Hydrophobic hydration at the level of primitive models

Structural changes which take place in bulk water when a molecule of an apolar solute is brought therein are studied at a very basic elementary level. Water is modelled by two different types of extended primitive models and the solute is a hard sphere. The model mixture, which does not incorporate any water—solute interaction but the hard-core repulsion and is free of any adjustable parameter, is shown to predict the site—site correlation functions and details of the orientational arrangement of water molecules in the first hydration shell in full agreement with results obtained using complex realistic potentials.     

Cluster integrals of convex molecule systems

Cluster integrals assigned to particles interacting via the Kihara non-spherical potential are studied theoretically. An exact formula is derived which allows one to consider the effect of molecular shape separately from the effect of soft interactions. Employing the proposed formalism, the cluster integrals are analysed. The approach is applied to determine the third virial coefficient and an efficient computational method is developed. The third virial coefficient was calculated for a combination of molecules with hard cores of prolate spher-ocylindrical- and spherical shapes interacting via the square-well, triangle-well and 12-6 pair potentials. Comparison with numerical results obtained by Monte Carlo integration is made and fair agreement is found.     

Pair approximation for polarization interaction and adiabatic nuclear and electronic sampling method for fluids with dipole polarizability

The adiabatic nuclear and electronic sampling method (ANES), originally formulated as an efficient Monte Carlo algorithm for systems with fluctuating charges, is applied to the simulation of a polarizable water model with induced dipole moments. Structural, thermodynamic and dipolar properties obtained by ANES and a newer algorithm, the pair approximation for polarization interaction (PAPI), are compared with full iteration. With the best parameters, the inaccuracy of both approximate methods was found to be comparable with the uncertainty of the full iteration. The PAPI method with iteration radius equal to the second minimum of the oxygen—oxygen correlation function is, depending on the convergence tolerance, 10–15 times faster than the full iteration for 256 molecules, and yields very accurate structure and thermodynamics with deviation about 0.3%. When the iteration radius is increased to the cutoff distance, exact results are recovered at the cost of decreased efficiency. The ANES method with small nuclear displacements proved to inefficiently sample the configurational space. Simulations at low electronic temperatures with large nuclear displacements are inaccurate for up to 100 electronic moves, and increasing this number would make the simulations as slow as the full iteration. The most accurate and efficient adiabatic ANES simulations are those with infinite electronic temperature, large nuclear displacements and 1–10 electronic moves. The extra freedom of induced dipoles in the ANES method at high electronic temperatures modifies the observed dipolar properties; however, the question of whether the dielectric constant is also modified needs further consideration.     

About one - an inquiry about the meanings and uses of the number one

The story of the number one is told. The long struggle to recognize one as a number is described. The role of the number one in philosophy, religion, mathematics and science is briefly discussed. Finally, the relationship between one and some other numbers is presented.     

Fluids of pseudo-hard bodies II. Reference models for water,methanol, and ammonia

Pseudo-hard body fluids resulting from extended primitive models of water, methanol, and ammonia have been investigated both by computer simulations and theory for a number of geometrical parameters. It is shown that none of the existing equations of state and integral equations for the site-site correlation functions is able to describe the properties of the pseudohard body fluids reasonably accurately. For the equation of state an accurate semi-empirical method is proposed and for the site-site correlation functions the reference average Mayer function perturbation theory has been found to perform at least qualitatively correctly, which is not the case with Ornstein-Zernike equation based theories.     

Thermodynamics of binding of Zn2+ to carbonic anhydrase inhibitors

The Becke3LYP functional of DFT theory and the two-layered ONIOM (B3LYP/6–311 + G(d,p): MNDO) method were used to characterize 46 gas-phase complexes of 34 neutral and anionic ligands (H₂O, CH₃OH, CH₃COOH, CH₃CONH₂, HOSO₂NH₂, CO₂, HSO₂NH₂, CH₃SO₂NH₂, CH₃C(= O)NHOH, imidazole, NH₂SO₂NH₂, anions of 4-aminobenzenesulphonamide, saccharin, 1I9L, brinzolamide, dorzolamide, acetazolamide, further HO^(?), CH₃CO^(?), CH₃COO^(?), CH₃CONH^(?), N = N = N^(?), S = C = N^(?), CH₃C(= O)NHO^(?), HOCOO^(?), imidazoleN^(?), phenol-O^(?), HOSO₂NH^(?), ^(?)OSO₂NH^(?), ^(?)OSO₂NH₂, H₂NSO₂NH^(?), HSO₂NH^(?), CH₃SO₂NH^(?), and CF₃SO₂NH^(?), respectively) with Zn²⁺. Proton dissociation enthalpies and Gibbs energies of acidic inhibitors in the presence of zinc were computed. Their gas-phase acidity considerably increases upon chelation. Of the bases investigated, the weakest zinc affinity is exhibited by carbon dioxide (- 313.5 kJ mol^?1). Deprotonated inhibitors have higher affinities for zinc than the neutral ones. Compared to the other mono-deprotonated ligands the acetohydroxamic acid anion has the highest affinity for zinc (- 1872.7 kJ mol^?1). The zinc affinity of the acetazolamide anion computed using the hybrid ONIOM (B3LYP/6-311 + G(d,p): MNDO) method is in very good agreement with the full DFT ones and this method can be adopted to model large complexes of inhibitors with the active site of carbonic anhydrase.     

Substituent effects on gas-phase acidities of formic acid and its silicon and sulphur derivatives R − M(= X)XH(M = C., Si; X = O,S; R = H,F, CI,OH, NH2 and CH3)

Ab initio molecular orbital methods at the CBS-Q level of theory have been used to study the effect of substituent (F, Cl, NH₂, OH and CH₃) on the gas-phase acidities of formic acid, HCOOH, its silicon and sulphur derivatives R-M(= X)XH(M = C., Si; X = 0, S; R = F, Cl, OH, NH₂ and CH₃). For formic acid and its thio and dithio derivatives the acidity changes upon substitution are irregular and depend on both the type of substituent, position and degree of replacement of oxygen atoms by sulphur atoms. For sila carboxylic acids and their thio and dithio derivatives the calculated acidities regularly increase in the order: R-SiOOH < R-Si(=S)OH ? R-Si(=O)SH < R-SiSSH(R = H, F, Cl, OH, NH₂ and CH₃). The chloro derivatives are the strongest among the acids studied. The highest gas phase acidity (1277.6 kJmol^?1) has been calculated for ClC(=S)OH.     

Hydrophobic hydration at the level of primitive models. II: Large solutes and water restructuring

Details of structural changes that take place in water near an apolar solute have been studied by Monte Carlo simulations for hard sphere solutes of increasing size, including the limiting case of water at a hard structureless wall. Water has been modelled by two different types of extended primitive model, the four-site EPM4 model and five-site EPM5 model. Two different patterns of the orientational ordering of the water molecules around the solute as a function of its size have been found. For the EPM5 model, the structure of water and the orientation of its molecules near an apolar solute of finite diameter do not seem to be sensitive to the size of the solute, and only become more pronounced when the solute becomes a hard wall. On the other hand, the orientation ordering of the EPM4 molecules gradually changes with increasing size of the solute, and for solutes larger than approximately five times the size of the water molecule it is opposite to that near a small solute. A novel method to evaluate the excess chemical potential of large solutes has been implemented, and some thermodynamic quantities for water (distribution of hydrogen bonds and the excess chemical potential) have been computed as a function of the distance from the solute.