1
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Behara PK, Jang H, Horton JT, Gokey T, Dotson DL, Boothroyd S, Bayly CI, Cole DJ, Wang LP, Mobley DL. Benchmarking Quantum Mechanical Levels of Theory for Valence Parametrization in Force Fields. J Phys Chem B 2024; 128:7888-7902. [PMID: 39087913 PMCID: PMC11331531 DOI: 10.1021/acs.jpcb.4c03167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/09/2024] [Accepted: 07/15/2024] [Indexed: 08/02/2024]
Abstract
A wide range of density functional methods and basis sets are available to derive the electronic structure and properties of molecules. Quantum mechanical calculations are too computationally intensive for routine simulation of molecules in the condensed phase, prompting the development of computationally efficient force fields based on quantum mechanical data. Parametrizing general force fields, which cover a vast chemical space, necessitates the generation of sizable quantum mechanical data sets with optimized geometries and torsion scans. To achieve this efficiently, choosing a quantum mechanical method that balances computational cost and accuracy is crucial. In this study, we seek to assess the accuracy of quantum mechanical theory for specific properties such as conformer energies and torsion energetics. To comprehensively evaluate various methods, we focus on a representative set of 59 diverse small molecules, comparing approximately 25 combinations of functional and basis sets against the reference level coupled cluster calculations at the complete basis set limit.
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Affiliation(s)
- Pavan Kumar Behara
- Center
for Neurotherapeutics, University of California, Irvine, California 92697, United States
| | - Hyesu Jang
- Chemistry
Department, University of California at
Davis, Davis, California 95616, United States
- OpenEye
Scientific Software, Santa
Fe, New Mexico 87508, United States
| | - Joshua T. Horton
- School
of Natural and Environmental Sciences, Newcastle
University, Newcastle
upon Tyne NE1 7RU, U.K.
| | - Trevor Gokey
- Department
of Chemistry, University of California, Irvine, California 92697, United States
| | - David L. Dotson
- The
Open Force Field Initiative, Open Molecular Software Foundation, Davis, California 95616, United States
- Datryllic
LLC, Phoenix, Arizona 85003, United States
| | | | | | - Daniel J. Cole
- School
of Natural and Environmental Sciences, Newcastle
University, Newcastle
upon Tyne NE1 7RU, U.K.
| | - Lee-Ping Wang
- Chemistry
Department, University of California at
Davis, Davis, California 95616, United States
| | - David L. Mobley
- Center
for Neurotherapeutics, University of California, Irvine, California 92697, United States
- Department
of Chemistry, University of California, Irvine, California 92697, United States
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2
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Wang L, Behara PK, Thompson MW, Gokey T, Wang Y, Wagner JR, Cole DJ, Gilson MK, Shirts MR, Mobley DL. The Open Force Field Initiative: Open Software and Open Science for Molecular Modeling. J Phys Chem B 2024; 128:7043-7067. [PMID: 38989715 DOI: 10.1021/acs.jpcb.4c01558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
Force fields are a key component of physics-based molecular modeling, describing the energies and forces in a molecular system as a function of the positions of the atoms and molecules involved. Here, we provide a review and scientific status report on the work of the Open Force Field (OpenFF) Initiative, which focuses on the science, infrastructure and data required to build the next generation of biomolecular force fields. We introduce the OpenFF Initiative and the related OpenFF Consortium, describe its approach to force field development and software, and discuss accomplishments to date as well as future plans. OpenFF releases both software and data under open and permissive licensing agreements to enable rapid application, validation, extension, and modification of its force fields and software tools. We discuss lessons learned to date in this new approach to force field development. We also highlight ways that other force field researchers can get involved, as well as some recent successes of outside researchers taking advantage of OpenFF tools and data.
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Affiliation(s)
- Lily Wang
- Open Force Field, Open Molecular Software Foundation, Davis, California 95616, United States
| | - Pavan Kumar Behara
- Center for Neurotherapeutics, University of California, Irvine, California 92697, United States
| | - Matthew W Thompson
- Open Force Field, Open Molecular Software Foundation, Davis, California 95616, United States
| | - Trevor Gokey
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Yuanqing Wang
- Simons Center for Computational Physical Chemistry and Center for Data Science, New York, New York 10004, United States
| | - Jeffrey R Wagner
- Open Force Field, Open Molecular Software Foundation, Davis, California 95616, United States
| | - Daniel J Cole
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California at San Diego, La Jolla, California 92093, United States
| | - Michael R Shirts
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80305, United States
| | - David L Mobley
- Department of Chemistry, University of California, Irvine, California 92697, United States
- Department of Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
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3
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Di Grande S, Barone V. Toward Accurate Quantum Chemical Methods for Molecules of Increasing Dimension: The New Family of Pisa Composite Schemes. J Phys Chem A 2024; 128:4886-4900. [PMID: 38847454 DOI: 10.1021/acs.jpca.4c01673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
The new versions of the Pisa composite scheme introduced in the present paper are based on the careful selection of different quantum chemical models for energies, geometries, and vibrational frequencies, with the aim of maximizing the accuracy of the overall description while retaining a reasonable cost for all the steps. In particular, the computation of accurate electronic energies has been further improved introducing more reliable complete basis set extrapolations and estimation of core-valence correlation, together with improved basis sets for third-row atoms. Furthermore, the reduced-cost frozen natural orbital (FNO) model has been introduced and validated for large molecules. Accurate molecular structures can be obtained avoiding complete basis set extrapolation and evaluating core-valence correlation at the MP2 level. Unfortunately, analytical gradients are not available for the FNO version of the model. Therefore, for large molecules, an accurate reduced-cost alternative is offered by evaluation of valence contributions with a double-hybrid functional in conjunction with the same MP2 contribution for core-valence correlation or by means of a one-parameter approximation. The same double-hybrid functional and basis set are employed to evaluate zero-point energies and partition functions. After the validation of the new models for small systems, a panel of molecular bricks of life has been used to analyze their performances for problems of current fundamental or technological interest. The fully black-box implementation of the computational workflow paves the way toward the accurate yet not prohibitively expensive study of medium- to large-sized molecules also by experimentally oriented researchers.
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Affiliation(s)
- Silvia Di Grande
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Scuola Superiore Meridionale, Largo San Marcellino 10, 80138 Napoli, Italy
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4
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Mun H, Lorpaiboon W, Ho J. In Search of the Best Low-Cost Methods for Efficient Screening of Conformers. J Phys Chem A 2024; 128:4391-4400. [PMID: 38754085 DOI: 10.1021/acs.jpca.4c01407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Locating the lowest energy conformer is crucial for the accurate computation of equilibrium properties of molecular systems. This paper examines the performance of efficient low-cost methods in terms of the alignment and relative energies of their energy minima against the benchmark revDSD-PBEP86-D4/def2-TZVPP//MP2/cc-pVTZ potential energy surface. The low-cost methods considered include GFN-FF, GFN2-xTB, DFTB3, HF-3c, B97-3c, PBEh-3c, and r2SCAN-3c composite methods against a diverse test set of 20 compounds including alkanes, perfluoroalkyl molecules, peptides, open-shell radicals, and Zn(II) complexes of varying sizes. The "3c" composite methods are generally more accurate, but are at least 2-3 orders of magnitude more expensive than tight-binding methods which have energy minima that align well with the benchmark potential energy surface. The findings of this paper were further exploited to introduce a simple strategy involving Grimme's CENSO energy-sorting algorithm that resulted in up to an order of magnitude reduction in computational time for locating the lowest energy conformer on the revDSD-PBEP86-D4/def2-TZVPP//MP2/cc-pVTZ surface.
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Affiliation(s)
- Haedam Mun
- School of Chemistry, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Wanutcha Lorpaiboon
- School of Chemistry, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Junming Ho
- School of Chemistry, The University of New South Wales, Sydney, NSW 2052, Australia
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5
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Agbaglo DA, Summers TJ, Cheng Q, DeYonker NJ. The influence of model building schemes and molecular dynamics sampling on QM-cluster models: the chorismate mutase case study. Phys Chem Chem Phys 2024; 26:12467-12482. [PMID: 38618904 PMCID: PMC11090134 DOI: 10.1039/d3cp06100k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Most QM-cluster models of enzymes are constructed based on X-ray crystal structures, which limits comparison to in vivo structure and mechanism. The active site of chorismate mutase from Bacillus subtilis and the enzymatic transformation of chorismate to prephenate is used as a case study to guide construction of QM-cluster models built first from the X-ray crystal structure, then from molecular dynamics (MD) simulation snapshots. The Residue Interaction Network ResidUe Selector (RINRUS) software toolkit, developed by our group to simplify and automate the construction of QM-cluster models, is expanded to handle MD to QM-cluster model workflows. Several options, some employing novel topological clustering from residue interaction network (RIN) information, are evaluated for generating conformational clustering from MD simulation. RINRUS then generates a statistical thermodynamic framework for QM-cluster modeling of the chorismate mutase mechanism via refining 250 MD frames with density functional theory (DFT). The 250 QM-cluster models sampled provide a mean ΔG‡ of 10.3 ± 2.6 kcal mol-1 compared to the experimental value of 15.4 kcal mol-1 at 25 °C. While the difference between theory and experiment is consequential, the level of theory used is modest and therefore "chemical" accuracy is unexpected. More important are the comparisons made between QM-cluster models designed from the X-ray crystal structure versus those from MD frames. The large variations in kinetic and thermodynamic properties arise from geometric changes in the ensemble of QM-cluster models, rather from the composition of the QM-cluster models or from the active site-solvent interface. The findings open the way for further quantitative and reproducible calibration in the field of computational enzymology using the model construction framework afforded with the RINRUS software toolkit.
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Affiliation(s)
- Donatus A Agbaglo
- Department of Chemistry, University of Memphis, Memphis, TN 38152, USA.
| | - Thomas J Summers
- Department of Chemistry, University of Memphis, Memphis, TN 38152, USA.
| | - Qianyi Cheng
- Department of Chemistry, University of Memphis, Memphis, TN 38152, USA.
| | - Nathan J DeYonker
- Department of Chemistry, University of Memphis, Memphis, TN 38152, USA.
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6
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Uribe L, Di Grande S, Crisci L, Lazzari F, Mendolicchio M, Barone V. Accurate Structures and Rotational Constants of Steroid Hormones at DFT Cost: Androsterone, Testosterone, Estrone, β-Estradiol, and Estriol. J Phys Chem A 2024; 128:2629-2642. [PMID: 38530336 DOI: 10.1021/acs.jpca.4c00573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
A comprehensive analysis of the structural, conformational, and spectroscopic properties in the gas phase has been performed for five prototypical steroid hormones, namely, androsterone, testosterone, estrone, β-estradiol, and estriol. The revDSD-PBEP86 double-hybrid functional in conjunction with the D3BJ empirical dispersion and a suitable triple-ζ basis set provides accurate conformational energies and equilibrium molecular structures, with the latter being further improved by proper account of core-valence correlation. Average deviations within 0.1% between computed and experimental ground state rotational constants are reached when adding to those equilibrium values vibrational corrections obtained at the cost of standard harmonic frequencies thanks to the use of a new computational tool. Together with the intrinsic interest of the studied hormones, the accuracy of the results obtained at DFT cost for molecules containing about 50 atoms paves the way toward the accurate investigations of other flexible bricks of life.
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Affiliation(s)
- Lina Uribe
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Scuola Superiore Meridionale, Largo San Marcellino 10, 80138 Napoli, Italy
| | - Silvia Di Grande
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Scuola Superiore Meridionale, Largo San Marcellino 10, 80138 Napoli, Italy
| | - Luigi Crisci
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Federico Lazzari
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Marco Mendolicchio
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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7
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Barone V. Quantum chemistry meets high-resolution spectroscopy for characterizing the molecular bricks of life in the gas-phase. Phys Chem Chem Phys 2024; 26:5802-5821. [PMID: 38099409 DOI: 10.1039/d3cp05169b] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
Computation of accurate geometrical structures and spectroscopic properties of large flexible molecules in the gas-phase is tackled at an affordable cost using a general exploration/exploitation strategy. The most distinctive feature of the approach is the careful selection of different quantum chemical models for energies, geometries and vibrational frequencies with the aim of maximizing the accuracy of the overall description while retaining a reasonable cost for all the steps. In particular, a composite wave-function method is used for energies, whereas a double-hybrid functional (with the addition of core-valence correlation) is employed for geometries and harmonic frequencies and a cheaper hybrid functional for anharmonic contributions. A thorough benchmark based on a wide range of prototypical molecular bricks of life shows that the proposed strategy is close to the accuracy of state-of-the-art composite wave-function methods, and is applicable to much larger systems. A freely available web-utility post-processes the geometries optimized by standard electronic structure codes paving the way toward the accurate yet not prohibitively expensive study of medium- to large-sized molecules by experimentally-oriented researchers.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy.
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8
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Barone V, Uribe Grajales LM, Di Grande S, Lazzari F, Mendolicchio M. DFT Meets Wave-Function Methods for Accurate Structures and Rotational Constants of Histidine, Tryptophan, and Proline. J Phys Chem A 2023; 127:7534-7543. [PMID: 37665117 PMCID: PMC10510395 DOI: 10.1021/acs.jpca.3c04227] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/12/2023] [Indexed: 09/05/2023]
Abstract
A new computational strategy has been applied to the conformational and spectroscopic properties in the gas phase of amino acids with very distinctive features, ranging from different tautomeric forms (histidine) to ring puckering (proline), and heteroaromatic structures with non-equivalent rings (tryptophan). The integration of modern double-hybrid functionals and wave-function composite methods has allowed us to obtain accurate results for a large panel of conformers with reasonable computer times. The remarkable agreement between computations and microwave experiments allows an unbiased interpretation of the latter in terms of stereoelectronic effects.
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Affiliation(s)
- Vincenzo Barone
- Scuola
Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Lina Marcela Uribe Grajales
- Scuola
Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Scuola
Superiore Meridionale, Largo San Marcellino 10, 80138 Napoli, Italy
| | - Silvia Di Grande
- Scuola
Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Scuola
Superiore Meridionale, Largo San Marcellino 10, 80138 Napoli, Italy
| | - Federico Lazzari
- Scuola
Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Marco Mendolicchio
- Scuola
Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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9
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Semidalas E, Martin JML. Correlation Consistent Basis Sets for Explicitly Correlated Theory: The Transition Metals. J Chem Theory Comput 2023; 19:5806-5820. [PMID: 37540641 PMCID: PMC10500978 DOI: 10.1021/acs.jctc.3c00506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Indexed: 08/06/2023]
Abstract
We present correlation consistent basis sets for explicitly correlated (F12) calculations, denoted VnZ(-PP)-F12-wis (n = D,T), for the d-block elements. The cc-pVDZ-F12-wis basis set is contracted to [8s7p5d2f] for the 3d-block, while its ECP counterpart for the 4d and 5d-blocks, cc-pVDZ-PP-F12-wis, is contracted to [6s6p5d2f]. The corresponding contracted sizes for cc-pVTZ(-PP)-F12-wis are [9s8p6d3f2g] for the 3d-block elements and [7s7p6d3f2g] for the 4d and 5d-block elements. Our VnZ(-PP)-F12-wis basis sets are evaluated on challenging test sets for metal-organic barrier heights (MOBH35) and group-11 metal clusters (CUAGAU-2). In F12 calculations, they are found to be about as close to the complete basis set limit as the combination of standard cc-pVnZ-F12 on main-group elements with the standard aug-cc-pV(n+1)Z(-PP) basis sets on the transition metal(s). While our basis sets are somewhat more compact than aug-cc-pV(n+1)Z(-PP), the CPU time benefit is negligible for catalytic complexes that contain only one or two transition metals among dozens of main-group elements; however, it is somewhat more significant for metal clusters.
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Affiliation(s)
- Emmanouil Semidalas
- Department of Molecular Chemistry
and Materials Science, Weizmann Institute
of Science, 7610001 Reḥovot, Israel
| | - Jan M. L. Martin
- Department of Molecular Chemistry
and Materials Science, Weizmann Institute
of Science, 7610001 Reḥovot, Israel
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10
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Barone V. Accurate structures and spectroscopic parameters of α,α-dialkylated α-amino acids in the gas-phase: a joint venture of DFT and wave-function composite methods. Phys Chem Chem Phys 2023; 25:22768-22774. [PMID: 37591810 DOI: 10.1039/d3cp02503a] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
Accurate computations of structural, conformational and spectroscopic properties in the gas phase have been performed for two α,α-dialkylated α-amino acids, namely aminoisobutyric acid and cyclopropylglycine. Thanks to the integration of modern double hybrid functionals and wave-function methods, several low-energy structures of the title molecules could be analyzed employing standard computer resources. The computed features of all the most stable conformers of the target amino acids closely match the corresponding spectroscopic parameters issued from microwave spectroscopic studies in the gas-phase. Together with their intrinsic interest, the accuracy of the results obtained with reasonable computer times paves the way for accurate investigations of other flexible bricks of life.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy.
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11
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Zhang P, Yang W. Toward a general neural network force field for protein simulations: Refining the intramolecular interaction in protein. J Chem Phys 2023; 159:024118. [PMID: 37431910 PMCID: PMC10481389 DOI: 10.1063/5.0142280] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 06/22/2023] [Indexed: 07/12/2023] Open
Abstract
Molecular dynamics (MD) is an extremely powerful, highly effective, and widely used approach to understanding the nature of chemical processes in atomic details for proteins. The accuracy of results from MD simulations is highly dependent on force fields. Currently, molecular mechanical (MM) force fields are mainly utilized in MD simulations because of their low computational cost. Quantum mechanical (QM) calculation has high accuracy, but it is exceedingly time consuming for protein simulations. Machine learning (ML) provides the capability for generating accurate potential at the QM level without increasing much computational effort for specific systems that can be studied at the QM level. However, the construction of general machine learned force fields, needed for broad applications and large and complex systems, is still challenging. Here, general and transferable neural network (NN) force fields based on CHARMM force fields, named CHARMM-NN, are constructed for proteins by training NN models on 27 fragments partitioned from the residue-based systematic molecular fragmentation (rSMF) method. The NN for each fragment is based on atom types and uses new input features that are similar to MM inputs, including bonds, angles, dihedrals, and non-bonded terms, which enhance the compatibility of CHARMM-NN to MM MD and enable the implementation of CHARMM-NN force fields in different MD programs. While the main part of the energy of the protein is based on rSMF and NN, the nonbonded interactions between the fragments and with water are taken from the CHARMM force field through mechanical embedding. The validations of the method for dipeptides on geometric data, relative potential energies, and structural reorganization energies demonstrate that the CHARMM-NN local minima on the potential energy surface are very accurate approximations to QM, showing the success of CHARMM-NN for bonded interactions. However, the MD simulations on peptides and proteins indicate that more accurate methods to represent protein-water interactions in fragments and non-bonded interactions between fragments should be considered in the future improvement of CHARMM-NN, which can increase the accuracy of approximation beyond the current mechanical embedding QM/MM level.
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Affiliation(s)
- Pan Zhang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| | - Weitao Yang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
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12
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Boothroyd S, Behara PK, Madin OC, Hahn DF, Jang H, Gapsys V, Wagner JR, Horton JT, Dotson DL, Thompson MW, Maat J, Gokey T, Wang LP, Cole DJ, Gilson MK, Chodera JD, Bayly CI, Shirts MR, Mobley DL. Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field. J Chem Theory Comput 2023; 19:3251-3275. [PMID: 37167319 PMCID: PMC10269353 DOI: 10.1021/acs.jctc.3c00039] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Indexed: 05/13/2023]
Abstract
We introduce the Open Force Field (OpenFF) 2.0.0 small molecule force field for drug-like molecules, code-named Sage, which builds upon our previous iteration, Parsley. OpenFF force fields are based on direct chemical perception, which generalizes easily to highly diverse sets of chemistries based on substructure queries. Like the previous OpenFF iterations, the Sage generation of OpenFF force fields was validated in protein-ligand simulations to be compatible with AMBER biopolymer force fields. In this work, we detail the methodology used to develop this force field, as well as the innovations and improvements introduced since the release of Parsley 1.0.0. One particularly significant feature of Sage is a set of improved Lennard-Jones (LJ) parameters retrained against condensed phase mixture data, the first refit of LJ parameters in the OpenFF small molecule force field line. Sage also includes valence parameters refit to a larger database of quantum chemical calculations than previous versions, as well as improvements in how this fitting is performed. Force field benchmarks show improvements in general metrics of performance against quantum chemistry reference data such as root-mean-square deviations (RMSD) of optimized conformer geometries, torsion fingerprint deviations (TFD), and improved relative conformer energetics (ΔΔE). We present a variety of benchmarks for these metrics against our previous force fields as well as in some cases other small molecule force fields. Sage also demonstrates improved performance in estimating physical properties, including comparison against experimental data from various thermodynamic databases for small molecule properties such as ΔHmix, ρ(x), ΔGsolv, and ΔGtrans. Additionally, we benchmarked against protein-ligand binding free energies (ΔGbind), where Sage yields results statistically similar to previous force fields. All the data is made publicly available along with complete details on how to reproduce the training results at https://github.com/openforcefield/openff-sage.
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Affiliation(s)
| | - Pavan Kumar Behara
- Department
of Pharmaceutical Sciences, University of
California, Irvine, California 92697, United States
| | - Owen C. Madin
- Chemical
& Biological Engineering Department, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - David F. Hahn
- Computational
Chemistry, Janssen Research & Development, Turnhoutseweg 30, Beerse B-2340, Belgium
| | - Hyesu Jang
- Chemistry
Department, The University of California
at Davis, Davis, California 95616, United States
- OpenEye
Scientific Software, Santa
Fe, New Mexico 87508, United States
| | - Vytautas Gapsys
- Computational
Chemistry, Janssen Research & Development, Turnhoutseweg 30, Beerse B-2340, Belgium
- Computational
Biomolecular Dynamics Group, Department of Theoretical and Computational
Biophysics, Max Planck Institute for Multidisciplinary
Sciences, Am Fassberg 11, D-37077, Göttingen, Germany
| | - Jeffrey R. Wagner
- Department
of Pharmaceutical Sciences, University of
California, Irvine, California 92697, United States
- The Open
Force Field Initiative, Open Molecular Software
Foundation, Davis, California 95616, United States
| | - Joshua T. Horton
- School
of Natural and Environmental Sciences, Newcastle
University, Newcastle
upon Tyne NE1 7RU, U.K.
| | - David L. Dotson
- The Open
Force Field Initiative, Open Molecular Software
Foundation, Davis, California 95616, United States
- Datryllic LLC, Phoenix, Arizona 85003, United
States
| | - Matthew W. Thompson
- Chemical
& Biological Engineering Department, University of Colorado Boulder, Boulder, Colorado 80309, United States
- The Open
Force Field Initiative, Open Molecular Software
Foundation, Davis, California 95616, United States
| | - Jessica Maat
- Department
of Chemistry, University of California, Irvine, California 92697, United States
| | - Trevor Gokey
- Department
of Chemistry, University of California, Irvine, California 92697, United States
| | - Lee-Ping Wang
- Chemistry
Department, The University of California
at Davis, Davis, California 95616, United States
| | - Daniel J. Cole
- School
of Natural and Environmental Sciences, Newcastle
University, Newcastle
upon Tyne NE1 7RU, U.K.
| | - Michael K. Gilson
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, The University of California at San Diego, La Jolla, California 92093, United States
| | - John D. Chodera
- Computational
& Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | | | - Michael R. Shirts
- Chemical
& Biological Engineering Department, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - David L. Mobley
- Department
of Pharmaceutical Sciences, University of
California, Irvine, California 92697, United States
- Department
of Chemistry, University of California, Irvine, California 92697, United States
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13
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Barone V, Fusè M. Accurate Structures and Spectroscopic Parameters of Phenylalanine and Tyrosine in the Gas Phase: A Joint Venture of DFT and Composite Wave-Function Methods. J Phys Chem A 2023; 127:3648-3657. [PMID: 37052318 PMCID: PMC10150396 DOI: 10.1021/acs.jpca.3c01174] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
A general strategy for the accurate computation of conformational and spectroscopic properties of flexible molecules in the gas phase is applied to two representative proteinogenic amino acids with aromatic side chains, namely, phenylalanine and tyrosine. The main features of all the most stable conformers predicted by this computational strategy closely match those of the species detected in microwave and infrared experiments. Together with their intrinsic interest, the accuracy of the results obtained with reasonable computer times paves the route for accurate investigations of other flexible bricks of life.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Marco Fusè
- DMMT-sede Europa, Università di Brescia, Viale Europa 11, 25121 Brescia, Italy
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14
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Barone V, Fusè M, Lazzari F, Mancini G. Benchmark Structures and Conformational Landscapes of Amino Acids in the Gas Phase: A Joint Venture of Machine Learning, Quantum Chemistry, and Rotational Spectroscopy. J Chem Theory Comput 2023; 19:1243-1260. [PMID: 36731119 PMCID: PMC9979611 DOI: 10.1021/acs.jctc.2c01143] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The accurate characterization of prototypical bricks of life can strongly benefit from the integration of high resolution spectroscopy and quantum mechanical computations. We have selected a number of representative amino acids (glycine, alanine, serine, cysteine, threonine, aspartic acid and asparagine) to validate a new computational setup rooted in quantum-chemical computations of increasing accuracy guided by machine learning tools. Together with low-lying energy minima, the barriers ruling their interconversion are evaluated in order to unravel possible fast relaxation paths. Vibrational and thermal effects are also included in order to estimate relative free energies at the temperature of interest in the experiment. The spectroscopic parameters of all the most stable conformers predicted by this computational strategy, which do not have low-energy relaxation paths available, closely match those of the species detected in microwave experiments. Together with their intrinsic interest, these accurate results represent ideal benchmarks for more approximate methods.
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Affiliation(s)
- Vincenzo Barone
- Scuola
Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy,
| | - Marco Fusè
- DMMT-sede
Europa, Universitá di Brescia, viale Europa 11, 25121 Brescia, Italy
| | - Federico Lazzari
- Scuola
Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Giordano Mancini
- Scuola
Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy
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15
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Energetic, conformational and vibrational features of the tripeptide (Gly)3. Data from MP2 and DFT calculations. COMPUT THEOR CHEM 2023. [DOI: 10.1016/j.comptc.2022.113989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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16
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de Oliveira MT, Alves JMA, Vrech NL, Braga AAC, Barboza CA. A comprehensive benchmark investigation of quantum chemical methods for carbocations. Phys Chem Chem Phys 2023; 25:1903-1922. [PMID: 36541431 DOI: 10.1039/d2cp04603b] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The application of various density functional approximations (DFAs) and an emphasis on popular methods without any consensus have prevailed in computational studies dedicated to carbocations. More importantly, an extensive and rigorous benchmark investigation on density functionals for the class is still lacking. To close this gap, we present a comprehensive benchmark study of quantum chemical methods on a series of classical and nonclassical carbocations, the CARBO33 dataset. We evaluate a total of 107 DFT methods from all rungs giving particular attention to double hybrid density functionals as the potential of the class has been largely undermined in the context of carbocations. To support our findings, DLPNO-CCSD(T) at the complete basis set (CBS) limit and W1-F12 are used as reference methods. Our results indicate that the composite CBS-QB3 method performs poorly and should not be adopted for target energies. Oftentimes, the tested DFAs of a lower rung perform better than several DFAs in a higher rung of Perdew's "Jacob's ladder". Nonetheless, double hybrids DSD-PBEP86-NL and ωB97X-2-D3(BJ) stand out by showing the overall best performance. Among the hybrids evaluated, about half of them show mean absolute deviation (MAD) below 1.1 kcal mol-1, including the popular hybrids M06-2X and mPW1PW91. In this family, MN15-D3(BJ) performs particularly well (MAD = 0.77 kcal mol-1) displaying reliable results across various tests. Highly popular B3LYP exhibited one of the worst performances (MAD = 4.74 kcal mol-1), and we do not recommend its application to carbocations. We also assess the 24 general-purpose basis sets of single- up to quadruple-ζ quality. The best compromise between accuracy and computational cost is achieved with cc-pVTZ followed by def2-TZVP. Computations on larger structures of general interest, including terpene carbocations, are also presented for selected DFT methods confirming general trends in the results.
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Affiliation(s)
- Marcelo T de Oliveira
- Department of Chemistry and Physics, La Trobe Institute of Molecular Sciences, La Trobe University, Melbourne, Victoria 3086, Australia. .,Chemistry Institute of São Carlos, University of São Paulo, Av. Trabalhador São Carlense 400, 13566-590, São Carlos, SP, Brazil
| | - Júlia M A Alves
- Chemistry Institute of São Carlos, University of São Paulo, Av. Trabalhador São Carlense 400, 13566-590, São Carlos, SP, Brazil
| | - Natália L Vrech
- Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-000, São Paulo, SP, Brazil
| | - Ataualpa A C Braga
- Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-000, São Paulo, SP, Brazil
| | - Cristina A Barboza
- Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland.,Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, Warsaw, Poland
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17
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Barone V, Di Grande S, Puzzarini C. Toward Accurate yet Effective Computations of Rotational Spectroscopy Parameters for Biomolecule Building Blocks. MOLECULES (BASEL, SWITZERLAND) 2023; 28:molecules28020913. [PMID: 36677970 PMCID: PMC9863398 DOI: 10.3390/molecules28020913] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 01/01/2023] [Accepted: 01/12/2023] [Indexed: 01/19/2023]
Abstract
The interplay of high-resolution rotational spectroscopy and quantum-chemical computations plays an invaluable role in the investigation of biomolecule building blocks in the gas phase. However, quantum-chemical methods suffer from unfavorable scaling with the dimension of the system under consideration. While a complete characterization of flexible systems requires an elaborate multi-step strategy, in this work, we demonstrate that the accuracy obtained by quantum-chemical composite approaches in the prediction of rotational spectroscopy parameters can be approached by a model based on density functional theory. Glycine and serine are employed to demonstrate that, despite its limited cost, such a model is able to predict rotational constants with an accuracy of 0.3% or better, thus paving the way toward the accurate characterization of larger flexible building blocks of biomolecules.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-50126 Pisa, Italy
- Correspondence: (V.B.); (C.P.)
| | - Silvia Di Grande
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-50126 Pisa, Italy
- Scuola Superiore Meridionale, Largo San Marcellino 10, I-80138 Napoli, Italy
| | - Cristina Puzzarini
- Rotational and Computational Spectroscopy Lab, Department of Chemistry “Giacomo Ciamician”, University of Bologna, Via F. Selmi 2, I-40126 Bologna, Italy
- Correspondence: (V.B.); (C.P.)
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18
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D’Amore L, Hahn DF, Dotson DL, Horton JT, Anwar J, Craig I, Fox T, Gobbi A, Lakkaraju SK, Lucas X, Meier K, Mobley DL, Narayanan A, Schindler CE, Swope WC, in ’t Veld PJ, Wagner J, Xue B, Tresadern G. Collaborative Assessment of Molecular Geometries and Energies from the Open Force Field. J Chem Inf Model 2022; 62:6094-6104. [PMID: 36433835 PMCID: PMC9873353 DOI: 10.1021/acs.jcim.2c01185] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Force fields form the basis for classical molecular simulations, and their accuracy is crucial for the quality of, for instance, protein-ligand binding simulations in drug discovery. The huge diversity of small-molecule chemistry makes it a challenge to build and parameterize a suitable force field. The Open Force Field Initiative is a combined industry and academic consortium developing a state-of-the-art small-molecule force field. In this report, industry members of the consortium worked together to objectively evaluate the performance of the force fields (referred to here as OpenFF) produced by the initiative on a combined public and proprietary dataset of 19,653 relevant molecules selected from their internal research and compound collections. This evaluation was important because it was completely blind; at most partners, none of the molecules or data were used in force field development or testing prior to this work. We compare the Open Force Field "Sage" version 2.0.0 and "Parsley" version 1.3.0 with GAFF-2.11-AM1BCC, OPLS4, and SMIRNOFF99Frosst. We analyzed force-field-optimized geometries and conformer energies compared to reference quantum mechanical data. We show that OPLS4 performs best, and the latest Open Force Field release shows a clear improvement compared to its predecessors. The performance of established force fields such as GAFF-2.11 was generally worse. While OpenFF researchers were involved in building the benchmarking infrastructure used in this work, benchmarking was done entirely in-house within industrial organizations and the resulting assessment is reported here. This work assesses the force field performance using separate benchmarking steps, external datasets, and involving external research groups. This effort may also be unique in terms of the number of different industrial partners involved, with 10 different companies participating in the benchmark efforts.
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Affiliation(s)
- Lorenzo D’Amore
- Computational Chemistry, Janssen R&D, C/ Jarama 75A, 45007 Toledo, Spain
| | - David F. Hahn
- Computational Chemistry, Janssen R&D, Turnhoutseweg 30, Beerse B-2340, Belgium
| | - David L. Dotson
- The Open Force Field Initiative, Open Molecular Software Foundation, Davis, California 95616, USA
| | - Joshua T. Horton
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Jamshed Anwar
- Department of Chemistry, Lancaster University, Lancaster LA1 4YW, UK
| | - Ian Craig
- Molecular Modeling & Drug Discovery, BASF SE, 67056 Ludwigshafen, Germany
| | - Thomas Fox
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co KG, 88397 Biberach/Riss, Germany
| | - Alberto Gobbi
- Genentech, Inc., 1 DNA Way, South San Francisco, California, 94080, USA
| | | | - Xavier Lucas
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Katharina Meier
- Computational Life Science Technology Functions, Crop Science, R&D, Bayer AG, 40789 Monheim, Germany
| | - David L. Mobley
- Departments of Pharmaceutical Sciences and Chemistry, University of California 92617, Irvine, USA
| | - Arjun Narayanan
- Data and Computational Sciences, Vertex Pharmaceuticals, 50 Northern Ave, Boston, MA 02210, USA
| | | | - William C. Swope
- Genentech, Inc., 1 DNA Way, South San Francisco, California, 94080, USA
| | | | - Jeffrey Wagner
- The Open Force Field Initiative, Open Molecular Software Foundation, Davis, California, 95616, USA,Chemistry Department, The University of California at Irvine, Irvine, California, 92617, USA
| | - Bai Xue
- XtalPi Inc. Floor 3, International Biomedical Innovation Park II, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen, Guangdong, 518040 China
| | - Gary Tresadern
- Computational Chemistry, Janssen R&D, Turnhoutseweg 30, Beerse B-2340, Belgium
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19
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Wang Y, Walker BD, Liu C, Ren P. An Efficient Approach to Large-Scale Ab Initio Conformational Energy Profiles of Small Molecules. Molecules 2022; 27:8567. [PMID: 36500658 PMCID: PMC9738817 DOI: 10.3390/molecules27238567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/19/2022] [Accepted: 11/27/2022] [Indexed: 12/12/2022] Open
Abstract
Accurate conformational energetics of molecules are of great significance to understand maby chemical properties. They are also fundamental for high-quality parameterization of force fields. Traditionally, accurate conformational profiles are obtained with density functional theory (DFT) methods. However, obtaining a reliable energy profile can be time-consuming when the molecular sizes are relatively large or when there are many molecules of interest. Furthermore, incorporation of data-driven deep learning methods into force field development has great requirements for high-quality geometry and energy data. To this end, we compared several possible alternatives to the traditional DFT methods for conformational scans, including the semi-empirical method GFN2-xTB and the neural network potential ANI-2x. It was found that a sequential protocol of geometry optimization with the semi-empirical method and single-point energy calculation with high-level DFT methods can provide satisfactory conformational energy profiles hundreds of times faster in terms of optimization.
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Affiliation(s)
| | | | | | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
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20
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Ehrhard AA, Gunkel L, Jäger S, Sell AC, Nagata Y, Hunger J. Elucidating Conformation and Hydrogen-Bonding Motifs of Reactive Thiourea Intermediates. ACS Catal 2022; 12:12689-12700. [PMID: 36313523 PMCID: PMC9594049 DOI: 10.1021/acscatal.2c03382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/19/2022] [Indexed: 11/29/2022]
Abstract
![]()
Substituted diphenylthioureas (DPTUs) are efficient hydrogen-bonding
organo-catalysts, and substitution of DPTUs has been shown to greatly
affect catalytic activity. Yet, both the conformation of DPTUs in
solution and the conformation and hydrogen-bonded motifs within catalytically
active intermediates, pertinent to their mode of activation, have
remained elusive. By combining linear and ultrafast vibrational spectroscopy
with spectroscopic simulations and calculations, we show that different
conformational states of thioureas give rise to distinctively different
N–H stretching bands in the infrared spectra. In the absence
of hydrogen-bond-accepting substrates, we show that vibrational structure
and dynamics are highly sensitive to the substitution of DPTUs with
CF3 groups and to the interaction with the solvent environment,
allowing for disentangling the different conformational states. In
contrast to bare diphenylthiourea (0CF-DPTU), we find the catalytically
superior CF3-substituted DPTU (4CF-DPTU) to favor the trans–trans conformation in solution,
allowing for donating two hydrogen bonds to the reactive substrate.
In the presence of a prototypical substrate, DPTUs in trans–trans conformation hydrogen bond to the
substrate’s C=O group, as evidenced by a red-shift of
the N–H vibration. Yet, our time-resolved infrared experiments
indicate that only one N–H group forms a strong hydrogen bond
to the carbonyl moiety, while thiourea’s second N–H
group only weakly interacts with the substrate. Our data indicate
that hydrogen-bond exchange between these N–H groups occurs
on the timescale of a few picoseconds for 0CF-DPTU and is significantly
accelerated upon CF3 substitution. Our results highlight
the subtle interplay between conformational equilibria, bonding states,
and bonding lifetimes in reactive intermediates in thiourea catalysis,
which help rationalize their catalytic activity.
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Affiliation(s)
- Amelie A. Ehrhard
- Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Lucas Gunkel
- Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Sebastian Jäger
- Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Arne C. Sell
- Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Yuki Nagata
- Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Johannes Hunger
- Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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21
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Mehta N, Martin JML. Explicitly Correlated Double-Hybrid DFT: A Comprehensive Analysis of the Basis Set Convergence on the GMTKN55 Database. J Chem Theory Comput 2022; 18:5978-5991. [PMID: 36099641 PMCID: PMC9558368 DOI: 10.1021/acs.jctc.2c00426] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Double-hybrid density functional theory (DHDFT) offers
a pathway
to accuracy approaching composite wavefunction approaches such as
G4 theory. However, the Görling–Levy second-order perturbation
theory (GLPT2) term causes them to partially inherit the slow ∝L–3 (with L the maximum
angular momentum) basis set convergence of correlated wavefunction
methods. This could potentially be remedied by introducing F12 explicit
correlation: we investigate the basis set convergence of both DHDFT
and DHDFT-F12 (where GLPT2 is replaced by GLPT2-F12) for the large
and chemically diverse general main-group thermochemistry, kinetics,
and noncovalent interactions (GMTKN55) benchmark suite. The B2GP-PLYP-D3(BJ)
and revDSD-PBEP86-D4 DHDFs are investigated as test cases, together
with orbital basis sets as large as aug-cc-pV5Z and F12 basis sets
as large as cc-pVQZ-F12. We show that F12 greatly accelerates basis
set convergence of DHDFs, to the point that even the modest cc-pVDZ-F12
basis set is closer to the basis set limit than cc-pV(Q+d)Z or def2-QZVPPD
in orbital-based approaches, and in fact comparable in quality to
cc-pV(5+d)Z. Somewhat surprisingly, aug-cc-pVDZ-F12 is not required
even for the anionic subsets. In conclusion, DHDF-F12/VDZ-F12 eliminates
concerns about basis set convergence in both the development and applications
of double-hybrid functionals. Mass storage and I/O bottlenecks for
larger systems can be circumvented by localized pair natural orbital
approximations, which also exhibit much gentler system size scaling.
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Affiliation(s)
- Nisha Mehta
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 7610001 Reḥovot, Israel
| | - Jan M L Martin
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 7610001 Reḥovot, Israel
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22
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Oh L, Varki A, Chen X, Wang LP. SARS-CoV-2 and MERS-CoV Spike Protein Binding Studies Support Stable Mimic of Bound 9- O-Acetylated Sialic Acids. Molecules 2022; 27:5322. [PMID: 36014560 PMCID: PMC9415320 DOI: 10.3390/molecules27165322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/13/2022] [Accepted: 08/16/2022] [Indexed: 11/18/2022] Open
Abstract
Many disease-causing viruses target sialic acids (Sias), a class of nine-carbon sugars known to coat the surface of many cells, including those in the lungs. Human beta coronaviridae, known for causing respiratory tract diseases, often bind Sias, and some preferentially bind to those with 9-O-Ac-modification. Currently, co-binding of SARS-CoV-2, a beta coronavirus responsible for the COVID-19 pandemic, to human Sias has been reported and its preference towards α2-3-linked Neu5Ac has been shown. Nevertheless, O-acetylated Sias-protein binding studies are difficult to perform, due to the ester lability. We studied the binding free energy differences between Neu5,9Ac2α2-3GalβpNP and its more stable 9-NAc mimic binding to SARS-CoV-2 spike protein using molecular dynamics and alchemical free energy simulations. We identified multiple Sia-binding pockets, including two novel sites, with similar binding affinities to those of MERS-CoV, a known co-binder of sialic acid. In our binding poses, 9-NAc and 9-OAc Sias bind similarly, suggesting an experimentally reasonable mimic to probe viral mechanisms.
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Affiliation(s)
- Lisa Oh
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | - Ajit Varki
- Glycobiology Research and Training Center, Departments of Medicine and Cellular and Molecular Medicine, University of California, San Diego, CA 92093, USA
| | - Xi Chen
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | - Lee-Ping Wang
- Department of Chemistry, University of California, Davis, CA 95616, USA
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23
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Sparrow ZM, Ernst BG, Quady TK, DiStasio RA. Uniting Nonempirical and Empirical Density Functional Approximation Strategies Using Constraint-Based Regularization. J Phys Chem Lett 2022; 13:6896-6904. [PMID: 35863751 DOI: 10.1021/acs.jpclett.2c00643] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In this work, we present a general framework that unites the two primary strategies for constructing density functional approximations (DFAs): nonempirical (NE) constraint satisfaction and empirical (E) data-driven optimization. The proposed method employs B-splines, bell-shaped spline functions with compact support, to construct each inhomogeneity correction factor (ICF). This choice offers several distinct advantages over traditional polynomial expansions by enabling explicit enforcement of linear and nonlinear constraints as well as ICF smoothness using Tikhonov and penalized B-splines (P-splines) regularization. As proof-of-concept, we use the so-called CASE (constrained and smoothed empirical) framework to construct a constraint-satisfying and data-driven global hybrid that exhibits enhanced performance across a diverse set of chemical properties. We argue that the CASE approach can be used to generate DFAs that maintain the physical rigor and transferability of NE-DFAs while leveraging high-quality quantum-mechanical data to remove the arbitrariness of ansatz selection and improve performance.
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Affiliation(s)
- Zachary M Sparrow
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Brian G Ernst
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Trine K Quady
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Robert A DiStasio
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
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24
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Ehlert S, Grimme S, Hansen A. Conformational Energy Benchmark for Longer n-Alkane Chains. J Phys Chem A 2022; 126:3521-3535. [PMID: 35616628 DOI: 10.1021/acs.jpca.2c02439] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present the first benchmark set focusing on the conformational energies of highly flexible, long n-alkane chains, termed ACONFL. Unbranched alkanes are ubiquitous building blocks in nature, so the goal is to be able to calculate their properties most accurately to improve the modeling of, e.g., complex (biological) systems. Very accurate DLPNO-CCSD(T1)/CBS reference values are provided, which allow for a statistical meaningful evaluation of even the best available density functional methods. The performance of established and modern (dispersion corrected) density functionals is comprehensively assessed. The recently introduced r2SCAN-V functional shows excellent performance, similar to efficient composite DFT methods like B97-3c and r2SCAN-3c, which provide an even better cost-accuracy ratio, while almost reaching the accuracy of much more computationally demanding hybrid or double hybrid functionals with large QZ AO basis sets. In addition, we investigated the performance of common wave function methods, where MP2/CBS surprisingly performs worse compared to the simple D4 dispersion corrected Hartree-Fock. Furthermore, we investigate the performance of several semiempirical and force field methods, which are commonly used for the generation of conformational ensembles in multilevel workflows or in large scale molecular dynamics studies. Outstanding performance is obtained by the recently introduced general force field, GFN-FF, while other commonly applied methods like the universal force field yield large errors. We recommend the ACONFL as a helpful benchmark set for parametrization of new semiempirical or force field methods and machine learning potentials as well as a meaningful validation set for newly developed DFT or dispersion methods.
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Affiliation(s)
- Sebastian Ehlert
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstrasse 4, 53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstrasse 4, 53115 Bonn, Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstrasse 4, 53115 Bonn, Germany
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25
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Prasad VK, Otero-de-la-Roza A, DiLabio GA. Small-Basis Set Density-Functional Theory Methods Corrected with Atom-Centered Potentials. J Chem Theory Comput 2022; 18:2913-2930. [PMID: 35412817 DOI: 10.1021/acs.jctc.2c00036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Density functional theory (DFT) is currently the most popular method for modeling noncovalent interactions and thermochemistry. The accurate calculation of noncovalent interaction energies, reaction energies, and barrier heights requires choosing an appropriate functional and, typically, a relatively large basis set. Deficiencies of the density-functional approximation and the use of a limited basis set are the leading sources of error in the calculation of noncovalent and thermochemical properties in molecular systems. In this article, we present three new DFT methods based on the BLYP, M06-2X, and CAM-B3LYP functionals in combination with the 6-31G* basis set and corrected with atom-centered potentials (ACPs). ACPs are one-electron potentials that have the same form as effective-core potentials, except they do not replace any electrons. The ACPs developed in this work are used to generate energy corrections to the underlying DFT/basis-set method such that the errors in predicted chemical properties are minimized while maintaining the low computational cost of the parent methods. ACPs were developed for the elements H, B, C, N, O, F, Si, P, S, and Cl. The ACP parameters were determined using an extensive training set of 118655 data points, mostly of complete basis set coupled-cluster level quality. The target molecular properties for the ACP-corrected methods include noncovalent interaction energies, molecular conformational energies, reaction energies, barrier heights, and bond separation energies. The ACPs were tested first on the training set and then on a validation set of 42567 additional data points. We show that the ACP-corrected methods can predict the target molecular properties with accuracy close to complete basis set wavefunction theory methods, but at a computational cost of double-ζ DFT methods. This makes the new BLYP/6-31G*-ACP, M06-2X/6-31G*-ACP, and CAM-B3LYP/6-31G*-ACP methods uniquely suited to the calculation of noncovalent, thermochemical, and kinetic properties in large molecular systems.
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Affiliation(s)
- Viki Kumar Prasad
- Department of Chemistry, University of British Columbia, Okanagan, 3247 University Way, Kelowna, British Columbia V1V 1V7, Canada
| | - Alberto Otero-de-la-Roza
- Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, MALTA Consolider Team, Oviedo E-33006, Spain
| | - Gino A DiLabio
- Department of Chemistry, University of British Columbia, Okanagan, 3247 University Way, Kelowna, British Columbia V1V 1V7, Canada
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26
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Prasad VK, Otero-de-la-Roza A, DiLabio GA. Fast and Accurate Quantum Mechanical Modeling of Large Molecular Systems Using Small Basis Set Hartree-Fock Methods Corrected with Atom-Centered Potentials. J Chem Theory Comput 2022; 18:2208-2232. [PMID: 35313106 DOI: 10.1021/acs.jctc.1c01128] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
There has been significant interest in developing fast and accurate quantum mechanical methods for modeling large molecular systems. In this work, by utilizing a machine learning regression technique, we have developed new low-cost quantum mechanical approaches to model large molecular systems. The developed approaches rely on using one-electron Gaussian-type functions called atom-centered potentials (ACPs) to correct for the basis set incompleteness and the lack of correlation effects in the underlying minimal or small basis set Hartree-Fock (HF) methods. In particular, ACPs are proposed for ten elements common in organic and bioorganic chemistry (H, B, C, N, O, F, Si, P, S, and Cl) and four different base methods: two minimal basis sets (MINIs and MINIX) plus a double-ζ basis set (6-31G*) in combination with dispersion-corrected HF (HF-D3/MINIs, HF-D3/MINIX, HF-D3/6-31G*) and the HF-3c method. The new ACPs are trained on a very large set (73 832 data points) of noncovalent properties (interaction and conformational energies) and validated additionally on a set of 32 048 data points. All reference data are of complete basis set coupled-cluster quality, mostly CCSD(T)/CBS. The proposed ACP-corrected methods are shown to give errors in the tenths of a kcal/mol range for noncovalent interaction energies and up to 2 kcal/mol for molecular conformational energies. More importantly, the average errors are similar in the training and validation sets, confirming the robustness and applicability of these methods outside the boundaries of the training set. In addition, the performance of the new ACP-corrected methods is similar to complete basis set density functional theory (DFT) but at a cost that is orders of magnitude lower, and the proposed ACPs can be used in any computational chemistry program that supports effective-core potentials without modification. It is also shown that ACPs improve the description of covalent and noncovalent bond geometries of the underlying methods and that the improvement brought about by the application of the ACPs is directly related to the number of atoms to which they are applied, allowing the treatment of systems containing some atoms for which ACPs are not available. Overall, the ACP-corrected methods proposed in this work constitute an alternative accurate, economical, and reliable quantum mechanical approach to describe the geometries, interaction energies, and conformational energies of systems with hundreds to thousands of atoms.
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Affiliation(s)
- Viki Kumar Prasad
- Department of Chemistry, University of British Columbia, Okanagan, 3247 University Way, Kelowna, British Columbia, Canada V1V 1V7
| | - Alberto Otero-de-la-Roza
- MALTA Consolider Team, Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, E-33006 Oviedo, Spain
| | - Gino A DiLabio
- Department of Chemistry, University of British Columbia, Okanagan, 3247 University Way, Kelowna, British Columbia, Canada V1V 1V7
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27
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Dey G, Chakraborty A. Conformational Landscape and Tautomerisation in (Z)-4-(hydroxymethylene) isochroman-1,3-dione: Analysis through Energy and Hardness profiles. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130859] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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28
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Qiu Y, Smith DGA, Boothroyd S, Jang H, Hahn DF, Wagner J, Bannan CC, Gokey T, Lim VT, Stern CD, Rizzi A, Tjanaka B, Tresadern G, Lucas X, Shirts MR, Gilson MK, Chodera JD, Bayly CI, Mobley DL, Wang LP. Development and Benchmarking of Open Force Field v1.0.0-the Parsley Small-Molecule Force Field. J Chem Theory Comput 2021; 17:6262-6280. [PMID: 34551262 PMCID: PMC8511297 DOI: 10.1021/acs.jctc.1c00571] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We present a methodology for defining and optimizing a general force field for classical molecular simulations, and we describe its use to derive the Open Force Field 1.0.0 small-molecule force field, codenamed Parsley. Rather than using traditional atom typing, our approach is built on the SMIRKS-native Open Force Field (SMIRNOFF) parameter assignment formalism, which handles increases in the diversity and specificity of the force field definition without needlessly increasing the complexity of the specification. Parameters are optimized with the ForceBalance tool, based on reference quantum chemical data that include torsion potential energy profiles, optimized gas-phase structures, and vibrational frequencies. These quantum reference data are computed and are maintained with QCArchive, an open-source and freely available distributed computing and database software ecosystem. In this initial application of the method, we present essentially a full optimization of all valence parameters and report tests of the resulting force field against compounds and data types outside the training set. These tests 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, as is accuracy on binding free energies. We find that this initial Parsley force field affords accuracy similar to that of other general force fields when used to calculate relative binding free energies spanning 199 protein-ligand systems. Additionally, the resulting infrastructure allows us to rapidly optimize an entirely new force field with minimal human intervention.
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Affiliation(s)
- Yudong Qiu
- Chemistry Department, The University of California at Davis, Davis, California 95616, United States
| | - Daniel G A Smith
- The Molecular Sciences Software Institute (MolSSI), Blacksburg, Virginia 24060, United States
| | - Simon Boothroyd
- Computational & Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Hyesu Jang
- Chemistry Department, The University of California at Davis, Davis, California 95616, United States
| | - David F Hahn
- Computational Chemistry, Janssen Research & Development, Turnhoutseweg 30, Beerse B-2340, Belgium
| | - Jeffrey Wagner
- Chemistry Department, The University of California at Irvine, Irvine, California 92617, United States
| | - Caitlin C Bannan
- Chemistry Department, The University of California at Irvine, Irvine, California 92617, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California at San Diego, La Jolla, California 92093, United States
| | - Trevor Gokey
- Chemistry Department, The University of California at Irvine, Irvine, California 92617, United States
| | - Victoria T Lim
- Chemistry Department, The University of California at Irvine, Irvine, California 92617, United States
| | - Chaya D Stern
- Computational & Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Andrea Rizzi
- Computational & Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
- Tri-Institutional Training Program in Computational Biology and Medicine, New York, New York 10065, United States
| | - Bryon Tjanaka
- Chemistry Department, The University of California at Irvine, Irvine, California 92617, United States
| | - Gary Tresadern
- Computational Chemistry, Janssen Research & Development, Turnhoutseweg 30, Beerse B-2340, Belgium
| | - Xavier Lucas
- F. Hoffmann-La Roche AG, Basel 4070, Switzerland
| | - Michael R Shirts
- Chemical & Biological Engineering Department, The University of Colorado at Boulder, Boulder, Colorado 80309, United States
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California at San Diego, La Jolla, California 92093, United States
| | - John D Chodera
- Computational & Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | | | - David L Mobley
- Chemistry Department, The University of California at Irvine, Irvine, California 92617, United States
| | - Lee-Ping Wang
- Chemistry Department, The University of California at Davis, Davis, California 95616, United States
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29
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Kraus P. Extrapolating DFT Toward the Complete Basis Set Limit: Lessons from the PBE Family of Functionals. J Chem Theory Comput 2021; 17:5651-5660. [PMID: 34351738 DOI: 10.1021/acs.jctc.1c00542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Extrapolation of density functional theory results from 2- and 3-ζ calculations is a promising method for extracting higher accuracy data from calculations of systems at the affordability limit. In this work, the author presents formulas for the determination of extrapolation parameters, which account for the makeup of the density functional approximation. The formulas are fitted to reproduce the complete basis set limit energies of PBE and related density functional approximations, using a set of 30 singlet diatomics. Their performance is extensively evaluated using standard benchmark data sets. The current systematically derived expressions are shown to be transferrable outside the PBE family of functional approximations, with the resulting extrapolation parameters outperforming the previous, less-systematic values. A good performance of [2,3]-ζ extrapolations for interaction energies of systems with significant noncovalent character is confirmed and holds even in systems of ∼100 atoms in size.
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Affiliation(s)
- Peter Kraus
- School of Molecular and Life Sciences, Curtin University, G.P.O. Box U1987, Perth 6845, Western Australia, Australia
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30
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Mehta N, Fellowes T, White JM, Goerigk L. CHAL336 Benchmark Set: How Well Do Quantum-Chemical Methods Describe Chalcogen-Bonding Interactions? J Chem Theory Comput 2021; 17:2783-2806. [PMID: 33881869 DOI: 10.1021/acs.jctc.1c00006] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We present the CHAL336 benchmark set-the most comprehensive database for the assessment of chalcogen-bonding (CB) interactions. After careful selection of suitable systems and identification of three high-level reference methods, the set comprises 336 dimers each consisting of up to 49 atoms and covers both σ- and π-hole interactions across four categories: chalcogen-chalcogen, chalcogen-π, chalcogen-halogen, and chalcogen-nitrogen interactions. In a subsequent study of DFT methods, we re-emphasize the need for using proper London dispersion corrections when treating noncovalent interactions. We also point out that the deterioration of results and systematic overestimation of interaction energies for some dispersion-corrected DFT methods does not hint at problems with the chosen dispersion correction but is a consequence of large density-driven errors. We conclude this work by performing the most detailed DFT benchmark study for CB interactions to date. We assess 109 variations of dispersion-corrected and dispersion-uncorrected DFT methods and carry out a detailed analysis of 80 of them. Double-hybrid functionals are the most reliable approaches for CB interactions, and they should be used whenever computationally feasible. The best three double hybrids are SOS0-PBE0-2-D3(BJ), revDSD-PBEP86-D3(BJ), and B2NCPLYP-D3(BJ). The best hybrids in this study are ωB97M-V, PW6B95-D3(0), and PW6B95-D3(BJ). We do not recommend using the popular B3LYP functional nor the MP2 approach, which have both been frequently used to describe CB interactions in the past. We hope to inspire a change in computational protocols surrounding CB interactions that leads away from the commonly used, popular methods to the more robust and accurate ones recommended herein. We would also like to encourage method developers to use our set for the investigation and reduction of density-driven errors in new density functional approximations.
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Affiliation(s)
- Nisha Mehta
- School of Chemistry, The University of Melbourne, Victoria 3010, Australia
| | - Thomas Fellowes
- School of Chemistry, The University of Melbourne, Victoria 3010, Australia.,Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia
| | - Jonathan M White
- School of Chemistry, The University of Melbourne, Victoria 3010, Australia.,Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia
| | - Lars Goerigk
- School of Chemistry, The University of Melbourne, Victoria 3010, Australia
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31
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Gutten O, Jurečka P, Aliakbar Tehrani Z, Buděšínský M, Řezáč J, Rulíšek L. Conformational energies and equilibria of cyclic dinucleotides in vacuo and in solution: computational chemistry vs. NMR experiments. Phys Chem Chem Phys 2021; 23:7280-7294. [PMID: 33876088 DOI: 10.1039/d0cp05993e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Performance of computational methods in modelling cyclic dinucleotides - an important and challenging class of compounds - has been evaluated by two different benchmarks: (1) gas-phase conformational energies and (2) qualitative agreement with NMR observations of the orientation of the χ-dihedral angle in solvent. In gas-phase benchmarks, where CCSD(T) and DLPNO-CCSD(T) methods have been used as the reference, most of the (dispersion corrected) density functional approximations are accurate enough to justify prioritizing computational cost and compatibility with other modelling options as the criterion of choice. NMR experiments of 3'3'-c-di-AMP, 3'3'-c-GAMP, and 3'3'-c-di-GMP show the overall prevalence of the anti-conformation of purine bases, but some population of syn-conformations is observed for guanines. Implicit solvation models combined with quantum-chemical methods struggle to reproduce this behaviour, probably due to a lack of dynamics and explicitly modelled solvent, leading to structures that are too compact. Molecular dynamics simulations overrepresent the syn-conformation of guanine due to the overestimation of an intramolecular hydrogen bond. Our combination of experimental and computational benchmarks provides "error bars" for modelling cyclic dinucleotides in solvent, where such information is generally difficult to obtain, and should help gauge the interpretability of studies dealing with binding of cyclic dinucleotides to important pharmaceutical targets. At the same time, the presented analysis calls for improvement in both implicit solvation models and force-field parameters.
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Affiliation(s)
- Ondrej Gutten
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10, Praha 6, Czech Republic.
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32
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Santra G, Martin JML. What Types of Chemical Problems Benefit from Density-Corrected DFT? A Probe Using an Extensive and Chemically Diverse Test Suite. J Chem Theory Comput 2021; 17:1368-1379. [PMID: 33625863 PMCID: PMC8028055 DOI: 10.1021/acs.jctc.0c01055] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
![]()
For the large and
chemically diverse GMTKN55 benchmark suite, we
have studied the performance of density-corrected density functional
theory (HF-DFT), compared to self-consistent DFT, for several pure
and hybrid GGA and meta-GGA exchange–correlation (XC) functionals
(PBE, BLYP, TPSS, and SCAN) as a function of the percentage of HF
exchange in the hybrid. The D4 empirical dispersion correction has
been added throughout. For subsets dominated by dynamical correlation,
HF-DFT is highly beneficial, particularly at low HF exchange percentages.
This is especially true for noncovalent interactions where the electrostatic
component is dominant, such as hydrogen and halogen bonds: for π-stacking,
HF-DFT is detrimental. For subsets with significant nondynamical correlation
(i.e., where a Hartree–Fock determinant is not a good zero-order
wavefunction), HF-DFT may do more harm than good. While the self-consistent
series show optima at or near 37.5% (i.e., 3/8) for all four XC functionals—consistent
with Grimme’s proposal of the PBE38 functional—HF-BnLYP-D4, HF-PBEn-D4, and HF-TPSSn-D4 all exhibit minima nearer 25% (i.e., 1/4) as the use
of HF orbitals greatly mitigates the error at 25% for barrier heights.
Intriguingly, for HF-SCANn-D4, the minimum is near
10%, but the weighted mean absolute error (WTMAD2) for GMTKN55 is
only barely lower than that for HF-SCAN-D4 (i.e., where the post-HF
step is a pure meta-GGA). The latter becomes an attractive option,
only slightly more costly than pure Hartree–Fock, and devoid
of adjustable parameters other than the three in the dispersion correction.
Moreover, its WTMAD2 is only surpassed by the highly empirical M06-2X
and by the combinatorially optimized empirical range-separated hybrids
ωB97X-V and ωB97M-V.
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Affiliation(s)
- Golokesh Santra
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 7610001 Reḥovot, Israel
| | - Jan M L Martin
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 7610001 Reḥovot, Israel
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33
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Varandas AJC. Canonical and explicitly-correlated coupled cluster correlation energies of sub-kJ mol -1 accuracy via cost-effective hybrid-post-CBS extrapolation. Phys Chem Chem Phys 2021; 23:9571-9584. [PMID: 33885095 DOI: 10.1039/d1cp00357g] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cost-effectiveness and accuracy are two basic pillars in electronic structure calculations. While cost-effectiveness enhances applicability, high accuracy is sustained when employing advanced computational tools. With the gold standard method of ab initio quantum chemistry at the focal point, canonical CCSD(T) and modern explicitly correlated CCSD(T)-F12 calculations are employed hand in hand to develop accurate hybrid post-CBS extrapolation schemes, which are validated using popular training sets involving a total of 130 molecules. By using raw valence-only calculations at CCSD(T)/VDZ and CCSD(T)/VQZ-F12 levels of theory, the novel scheme leads to the prediction of absolute energies that differ on average (-0.170 ± 0.224) kcal mol-1 from the highest affordable CCSD(T)-F12b/V(Q,5)Z-F12 extrapolations, but only (-0.048 ± 0.228) kcal mol-1 from the post-CBS extrapolated values based on CBS(D,T), CBS(D,Q) and CBS(T,Q) energies. From the cost-effectiveness standpoint, the approach is a kind of pseudo one-point extrapolation scheme since its cost is basically that of the highest-rung raw energy where it is based. Variants that imply no additional cost are also discussed, emerging h-pCBS(dt,dq)ab as the most effective. The approach can also be used with PNO-based local correlation methods that gained popularity due to allowing coupled-cluster calculations even for large molecules at reduced computational cost, namely local PNO-CCSD(T) and PNO-CCSD(T)-F12b. To gauge the approach performance, both the hydrogen molecule and the O-C2H5 torsion path of ethyl-methyl-ether, an extra molecule here considered with presupposed existence in astrophysical objects, are also studied. Additionally, the nonbonding interactions in the A24 test set are revisited per se. The results show that the title approach may be useful in high-accuracy quantum chemistry, with further improvements requiring the inclusion of contributions beyond the theory here employed such as the ones due to relativistic and nonadiabatic effects.
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Affiliation(s)
- A J C Varandas
- School of Physics and Physical Engineering, Qufu Normal University, 273165 Qufu, China
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34
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Mehta N, Goerigk L. Assessing the Applicability of the Geometric Counterpoise Correction in B2PLYP/Double-ζ Calculations for Thermochemistry, Kinetics, and Noncovalent Interactions. Aust J Chem 2021. [DOI: 10.1071/ch21133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We present a proof-of-concept study of the suitability of Kruse and Grimme’s geometric counterpoise correction (gCP) for basis set superposition errors (BSSEs) in double-hybrid density functional calculations with a double-ζ basis set. The gCP approach only requires geometrical information as an input and no orbital/density information is needed. Therefore, this correction is practically free of any additional cost. gCP is trained against the Boys and Bernardi counterpoise correction across a set of 528 noncovalently bound dimers. We investigate the suitability of the approach for the B2PLYP/def2-SVP level of theory, and reveal error compensation effects—missing London dispersion and the BSSE—associated with B2PLYP/def2-SVP calculations, and present B2PLYP-gCP-D3(BJ)/def2-SVP with the reparametrised DFT-D3(BJ) and gCP corrections as a more balanced alternative. Benchmarking results on the S66x8 benchmark set for noncovalent interactions and the GMTKN55 database for main-group thermochemistry, kinetics, and noncovalent interactions show a statistical improvement of the B2PLYP-gCP-D3(BJ) scheme over plain B2PLYP and B2PLYP-D3(BJ). B2PLYP-D3(BJ) shows significant overestimation of interaction energies, barrier heights with larger deviations from the reference values, and wrong relative stabilities in conformers, all of which can be associated with BSSE. We find that the gCP-corrected method represents a significant improvement over B2PLYP-D3(BJ), particularly for intramolecular noncovalent interactions. These findings encourage future developments of efficient double-hybrid DFT strategies that can be applied when double-hybrid calculations with large basis sets are not feasible due to system size.
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35
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Lim VT, Hahn DF, Tresadern G, Bayly CI, Mobley DL. Benchmark assessment of molecular geometries and energies from small molecule force fields. F1000Res 2020; 9:Chem Inf Sci-1390. [PMID: 33604023 PMCID: PMC7863993 DOI: 10.12688/f1000research.27141.1] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/18/2020] [Indexed: 12/22/2022] Open
Abstract
Background: Force fields are used in a wide variety of contexts for classical molecular simulation, including studies on protein-ligand binding, membrane permeation, and thermophysical property prediction. The quality of these studies relies on the quality of the force fields used to represent the systems. Methods: Focusing on small molecules of fewer than 50 heavy atoms, our aim in this work is to compare nine force fields: GAFF, GAFF2, MMFF94, MMFF94S, OPLS3e, SMIRNOFF99Frosst, and the Open Force Field Parsley, versions 1.0, 1.1, and 1.2. On a dataset comprising 22,675 molecular structures of 3,271 molecules, we analyzed force field-optimized geometries and conformer energies compared to reference quantum mechanical (QM) data. Results: We show that while OPLS3e performs best, the latest Open Force Field Parsley release is approaching a comparable level of accuracy in reproducing QM geometries and energetics for this set of molecules. Meanwhile, the performance of established force fields such as MMFF94S and GAFF2 is generally somewhat worse. We also find that the series of recent Open Force Field versions provide significant increases in accuracy. Conclusions: This study provides an extensive test of the performance of different molecular mechanics force fields on a diverse molecule set, and highlights two (OPLS3e and OpenFF 1.2) that perform better than the others tested on the present comparison. Our molecule set and results are available for other researchers to use in testing.
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Affiliation(s)
- Victoria T. Lim
- Department of Chemistry, University of California, Irvine, CA, 92697, USA
| | - David F. Hahn
- Computational Chemistry, Janssen Research & Development, Beerse, B-2340, Belgium
| | - Gary Tresadern
- Computational Chemistry, Janssen Research & Development, Beerse, B-2340, Belgium
| | | | - David L. Mobley
- Department of Chemistry, University of California, Irvine, CA, 92697, USA
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, USA
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36
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König G, Riniker S. On the faithfulness of molecular mechanics representations of proteins towards quantum-mechanical energy surfaces. Interface Focus 2020; 10:20190121. [PMID: 33184586 DOI: 10.1098/rsfs.2019.0121] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2020] [Indexed: 12/11/2022] Open
Abstract
Force fields based on molecular mechanics (MM) are the main computational tool to study the relationship between protein structure and function at the molecular level. To validate the quality of such force fields, high-level quantum-mechanical (QM) data are employed to test their capability to reproduce the features of all major conformational substates of a series of blocked amino acids. The phase-space overlap between MM and QM is quantified in terms of the average structural reorganization energies over all energy minima. Here, the structural reorganization energy is the MM potential-energy difference between the structure of the respective QM energy minimum and the structure of the closest MM energy minimum. Thus, it serves as a measure for the relative probability of visiting the QM minimum during an MM simulation. We evaluate variants of the AMBER, CHARMM, GROMOS and OPLS biomolecular force fields. In addition, the two blocked amino acids alanine and serine are used to demonstrate the dependence of the measured agreement on the QM method, the phase, and the conformational preferences. Blocked serine serves as an example to discuss possible improvements of the force fields, such as including polarization with Drude particles, or using tailored force fields. The results show that none of the evaluated force fields satisfactorily reproduces all energy minima. By decomposing the average structural reorganization energies in terms of individual energy terms, we can further assess the individual weaknesses of the parametrization strategies of each force field. The dominant problem for most force fields appears to be the van der Waals parameters, followed to a lesser degree by dihedral and bonded terms. Our results show that performing a simple QM energy optimization from an MM-optimized structure can be a first test of the validity of a force field for a particular target molecule.
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Affiliation(s)
- Gerhard König
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany.,Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Sereina Riniker
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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37
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Li W, Battistel MD, Reeves H, Oh L, Yu H, Chen X, Wang LP, Freedberg DI. A combined NMR, MD and DFT conformational analysis of 9-O-acetyl sialic acid-containing GM3 ganglioside glycan and its 9-N-acetyl mimic. Glycobiology 2020; 30:787-801. [PMID: 32350512 PMCID: PMC8179627 DOI: 10.1093/glycob/cwaa040] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/22/2020] [Accepted: 04/22/2020] [Indexed: 01/30/2023] Open
Abstract
O-Acetylation of carbohydrates such as sialic acids is common in nature, but its role is not clearly understood due to the lability of O-acetyl groups. We demonstrated previously that 9-acetamido-9-deoxy-N-acetylneuraminic acid (Neu5Ac9NAc) is a chemically and biologically stable mimic of the 9-O-acetyl-N-acetylneuraminic acid (Neu5,9Ac2) of the corresponding sialoglycans. Here, a systematic nuclear magnetic resonance (NMR) spectroscopic and molecular dynamics (MD) simulation study was undertaken for Neu5,9Ac2-containing GM3 ganglioside glycan (GM3-glycan) and its Neu5Ac9NAc analog. GM3-glycan with Neu5Ac as the non-O-acetyl form of Neu5,9Ac2 was used as a control. Complete 1H and 13C NMR chemical shift assignments, three-bond 1H-13C trans-glycosidic coupling constants (3JCH), accurate 1H-1H coupling constants (3JHH), nuclear Overhauser effects and hydrogen bonding detection were carried out. Results show that structural modification (O- or N-acetylation) on the C-9 of Neu5Ac in GM3 glycan does not cause significant conformational changes on either its glycosidic dihedral angles or its secondary structure. All structural differences are confined to the Neu5Ac glycerol chain, and minor temperature-dependent changes are seen in the aglycone portion. We also used Density Functional Theory (DFT) quantum mechanical calculations to improve currently used 3JHH Karplus relations. Furthermore, OH chemical shifts were assigned at -10°C and no evidence of an intramolecular hydrogen bond was observed. The results provide additional evidence regarding structural similarities between sialosides containing 9-N-acetylated and 9-O-acetylated Neu5Ac and support the opportunity of using 9-N-acetylated Neu5Ac as a stable mimic to study the biochemical role of 9-O-acetylated Neu5Ac.
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Affiliation(s)
- Wanqing Li
- Department of Chemistry, University of California-Davis, One Shields Avenue, Davis, California 95616, USA
| | - Marcos D Battistel
- Laboratory of Bacterial Polysaccharides, Food and Drug Administration (FDA), Silver Spring, MD 20993, USA
| | - Hannah Reeves
- Department of Chemistry, University of California-Davis, One Shields Avenue, Davis, California 95616, USA
| | - Lisa Oh
- Department of Chemistry, University of California-Davis, One Shields Avenue, Davis, California 95616, USA
| | - Hai Yu
- Department of Chemistry, University of California-Davis, One Shields Avenue, Davis, California 95616, USA
| | - Xi Chen
- Department of Chemistry, University of California-Davis, One Shields Avenue, Davis, California 95616, USA
| | - Lee-Ping Wang
- Department of Chemistry, University of California-Davis, One Shields Avenue, Davis, California 95616, USA
| | - Darón I Freedberg
- Laboratory of Bacterial Polysaccharides, Food and Drug Administration (FDA), Silver Spring, MD 20993, USA
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38
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Williams ZM, Wiles TC, Manby FR. Accurate Hybrid Density Functionals with UW12 Correlation. J Chem Theory Comput 2020; 16:6176-6194. [PMID: 32820918 DOI: 10.1021/acs.jctc.0c00442] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In previous work, we suggested a single-parameter hybrid functional containing a novel correlation contribution based on the Unsöld approximation, UW12. This model resembles the explicitly correlated part of MP2-F12 theory and can be written as an explicit formula in terms of the single-particle reduced density matrix. Here, we further investigate hybrid functionals containing UW12 correlation and in particular look at functionals with a large fraction of exact exchange to reduce the self-interaction error. We suggest two new hybrid functionals B-LYP-osUW12 and fB-LYP-osUW12. On the test sets we use, our best hybrid functional overall (B-LYP-osUW12) is of similar accuracy to the best double hybrids considered while eliminating the need for virtual orbitals.
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Affiliation(s)
- Zack M Williams
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K
| | - Timothy C Wiles
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K
| | - Frederick R Manby
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K
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39
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Patra A, Jana S, Constantin LA, Samal P. Efficient yet accurate dispersion-corrected semilocal exchange–correlation functionals for non-covalent interactions. J Chem Phys 2020; 153:084117. [DOI: 10.1063/5.0011849] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Abhilash Patra
- School of Physical Sciences, National Institute of Science Education and Research, HBNI, Bhubaneswar 752050, India
| | - Subrata Jana
- School of Physical Sciences, National Institute of Science Education and Research, HBNI, Bhubaneswar 752050, India
| | - Lucian A. Constantin
- Istituto di Nanoscienze, Consiglio Nazionale delle Ricerche CNR-NANO, 41125 Modena, Italy
| | - Prasanjit Samal
- School of Physical Sciences, National Institute of Science Education and Research, HBNI, Bhubaneswar 752050, India
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40
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Kang YK, Park HS. Conformational preferences of cationic β-peptide in water studied by CCSD(T), MP2, and DFT methods. Heliyon 2020; 6:e04721. [PMID: 32904383 PMCID: PMC7452530 DOI: 10.1016/j.heliyon.2020.e04721] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/14/2020] [Accepted: 08/11/2020] [Indexed: 11/28/2022] Open
Abstract
The conformational preferences of the cationic nylon-3 βNM [(3R,4)-diaminobutanoic acid, dAba] dipeptide in water were explored as the first step to understand the mode of action of polymers of βNM against phylogenetically diverse and intrinsically drug-resistant pathogenic fungi. The CCSD(T), MP2, M06-2X, ωB97X-D, B2PLYP-D3BJ, and DSD-PBEP86-D3BJ levels of theory with various basis sets were assessed for relative energies of the 45 local minima of the cationic Ac-dAba-NHMe located at the SMD M06-2X/6-31+G(d) level of theory in water against the benchmark CCSD(T)/CBS-limit energies in water. The best performance was obtained at the double-hybrid DSD-PBEP86-D3BJ/def2-QZVP level of theory with RMSD = 0.12 kcal/mol in water. The M06-2X/def2-QZVP level of theory predicted reasonably the conformational preference with RMSD = 0.38 kcal/mol in water and may be an alternative level of theory with marginal deviations for the calculation of conformational energies of relatively longer cationic peptides in water. In particular, the H14–helical structures appeared to be the most feasible conformations for the cationic Ac-dAba-NHMe populated at 48–64% by relative free energies in water. The hexamer built from the H14–structure of the cationic Ac-dAba-NHMe adopted a left-handed 314-helix, which has a slightly narrower radius and a longer rise than the regular 314-helix of β-peptides. Hence, the 314-helices of oligomers or polymers of the cationic dAba residues are expected to be the active conformation to exhibit the ability to bridge between charged lipid head groups that might cause a local depression or invagination of the membrane of fungi.
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Affiliation(s)
- Young Kee Kang
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk 28644, Republic of Korea
| | - Hae Sook Park
- Department of Nursing, Cheju Halla University, Cheju 63092, Republic of Korea
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41
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Förster A, Visscher L. Double hybrid DFT calculations with Slater type orbitals. J Comput Chem 2020; 41:1660-1684. [PMID: 32297682 PMCID: PMC7317772 DOI: 10.1002/jcc.26209] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/31/2020] [Accepted: 04/01/2020] [Indexed: 12/14/2022]
Abstract
On a comprehensive database with 1,644 datapoints, covering several aspects of main-group as well as of transition metal chemistry, we assess the performance of 60 density functional approximations (DFA), among them 36 double hybrids (DH). All calculations are performed using a Slater type orbital (STO) basis set of triple-ζ (TZ) quality and the highly efficient pair atomic resolution of the identity approach for the exchange- and Coulomb-term of the KS matrix (PARI-K and PARI-J, respectively) and for the evaluation of the MP2 energy correction (PARI-MP2). Employing the quadratic scaling SOS-AO-PARI-MP2 algorithm, DHs based on the spin-opposite-scaled (SOS) MP2 approximation are benchmarked against a database of large molecules. We evaluate the accuracy of STO/PARI calculations for B3LYP as well as for the DH B2GP-PLYP and show that the combined basis set and PARI-error is comparable to the one obtained using the well-known def2-TZVPP Gaussian-type basis set in conjunction with global density fitting. While quadruple-ζ (QZ) calculations are currently not feasible for PARI-MP2 due to numerical issues, we show that, on the TZ level, Jacob's ladder for classifying DFAs is reproduced. However, while the best DHs are more accurate than the best hybrids, the improvements are less pronounced than the ones commonly found on the QZ level. For conformers of organic molecules and noncovalent interactions where very high accuracy is required for qualitatively correct results, DHs provide only small improvements over hybrids, while they still excel in thermochemistry, kinetics, transition metal chemistry and the description of strained organic systems.
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Affiliation(s)
- Arno Förster
- Theoretical ChemistryVrije UniversiteitAmsterdamThe Netherlands
| | - Lucas Visscher
- Theoretical ChemistryVrije UniversiteitAmsterdamThe Netherlands
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42
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Orján EM, Nacsa AB, Czakó G. Conformers of dehydrogenated glycine isomers. J Comput Chem 2020; 41:2001-2014. [DOI: 10.1002/jcc.26375] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/05/2020] [Accepted: 06/10/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Erik M. Orján
- MTA‐SZTE Lendület Computational Reaction Dynamics Research Group, Interdisciplinary Excellence Centre and Department of Physical Chemistry and Materials ScienceInstitute of Chemistry, University of Szeged Szeged Hungary
| | - András B. Nacsa
- MTA‐SZTE Lendület Computational Reaction Dynamics Research Group, Interdisciplinary Excellence Centre and Department of Physical Chemistry and Materials ScienceInstitute of Chemistry, University of Szeged Szeged Hungary
| | - Gábor Czakó
- MTA‐SZTE Lendület Computational Reaction Dynamics Research Group, Interdisciplinary Excellence Centre and Department of Physical Chemistry and Materials ScienceInstitute of Chemistry, University of Szeged Szeged Hungary
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43
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Toward accurate prediction of amino acid derivatives structure and energetics from DFT: glycine conformers and their interconversions. J Mol Model 2020; 26:129. [DOI: 10.1007/s00894-020-4342-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 03/04/2020] [Indexed: 12/30/2022]
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44
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Calvelo M, Lamas A, Guerra A, Amorín M, Garcia-Fandino R, Granja JR. Parallel Versus Antiparallel β-Sheet Structure in Cyclic Peptide Hybrids Containing γ- or δ-Cyclic Amino Acids. Chemistry 2020; 26:5846-5858. [PMID: 31999874 DOI: 10.1002/chem.201905554] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Indexed: 11/07/2022]
Abstract
Cyclic peptides with disc-shaped structures have emerged as potent building blocks for the preparation of new biomaterials in fields ranging from biological to material science. In this work, we analyze in depth the self-assembling properties of a new type of cyclic peptides based on the alternation of α-residues and cyclic δ-amino acids (α,δ-CPs). To examine the preferred stacking properties adopted by cyclic peptides bearing this type of amino acids, we carried out a synergistic in vitro/in silico approximation by using simple dimeric models and then extended to nanotubes. Although these new cyclic peptides (α,δ-CPs) can interact either in a parallel or antiparallel fashion, our results confirm that although the parallel β-sheet is more stable, it can be switched to the antiparallel stacking by choosing residues that can establish favorable cross-strand interactions. Moreover, the subsequent comparison by using the same methodology but applied to α,γ-CPs models, up to the moment assumed as antiparallel-like d,l-α-CPs, led to unforeseen conclusions that put into question preliminary conjectures about these systems. Surprisingly, they tend to adopt a parallel β-sheet directed by the skeleton interactions. These results imply a change of paradigm with respect to cyclic peptide designs that should be considered for dimers and nanotubes.
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Affiliation(s)
- Martín Calvelo
- Centro Singular de Investigación en Química Biolóxica e, Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Alejandro Lamas
- Centro Singular de Investigación en Química Biolóxica e, Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Arcadio Guerra
- Centro Singular de Investigación en Química Biolóxica e, Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Manuel Amorín
- Centro Singular de Investigación en Química Biolóxica e, Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Rebeca Garcia-Fandino
- Centro Singular de Investigación en Química Biolóxica e, Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Juan R Granja
- Centro Singular de Investigación en Química Biolóxica e, Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
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45
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Yu F, Wang Y. Dual‐hybrid direct random phase approximation and second‐order screened exchange with nonlocal van der Waals correlations for noncovalent interactions. J Comput Chem 2020; 41:1018-1025. [DOI: 10.1002/jcc.26149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/05/2020] [Accepted: 01/06/2020] [Indexed: 11/09/2022]
Affiliation(s)
- Feng Yu
- Department of Physics, School of ScienceXi'an Technological University Xi'an Shaanxi China
| | - Yaoting Wang
- Department of Physics, School of ScienceXi'an Technological University Xi'an Shaanxi China
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46
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Chen J, Chan B, Shao Y, Ho J. How accurate are approximate quantum chemical methods at modelling solute-solvent interactions in solvated clusters? Phys Chem Chem Phys 2020; 22:3855-3866. [PMID: 32022044 PMCID: PMC7394230 DOI: 10.1039/c9cp06792b] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In this paper, the performance of a wide range of DFT methods is assessed for the calculation of interaction energies of thermal clusters of a solute in water. Three different charge states (neutral, proton transfer transition state and zwitterion) of glycine were solvated by 1 to 40 water molecules as sampled from molecular dynamics simulations. While some ab initio composite methods that employ insufficiently large basis sets incurred significant errors even for a cluster containing only 5 water molecules relative to the W1X-2 benchmark, the DLPNO-CCSD(T)/CBS and DSD-PBEP86 (triple zeta basis set) levels of theory predicted very accurate interaction energies. These levels of theory were used to benchmark the performance of 16 density functionals from different rungs of Jacob's Ladder. Of the Rung 4 functionals examined, the ωB97M-V and ωB97X-V functionals stood out for predicting absolute interaction energies in 40-water clusters with mean absolute deviations (MAD) ∼4 kJ mol-1. The B3LYP-D3(BJ) functional performed exceptionally well with a MAD ∼1.7 kJ mol-1 and is the overall best performing method. Calculations of relative interaction energies allow for cancellation of systematic errors, including basis set truncation and superposition errors, and the ωB97M-V and B3LYP-D3(BJ) double zeta basis set calculations yielded relative interaction energies that are within ∼3 kJ mol-1 of the benchmark. The ONIOM approximation provides another strategy for accelerating the calculation of accurate absolute interaction energies provided that the calculations have converged with respect to the size of the "high-level-layer".
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Affiliation(s)
- Junbo Chen
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Bun Chan
- Graduate School of Engineering, Nagasaki University, Bunkyo-Machi 1-14, Nagasaki 852-8521, Japan.
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, USA
| | - Junming Ho
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia.
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47
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Förster A, Franchini M, van Lenthe E, Visscher L. A Quadratic Pair Atomic Resolution of the Identity Based SOS-AO-MP2 Algorithm Using Slater Type Orbitals. J Chem Theory Comput 2020; 16:875-891. [PMID: 31930915 PMCID: PMC7027358 DOI: 10.1021/acs.jctc.9b00854] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Indexed: 01/04/2023]
Abstract
We report a production level implementation of pair atomic resolution of the identity (PARI) based second-order Møller-Plesset perturbation theory (MP2) in the Slater type orbital (STO) based Amsterdam Density Functional (ADF) code. As demonstrated by systematic benchmarks, dimerization and isomerization energies obtained with our code using STO basis sets of triple-ζ-quality show mean absolute deviations from Gaussian type orbital, canonical, basis set limit extrapolated, global density fitting (DF)-MP2 results of less than 1 kcal/mol. Furthermore, we introduce a quadratic scaling atomic orbital based spin-opposite-scaled (SOS)-MP2 approach with a very small prefactor. Due to a worst-case scaling of [Formula: see text], our implementation is very fast already for small systems and shows an exceptionally early crossover to canonical SOS-PARI-MP2. We report computational wall time results for linear as well as for realistic three-dimensional molecules and show that triple-ζ quality calculations on molecules of several hundreds of atoms are only a matter of a few hours on a single compute node, the bottleneck of the computations being the SCF rather than the post-SCF energy correction.
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Affiliation(s)
- Arno Förster
- Theoretical Chemistry, Vrije
Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The
Netherlands
| | - Mirko Franchini
- Theoretical Chemistry, Vrije
Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The
Netherlands
- Scientific Computing & Modelling
NV, De Boelelaan 1083, NL-1081 HV Amsterdam, The
Netherlands
| | - Erik van Lenthe
- Scientific Computing & Modelling
NV, De Boelelaan 1083, NL-1081 HV Amsterdam, The
Netherlands
| | - Lucas Visscher
- Theoretical Chemistry, Vrije
Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The
Netherlands
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48
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Chan B. Aqueous-Phase Conformations of Lactose, Maltose, and Sucrose and the Assessment of Low-Cost DFT Methods with the DSCONF Set of Conformers for the Three Disaccharides. J Phys Chem A 2020; 124:582-590. [PMID: 31927999 DOI: 10.1021/acs.jpca.9b10932] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In the present study, we have examined a range of quantum chemistry methods for the calculation of conformers for lactose, maltose, and sucrose. We find that the DSD-PBE-P86/aug'-cc-pVTZ//B3-LYP-D3BJ/6-311+G(2d,p) protocol yields good relative energies in comparison with reference CCSD(T)/CBS//B3-LYP-D3BJ/maug-cc-pVTZ values. We have surveyed a total of ∼550 conformers for the three disaccharides with the chosen DSD-PBE-P86 method in conjunction with continuum aqueous solvation. In each case, the lowest free energy conformer is characterized by hydrogen bond(s) between the two rings. Another finding is that the major contributors to the overall variations in aqueous free energies are the electronic energies and the solvation energies. To facilitate investigations of larger systems, we have compiled the DSCONF set of conformers for the three disaccharides, and we have assessed lower cost methods with this set. We find MS1-D3/6-31+G(2d,p) to be cost-effective and accurate for both geometry optimization and the calculation of relative energies for disaccharides. In addition, we note that MS1-D3 has previously been found to yield good relative energies for the WATER27 set of water clusters. We thus deem this method to be appropriate for the study of saccharide conformations in both gas phase and aqueous solution.
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Affiliation(s)
- Bun Chan
- Graduate School of Engineering , Nagasaki University , Bunkyo 1-14 , Nagasaki 852-8521 , Japan
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49
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Henao A, Ruiz GN, Steinke N, Cerveny S, Macovez R, Guàrdia E, Busch S, McLain SE, Lorenz CD, Pardo LC. On the microscopic origin of the cryoprotective effect in lysine solutions. Phys Chem Chem Phys 2020; 22:6919-6927. [DOI: 10.1039/c9cp06192d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Lysine cryoprotective properties are due to the tight bonding of the first hydration Shell to the amino acid. However this effect is only possible for concentration up to 5.4 water molecules per lysine.
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Affiliation(s)
- Andrés Henao
- Grup de Caracterització de Materials
- Departament de Física
- ETSEIB, Universitat Politècnica de Catalunya
- E-08019 Barcelona
- Spain
| | - Guadalupe N. Ruiz
- Grup de Caracterització de Materials
- Departament de Física
- ETSEIB, Universitat Politècnica de Catalunya
- E-08019 Barcelona
- Spain
| | - Nicola Steinke
- Center for Marine Environmental Sciences (MARUM)
- University of Bremen
- 28359 Bremen
- Germany
| | - Silvina Cerveny
- Centro de Física de Materiales (CSIC-UPV/EHU)-Material Physics Centre (MPC)
- Donostia International Physics Center (DIPC)
- 20018 San Sebastián
- Spain
| | - Roberto Macovez
- Grup de Caracterització de Materials
- Departament de Física
- ETSEIB, Universitat Politècnica de Catalunya
- E-08019 Barcelona
- Spain
| | - Elvira Guàrdia
- Grup de Simulació per Ordinador en Matèria Condensada
- Departament de Física
- Universitat Politècnica de Catalunya
- E-08034 Barcelona
- Spain
| | - Sebastian Busch
- German Engineering Materials Science Centre (GEMS) at Heinz Maier-Leibnitz Zentrum (MLZ)
- Helmholtz-Zentrum Geesthacht GmbH
- 85747 Garching bei München
- Germany
| | - Sylvia E. McLain
- Department of Chemistry
- School of Life Sciences
- University of Sussex
- Brighton
- UK
| | | | - Luis Carlos Pardo
- Grup de Caracterització de Materials
- Departament de Física
- ETSEIB, Universitat Politècnica de Catalunya
- E-08019 Barcelona
- Spain
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50
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Mezei PD, Kállay M. Construction of a Range-Separated Dual-Hybrid Direct Random Phase Approximation. J Chem Theory Comput 2019; 15:6678-6687. [PMID: 31693355 DOI: 10.1021/acs.jctc.9b00891] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Blending the good performance of the global hybrid PBE0 functional at short-range and the dual-hybrid dRPA75 functional at long range, we propose a new range-separated direct random phase approximation (dRPA75rs), which considerably improves on the accuracy of the calculated reaction energies and barrier heights compared to the parent approaches and provides a good description of noncovalent interactions without any dispersion correction. We also combine the new scheme with spin-component scaling (SCS-dRPA75rs), which enables the accurate calculation of energy differences for processes involving electron pair breaking, such as atomization. The new method scaling as the fourth power of the system size shows a balanced performance on a broad test set involving radicals, transition metal atoms, and heavy atoms, which makes it competitive with the best double-hybrid functionals based on the second-order perturbation theory. According to the results for the homogeneous electron gas, our dRPA75rs method expectedly gives errors for metallic systems similar to the dRPA approach with an additional error cancellation in the case of partial spin polarization.
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Affiliation(s)
- Pál D Mezei
- Department of Chemistry , University of Basel , Basel 4056 , Switzerland
| | - Mihály Kállay
- Department of Physical Chemistry and Materials Science , Budapest University of Technology and Economics , P.O. Box 91, H-1521 Budapest , Hungary
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