COMPASS Force Field for 14 Inorganic Molecules, He, Ne, Ar, Kr, Xe, H2, O2, N2, NO, CO, CO2, NO2, CS2, and SO2, in Liquid Phases

2000 ◽  
Vol 104 (20) ◽  
pp. 4951-4957 ◽  
Author(s):  
Jie Yang ◽  
Yi Ren ◽  
An-min Tian ◽  
Huai Sun
Keyword(s):  
Force Field ◽  
Liquid Phases ◽  
Inorganic Molecules

scholarly journals A general-purpose machine-learning force field for bulk and nanostructured phosphorus

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Volker L. Deringer ◽  
Miguel A. Caro ◽  
Gábor Csányi
Keyword(s):  
Machine Learning ◽  
Force Field ◽  
Density Functional ◽  
Materials Science ◽  
General Purpose ◽  
Many Body ◽  
Functional Theory ◽  
Liquid Phases ◽  
Materials Modelling ◽  
Applied Fields

Abstract Elemental phosphorus is attracting growing interest across fundamental and applied fields of research. However, atomistic simulations of phosphorus have remained an outstanding challenge. Here, we show that a universally applicable force field for phosphorus can be created by machine learning (ML) from a suitably chosen ensemble of quantum-mechanical results. Our model is fitted to density-functional theory plus many-body dispersion (DFT + MBD) data; its accuracy is demonstrated for the exfoliation of black and violet phosphorus (yielding monolayers of “phosphorene” and “hittorfene”); its transferability is shown for the transition between the molecular and network liquid phases. An application to a phosphorene nanoribbon on an experimentally relevant length scale exemplifies the power of accurate and flexible ML-driven force fields for next-generation materials modelling. The methodology promises new insights into phosphorus as well as other structurally complex, e.g., layered solids that are relevant in diverse areas of chemistry, physics, and materials science.

Millimetre-wave and infrared spectroscopy of Br13 CN: anharmonic force field of cyanogen bromide from spectroscopic data and ab initio calculations

1997 ◽  
Vol 90 (3) ◽  
pp. 495-497
Author(s):  
CLAUDIO ESPOSTI ◽  
FILIPPO TAMASSIA ◽  
CRISTINA PUZZARINI ◽  
RICCARDO TARRONI ◽  
ZDENEK ZELINGER
Keyword(s):  
Infrared Spectroscopy ◽  
Force Field ◽  
Ab Initio Calculations ◽  
Ab Initio ◽  
Spectroscopic Data ◽  
Cyanogen Bromide ◽  
Millimetre Wave ◽  
Anharmonic Force

Molecular force field evaluation by empirical constraints

1976 ◽  
Vol 73 ◽  
pp. 1051-1057
Author(s):  
Sadao Isotani ◽  
Alain J.-P. Alix
Keyword(s):  
Force Field ◽  
Field Evaluation ◽  
Molecular Force ◽  
Molecular Force Field

In Memoriam. Professor Stefan ERNST

2015 ◽  
Vol 39 (4) ◽  
pp. 665-666
Author(s):  
Mirosław Chorazewski
Keyword(s):  
Secondary Education ◽  
Primary Education ◽  
Unexpected Death ◽  
Uranyl Compounds ◽  
Liquid Phases ◽  
German Speaking ◽  
In Memoriam ◽  
The University ◽  
Phd Thesis ◽  
Molecular Acoustics

Abstract It is with great sadness that we inform our readers about the recent death of Professor Stefan Ernst. Stefan Ernst was born in Piaśniki, Upper Silesia, on November 03, 1934, to parents of Polish-German descent. His primary education started during the war at a German-speaking school in Wirek and continued in Olesno, where he also got his secondary education. As chemistry studies were not yet available at the University ofWrocław in 1953, he started studying biology and switched to chemistry a year later. He received his master’s degree in chemistry in 1959, as one of the first graduates in that major. Then, he started his work on application of thermodynamics and molecular acoustics in investigation of liquid phases under the guidance of the Prof. Bogusława Jeżowska-Trzebiatowska. On 28 November 1967, he defended his PhD thesis entitled “Association-Dissociation Equilibria and the Structure of Uranyl Compounds in Organic Solvents” at the University of Wrocław. Professor Stefan Ernst was a linguist, a polyglot, a renowned thermodynamisist and a researcher of molecular acoustics. With great regret and shock we have learned of his sudden and unexpected death on August 03, 2014, in a hospital in Kraków.

Advances in Force Field Tailoring for Construction...

2005 ◽  
Author(s):  
Sam Wanis ◽  
Narayanan Komerath
Keyword(s):  
Force Field

Force-field tailoring: First-principles derivation of wall formation physics

2006 ◽  
Author(s):  
Sam Wanis ◽  
Narayanan Komerath
Keyword(s):  
Force Field ◽  
First Principles ◽  
Wall Formation

Optimization of a New Reactive Force Field for Silver - Based Materials

2020 ◽  
Author(s):  
Clément Dulong ◽  
Bruno Madebène ◽  
Susanna Monti ◽  
Johannes Richardi
Keyword(s):  
Force Field ◽  
Self Assembled Monolayers ◽  
The Novel ◽  
Reactive Force ◽  
Reactive Force Field ◽  
Energetic Properties ◽  
Extended Training ◽  
Geometrical Features ◽  
Assembled Monolayers ◽  
Gold Thiolate

<div><div><div><p>A new reactive force field based on the ReaxFF formalism is effectively parametrized against an extended training set of quantum chemistry data (containing more than 120 different structures) to describe accurately silver- and silver-thiolate systems. The results obtained with this novel representation demonstrate that the novel ReaxFF paradigm is a powerful methodology to reproduce more appropriately average geometric and energetic properties of metal clusters and slabs when compared to the earlier ReaxFF parametrizations dealing with silver and gold. ReaxFF cannot describe adequately specific geometrical features such as the observed shorter distances between the under-coordinated atoms at the cluster edges. Geometric and energetic properties of thiolates adsorbed on a silver Ag20 pyramid are correctly represented by the new ReaxFF and compared with results for gold. The simulation of self-assembled monolayers of thiolates on a silver (111) surface does not indicate the formation of staples in contrast to the results for gold-thiolate systems.</p></div></div></div>

Driving Torsion Scans with Wavefront Propagation

2020 ◽  
Author(s):  
Yudong Qiu ◽  
Daniel Smith ◽  
Chaya Stern ◽  
mudong feng ◽  
Lee-Ping Wang
Keyword(s):  
Potential Energy ◽  
Force Field ◽  
Degrees Of Freedom ◽  
Computational Cost ◽  
Initial Guess ◽  
Field Development ◽  
Force Field Development ◽  
Wavefront Propagation ◽  
Open Source Software Package

<div>The parameterization of torsional / dihedral angle potential energy terms is a crucial part of developing molecular mechanics force fields.</div><div>Quantum mechanical (QM) methods are often used to provide samples of the potential energy surface (PES) for fitting the empirical parameters in these force field terms.</div><div>To ensure that the sampled molecular configurations are thermodynamically feasible, constrained QM geometry optimizations are typically carried out, which relax the orthogonal degrees of freedom while fixing the target torsion angle(s) on a grid of values.</div><div>However, the quality of results and computational cost are affected by various factors on a non-trivial PES, such as dependence on the chosen scan direction and the lack of efficient approaches to integrate results started from multiple initial guesses.</div><div>In this paper we propose a systematic and versatile workflow called \textit{TorsionDrive} to generate energy-minimized structures on a grid of torsion constraints by means of a recursive wavefront propagation algorithm, which resolves the deficiencies of conventional scanning approaches and generates higher quality QM data for force field development.</div><div>The capabilities of our method are presented for multi-dimensional scans and multiple initial guess structures, and an integration with the MolSSI QCArchive distributed computing ecosystem is described.</div><div>The method is implemented in an open-source software package that is compatible with many QM software packages and energy minimization codes.</div>

Statistical Force-Field for Structural Modeling Using Chemical Cross-Linking/mass Spectrometry Distance Constraints

2018 ◽  
Author(s):  
Allan J. R. Ferrari ◽  
Fabio C. Gozzo ◽  
Leandro Martinez
Keyword(s):  
Mass Spectrometry ◽  
Amino Acid ◽  
Force Field ◽  
Protein Structures ◽  
Protein Structure Determination ◽  
Structural Modeling ◽  
Cross Linking ◽  
Amino Acid Residues ◽  
Distance Constraints ◽  
Chemical Cross Linking

<div><p>Chemical cross-linking/Mass Spectrometry (XLMS) is an experimental method to obtain distance constraints between amino acid residues, which can be applied to structural modeling of tertiary and quaternary biomolecular structures. These constraints provide, in principle, only upper limits to the distance between amino acid residues along the surface of the biomolecule. In practice, attempts to use of XLMS constraints for tertiary protein structure determination have not been widely successful. This indicates the need of specifically designed strategies for the representation of these constraints within modeling algorithms. Here, a force-field designed to represent XLMS-derived constraints is proposed. The potential energy functions are obtained by computing, in the database of known protein structures, the probability of satisfaction of a topological cross-linking distance as a function of the Euclidean distance between amino acid residues. The force-field can be easily incorporated into current modeling methods and software. In this work, the force-field was implemented within the Rosetta ab initio relax protocol. We show a significant improvement in the quality of the models obtained relative to current strategies for constraint representation. This force-field contributes to the long-desired goal of obtaining the tertiary structures of proteins using XLMS data. Force-field parameters and usage instructions are freely available at http://m3g.iqm.unicamp.br/topolink/xlff <br></p></div><p></p><p></p>

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>

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