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Register a new userUsing nonlocal electrostatics for solvation free energy computations: ions and small molecules
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Added by
Andreas Hildebrandt
Publication date
2002
fields
Physics
and research's language is
English
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Solvation free energy is an important quantity in Computational Chemistry with a variety of applications, especially in drug discovery and design. The accurate prediction of solvation free energies of small molecules in water is still a largely unsolved problem, which is mainly due to the complex nature of the water-solute interactions. In this letter we develop a scheme for the determination of the electrostatic contribution to the solvation free energy of charged molecules based on nonlocal electrostatics involving a minimal parameter set which in particular allows to introduce atomic radii in a consistent way. We test our approach on simple ions and small molecules for which both experimental results and other theoretical descriptions are available for quantitative comparison. We conclude that our approach is both physically transparent and quantitatively reliable.
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A high level polarizable force field is used to study the temperature dependence of hydrophobic hydration of small-sized molecules from computer simulations. Molecular dynamics (MD) simulations of liquid water at various temperatures form the basis of free energy perturbation calculations that consider the onset and growth of a repulsive sphere. This repulsive sphere acts as a model construct for the hydrophobic species. In the present study, an extension is pursued for seven independent target temperatures, ranging from close to the freezing point almost up to the boiling point of liquid water under standard conditions. Care is taken to maintain proper physico-chemical model descriptions by cross-checking with experimental water densities at the selected target temperatures. The polarizable force field description of molecular water turns out to be suitable throughout the entire temperature domain considered. Derivatives of the computed free energies of hydrophobic hydration with respect to the temperature give access to the changes in entropy. In practice the entropy differential is determined from the negative of the slope of tangential lines formed at a certain target temperature in the free energy profile. The obtained changes in entropy are negative for small-sized cavities, and hence reconfirm the basic ideas of the Lum Chandler Weeks theory on hydrophobic hydration of small-sized solutes.
In the molecular dynamics calculations for the free energy of ions and ionic molecules, we often encounter wet charged molecular systems where electrical neutrality condition is broken. This causes a problem in the evaluation of electrostatic interaction under periodic boundary condition. A standard remedy for the problem is to consider a hypothetical homogeneous background charge density to neutralize the total system. Here, we present a new expression for the evaluation of electrostatic interactions for the system including the background charge by fast multipole method (FMM). Further, an efficient scheme to evaluate solute-solvent interaction energy by FMM has been developed to reduce the computation of far-field part. We have calculated hydration free energy of ions, Mg$^{2+}$, Na$^{+}$, and Cl$^{-}$ dissolved in neutral solvent using the new expression. The calculated free energy showed a good agreement with the result using well-established particle mesh Ewald method, demonstrating the validity of the present expression in the framework of FMM. An advantage of the present scheme is in an efficient free energy calculation of a large-scale charged systems (particularly over million particles) based on highly parallel computations.
The accurate modeling of the dielectric properties of water is crucial for many applications in physics, computational chemistry and molecular biology. This becomes possible in the framework of nonlocal electrostatics, for which we propose a novel formulation allowing for numerical solutions for the nontrivial molecular geometries arising in the applications mentioned before. Our approach is based on the introduction of a secondary field, $psi$, which acts as the potential for the rotation free part of the dielectric displacement field ${bf D}$. For many relevant models, the dielectric function of the medium can be expressed as the Greens function of a local differential operator. In this case, the resulting coupled Poisson (-Boltzmann) equations for $psi$ and the electrostatic potential $phi$ reduce to a system of coupled PDEs. The approach is illustrated by its application to simple geometries.
In the present work, we investigate the ionization of molecules of biological interest by the impact of multicharged ions in the intermediate to high energy range. We performed full non-perturbative distorted-wave calculations (CDW) for thirty-six collisional systems composed by six atomic targets: H, C, N, O, F, and S -which are the constituents of most of the DNA and biological molecules- and six charged projectiles (antiprotons, H, He, B, C, and O). On account of the radiation damage caused by secondary electrons, we inspect the energy and angular distributions of the emitted electrons from the atomic targets. We examine seventeen molecules: DNA and RNA bases, DNA backbone, pyrimidines, tetrahydrofuran (THF), and C n H n compounds. We show that the simple stoichiometric model (SSM), which approximates the molecular ionization cross sections as a linear combination of the atomic ones, gives reasonably good results for complex molecules. We also inspect the extensively used Toburen scaling of the total ionization cross sections of molecules with the number of weakly bound electrons. Based on the atomic CDW results, we propose new active electron numbers, which leads to a better universal scaling for all the targets and ions studied here in the intermediate to the high energy region. The new scaling describes well the available experimental data for proton impact, including small molecules. We perform full molecular calculations for five nucleobases and test a modified stoichiometric formula based on the Mulliken charge of the composite atoms. The difference introduced by the new stoichiometric formula is less than 3%, which indicates the reliability of the SSM to deal with this type of molecules. The results of the extensive ion-target examination included in the present study allow us to assert that the SSM and the CDW-based scaling will be useful tools in this area.
Transitional metal ions widely exist in biological environments and are crucial to many life-sustaining physiological processes. Recently, transition metal ion such as Cu$^{2+}$, Zn$^{2+}$, Ni$^{2+}$, have been shown can increase the solubilities of aromatic biomolecules. Comparing with Cu$^{2+}$, Zn$^{2+}$ shows less enhancement to the solubilities of biomolecules such as tryptophan (Trp). On the other hand, Zn$^{2+}$ has a higher concentration in human blood plasma and appears in protein the most among transition metal ions, clarifying whether Zn$^{2+}$ can enhance the solubilities of other aromatic amino acids is significantly important. Herein, we observed that the solubility of aromatic amino acid histidine (His) is greatly enhanced in ZnCl$_2$ solution. Based on first principle calculations, this enhancement of solubility is attributed to cation-$pi$ interaction between His and Zn$^{2+}$. Our results here are of great importance for the bioavailability of aromatic drugs and provide new insights for the understanding of physiological functions of Zn$^{2+}$.
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