scholarly journals A unified picture of the covalent bond within quantum-accurate force fields: From organic molecules to metallic complexes’ reactivity

2019 ◽  
Vol 5 (5) ◽  
pp. eaaw2210 ◽  
Author(s):  
Alessandro Lunghi ◽  
Stefano Sanvito
Keyword(s):  
Organic Molecules ◽  
Energy Surface ◽  
Force Fields ◽  
Covalent Bond ◽  
Organometallic Compounds ◽  
Molecular Systems ◽  
Physical Chemical ◽  
Atomistic Models ◽  
General Potential ◽  
Unified Description

Computational studies of chemical processes taking place over extended size and time scales are inaccessible by electronic structure theories and can be tackled only by atomistic models such as force fields. These have evolved over the years to describe the most diverse systems. However, as we improve the performance of a force field for a particular physical/chemical situation, we are also moving away from a unified description. Here, we demonstrate that a unified picture of the covalent bond is achievable within the framework of machine learning–based force fields. Ridge regression, together with a representation of the atomic environment in terms of bispectrum components, can be used to map a general potential energy surface for molecular systems at chemical accuracy. This protocol sets the ground for the generation of an accurate and universal class of potentials for both organic and organometallic compounds with no specific assumptions on the chemistry involved.

Hydration Free Energies of Organic Molecules in the FreeSolv Database Calculated with Polarized Atom In Molecules Atomic Charges and the GAFF Force Field.

2018 ◽  
Author(s):  
Maximiliano Riquelme ◽  
Alejandro Lara ◽  
David L. Mobley ◽  
Toon Vestraelen ◽  
Adelio R Matamala ◽  
...  
Keyword(s):  
Force Field ◽  
Functional Groups ◽  
Electrostatic Interactions ◽  
Organic Molecules ◽  
Force Fields ◽  
Chemical Elements ◽  
Atomic Charges ◽  
Free Energies ◽  
Molecular Systems ◽  
Solvent Model

<div>Computer simulations of bio-molecular systems often use force fields, which are combinations of simple empirical atom-based functions to describe the molecular interactions. Even though polarizable force fields give a more detailed description of intermolecular interactions, nonpolarizable force fields, developed several decades ago, are often still preferred because of their reduced computation cost. Electrostatic interactions play a major role in bio-molecular systems and are therein described by atomic point charges.</div><div>In this work, we address the performance of different atomic charges to reproduce experimental hydration free energies in the FreeSolv database in combination with the GAFF force field. Atomic charges were calculated by two atoms-in-molecules approaches, Hirshfeld-I and Minimal Basis Iterative Stockholder (MBIS). To account for polarization effects, the charges were derived from the solute's electron density computed with an implicit solvent model and the energy required to polarize the solute was added to the free energy cycle. The calculated hydration free energies were analyzed with an error model, revealing systematic errors associated with specific functional groups or chemical elements. The best agreement with the experimental data is observed for the MBIS atomic charge method, including the solvent polarization, with a root mean square error of 2.0 kcal mol<sup>-1</sup> for the 613 organic molecules studied. The largest deviation was observed for phosphor-containing molecules and the molecules with amide, ester and amine functional groups.</div>

scholarly journals Linear Atomic Cluster Expansion Force Fields for Organic Molecules: beyond RMSE

2021 ◽  
Author(s):  
David Peter Kovacs ◽  
Cas van der Oord ◽  
Jiri Kucera ◽  
Alice Allen ◽  
Daniel Cole ◽  
...  
Keyword(s):  
Potential Energy ◽  
Potential Energy Surface ◽  
Cluster Expansion ◽  
Organic Molecules ◽  
Energy Surface ◽  
Force Fields ◽  
Atomic Cluster ◽  
Symmetric Polynomials ◽  
Benchmark Datasets ◽  
Expansion Force

We demonstrate that fast and accurate linear force fields can be built for molecules using the Atomic Cluster Expansion (ACE) framework. The ACE models parametrize the Potential Energy Surface in terms of body ordered symmetric polynomials making the functional form reminiscent of traditional molecular mechanics force fields. We show that the 4 or 5-body ACE force fields improve on the accuracy of the empirical force fields by up to a factor of 10, reaching the accuracy typical of recently proposed machine learning based approaches. We not only show state of the art accuracy and speed on the widely used MD17 and ISO17 benchmark datasets, but also go beyond RMSE by comparing a number of ML and empirical force fields to ACE on more important tasks such as normal mode prediction, high temperature molecular dynamics, dihedral torsional profile prediction and even bond breaking. We also demonstrate the smoothness, transferability and extrapolation capabilities of ACE on a new challenging benchmark dataset comprising a potential energy surface of a flexible drug-like molecule.

Hydration Free Energies of Organic Molecules in the FreeSolv Database Calculated with Polarized Atom In Molecules Atomic Charges and the GAFF Force Field.

2018 ◽  
Author(s):  
Maximiliano Riquelme ◽  
Alejandro Lara ◽  
David L. Mobley ◽  
Toon Vestraelen ◽  
Adelio R Matamala ◽  
...  
Keyword(s):  
Force Field ◽  
Functional Groups ◽  
Electrostatic Interactions ◽  
Organic Molecules ◽  
Force Fields ◽  
Chemical Elements ◽  
Atomic Charges ◽  
Free Energies ◽  
Molecular Systems ◽  
Solvent Model

<div>Computer simulations of bio-molecular systems often use force fields, which are combinations of simple empirical atom-based functions to describe the molecular interactions. Even though polarizable force fields give a more detailed description of intermolecular interactions, nonpolarizable force fields, developed several decades ago, are often still preferred because of their reduced computation cost. Electrostatic interactions play a major role in bio-molecular systems and are therein described by atomic point charges.</div><div>In this work, we address the performance of different atomic charges to reproduce experimental hydration free energies in the FreeSolv database in combination with the GAFF force field. Atomic charges were calculated by two atoms-in-molecules approaches, Hirshfeld-I and Minimal Basis Iterative Stockholder (MBIS). To account for polarization effects, the charges were derived from the solute's electron density computed with an implicit solvent model and the energy required to polarize the solute was added to the free energy cycle. The calculated hydration free energies were analyzed with an error model, revealing systematic errors associated with specific functional groups or chemical elements. The best agreement with the experimental data is observed for the MBIS atomic charge method, including the solvent polarization, with a root mean square error of 2.0 kcal mol<sup>-1</sup> for the 613 organic molecules studied. The largest deviation was observed for phosphor-containing molecules and the molecules with amide, ester and amine functional groups.</div>

QUBEKit: Automating the Derivation of Force Field Parameters from Quantum Mechanics

2019 ◽  
Author(s):  
Joshua Horton ◽  
Alice Allen ◽  
Leela Dodda ◽  
Daniel Cole
Keyword(s):  
Quantum Mechanics ◽  
Force Field ◽  
Organic Molecules ◽  
Force Fields ◽  
Liquid Density ◽  
Small Organic Molecules ◽  
Automated Generation ◽  
Energy Of Hydration ◽  
Novel Method ◽  
Force Field Parameters

<div><div><div><p>Modern molecular mechanics force fields are widely used for modelling the dynamics and interactions of small organic molecules using libraries of transferable force field parameters. For molecules outside the training set, parameters may be missing or inaccurate, and in these cases, it may be preferable to derive molecule-specific parameters. Here we present an intuitive parameter derivation toolkit, QUBEKit (QUantum mechanical BEspoke Kit), which enables the automated generation of system-specific small molecule force field parameters directly from quantum mechanics. QUBEKit is written in python and combines the latest QM parameter derivation methodologies with a novel method for deriving the positions and charges of off-center virtual sites. As a proof of concept, we have re-derived a complete set of parameters for 109 small organic molecules, and assessed the accuracy by comparing computed liquid properties with experiment. QUBEKit gives highly competitive results when compared to standard transferable force fields, with mean unsigned errors of 0.024 g/cm3, 0.79 kcal/mol and 1.17 kcal/mol for the liquid density, heat of vaporization and free energy of hydration respectively. This indicates that the derived parameters are suitable for molecular modelling applications, including computer-aided drug design.</p></div></div></div>

QUBEKit: Automating the Derivation of Force Field Parameters from Quantum Mechanics

2019 ◽  
Author(s):  
Joshua Horton ◽  
Alice Allen ◽  
Leela Dodda ◽  
Daniel Cole
Keyword(s):  
Quantum Mechanics ◽  
Force Field ◽  
Organic Molecules ◽  
Force Fields ◽  
Liquid Density ◽  
Small Organic Molecules ◽  
Automated Generation ◽  
Energy Of Hydration ◽  
Novel Method ◽  
Force Field Parameters

<div><div><div><p>Modern molecular mechanics force fields are widely used for modelling the dynamics and interactions of small organic molecules using libraries of transferable force field parameters. For molecules outside the training set, parameters may be missing or inaccurate, and in these cases, it may be preferable to derive molecule-specific parameters. Here we present an intuitive parameter derivation toolkit, QUBEKit (QUantum mechanical BEspoke Kit), which enables the automated generation of system-specific small molecule force field parameters directly from quantum mechanics. QUBEKit is written in python and combines the latest QM parameter derivation methodologies with a novel method for deriving the positions and charges of off-center virtual sites. As a proof of concept, we have re-derived a complete set of parameters for 109 small organic molecules, and assessed the accuracy by comparing computed liquid properties with experiment. QUBEKit gives highly competitive results when compared to standard transferable force fields, with mean unsigned errors of 0.024 g/cm3, 0.79 kcal/mol and 1.17 kcal/mol for the liquid density, heat of vaporization and free energy of hydration respectively. This indicates that the derived parameters are suitable for molecular modelling applications, including computer-aided drug design.</p></div></div></div>

Insight into structure, stability and hydrogen bond in complexes of guanine and thymine at the molecular level using computational chemical method

2021 ◽  
Vol 11 (1) ◽  
pp. 127-134
Author(s):  
Nhung Ngo Thi Hong ◽  
Huong Dau Thi Thu ◽  
Trung Nguyen Tien
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Energy Surface ◽  
Covalent Bond ◽  
Electrostatic Energy ◽  
Substantial Contribution ◽  
Structure Stability ◽  
Dispersion Terms ◽  
Insight Into

Nine stable structures of complexes formed by interaction of guanine with thymine were located on potential energy surface at B3LYP/6-311++G(2d,2p). The complexes are quite stable with interaction energy from -5,8 to -17,7 kcal.mol-1. Strength of complexes are contributed by hydrogen bonds, in which a pivotal role of N−H×××O/N overcoming C−H×××O/N hydrogen bond, up to to 3.5 times, determines stabilization of complexes investigated. It is found that polarity of N/C−H covalent bond over proton affinity of N/O site governs stability of hydrogen bond in the complexes. The obtained results show that the N/C−H×××O/N red-shifting hydrogen bonds occur in all complexes, and a larger magnitude of an elongation of N−H compared C-H bond length accompanied by a decrease of its stretching frequency is detected in the N/C−H×××O/N hydrogen bond upon complexation. The SAPT2+ analysis indicates the substantial contribution of attractive electrostatic energy versus the induction and dispersion terms in stabilizing the complexes.

scholarly journals Low temperature reaction dynamics for CH3OH + OH collisions on a new full dimensional potential energy surface

2018 ◽  
Vol 20 (40) ◽  
pp. 25951-25958 ◽  
Author(s):  
Octavio Roncero ◽  
Alexandre Zanchet ◽  
Alfredo Aguado
Keyword(s):  
Low Temperature ◽  
Potential Energy ◽  
Potential Energy Surface ◽  
Low Temperatures ◽  
Organic Molecules ◽  
Energy Surface ◽  
Reaction Dynamics ◽  
Buffer Gas ◽  
Temperature Reaction ◽  
Formation Of Complexes

Is the rise of the rate constant measured in laval expansion experiments of OH with organic molecules at low temperatures due to the reaction between the reactants or due to the formation of complexes with the buffer gas?

scholarly journals Linear Atomic Cluster Expansion Force Fields for Organic Molecules: beyond RMSE

2021 ◽  
Author(s):  
David Peter Kovacs ◽  
Cas van der Oord ◽  
Jiri Kucera ◽  
Alice Allen ◽  
Daniel Cole ◽  
...  
Keyword(s):  
Cluster Expansion ◽  
Organic Molecules ◽  
Force Fields ◽  
Atomic Cluster ◽  
Expansion Force

scholarly journals Single Molecule Techniques Can Distinguish the Photophysical Processes Governing Metal-Enhanced Fluorescence

2022 ◽  
Author(s):  
Stefania Impellizzeri ◽  
Gregory J, Hodgson ◽  
Nicholas P. Dogantzis
Keyword(s):  
Single Molecule ◽  
Organic Molecules ◽  
Near Field ◽  
Comprehensive Understanding ◽  
Enhanced Fluorescence ◽  
Metal Enhanced Fluorescence ◽  
Maximum Enhancement ◽  
Molecular Systems ◽  
Photophysical Processes ◽  
Underlying Processes

<p>Plasmonic metal nanoparticles can impact the behaviour of organic molecules in a number of ways, including enhancing or quenching fluorescence. Only through a comprehensive understanding of the fundamental photophysical processes regulating nano-molecular interactions can these effects be controlled, and exploited to the fullest extent possible. Metal-enhanced fluorescence (MEF) is governed by two underlying processes, increased rate of fluorophore excitation and increased fluorophore emission, the balance between which has implications for optimizing hybrid nanoparticle-molecular systems for various applications. We report groundbreaking work on the use of single molecule fluorescence microscopy to distinguish between the two mechanistic components of MEF, in a model system consisting of two analogous boron dipyrromethene (BODIPY) fluorophores and triangular silver nanoparticles (AgNP). We demonstrate that the increased excitation MEF mechanism occurs to approximately the same extent for both dyes, but that the BODIPY with the higher quantum yield of fluorescence experiences a greater degree of MEF via the increased fluorophore emission mechanism, and higher overall enhancement, as a result of its superior ability to undergo near-field interactions with AgNP. We foresee that this knowledge and methodology will be used to tailor MEF to meet the needs of different applications, such as those requiring maximum enhancement of fluorescence intensity or instead prioritizing excited-state photochemistry. </p>

scholarly journals Linear Atomic Cluster Expansion Force Fields for Organic Molecules: beyond RMSE

2021 ◽  
Author(s):  
David Peter Kovacs ◽  
Cas van der Oord ◽  
Jiri Kucera ◽  
Alice Allen ◽  
Daniel Cole ◽  
...  
Keyword(s):  
Cluster Expansion ◽  
Organic Molecules ◽  
Force Fields ◽  
Atomic Cluster ◽  
Expansion Force
Sign in / Sign up

Export Citation Format

Share Document