Comparative study of liquid uptake and permeation characteristics of sulfonated cation-exchange membranes in water and methanol

Liquid permeation and uptake measurements of pure water and methanol were carried out using three commercial cation-exchange membranes: Nafion-117 (perfluorinated polyethylene with pendant ether-linked side chains terminated with sulfonated groups), MK-40 (microparticles of polystyrene–divinylbenzene with sulfonic groups randomly dispersed in a polyethylene matrix) and CR61-CZL-412 (crosslinked sulfonated copolymer of styrene–divinylbenzene). Methanol uptake by the Nafion-117 membrane was higher than that of water, in contrast, for MK-40 and CR61-CZL-412 membranes the opposite behavior is observed. Differences in the water and methanol liquid uptakes by the membranes were discussed in terms of the chemical interaction between the liquids and the polymers, and also on the size of the liquid molecules. On the other hand, the methanol permeation flow values through the membranes were higher than those of water for all the studied membranes.     

Conformational equilibrium of 1,2-dichloroethane in water: comparison of PCM and RISM-SCF methods

The RISM-SCF and polarizable continuum model (PCM) approaches have been applied to study the conformational equilibrium of 1,2-dichloroethane (DCE) in water. Both the electron correlation effect and basis sets play an important role in the relative energies of the gauche and trans conformers in gas and solution phases. Both PCM and RISM-MP2 methods resulted in a consistent trend with the previous experimental and theoretical studies that the population of the gauche conformer increases in going from the gas phase to the aqueous solution. However, the PCM treatment could not describe the solvent effect completely in that the sign of the relative free energy of the gauche and trans forms is opposite to the most recent experimental and theoretical data, while the RISM-MP2 gives the right sign in the free energy difference. We found that the larger excess chemical potential gain (by ca. -4.1 kcal/mol) for the gauche conformer is large enough to result in the gauche preference of DCE in water, though it has to compensate for more solute reorganization energy (approximately 1.6 kcal/mol) and overcome the energy difference (approximately 1.6 kcal/mol) in the gas phase. The radial distribution functions between DCE and the nearest water shows that the electrostatic repulsion between chlorine and oxygen atoms is higher in the trans conformer than in the gauche one, while the attractive interaction between chlorine and hydrogen of water is higher in the gauche conformer.     

Quantifying the electrostatic driving force behind SmI2 reductions

The equilibrium constant for the electron transfer between SmI2 and substituted benzophenones was determined. The electron transfer reactions are exothermic with DeltaG(eq) ranging from -5.1 to -1.6 kcal/mol. Redox potentials suggest that the electron transfer reactions should be endothermic by ca. 25 kcal/mol, contrary to the experimental observation. It is suggested that the change from endothermicity to exothermicity stems from the electrostatic attraction between the negatively charged radical anion and Sm(3+).     

Thermodynamics and kinetics of intramolecular proton transfer in Guanine. Post Hartree-Fock study

The most stable tautomers and rotamers of guanine are characterized by post Hartree-Fock ab initio calculations at the MP2 and CCSD(T) levels employing extended basis sets. Four of the lowest-energy structures (7H-oxo-amino- < 9H-oxo-amino- < 9H-syn-hydroxo-amino- < 9H-anti-hydroxo-amino-guanine) are found to lie within ca. 1 kcal/mol. The next form of guanine is established to lie more than 3 kcal/mol higher than the global minimum tautomer. The transition states of the following reversible reactions: 9H-oxo-amino-guanine right harpoon over left harpoon 9H-syn-hydroxo-amino-guanine right harpoon over left harpoon 9H-anti-hydroxo-amino-guanine have been studied. The calculated energy data were used to obtain thermodynamic parameters and to estimate the composition of the equilibrium mixture of conformers at 0 K and room temperature. The rate constants for the tautomerization of 9H-oxo-amino-guanine were determined by using the instanton approach. Their predicted values characterize an extremely slow chemical process, which is expected to reach the equilibrium in ca. 2500 h. Despite being so slow, we have shown that such a rate of the tautomerization describes a process that is much faster than the one characterized by the observed frequency of spontaneous point mutations. Therefore, additional stabilization factors, e.g., hydrations and interactions with enzymes are necessary to secure the known fidelity of DNA synthesis.     

Interactions in large, polyaromatic hydrocarbon dimers: application of density functional theory with dispersion corrections

The interactions within two models for graphene, coronene and hexabenzocoronene (HBC), and (H 3C(CH 2) 5) 6-HBC, a synthesizable model for asphaltenes, were studied using density functional theory (DFT) with dispersion corrections. The corrections were implemented using carbon atom-centered effective core-type potentials that were designed to correct the erroneous long-range behavior of several DFT methods. The potentials can be used with any computational chemistry program package that can handle standard effective core potential input, without the need for software modification. Testing on a set of common noncovalently bonded dimers shows that the potentials improve calculated binding energies by factors of 2-3 over those obtained without the potentials. Binding energies are predicted to within ca. 15%, and monomer separations to within ca. 0.1 A, of high-level wave function data. The application of the present approach predicts binding energies and structures of the coronene dimer that are in excellent agreement with the results of other DFT methods in which dispersion is taken into account. Dimers of HBC show extensive binding in pi-stacking arrangements, with the largest binding energy, 44.8 kcal/mol, obtained for a parallel-displaced structure. This structure is inline with the published crystal structure. Conformations in which the monomers are perpendicular to one another are much more weakly bound and have binding energies less than 10 kcal/mol. For dimers of (H 3C(CH 2) 5) 6-HBC, which contain 336 atoms, we find that a slipped-parallel structure with C s symmetry has a binding energy of 52.4 kcal/mol, 8.9 kcal/mol lower than that of a bowl-like, C 6 v -symmetric structure.     

Improved interaction potentials for charged residues in proteins

Electrostatic interactions dominate the structure and free energy of biomolecules. To obtain accurate free energies involving charged groups from molecular simulations, OPLS-AA parameters have been reoptimized using Monte Carlo free energy perturbation. New parameters fit a self-consistent, experimental set of hydration free energies for acetate (Asp), propionate (Glu), 4-methylimidazolium (Hip), n-butylammonium (Lys), and n-propylguanidinium (Arg), all resembling charged residue side chains, including beta-carbons. It is shown that OPLS-AA free energies depend critically on the type of water model, TIP4P or TIP3P; i.e., each water model requires specific water-charged molecule interaction potentials. New models (models 1 and 3) are thus described for both water models. Uncertainties in relative free energies of charged residues are approximately 2 kcal/mol with the new parameters, due to variations in system setup (MAEs of ca. 1 kcal/mol) and noise from simulations (ca. 1 kcal/mol). The latter error of approximately 1 kcal/mol contrasts MAEs from standard OPLS-AA of up to 13 kcal/mol for the entire series of charged residues or up to 5 kcal/mol for the cationic series Lys, Arg, and Hip. The new parameters can be used directly in molecular simulations with no modification of neutral residues needed and are envisioned to be particular important in simulations where charged residues change environment.     

Ab initio/GIAO-CCSD(T) study of structures, energies, and 13C NMR chemical shifts of C4H7(+) and C5H9(+) ions: relative stability and dynamic aspects of the cyclopropylcarbinyl vs bicyclobutonium ions

The structures and energies of the carbocations C 4H 7 (+) and C 5H 9 (+) were calculated using the ab initio method. The (13)C NMR chemical shifts of the carbocations were calculated using the GIAO-CCSD(T) method. The pisigma-delocalized bisected cyclopropylcarbinyl cation, 1 and nonclassical bicyclobutonium ion, 2 were found to be the minima for C 4H 7 (+) at the MP2/cc-pVTZ level. At the MP4(SDTQ)/cc-pVTZ//MP2/cc-pVTZ + ZPE level the structure 2 is 0.4 kcal/mol more stable than the structure 1. The (13)C NMR chemical shifts of 1 and 2 were calculated by the GIAO-CCSD(T) method. Based on relative energies and (13)C NMR chemical shift calculations, an equilibrium involving the 1 and 2 in superacid solutions is most likely responsible for the experimentally observed (13)C NMR chemical shifts, with the latter as the predominant equilibrating species. The alpha-methylcyclopropylcarbinyl cation, 4, and nonclassical bicyclobutonium ion, 5, were found to be the minima for C 5H 9 (+) at the MP2/cc-pVTZ level. At the MP4(SDTQ)/cc-pVTZ//MP2/cc-pVTZ + ZPE level ion 5 is 5.9 kcal/mol more stable than the structure 4. The calculated (13)C NMR chemical shifts of 5 agree rather well with the experimental values of C 5H 9 (+).     

Self-diffusion coefficient of water in Nafion-117 membrane with different monovalent counterions: a radiotracer study

The self-diffusion coefficient of water in Nafion-117 membrane in different cationic forms was measured by the transient radiotracer method, which is based on an analytical solution of Fick's second law. The self-diffusion coefficient of water in the membrane was obtained from the analysis of time-dependent isotopic-exchange rates of tritium tagged water between sample of Nafion-117 membrane and equilibrating water. This transient method does not require the knowledge of partition coefficient of water, which is an essential parameter in the radiotracer permeation method. In present work, self-diffusion coefficients of water in the Nafion-117 membrane with H⁺, Li⁺, Ag⁺, Na⁺, K⁺, Rb⁺ and Cs⁺ monovalent counterions were obtained. The values of logarithm of self-diffusion coefficients were found to vary linearly as a function of polymer volume fraction except for membrane sample with H⁺ counterions. The self-diffusion coefficient of water in Nafion-117 membrane with H⁺ counterions was significantly different from the trend observed in the variation of self-diffusion coefficient of water as a function of polymer volume fraction in the membrane with other monovalent counterions. This observation seems to suggest that the physical structure of Nafion-117 membrane in H⁺ form may be quite different from the Nafion-117 membrane with other monovalent counterions. The high self-diffusion coefficient of water (1.67 × 10⁻⁶ cm²/s) in Nafion-117 membrane with Cs⁺ counterions indicates that the ionic clusters in Nafion-117 membrane are well connected even at low water content (8.2 wt.%) in the membrane.     

Potential energy scans and vibrational assignments of cyclopropanecarboxylic acid and cyclopropanecarboxamide

The structural stability and internal rotations in cyclopropanecarboxylic acid and cyclopropanecarboxamide were investigated by the DFT-B3LYP and the ab initio MP2 calculations using 6-311G** and 6-311+G** basis sets. The computations were extended to the MP4//MP2/6-311G** and CCSD(T)//MP2/6-311G** single-point calculations. From the calculations the molecules were predicted to exist predominantly in the cis (C=O group eclipses the cyclopropane ring) with a cis-trans barrier of about 4-6kcal/mol. The OCOH torsional barrier in the acid was estimated to be about 12-13kcal/mol while the corresponding OCNH torsional barrier in the amide was calculated to be about 20kcal/mol. The equilibrium constant k for the cis<-->trans interconversion in cyclopropanecarboxylic acid was calculated to be 0.1729 at 298.15K that corresponds to an equilibrium mixture of about 85% cis and 15% trans. The vibrational frequencies were computed at the DFT-B3LYP level. Normal coordinate calculations were carried out and potential energy distributions were calculated for the low energy cis conformer of the molecules. Complete vibrational assignments were made on the basis of normal coordinate calculations and comparison with experimental data of the molecules.     

Average sequential water molecule binding enthalpies of M(H2O)(19-124)2+ (M = Co, Fe, Mn, and Cu) measured with ultraviolet photodissociation at 193 and 248 nm

The average sequential water molecule binding enthalpies to large water clusters (between 19 and 124 water molecules) containing divalent ions were obtained by measuring the average number of water molecules lost upon absorption of an UV photon (193 or 248 nm) and using a statistical model to account for the energy released into translations, rotations, and vibrations of the products. These values agree well with the trend established by more conventional methods for obtaining sequential binding enthalpies to much smaller hydrated divalent ions. The average binding enthalpies decrease to a value of ~10.4 kcal/mol for n > ~40 and are insensitive to the ion identity at large cluster size. This value is close to that of the bulk heat of vaporization of water (10.6 kcal/mol) and indicates that the structure of water in these clusters may more closely resemble that of bulk liquid water than ice, owing either to a freezing point depression or rapid evaporative cooling and kinetic trapping of the initial liquid droplet. A discrete implementation of the Thomson equation using parameters for liquid water at 0 °C generally fits the trend in these data but provides values that are ~0.5 kcal/mol too low.     

F+ and F⁻ affinities of simple N(x)F(y) and O(x)F(y) compounds

Atomization energies at 0 K and heats of formation at 0 and 298 K are predicted for the neutral and ionic N(x)F(y) and O(x)F(y) systems using coupled cluster theory with single and double excitations and including a perturbative triples correction (CCSD(T)) method with correlation consistent basis sets extrapolated to the complete basis set (CBS) limit. To achieve near chemical accuracy (±1 kcal/mol), three corrections to the electronic energy were added to the frozen core CCSD(T)/CBS binding energies: corrections for core-valence, scalar relativistic, and first order atomic spin-orbit effects. Vibrational zero point energies were computed at the CCSD(T) level of theory where possible. The calculated heats of formation are in good agreement with the available experimental values, except for FOOF because of the neglect of higher order correlation corrections. The F(+) affinity in the N(x)F(y) series increases from N(2) to N(2)F(4) by 63 kcal/mol, while that in the O(2)F(y) series decreases by 18 kcal/mol from O(2) to O(2)F(2). Neither N(2) nor N(2)F(4) is predicted to bind F(-), and N(2)F(2) is a very weak Lewis acid with an F(-) affinity of about 10 kcal/mol for either the cis or trans isomer. The low F(-) affinities of the nitrogen fluorides explain why, in spite of the fact that many stable nitrogen fluoride cations are known, no nitrogen fluoride anions have been isolated so far. For example, the F(-) affinity of NF is predicted to be only 12.5 kcal/mol which explains the numerous experimental failures to prepare NF(2)(-) salts from the well-known strong acid HNF(2). The F(-) affinity of O(2) is predicted to have a small positive value and increases for O(2)F(2) by 23 kcal/mol, indicating that the O(2)F(3)(-) anion might be marginally stable at subambient temperatures. The calculated adiabatic ionization potentials and electron affinities are in good agreement with experiment considering that many of the experimental values are for vertical processes.     

Investigation of excess adsorption, solvation force, and plate-fluid interfacial tension for Lennard-Jones fluid confined in slit pores

The excess Helmholtz free energy functional is formulated in terms of a modified fundamental measure theory [Y. X. Yu and J. Z. Wu, J. Chem. Phys. 117, 10156 (2002)] for a short ranged repulsion and a first-order mean-spherical approximation theory [Y. P. Tang, J. Chem. Phys. 118, 4140 (2003)] for a long ranged attraction. Within the framework of the density functional theory, the density profile, excess adsorption, solvation force, and plate-fluid interfacial tension of a Lennard-Jones fluid confined in slit pores are predicted, and the results agree well with the simulation data. The phase equilibria inside the slit pores are determined according to the requirement that temperature, chemical potential, and grand potential in coexistence phases should be equal, and the plate-fluid interfacial tensions at equilibrium states are predicted consequently.     

Dissolved organic carbon--contaminant interaction descriptors found by 3D force field calculations

Enthalpies of transfer at 300 K of various partitioning processes were calculated in order to study the suitability of 3D force fields for the calculation of partitioning constants. A 3D fulvic acid (FA) model of dissolved organic carbon (DOC) was built in a MM+ force field using AMI atomic charges and geometrical optimization (GO). 3,5-Dichlorobiphenyl (PCB14), 4,4'-dichlorobiphenyl (PCB15), 1,1,1-trichloro-2,2-bis-(4-chlorophenyl)-ethane (PPDDT) and 2-chloro-4-ethylamino-6-isopropylamino-s-triazine (Atrazine) were inserted into different sites and their interaction energies with FA were calculated. Energies of hydration were calculated and subtracted from FA-contaminant interactions of selected sites. The resulting values for the enthalpies of transfer from water to DOC were 2.8, -1.4, -6.4 and 0.0 kcal/mol for PCB 14, PCB15, PPDDT and Atrazine, respectively. The value of PPDDT compared favorably with the experimental value of -5.0 kcal/mol. Prior to this, the method was studied by the calculation of the enthalpies of vaporization and aqueous solution using various force fields. In the MM + force field GO predicted enthalpies of vaporization deviated by +0.7 (PCB14), +3.6 (PCB15) and -0.7 (PPDDT)kcal/mol from experimental data, whereas enthalpies of aqueous solution deviated by -3.6 (PCB14), +5.8 (PCB15) and +3.7 (PPDDT) kcal/mol. Only for PCB14 the wrong sign of this enthalpy value was predicted. Potential advantages and limitations of the approach were discussed.     

Reaction mechanism and tautomeric equilibrium of 2-mercaptopyrimidine in the gas phase and in aqueous solution: a combined Monte Carlo and quantum mechanics study

A combined Monte Carlo and quantum mechanical study was carried out to analyze the tautomeric equilibrium of 2-mercaptopyrimidine in the gas phase and in aqueous solution. Second- and fourth-order M?ller-Plesset perturbation theory calculations indicate that in the gas phase thiol (Pym-SH) is more stable than the thione (Pym-NH) by ca. 8 kcal/mol. In aqueous solution, thermodynamic perturbation theory implemented on a Monte Carlo NpT simulation indicates that both the differential enthalpy and Gibbs free energy favor the thione form. The calculated differential enthalpy is DeltaH(SH)(-->)(NH)(solv) = -1.7 kcal/mol and the differential Gibbs free energy is DeltaG(SH)(-->)(NH)(solv) = -1.9 kcal/mol. Analysis is made of the contribution of the solute-solvent hydrogen bonds and it is noted that the SH group in the thiol and NH group in the thione tautomers act exclusively as a hydrogen bond donor in aqueous solution. The proton transfer reaction between the tautomeric forms was also investigated in the gas phase and in aqueous solution. Two distinct mechanisms were considered: a direct intramolecular transfer and a water-assisted mechanism. In the gas phase, the intramolecular transfer leads to a large energy barrier of 34.4 kcal/mol, passing through a three-center transition state. The proton transfer with the assistance of one water molecule decreases the energy barrier to 17.2 kcal/mol. In solution, these calculated activation barriers are, respectively, 32.0 and 14.8 kcal/mol. The solvent effect is found to be sizable but it is considerably more important as a participant in the water-assisted mechanism than the solvent field of the solute-solvent interaction. Finally, the calculated total Gibbs free energy is used to estimate the equilibrium constant.     

Bond dissociation energies for removal of the hydroxyl group in some alcohols from quantum chemical calculations

In this theoretical work, 22 alcohols and their geometric structure properties have been investigated employing quantum chemical methods to calculate the C? OH equilibrium bond distances and bond dissociation energies (BDEs). Since DFT methods have been researched to have low basis sets sensitivity for small and medium molecules in our previous work (Zhao et al., J Mol Struct, 2006, 766, 87), 22 title compounds have been studied by employing the hybrid density functional theory (B3LYP, B3PW91, B3P86, PBE1PBE) in conjunction with the 6‐311G** basis set and the complete basis set (CBS–Q) method. Comparison with the available experimental data shows that CBS–Q and B3P86 methods calculated results agree very well with the experimental values, with the average absolute errors of 1.3 kcal/mol and 3.5 kcal/mol, respectively. So considering the expensive computational time, CBS–Q method can be chosen as a satisfactory method of predicting the accurate BDEs for removal of the OH group in small and medium size alcohols. And B3P86 method may give accurate BDEs for larger alcohols we haven't studied. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Hydration of small anions: Calculations by the AM1 semiempirical method

The AM1 semiempirical molecular orbital method has been used to calculate successive heats of hydration of small anions, including hydride, hydroxide, and the halogen ions, for cluster sizes up to 11 water molecules surrounding the central anion. Heats of hydration agree with available experimental data to within a few kcal/mol. Structures, however, do not always agree well with available ab initio calculations on clusters with one or two water molecules. The results indicate that the AM1 semiempirical technique applied to finite-sized clusters must be used with caution in understanding how hydration affects the chemical reactions of anions.     

The isomerization equilibrium between cis and trans chloride ruthenium olefin metathesis catalysts from quantum mechanics calculations

The cis-trans chloride isomerization of a ruthenium olefin metathesis catalyst is studied using quantum mechanics (B3LYP DFT), including the Poisson-Boltzmann (PBF) continuum approximation. The predicted geometries agree with experiment. The energies in methylene chloride, lead to DeltaG = -0.70 kcal/mol and a cis:trans ratio of 76:24, quite close to the experimental value of DeltaG = -0.78 kcal/mol or c:t 78:22. In contrast, we predict that in benzene c:t = 4:96 in agreement with the experimental observation of only the trans isomer. Our calculated relative activation energies explain the observed difference in initiation rates and suggest that each isomer should be isolable in high ratio by simply changing solvent.     

General base catalysis for cleavage by the active-site cytosine of the hepatitis delta virus ribozyme: QM/MM calculations establish chemical feasibility

The hepatitis delta virus (HDV) ribozyme is an RNA motif embedded in human pathogenic HDV RNA. Previous experimental studies have established that the active-site nucleotide C75 is essential for self-cleavage of the ribozyme, although its exact catalytic role in the process remains debated. Structural data from X-ray crystallography generally indicate that C75 acts as the general base that initiates catalysis by deprotonating the 2'-OH nucleophile at the cleavage site, while a hydrated magnesium ion likely protonates the 5'-oxygen leaving group. In contrast, some mechanistic studies support the role of C75 acting as general acid and thus being protonated before the reaction. We report combined quantum chemical/molecular mechanical calculations for the C75 general base pathway, utilizing the available structural data for the wild type HDV genomic ribozyme as a starting point. Several starting configurations differing in magnesium ion placement were considered and both one-dimensional and two-dimensional potential energy surface scans were used to explore plausible reaction paths. Our calculations show that C75 is readily capable of acting as the general base, in concert with the hydrated magnesium ion as the general acid. We identify a most likely position for the magnesium ion, which also suggests it acts as a Lewis acid. The calculated energy barrier of the proposed mechanism, approximately 20 kcal/mol, would lower the reaction barrier by approximately 15 kcal/mol compared with the uncatalyzed reaction and is in good agreement with experimental data.     

Deprotonation of a histidine residue in aqueous solution using constrained ab initio molecular dynamics

The dissociation of a weak acid - a histidine residue - in water was investigated by means of constrained Car-Parrinello ab initio molecular dynamics. Both linear and coordination constraints were employed, and the structural, electronic, and dynamical transformations along the respective reaction coordinates were analyzed. The calculated potentials of mean force for the dissociation of a hydrogen atom from the Nepsilon and Ndelta positions of the imidazole ring reveal that protonated forms are approximately 9.0-9.5 kcal/mol more stable than the deprotonated. This result seems to agree well with the experimental estimate based on pKa. A possible transition state for the deprotonation has also been identified. Analysis of the electron localization function indicates that the proton transfer along the selected reaction path is not a fully concerted process.