1 with 6 and 7 have very low activation barriers (ΔE _a = 4.7 and 4.4 kcal mol⁻¹, respectively; at the B3LYP level). For these reactions, the G2 method gives even smaller activation parameters (1.8 and 0.3 kcal mol⁻¹, respectively). The results of our calculations provide a good explanation for high reactivity of diazocyclopropane 1. Dedicated to Academician N. K. Kochetkov on the occasion of his 90th birthday. __________ Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 5, pp. 1072–1076, May, 2005.     

Structure of guest-host complexes of β-cyclodextrin with arenes: a quantum-chemical study

The structure of β-cyclodextrin (β-CD), as well as the structure and energetics of β-CD-naphthalene, β-CD-fluorene, β-CD-phenanthrene, β-CD-cyclohexane (1:1), and β-CD-naphthalene (2:2) inclusion complexes was studied by the semiempirical MNDO/PM3 method. Calculations of a β-CD-naphthalene-cyclohexane (1:1:1) complex were also performed. The minimum heat of formation was found for the symmetric β-CD conformation withC ₇ symmetry axis. The structure is stabilized by the ring of interunit H-bonds formed by the protons of the 2-OH groups and the O atoms of the 3′-OH groups of the glucose units. Preferableness of this orientation of interunit H-bonds was confirmed byab initio calculations of the molecule of α-(1–4)-glucobiose (maltose) in the MP2/6-31G(d,p)//6-31G(d,p) approximation. The formation of any inclusion compounds of β-CD with arenes is energetically favorable: the complexation energy varies in the range −9 to −12 kcal mol⁻¹. Among complexes with naphthalene, that of composition 2:2 is the most energetically favorable, which is in agreement with experimental data. In this complex, β-CD exists as a dimer of the “head-to-head” type, in which both partners are linked by a system of H-bonds. The structure of the “head-to-head” dimer of β-CD was simulated byab initio calculations of the H-bonded dimer of α-d-glucose in the RHF/6-31G(d,p) approximation. In the dimer, both components are linked by a pair of H-bonds formed by the protons of the 3-OH groups and the O atoms of the, 2-OH groups. The dimerization energies obtained fromab initio and semiempirical MNDO/PM3 and AM1 calculations differ by about 2.5 times (8.6vs 3.2 and 3.8 kcal mol⁻¹, respectively).     

Molecular structure, barriers to internal rotation, and the enthalpy of formation of cumene hydroperoxide PhCMe2OOH: a DFT study

Conformational analysis of cumene hydroperoxide PhCMe₂OOH (1) has been carried out using the density functional methods B3LYP/6-31G(d,p) and B3LYP/6-311+G(3df,2p). Ignoring rotation of methyl groups, molecule 1 has seven conformers differing in orientation of the — CMe₂OOH fragment relative to the benzene ring and in mutual position of atoms in this fragment. The molecular structures, relative energies, and statistical distribution of the conformers were determined, and intramolecular rotational barriers were estimated. The enthalpies of formation of all conformers of molecule 1 were calculated using two approximations with inclusion of zero-point vibrational energy and temperature correction. Calculations using the isodesmic reaction (IDR) scheme made it possible to reduce the systematic error of the determination of the enthalpy of reactions. The total enthalpy of formation of compound 1 calculated with inclusion of statistical distribution of rotamers equals −19.7±3.6 kcal mol⁻¹. The combination of the B3LYP/6-31G(d,p) approximation and the IDR scheme gives fairly accurate results (relative error is ±0.4 kcal mol⁻¹) as compared to those obtained with the extended basis set 6-311+G(3df,2p). Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 6, pp. 1157–1164, June, 2008.     

Hypercoordinate atoms of second-row elements in dodecahedrane endohedral complexes

The energy characteristics and geometric parameters of the dodecahedrane endohedral complexes X@C₂₀H₂₀ (X = C⁴⁻, N³⁻, O²⁻, F⁻, Ne) were studied by the density functional theory B3LYP method with the 6-311G(d,p), 6-311+G(d,p), and 6-311G(df,p)) basis sets. In all structures the central atoms X are characterized by a coordination number of 20. The energy of formation of the complexes decreases in the order X = C⁴⁻, N³⁻, O²⁻, F⁻, Ne. The coordination number of the central atom remains unchanged upon adding Li⁺ counterions to anionic systems. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 5, pp. 824–830, May, 2007.     

Molecular Structure and Conformational Composition of 1-[(Methylthio)methyl]-2-nitrobenzene (MTMNB): A Theoretical and Experimental Study

The conformational composition of gaseous MTMNB and the molecular structures of the rotational forms have been studied by electron diffraction at 130^∘C aided by results from ab initio and density functional theory calculations. The conformational potential energy surface has been investigated by using the B3LYP/6-31G(d,p) method. As a result, six minimum-energy conformers have been identified. Geometries of all conformers were optimized using MP2/6-31G(d,p), B3LYP/6-31G(d,p), and B3LYP/cc-pVTZ methods. These calculations resulted in accurate geometries, relative energies, and harmonic vibrational frequencies for all conformers. The B3LYP/cc-pVTZ energies were then used to calculate the Boltzmann distribution of conformers. The best fit of the electron diffraction data to calculated values was obtained for the six conformer model, in agreement with the theoretical predictions. Average parameter values (r_a in angstroms, angle α in degrees, and estimated total errors given in parentheses) weighted for the mixture of six conformers are r(C–C) = 1.507(5), r(C–C)_{ring, av} = 1.397(3), r(C–S)_av = 1.814(4), r(C–N) = 1.495(4), r(N–O)_av = 1.223(3), ∠(C–C–C)_ring = 116.0–122.5, ∠ C6–C4–C7 = 118.2(4), ∠ C–C–S = 113.6(6), ∠ C–S–C = 98.5(12), ∠ N–C–C4 = 121.9(3), ∠(O–N–C)_av = 116.8(3), ∠ O–N–O = 127.0(4). Torsional angles could not be refined. Theoretical B3LYP/cc-pVTZ torsional angles for the rotation about C–N bond, φ_C−N, were found to be 30.5–36.5^∘ for different conformers. As to internal rotation about C–C and C–S bonds, values of φ_C−C = 68–118^∘ and φ_C−S = 66–71^∘ were obtained for the three most stable conformers with gauche orientation with respect to these bonds. Some conclusions of this work were presented in a short communication in Russ. J. Phys. Chem. 2005, 79, 1701.     

Photoelectron spectrum and quantum chemical analysis of the structure of bis(1,3,6-trimethyluracilyl-5)methane

Photoelectron spectra of bis(1,3,6-trimethyluracilyl-5)methane (I) and 1,3,6-trimethyluracil (II) were studied; AM1 optimization of geometric characteristics was carried out. The total energy minimum and the best agreement between the values of IP_m and -ɛ_m were obtained for conformations with nearly orthogonal location of uracilyl fragments. In such conformations, the highest occupied orbitals are pseudodegenerate. To interpret the photoelectron spectra, we employed ab initio calculations in STO-3G and 4-31G basis sets. For uracil and its derivatives, all methods give the π, π, n⁻, n⁺, π sequence of the highest orbitals. A. E. Arbuzov Institute of Organic and Physical Chemistry, Kazan Scientific Center, Russian Academy of Sciences. Translated fromZhurnal Struktumoi Khimii, Vol. 36, No. 1, pp. 102–107, January–February, 1995. Translated by L. Smolina     

Vibrational spectra of 1,1,3,3-tetramethyl-2-nitroguanidine and their interpretation with the use of scaling of quantum-chemical force field

The IR (4000–50 cm⁻¹) and Raman (3500–170 cm⁻¹) spectra of solid 1,1,3,3-tetramethyl-2-nitroguanidine (TMNG) were obtained. The spectra were interpreted using the scaling of the TMNG quantum-chemical force field in the B3LYP/6-311G(d,p) approximation. Transferable scale factors necessary for the interpretation of spectra of more complex related compounds were determined. The scaled harmonic force field is supposed to be used in the analysis of the available gas-phase electron diffraction data for TMNG. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 495–498, March, 2008.     

Ab initio study of the ground state and conformational stability of peroxyacetyl nitrate in internal rotation about the peroxide bond

The molecular and electronic structure of the ground state of peroxyacetyl nitrate (PAN) was calculated by the unrestricted Hartree-Fock-Roothaan method with the use of the standard 3–21G and 6–31G basis set. The potential curve of the internal rotation about the peroxide bond of PAN was calculated with the 6–31G basis set. The curve contains two maxima. The ground state of PAN is characterized by a structure in which groups of atoms adjacent to the peroxide bond lie in planes that are perpendicular to each other (the dihedral angle ϱ(COON) is 89.9°). The calculated barriers to rotation are 19.6 and 66.8 kJ mol⁻¹. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 600–604, April, 1998.     

An ab initio Molecular Orbital Study of the Conformational Properties of all-( Z )-Cyclododeca-1,4,7,10-tetraene

 Ab initio HF/6-31G^* and MP2/6-31G^*//HF/6-31G^* methods were used to calculate the structure optimization and conformational interconversion pathways for all-(Z )-cyclododeca-1,4,7,10-tetraene. This compound adopts the symmetrical crown (C _4v) conformation. Ring inversion takes place via symmetrical intermediates, such as boat-chair (BC, C _s) and twist (C _2h) conformers and requires about 22.3 kJ · mol⁻¹. The calculated strain energies for BC and twist conformers are 5.9 and 13.5 kJ · mol⁻¹. The results of semiempirical AM1 calculations for structural parameters and relative energies of the important geometries of the title compound are in good agreement with the results of ab initio methods.     

Quantum chemical calculations for the geometry and intramolecular rearrangements of a model nickel(<Emphasis Type="SmallCaps">ii</Emphasis>) <Emphasis Type="Italic">o</Emphasis>-semiquinone complex with a PCP pincer ligand

The structure and intramolecular rearrangements of the model five-coordinate nickel PCP-pincer complex with the o-semiquinone ligand were studied by the density functional theory method at the B3LYP/6-311++G(d,p) level. The isomerization associated with swing vibrations of the o-semiquinone ligand can occur virtually barrierless (0.7 kcal mol⁻¹). The dynamics of the coordination sphere determined by pendulum vibrations of the o-semiquinone ligand has the energy barriers of 4–5 kcal mol⁻¹, which is in good agreement with experimental data. A comparison of the results of calculations with the ESR spectroscopic data revealed the dependence of the types and the energy characteristics of intramolecular rearrangements on the nature of substituents at the phosphorus atom.     

Substrate and positional selectivity in electrophilic substitution reactions in pyrrole, furan, thiophene, and selenophene derivatives and related benzoannelated systems

Data on the relative reactivities (substrate selectivity) of five-membered heterocycles in electrophilic substitution reactions and positional selectivity (α : β ratio) in these reactions were analyzed. Unlike the substrate selectivity (pyrrole ≫ furan > selenophene > thiophene) determined by the position of heteroatoms in the Periodic Table, the positional selectivity decreases in the order corresponding to the change in the relative stability of the onium states of the elements (O⁺ < Se⁺ ≤ S⁺ < N⁺) and reflects the predominant role of heteroatoms in the stabilization of σ complexes formed upon β-substitution. These differences in the positional selectivity of the parent heterocycles have a substantial effect on the orientation in electrophilic substitution reactions in their derivatives and the corresponding benzoannelated systems. This interpretation was confirmed by ab initio quantum chemical calculations (RHF/6–31G(d) and MP2/6– 31G(d)//RHF/6–31G(d)) and density functional theory calculations (B3LYP/6–31G(d)). Quantum chemical calculations were performed by the above-mentioned methods for model N-R-pyrroles (R = Me, Et, Prⁱ, Bu^t, CH=CH₂, C≡CH, Ph, PhSO₂, and 4-O₂NC₆H₄) and their α- and β-protonated σ complexes. The results of these calculations demonstrated that it is the steric factors and charges on the β-C, α-C, and N atoms and the substituents at the N atom (the kinetic control), as well as the nature of the electrophile, rather than the difference in the relative stabilities of the onium states of N⁺ (which depends on the nature of the substituent at the N atom and reflects the role of the heteroatom in stabilization of σ complexes formed via β-substitution; the thermodynamic control) that are responsible for the type of orientation (α or β) that prevails. Dedicated to Academician V. I. Minkin on the occasion of his 70th birthday. __________ Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 837–846, April, 2005.     

Isomerism in OBe3F3 + cation: anab initio study

Ab initio MP2/6-31G^*//HF/6-31G^*+ZPE(HF/6-31G^*) calculations of the potential energy surface in the vicinity of stationary points and the pathways of intramolecular rearrangements between low-lying structures of the OBe₃F₃ ⁺ cation detected in the mass spectra of μ₄-Be₄O(CF₃COO)₆ were carried out. Ten stable isomers with di- and tricoordinate oxygen atoms were localized. The relative energies of six structures lie in the range 0–8 kcal mol⁻¹ and those of the remaining four structures lie in the range 20–40 kcal mol⁻¹. Two most favorable isomers, aC _2v isomer with a dicoordinate oxygen atom, planar six-membered cycle, and one terminal fluorine atom and a pyramidalC _3v isomer with a tricoordinate oxygen atom and three bridging fluorine atoms, are almost degenerate in energy. The barriers to rearrangements with the breaking of one fluorine bridge are no higher than 4 kcal mol⁻¹, except for the pyramidalC _3v isomer (∼16 kcal mol⁻¹). On the contrary, rearrangements with the breaking of the O−Be bond occur with overcoming of a high energy barrier (∼24 kcal mol⁻¹). A planarD _3h isomer with a tricoordinate oxygen atom and linear O−Be−H fragments was found to be the most favorable for the OBe₃H₃ ⁺ cation, a hydride analog of the OBe₃F₃ ⁺ ion; the energies of the remaining five isomers are more than 25 kcal mol⁻¹ higher. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 420–430, March, 1999.     

Theoretical study of structure and properties of hexuronic acid and <Emphasis Type="SmallCaps">d</Emphasis>-glucosamine structural units of glycosaminoglycans

The Becke3LYP functional of DFT theory was used to investigate molecular structure and sodium affinity of the systems CH₃CO₂Na (1), CH₃–O–SO₃Na (2), CH₃–NH–SO₃Na (3), saccharide_1Na₂ (4), saccharide_2Na (5), saccharide_3Na₃ (6), saccharide_4Na₂ (7), and saccharide_5Na₂ (8), respectively, which are models of N- and O-sulfate glycosaminoglycans. Interaction enthalpies, entropies and Gibbs energies of the sodium-coordinated systems in the gas phase were determined with the B3LYP/6-311+G(d,p) and B3LYP/6-31+G(d) methods. The computed Gibbs energies, ΔG ^o , of model systems 1–3 are negative and span a rather broad energy interval (from −500 to −1,500 kJ mol⁻¹). Gibbs interaction energies for sodium acetate, sodium sulfate and sodium sulfamate functions of the five saccharides, systems 4–8 are always lower than those values found for the model compounds 1–3. The ionization of sodium salts of saccharides studied in gas phase is in most cases connected with considerable conformational rearrangement of the ionic species. This rearrangement causes an additional energetic stabilization of anionic species and is connected with the substantial release of entropy.     

Dependence of geminal1H−1H and31P−1H spin-spin coupling constants on the specific intramolecular C−H...X interaction

Participation of the proton in a specific intramolecular C−H...X (X=N, 0) interaction leads to an increase in its geminal¹H−¹H and¹H−³¹P spin-spin coupling constants (SSCC). According toab initio calculations carried out in the 6–31G^** basis set, the observed effect is mainly due to the change in the diamagnetic spin-orbital contribution to SSCC. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 2, pp. 306–309, February, 1997.     

An ab initio Molecular Orbital Study of the Conformational Properties of all-(Z)-Cyclododeca-1,4,7,10-tetraene

Summary.  Ab initio HF/6-31G^* and MP2/6-31G^*//HF/6-31G^* methods were used to calculate the structure optimization and conformational interconversion pathways for all-(Z )-cyclododeca-1,4,7,10-tetraene. This compound adopts the symmetrical crown (C _4v) conformation. Ring inversion takes place via symmetrical intermediates, such as boat-chair (BC, C _s) and twist (C _2h) conformers and requires about 22.3 kJ · mol⁻¹. The calculated strain energies for BC and twist conformers are 5.9 and 13.5 kJ · mol⁻¹. The results of semiempirical AM1 calculations for structural parameters and relative energies of the important geometries of the title compound are in good agreement with the results of ab initio methods. Received July 9, 2001. Accepted September 26, 2001     

Pathways of the reaction of nucleophilic addition of ammonia to formaldehyde in the gas phase and in the complex with formic acid:ab initio calculations

The gradient pathways of the reaction of nucleophilic addition of ammonia to formaldehyde were calculated for free molecules and in the NH₃...H₂CO...HC(O)OH complex by theab initio RHF/6-31G^**, MP2(fc)/6-31G^**, and MP2(full)/6-311++G^** methods. Both reactions proceed concertedly. In the first case, the reaction successively passes through two transitional states with an energy barrier exceeding 35 kcal mol⁻¹. In the case of the complex with formic acid, the reaction follows a conventional pathway, although its activation barrier calculated by the RHF/6-31G^** and MP2(fc)/6-31G^** methods decreases to 12.6 and 3.8 kcal mol⁻¹, respectively. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 13–20, January, 1998.     

A naked-eye,selective and sensitive chemosensor for fluoride ion

Effect of the addition of six different anions on the absorption and fluorescence spectra of acridine yellow G (AYG) was examined. Only the F⁻ anion could induce a visible color change observable with naked eye and a strong fluorescence quenching with K _SV of 8.3 × 10⁴ mol⁻¹ L in CH₃CN solutions. Calculated results of the interaction between the F⁻ anion and acridine yellow G using the B3LYP/6-31G(d) program showed that the intermolecular charge transfer through the formation of an H-bond between AYG and F⁻ is an essential sensor mechanism.