A hybrid semiempirical quantum mechanical and lattice-sum method for electrostatic interactions in fluid simulations

1997 ◽  
Vol 107 (4) ◽  
pp. 1212-1217 ◽  
Author(s):  
Jiali Gao ◽  
Cristobal Alhambra
Keyword(s):  
Electrostatic Interactions ◽  
Quantum Mechanical ◽  
Lattice Sum

scholarly journals Long-ranged contributions to solvation free energies from theory and short-ranged models

2016 ◽  
Vol 113 (11) ◽  
pp. 2819-2826 ◽  
Author(s):  
Richard C. Remsing ◽  
Shule Liu ◽  
John D. Weeks
Keyword(s):  
Electrostatic Interactions ◽  
Large Contribution ◽  
Thermodynamic Quantities ◽  
Coulomb Interactions ◽  
Free Energies ◽  
Lattice Sum ◽  
Solvation Thermodynamics ◽  
Simulation Cell ◽  
Solvation Free Energies ◽  
Ionic Solutes

Long-standing problems associated with long-ranged electrostatic interactions have plagued theory and simulation alike. Traditional lattice sum (Ewald-like) treatments of Coulomb interactions add significant overhead to computer simulations and can produce artifacts from spurious interactions between simulation cell images. These subtle issues become particularly apparent when estimating thermodynamic quantities, such as free energies of solvation in charged and polar systems, to which long-ranged Coulomb interactions typically make a large contribution. In this paper, we develop a framework for determining very accurate solvation free energies of systems with long-ranged interactions from models that interact with purely short-ranged potentials. Our approach is generally applicable and can be combined with existing computational and theoretical techniques for estimating solvation thermodynamics. We demonstrate the utility of our approach by examining the hydration thermodynamics of hydrophobic and ionic solutes and the solvation of a large, highly charged colloid that exhibits overcharging, a complex nonlinear electrostatic phenomenon whereby counterions from the solvent effectively overscreen and locally invert the integrated charge of the solvated object.

Lattice‐sum methods for calculating electrostatic interactions in molecular simulations

1995 ◽  
Vol 103 (8) ◽  
pp. 3014-3021 ◽  
Author(s):  
Brock A. Luty ◽  
Ilario G. Tironi ◽  
Wilfred F. van Gunsteren
Keyword(s):  
Electrostatic Interactions ◽  
Molecular Simulations ◽  
Lattice Sum

The docking manoeuvre at a drug receptor: a quantum mechanical study of intercalative attack of ethidium and its carboxylated derivative on a DNA fragment

1979 ◽  
Vol 287 (1025) ◽  
pp. 571-604 ◽  
Keyword(s):  
Electrostatic Potential ◽  
Electrostatic Interactions ◽  
Dimensional Space ◽  
Receptor Interaction ◽  
Quantum Mechanical ◽  
Space Vehicles ◽  
Drug Molecule ◽  
Drug Molecules ◽  
Mechanical Methods ◽  
Drug Receptor

Various semi-empirical quantum mechanical methods have been used to investigate the docking manoeuvre of ethidium and of its carboxylated derivative at the (dC-dG) • (dC-dG) receptor. The objective of the work was to determine whether the drug attacks the receptor in a random orientation or is pre-aligned for effective docking. An analogy was made between the interaction and two docking space vehicles. Charge distributions were computed for the intercalative site and the drug molecules; from these distributions it was possible to map, in three-dimensional space, the molecular electrostatic potential surrounding the receptor. Perturbation of the receptor fields by an approaching drug molecule showed field neutralization and a shifting local minimum as docking proceeds. Most of the electrostatic potential surrounding the receptor was shown to be derived from the two ionized phosphate groups. The orientation of the drug molecule was studied in a simplified anionic field constructed to reproduce that of the receptor phosphates. Rotation of ethidium and p -carboxyphenylethidium round the Eulerian axes in this simulated anionic field showed up distinct preferences for orientation of drug molecules in the vicinity of the receptor. Probability distributions for rotational populations demonstrated clearly that the receptor induces an orientation in the approaching ligand. The energy involved in modification of the alignment could be attributed to electrostatic interactions over large separation distances and to induced electron delocalization as the drug approaches closer to the receptor. This partition of the energy was considered further by monitoring electron migration in the drug molecules and analysis of dipole moment fluctuations. Orientation restrictions reflect entropy changes in the association reaction; these are discussed with respect to their importance in determination of reaction kinetics, and in two established models for drug- receptor interaction, namely, the ‘lock and key’ and ‘zipper’ mechanisms.

scholarly journals Reinterpreting π-Stacking

2020 ◽  
Author(s):  
Kevin Carter-Fenk ◽  
John Herbert
Keyword(s):  
Electrostatic Interactions ◽  
Mechanical Energy ◽  
Intermolecular Forces ◽  
Protein Crystal ◽  
Energy Decomposition Analysis ◽  
Quantum Mechanical ◽  
Electrostatic Repulsion ◽  
Pi Stacking ◽  
Intermolecular Distances ◽  
Pi Interactions

The nature of pi-pi interactions has long been debated. The term "pi-stacking" is considered by some to be a misnomer, in part because overlapping pi-electron densities are thought to incur steric repulsion, and the physical origins of the widely-encountered "slip-stacked" motif have variously been attributed to either sterics or electrostatics, in competition with dispersion. Here, we use quantum-mechanical energy decomposition analysis to investigate pi-pi interactions in supramolecular complexes of polycyclic aromatic hydrocarbons, ranging in size up to realistic models of graphene, and for comparison we perform the same analysis on stacked complexes of polycyclic <i>saturated</i> hydrocarbons, which are cyclohexane-based analogues of graphane. Our results help to explain the short-range structure of liquid hydrocarbons that is inferred from neutron scattering, trends in melting-point data, the interlayer separation of graphene sheets, and finally band gaps and observation of molecular plasmons in graphene nanoribbons. Analysis of intermolecular forces demonstrates that aromatic pi-pi interactions constitute a unique and fundamentally quantum-mechanical form of non-bonded interaction. Not only do stacked pi-pi architectures enhance dispersion, but quadrupolar electrostatic interactions that may be repulsive at long range are rendered attractive at the intermolecular distances that characterize pi-stacking, as a result of charge penetration effects. The planar geometries of aromatic sp<sup>2</sup> carbon networks lead to attractive interactions that are "served up on a molecular pizza peel", and adoption of slip-stacked geometries minimizes steric (rather than electrostatic) repulsion. The slip-stacked motif therefore emerges not as a defect induced by electrostatic repulsion but rather as a natural outcome of a conformation landscape that is dominated by van der Waals interactions (dispersion plus Pauli repulsion), and is therefore fundamentally quantum-mechanical in its origins. This reinterpretation of the forces responsible for pi-stacking has important implications for the manner in which non-bonded interactions are modeled using classical force fields, and for rationalizing the prevalence of the slip-stacked pi-pi motif in protein crystal structures.<br><br>

scholarly journals Reinterpreting π-Stacking

2020 ◽  
Author(s):  
Kevin Carter-Fenk ◽  
John Herbert
Keyword(s):  
Electrostatic Interactions ◽  
Mechanical Energy ◽  
Intermolecular Forces ◽  
Protein Crystal ◽  
Energy Decomposition Analysis ◽  
Quantum Mechanical ◽  
Electrostatic Repulsion ◽  
Pi Stacking ◽  
Intermolecular Distances ◽  
Pi Interactions

The nature of pi-pi interactions has long been debated. The term "pi-stacking" is considered by some to be a misnomer, in part because overlapping pi-electron densities are thought to incur steric repulsion, and the physical origins of the widely-encountered "slip-stacked" motif have variously been attributed to either sterics or electrostatics, in competition with dispersion. Here, we use quantum-mechanical energy decomposition analysis to investigate pi-pi interactions in supramolecular complexes of polycyclic aromatic hydrocarbons, ranging in size up to realistic models of graphene, and for comparison we perform the same analysis on stacked complexes of polycyclic <i>saturated</i> hydrocarbons, which are cyclohexane-based analogues of graphane. Our results help to explain the short-range structure of liquid hydrocarbons that is inferred from neutron scattering, trends in melting-point data, the interlayer separation of graphene sheets, and finally band gaps and observation of molecular plasmons in graphene nanoribbons. Analysis of intermolecular forces demonstrates that aromatic pi-pi interactions constitute a unique and fundamentally quantum-mechanical form of non-bonded interaction. Not only do stacked pi-pi architectures enhance dispersion, but quadrupolar electrostatic interactions that may be repulsive at long range are rendered attractive at the intermolecular distances that characterize pi-stacking, as a result of charge penetration effects. The planar geometries of aromatic sp<sup>2</sup> carbon networks lead to attractive interactions that are "served up on a molecular pizza peel", and adoption of slip-stacked geometries minimizes steric (rather than electrostatic) repulsion. The slip-stacked motif therefore emerges not as a defect induced by electrostatic repulsion but rather as a natural outcome of a conformation landscape that is dominated by van der Waals interactions (dispersion plus Pauli repulsion), and is therefore fundamentally quantum-mechanical in its origins. This reinterpretation of the forces responsible for pi-stacking has important implications for the manner in which non-bonded interactions are modeled using classical force fields, and for rationalizing the prevalence of the slip-stacked pi-pi motif in protein crystal structures.<br><br>

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