Solvent dependence on conformational transition, dipole moment, and molecular geometry of 1,2-dichloroethane: insight from Car-Parrinello molecular dynamics calculations

We have investigated the molecular geometry and dipole moment distribution for the major conformational states of 1,2-dichloroethane (DCE) in three different solvents under ambient conditions using the Car-Parrinello mixed quantum mechanics/molecular mechanics method. The solvents studied were water, DCE, and chloroform. Within the time scale investigated, we find a conformational equilibrium existing between the gauche and trans forms of DCE in all three solvents. In the chloroform solvent, the conformational transition occurs more frequently than in water solvent and in liquid DCE (i.e., DCE solute in DCE solvent). The population of gauche conformer is more in the case of water solvent, while the trans conformer dominates in chloroform solvent. We report a bimodal nature of the dipole moment distribution for DCE in all three solute-solvents studied, where the peaks are attributed to the trans and gauche conformational states. The dipole moments of both of the conformational states increase with increasing polarity of the solvent. Also, with an increase in solvent polarity, an increase in the C-Cl bond length and magnitude of atomic charges in DCE has been observed. The increase in atomic charges of DCE is almost twice when the solvent is changed from chloroform to water.     

Chlorocarbonyl trifluoromethanesulfonate, ClC(O)OSO2CF3: structure and conformational properties in the gaseous and condensed phases

Pure chlorocarbonyl trifluoromethanesulfonate, ClC(O)OSO(2)CF(3), has been prepared in about 58% yield by the ambient-temperature reaction between ClC(O)SCl and AgCF(3)SO(3). The conformational properties of the gaseous molecule have been studied by vibrational spectroscopy [IR(gas), IR(matrix), and Raman(liquid)] and quantum chemical calculations (HF and B3LYP with 6-31+G* basis sets); in addition, the solid-state structure has been determined by X-ray crystallography. ClC(O)OSO(2)CF(3) exists in the gas phase as a mixture of trans [ClC(O) group trans with respect to the CF(3) group] and gauche conformers, with the trans form being the more abundant [66(8)% from IR(matrix) measurements]. In both conformers, the C=O bond of the ClC(O) group is oriented synperiplanar with respect to the S-O single bond. The experimental free energy difference between the two forms, DeltaG degrees = 0.8(2) kcal mol(-1) (IR), is slightly smaller than the calculated value (1.0-1.5 kcal mol(-1)). The crystalline solid at 150 K [monoclinic, P2(1)/n, a = 7.3951(9) angstroms, b = 24.897(3) angstroms, c = 7.4812(9) angstroms, beta = 99.448(2) degrees, Z = 8] consists surprisingly of both trans and gauche forms. Whereas the more stable conformer for the more or less discrete molecules and the polarization effects would tend to favor the trans form, the packing effects would stabilize the gauche rotamer in the solid state.     

The extremely flat torsional potential energy surface of oxalyl chloride

The conformational behavior of oxalyl chloride has been investigated using ab initio Hartree-Fock (HF) and second-order Moller-Plesset (MP2) perturbation theories, and the coupled-cluster singles and doubles method appended with a perturbative inclusion of connected triple excitations [CCSD(T)]. Correlation consistent polarized valence quadruple-zeta (cc-pVQZ) and quintuple-zeta (cc-pV5Z) basis sets were used in this research. At the cc-pVQZ and cc-pV5Z HF levels, there is no stationary point corresponding to a stable gauche conformer. On the other hand, at the cc-pVQZ and cc-pV5Z MP2 levels and with the cc-pVQZ CCSD(T) method, the gauche conformer of oxalyl chloride was found at O[Double Bond]C-C[Double Bond]O dihedral angles of 81.9 degrees , 79.4 degrees , and 83.4 degrees , respectively. At the cc-pV5Z MP2 level, the energy barrier from trans to gauche was predicted to be 0.74 kcal mol(-1) and that from gauche to trans to be 0.09 kcal mol(-1). Thus, the potential-energy surface along the O[Double Bond]C-C[Double Bond]O torsional mode is exceedingly flat. The existence of the gauche conformation is mainly due to the minimization of steric repulsion.     

Is there a general rule for the gauche effect in the conformational isomerism of 1,2-disubstituted ethanes?

The stabilities of the gauche and anti conformations of butane, 1,2-dicyanoethane (DCE), and 1,2-dinitroethane (DNE) have been investigated through theoretical calculations. The gauche effect-the tendency of keeping close vicinal electronegative substituents (thetaX-C-C-X approximately 60 degrees ) in an ethane fragment-is expected to drive the conformational equilibrium of DCE and DNE toward the gauche conformation. It was found that, for butane, where the gauche effect is supposed to be poor/null, the hyperconjugation effect contributes mostly to the anti stabilization in opposition to the traditional sense that the methyl groups repel each other, and this should govern its conformational equilibrium. For DCE the equilibrium was shifted to the anti conformer, essentially due to a gauche repulsion, while for DNE, despite the higher electronic delocalization energies, a predominance of the gauche conformer was obtained, and this was attributed mainly to the attractive dipolar interaction between the two nitro groups. A full orbital energy analysis was performed using the natural bond orbital approach, which showed that bond bending and anti-C-H/C-X* hyperconjugation models, usually applied to explain the origin of the gauche effect in fluorinated derivatives, are not adequate to completely explain the conformational behavior of the titled compounds.     

Stereochemistry of 1,2-dichloroethane adsorbed on Pt(111)

The rotational isomerism of 1,2-dichloroethane (DCE, CH2ClCH2Cl) adsorbed on Pt(111) was studied in the temperature range of 35-100 K using high-resolution electron energy loss spectroscopy and metastable atom electron spectroscopy. In the coverage below monolayer the physisorbed and chemisorbed species coexist at 35 K in the gauche and slightly distorted trans form, respectively. Owing to the direct Pt-Cl interactions, the nonbonding Cl 3p states of the chemisorbed DCE are split off, giving rise to degradation in symmetry from the pure trans form (C2h). The physisorbed gauche conformers are arranged with the C2 axis parallel (or heavily tilted) to the substrate and converted irreversibly to the pseudo-trans form by heating at 70 K. In the multilayer, the trans and gauche conformers exist at 35 K, where the former population is increased with increasing layer thickness. Upon annealing the bilayer at 80 K, the irreversible conversion takes place to yield a higher population of the gauche conformer in the topmost layer. The conformational stabilities and mutual changes of DCE adsorbed on a metal surface are discussed in terms of intramolecular rotational potential.     

Fluorocarbonyl trifluoromethanesulfonate, FC(O)OSO2CF3: structure and conformational properties in the gaseous and condensed phases

Pure fluorocarbonyl trifluoromethanesulfonate, FC(O)OSO(2)CF(3), is prepared in about 70% yield by the ambient-temperature reaction between FC(O)SCl and AgCF(3)SO(3). The geometric structure and conformational properties of the gaseous molecule have been studied by gas electron diffraction (GED), vibrational spectroscopy [IR(gas), IR(matrix), and Raman(liquid)] and quantum chemical calculations (HF, MP2, and B3LYP with 6-311G basis sets); in addition, the solid-state structure has been determined by X-ray crystallography. FC(O)OSO(2)CF(3) exists in the gas phase as a mixture of trans [FC(O) group trans with respect to the CF(3) group] and gauche conformers with the trans form prevailing [67(8)% from GED and 59(5)% from IR(matrix) measurements]. In both conformers the C=O bond of the FC(O) group is oriented synperiplanar with respect to the S-O single bond. The experimental free energy difference between the two forms, DeltaG degrees = 0.49(13) kcal mol(-1) (GED) and 0.22(12) kcal mol(-1) (IR), is slightly smaller than the calculated value (0.74-0.94 kcal mol(-1)). The crystalline solid at 150 K [monoclinic, P2(1)/c, a = 10.983(1) A, b = 6.4613(6) A, c = 8.8508(8) A, beta = 104.786(2) degrees ] consists exclusively of the trans conformer.     

Gas-phase Raman spectra and the potential energy function for the internal rotation of 1,3-butadiene and its isotopologues

The gas-phase Raman spectra of 1,3-butadiene and its 2,3-d(2), 1,1,4,4-d(4), and -d(6) isotopologues have been recorded with high sensitivity in the region below 350 cm(-1) in order to investigate the internal rotation (torsional) vibration. Based on more accurate structural information, the internal rotor constants F(n) were calculated as a function of rotation angle (?). The data for all the isotopologues were then fit using a one-dimensional potential energy function of the form V = (1)/(2)∑V(n)(1 - cos ?). Initial V(n) values were based on those generated from theoretical calculations. The agreement between observed and calculated frequencies is very good, although bands not taken into account were present in the spectra. The energy difference between the trans and gauche forms was determined to be about 1030 cm(-1) (2.94 kcal/mol), and the barrier between the two equivalent gauche forms was determined to be about 180 cm(-1) (0.51 kcal/mol), which agrees well with high-level ab initio calculations. An alternative set of assignments also fits the data quite well for all of the isotopologues. For this model, the energy difference between the trans and gauche forms is about 1080 cm(-1) (3.09 kcal/mol), and the barrier between gauche forms is about 405 cm(-1) (1.16 kcal/mol).     

Structural relaxation in amorphous 1,2-dichloroethane studied by transformation between conformation isomers

Structural relaxation in amorphous 1,2-dichloroethane (DCE) samples prepared by vapor deposition on cold substrates were studied by Raman scattering. The gauche and trans molecules of DCE were found to coexist in amorphous states immediately after the deposition, and structural relaxation occurred with temperature elevation before crystallization. Mole fraction of the gauche isomer increased during this relaxation process, although trans is the stable isomer in gaseous and crystalline states. At the final amorphous stage immediately before crystallization, the gauche mole fraction was close to the mole fraction of the supercooled liquid state. It was also found that trans molecules located at positions with lower density were more easily transformed into the gauche conformation, while the distribution of the local structure around the resultant gauche molecules remained almost unchanged during the structural relaxation. Such behaviors of amorphous DCE are discussed from the viewpoint of the characteristic molecular structure of DCE.     

Mechanism of the hydration of carbon dioxide: direct participation of H2O versus microsolvation

Thermochemical parameters of carbonic acid and the stationary points on the neutral hydration pathways of carbon dioxide, CO 2 + nH 2O --> H 2CO 3 + ( n - 1)H 2O, with n = 1, 2, 3, and 4, were calculated using geometries optimized at the MP2/aug-cc-pVTZ level. Coupled-cluster theory (CCSD(T)) energies were extrapolated to the complete basis set limit in most cases and then used to evaluate heats of formation. A high energy barrier of approximately 50 kcal/mol was predicted for the addition of one water molecule to CO 2 ( n = 1). This barrier is lowered in cyclic H-bonded systems of CO 2 with water dimer and water trimer in which preassociation complexes are formed with binding energies of approximately 7 and 15 kcal/mol, respectively. For n = 2, a trimeric six-member cyclic transition state has an energy barrier of approximately 33 (gas phase) and a free energy barrier of approximately 31 (in a continuum solvent model of water at 298 K) kcal/mol, relative to the precomplex. For n = 3, two reactive pathways are possible with the first having all three water molecules involved in hydrogen transfer via an eight-member cycle, and in the second, the third water molecule is not directly involved in the hydrogen transfer but solvates the n = 2 transition state. In the gas phase, the two transition states have comparable energies of approximately 15 kcal/mol relative to separated reactants. The first path is favored over in aqueous solution by approximately 5 kcal/mol in free energy due to the formation of a structure resembling a (HCO 3 (-)/H 3OH 2O (+)) ion pair. Bulk solvation reduces the free energy barrier of the first path by approximately 10 kcal/mol for a free energy barrier of approximately 22 kcal/mol for the (CO 2 + 3H 2O) aq reaction. For n = 4, the transition state, in which a three-water chain takes part in the hydrogen transfer while the fourth water microsolvates the cluster, is energetically more favored than transition states incorporating two or four active water molecules. An energy barrier of approximately 20 (gas phase) and a free energy barrier of approximately 19 (in water) kcal/mol were derived for the CO 2 + 4H 2O reaction, and again formation of an ion pair is important. The calculated results confirm the crucial role of direct participation of three water molecules ( n = 3) in the eight-member cyclic TS for the CO 2 hydration reaction. Carbonic acid and its water complexes are consistently higher in energy (by approximately 6-7 kcal/mol) than the corresponding CO 2 complexes and can undergo more facile water-assisted dehydration processes.     

Adjacent gauche stabilization in linear alkanes: implications for polymer models and conformational analysis

High-level ab initio quantum mechanical calculations are used to study various gauche conformational energies of n-pentane to n-decane. The destabilizing "pentane effect" (adjacent gauche states of opposite sign) for alkanes is confirmed, but the energies were found to depend slightly on chain length. In contrast, introducing an adjacent gauche of the same sign requires only 0.22-0.37 kcal/mol, approximately half of the single gauche state energy. This adjacent gauche stabilization should be taken into account when formulating or analyzing rotational isomeric models, carrying out conformational analysis, and developing force fields for alkanes, lipids, and related polymers.     

Theoretical conformational analysis for neurotransmitters in the gas phase and in aqueous solution. Norepinephrine

The natural neurotransmitter (R)-norepinephrine takes the monocationic form in 93% abundance at the physiological tissue pH of 7.4. Ab initio and DFT/B3LYP calculations were performed for 12 protonated conformers of (R)-norepinephrine in the gas phase with geometry optimizations up to the MP2/6-311++G level, and with single-point calculations up to the QCISD(T) level at the HF/6-31G-optimized geometries. Four monohydrates were studied at the MP2/6-31G//HF/6-31G level. In the gas phase, the G1 conformer is the most stable with phenyl.NH(3)(+) gauche and HO(alc).NH(3)(+) gauche arrangements. A strained intramolecular hydrogen bond was found for conformers (G1 and T) with close NH(3)(+) and OH groups. Upon rotation of the NH(3)(+) group as a whole unit about the C(beta)-C(alpha) axis, a 3-fold potential was calculated with free energies for barriers of 3-12 kcal/mol at the HF/6-31G level. Only small deviations were found in MP2/6-311++G single-point calculations. A 2-fold potential was calculated for the phenyl rotation with free energies of 11-13 kcal/mol for the barriers at T = 310 K and p = 1 atm. A molecular mechanics docking study of (R)-norepinephrine in a model binding pocket of the beta-adrenergic receptor shows that the ligand takes a conformation close to the T(3) arrangement. The effect of aqueous solvation was considered by the free energy perturbation method implemented in Monte Carlo simulations. There are 4-5 strongly bound water molecules in hydrogen bonds to the conformers. Although hydration stabilizes mostly the G2 form with gauche phenyl.NH(3)(+) arrangement and a water-exposed NH(3)(+) group, the conformer population becomes T > G1 > G2, in agreement with the PMR spectroscopy measurements by Solmajer et al. (Z. Naturforsch. 1983, 38c, 758). Solvent effects reduce the free energies for barriers to 3-6 and 9-12 kcal/mol for rotations about the C(beta)-C(alpha) and the C(1)(ring)-C(beta) axes, respectively.     

Vibrational-torsional excitation and direct overtone photodissociation of ethyl hydroperoxide at 5nuOH

We have observed OH radical products from the unimolecular dissociation of ethyl hydroperoxide (CH3-CH2OOH) excited to 5nuOH and have collected an action spectrum from 15,600 to 16,800 cm(-1) and an OH product state distribution at the maximum (16,119 cm(-1)). We use a vibrational-torsional model to simulate spectra in the 5nuOH region for the trans and gauche conformers. A combination of the two simulated spectra resembles the experimental action spectrum, provided that the trans conformer is assumed to dominate at room temperature. Energy disposal in the OH fragment yields an upper limit for the O-O bond dissociation energy at D0 < 44 kcal mol(-1).     

Photophysical studies of the trans to cis isomerization of the push-pull molecule: 1-(pyridin-4-yl)-2-(N-methylpyrrol-2-yl)ethene (mepepy)

Organic molecules possessing intramolecular charge-transfer properties (D-pi-A type molecules) are of key interest particularly in the development of new optoelectronic materials as well as photoinduced magnetism. One such class of D-pi-A molecules that is of particular interest contains photoswitchable intramolecular charge-transfer states via a photoisomerizable pi-system linking the donor and acceptor groups. Here we report the photophysical and electronic properties of the trans to cis isomerization of 1-(pyridin-4-yl)-2-(N-methylpyrrol-2-yl)ethene ligand (mepepy) in aqueous solution using photoacoustic calorimetry (PAC) and theoretical methods. Density functional theory (DFT) calculations demonstrate a global energy difference between cis and trans isomers of mepepy to be 8 kcal mol(-1), while a slightly lower energy is observed between the local minima for the trans and cis isomers (7 kcal mol(-1)). Interestingly, the trans isomer appears to exhibit two ground-state minima separated by an energy barrier of approximately 9 kcal mol(-1). Results from the PAC studies indicate that the trans to cis isomerization results in a negligible volume change (0.9 +/- 0.4 mL mol(-1)) and an enthalpy change of 18 +/- 3 kcal mol(-1). The fact that the acoustic waves associated with the trans to cis transition of mepepy overlap in frequency with those of a calorimetric reference implies that the conformational transition occurs faster than the approximately 50 ns response time of the acoustic detector. Comparison of the experimental results with theoretical studies provide evidence for a mechanism in which the trans to cis isomerization of mepepy results in the loss of a hydrogen bond between a water molecule and the pyridine ring of mepepy.     

Peroxy acid epoxidation of acyclic allylic alcohols. Competition between s-trans and s-cis peroxy acid conformers

[Reaction: see text]. RB3LYP calculations, reported here, indicate that peroxy acid s-cis conformer is more stable than its s-trans counterpart, in agreement with experimental data. Difference in stability is the highest in the gas phase, but it falls considerably on going from the gas phase to moderately polar solvent. In the case of peroxy formic acid, the enthalpy (free energy) difference is about 3.4 (2.5) kcal/mol, respectively, in the gas phase but decreases to 1.2 (0.6) kcal/mol in dichloromethane solution. Introduction of an alkyl or aryl substituent on the peroxy acid, that is, on passing to peroxy acetic, peroxy benzoic (PBA), and m-chloroperoxy benzoic acid (MCPBA), adds a further significant (1.0-1.5 kcal/mol) favor to the s-cis isomer. RB3LYP/6-31+G(2d,p) calculations on the epoxidation of 2-propenol with peroxy formic and peroxy benzoic acids, respectively, suggest that the less stable peroxy acid s-trans conformer can compete with the more stable s-cis form in epoxidation reaction of these substrates. Transition structures arising from s-trans peroxy acids ("trans" TSs) retain both the well-established, for "cis" TS, perpendicular orientation of the O-H peroxy acid bond relative to the C=C bond and the one-step oxirane ring formation. These TSs collapse to the final epoxide via a 1,2-H shift at variance with the 1,4-H transfer of the classical Bartlett's "cis" mechanism. The "trans" reaction pathways have a higher barrier in the gas phase than the "cis" reaction channels, but in moderately polar solvents they become competitive. In fact, the "trans" TSs are always significantly more stabilized than their "cis" counterparts by solvation effects. Calculations also suggest that going from peroxy formic to peroxy benzoic acid should slightly disfavor the "trans" route relative to the "cis" one, reflecting, in an attenuated way, the decrease in the peroxy acid s-trans/s-cis conformer ratio. The predicted behavior for MCPBA parallels that of PBA acid.     

13C NMR, infrared, solvation and theoretical investigation of the conformational isomerism in 1-haloacetones (X = Cl, Br and I)

The solvent dependence of the 13C NMR spectra of chloroacetone (CA), bromoacetone (BA) and iodoacetone (IA) are reported and the 3J(CH) couplings analysed using ab initio calculations and solvation theory. In CA the energy difference (E(cis) - E(gauche)) between the cis (Cl-C-C=O 0 degrees) and gauche (Cl-C-C=O 155 degrees) conformers is 1.7 kcal mol(-1) in the vapour, decreasing to 0.8 kcal mol(-1) in CCl4 solution and to -1.0 kcal mol(-1) in the pure liquid. The conformational equilibrium, in BA, is between the more polar cis (Br-C-C=O 0 degrees) and gauche (Br-C-C=O 132 degrees) conformations. The energy difference (E(cis) - E(gauche)) is 1.8 kcal mol(-1) in the vapour, decreasing to 0.9 kcal mol(-1) in CCl4 solution and to -0.4 kcal mol(-1) in the pure liquid. The energy difference (E(cis) - E(gauche)), in IA, between the cis (I-C-C=O 0 degrees) and gauche (I-C-C=O 104 degrees) conformers is 1.1 kcal mol(-1) in the vapour phase, decreasing to 0.5 kcal mol(-1) in CCl4 solution and to -0.5 kcal mol(-1) in the pure liquid. The vapour state energy difference for BA [1.4 kcal mol(-1) at B3LYP/6-311++G(d,p)] and for IA [1.6 kcal mol(-1) at B3LYP/6-311++G(d,p)/LANL2DZ)] are in very good agreement with the above values. For CA the agreement is also satisfactory [1.4 kcal mol(-1) at B3LYP/6-311++G(d,p)].     

Conformational stability and vibrations of aminopropylsilanol molecule

Density functional theory (DFT), using the B3-LYP/6-31G(d,p) method have been used to investigate the conformation and vibrational spectra of aminopropylsilanetriol (APST) NH2CH2CH2CH2Si(OH)3. The potential function for CCCSi torsion gives rise to two distinct conformers trans and gauche. The predicted energy of the more stable trans conformer is 337 cm-1 less than the energy of gauche conformer. The calculated barriers to the conformation interchange are: 1095, 2845 and 438 cm-1 for the trans to gauche, gauche to gauche and gauche to trans conformers, respectively. For the trans conformer the potential energy curve for the Si(OH)3 groups torsion in APST has been calculated changing the HOSiC dihedral angle. The barrier for the internal rotation of 3065 cm-1 has been obtained. The optimized molecular structure of APST dimer calculated for trans conformer has a SiOSi angle of 143.2 degrees, and a SiOSi bond length of 0.164 nm. A complete vibrational assignment for both conformers as well as for trans-dimer is supported by the normal coordinate analysis, calculated IR intensities as well as Raman activities. On the basis of the results, the vibrational spectra of APST aqueous solution and APST polymer have been analyzed. The average error between the observed and calculated frequencies is 14 cm-1.     

Dissociation of carbonic acid: gas phase energetics and mechanism from ab initio metadynamics simulations

A comprehensive metadynamics study of the energetics, stability, conformational changes, and mechanism of dissociation of gas phase carbonic acid, H2CO3, yields significant new insight into these reactions. The equilibrium geometries, vibrational frequencies, and conformer energies calculated using the density functional theory are in good agreement with the previous theoretical predictions. At 315 K, the cis-cis conformer has a very short life time and transforms easily to the cis-trans conformer through a change in the O=C-O-H dihedral angle. The energy difference between the trans-trans and cis-trans conformers is very small (approximately 1 kcal/mol), but the trans-trans conformer is resistant to dissociation to carbon dioxide and water. The cis-trans conformer has a relatively short path for one of its hydroxyl groups to accept the proton from the other end of the molecule, resulting in a lower activation barrier for dissociation. Comparison of the free and potential energies of dissociation shows that the entropic contribution to the dissociation energy is less than 10%. The potential energy barrier for dissociation of H2CO3 to CO2 and H2O from the metadynamics calculations is 5-6 kcal/mol lower than in previous 0 K studies, possibly due to a combination of a finite temperature and more efficient sampling of the energy landscape in the metadynamics calculations. Gas phase carbonic acid dissociation is triggered by the dehydroxylation of one of the hydroxyl groups, which reorients as it approaches the proton on the other end of the molecule, thus facilitating a favorable H-O-H angle for the formation of a product H2O molecule. The major atomic reorganization of the other part of the molecule is a gradual straightening of the O=C=O bond. The metadynamics results provide a basis for future simulation of the more challenging carbonic acid-water system.     

Gauche effect in 1,2-difluoroethane. Hyperconjugation, bent bonds, steric repulsion

Natural bond orbital deletion calculations show that whereas the gauche preference arises from vicinal hyperconjugative interaction between anti C-H bonds and C-F* antibonds, the cis C-H/C-F* interactions are substantial (approximately 25% of the anti interaction). The established significantly >60 degrees FCCF dihedral angle for the equilibrium conformer can then be rationalized in terms of the hyperconjugation model alone by taking into account both anti interactions that maximize near 60 degrees and the smaller cis interactions that maximize at a much larger dihedral angle. This explanation does not invoke repulsive forces to rationalize the 72 degrees equilibrium conformer angle. The relative minimum energy for the trans conformer is the consequence of a balance between decreasing hyperconjugative stabilization and decreasing steric destabilization as the FCCF torsional angle approaches 180 degrees . The torsional coordinate is predicted to be strongly contaminated by CCF bending, with the result that approximately half of the trans --> gauche stabilization energy stems from mode coupling.     

Comparative assessment of computational methods for the determination of solvation free energies in alcohol‐based molecules

The determination of differences in solvation free energies between related drug molecules remains an important challenge in computational drug optimization, when fast and accurate calculation of differences in binding free energy are required. In this study, we have evaluated the performance of five commonly used polarized continuum model (PCM) methodologies in the determination of solvation free energies for 53 typical alcohol and alkane small molecules. In addition, the performance of these PCM methods, of a thermodynamic integration (TI) protocol and of the Poisson–Boltzmann (PB) and generalized Born (GB) methods, were tested in the determination of solvation free energies changes for 28 common alkane‐alcohol transformations, by the substitution of an hydrogen atom for a hydroxyl substituent. The results show that the solvation model D (SMD) performs better among the PCM‐based approaches in estimating solvation free energies for alcohol molecules, and solvation free energy changes for alkane‐alcohol transformations, with an average error below 1 kcal/mol for both quantities. However, for the determination of solvation free energy changes on alkane‐alcohol transformation, PB and TI yielded better results. TI was particularly accurate in the treatment of hydroxyl groups additions to aromatic rings (0.53 kcal/mol), a common transformation when optimizing drug‐binding in computer‐aided drug design. © 2013 Wiley Periodicals, Inc.     

Computational study on kinetics and mechanisms of unimolecular decomposition of succinic acid and its anhydride

The mechanisms and kinetics of unimolecular decomposition of succinic acid and its anhydride have been studied at the G2M(CC2) and microcanonical RRKM levels of theory. It was shown that the ZsgsZ conformer of succinic acid, with the Z-acid form and the gauche conformation around the central C-C bond, is its most stable conformer, whereas the lowest energy conformer with the E-acid form, ECGsZ, is only 3.1 kcal/mol higher in energy than the ZsgsZ. Three primary decomposition channels of succinic acid producing H2O + succinic anhydride with a barrier of 51.0 kcal/mol, H2O + OCC2H3COOH with a barrier of 75.7 kcal/mol and CO2 + C2H5COOH with a barrier of 71.9 kcal/mol were predicted. The dehydration process starting from the ECGCZ-conformer is found to be dominant, whereas the decarboxylation reaction starting from the ZsgsZ-conformer is only slightly less favorable. It was shown that the decomposition of succinic anhydride occurs via a concerted fragmentation mechanism (with a 69.6 kcal/mol barrier), leading to formation of CO + CO2 + C2H4 products. On the basis of the calculated potential energy surfaces of these reactions, the rate constants for unimolecular decomposition of succinic acid and its anhydride were predicted. In addition, the predicted rate constants for the unimolecular decomposition of C2H5COOH by decarboxylation (giving C2H6 + CO2) and dehydration (giving H3CCHCO + H2O) are in good agreement with available experimental data.