Hydrophobic effect on chain folding. The trans to gauche isomerization of n-butane in water

Rosenberg, Robert; Mikkilineni, R.; Berne, B. J.

doi:10.1021/ja00390a043

Cited by 63 publications

(30 citation statements)

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“…Perhaps we should emphasize that the two calculations agree within 0.04 kcal/mol. Earlier values in the literature include -0.18 kcal/mol [50] and -0.10 kcal/mol [51] for simulations with the ST2 and TIPS2 water models, respectively.…”

Section: Equilibriamentioning

confidence: 99%

AM1-SM2 and PM3-SM3 parameterized SCF solvation models for free energies in aqueous solution

Cramer

Truhlar

1992

J Computer-Aided Mol Des

330

306

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Two new continuum solvation models have been presented recently, and in this paper they are explained and reviewed in detail with further examples. Solvation Model 2 (AM1-SM2) is based on the Austin Model 1 and Solvation Model 3 (PM3-SM3) on the Parameterized Model 3 semiempirical Hamiltonian. In addition to the incorporation of phosphorus parameters, both of these new models address specific deficiencies in the original Solvation Model 1 (AM1-SM1), viz., (1) more accurate account is taken of the hydrophobic effect of hydrocarbons, (2) assignment of heavy-atom surface tensions is based on the presence or absence of bonded hydrogen atoms, and (3) the treatment of specific hydration-shell water molecules is more consistent. The new models offer considerably improved performance compared to AM1-SM1 for neutral molecules and essentially equivalent performance for ions. The solute charges within the Parameterized Model 3 Hamiltonian limit the utility of PM3-SM3 for compounds containing nitrogen and possibly phosphorus. For other systems both AM1-SM2 and PM3-SM3 give realistic results, but AM1-SM2 in general outperforms PM3-SM3. Key features of the models are discussed with respect to alternative approaches.

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Section: Equilibriamentioning

confidence: 99%

AM1-SM2 and PM3-SM3 parameterized SCF solvation models for free energies in aqueous solution

Cramer

Truhlar

1992

J Computer-Aided Mol Des

330

306

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“…In computer simulation studies, 16,17,23,[26][27][28][29] both united-atom and all-atom solute models have been employed. Tobias and…”

Section: Introductionmentioning

confidence: 99%

“…The other one is an all-atom model, namely that all atoms of the n-butane molecule are considered as the sites of pair interactions. In this model, the hydrogens of the CH n groups are explicitly treated, each atom is assigned an atomic charge, and the CH n groups need not be neutral.In computer simulation studies, 16,17,23,[26][27][28][29] both united-atom and all-atom solute models have been employed. Tobias and…”

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confidence: 99%

Solvation Structure, Thermodynamics, and Molecular Conformational Equilibria for n-Butane in Water Analyzed by Reference Interaction Site Model Theory Using an All-Atom Solute Model

Cui

Smith

2002

J. Phys. Chem. B

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For the four thermodynamic states: temperature T ) 283. 15, 298.15, 313.15, and 328.15 K and the corresponding bulk water density F ) 0.9997, 0.9970, 0.9922, and 0.9875 g cm -3 , for which experimental data are available, we have studied hydration structure, hydration thermodynamics, and molecular conformational equilibria for n-butane in water at infinite dilution, by means of the hypernetted chain closure reference interaction site model (HNC-RISM) theory with an all-atom solute model. The hydration structures of the trans and the gauche conformers of n-butane are presented and analyzed at the atomic level in terms of the atomic solute-solvent radial distribution functions. With these radial distribution functions as input, the n-butane conformational average hydration free energies, energies, enthalpies, and entropies are calculated. At room temperature, the normalized equilibrium distribution of n-butane conformers, the water solvent-induced rotational free energy surface and the trans-gauche and trans-cis cavity thermodynamic properties are calculated. With the optimized nonbonded potential parameters based on the CHARMM96 all-atom model for alkanes (Yin, D.; Mackerell, A. D., Jr. J. Comput. Chem. 1998, 19, 334), n-butane hydration thermodynamics and its conformational equilibria in water are well described by the HNC-RISM theory in comparison with the available experimental and computer simulation results. We also calculated the solute density derivatives of the water-water radial distribution functions δh vv , with the optimized CHARMM96 all-atom model, the united-atom OPLS (optimized potentials for liquid simulations), and the all-atom OPLS models for n-butane, respectively. The δh vv (r) reflect the effect of increased pressure disrupting the hydrogen bonding between water molecules. The all-atom model seems to enhance such an effect due to the well-documented shortcoming of the RISM theory in the treatment of the excluded volume of so-called auxiliary sites. I. IntroductionTwo important problems in the study of the aqueous solution behavior of biomolecules are the restructuring of water around the molecules and the solvent influence on the conformational structure of the molecules. Small flexible hydrocarbon molecules have been used as models for studying those problems. 1 Among them, n-butane, which has only one conformational degree of freedom, is perhaps the simplest molecule available for studying the two problems at the same time. n-butane has been studied extensively in the gas phase, 1-8 in the neat liquid, 9-17 and in apolar 15,18-23 and aqueous solutions. 15,16,23-33 There are two kinds of models for representing the n-butane molecule. One is a united-atom model, namely that the methyl and methylene groups are approximately considered as one site of pair interactions, respectively. In this model, the hydrogens of the CH n groups are implicitly treated, the interaction sites for the CH n groups are centered on the carbons, and the CH n groups are all taken as neutral. The other one is an all-...

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“…[ kBT ] ( 8 ) Pu(A; A') cc P(A)exp from which we find for the unrestrained probability distribution P ( A):…”

Section: Construction Of the Free Energy Profile From The Reaction Comentioning

confidence: 99%

Conformational transitions of a dipeptide in water: Effects of imposed pathways using umbrella sampling techniques

Fraternali

Gunsteren

1994

Biopolymers

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SYNOPSISThe free energy difference between two states of a molecular system separated by an energy barrier can generally be computed using the technique of umbrella sampling along a chosen reaction coordinate or pathway. The effect of a particular choice of pathway upon the obtained free energy difference is investigated by molecular dynamics simulation of a model system consisting of a glycine dipeptide in aqueous solution. Two different reaction coordinates connecting the so-called C5 and C, conformations, one involving intramolecular hydrogen bonds and the other involving the peptide I #& angles, are considered.The Gibbs free energy differences AG( C5 -C,) are small in both cases, 1.5 f 1 kJ mol-' and 2.2 f 1 kJ mol-', respectively. The two different reaction coordinates yield free energy differences that are identical to within their statistical error. It is found that the exchange of solute-solute, solute-water, and water-water hydrogen bonds involves free energy changes of less than kBT, which points at the existence of a multitude of low free energy pathways connecting the C5 and C, dipeptide conformations. 0 1994 John Wiley & Sons, Inc. I NTRO DUCT10 NConformational equilibria, folding processes, complex formation, and reactions occurring in peptides and proteins happen on a great variety of time scales, ranging from picoseconds to minutes.' This poses severe problems to a theoretical treatment of these phenomena, e.g., by computer simulation methods. The most interesting transition processes have time scales much longer than the period of about 1 ns typical for present day molecular dynamics (MD) computer simulations, and therefore cannot realistically be studied by conventional MD simulations. The time period covered by a MD simulation should even be much longer than the relaxation time of the process of interest in order to perform a sufficiently extensive sampling of phase space and so allow for reliable averaging of the relevant physical quantities.In view of this state of affairs, it is of central importance to use and develop time-saving techniques, which allow for simulation on a longer time scale, or fnr an improved sampling of configuration Biopolymers, Vol. 34, 347-355 (1994) space. Such time-saving techniques, as they are used in classical simulations of molecular systems, have recently been reviewed.' One approach to enhance the efficiency of a simulation involving a transition process is to deform the potential energy function Vphys of the molecular system in such a manner that energy barriers to the configurational transition to be studied are lowered or circumvented. When the energy barrier that inhibits a configurational transition of a molecular system can be identified, one may force the system over the barrier by the application of umbrella sampling techniques3: an additional term V" that lowers the energy barrier is added to Vphys and the resulting relative probabilities of the configurations along the pathway over the (reduced) barrier are corrected for the effect of the addition...

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Hydrophobic effect on chain folding. The trans to gauche isomerization of n-butane in water

Cited by 63 publications

References 1 publication

AM1-SM2 and PM3-SM3 parameterized SCF solvation models for free energies in aqueous solution

AM1-SM2 and PM3-SM3 parameterized SCF solvation models for free energies in aqueous solution

Solvation Structure, Thermodynamics, and Molecular Conformational Equilibria for n-Butane in Water Analyzed by Reference Interaction Site Model Theory Using an All-Atom Solute Model

Conformational transitions of a dipeptide in water: Effects of imposed pathways using umbrella sampling techniques

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