The <scp>MolSSI</scp> QCA<scp>rchive</scp> project: An open‐source platform to compute, organize, and share quantum chemistry data

Smith, Daniel G. A.; Altarawy, Doaa; Burns, Lori A.; Welborn, Matthew; Naden, Levi N.; Ward, Logan; Ellis, Sam; Pritchard, Benjamin P.; Crawford, T. Daniel

doi:10.1002/wcms.1491

Cited by 70 publications

(73 citation statements)

References 60 publications

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“…The torsion scans shown in Figure 11 were run on QCArchive [18]. They were computed with TorsionDrive [20] and geomeTRIC [54], as standalone geometry optimizer interfaced with the QCEngine [55] project.…”

Section: Detailed Methodsmentioning

confidence: 99%

“…Formally, M ≤ 4 for hybrid DFT, although modern implementations of hybrid DFT scale asymptotically as N 2.2–2.3 [16]. Using QCArchive data [17,18], we found that empirically, hybrid DFT grows like N 2.6 for the DZVP basis [15] as shown for gradient evaluations in Figure 1, A. To achieve good sampling of the torsion profiles for adequate potential fits, constrained geometry optimizations need to be calculated at ≤ 15 0 intervals, for a minimum of 24 constrained geometry optimizations for a 1D torsion profile.…”

Section: Introductionmentioning

confidence: 99%

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Capturing non-local through-bond effects in molecular mechanics force fields I: Fragmenting molecules for quantum chemical torsion scans [Article v1.1]

Stern

Bayly²,

Smith

et al. 2020

Preprint

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Accurate molecular mechanics force fields for small molecules are essential for predicting protein-ligand binding affinities in drug discovery and understanding the biophysics of biomolecular systems. Torsion potentials derived from quantum chemical (QC) calculations are critical for determining the conformational distributions of small molecules, but are computationally expensive and scale poorly with molecular size. To reduce computational cost and avoid the complications of distal through-space intramolecular interactions, molecules are generally fragmented into smaller entities to carry out QC torsion scans. However, torsion potentials, particularly for conjugated bonds, can be strongly affected by through-bond chemistry distal to the torsion itself. Poor fragmentation schemes have the potential to significantly disrupt electronic properties in the region around the torsion by removing important, distal chemistries, leading to poor representation of the parent molecule’s chemical environment and the resulting torsion energy profile. Here we show that a rapidly computable quantity, the fractional Wiberg bond order (WBO), is a sensitive reporter on whether the chemical environment around a torsion has been disrupted. We show that the WBO can be used as a surrogate to assess the robustness of fragmentation schemes and identify conjugated bond sets. We use this concept to construct a validation set by exhaustively fragmenting a set of druglike organic molecules and examine their corresponding WBO distributions derived from accessible conformations that can be used to evaluate fragmentation schemes. To illustrate the utility of the WBO in assessing fragmentation schemes that preserve the chemical environment, we propose a new fragmentation scheme that uses rapidly-computable AM1 WBOs, which are available essentially for free as part of standard AM1-BCC partial charge assignment. This approach can simultaneously maximize the chemical equivalency of the fragment and the substructure in the larger molecule while minimizing fragment size to accelerate QC torsion potential computation for small molecules and reducing undesired through-space steric interactions.

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Section: Detailed Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Capturing non-local through-bond effects in molecular mechanics force fields I: Fragmenting molecules for quantum chemical torsion scans [Article v1.1]

Stern

Bayly²,

Smith

et al. 2020

Preprint

Self Cite

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“…Quantum chemical calculations (geometry optimizations and torsion scans) were performed on a distributed set of high-performance computing clusters using the MolSSI QCFractal [41] distributed quantum chemistry engine, with results deposited in the public MolSSI QCArchive Server (MQCAS) [42,43] to allow open public access to all data. We used a single level of theory for all QM calculations, B3LYP-D3(BJ) / DZVP [44][45][46][47].…”

Section: Selection Of Quantum Chemistry Methodologymentioning

confidence: 99%

Development and Benchmarking of Open Force Field v1.0.0, the Parsley Small Molecule Force Field

Qiu¹,

Smith²,

Boothroyd³

et al. 2020

Preprint

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We describe the structure and optimization of the Open Force Field 1.0.0 small molecule force field, code-named Parsley. Parsley uses the SMIRKS-native Open Force Field (SMIRNOFF) parameter assignment formalism in which parameter types are assigned directly by chemical perception, in contrast to traditional atom type-based approaches. This method provides a natural means to incorporate increasingly diverse chemistry without needlessly increasing force field complexity. In this work, we present essentially a full optimization of the valence parameters in the force field. The optimization was carried out with the ForceBalance tool and was informed by reference quantum chemical data that include torsion potential energy profiles, optimized gas-phase structures, and vibrational frequencies. These data were computed and are maintained with QCArchive, an open-source and freely available distributed computing and database software ecosystem. Tests of the resulting force field against compounds and data types outside the training set show improvements in optimized geometries and conformational energetics and demonstrate that Parsley's accuracy for liquid properties is similar to that of other general force fields. <br>

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“…What is the future direction of IOData? We aim to support parsing and writing additional file formats, and also to extend our support for writing input files and enable direct integration with QCEngine 21 . Our current to‐do list for IOData can be found on its GitHub's issue page, and we anticipate that most items will be resolved by the end of 2020.…”

Section: Frequently Asked Questionsmentioning

confidence: 99%

IOData: A python library for reading, writing, and converting computational chemistry file formats and generating input files

et al. 2020

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IOData is a free and open‐source Python library for parsing, storing, and converting various file formats commonly used by quantum chemistry, molecular dynamics, and plane‐wave density‐functional‐theory software programs. In addition, IOData supports a flexible framework for generating input files for various software packages. While designed and released for stand‐alone use, its original purpose was to facilitate the interoperability of various modules in the HORTON and ChemTools software packages with external (third‐party) molecular quantum chemistry and solid‐state density‐functional‐theory packages. IOData is designed to be easy to use, maintain, and extend; this is why we wrote IOData in Python and adopted many principles of modern software development, including comprehensive documentation, extensive testing, continuous integration/delivery protocols, and package management. This article is the official release note of the IOData library.

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The MolSSI QCArchive project: An open‐source platform to compute, organize, and share quantum chemistry data

Cited by 70 publications

References 60 publications

Capturing non-local through-bond effects in molecular mechanics force fields I: Fragmenting molecules for quantum chemical torsion scans [Article v1.1]

Capturing non-local through-bond effects in molecular mechanics force fields I: Fragmenting molecules for quantum chemical torsion scans [Article v1.1]

Development and Benchmarking of Open Force Field v1.0.0, the Parsley Small Molecule Force Field

IOData: A python library for reading, writing, and converting computational chemistry file formats and generating input files

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