Solvation of the tautomeric forms of 2-oxopyrimidine in carbon tetrachloride solution: A Monte Carlo simulation

Solvation of both tautomeric forms of 2-oxopyrimidine by carbon tetrachloride has been investigated using the Monte Carlo method for a cluster consisting of 50 molecules at T=300 K. The results indicate that, in oposition to hydration, this solvation shifts the tautomeric equilibrium a little towards the lactim form, in agreement with experiment. The structure of the solvation shell in both tautomers closely resembles that of the pure solvent. Local minima of the interaction energy between n = 1, 2, 3, 4, 6 and 8 CCl₄ molecules and 2-oxopyrimidine have been examined. The results shed some light on the nature of the poor solubility of purines and pyrimidines in carbon tetrachloride.     

Solvent effects on the UV-visible absorption spectrum of benzophenone in water: a combined Monte Carlo quantum mechanics study including solute polarization

The entire ultraviolet-visible absorption spectrum of benzophenone in water is studied and compared with the same spectrum in gas phase. Five transitions are considered, and the corresponding solvatochromic shifts are obtained and compared to experiment. Using a sequential procedure of Monte Carlo simulations and quantum mechanical calculations, liquid configurations were generated and an averaged spectrum of the solution was calculated. The solute polarization was included by an iterative procedure where the atomic charges of the solute were obtained as an average with the solvent distribution. The calculated average dipole moment of benzophenone in water, with MP26-31++G(d,p), converges to the value of 5.84+/-0.05 D, 88% larger than the gas-phase value of 3.11 D. Using 100 statistically uncorrelated configurations and solvation shells with 235 explicit water molecules selected by a minimum-distance distribution of solvent shells, instead of the usual radial distribution, the excitation energies were obtained from solute-solvent all-valence-electron INDO/CIS calculations. The shift of the weak n-pi(*) transition is obtained as 2045+/-40 cm(-1) and the strong and broad pi-pi(*) shift as -1790+/-30 cm(-1). These results are in good agreement with the experimental values of 2200 and -1600 cm(-1), respectively. Standard procedure used by common force fields to generate atomic charges to describe the electrostatic moments of the solute, with HF6-31G(d), gives a dipole moment of 3.64 D. Using these standard charges in the simulation, the average shifts are calculated as 1395+/-35 and -1220+/-25 cm(-1), both about 600 cm(-1) smaller in magnitude than those obtained with the average converged fully polarized solute. The influence of the solute polarization in the solute-solvent interaction and, in particular, in solute-solvent hydrogen bonds is analyzed.     

Investigation of the tautomeric equilibrium of nucleic acid bases in aqueous solution

Relative constants of acidity and basicity of nucleic acid bases (NABs) and their tautomeric forms are calculated. The general characteristic of the effect of an aqueous solvent on the tautomeric equilibrium of NABs is formulated. It is shown that during the tautomeric transformation of NABs their acid-base properties change to the opposite ones. One of possible causes of the formation of complementary pairs with rare tautomeric forms of NABs is considered.     

Absorption and fluorescence spectra of uracil in the gas phase and in aqueous solution: a TD-DFT quantum mechanical study

Here we present the first computations of fluorescence spectra in aqueous solution at an accurate quantum mechanical level. From a methodological point of view, our study shows that by only taking into account both bulk effects and explicit solvent molecules it is possible to reproduce solvent effects on the energy and the intensities of the electronic spectra, especially for what concerns pi/pi* transition. The computed absorption and fluorescence spectra are in a good agreement with the available experimental results. The energy ordering between the lowest energy n-pi* and the pi/pi* transitions in uracil strongly depends on the nature of the embedding medium. The geometry of the first solvation shell is remarkably sensitive to the specific electronic state, suggesting that solvent degrees of freedom can act as S1/S2 coupling modes.     

Lactam/lactim tautomeric interconversion mechanism of 2-pyridone in aqueous solution

By means of the CNDO/2 method, the participation of a water molecule in the process of interconversion from the form lactam to lactim is rationalised.     

Probing supercritical water with the n-pi* transition of acetone: a Monte Carlo/quantum mechanics study

The n-pi(*) electronic transition of acetone is a convenient and important probe to study supercritical water. The solvatochromic shift of this transition in supercritical water (adopting the experimental condition of P=340.2 atm and T=673 K) has been studied theoretically using Metropolis NPT Monte Carlo (MC) simulation and quantum mechanics (QM) calculations based on INDO/CIS and TDDFT-B3LYP6-31+G(d) methods. MC simulations are used to analyze hydration shells, solute-solvent interaction, and for generating statistically relevant configurations for subsequent QM calculations of the n-pi(*) transition of acetone. The results show that the average number of hydrogen bonds between acetone and water is essentially 13 of that in normal water condition of temperature and pressure. But these hydrogen bonds have an important contribution in the solute stabilization and in the solute-solvent interaction. In addition, they respond for nearly half of the solvatochromic shift. The INDO/CIS calculations explicitly considering all valence electrons of the water molecules, using different solvation shells, up to the third shell (170 water molecules), give a solvatochromic shift of 670+/-36 cm(-1) in very good agreement with the experimentally inferred result of 500-700 cm(-1). It is found that the solvatochromic effect on n-pi(*) transition of acetone in the supercritical condition is essentially given by the first solvation shell. The time-dependent density-functional theory (TDDFT) calculations are also performed including all solvent molecules up to the third shell, now represented by point charges. This TDDFT-B3LYP6-31+G(d) also gives a good but slightly overestimated result of 825+/-65 cm(-1). For comparison the same study is also made for acetone in water at normal condition. Finally, all average results reported here are statistically converged.     

Reagents for electrophilic amination: a quantum Monte Carlo study

Electrophilic amination is an appealing synthetic strategy to construct carbon-nitrogen bonds. The authors explore the use of the quantum Monte Carlo method and a proposed variant of the electron pair localization function--the electron pair localization function density--as a measure of the nucleophilicity of nitrogen lone pairs as a possible screening procedure for electrophilic reagents.     

Quantum-chemical study of the mechanism of the hydrolysis of amides in the gas phase and in aqueous solution

The MNDO, AM1, and MNDO/M methods have been used to calculate the profile of the potential energy surface for the hydrolysis of formamide in the gas phase and in aqueous solution. Estimates have been made of the changes in the energy barrier in specific acid and base catalysis, and it is shown that in the absence of proton exchange between the reacting system and the solvent the interaction of the charged reactants with a polar medium impedes the reaction.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 8, pp. 1785–1792, August 1989.     

Uranyl complexes with diamide ligands: a quantum mechanics study of chelating properties in the gas phase

We report a quantum mechanical study on the complexes of UO(2)(2+) with diamide ligands L of malonamide and succinamide type, respectively, forming 6- and 7-chelate rings in their bidentate coordination to uranium. The main aims are to (i) assess how strong the chelate effect is (i.e., the preference for bi- versus monodentate binding modes of L), (ii) compare these ligands as a function of the chelate ring size, and (iii) assess the role of neutralizing counterions. For this purpose, we consider UO(2)L(2+), UO(2)L(2)(2+), UO(2)L(3)(2+), and UO(2)X(2)L type complexes with X(-) = Cl(-) versus NO(3)(-). Hartree-Fock and DFT calculations lead to similar trends and reveal the importance of saturation and steric repulsions ("strain") in the first coordination sphere. In the unsaturated UO(2)L(2+), UO(2)L(2)(2+), and UO(2)Cl(2)L complexes, the 7-ring chelate is preferred over the 6-ring chelate, and bidentate coordination is preferred over the monodentate one. However, in the saturated UO(2)(NO(3))(2)L complexes, the 6- and 7-chelating ligands have similar binding energies, and for a given ligand, the mono- and bidentate binding modes are quasi-isoenergetic. These conclusions are confirmed by the calculations of free energies of complexation in the gas phase. In condensed phases, the monodentate form of UO(2)X(2)L complexes should be further stabilized by coordination of additional ligands, as well as by interactions (e.g., hydrogen bonding) of the "free" carbonyl oxygen, leading to an enthalpic preference for this form, compared to the bidentate one. We also considered an isodesmic reaction exchanging one bidentate ligand L with two monoamide analogues, which reveals that the latter are clearly preferred (by 23-14 kcal/mol at the HF level and 24-12 kcal/mol at the DFT level). Thus, in the gas phase, the studied bidentate ligands are enthalpically disfavored, compared to bis-monodentate analogues. The contrast with trends observed in solution hints at the importance of "long range" forces (e.g., second shell interactions) and entropy effects on the chelate effect in condensed phases.     

Monte Carlo simulation of phase separation kinetics in a concentrated polymer solution

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Phase behavior of n-alkanes in supercritical solution: a Monte Carlo study

We present a coarse-grained model for n-alkanes in a supercritical solution, which is exemplified by a mixture of hexadecane and CO2. For pure hexadecane, the Monte Carlo simulations of the coarse-grained model reproduce the experimental phase diagram and the interfacial tension with good accuracy. For the mixture, the phase behavior sensitively depends on the compatibility of the polymer with the solvent. We present a global phase diagram with critical lines, which is in semiquantitative agreement with experiments. In this context we developed two computational schemes: The first adopts Wang-Landau sampling to the off-lattice grand canonical ensemble, the second combines umbrella sampling with an extrapolation scheme to determine the weight function. Additionally, we use Wertheim's theory (TPT1) to obtain the equation of state for our coarse-grained model of supercritical mixtures and discuss the behavior for longer alkanes.     

Monte Carlo simulation of a 1,4,7,10-tetraazacyclododecane/lithium complex in aqueous solution

Monte Carlo simulations have been carried out for the system consisting of a 1,4,7,10-tetraazacyclododecane (cyclen)-lithium complex in 201 water molecules. The volume of the periodic cube was calculated using the experimental density of pure water at 298 K and 1 atm of 1 g.cm(-)(3), plus additional space occupied by the complex. The geometry of the complex is the alternated form, where the ion is located at the center of the cyclen. The complex-water interaction was represented by the cyclen-water and lithium-water pair potentials, both of which were developed on the basis of ab initio calculations. The results show two layers of solvation shells consisting of 2 and 6.9 water molecules. Two water molecules in the first solvation shell (O(1) and O(2)) bind directly to the ion in which the ion-oxygen distance is 2.38 A, the dipole vector points to the ion, and rotation takes place around the ion-oxygen axis. In the next layer, 4 water molecules coordinate simultaneously to the first 2 water molecules in the first shell and the NH functional groups of cyclen. The remaining 2.9 water molecules in the second layer are also coordinated to be in the first half-hydration shell of O(1) and O(2).     

Bond dissocation and conformational energetics of tetrasulfur: a quantum Monte Carlo study

Variational Monte Carlo (VMC) and fixed-node diffusion Monte Carlo (DMC) calculations are performed for S4. The effect of single- and multireference trial functions, as well as choice of orbitals, is investigated for its effect on the quality of the Monte Carlo estimates. Estimates of symmetric (two S2 molecules) and asymmetric (S atom and S3 molecule) bond dissociation are reported. The conformational change of S4 from C2v to D2h defines a double-well potential and is also estimated. Multireference DMC with natural orbitals (DMC/NO) estimates the energy of the conformational change as 1.20(20) kcal/mol; the dissociation of the long S-S single bond is estimated at 21.1(1.3) kcal/mol, and the asymmetric bond energy is estimated as 53.2(2.4) kcal/mol. An estimate of the total atomization energy using multireference DMC/NO gives a value of 219.5(2.2) kcal/mol. The relative quality of result and implications for simplified trial function design are discussed.     

Ground and excited electronic states of azobenzene: a quantum Monte Carlo study

Large-scale quantum Monte Carlo (QMC) calculations of ground and excited singlet states of both conformers of azobenzene are presented. Remarkable accuracy is achieved by combining medium accuracy quantum chemistry methods with QMC. The results not only reproduce measured values with chemical accuracy but the accuracy is sufficient to identify part of experimental results which appear to be biased. Novel analysis of nodal surface structure yields new insights and control over their convergence, providing boost to the chemical accuracy electronic structure methods of large molecular systems.     

Theoretical study of the kojic acid structure in gas phase and aqueous solution

Density functional calculations at the B3LYP/6‐311++G** level have been performed to determine the ground‐state conformational preference for kojic acid, a widely used skin‐whitening, antibrowning, and antibacterial agent. It is found that the gas phase consists almost entirely of the 5‐hydroxy‐2‐(hydroxymethyl)‐4H‐pyran‐4‐one tautomer, although several rotamers of this are prevalent. In aqueous solution, however, other tautomers are also present. The validity of the calculations is confirmed by the observed FTIR, NMR, and UV–vis spectra, which show good correspondence with the theoretical spectra. The electronic interactions are interpreted in terms of charge and bond order analysis as well as the composition of the HOMO and LUMO. The calculations show that kojic acid has partial aromatic character and is a good nucleophile. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Polyelectrolyte shells of copolymer micelles in aqueous solutions: a Monte Carlo study

Multimolecular micelles, formed by polystyrene-block-poly(methacrylic acid) in water, are studied by lattice Monte Carlo method. Electrostatic interactions are calculated in the mean-field approximation by solving the Poisson-Boltzmann equation. The model is parametrized according to available experimental data. The dependence of micellar size on pH and ionic strength is calculated and compared with experimental data. A special attention is devoted to the behavior in solutions with a low ionic strength.     

Monte Carlo simulation of the self-assembly and phase behavior of semiflexible equilibrium polymers

Grand canonical Monte Carlo simulations of a simple model semiflexible equilibrium polymer system, consisting of hard sphere monomers reversibly self-assembling into chains of arbitrary length, have been performed using a novel sampling method to add or remove multiple monomers during a single MC move. Systems with two different persistence lengths and a range of bond association constants have been studied. We find first-order lyotropic phase transitions between isotropic and nematic phases near the concentrations predicted by a statistical thermodynamic theory, but with significantly narrower coexistence regions. A possible contribution to the discrepancy between theory and simulation is that the length distribution of chains in the nematic phase is bi-exponential, differing from the simple exponential distribution found in the isotropic phase and predicted from a mean-field treatment of the nematic. The additional short length-scale characterizing the distribution appears to arise from the lower orientational order of short chains. The dependence of this length-scale on chemical potential, bond association constant, and total monomer concentration has been examined.     

Freezing line of the Lennard-Jones fluid: a phase switch Monte Carlo study

We report a phase switch Monte Carlo (PSMC) method study of the freezing line of the Lennard-Jones (LJ) fluid. Our work generalizes to soft potentials the original application of the method to hard-sphere freezing and builds on a previous PSMC study of the LJ system by Errington [J. Chem. Phys. 120, 3130 (2004)]. The latter work is extended by tracing a large section of the Lennard-Jones freezing curve, the results of which we compare with a previous Gibbs-Duhem integration study. Additionally, we provide new background material regarding the statistical-mechanical basis of the PSMC method and extensive implementation details.