Theoretical model of internal rotation in monosubstituted derivatives of furfural

The present work explores the effect of substitution in all free positions of furfural on conformational preferences of formyl group by using ab-initio calculations at the MP2/6-31G(p,d) level of theory. Theoretical modeling was made in vacuo. The selected substituents were -CH(3), NH(2), NO(2) and F groups in 3, 4, 5 and ipso carbonyl positions. Geometries of all derivatives were analyzed and it is ascertained that substitution has not important consequences on furan ring geometry. Differences of energy between OO-cis and trans conformers and energy barriers between them are described and extreme cases are explained. Interesting features appear in the cases of -NH(2) and -NO(2) groups, and particularly when the 3 and ipso carbonyl positions are substituted. Variations in energy barriers are correlated with variations in C2-C6 distances for the transition states and planar forms. Substitution effect on Mülliken charges are analyzed and related with internal rotation energy barriers and differences between conformers.     

A theoretical study on three conformational structures of 2,6‐distyrylpyridine

Ab initio methods at the levels HF/cc‐pVDZ, HF/6‐31G(d,p), MP2/cc‐pVDZ, and MP2/6‐31G(d,p), as well as methods based on density functional theory (DFT) employing the hybrid functional B3LYP with the basis sets cc‐pVDZ and 6‐31G(d,p), have been applied to study the conformers of 2,6‐distyrylpyridine. Bond distances, bond angles, and dihedral angles have been calculated at the B3LYP level. The calculated values were in good agreement with those measured by X‐ray diffraction analysis of 2,6‐distyrylpyridine. The values calculated using the Hartree‐Fock method and second‐order perturbation theory (MP2) were inconsistent. The optimized lowest‐energy geometries were calculated from the reported X‐ray structural data by the B3LYP/cc‐pVDZ method. Three conformations, A, B, and C, were proposed for 2,6‐distyrylpyridine. Calculations at the three levels of theory indicated that conformation A was the most stable structure, with conformations C and B being higher in energy by 1.10 and 2.57 kcal/mol, respectively, using the same method and basis function. The same trend in the relative energies of the three possible conformations was observed at the two levels of theory and with the different basis sets employed. The reported X‐ray data were utilized to optimize total molecular energy of conformation A at the different calculation levels. The bond lengths, bond angles, and dihedral angles were then obtained from the optimized geometries by ab initio methods and by applying DFT using the two basis functions cc‐pVDZ and 6‐31G(d,p). The values were analyzed and compared. The calculated total energies, the relative energies of the molecular orbitals, the gap between them, and the dipole moment for each conformational structure proposed for 2,6‐distyrylpyridine are also reported. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Conformational analysis of model compounds of vitamin D by theoretical calculations

A conformational analysis of two model compounds of vitamin D was carried out by means of theoretical computations, Ab initio calculations were carried out using the standard 6-31G* basis set at the Hartree–Fock (HF) level of theory. In addition, the Møller–Plesset (MP2) correlation treatment was applied on the simplest model. Semiempirical calculations were also performed using the AM1 Hamiltonian. The results predict stable A-ring twist forms with energies in the order of 4–6 kcal/mol relative to the global minimum, significantly higher than those reported from molecular mechanics calculations. In addition, a folded conformation was found by the HF optimizations; however, its stability is predicted to be very poor. Comparison of the theoretical results with experimental data is discussed. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 1647–1655, 1997     

Equilibrium geometry and gas‐phase proton affinity of 2‐thiouracil derivatives

The ground‐state geometries of uracil, 6‐hydroxy‐uracil, and 6‐hydroxy‐, 6‐amino‐, 6‐methyl‐, 6‐trifluoro‐, and 6‐phenyl‐2‐thiouracil were optimized at the Hartree–Fock level. The molecular structures were fully optimized using the 6‐31G and 6‐31G* basis sets. The effect of substituents on the geometry and electronic structural features of 2‐thiouracils were examined. The perturbation effects of the OH and NH₂ groups are by far more pronounced on the geometric features and the dipole moment magnitude and direction of 2‐thiouracil. The potential energy per atom criteria was used to compare the relative tightness of binding in the studied series. Proton affinity and deprotonation enthalpy on each of the possible sites in 2‐thiouracil and its derivatives have been calculated at the 6‐31G/MP2 level of theory. The obtained results show that thiouracils behave as bases where they possess a high tendency to abstract protons. Substituents in the 6‐position have the general effect of enhancing the basicity strength of the thiocabonyl site in the order Ph < CH3 ≈ NH2 < OH. The CF3 group has the effect of reducing considerably the basicity strength and enhances the acidity strength at both N1 and N3. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

Amphiphilic organic ion pairs in solution: a theoretical study.

The macroscopic manifestation of hydrophobic interactions for amphiphilic organic ion pairs (tetraalkylammonium-anion) has been shown experimentally by measuring their association constants and their affinity with the organic phase. Beyond a certain size, there is a direct relation between association constants and chain lengths in tetraalkylammonium ions. We propose to cast a bridge between these results and geometrical properties considered at the level of a single ion pair by means of quantum chemistry calculations performed on model systems: trimethylalkylammonium-pentyl sulfate instead of tetraalkylammonium-dodecyl sulfate. Two limiting cases are considered: head-to-head configurations, which yield an optimal electrostatic interaction between polar heads, and parallel configurations with a balance between electrostatic and hydrophobic interactions. All properties (geometries, complexation energies, and atomic charges) were obtained at the MP2 level of calculation, with water described by a continuum model (CPCM). Dispersion forces link hydrocarbon chains of tetraalkylammonium ions and pentyl sulfate, thus yielding (for the largest ion pairs) parallel configurations favored with respect to head-to-head geometries by solute-solvent electrostatic interactions. Given the small experimental association energies, we probe the accuracy limit of the MP2 and CPCM methods. However, clear trends are obtained as a function of chain length, which agree with the experimental observations. The calculated monotonic stabilization of ion pairs when the hydrocarbon chain increases in length is discussed in terms of electrostatic interactions (between ions and between ion pairs and water), dispersion forces, and cavitation energies.     

Electronic and steric substituent influences on the conformational equilibria of cyclohexyl esters: the anomeric effect is not anomalous!

The cyclohexyl esters of a series of carboxylic acids, RCO₂H, spanning a range of electronegativities and quotients of steric hindrance for the R substituent (R=Me, Et, iPr, tBu, CF₃, CH₂Cl, CHCl₂, CCl₃, CH₂Br, CHBr₂, and CBr₃) were prepared. Their conformational equilibria in CD₂Cl₂ were examined by low‐temperature ¹H NMR spectroscopy to study the axial or equatorial orientation of the ester functionality with respect to the adopted chair conformation of the cyclohexane ring. The ab initio and DFT geometry‐optimized structures and relative free energies of the axial and equatorial conformers were also calculated at the HF/6‐311G**, MP2/6‐311G**, and B3LYP/6‐31G** levels of theory, both in the gas phase and in solution. In the latter case, a self‐consistent isodensity polarized continuum model was employed. Only by including electron correlation in the modeling calculations for the solvated molecules was it possible to obtain a reasonable correlation between ΔG°_calcd and ΔG°_exp. Both the structures and the free energy differences of the axial and equatorial conformers were evaluated with respect to the factors normally influencing conformational preference, namely, 1,3‐diaxial steric interactions in the axial conformer and hyperconjugation. It was assessed that hyperconjugative interactions, σ_{C? C}/σ_{C? H} and σ*_{C? O}, together with a steric effect—the destabilization of the equatorial conformer with increasing bulk of the R group—were the determinant factors for the position of the conformational equilibria. Thus, because hyperconjugation is held responsible as the mitigating factor for the anomeric effect in 2‐substituted, six‐membered saturated heterocyclic rings, and since it is also similarly responsible, at least partly, in these monosubstituted cyclohexanes for a preferential shift towards the axial conformer, the question is therefore raised: can the anomeric effect really be construed as anomalous?     

A theoretical study of the reaction of HCO+ with C2H2

A theoretical study was performed for the reaction of formyl cation and acetylene to give C₃H+O in flames and C₂H (nonclassical)+CO, both in flames and in interstellar clouds. The corresponding Potential Energy Surface (PES) was studied at the B3LYP/cc‐pVTZ level of theory, and single‐point calculations on the B3LYP geometries were carried out at the CCSD(T)/cc‐pVTZ level. Our results display a route to propynal evolving energetically under C₂H (nonclassical)+CO and, consequently, accessible in interstellar clouds conditions. This route connects the most stable C₃H₃O⁺ isomer (C2‐protonated propadienone) with a species from which propynal may be produced in a dissociative electron recombination reaction. The reaction channel to produce the C₃H+O evolves basically through two TSs and presents an endothermicity of 63.9 kcal/mol at 2000 K. According to our Gibbs energy profiles, the C2‐protonated propadienone is the most stable species at low–moderate temperatures and, consequently, could play a certain role in interstellar chemistry. On the contrary, in combustion chemistry conditions (2000 K) the C₂H (nonclassical)+CO products are the most thermodynamically favored species. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 35–42, 2000     

The gas phase acidity of oligofluorobenzenes and oligochlorobenzenes: about the additivity or non-additivity of substituent effects

The deprotonation energies of benzene, fluorobenzene, all di-, tri-, and tetrafluorobenzenes, pentafluorobenzene, chlorobenzene, all di-, tri-, and tetrachlorobenzenes, and pentachlorobenzene have been calculated at various levels of second-order Moller-Plesset and density functional theory. Taking the previously determined experimental data as a benchmark, good agreement was achieved in the chloro series even with moderate computational effort, whereas more extended basis sets have to be used to obtain meaningful numbers in the fluoro series. Apparently, most extensive electron correlation is required to avoid artifacts caused by the proximity of nonbonding lone pairs at the carbanionic center and at the fluorine atoms. When two or more fluorine substituents were introduced in the same aromatic ring, their individual effects (as defined by position-dependent acidity increments) proved to be perfectly additive in the entire series. In contrast, the acidifying effect of chloro substituents was found to level off when the number of such halogens increases. Additivity or non-additivity of element effects cannot be ascertained after having merely compared the acidity of mono- and disubstituted substrates, but only after having moved to higher degrees of substitution.     

The vibrational and NMR spectra,conformations and ab initio calculations of aminomethylene,propanedinitrile and itsN-methyl derivatives

The IR and Raman spectra of aminomethylene propanedinitrile (AM) [H₂N-CH=C(CN)₂], (methylamino)methylene propanedinitrile (MAM) [CH₃NH-CH=C(CN)₂] and (dimethylamino)methylene propanedinitrile (DMAM) [(CH₃)₂N-CH=C(CN)₂] as solids and solutes in various solvents have been recorded in the region 4000-50 cm^–1. AM and DMAM can exist only as one conformer. From the vibrational and NMR spectra of MAM in solutions, the existence of two conformers with the methyl group orientedanti andsyn toward the double C=C bond were confirmed. The enthalpy difference H ⁰ between the conformers was measured to be 3.7±1.4 kJ mol^–1 from the IR spectra in acetonitrile solution and 3.4±1.1 kJ mol^–1 from the NMR spectra in DMSO solution. Semiempirical (AM1, PM3, MNDO, MINDO3) and ab initio SCF calculations using a DZP basis set were carried out for all three compounds. The calculations support the existence of two conformersanti andsyn for MAM, withanti being 7.8 kJ mol^–1 more stable thansyn from ab initio and 8.6, 13.4, 11.6, and 10.8 kJ mor^–1 from AM1, PM3, MNDO, and MINDO3 calculations, respectively. Finally, complete assignments of the vibrational spectra for all three compounds were made with the aid of normal coordinate calculations employing scaled ab initio force constants. The same scale factors were optimized on the experimental frequencies of all three compounds, and a very good agreement between calculated and experimental frequencies was achieved.     

On the origin of red and blue shifts of X-H and C-H stretching vibrations in formic acid (formate ion) and proton donor complexes.

Complexes between formic acid or formate anion and various proton donors (HF, H(2)O, NH(3), and CH(4)) are studied by the MP2 and B3LYP methods with the 6-311++G(3df,3pd) basis set. Formation of a complex is characterized by electron-density transfer from electron donor to ligands. This transfer is much larger with the formate anion, for which it exceeds 0.1 e. Electron-density transfer from electron lone pairs of the electron donor is directed into sigma* antibonding orbitals of X--H bonds of the electron acceptor and leads to elongation of the bond and a red shift of the X--H stretching frequency (standard H-bonding). However, pronounced electron-density transfer from electron lone pairs of the electron donor also leads to reorganization of the electron density in the electron donor, which results in changes in geometry and vibrational frequency. These changes are largest for the C--H bonds of formic acid and formate anion, which do not participate in H-bonding. The resulting blue shift of this stretching frequency is substantial and amounts to almost 35 and 170 cm(-1), respectively.     

A C‐linked Glycomimetic in the Gas Phase and in Solution: Synthesis and Conformation of the Disaccharide Manα(1,6)‐C‐ManαOPh

The effect of carbon is subtle but sweet : The flexible C‐linkage in the newly synthesised C‐glycosyl mimetic, Manα(1,6)‐C‐ManαOPh allows OH? π bonding, both in the gas phase and in aqueous solution. This interaction is absent in the O‐linked disaccharide (see figure).

     

A theoretical case study of type I and type II beta-turns

NMR chemical shielding anisotropy tensors have been computed by employing a medium size basis set and the GIAO-DFT(B3LYP) formalism of electronic structure theory for all of the atoms of type I and type II beta-turn models. The models contain all possible combinations of the amino acid residues Gly, Ala, Val, and Ser, with all possible side-chain orientations where applicable in a dipeptide. The several hundred structures investigated contain either constrained or optimized phi, psi, and chi dihedral angles. A statistical analysis of the resulting large database was performed and multidimensional (2D and 3D) chemical-shift/chemical-shift plots were generated. The (1)H(alpha-13)C(alpha), (13)C(alpha-1)H(alpha-13)C(beta), and (13)C(alpha-1)H(alpha-13)C' 2D and 3D plots have the notable feature that the conformers clearly cluster in distinct regions. This allows straightforward identification of the backbone and side-chain conformations of the residues forming beta-turns. Chemical shift calculations on larger For-(L-Ala)(n)-NH(2) (n=4, 6, 8) models, containing a single type I or type II beta-turn, prove that the simple models employed are adequate. A limited number of chemical shift calculations performed at the highly correlated CCSD(T) level prove the adequacy of the computational method chosen. For all nuclei, statistically averaged theoretical and experimental shifts taken from the BioMagnetic Resonance Bank (BMRB) exhibit good correlation. These results confirm and extend our previous findings that chemical shift information from selected multiple-pulse NMR experiments could be employed directly to extract folding information for polypeptides and proteins.     

Ab initio study on the electronic structures of styrene in the Franck-Condon region

The electronic structures of styrene in the Franck‐Condon region have been theoretically examined by means of ab initio complete active space self‐consistent field (CASSCF) and the second order multireference Møller‐Plesset calculations. The optimized structure of styrene in S₀ is planar but the torsional motion of the phenyl group is very floppy. The S₁ state is assigned to the local π–π* excitation within the benzene ring. On the other hand, S₂, above S₁ by 0.561 eV, is assigned to a state that resembles the so‐called V‐state of ethylene. The transition intensity of S₀–S₁ is weak, while that of S₀–S₂ is strong. This is in good agreement with the experimental absorption spectrum where the S₀–S₁ and S₀–S₂ transitions are in the energy range of 290–220 nm. The optimized geometry of S₁, characterized by an enlarged benzene ring and its vibrational analyses, further justifies the assignment of the S₁ state. © 2002 Wiley Periodicals, Inc. J Comput Chem 9: 928–937, 2002     

1,3-D,A取代方酸极化率和一阶超极化率的从头算研究

本文在RHF／6-311 G(3d，2p)水平上，对一系列1，3取代方酸衍生物的几何构型进行了全优化，得到分子最稳定构型，并用CPHF方法计算了分子线性极化率和一阶超极化率，分析了取代基对分子线性和非线性光学性质的影响。     

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.     

Structure of the HOOO radical in liquid water: a theoretical study.

The HOOO radical is supposed to play a role in ozone chemistry, both in the gas phase and aqueous media. We discuss the influence of the solvent on the electronic and geometrical structure of this radical using density functional and high-level ab initio calculations together with continuum, discrete, and discrete-continuum solvent models. Solute-solvent electrostatic interactions are shown to be fundamental, and lead to a noticeable stabilization of the radical, which should adopt a trans conformation in aqueous media. In fact, no energy minimum for the cis conformation is predicted in these conditions.     

A theoretical study of anion-pi interactions in seven-membered rings.

Several complexes of tropylium (1) with anions are optimized at the RI-MP2(full)/6-31++G** level of theory. This binding unit can interact very favorably with anions, and it combines the strength of the electrostatic interaction with the directionality of the anion-pi interaction. The complexes of 1 with anions are characterized by means of the Bader theory of "atoms-in-molecules," and the physical nature of the interaction has been analyzed by means of the molecular interaction potential with polarization tool. Experimental evidence of anion-pi interactions involving seven-membered rings has been found in the solid state.     

Probing the Methyl Torsional Barriers of the E and Z Isomers of Butadienyl Acetate by Microwave Spectroscopy

The Fourier transform microwave spectra of the E and Z isomers of butadienyl acetate were measured in the frequency range from 2 to 26.5 GHz under molecular‐jet conditions. The most stable conformer of each isomer, in which all heavy atoms are located in a symmetry plane, was identified after analyzing the spectrum by comparison with the results from quantum‐chemical calculations. The barriers to internal rotation of the acetyl methyl group were found to be 149.1822(20) and 150.2128(48) cm^?1 for the E and Z isomers, respectively, which are similar to that of vinyl acetate. A comparison between two theoretical approaches treating internal rotation, the rho axis method and combined axis method, was also performed. The influence of the alkyl R chain on the methyl torsional barriers in CH₃ ‐COOR acetates was explored.     

Experimental and theoretical multiple kinetic isotope effects for an SN2 reaction. An attempt to determine transition-state structure and the ability of theoretical methods to predict experimental kinetic isotope effects

The secondary alpha-deuterium, the secondary beta-deuterium, the chlorine leaving-group, the nucleophile secondary nitrogen, the nucleophile (12)C/(13)C carbon, and the (11)C/(14)C alpha-carbon kinetic isotope effects (KIEs) and activation parameters have been measured for the S(N)2 reaction between tetrabutylammonium cyanide and ethyl chloride in DMSO at 30 degrees C. Then, thirty-nine readily available different theoretical methods, both including and excluding solvent, were used to calculate the structure of the transition state, the activation energy, and the kinetic isotope effects for the reaction. A comparison of the experimental and theoretical results by using semiempirical, ab initio, and density functional theory methods has shown that the density functional methods are most successful in calculating the experimental isotope effects. With two exceptions, including solvent in the calculation does not improve the fit with the experimental KIEs. Finally, none of the transition states and force constants obtained from the theoretical methods was able to predict all six of the KIEs found by experiment. Moreover, none of the calculated transition structures, which are all early and loose, agree with the late (product-like) transition-state structure suggested by interpreting the experimental KIEs.     

A theoretical study of the structure and bonding of UOX4 (X = F, Cl, Br, I) molecules: the importance of inverse trans influence.

During nitroxide-mediated polymerization (NMP) in the presence of a nitroxide R2(R1)NO*, the reversible formation of N-alkoxyamines [P-ON(R1)R2] reduces significantly the concentration of polymer radicals (P*) and their involvement in termination reactions. The control of the livingness and polydispersity of the resulting polymer depends strongly on the magnitude of the bond dissociation energy (BDE) of the C-ON(R1)R2 bond. In this study, theoretical BDEs of a large series of model N-alkoxyamines are calculated with the PM3 method. In order to provide a predictive tool, correlations between the calculated BDEs and the cleavage temperature (T(c)), and the dissociation rate constant (k(d)), of the N-alkoxyamines are established. The homolytic cleavage of the N-OC bond is also investigated at the B3P86/6-311++G(d,p)//B3LYP/6-31G(d), level. Furthermore, a natural bond orbital analysis is carried out for some N-alkoxyamines with a O-C-ON(R1)R2 fragment, and the strengthening of their C-ON(R1)R2 bond is interpreted in terms of stabilizing anomeric interactions.