Computer simulation of aqueous Na-Cl electrolytes

Hummer, Gerhard; Soumpasis, Dikeos Mario; Neumann, Martin

doi:10.1088/0953-8984/6/23a/018

Cited by 96 publications

(97 citation statements)

References 5 publications

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“…LMF theory suggests simplified simulation models for general Coulomb systems based on the mimic system that do not require special treatment of periodic boundary conditions. The shortranged intermolecular interactions in the Coulomb mimic system are reminiscent of the truncated interactions used in reaction field methods (18), but it was not very clear in those approaches how to choose an appropriate cutoff and how to treat nonuniform environments. The determination of min and the effective field in LMF theory provides a way to deal with both problems.…”

Section: Discussionmentioning

confidence: 99%

Local molecular field theory for effective attractions between like charged objects in systems with strong Coulomb interactions

Chen

Weeks

2006

Proc. Natl. Acad. Sci. U.S.A.

103

142

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Strong, short-ranged positional correlations involving counterions can induce a net attractive force between negatively charged strands of DNA and lead to the formation of ion pairs in dilute ionic solutions. However, the long range of the Coulomb interactions impedes the development of a simple local picture. We address this general problem by mapping the properties of a nonuniform system with Coulomb interactions onto those of a simpler system with short-ranged intermolecular interactions in an effective external field that accounts for the averaged effects of appropriately chosen long-ranged and slowly varying components of the Coulomb interactions. The remaining short-ranged components combine with the other molecular core interactions and strongly affect pair correlations in dense or strongly coupled systems. We show that pair correlation functions in the effective short-ranged system closely resemble those in the uniform primitive model of ionic solutions and illustrate the formation of ion pairs and clusters at low densities. The theory accurately describes detailed features of the effective attraction between two equally charged walls at strong coupling and intermediate separations of the walls. Analytical results for the minimal coupling strength needed to get any attraction and for the separation at which the attractive force is a maximum are presented.effective short-ranged model ͉ ion pairing ͉ mean field theory ͉ Poission-Boltzmann S trong Coulomb interactions in crowded, nonuniform environments have important experimental consequences in a wide variety of biophysical applications ranging from DNA packaging in viruses to transport in ion channels (1-4). These interactions present major challenges to theory and computer simulations not only because of their characteristic long range but also because they can be very strong at short distances. Here, we present a local molecular field (LMF) theory (5) that averages over particular long-ranged and slowly varying components of the Coulomb interactions (6) while still maintaining an accurate description of the short-ranged components. Our model provides a general and physically suggestive theory for strongly coupled Coulomb systems and reduces exactly to the classical Poisson-Boltzmann (PB) approximation for dilute, weakly coupled systems.We consider a general starting point where a molecule of species i, described by a rigid body frame with center at r i , interacts with an external field, fi (r i ), that comes from fixed charged solutes, or walls, or particular fixed molecules of a mobile species, as illustrated below. The subscript f indicates the source of the field, which we treat as a special fixed species f. The interaction between a pair of molecules of species i and j is assumed to have the general form w ij (r ij ) ϭ w s,ij (r ij ) ϩ w q,ij (r ij ), where r ij ϵ r j Ϫ r i . The w s,ij (r ij ) denote general (repulsive core and other), short-ranged intermolecular interactions. There are angular coordinates expressing orientations of the body fram...

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Section: Discussionmentioning

confidence: 99%

Local molecular field theory for effective attractions between like charged objects in systems with strong Coulomb interactions

Chen

Weeks

2006

Proc. Natl. Acad. Sci. U.S.A.

103

142

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“…The solvated systems are subjected to 500 steps of steepestdescent energy minimization and a 100-ps MD simulation at constant pressure and temperature, with P ϭ 1 atm (1 atm ϭ 101.3 kPa) and T ϭ 300 K. We use the force field of Cornell et al (39) and the suite of programs in AMBER 4.1 (40), modified to include the generalized reaction field treatment of electrostatic interactions (41,42) (with a cutoff of 8.0 Å) and the REMD algorithm. Nonbonded pair lists were updated every 10 integration steps.…”

Section: Methodsmentioning

confidence: 99%

α-Helical stabilization by side chain shielding of backbone hydrogen bonds

Garcı́a

Sanbonmatsu

2002

Proc. Natl. Acad. Sci. U.S.A.

442

470

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We study atomic models of the thermodynamics of the structural transition of peptides that form ␣-helices. The effect of sequence variation on ␣-helix formation for alanine-rich peptides, Ac-Ala21-methyl amide (A21) and Ac-A5 (AAARA)3A-methyl amide (Fs peptide), is investigated by atomic simulation studies of the thermodynamics of the helix-coil transition in explicit water. The simulations show that the guanidinium group in the Arg side chains in the Fs peptide interacts with the carbonyl group four amino acids upstream in the chain and desolvates backbone hydrogen bonds. This desolvation can be directly correlated with a higher probability of hydrogen bond formation. We find that Fs has higher helical content than A21 at all temperatures. A small modification in the AMBER force field reproduces the experimental helical content and helix-coil transition temperatures for the Fs peptide.D etailed all-atom molecular simulation of protein folding has been limited by the inadequacy of sampling and possible inaccuracies of the semiempirical force fields used in classical simulations. The development of techniques for efficient sampling and the refinement of semiempirical force fields are crucial for modeling protein folding, structure prediction, and complex formation. Small peptides have many of the complexities associated with the energy landscape of proteins (1) and are ideal systems to understand the role of competing interactions in determining protein structures. In this work, we study the thermodynamics of the helix-coil transition of short peptides for which ample experimental data exist. We use highly parallel algorithms that enable the efficient sampling of configurational space. We validate our results through comparison with experimental data and test the sensitivity of our results to small changes in the semiempirical force field.The elucidation of ␣-helical formation energetics is relevant for understanding protein folding mechanisms. In spite of the large number of experimental studies conducted in peptides, there is still much debate concerning the propensity of Ala residues to stabilize ␣-helices. Ingwall et al. (2) studied runs of Ala n , with n ϭ 10-1,000, flanked by Lys runs, and concluded that short (n ϳ 10) sequences of Ala peptides do not form helices in water (2, 3). Similar conclusions were drawn from studies of Ala-rich random sequences. However, short (13-21) Ala-rich peptides containing interior charged amino acid side chains are found to form helices with 70-90% helical content (4-7), and short runs of Ala n (n ϭ 13) flanked by two ornithine charged amino acid are found to be about 40% helical in water (8, 9). These data have been interpreted in terms of a large intrinsic propensity of Ala residues to form helices in water. Within the Lifson-Roig (10, 11) and Zimm-Bragg (12) models for the helix-coil transition, the intrinsic propensity of an amino acid to form a helix is a measure of the interactions of the amino acid with its own and nearest-neighbor amino acid backbone (11, 13). Theore...

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“…For simulation details, see Ref. 99. Figure 15 shows the excess chemical potential of spherical solutes as a function of their exclusion radius d with water.…”

Section: Salt Effects On Hydrophobic Hydrationmentioning

confidence: 99%

Hydrophobic Effects on a Molecular Scale

et al. 1998

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A theoretical approach is developed to quantify hydrophobic hydration and interactions on a molecular scale, with the goal of insight into the molecular origins of hydrophobic effects. The model is based on the fundamental relation between the probability for cavity formation in bulk water resulting from molecular-scale density fluctuations, and the hydration free energy of the simplest hydrophobic solutes, hard particles. This probability is estimated using an information theory (IT) approach, incorporating experimentally available properties of bulk water -the density and radial distribution function. The IT approach reproduces the simplest hydrophobic effects: hydration of spherical nonpolar solutes, the potential of mean force (PMF) between methane molecules, and solvent contributions to the torsional equilibrium of butane. Applications of this approach to study temperature and pressure effects provide new insights into the thermodynamics and kinetics of protein folding. The IT model relates the hydrophobic-entropy convergence observed in protein unfolding experiments to the macroscopic isothermal compressibility of water. A novel explanation for pressure denaturation of proteins follows from an analysis of the pressure stability of hydrophobic aggregates, suggesting that water penetrates the hydrophobic core of proteins at high pressures. This resolves a long-standing puzzle, whether pressure denaturation contradicts the hydrophobic-core model of protein stability. Finally, issues of "dewetting" of molecularly large nonpolar solutes are discussed in the context of a recently developed perturbation theory approach.

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Computer simulation of aqueous Na-Cl electrolytes

Cited by 96 publications

References 5 publications

Local molecular field theory for effective attractions between like charged objects in systems with strong Coulomb interactions

Local molecular field theory for effective attractions between like charged objects in systems with strong Coulomb interactions

α-Helical stabilization by side chain shielding of backbone hydrogen bonds

Hydrophobic Effects on a Molecular Scale

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