Trichloromethyl chloroformate ("diphosgene"), ClCOOCCl3: structure and conformational properties in the gaseous and condensed phases

The conformational properties of gaseous trichloromethyl chloroformate (or "diphosgene"), ClC(O)OCCl3, have been studied by vibrational spectroscopy [IR (gas), IR (matrix), and Raman (liquid)] and quantum chemical calculations (MP2 and B3LYP with 6-311G basis sets); in addition, the structure of a single crystal at low temperature has been determined by X-ray diffraction. ClC(O)OCCl3 exhibits only one conformational form having Cs symmetry with a synperiplanar orientation of the C-O single bond relative to the C=O double bond. The calculated energy difference between the syn and anti forms, 5.73 kcal mol(-1) (B3LYP) or 7.06 kcal mol(-1) (MP2), is consistent with the experimental findings for the gas and liquid phases. The crystalline solid at 150 K [monoclinic, P2(1)/n, a = 5.5578(5) angstroms, b = 14.2895(12) angstroms, c = 8.6246(7) angstroms, beta = 102.443(2) degrees, Z = 4] likewise consists only of molecules in the syn form.     

Predicting the binding capability of benzothiazoline-2-thione and its derivatives with gold: a DFT and FT-Raman combined studies

The activities of chemical systems can be evaluated successfully by combining vibrational spectroscopic analysis and quantum chemical calculation based on density functional theory (DFT). Two tautomers of 5-fluorobenzo[d]thiazole-2(3H)-thione (FBTT), 7H-[1,3]dioxolo[4',5',4,5]benzo[1,2-d]thiazole-6-thione (DBTT) and 5-chloro-6-methylbenzo[d]thiazole-2(3H)-thione (CMBTT) were investigated by FT-Raman spectroscopy and DFT calculations at B3LYP/6-311+G** level. The molecular properties and activity relationships were determined by the HOMO energies, Mulliken charges and the binding energies with metal. It is concluded that three derivatives exhibited stable conformation of the thione form both in the isolated powder monomers and in their complexes with gold. The binding capability with gold was in the order of DBTT>BTT approximately CMBTT>FBTT. The derivatives with the electron-donor substitutes in benzene ring were favorable to metal for the p-pi conjugate effect.     

C(Ar)-H···O hydrogen bonds in substituted isobenzofuranone derivatives: geometric, topological, and NMR characterization

Substituted isobenzofuranone derivatives 1a-3a and bindone 4 are characterized by the presence of an intramolecular C(Ar)-H···O hydrogen bond in the crystal (X-ray), solution ((1)H NMR and specific and nonspecific IEF-PCM solvation model combined with MP2 and B3LYP methods), and gas (MP2 and B3LYP) phases. According to geometric and AIM criteria, the C(Ar)-H···O interaction weakens in 1a-3a (independent of substituent nature) and in 4 with the change in media in the following order: gas phase > CHCl(3) solution > DMSO solution > crystal. The maximum value of hydrogen bond energy is 4.6 kcal/mol for 1a-3a and 5.6 kcal/mol for 4. Both in crystals and in solutions, hydrogen bond strength increases in the order 1a < 2a < 3a with the rising electronegativity of the ring substituents (H < OMe < Cl). The best method for calculating (1)H NMR chemical shifts (δ(calcd) - δ(expl) < 0.7 ppm) of hydrogen bonded and nonbonded protons in 1a-3a and 1b-3b (isomers without hydrogen bonds) is the GIAO method at the B3LYP level with the 6-31G** and 6-311G** basis sets. For the C-H moiety involved in the hydrogen bond, the increase of the spin-spin coupling constant (1)J((13)C-(1)H) by about 7.5 Hz is in good agreement with calculations for C-H bond shortening and for blue shifts of C-H stretching vibrations (by 55-75 cm(-1)).     

Noble gas-transition-metal complexes: coordination of VO2 and VO4 by Ar and Xe atoms in solid noble gas matrixes

The matrix isolation infrared spectroscopic and quantum chemical calculation results indicate that vanadium oxides, VO2 and VO4, coordinate noble gas atoms in forming noble gas complexes. The results showed that VO2 coordinates two Ar or Xe atoms and that VO4 coordinates one Ar or Xe atom in solid noble gas matrixes. Hence, the VO2 and VO4 molecules trapped in solid noble gas matrixes should be regarded as the VO2(Ng)2 and VO4(Ng) (Ng = Ar or Xe) complexes. The total V-Ng binding energies were predicted to be 12.8, 18.2, 5.0, and 7.3 kcal/mol, respectively, for the VO2(Ar)2, VO2(Xe)2, VO4(Ar), and VO4(Xe) complexes at the CCSD(T)//B3LYP level of theory.     

A combined experimental and theoretical approach for structural study on a new cinnamoyl derivative of 2-acetyl-1,3-indandione and its metal(II) complexes

The synthesis, structure and spectral properties of a new cinnamoyl derivative of 2-acetyl-1,3-indandione (2AID), p-fluoro-cinnamoyl-1,3-indandione, LH and its metal(II) complexes with Cu(II), Zn(II) and Cd(II), are described. In order to verify the molecular structure of the free ligand and its metal complexes, model geometries based on the spectroscopic data were optimized using quantum chemical methods. The experimental spectroscopic data (IR and NMR) of the ligand, LH, complemented by the calculated ones, show that it exists in the exocyclic enolic form in the gas phase, solution and solid state. Good quality single crystals of Cd(II) complex were obtained from a DMSO solution and were studied by means of single-crystal X-ray diffraction. The data show bidentate coordination of the ligand and two DMSO molecules coordinated to the metal centre, thus forming a complex with octahedral geometry. On the contrary, the spectroscopic data on the amorphous samples indicate a square planar geometry of the Cu(II) complex and distorted octahedral geometry for Zn(II) and Cd(II) complexes with two water molecules coordinated to the metal centre. The used quantum chemical method for structure optimization of the transition metal complexes, B3LYP/LANL2DZ, shows very good agreement with the crystallographic data and, therefore, was also employed for structural determination for the non-crystalline complexes. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Vibrational spectra and gas-phase structure of N-methyl-S,S-bis(trifluoromethyl)sulfimide, CH3N=S(CF3)2

The molecular structure of N-methyl-S,S-bis(trifluoromethyl)sulfimide, CH3N=S(CF3)2, was determined by gas electron diffraction and quantum chemical calculations [B3LYP and MP2 with 6-31+G(2df,p) basis sets]. Furthermore, vibrational spectra, IR (gas) and Raman (liquid), were recorded. These spectra were assigned by comparison with analogous molecules and with calculated frequencies and intensities (HF, B3LYP, and MP2 with 6-311G basis sets). All experimental data and computational methods result in a single conformer with syn orientation of the CH3 group relative to the bisector of the two CF3 groups. The molecule possesses C1 symmetry, slightly distorted from CS symmetry. The N=S bond length in this compound [1.522(10) A] is longer than that in imidosulfur difluorides RN=SF2 [1.476(4) A - 1.487(5) A].     

Molecular structure and conformations of para-methylbenzene sulfonamide and ortho-methylbenzene sulfonamide: gas electron diffraction and quantum chemical calculations study

The molecular structure and conformational properties of para-methylbenzene sulfonamide (4-MBSA) and ortho-methylbenzene sulfonamide (2-MBSA) have been studied by gas electron diffraction (GED) and quantum chemical methods (B3LYP/6-311+G** and MP2/6-31G**). Quantum chemical calculations predict the existence of two conformers for 4-MBSA with the S-N bond perpendicular to the benzene plane and the NH2 group either eclipsing or staggering the S-O bonds of the SO2 group. Both conformers possess CS symmetry. The eclipsed form is predicted to be favored by DeltaE = 0.63 kcal/mol (B3LYP) or 1.00 kcal/mol (MP2). According to the calculations, the S-N bond in 2-MBSA can possess planar direction opposite the methyl group (phi(C2C1SN) = 180 degrees ) or nonplanar direction (phi(C2C1SN) approximately 60 degrees ). In both cases, the NH2 group can adopt eclipsed or staggered orientation, resulting in a total of four stable conformers. The nonplanar eclipsed conformer (C1 symmetry) and the planar eclipsed form (CS symmetry) are predicted to be favored. According to the GED analysis, the saturated vapor over solid 4-MBSA at T = 151(3) degrees C consists as mixture of the eclipsed (78(19) %) and staggered (22(19) %) forms. The saturated vapor over solid 2-MBSA at T = 157(3) degrees C consists as a mixture of the nonplanar eclipsed (69(11) %) and planar eclipsed (31(11) %) forms.     

Structural and conformational properties of fluoroformic acid anhydride, FC(O)OC(O)F

The conformational properties and geometric structures of fluoroformic acid anhydride, FC(O)OC(O)F, have been studied by vibrational spectroscopy, gas electron diffraction (GED), single-crystal X-ray diffraction, and quantum chemical calculations (HF, MP2, and B3LYP methods with 6-31G* and B3LYP/6-311+G* basis sets). Satellite bands in the IR matrix spectra, which increase in intensity when the matrix gas mixture is heated prior to deposition as a matrix, indicate the presence of two conformers at room temperature. According to the electron diffraction analysis, the prevailing conformer is of C(2) symmetry with both C=O bonds synperiplanar with respect to the opposite C-O bond ([sp, sp] conformer). The minor conformer [15(5)% from IR matrix and 6(11)% from GED] is predicted by quantum chemical calculations to possess an [sp, ac] structure. FC(O)OC(O)F crystallizes in the orthorhombic system in the space group P2(1)2(1)2(1) with a = 6.527(1) angstroms, b = 7.027(1) angstroms, and c = 16.191(1) angstroms and four formula units per unit cell. In the crystal, only the [sp, sp] conformer is present, and the structural parameters are very similar to those determined by GED.     

Tautomeric and conformational properties of malonamic acid methyl ester, NH2C(O)-CH2-C(O)OCH3: electron diffraction and quantum chemical study

The tautomeric and conformational properties of malonamic acid methyl ester, NH2C(O)-CH2-C(O)OCH3, have been investigated by means of gas-phase electron diffraction (GED) and quantum chemical calculations (HF, B3LYP, and MP2 approximations with different basis sets up to 6-311++G(3df,pd)). Both quantum chemistry and GED at 360(8) K result in the existence of a single diketo conformer in the gas phase. According to GED refinement, this conformer possesses an (ac, sc) conformation with dihedral angles C-C-C(NH2)=O of 140.3(3.0) degrees and C-C-C(OCH3)=O of 31.1(7.2) degrees. The experimental geometric parameters are reproduced very closely by MP2 and B3LYP methods with large basis sets.     

Structural study and thermal behavior of novel interaction product of 4-amino-5-(furan-2-yl)-4H-1,2,4-triazole-3-thione with molecular iodine

Abstract

As a part of investigation of thyreostatic activity of mercapto-substituted triazoles, the structure, spectroscopic properties of 4-amino-5-(furan-2-yl)-4H-1,2,4-triazole-3-thione were obtained. 4-amino-5-(furan-2-yl)-4H-1,2,4-triazole-3-thione forms steady charge-transfer complex in dilute chloroform solution, coordinating one iodine molecule (lgβ?=?3.47). The reaction product of 4-amino-5-(furan-2-yl)-4H-1,2,4-triazole-3-thione is presented by uncharged adduct: C₆H₆N₄OS·I₂. The crystal structure of the adduct was studied in detail by single crystal X-ray diffraction. The results of thermogravimetric analysis revealed the stability of adduct in a solid state at the temperature range 50–500?°C.     

Toward an intimate understanding of the structural properties and conformational preference of oxoesters and thioesters: gas and crystal structure and conformational analysis of dimethyl monothiocarbonate, CH3OC(O)SCH3

[structure: see text] The molecular structure and conformational properties of dimethyl monothiocarbonate, CH3OC(O)SCH3, have been studied in the gas phase by gas electron diffraction (GED) and vibrational spectroscopy and in the solid state by X-ray crystallography. The experimental investigations were supplemented by quantum chemical calculations at the B3LYP/6-311++G(3df,2p) and MP2/6-311++G(2df,p) levels of approximation. The gaseous molecule exhibits only one conformation having Cs symmetry with synperiplanar orientation of both the C-S and the C-O single bonds relative to the C=O double bond. The following skeletal geometric parameters were derived from the GED analysis (r(hl) values with 3sigma uncertainties): C=O = 1.203(4) A, C(sp(2))-O = 1.335(5) A, C(sp(3))-O = 1.437(5) A, C(sp(2))-S = 1.763(5) A, and C(sp(3))-S = 1.803(5) A; O=C-O = 125.9(8) degrees , O=C-S = 125.7(7) degrees , O-C-S = 108.4(9) degrees , and C-O-C = 113.4(15) degrees . The structure of a single crystal, grown by a miniature zone-melting procedure, was determined by X-ray diffraction analysis at a low temperature. The crystalline solid [monoclinic, P2(1)/n, a = 12.6409(9) A, b = 4.1678(3) A, and c = 19.940(1) A, beta = 98.164(1) degrees ] exists exclusively as molecules in the synperiplanar conformation and with geometrical parameters that agree with those of the molecule in the gas phase. The results are discussed in terms of anomeric and mesomeric effects and in terms of a natural bond orbital analysis.     

X-Ray, MP2 and DFT studies of the structure and vibrational spectra of homarinium chloride

The effects of hydrogen bonding, inter- and intramolecular electrostatic interactions on the structure of homarinium chloride, HOMH·Cl, in the crystal and its isolated molecule have been studied by X-ray diffraction, FT-IR, Raman, ¹H and ¹³C NMR spectroscopies, and by the MP2 and DFT theoretical methods. In the crystal, the Cl⁻ anion is connected with protonated homarine via the O–HCl⁻ hydrogen bond of the length of 2.937(4) Å, and two N⁺Cl⁻ intermolecular electrostatic interactions. In the isolated molecule, according to the MP2 and B3LYP calculations, the Cl⁻ anion is engaged in a shorter hydrogen bond (O–HCl⁻ of 2.811–2.861 Å) and in one type of intramolecular electrostatic interactions. The calculated bond lengths and bond angles at the MP2 and B3LYP levels of theory are in good agreement with the X-ray data, except the conformation of the COOH group, which is cis (syn) in the crystal and trans (anti) in the isolated molecule. The tentative assignments for the experimental solid state vibrational spectra of HOMH·Cl and HOMD·Cl have been made on the basis of the B3LYP/6-31G(d,p) calculated frequencies and intensities. The effect of quaternization of picolinic acid on the chemical shifts of the ring protons and carbons is analyzed.     

((Fluoroformyl)imido)sulfuryl difluoride, FC(O)N=S(O)F2: structural, conformational, and configurational properties in the gaseous and condensed phases

Structural, conformational, and configurational properties of the gaseous molecule ((fluoroformyl)imido)sulfuryl difluoride, FC(O)N=S(O)F(2), have been studied by vibrational spectroscopy (IR (gas) and Raman (liquid)) and quantum chemical calculations (HF, MP2, and B3LYP with 6-31+G* and 6-311+G* basis sets); in addition, the solid-state structure has been determined by X-ray crystallography. FC(O)N=S(O)F(2) exists in the gas phase as a mixture of a favored antiperiplanar-synperiplanar form (the S=O double bond antiperiplanar with respect to the C-N single bond, and the C=O group synperiplanar with respect to the S=N double bond) in equilibrium with less abundant antiperiplanar-antiperiplanar, synclinal-synperiplanar, and synclinal-antiperiplanar structures. The crystalline solid at 163 K (monoclinic, P2(1)/c, a = 5.1323(7) A, b = 15.942(2) A, c = 16.798(2) A, beta = 95.974(3) degrees , Z = 12) consists of three similar antiperiplanar-synperiplanar forms.     

Conformations of silicon-containing rings. 5. Conformational properties of 1-methyl-1-silacyclohexane: gas electron diffraction,low-temperature NMR,and quantum chemical calculations

The molecular structure of 1-methyl-1-silacyclohexane 3 has been determined by gas electron diffraction (GED). The conformational preference of the methyl group was studied experimentally in the gas phase (GED) and in solution (low-temperature (13)C NMR) and by quantum chemical calculations (HF, MP2, and B3LYP with 6-31G basis sets and mPW1PW91/6-311G(2df,p)). Both experimental methods result in a preference of the equatorial position of the methyl group, 68(7)% in the gas phase at 298 K and 74(1)% in solution at 110 K. The calculations predict 68-73% equatorial conformer at room temperature. From coalescence temperatures, Gibbs free energies of activation for ring inversion DeltaG++ (eq --> ax) = 5.81(18) and DeltaG++ (ax --> eq) = 5.56(18) kcal mol(-1) were derived. The calculated values for DeltaG++ (eq --> ax) are 5.92 (B3LYP) and 5.84 kcal mol(-1) (mPW1PW91).     

Thermochemistry of Lewis adducts of BH3 and nucleophilic substitution of triethylamine on NH3BH3 in tetrahydrofuran

The thermochemistry of the formation of Lewis base adducts of BH(3) in tetrahydrofuran (THF) solution and the gas phase and the kinetics of substitution on ammonia borane by triethylamine are reported. The dative bond energy of Lewis adducts were predicted using density functional theory at the B3LYP/DZVP2 and B3LYP/6-311+G** levels and correlated ab initio molecular orbital theories, including MP2, G3(MP2), and G3(MP2)B3LYP, and compared with available experimental data and accurate CCSD(T)/CBS theory results. The analysis showed that the G3 methods using either the MP2 or the B3LYP geometries reproduce the benchmark results usually to within ~1 kcal/mol. Energies calculated at the MP2/aug-cc-pVTZ level for geometries optimized at the B3LYP/DZVP2 or B3LYP/6-311+G** levels give dative bond energies 2-4 kcal/mol larger than benchmark values. The enthalpies for forming adducts in THF were determined by calorimetry and compared with the calculated energies for the gas phase reaction: THFBH(3) + L → LBH(3) + THF. The formation of NH(3)BH(3) in THF was observed to yield significantly more heat than gas phase dative bond energies predict, consistent with strong solvation of NH(3)BH(3). Substitution of NEt(3) on NH(3)BH(3) is an equilibrium process in THF solution (K ≈ 0.2 at 25 °C). The reaction obeys a reversible bimolecular kinetic rate law with the Arrhenius parameters: log A = 14.7 ± 1.1 and E(a) = 28.1 ± 1.5 kcal/mol. Simulation of the mechanism using the SM8 continuum solvation model shows the reaction most likely proceeds primarily by a classical S(N)2 mechanism.     

Are AM1 ligand‐protein binding enthalpies good enough for use in the rational design of new drugs?

We have examined the performance of semiempirical quantum mechanical methods in solving the problem of accurately predicting protein-ligand binding energies and geometries. Firstly, AM1 and PM3 geometries and binding enthalpies between small molecules that simulate typical ligand-protein interactions were compared with high level quantum mechanical techniques that include electronic correlation (e.g., MP2 or B3LYP). Species studied include alkanes, aromatic systems, molecules including groups with hypervalent sulfur or with donor or acceptor hydrogen bonding capability, as well as ammonium or carboxylate ions. B3LYP/6-311+G(2d,p) binding energies correlated very well with the BSSE corrected MP2/6-31G(d) values. AM1 binding enthalpies also showed good correlation with MP2 values, and their systematic deviation is acceptable when enthalpies are used for the comparison of interaction energies between ligands and a target. PM3 otherwise gave erratic energy differences in comparison to the B3LYP or MP2 approaches. As one would expect, the geometries of the binding complexes showed the known limitations of the semiempirical and DFT methods. AM1 calculations were subsequently applied to a test set consisting of "real" protein active site-ligand complexes. Preliminary results indicate that AM1 could be a valuable tool for the design of new drugs using proteins as templates. This approach also has a reasonable computational cost. The ligand-protein X-ray structures were reasonably reproduced by AM1 calculations and the corresponding AM1 binding enthalpies are in agreement with the results from the "small molecules" test set.     

Tautomeric and conformational properties of malonamide, NH2C(O)-CH2-C(O)NH2: electron diffraction and quantum chemical study

The geometric structure of malonamide, NH2C(O)-CH2-C(O)NH2, has been investigated by gas electron diffraction (GED) and quantum chemical calculations (B3LYP and MP2 approximations with 6-311++G(3df,pd) basis sets). Both GED and quantum chemistry result in the existence of a single diketo conformer in the gas phase. According to GED refinement this conformer possesses (sc,ac) conformation with one C=O bond in synclinal orientation (dihedral angle tau(O=C-C-C)=49.0(3.0) degrees) and the other C=O bond in anticlinal orientation (dihedral angle tau(O=C-C-C)=139.5(3.3) degrees). The experimental geometric parameters are reproduced very closely by the B3LYP method.     

Zwitterionic spirocycles based on dinitrobenzofurazan and tropolone heteroanalogs

Zwitterionic spirocyclic σ-complexes were synthesized by reaction of 7-chloro-4,6-dinitrobenzofurazan with 2-(benzylamino)cyclohepta-2,4,6-trien-1-one, 2-(benzylamino)cyclohepta-2,4,6-triene-1-thione, and N-benzyl-7-(benzylimino)cyclohepta-1,3,5-trien-1-amine. The structure, stereodynamics, and stability of the spirocycles were studied by NMR spectroscopy, X-ray analysis, and DFT quantum chemical calculations at the B3LYP/6-31G** level of theory. The contribution of heteroatoms to positive charge delocalization and the thermodynamic and kinetic stabilities of the spirocycles increase in the series aminotropone < aminothiotropone < aminotropone imine.     

Synthesis and spectral studies of organotin(IV) 4-amino-3-alkyl-1,2,4-triazole-5-thionates: in vitro antimicrobial activity

Some di- and triorganotin(IV) triazolates of general formula, R(4-n)SnLn (where n=2; R=Me, n-Bu and Ph; n=1; R=Me, n-Pr, n-Bu and Ph and HL=4-amino-3-methyl-1,2,4-triazole-5-thiol (HL-1); and 4-amino-3-ethyl-1,2,4-triazole-5-thiol (HL-2)) were synthesized by the reaction of R(4-n)SnCln with sodium salt of HL-1 and HL-2. The bonding and coordination behavior in these derivatives have been discussed on the basis of IR and 119Sn M?ssbauer spectroscopic studies in the solid state. Their coordination behavior in solution is discussed by multinuclear (1H, 13C and 119Sn) NMR spectral studies. The IR and 119Sn M?ssbauer spectroscopic studies indicate that the ligands, HL-1 and HL-2 act as a monoanionic bidentate ligand, coordinating through Sexo- and Nring. The distorted skew trapezoidal-bipyramidal and distorted trigonal bipyramidal geometries have been proposed for R2SnL2 and R3SnL, respectively, in the solid state. In vitro antimicrobial screening of some of the newly synthesized derivatives and of some di- and triorganotin(IV) derivatives of 3-amino-1,2,4-triazole-5-thiol (HL-3) and 5-amino-3H-1,3,4-thiadiazole-2-thiol (HL-4) along with two standard drugs such as fluconazole and ciprofloxacin have been carried out against the bacteria, viz. Staphylococcus aureus and Escherichia coli, and against some fungi, viz. Aspergillus fumigatus, Candida albicans, Candida albicans (ATCC 10231), Candida krusei (GO3) and Candida glabrata (HO5) by the filter paper disc method. The studied organotin(IV) compounds show mild antifungal activity as compared to that of fluconazole, however, they show almost insignificant activity against the studied Gram-positive (Staphylococcus aureas) and Gram-negative (Escherichia coli) bacteria as compared to that of standard drug, ciprofloxacin.     

Conformational properties of penicillins: quantum chemical calculations and molecular dynamics simulations of benzylpenicillin

Herein, we present theoretical results on the conformational properties of benzylpenicillin, which are characterized by means of quantum chemical calculations (MP2/6-31G* and B3LYP/6-31G*) and classical molecular dynamics simulations (5 ns) both in the gas phase and in aqueous solution. In the gas phase, the benzylpenicillin conformer in which the thiazolidine ring has the carboxylate group oriented axially is the most favored one. Both intramolecular CH. O and dispersion interactions contribute to stabilize the axial conformer with respect to the equatorial one. In aqueous solution, a molecular dynamics simulation predicts a relative population of the axial:equatorial conformers of 0.70:0.30 in consonance with NMR experimental data. Overall, the quantum chemical calculations as well as the simulations give insight into substituent effects, the conformational dynamics of benzylpenicillin, the frequency of ring-puckering motions, and the correlation of side chain and ring-puckering motions.