scispace - formally typeset
Open AccessJournal ArticleDOI

Molecular simulation by knowledgeable quantum atoms

Paul L. A. Popelier
- 24 Feb 2016 - 
- Vol. 91, Iss: 3, pp 033007
Reads0
Chats0
TLDR
The next-next-generation force field (QCTFF) as mentioned in this paper is a force field based on the atomistic kriging model, which can learn how fundamental energy quantities, as well as high-rank multipole moments, all associated with an atom of interest, vary with the precise positions of atomic neighbors.
Abstract
We are at the dawn of molecular simulations being carried out, literally, by atoms endowed by knowledge of how to behave quantum mechanically in the vicinity of other atoms. The 'next–next-generation' force field that aims to achieve this is called QCTFF, for now, although a more pronounceable name will be suggested in the conclusion. Classical force fields such as AMBER mimic the interatomic energy experienced by atoms during a molecular simulation, with simple expressions capturing a relationship between energy and nuclear position. Such force fields neither see the electron density nor exchange-delocalization itself, or exact electrostatic interaction; they only contain simple equations and elementary parameters such as point charges to imitate the energies between atoms. Next-generation force fields, such as AMOEBA, go further and make the electrostatics more accurate by introducing multipole moments and dipolar polarization. However, QCTFF goes even further and abolishes all traditional force field expressions (e.g. Hooke's law and extensions, Lennard-Jones) in favor of atomistic kriging models. These machine learning models learn how fundamental energy quantities, as well as high-rank multipole moments, all associated with an atom of interest, vary with the precise positions of atomic neighbors. As a result, all structural phenomena can be rapidly calculated as an interplay of intra-atomic energy, exchange-delocalization energy, electrostatic energy and dynamic correlation energy. The final QCTFF force field will generate a wealth of localized quantum information while being faster than a Car–Parrinello simulation (which does not generate local information). Isn't it enough to see that a garden is beautiful without having to believe that there are fairies at the bottom of it too? (Douglas Adams).

read more

Citations
More filters
Journal ArticleDOI

Fluorine Gauche Effect Explained by Electrostatic Polarization Instead of Hyperconjugation: An Interacting Quantum Atoms (IQA) and Relative Energy Gradient (REG) Study.

TL;DR: It is proposed that the cause of gauche stability is 1,3 C···F electrostatic polarization interactions, which means that if a number of fluorine atoms are aligned, then the stability due to polarization of nearby carbon atoms is increased.
Journal ArticleDOI

Quantifying Electron Correlation of the Chemical Bond

TL;DR: The Interacting Quantum Atoms (IQA) method is used to analyze the correlated part of the Møller-Plesset (MP) perturbation theory two-particle density matrix, which covers both bonds and nonbonded through-space atom-atom interactions within a molecule or molecular complex.
Journal ArticleDOI

The ANANKE relative energy gradient (REG) method to automate IQA analysis over configurational change.

TL;DR: The ANANKE method is proposed, which is based on the topological energy partitioning method called interacting quantum atoms (IQA), and able to explain the gauche effect, the torsional barrier in biphenyl, the arrow-pushing scheme of an enzymatic reaction, and halogen-alkane nucleophilic substitution reactions.
Journal ArticleDOI

Exponential Relationships Capturing Atomistic Short-Range Repulsion from the Interacting Quantum Atoms (IQA) Method.

TL;DR: It is shown that the corresponding atomic deformation energy is very well described by an exponential function, which matches the well-known Buckingham repulsive potential.
Journal ArticleDOI

Utilizing Machine Learning for Efficient Parameterization of Coarse Grained Molecular Force Fields.

TL;DR: It is found that Bayesian optimization is capable of reaching a force field of comparable performance to the the current state-of-the-art within 40 iterations.
References
More filters
Proceedings ArticleDOI

Particle swarm optimization

TL;DR: A concept for the optimization of nonlinear functions using particle swarm methodology is introduced, and the evolution of several paradigms is outlined, and an implementation of one of the paradigm is discussed.
Journal ArticleDOI

A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu

TL;DR: The revised DFT-D method is proposed as a general tool for the computation of the dispersion energy in molecules and solids of any kind with DFT and related (low-cost) electronic structure methods for large systems.
Journal ArticleDOI

Differential Evolution – A Simple and Efficient Heuristic for Global Optimization over Continuous Spaces

TL;DR: In this article, a new heuristic approach for minimizing possibly nonlinear and non-differentiable continuous space functions is presented, which requires few control variables, is robust, easy to use, and lends itself very well to parallel computation.
Journal ArticleDOI

Development and testing of a general amber force field.

TL;DR: A general Amber force field for organic molecules is described, designed to be compatible with existing Amber force fields for proteins and nucleic acids, and has parameters for most organic and pharmaceutical molecules that are composed of H, C, N, O, S, P, and halogens.
Journal ArticleDOI

5. Statistics for Spatial Data

TL;DR: Cressie et al. as discussed by the authors presented the Statistics for Spatial Data (SDS) for the first time in 1991, and used it for the purpose of statistical analysis of spatial data.
Related Papers (5)