Crystal Structure and Quantum Chemical Ab Initio Calculations of Ibotenic Acid,an Excitatory Amino Acid Receptor Agonist

Ibotenic acid, a constituent of Amanita muscaria, is a potent NMDA receptor agonist. The structure of the ibotenic acid zwitterion monohydrate in the crystalline state has been determined by X-ray crystallography. The crystal structure has two ibotenic acid monohydrate formula units in the asymmetric unit and features an extensive hydrogen bond network. The ibotenic acid zwitter-ions in the crystalline state are compared to the in vacuo structure calculated by quantum chemical ab initio calculations at the HF/6-31+G* level and the effects of the hydrogen bond network on the structures in the solid state are discussed. The calculated potential energy curve with respect to side-chain orientation displays a single energy minimum. The conformations corresponding to the solid-state conformations are calculated to be ca. 2 kcal/mol higher in energy than the minimum-energy conformation in vacuo.     

Ab initio calculations of methionines and their protonated forms

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

Molecular structure,conformational mobility,vibrational spectra,and thermochemistry of peroxyacetic acid: an ab initio and density functional study

The structure of the peroxyacetic acid (PAA) molecule and its conformational mobility under rotation about the peroxide bond was studied by ab initio and density functional methods. The free rotation is hindered by the trans-barrier of height 22.3 kJ mol^–1. The equilibrium molecular structure of AcOOH (C _s symmetry) is a result of intramolecular hydrogen bond. The high energy of hydrogen bonding (46 kJ mol^–1 according to natural bonding orbital analysis) hampers formation of intermolecular associates of AcOOH in the gas and liquid phases. The standard enthalpies of formation for AcOOH (–353.2 kJ mol^–1) and products of radical decomposition of the peroxide — AcO^· (–190.2 kJ mol^–1) and AcOO^· (–153.4 kJ mol^–1) — were determined by the G2 and G2(MP2) composite methods. The O—H and O—O bonds in the PAA molecule (bond energies are 417.8 and 202.3 kJ mol^–1, respectively) are much stronger than in alkyl hydroperoxide molecules. This provides an explanation for substantial contribution of non-radical channels of the decomposition of peroxyacetic acid. The electron density distribution and gas-phase acidity of PAA were determined. The transition states of the ethylene and cyclohexene epoxidation reactions were located (E _a = 71.7 and 50.9 kJ mol^–1 respectively).     

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

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

Ab initio calculation of the band structure of some boron polymers

Ab initio calculations using a STO-3G basis set have been performed on the polymer systems (HBX) _n where X = Be, BH, CH₂, NH, and O. Energy band diagrams and accompanying density-of-states plots have been obtained. The highest filled orbital of (HBNH) _n and (HBO) _n occurs at the X-point and possesses character while the - framework orbital at the X- point is the highest filled level for (HBBe) _n , (HBBH) _n , and (HBCH₂) _n . The conduction band for all five species has symmetry and the band gap of the (HBX) _n species increases in the order X = Be < BH < NH < O < CH₂. An estimate of the energy of polymerisation of the (HBX) _n systems suggests that HBNH is particularly stabilised by polymerisation. The electron distribution in (HBBe) _n shows a - electron drift towards boron, while in the other four systems the net electron transfer is directed away from boron. There is significant electron back-donation to boron in (HBO) _n and (HBNH) _n .     

Alkylhydrazides and their protonated forms: Physical methods andab initio calculations

The basicity of hydrazides of the highest aliphatic carboxylic acids RC(O)NHNH₂ (R = C_nH_2n+1,n = 5-12) has been studied by potentiometric titration, and IR and¹H NMR spectroscopy.Ab initio Hartree-Fork calculations using the 6–31G^* basis set with full optimization of geometry were carried out on the simplest acy1hydrazines and their possible protonated forms. Based on these calculations, and the 1R and¹H NMR spectra, the tautomerism of alkylhydrazides and the structures of their protonated forms are discussed.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 11, pp. 2645–2649, November, 1996.     

FTIR and FT-Raman spectra, assignments, ab initio HF and DFT analysis of xanthine

The molecular vibrations of xanthine were investigated in polycrystalline sample, at room temperature by Fourier transform infrared (FTIR) and FT-Raman spectroscopies. The spectra of the molecule have been recorded in the regions 4000-50 cm(-1) and 3500-100 cm(-1), respectively. Theoretical information on the optimized geometry, harmonic vibrational frequencies, infrared and Raman intensities were obtained by means of ab initio Hartree-Fock (HF) and density functional theory (DFT) gradient calculations with complete relaxation in the potential energy surface using 6-311++G(d,p) basis set. The vibrational frequencies which were determined experimentally from the spectral data are compared with those obtained theoretically from ab initio and DFT calculations. A close agreement was achieved between the observed and calculated frequencies by refinement of the scale factors. The infrared and Raman spectra were also predicted from the calculated intensities. Thermodynamic properties like entropy, heat capacity, zero point energy have been calculated for the molecule. Unambiguous vibrational assignment of all the fundamentals was made using the potential energy distribution (PED).     

Molecular and electronic structures of anionic σ-complexes of 9-nitroanthracene and its derivatives studied byab initio HF/6-31G** calculations

The molecular structures of anionic σ-complexes of 9-nitroanthracene and its 10-methoxy and 10-acetonyl derivatives were calculated by theab initio quantum-chemical HF/6-31G^** method. The central ring of the anthracene fragment adopts a boat conformation. The values of the bond lengths and bond orders in the compounds under study indicate that the contribution of theaci-resonance form to the structure of the nitro group is substantially larger than that estimated for 2,4,6-trinitrobenzene derivatives. The substituents have no substantial effect on the geometry of the anion. The negative charge is localized mainly on the oxygen atoms of the nitro group and of the substituents. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 11, pp. 2142–2145, November, 1998.     

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.     

Electronic structure and reactivity of S—S dications

The electronic structure and reactivity of some S—S dications were studied at the MP2/6-31G* level of theory. The results obtained indicate a stepwise electrophilic addition of disulfonium dication moiety to the double C=C bond to be the preferable mechanism.     

Scopolamine and atropineN-methyl diastereomer stability.Ab initio calculations onO-formylscopine andO-formyltropine model compounds

Ab initio geometry optimizations at the RHF-21G basis set level were calculated forequatorial andaxial N-methyl diastereomers ofO-formyltropine andO-formylscopine esters and other model compounds. These optimized geometries were then utilized as input for single-point energy calculations using the higher level RHF/6-31G^* basis set to afford a more precise estimation of the total energies and atomic charges. Ethano bridge pinching of theN-protonated tropanyl piperidine moiety pushes the smalleraxial N-proton closer toward the neighboring twoaxial C-H bonds compared with the analogous case for a bulkyaxial N-methyl. Increasedcis 1,3-diaxial interactions in theaxial N-methyl diastereomer destabilize this epimer in favor of theequatorial N-methyl counterpart [e.g., 2.121 kcal/mol lower energy for theequatorial N-methylO-formyltropineN-protonated diastereomer (12) than for theaxial epimer (13)]. Lower pyramidality at nitrogen in the free base maintains the relative stability of theequatorial N-methyl free base diastereomer (14) (1.120 kcal/mol more stable than theaxial free base15). A nonprotonated carbon atom at the apex of a three-membered ring fused to the 6,7-positions of theO-formyltropine skeleton results in severe transannular nonbonding steric interactions involving the neighboringequatorial N-methyl group inN-protonated16 (3.335 kcal/mol less stable than theaxial N-methyl epimer17, where these transannular interactions are reduced due to the smallerequatorial N-H proton). Oxygen atom occupation of the apex of a similar fused three-membered ring retains the same severe transannular nonbonding steric interactions involving the neighboringequatorial N-methyl group inN-protonated18. These transannular interactions now become electrostatically attractive in theN-protonatedaxial N-methyl epimer19 (2.031 kcal/mol more stable than theequatorial epimer). Reduced pyramidality at nitrogen in theO-formylscopine free base reduces the repulsive transannular interaction with the neighboringequatorial N-methyl group compared to that in theN-protonated form. Lowered pyramidality also reduces thecis-1,3-diaxial interactions in theaxial N-methyl epimer, but the nitrogen lone pair is pushed close to the transannular oxygen lone pair as a result (theequatorial N-methyl free base20 is 3.870 kcal/mol more stable than theaxial epimer21). Theseab initio-calculated models ofO-formyltropines andO-formylscopineN-methyl diastereomeric protonated cations and free bases provide stereochemical insight into the relative stabilities of solution-state atropine and scopolamineN-methyl species previously observed by NMR spectroscopic methods.     

Ab initio investigation of tautomeric stability,molecular structure,and internal rotation of methylphosphonic dicyanide,methoxydicyanophosphine, and their isocyano analogs

The equilibrium geometric parameters and structures of the transition states of internal rotation for MeP(O)(CN)₂, McOP(CN)₂, and their isocyano analogs, MeP(O)(NC)₂ and MeOP(NC)₂, have been calculated by theab initio SCF method and with inclusion of electron correlation effects according to the second-order Muuller-Plesset perturbation theory (MP2). At both levels the 6-31G* basis set has been used. The estimation of relative stability of these tautomeric forms depends largely on the calculation level. The total energies of the cyanides calculated by the MP2 method are 25–30 kcal mol^–1 lower than those of the corresponding isocyanides. The oxo-tautomeric forms containing four-coordinate phosphorus are 15–25 kcal mol^–1 more stable than the three-coordinate phosphorus aci-derivatives. The internal rotation potential curves of the aci-forms are characterized by a deep minimum for thetrans-arrangement of the methoxy group and phosphorus lone electron pair. Two additional less clearly pronounced minima are located symmetrically on both sides of the weak maximum, which corresponds to thecis-arrangement. The equilibrium oxo-form structures have a staggered configuration of the methyl group with respect to the phosphorus atom bonds.Translated from izvestiyaAkademii Nauk. Seriya Khimicheskaya, No. 5, pp. 1104–1115, May, 1996.     

Ab initio calculations of activation energy of the reaction of hydrogen exchange on strongly acidic centers

Ab initio calculations of fragments of the potential energy surfaces of hydrogen exchange reactions between H₂, CH₄, and alanine molecules and the H₃O⁺ ion were performed by the restricted Hartree-Fock method, at the second-order Møller-Plesset level of perturbation theory, and by the method of coupled clusters using the 6–31G^* and aug-cc-pVDZ basis sets. The one-center synchronous mechanism of hydrogen exchange reaction was studied and the activation energies and structures of transition states were determined. It was found that the geometric parameters of the H₂ and CH₄ molecules in the transition states are close to those of the H₃ ⁺ and CH₅ ⁺ ions. The higher the proton affinity of the reacting molecule in the reaction studied the lower the activiation energy of hydrogen exchange. The one-center mechanism studied can be used to describe the high-temperature solid-state catalytic isotope exchange (HSCIE) reaction. The results ofab initio calculations of synchronous hydrogen exchange between the H₃O⁺ ion and hydrogen atoms in different positions of the alanine molecule are in good agreement with experimental data on the regioselectivity and stereoselectivity of the HSCIE reaction with spillover-tritium.     

Molecular structure and decomposition mechanism of peracetic acid esters AcOOR (R = Me,Bu<Superscript>t</Superscript>)

The molecular structure and conformational mobility of methyl and tert-butyl esters of peracetic acid AcOOR (R = Me (1), Bu^t (2)) were studied by the ab initio MP4(SDQ)//MP2(FC)/6-31G(d,p) method and density functional B3LYP/6-31G(d,p) approach. The B3LYP calculated equilibrium conformations of the molecules are characterized by the C-O-O-C torsion angles of 93.6° (1) and 117.0° (2). Structural features of the molecules under study and a distortion of tetrahedral bond configuration at the C_α atom were explained using the natural bonding orbital approach. The standard enthalpies of formation of AcOOMe (−328.5 kJ mol⁻¹) and AcOOBu^t (−440.4 kJ mol⁻¹) were determined using the G2 and G2(MP2) computational schemes and the isodesmic reaction approach. The transition state of AcOOMe decomposition into AcOOH and formaldehyde was calculated (E _a = 122.8 kJ mol⁻¹). The thermal effects of homolytic decomposition of the peroxy esters following a concerted mechanism (Me^· + CO₂ + ^·OR) and simple homolysis of the peroxide bond (AcO^· + ^·OR) were found to be 97.5±0.3 and 155.1±0.3 kJ mol⁻¹, respectively. At temperatures below 400 K, the most probable decomposition mechanism of peroxy esters 1 and 2 involves simple homolysis of the O-O bond.__________Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 10, pp. 2021–2027, October, 2004.     

Molecular structure and conformational transitions of dichloroacetylchloride

RHF and MP2 techniques in 6–31G(d) basis set have been used to determine the structure of the isolated molecule CHCl₂COCl in two stable conformations (cis-and gosh-), as well as in transition states arising due to the rotary motion of CHCl₂ group around the C—C bond. The energy gap between the conformers and the relevant potential barriers has been calculated using the obtained potential dependence of the internal rotation. Plausible conformation of dichloroacetylchloride is discussed on the basis of ³⁵Cl NQR.     

Conformational flexibility and aromaticity of azanaphthalenes

Conformational flexibility of naphthalene and its different mono-and diaza analogues has been studied by MP2/6-31G(d, p) quantum chemical computations. It is shown that all molecules possess a considerable conformational flexibility. The out-of-plane deformation energy of both a bicyclic π-system on the whole and separate rings directly depends on the degree of aromaticity of the conjugated system. Effects of the amount and arrangement of nitrogen atoms on conformational features and aromaticity of the molecules considered were analyzed.     

Crystal structure and ab initio calculations of a cyano-carbamimidic acid ethyl ester

The structure of one tautomer (amine form) of cyano-carbamimidic acid ethyl ester or (amino-ethoxy-methylidene)aminoformonitrile (CAS: 13947-84-7) was determined by single crystal X-ray diffraction. Ab initio quantum chemical calculations at the B3LYP, MP2 and G3 levels were performed to investigate the stability and the formation of the different tautomers and conformers. The calculations indicate that the amine form is the more stable tautomer, showing a high degree of electron conjugation. The most stable amine conformer located by the calculations corresponds to the crystallized structure. On the contrary, in the less stable imine form, the conjugation is separated by a N2–C2 single bond.     

Comparative Study of the Structure of Rhodanine, Isorhodanine, Thiazolidine-2,4-dione, and Thiorhodanine

Ab initio (HF and MP2 level) and semiempirical (AM1, PM3, MNDO) calculations on the relative stabilities and structures of the potential tautomeric forms of rhodanine, isorhodanine, thiazolidine-2,4-dione, and thiorhodanine are reported. Ab initio calculations predict that the thiooxo, oxothio, dioxo, and dithio tautomers are the most stable. These results correspond to the known experimental data. Infrared spectra of the investigated compounds were recorded for the region 4000-150 cm^-1, and the characteristic bands were compared with ab initio calculated frequencies at the HF/3-21G^(*)* level.     

Gas electron diffraction study of the geometric structure of triallylborane molecule

The main structural parameters of the triallylborane molecule having the C ₃ symmetry were determined by gas electron diffraction and quantum-chemical calculations at the MP2/6-31G(d,p) and B3LYP/6-31G(d,p) levels. The parameters calculated by the MP2/6-31G(d,p) method are in better agreement with the experimental data than those calculated by the B3LYP/6-31G(d,p) method.__________Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 98–101, January, 2005.