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Chan M, Verstraelen T, Tehrani A, Richer M, Yang XD, Kim TD, Vöhringer-Martinez E, Heidar-Zadeh F, Ayers PW. The tale of HORTON: Lessons learned in a decade of scientific software development. J Chem Phys 2024; 160:162501. [PMID: 38651814 DOI: 10.1063/5.0196638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 02/28/2024] [Indexed: 04/25/2024] Open
Abstract
HORTON is a free and open-source electronic-structure package written primarily in Python 3 with some underlying C++ components. While HORTON's development has been mainly directed by the research interests of its leading contributing groups, it is designed to be easily modified, extended, and used by other developers of quantum chemistry methods or post-processing techniques. Most importantly, HORTON adheres to modern principles of software development, including modularity, readability, flexibility, comprehensive documentation, automatic testing, version control, and quality-assurance protocols. This article explains how the principles and structure of HORTON have evolved since we started developing it more than a decade ago. We review the features and functionality of the latest HORTON release (version 2.3) and discuss how HORTON is evolving to support electronic structure theory research for the next decade.
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Affiliation(s)
- Matthew Chan
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S-4L8, Canada
| | - Toon Verstraelen
- Center for Molecular Modeling (CMM), Ghent University, Technologiepark-Zwijnaarde 46, B-9052 Ghent, Belgium
| | - Alireza Tehrani
- Department of Chemistry, Queen's University, Kingston, Ontario K7L-3N6, Canada
| | - Michelle Richer
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S-4L8, Canada
| | - Xiaotian Derrick Yang
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S-4L8, Canada
| | - Taewon David Kim
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S-4L8, Canada
| | - Esteban Vöhringer-Martinez
- Departamento de Físico Química, Facultad de Ciencias Químicas, Universidad de Concepción, 4070371 Concepción, Chile
| | - Farnaz Heidar-Zadeh
- Department of Chemistry, Queen's University, Kingston, Ontario K7L-3N6, Canada
| | - Paul W Ayers
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S-4L8, Canada
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Petris PC, Becherer P, Fraaije JGEM. Alkane/Water Partition Coefficient Calculation Based on the Modified AM1 Method and Internal Hydrogen Bonding Sampling Using COSMO-RS. J Chem Inf Model 2021; 61:3453-3462. [PMID: 34165298 PMCID: PMC8317156 DOI: 10.1021/acs.jcim.0c01478] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
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We introduce a physics-based
model for calculating partition coefficients
of solutes between water and alkanes, using a combination of a semi-empirical
method for COSMO charge density calculation and statistical sampling
of internal hydrogen bonds (IHBs). We validate the model on the experimental
partition data (∼3500 molecules) of small organics, drug-like
molecules, and statistical assessment of modeling of proteins and
ligand drugs. The model combines two novel algorithms: a bond-correction
method for improving the calculation of COSMO charge density from
AM1 calculations and a sampling method to deal with IHBs. From a comparison
of simulated and experimental partition coefficients, we find a root-mean-square
deviation of roughly one log 10 unit. From IHB analysis, we know that
IHBs can be present in two states: open (in water) and closed (in
apolar solvent). The difference can lead to a shift of as much as
two log 10 units per IHB; not taking this effect into account can
lead to substantial errors. The method takes a few minutes of calculation
time on a single core, per molecule. Although this is still much slower
than quantitative structure–activity relationship, it is much
faster than molecular simulations and can be readily incorporated
into any screening method.
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Affiliation(s)
- Panagiotis C Petris
- Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands.,Siemens Industry Software Netherlands B.V., Galileiweg 8, 2333 BD Leiden, The Netherlands
| | - Paul Becherer
- Siemens Industry Software Netherlands B.V., Galileiweg 8, 2333 BD Leiden, The Netherlands
| | - Johannes G E M Fraaije
- Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands.,Siemens Industry Software Netherlands B.V., Galileiweg 8, 2333 BD Leiden, The Netherlands
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Riquelme M, Vöhringer-Martinez E. SAMPL6 Octanol-water partition coefficients from alchemical free energy calculations with MBIS atomic charges. J Comput Aided Mol Des 2020; 34:327-334. [PMID: 31960251 DOI: 10.1007/s10822-020-00281-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 01/08/2020] [Indexed: 12/14/2022]
Abstract
In molecular modeling the description of the interactions between molecules forms the basis for a correct prediction of macroscopic observables. Here, we derive atomic charges from the implicitly polarized electron density of 11 molecules in the SAMPL6 challenge using the Hirshfeld-I and Minimal Basis Set Iterative Stockholder (MBIS) partitioning method. These atomic charges combined with other parameters in the GAFF force field and different water/octanol models were then used in alchemical free energy calculations to obtain hydration and solvation free energies, which after correction for the polarization cost, result in the blind prediction of the partition coefficient. From the tested partitioning methods and water models the S-MBIS atomic charges with the TIP3P water model presented the smallest deviation from the experiment. Conformational dependence of the free energies and the energetic cost associated with the polarization of the electron density are discussed.
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Affiliation(s)
- Maximiliano Riquelme
- Instituto de Ciencias Químicas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Esteban Vöhringer-Martinez
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, Chile.
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