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.     

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.     

Tautomeric and conformational properties of benzoylacetone, CH3-C(O)-CH2-C(O)-C6H5: gas-phase electron diffraction and quantum chemical study

Tautomeric and structural properties of benzoylacetone, CH(3)-C(O)-CH(2)-C(O)-C(6)H(5), have been studied by gas-phase electron diffraction (GED) and quantum chemical calculations (B3LYP and MP2 approximation with different basis sets up to aug-cc-pVTZ). Analysis of GED intensities resulted in the presence of 100% enol tautomer at 331(5) K. The existence of two possible enol conformers in about equal amounts is confirmed by both GED and quantum chemical results. In both conformers the enol ring possesses C(s) symmetry with a strongly asymmetric hydrogen bond. The experimental geometric parameters are reproduced very closely by the B3LYP/cc-pVTZ method.     

Tautomeric and conformational properties of acetoacetamide: electron diffraction and quantum chemical study

The tautomeric properties of acetoacetamide, CH3C(O)CH2C(O)NH2, have been investigated by gas electron diffraction (GED) and quantum chemical calculations (B3LYP and MP2 approximations with 6-31G(d,p) and 6-311++G(3df,pd) basis sets). GED results in a mixture of 63(7)% enol tautomer and 37(7)% diketo form at 74(5) degrees C. Only one enol form with the O-H bond adjacent to the methyl group (CH3C(OH)=CHC(O)NH2) and only one diketo conformer (with dihedral angles tau(O=C(CH3)-C-C) = 31.7(7.5) degrees and tau(O=C(NH2)-C(H2)-C(O)) = 130.9(4.5) degrees ) are present. The calculated tautomeric composition varies in a wide range depending on the quantum chemical method and basis set. Only the B3LYP method with small basis sets reproduces the experimental composition correctly.     

Tautomeric and conformational properties of dimethyl malonate, CH3OC(O)-CH2-C(O)OCH3: electron diffraction and quantum chemical study

The geometric structure of dimethyl malonate, CH₃OC(O)-CH₂-C(O)OCH₃, was studied by gas electron diffraction (GED) and quantum chemical methods. We conclude that only diketo conformers exist in the gas phase. According to the GED refinement, a mixture of two diketo conformers is present: 69(10)% (ac,ac) conformer with C₂ symmetry (both CO bonds anticlinal relative to the opposite C-C bond) and 31(10)% (sp,ac) conformer with C₁ symmetry (one CO bond with synperiplanar, the other CO bond with anticlinal orientation). Ab initio calculations, however, predict a preference of the (sp,ac) conformer rather than the (ac,ac) form.     

DFT Studies on Thermal Stabilities,Electronic Structures,and ~（13）C Chemical Shifts of C_（24）O_2 Based on Fullerene C_（24）（D_6）

Quantum chemical calculations on some possible equilibrium geometries of C24O2 isomers derived from C24 (D6) and C24O have been performed using density functional theory (DFT) method. The geometric and electronic structures as well as the relative energies and thermal stabilities of various C24O2 isomers at the ground state have been calculated at the B3LYP/6-31G(d) level of theory. And the 1,4,2,5-C24O2 isomer was found to be the most stable geometry where two oxygen atoms were added to the longest carbon-carbon bonds in the same pentagon from a thermodynamic point of view. Based on the optimized neutral geometries, the vertical ionization potential and vertical electron affinity have been obtained. Meanwhile, the vibrational frequencies, IR spectrum, and 13C chemical shifts of various C24O2 isomers have been calculated and analyzed.     

Computational study of the deamination reaction of cytosine with H2O and OH-

The mechanism for the deamination reaction of cytosine with H(2)O and OH(-) to produce uracil was investigated using ab initio calculations. Optimized geometries of reactants, transition states, intermediates, and products were determined at RHF/6-31G(d), MP2/6-31G(d), and B3LYP/6-31G(d) levels and for anions at the B3LYP/6-31+G(d) level. Single-point energies were also determined at B3LYP/6-31+G(d), MP2/GTMP2Large, and G3MP2 levels of theory. Thermodynamic properties (DeltaE, DeltaH, and DeltaG), activation energies, enthalpies, and free energies of activation were calculated for each reaction pathway that was investigated. Intrinsic reaction coordinate analysis was performed to characterize the transition states on the potential energy surface. Two pathways for deamination with H(2)O were found, a five-step mechanism (pathway A) and a two-step mechanism (pathway B). The activation energy for the rate-determining steps, the formation of the tetrahedral intermediate for pathway A and the formation of the uracil tautomer for pathway B, are 221.3 and 260.3 kJ/mol, respectively, at the G3MP2 level of theory. The deamination reaction by either pathway is therefore unlikely because of the high barriers that are involved. Two pathways for deamination with OH(-) were also found, and both of them are five-step mechanisms. Pathways C and D produce an initial tetrahedral intermediate by adding H(2)O to deprotonated cytosine which then undergoes three conformational changes. The final intermediate dissociates to product via a 1-3 proton shift. Deamination with OH(-), through pathway C, resulted in the lowest activation energy, 148.0 kJ/mol, at the G3MP2 level of theory.     

Structure and conformations of N-(fluoroformyl)imidosulfurous dichloride,FC(O)N=SCl2

The IR (gas) and Raman (liquid) spectra of FC(O)NSCl(2) demonstrate the presence of a conformational mixture in both phases. According to a gas electron diffraction study, the main conformer (94(8)%) possesses a syn-syn structure (C(O)F group synperiplanar with respect to the SCl(2) bisector and the C=O bond synperiplanar to the N=S bond). Quantum chemical calculations (HF, B3LYP and MP2 with 6-31G basis set, and MP2/6-311(2df)) predict a syn-anti structure for the second conformer. Analysis of the IR (gas) spectrum results in a contribution of 5(1)% of the minor form, corresponding to a Gibbs free energy difference DeltaG degrees = G degrees (syn-anti) - G degrees (syn-syn) = 1.75(15) kcal/mol. This value is reproduced very well by quantum chemical calculations, which include electron correlation effects (DeltaG degrees = 1.28-1.56 kcal/mol). The HF approximation overestimates this energy difference (DeltaG degrees = 3.24 kcal/mol).     

CH···O interaction lowers hydrogen transfer barrier to keto-enol tautomerization of β-cyclohexanedione: combined infrared spectroscopic and electronic structure calculation study

Molecular association and keto-enol tautomerization of β-cyclohexanedione (β-CHD) have been investigated in argon matrix and also in a thin solid film prepared by depositing pure β-CHD vapor on a cold (8 K) KBr window. Infrared spectra reveal that, in low-pressure vapor and argon matrix, the molecules are exclusively in diketo tautomeric form. The CH···O hydrogen bonded dimers of the diketo tautomer are produced by annealing the matrix at 28 K. No indication is found for keto-enol tautomerization of β-CHD in dimeric complexes in argon matrix within the temperature range of 8-28 K. On the other hand, in thin film of pure diketo tautomer, the conversion initiates only when the film is heated at temperatures above 165 K. The observed threshold appears to be associated with excitation of the intermolecular modes, and the IR spectra recorded at high temperatures display narrowing of vibrational bandwidths, which has been associated with reorientations of the molecules in the film. The nonoccurrence of tautomerization of the matrix isolated dimer is consistent with the barrier predicted by electronic structure calculations at B3LYP/6-311++G** and MP2/6-311++G** levels of theory. The transition state calculation predicts that CH···O interaction has a dramatic effect on lowering of the tautomerization barrier, from more than 60 kcal/mol for the bare molecule to ~35-45 kcal/mol for dimers.     

Ab initio studies of F−(H2O)n and Cl−(H2O)n clusters for n = 1, 2

Ab initio Hartree–Fock calculations are performed on hydrates of the F^? and Cl^? ions using 6-31G, 6-31G**, and 6-21G basis sets. Geometries and binding energies are obtained. An estimate of the correlation energy is provided by an MP2/6-31G (Møller-Plesset second-order perturbation) calculation. Comparisons are made between the Cl^?(SO₂) and the Cl^?(H₂O) complexes.     

2-(2-巯苯基)苯并噁唑分子内质子转移的理论研究

在B3LYP/6-31G(d,p)水平上研究了2-(2-巯苯基)苯并噁唑气态中五种异构体(E1, E2, E3, E4和K)在气态中的稳定性及其在基态下的质子转移, 同时结合极化连续介质模型(PCM)研究了水、二甲亚砜、乙腈、乙醇、苯胺和环己烷等对2-(2-巯苯基)苯并噁唑溶剂化作用的影响. 研究结果表明, 醇式异构体E1为2-(2-巯苯基)苯并噁唑的优势构型; 在E1向K(酮式异构体)转变过程中, 存在一个较小的能垒; 当考虑零点振动能(ZPVE)后, 逆向能垒消失. 在溶液中, 随着溶剂极性的增强, 醇式异构体E1与K之间的反应平衡向K方向移动, 在非极性溶剂环己烷中, E1为优势构型, 而在强极性水溶液中, K为优势构型.     

S-(fluoroformyl)O-(trifluoroacetyl) thioperoxide, FC(O)S-OC(O)CF3: gas-phase structure and conformational properties

The geometric structure and conformational properties of S-(fluoroformyl)O-(trifluoroacetyl) thioperoxide, FC(O)S-OC(O)CF3, were investigated by gas electron diffraction, matrix isolation infrared spectroscopy, and quantum chemical calculations (B3LYP with the 6-31G and aug-cc-pVTZ basis sets and MP2 with the 6-31G basis set). The experimental methods result in a mixture of two conformers with gauche conformation around the S-O bond. In the main conformer (82(7)% according to GED at 298 K), the C=O bond of the FC(O) group is oriented syn with respect to the S-O bond and phi(C-S-O-C) = 75(3) degrees . In the minor conformer (18(7)%), this C=O is oriented anti. Both conformers possess syn orientation of the C=O bond of the CF3C(O) group. The conformational properties and geometric parameters are reproduced reasonably well by the quantum chemical calculations, except for the S-O bond length, which is predicted too long by 0.04 A (B3LYP/aug-cc-pVTZ).     

Ab initio studies on Al(+)(H(2)O)(n), HAlOH(+)(H(2)O)(n-1), and the size-dependent H(2) elimination reaction

We report computational studies on Al(+)(H(2)O)(n), and HAlOH(+)(H(2)O)(n-1), n = 6-14, by the density functional theory based ab initio molecular dynamics method, employing a planewave basis set with pseudopotentials, and also by conventional methods with Gaussian basis sets. The mechanism for the intracluster H(2) elimination reaction is explored. First, a new size-dependent insertion reaction for the transformation of Al(+)(H(2)O)(n), into HAlOH(+)(H(2)O)(n-1) is discovered for n > or = 8. This is because of the presence of a fairly stable six-water-ring structure in Al(+)(H(2)O)(n) with 12 members, including the Al(+). This structure promotes acidic dissociation and, for n > or = 8, leads to the insertion reaction. Gaussian based BPW91 and MP2 calculations with 6-31G* and 6-31G** basis sets confirmed the existence of such structures and located the transition structures for the insertion reaction. The calculated transition barrier is 10.0 kcal/mol for n = 9 and 7.1 kcal/mol for n = 8 at the MP2/6-31G** level, with zero-point energy corrections. Second, the experimentally observed size-dependent H(2) elimination reaction is related to the conformation of HAlOH(+)(H(2)O)(n-1), instead of Al(+)(H(2)O)(n). As n increases from 6 to 14, the structure of the HAlOH(+)(H(2)O)(n-1) cluster changes into a caged structure, with the Al-H bond buried inside, and protons produced in acidic dissociation could then travel through the H(2)O network to the vicinity of the Al-H bond and react with the hydride H to produce H(2). The structural transformation is completed at n = 13, coincident approximately with the onset of the H(2) elimination reaction. From constrained ab initio MD simulations, we estimated the free energy barrier for the H(2) elimination reaction to be 0.7 eV (16 kcal/mol) at n = 13, 1.5 eV (35 kcal/mol) at n = 12, and 4.5 eV (100 kcal/mol) at n = 8. The existence of transition structures for the H(2) elimination has also been verified by ab initio calculations at the MP2/6-31G** level. Finally, the switch-off of the H(2) elimination for n > 24 is explored and attributed to the diffusion of protons through enlarged hydrogen bonded H(2)O networks, which reduces the probability of finding a proton near the Al-H bond.     

Mechanisms for the deamination reaction of cytosine with H2O/OH(-) and 2H2O/OH(-): a computational study

Mechanisms for the deamination reaction of cytosine with H 2O/OH (-) and 2H 2O/OH (-) to produce uracil were investigated using ab initio calculations. Optimized geometries of reactants, transition states, intermediates, and products were determined at MP2 and B3LYP using the 6-31G(d) basis set and at B3LYP/6-31+G(d) levels of theory. Single point energies were also determined at MP2/G3MP2Large and G3MP2 levels of theory. Thermodynamic properties (Delta E, Delta H, and Delta G), activation energies, enthalpies, and free energies of activation were calculated for each reaction pathway investigated. Intrinsic reaction coordinate (IRC) analysis was performed to characterize the transition states on the potential energy surface. Seven pathways for the deamination reaction were found. All pathways produce an initial tetrahedral intermediate followed by several conformational changes. The final intermediate for all pathways dissociates to product via a 1-3 proton shift. The activation energy for the rate-determining step, the formation of the tetrahedral intermediate for pathway D, the only pathway that can lead to uracil, is 115.3 kJ mol (-1) at the G3MP2 level of theory, in excellent agreement with the experimental value (117 +/- 4 kJ mol (-1)).     

Solid-state structures of 2-(4-hydroxyphenyl)-substituted phenalene-1,3-dione and indan-1,3-dione

The structure of 2-(4-hydroxyphenyl)-substituted indan-1,3-dione and phenalene-1,3-dione is investigated using a combination of solid-state NMR, single crystal X-ray analyses and quantum chemical calculations. It is shown that 2-(4-hydroxyphenyl)-1,3-indandione exists as a diketo tautomer while 2-(4-hydroxyphenyl)-1,3-phenalenedione exists in the enol form.     

Tautomeric and conformational equilibrium of 2-nitrosophenol and 9,10-phenanthrenequinonemonooxime: ab initio and NMR study

The tautomeric and conformational equilibrium of 2-nitrosophenol and 9,10-phenanthrenequinonemonooxime was studied by ab initio methods. The geometry optimizations of the structures investigated were done without any geometrical restrictions at HF/6-31G** and MP2/6-31G** levels of theory. The transition structures for tautomeric and rotameric conversions were located. To correct for electron correlation, single-point calculations were carried out up to MP4/6-311G*//MP2/6-31G* level of theory.

Ab initio calculations for 2-nitrosophenol in agreement with the available experimental data define the nitroso form as more stable. It was found that the influence of the correlation energy on the relative stabilities is smaller for the rotamers of the nitroso tautomer but substantially (4–6 kcal/mol) for the oxime forms. It was found that the barrier height of tautomerization reaction is 10.24 kcal/mol.

The structure of the 9,10-phenanthrenequinonemonooxime was studied by solid and liquid state NMR spectroscopy. Ab initio calculations in agreement with our experimental data predict that the compound exists as oxime tautomer and the syn-oxime is most stable. It was found that the solvent influence on the relative stabilities of both isomers: syn- and anti-oxime. While in chloroform solution the syn-oxime is preferred but in DMSO anti-oxime is more stable in energy.

At the MP4/6-311G*//MP2/6-31G**+ZPE level of theory the barrier of tautomerization was predicted to be 10.96 kcal/mol and the rotational barrier around the single C–O bond in the syn-oxime was found to be 7.57 kcal/mol. The rotation is facile and this explains the absence of nitroso tautomers in solution.     

Tautomerism and Regioselectivity of the Protonation of 2-Pyrrolidone. Stereoselectivity of Complexation between Palladium(II), Chloride Ion,and 2-Pyrrolidone

According to the AM1, PM3, HF/6-31G(d,p), and MP2/6-31G(d,p)//HF/6-31G(d,p) calculations, it is the lactam tautomer of 2-pyrrolidone that is thermodynamically most stable in both the gas phase and an aqueous solution. Analysis of the PM3 data with consideration of the medium showed that the tautomeric equilibrium of 2-pyrrolidone (pyrroline-2-ol) in aqueous solution is shifted to the lactim form, which thus can be involved in complexation with palladium(II). 2-Pyrrolidone was found to be protonated at the O atom in both the gas phase and aqueous solution, in agreement with the concept of the mesomeric displacement of the electron density in the amide fragment. The aqueous medium stabilizes the lactim tautomer of 2-pyrrolidone more strongly than the lactam tautomer and the O-protonated cyclic amide than the N-protonated one. The stereoselectivity of complexation between palladium(II), chloride ion, and pyrroline-2-ol was explained. The initially formed tetragonal-pyramidal adduct with an axial organic ligand undergoes rearrangement into an intermediate with an extra axial Cl atom, which is a precursor of the cis-product. The thermodynamically less stable cis-isomer of the complex [PdCl₂(pyrrolin-2-ol)₂] is formed from the thermodynamically most favorable intermediate in associative nucleophilic substitution. At the supramolecular level, the cis-product can be stabilized by intermolecular dipole-dipole association in the crystal.__________Translated from Koordinatsionnaya Khimiya, Vol. 31, No. 7, 2005, pp. 523–529.Original Russian Text Copyright © 2005 by Pankratov, Borodulin, Chaplygina.     

Trifluoromethanesulfenyl acetate, CF3S-OC(O)CH3, and trifluoromethanesulfenyl trifluoroacetate, CF3S-OC(O)CF3: unexpected conformational properties

Structural and conformational properties of two sulfenyl derivatives, trifluoromethanesulfenyl acetate, CF3S-OC(O)CH3 (1), and trifluoromethanesulfenyl trifluoroacetate, CF3S-OC(O)CF3 (2), were determined by gas electron diffraction, vibrational spectroscopy, in particular with IR (matrix) spectroscopy, which includes photochemical studies, and by quantum chemical calculations. Both compounds exist in the gas phase as a mixture of two conformers, with the prevailing component possessing a gauche structure around the S-O bond. The minor form, 15(5)% in 1 and 11(5)% in 2 according to IR(matrix) spectra, possesses an unexpected trans structure around the S-O bond. The C=O bond of the acetyl group is oriented syn with respect to the S-O bond in both conformers. UV-visible broad band irradiation of 1 and 2 isolated in inert gas matrixes causes various changes to occur. Conformational randomization clearly takes place in 2 with simultaneous formation of CF3SCF3. For 1 the only reaction channel detected leads to the formation of CH3SCF3 with the consequent extrusion of CO2. Quantum chemical calculations (B3LYP/6-31G and MP2 with 6-31G and 6-311G(2df,pd) basis sets) confirm the existence of a stable trans conformer. The calculations reproduce the conformational properties for both compounds qualitatively correct with the exception of the B3LYP method for compound 2 which predicts the trans form to be prevailing, in contrast to the experiment.