Explicit ion, implicit water solvation for molecular dynamics of nucleic acids and highly charged molecules

An explicit ion, implicit water solvent model for molecular dynamics was developed and tested with DNA and RNA simulations. The implicit water model uses the finite difference Poisson (FDP) model with the smooth permittivity method implemented in the OpenEye ZAP libraries. Explicit counter-ions, co-ions, and nucleic acid were treated with a Langevin dynamics molecular dynamics algorithm. Ion electrostatics is treated within the FDP model when close to the solute, and by the Coulombic model when far from the solute. The two zone model reduces computation time, but retains an accurate treatment of the ion atmosphere electrostatics near the solute. Ion compositions can be set to reproduce specific ionic strengths. The entire ion/water treatment is interfaced with the molecular dynamics package CHARMM. Using the CHARMM-ZAPI software combination, the implicit solvent model was tested on A and B form duplex DNA, and tetraloop RNA, producing stable simulations with structures remaining close to experiment. The model also reproduced the A to B duplex DNA transition. The effect of ionic strength, and the structure of the counterion atmosphere around B form duplex DNA were also examined.     

Theoretical calculations on the cycloreversion of oxetane radical cations

The molecular mechanism for the cycloreversion of oxetane radical cations has been studied at the UB3LYP/6-31G* level. Calculations support that the cycloreversion takes place via a concerted but asynchronous process, where C-C bond breaking at the transition state is more advanced than O-C breaking. This allows a favorable rearrangement of the spin electron density from the oxetane radical cation (with the spin density located mainly on the oxygen atom) to the alkene radical cation which is one of the final products. Inclusion of solvent effects does not modify the gas-phase results.     

DFT study on the cycloreversion of thietane radical cations

The molecular mechanism of the cycloreversion (CR) of thietane radical cations has been analyzed in detail at the UB3LYP/6-31G* level of theory. Results have shown that the process takes place via a stepwise mechanism leading to alkenes and thiobenzophenone; alternatively, formal [4+2] cycloadducts are obtained. Thus, the CR of radical cations 1a,b(?+) is initiated by C2-C3 bond breaking, giving common intermediates INa,b. At this stage, two reaction pathways are feasible involving ion molecule complexes IMCa,b (i) or radical cations 4a,b(?+) (ii). Calculations support that 1a(?+) follows reaction pathway ii (leading to the formal [4+2] cycloadducts 5a). By contrast, 1b(?+) follows pathway i, leading to trans-stilbene radical cation (2b(?+)) and thiobenzophenone.     

Stepwise cycloreversion of oxetane radical cations with initial C-O bond cleavage

2,4,6-Triaryl(thia)pyrylium salts have been used as electron-transfer photosensitizers for the cycloreversion of the oxetane ring system. The radical cation of 2,3-diphenyl-4-hydroxymethyloxetane (1) undergoes stepwise splitting via initial O-C2 cleavage. Spin and charge in the resulting intermediate are located in the oxygen and carbon atoms, respectively. Subsequent intramolecular nucleophilic attack produces 2,3-diphenyl-4-hydroxytetrahydrofuran (4a). Formation of this product occurs in the submicrosecond time scale, competing with C3-C4 cleavage to the detectable (lambdamax = 470 nm) trans-stilbene radical cation.     

Explicit and implicit multi‐center integrations

We present truncated expansions of multicenter one‐electron nuclear attraction and two‐electron repulsion integrals over localized basis functions in terms of one‐ and two‐center integrals of “Coulomb,” “exchange,” and “hybrid” type. Two variants are discussed: the “Explicit Multi‐center Integrations” and the “Implicit Multi‐Center Integrations” (abbreviated as “EMCI” and “IMCI”, respectively). While EMCI also deals with individual integrals, the IMCI option is the more appealing one: it enables us to evaluate the entire matrix elements of “Restricted Hartree–Fock”‐type in a very effective and chemically meaningful way. Due to the diatomic nature of our expansions, integrations over “Slater‐Type Orbitals” become well‐feasible, too. © 2012 Wiley Periodicals, Inc.     

The solvation number of ions obtained from their entropies of solvation

The entropy of solvation of an ion contains contributions from i) the change of the volume at its disposal, ii) long-range electrostatic effects, iii) immobilization of solvent molecules in the first solvation shell, and iv) effects on the structure of the solvent. The last item is important in water, but can be ignored in less structured solvents. Standard ionic entropies of transfer from water to a dozen solvents are used for the estimation of the entropy of solvent immobilization, and the (extrapolated) entropy of freezing of the solvent is then used to estimate the number of solvent molecules immobilized.Presented in part at the IX ICNAS (International Conference on Non-Aqueous Solutions), Pittsburgh, PA, August 1984.     

Postprocessing of docked protein-ligand complexes using implicit solvation models

Molecular docking plays an important role in drug discovery as a tool for the structure-based design of small organic ligands for macromolecules. Possible applications of docking are identification of the bioactive conformation of a protein-ligand complex and the ranking of different ligands with respect to their strength of binding to a particular target. We have investigated the effect of implicit water on the postprocessing of binding poses generated by molecular docking using MM-PB/GB-SA (molecular mechanics Poisson-Boltzmann and generalized Born surface area) methodology. The investigation was divided into three parts: geometry optimization, pose selection, and estimation of the relative binding energies of docked protein-ligand complexes. Appropriate geometry optimization afforded more accurate binding poses for 20% of the complexes investigated. The time required for this step was greatly reduced by minimizing the energy of the binding site using GB solvation models rather than minimizing the entire complex using the PB model. By optimizing the geometries of docking poses using the GB(HCT+SA) model then calculating their free energies of binding using the PB implicit solvent model, binding poses similar to those observed in crystal structures were obtained. Rescoring of these poses according to their calculated binding energies resulted in improved correlations with experimental binding data. These correlations could be further improved by applying the postprocessing to several of the most highly ranked poses rather than focusing exclusively on the top-scored pose. The postprocessing protocol was successfully applied to the analysis of a set of Factor Xa inhibitors and a set of glycopeptide ligands for the class II major histocompatibility complex (MHC) A(q) protein. These results indicate that the protocol for the postprocessing of docked protein-ligand complexes developed in this paper may be generally useful for structure-based design in drug discovery.     

Density functional investigation on electron-transfer catalysis of cycloreversion of cyclobutane: radical anion mechanism

The mechanism of cycloreversion of cyclobutane radical anion (c-C(4)H(8) (-)) has been investigated at the UB3LYP/6-31++G(d,p) level, and compared with those of neutral c-C(4)H(8) and c-C(4)H(8) (+) radical cation. Although both c-C(4)H(8) (-) and C(2)H(4) are shown to be Rydberg states unstable with respect to electron ejection, the activation barrier for the "rotating" cycloreversion of c-C(4)H(8) (-) (37.3 kcal/mol) is lower by about 25.2 kcal/mol than that of c-C(4)H(8), and even the intervention of tetramethylene radical anion intermediate may reduce the activation barrier for the cycloreversion of c-C(4)H(8) by about 8.4 kcal/mol, mainly due to stronger electron-deficiency of intermediate biradical species than close-shell cyclobutanes. For the cycloreversion for c-C(4)H(8) (-), side isomerization reaction may be efficiently prevented by the low kinetic stability of tetramethylene radical anion intermediate towards dissociation, just different from the radical cation case. Our theoretical results have suggested the possibility of electron-attachment catalysis of the cycloreversion of some electron-deficient substituted cyclobutanes.     

Application of the level-set method to the implicit solvation of nonpolar molecules

A level-set method is developed for numerically capturing the equilibrium solute-solvent interface that is defined by the recently proposed variational implicit solvent model [Dzubiella, Swanson, and McCammon, Phys. Rev. Lett. 104, 527 (2006); J. Chem. Phys. 124, 084905 (2006)]. In the level-set method, a possible solute-solvent interface is represented by the zero level set (i.e., the zero level surface) of a level-set function and is eventually evolved into the equilibrium solute-solvent interface. The evolution law is determined by minimization of a solvation free energy functional that couples both the interfacial energy and the van der Waals type solute-solvent interaction energy. The surface evolution is thus an energy minimizing process, and the equilibrium solute-solvent interface is an output of this process. The method is implemented and applied to the solvation of nonpolar molecules such as two xenon atoms, two parallel paraffin plates, helical alkane chains, and a single fullerence C(60). The level-set solutions show good agreement for the solvation energies when compared to available molecular dynamics simulations. In particular, the method captures solvent dewetting (nanobubble formation) and quantitatively describes the interaction in the strongly hydrophobic plate system.     

Reductive PET cycloreversion of oxetanes: singlet multiplicity, regioselectivity, and detection of olefin radical anion

Cycloreversion of 2-(p-cyanophenyl)-4-methyl-3-phenyloxetane (1) is achieved using 1-methoxynaphthalene (2) as electron-transfer photosensitizer. The experimental results are consistent with the reaction taking place from the singlet excited state of the sensitizer. Ring splitting of the radical anion 1*- occurs with cleavage of O-C2 and C3-C4 bonds, leading to products (acetaldehyde and p-cyanostilbene) different from the reagents used in the Paterno-Büchi synthesis of 1. The olefin radical anion involved in the electron-transfer process has been detected by means of laser flash photolysis.     

Negative solvation of diamagnetic ions in methanol

Analysis of intramolecular contributions calculated from selective T₁ measurements for hydroxyl and methyl protons of methanol solutions of diamagnetic salts provides evidence of a negative solvation effect for I^?, ClO₄^? and CNS^? ions. At low concentrations the microdynamic behaviour of the hydroxyl group is strongly affected whereas that of the methyl group appears to be unchanged.     

On the solvation of ions in small water droplets

The solvations of positively and negatively charged model ions in water droplets have been studied using Monte Carlo simulations performed with a polarizable intermolecular potential function model. Special focus has been placed on the position of the ion in the water droplet. It was found that the sign of the ionic charge is of minor importance but an increased ionic charge localizes the ion to the central regions of the droplet, whereas a large polarizability and a large ionic radius favor locations close to the surface of the water droplet.     

Shared solvation of sodium ions in alcohol-water solutions explains the non-ideality of free energy of solvation

In order to explain the discrepancies between theories and experiments regarding the non-ideality in the free energy of solvation, here we present a microscopic picture of sodium ions dissolved in water-alcohol mixed solvents. We used X-ray absorption spectroscopy to probe the K-edge of sodium ions in mixed solvents of water and alcohols (methanol, ethanol) and in the respective pure solvents. In the mixed solvents a shared solvation of the sodium ions is observed. We find that specifically the water component plays a key role in stabilizing the solvation shell in mixed solvents, which was revealed by a selective photochemical process occurring only in the pure alcohol solvents.     

Single ionic partial molar volumes and solvation of ions

The limiting partial molar volumes of alkali metal halides in water and some other protic solvents have been dissected into individual ionic contributions. The extra-thermodynamic procedure employed assumes independent contributions of ion-solvent and solvent-solvent interactions to this property. The resulting parameters are found to be chemically reasonable and consistent with the molecular properties of the solvents. The limiting partial molar volume of the hydrogen ion has been calculated to be –4.2 cm³-mol^–1 in water at 25°C. Analysis of data for aqueous solutions from 0 to 50°C permits the evaluation of the energy change associated with the transfer of a water molecule from the bulk to the hydration zone. Results from the present work are compared with those obtained from the scaled particle theory.