Full MP2 study of solvent implicit and explicit effect on tautomers of Dithio-Biuret

Dithio biuret conformers were optimised and frequency calculations were performed at MP2/6–311++G(d,p) level of theory. Classification of conformers was done to five different tautomers and the most stable conformer of each tautomer was selected. Tautomer 3 having trans conformation of amino and thiocarbonyl functional group was the most stable tautomer in the gas phase. Optimisation and frequency calculations were also done in four different solvents as follows: benzene, acetonitrile, DMSO and water. Stability of tautomers were compared in these solvents to explore effect of polarity on stabilisation of tautomers. Inter-conversion of selected tautomers was investigated both in the gas phase and in four different media. Results showed that when solvent is used as an implicit media, it has negligible effect on proton transfer. Water-explicit effect was also investigated and the results exhibited high dependency of proton transfer mechanism on water molecules when they participate in breaking and formation of bonds.     

DFT and MP2 study of simple and water-assisted tautomerism in amidrazones

DFT and MP2 methods were used to calculate structural parameters, vibrational modes, solvent effect, and energetic properties of amidrazones. Amidrazones can be presented by three tautomeric forms and six isomers. All tautomers and transition states were optimized at the B3LYP/6-311++g** and MP2/6-311++G** levels of theory. The relative stabilities of amidrazone isomers in the gas phase were found to be as 1Z > 1E > 2E > 2Z > 3E > 3Z > TS(1–2) > TS(1–3). The calculated energy differences between E and Z isomers are very low and between different tautomers are nearly low, but the energy barriers for tautomerism interconversions at the gas phase are high. The kinetic and thermodynamic data in solvents (chloroform, tetrahydrofuran, acetone, and water) are nearly similar to those in the gas phase but their rate constants are slightly less than those in the gas phase. Moreover, equilibrium and rate constants of intermolecular tautomerism in presence of 1–3 molecules of water were calculated. Computed energy barriers show that the barrier energy of water-assisted tautomerism is very lower than that in simple tautomerism and also calculated binding energies show that water can stabilize transition states more than tautomers. Therefore, this water-assisted tautomerism can be performed fast, especially with the assistance of two molecules of water.     

Study on the conformational equilibrium of the alanine dipeptide in water solution by using the averaged solvent electrostatic potential from molecular dynamics methodology

The ASEP/MD method has been employed for studying the solvent effect on the conformational equilibrium of the alanine dipeptide in water solution. MP2 and density functional theory (DFT) levels of theory were used and results were compared. While in gas phase cyclic structures showing intramolecular hydrogen bonds were found to be the most stable, the stability order is reversed in water solution. Intermolecular interaction with the solvent causes the predominance of extended structures as the stabilizing contacts dipeptide-water are favoured. Free-energy differences in solution were calculated and PPII, α(R), and C5 conformers were identified as the most stable at MP2 level. Experimental data from Raman and IR techniques show discrepancies about the relative abundance of α(R) y C5, our results support the Raman data. The DFT level of theory agrees with MP2 in the location and stability of PPII and α(R) forms but fails in the location of C5. MP2 results suggest the possibility of finding traces of C7eq conformer in water solution, in agreement with recent experiments.     

Solvent effects on the infrared spectra of beta-alkoxyvinyl methyl ketones I. Carbonyl and vinyl stretching vibrations

Infrared spectroscopy studies of six beta-alkoxyvinyl methyl ketones, with common structure R(1)O-CR(2)CH-COR(3), where R(1)=R(3)=CH(3), R(2)=H (1); R(1)=C(2)H(5), R(2)=H (2); R(3)=CF(3); R(1)=R(2)=CH(3), R(3)=CF(3) (3); R(1)=C(2)H(5), R(2)=C(6)H(5), R(3)=CF(3) (4); R(1)=C(2)H(5), R(2)=4-O(2)NC(6)H(4), R(3)=CF(3) (5); R(1)=C(2)H(5), R(2)=C(CH(3))(3), R(3)=CF(3) (6) in 11 pure organic solvents of different polarity were undertaken to investigate the solute-solvent interactions and to correlate solvent properties by means of linear solvation energy relationships (LSER) with the carbonyl and vinyl stretching vibrations of existing stereoisomeric forms. It was shown that contrary to simple carbonyl-containing compounds where solvent HBD acidity (alpha) has the largest influence on the nu (CO) band shift to lower wavenumbers, the dipolarity/polarizability (pi) term plays the main role in the interactions of conjugated enones with solvent molecules leading to the nu (CO) and nu (CC) bathochromic band shifts. The trifluoroacetyl group possesses a reduced ability to form hydrogen bonds with solvents. For the nu (CC) band of non-fluorinated enone 1 solvent HBD acidity (alpha) and solvent HBA basicity term (beta) play a perceptible role, whereas for 2 these terms are not significant. beta-Substituents in fluorinated enones such as R(2)=H, C(6)H(5), and C(CH(3))(3) assist in the intermolecular hydrogen bond formation of the carbonyl moiety with HBD solvents, while beta-substituents such as CH(3) and 4-NO(2)C(6)H(4) prevent the CO group to form the H-bonds with HBD solvents (the solvent HBD acidity term (alpha) is not significant). The comparison of four conformers of the enone 1 reveals that (EEE) form is the most polarizable conformer; the influences of the solvent dipolarity/polarizability (pi) and solvent HBD acidity (alpha) term on the bathochromic nu (CO) band shift are opposite to one another.     

Application of DFT and MP2 calculations on structural and water-assisted proton transfer in 3-amino-4-nitrofurazan

Density functional theory (DFT) and MP2 calculations have been employed to study of 3-amino-4-nitrofurazan molecule using the standard 6-311++G(d,p) basis set. The chemical properties of the 3-amino-4-nitrofurazan have been extensively studied. The geometries of molecules in the gas phase were optimized and compared with the crystallography of this substance. The results suggest that A form is the most stable form in the gas phase and it is the predominant tautomer in solution according to the DFT and MP2 calculations, respectively. In addition, variation of dipole moments in the gas phase, the specific solvent effects with addition of one molecule of water near the electrophilic centers of tautomers, the transition state of proton transfer assisted by a water molecule, the NBO charges of atoms and the potential energy surface were investigated. The calculated highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) are presented.     

Brønsted basicities of diamines in the gas phase, acetonitrile, and tetrahydrofuran

A comprehensive basicity study of alpha,omega-alkanediamines and related bases has been carried out. Basicities in acetonitrile (AN, pK(a) values), tetrahydrofuran (THF, pK(alpha) values), and gas phase (GP, GB values), were measured for 16, 14, and 9 diamine bases and for several related monoamines. In addition the gas-phase basicities and equilibrium geometries were computed for 19 diamino bases and several related monoamines at the DFT B3LYP 6-311+G** level. The effects of the different factors (intrinsic basicity of the amino groups, formation of intramolecular hydrogen bonds, and molecular strain) determining the diamine basicities were estimated by using the method of isodesmic reactions. The results are discussed in terms of molecular structure and solvation effects. The GP basicity is determined by the molecular size and polarizability, the extent of alkylation, and the energy effect of intramolecular hydrogen bond formation in the protonated base. The basicity trends in the solvents differ very much from those in GP: 1) The solvents severely compress the basicity range of the bases studied (3.5 times for the 1,3-propanediamine family in AN, and 7 times in THF), and 2) while stepwise alkylation of the basicity center leads to a steady basicity increase in the gas phase, the picture is complex in the solvents. Significant differences are also evident between THF and AN. The high hydrogen bond acceptor strength of THF leads to this solvent favoring the bases with "naked" protonation centers. In particular, the basicity order of N-methylated 1,3-propanediamines is practically inverse to that in the gas phase. The picture in AN is intermediate between that of GP and THF.     

The tautomerism of 1,2,3-triazole, 3(5)-methylpyrazole and their cations

The annular tautomerism of 1,2,3-triazole and 3(5)-methylpyrazole is discussed by means of a combination of theoretical calculations and experimental (ICR) gas-phase basicities and acidities. In the gas phase 1,2,3-triazole exists as the 2H-tautomer, whereas both tautomers of 3(5)-methylpyrazole are of similar energy. The solvent effects on these prototropic equilibria are discussed taking into account solvent properties as polarity/polarizability, acidity, and basicity. In nonhydrogen bonding solvents, the difference in dipole moments between both tautomers plays a role that has usually been underestimated.     

Solvent effects on the S0(1(1)Ag-) --> S2(1(1)Bu+) transition of beta-carotene, echinenone, canthaxanthin, and astaxanthin in supercritical CO2 and CF3H

Solvent-induced spectral shifts of the four C40 carotenoids, beta-carotene, echinenone, canthaxantin, and astaxanthin, have been studied in supercritical CO2 and CF3H. In situ absorption spectroscopic analysis was used to determine the maximum peak position of the electronic transitions from the ground state (1(1)Ag-) to the S2 state (1(1)Bu+) of the carotenoids. The medium polarizability function, R(n) = (n2 - 1)/(n2 + 2) of the refractive index of the solvent was varied over the range R(n) = 0.08-0.14, by changing the pressure of CO2 or CF3H between 90 and 300 bar at the temperature 308 K. For all the carotenoids studied here, a significant hypsochromic shift of ca. 20-30 nm was observed in supercritical fluids as compared to that in nonpolar liquids. The spectral shifts in supercritical fluids were compared with those in liquids and showed a clear linear dependence on the medium polarizability. The temperature-dependent shift of the absorption maxima was less significant. Interestingly, there was almost no difference in the energetic position of the absorption maxima in supercritical CO2 and CF3H at a given R(n) value. This is in contrast to previous extrapolations from studies in liquids at larger R(n) values, which yielded different slopes of the R(n)-dependent spectral shifts for polar and nonpolar solvents toward the gas-phase limit of R(n) = 0. The current experimental results in the gas-to-liquid range show that the polarity of the solvent has only a minor influence on the 1(1)Ag- --> 1(1)Bu+ transition energy in the region of low R(n). We also obtain more reliable extrapolations of this 0-0 transition energy to the gas-phase limit nu(0-0)(gas-phase) approximately (23,000 +/- 120) cm(-1) for beta-carotene.     

DFT and MP2 Calculations on Tautomers and Water-Assisted Proton Transfer on 1,2,5-Oxadiazol-4,3-diamine

In this work a detailed quantum-chemical comparison of the relative stability of six tautomers of 1,2,5-oxadiazol-4,3-diamine studied in the gas phase and solution. Theoretical calculations are carried out by the density functional theory (DFT/B3LYP) and MP2 methods using the standard 311++G(d,p) basis set. The results indicate that A is the most stable form in the gas phase and also is the predominant tautomer in solution at the DFT and MP2 methods. The transition states of proton transfer reaction are calculated. The variation of dipole moments and charges on atoms are studied in various solvent. Specific solvent effects with addition of one water molecule near the electrophilic centers of tautomer investigated. Also the transition state of proton transfer assisted by a water molecule was investigated.     

Conformation-changing aggregation in hydroxyacetone: a combined low-temperature FTIR, jet, and crystallographic study

Aggregation in hydroxyacetone (HA) is studied using low-temperature FTIR, supersonic jet expansion, and X-ray crystallographic (in situ cryocrystallization) techniques. Along with quantum chemical methods (MP2 and DFT), the experiments unravel the conformational preferences of HA upon aggregation to dimers and oligomers. The O-H···O═C intramolecular hydrogen bond present in the gas-phase monomer partially opens upon aggregation in supersonic expansions, giving rise to intermolecular cooperatively enhanced O-H···O-H hydrogen bonds in competition with isolated O-H···O═C hydrogen bonds. On the other hand, low-temperature IR studies on the neat solid and X-ray crystallographic data reveal that HA undergoes profound conformational changes upon crystallization, with the HOCC dihedral angle changing from ~0° in the gas phase to ~180° in the crystalline phase, hence giving rise to a completely new conformation. These conclusions are supported by theoretical calculations performed on the geometry derived from the crystalline phase.     

Conformational analysis of 2-acetylcyclopentanone by the density functional and MP2 methods

Two-dimensional potential energy surfaces for internal rotation of the acetyl substituent and inversion of the five-membered ring in the gas phase and in acetonitrile were constructed by the B3LYP/6-31G(d) method for the diketo form of the 2-acetylcyclopentanone (2-ACPN) molecule. The diketo form of 2-ACPN exists in the gas phase and in low-polarity cyclohexane as a mixture of four rotamers K1, K2, K3, and K4. The fifth isomeric form K3a exists in polar acetonitrile. The estimation of the tautomeric composition of 2-ACPN taking into account the influence of the cyclohexane medium in the framework of the polarizable continuum model (PCM) using the MP 2/cc-pVTZ method agrees better with experimental data than the estimate obtained by the B3LYP/cc-pVTZ method. The constants of the enol-enol and keto-enol tautomeric equilibria of the 2-ACPN tautomers in solutions of aprotic solvents were estimated.     

Calculation of relative energies of permethylated oligosilane conformers in vapor and in alkane solution

The geometries of 35 conformers of Me(SiMe2)nMe (n = 4, 1; n = 5, 2; n = 6, 3; n = 7, 4) were optimized at the MP2/VTDZ level, and CCSD(T) single-point calculations were done at three MP2/VTDZ conformer geometries of 1. The relative ground-state energies of the conformers of 1-4 in the gas phase were obtained from the MP2/VTDZ electronic energy, zero-point vibrational energy, and thermal corrections at 0, 77, and 298 K. Relative energies in an alkane solvent at 77 and 298 K were obtained by the addition of solvation energies, obtained from the SM5.42R model. The calculated energies of 26 of the conformers (n = 4-6) have been least-squares fitted to a set of 15 additive increments associated with each Si-Si bond conformation and each pair of adjacent bond conformations, with mean deviations of 0.06-0.20 kcal/mol. An even better fit for the energies of 24 conformers (mean deviations, 0.01-0.09 kcal/mol) has been obtained with a larger set of 19 increments, which also contained contributions from selected combinations of conformations of three adjacent bonds. The utility of the additive increments for the prediction of relative conformer energies in the gas phase and in solution has been tested on the remaining nine conformers (n = 6, 7). With the improved increment set, the average deviation from the SM5.42R//MP2 results for solvated conformers at 298 K was 0.18 kcal/mol, and the maximum error was 0.98 kcal/mol.     

Retention of C60 and C70 fullerenes on reversed-phase high-performance liquid chromatographic stationary phases.

The separation of C60 and C70 fullerenes on four different polysiloxane stationary phases was examined. It was determined that polar solvents can be used as mobile phases effectively for the separation of fullerene molecules. Unlike previously published work, a polymeric octadecyl siloxane (ODS) stationary phase provided higher separation factors for C70/C60 than did monomeric ODS stationary phases or phenyl substituted stationary phases. For example, for a methanol-diethyl ether (50:50, v/v) mobile phase and C60, k' approximately 5.0 separation factors, alpha = 3.3, were achieved with polymeric ODS compared to alpha = 2.2, with a monomeric ODS stationary phase. A linear solvation energy relationship (LSER) was used to model the importance of solvent interactions and stationary phase interaction to solute retention.     

Theoretical study of the elimination kinetics of several 2-substituted ethyl N,N-dimethylcarbamates in the gas phase, [(CH3)2NCOOCH2CH2Z, Z=CH2Cl, C≡CH, C≡N]

The theoretical studies of the gas-phase elimination of 2-substituted ethyl N,N-dimethylcarbamates (Z=CH₂Cl, C≡CH, C≡N) were performed using ab initio MP2/6-31G and MP2/6-31G(d) levels of theory. The gas phase elimination reaction of these carbamates yields N,N-dimethylcarbamic acid and the corresponding substituted olefin in a rate-determining step. The intermediate N,N-dimethylcarbamic acid is unstable and rapidly decomposes through a four-membered cyclic transition state to dimethylamine and CO₂ gas. The results of these calculations suggest a mechanism to be concerted, asynchronous, and a six-membered cyclic transition state structure. Plotting the relative theoretical rate coefficients against Taft's σ* values gave an approximate straight line (ρ*=0.4057, r=0.9894 at 360 °C). The correlation between experimental log k_rel vs. theoretical log k_rel. for these 2-substituted ethyl N,N-dimethylcarbamates gave an approximate straight line (r=0.9715 at 360 °C), suggesting the same type of mechanism.     

Ab initio study of hydrogen-bond formation between aliphatic and phenolic hydroxy groups and selected amino acid side chains

Hydrogen bonding was studied in 24 pairs of isopropyl alcohol and phenol as one partner, and water and amino-acid mimics (methanol, acetamide, neutral and protonated imidazole, protonated methylalamine, methyl-guanidium cation, and acetate anion) as the other partner. MP2/6-31+G* and MP2/aug-cc-pvtz calculations were conducted in the gas phase and in a model continuum dielectric environment with dielectric constant of 15.0. Structures were optimized in the gas phase with both basis sets, and zero-point energies were calculated at the MP2/6-31+G* level. At the MP2/aug-cc-pvtz level, the BSSE values from the Boys-Bernardi counterpoise calculations amount to 10-20 and 5-10% of the uncorrected binding energies of the neutral and ionic complexes, respectively. The geometry distortion energy upon hydrogen-bond formation is up to 2 kcal/mol, with the exception of the most strongly bound complexes. The BSSE-corrected MP2/aug-cc-pvtz binding energy of -27.56 kcal/mol for the gas-phase acetate...phenol system has been classified as a short and strong hydrogen bond (SSHB). The CH3NH3+...isopropyl alcohol complex with binding energy of -22.54 kcal/mol approaches this classification. The complete basis set limit (CBS) for the binding energy was calculated for twelve and six complexes on the basis of standard and counterpoise-corrected geometry optimizations, respectively. The X...Y distances of the X-H...Y bridges differ by up to 0.03 A as calculated by the two methods, whereas the corresponding CBS energy values differ by up to 0.03 kcal/mol. Uncorrected MP2/aug-cc-pvtz hydrogen-bonding energies are more negative by up to 0.35 kcal/mol than the MP2/CBS values, and overestimate the CCSD(T)/CBS binding energies generally by up to 5% for the eight studied complexes in the gas phase. The uncorrected MP2/aug-cc-pvtz binding energies decreased (in absolute value) by 11-18 kcal/mol for the ionic species and by up to 5 kcal/mol for the neutral complexes when the electrostatic effect of a polarizable model environment was considered. The DeltaECCSD(T) - DeltaEMP2 corrections still remained close to their gas-phase values for four complexes with 0, +/-1 net charges. Good correlations (R2 = 0.918-0.958) for the in-environment MP2/aug-cc-pvtz and MP2/6-31+G* hydrogen-bonding energies facilitate the high-level prediction of these energies on the basis of relatively simple MP2/6-31+G* calculations.     

Conformational preferences for some 5-substituted 2-acetylthiophenes through infrared spectroscopy and theoretical calculations

The s-cis-trans isomerisms of some derivatives of thiophene (2-acetyl, AT; 2-acetyl-5-bromo, ABT and 2-acetyl-5-chloro, ACT) were analyzed, using data from deconvolution of their carbonyl absorption bands in two solvents (CCl4 and CHCl3). These infrared data showed that the O,S-cis conformer largely predominates in the studied solvents and that the same occurs in the gas phase, as observed from theoretical calculations. The latter results were obtained using B3LYP/6-311++G(3df,3p) and MP2/6-311++G(3df,3p) levels of theory, with zero-point energy correction. Moreover, the use of the IEFPCM (Integral Equation Formalism Polarizable Continuum Model) to take into account the solvent effects, using the same levels of theory, confirmed the results observed from infrared data. Low temperature 13C NMR spectra in CS2/CD2Cl2 (-90 °C) and in acetone-d6 (-80°C) did not show pairs of signals for each carbon, due to the known low energy barrier (～8 kcal mol(-1)) for the cis-trans interconversion. Data from NBO calculations show that the nO(2)→σS-C5* and nO(2)→σC2-C3* interactions occur only in the O,S-cis isomer and can explain its conformational preference.     

Theoretical study of hydrogen bonding in homodimers and heterodimers of amide, boronic acid, and carboxylic acid, free and in encapsulation complexes

The homodimers and the heterodimers of two amides, two boronic acids, and two carboxylic acids have been calculated in the gas phase and in N,N-dimethylformamide (DMF) and CCl(4) solvents using the DFT (M06-2X and M06-L) and the MP2 methods in conjunction with the 6-31G(d,p) and 6-311+G(d,p) basis sets. Furthermore, their pairwise coencapsulation was studied to examine its effect on the calculated properties of the hydrogen bonds at the ONIOM[M06-2X/6-31G(d,p);PM6], ONIOM[MP2/6-31G(d,p); PM6], and M06-2X/6-31G(d,p) levels of theory. The present work is directed toward the theoretical rationalization and interpretation of recent experimental results on hydrogen bonding in encaptulation complexes [D. Ajami et al. J. Am. Chem. Soc. 2011, 133, 9689-9691]. The calculated dimerization energy (ΔE) values range from 0.74 to 0.35 eV for the different dimers in the gas phase, with the ordering carboxylic homodimers > amide-carboxylic dimers > amide homodimers > boronic-carboxylic dimers > amide-boronic dimers > boronic homodimers. In solvents, generally smaller ΔE values are calculated with only small variations in the ordering. In the capsule, the ΔE values range between 0.67 and 0.33 eV with practically the same ordering as in the gas phase. The calculated % distributions of the encapsulated dimers, taking into account statistical factors, are in agreement with the experimental distribution, where the occurrence of boronic homodimer dominates, even though it is calculated to have the smallest ΔE.     

A semi-empirical and ab initio combined approach for the full conformational searches of gaseous lysine and lysine–H2O complex

A full structural search of the canonical, zwitterionic, protonated and deprotonated lysine conformers in gas phase is presented. A total of 17,496 canonical, 972 zwitterionic, 11,664 protonated and 1458 trial deprotonated structures were generated by allowing for all combinations of internal single-bond rotamers. All the trial structures were initially optimized at the AM1 level, and the resulting structures were determined at the B3LYP/6-311G^* level. A total of 927 canonical, 730 protonated and 193 deprotonated conformers were found, but there were no stable zwitterionic structures in the gas phase. The most stable conformers of the canonical, protonated and deprotonated lysine were further optimized at the B3LYP/6-311++G^** level. The energies of the most stable structures were determined at the MP2/6-311G(2df,p) level and the vibrational frequencies were calculated at the B3LYP/6-311++G^** level. The rotational constants, dipole moments, zero-point vibrational energies, harmonic frequencies, vertical ionization energies, enthalpies, Gibbs free energies and conformational distributions of gaseous lysine were presented. Numerous new structures are found and the lowest-energy lysine conformer is more stable than the existing one by 1.1 kcal/mol. Hydrogen bonds are classified and may cause significant red-shifts to the associated vibrational frequencies. The calculated proton affinity/dissociation energy and gas-phase basicity/acidity are in good agreement with the experiments. Calculations are also presented for the canonical lysine–H₂O and zwitterionic lysine–H₂O clusters. Interaction between lysine and H₂O significantly affects the relative conformational stabilities. Only one water molecule is sufficient to produce the stable zwitterionic structures in gas phase. The lowest-energy structure is found to be zwitterions when applying the conductor-like polarized continuum solvent model (CPCM) to the lysine–H₂O complexes.     

On the accuracy of DFT-SAPT, MP2, SCS-MP2, MP2C, and DFT+Disp methods for the interaction energies of endohedral complexes of the C(60) fullerene with a rare gas atom

Selected points on the potential energy surface for the complexes Rg@C(60) (Rg = He, Ne, Ar, Kr) are calculated with various theoretical methods, like symmetry-adapted perturbation theory with monomers described by density functional theory (DFT-SAPT), supermolecular M?ller-Plesset theory truncated on the second order (MP2), spin-component-scaled MP2 (SCS-MP2), supermolecular density functional theory with empirical dispersion correction (DFT+Disp), and the recently developed MP2C method that improves the MP2 method for long-range electron correlation effects. A stabilization of the endohedral complex is predicted by all methods, but the depth of the potential energy well is overestimated by the DFT+Disp and MP2 approaches. On the other hand, the MP2C model agrees well with DFT-SAPT, which serves as the reference. The performance of SCS-MP2 is mixed: it produces too low interaction energies for the two heavier guests, while its accuracy for He@C(60) and Ne@C(60) is similar to that of MP2C. Fitting formulas for the main interaction energy components, i.e. the dispersion and first-order repulsion energies are proposed, which are applicable for both endo- and exohedral cases. For all examined methods density fitting is used to evaluate two-electron repulsion integrals, which is indispensable to allow studies of noncovalent complexes of this size. It has been found that density-fitting auxiliary basis sets cannot be used in a black-box fashion for the calculation of the first-order SAPT electrostatic energy, and that the quality of these basis sets should be always carefully examined in order to avoid an unphysical long-range behavior.