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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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2
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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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3
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Mazumdar P, Choudhury D. Study of the alkyl-π interaction between methane and few substituted pyrimidine systems using DFT, AIM and NBO calculations. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2021.113560] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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4
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Rowsey R, Taylor EE, Irle S, Stadie NP, Szilagyi RK. Methane Adsorption on Heteroatom-Modified Maquettes of Porous Carbon Surfaces. J Phys Chem A 2021; 125:6042-6058. [PMID: 34232640 DOI: 10.1021/acs.jpca.0c11284] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Experimental and theoretical studies disagree on the energetics of methane adsorption on carbon materials. However, this information is critical for the rational design and optimization of the structure and composition of adsorbents for natural gas storage. The delicate nature of dispersion interactions, polarization of both the adsorbent and the adsorbate, interplay between H-bonding and tetrel bonding, and induced dipole/Coulomb interactions inherent to methane physisorption require computational treatment at the highest possible level of theory. In this study, we employed the smallest reasonable computational model, a maquette of porous carbon surfaces with a central site for substitution and methane binding. The most accurate predictions of methane adsorption energetics were achieved by electron-correlated molecular orbital theory CCSD(T) and hybrid density functional theory MN15 calculations employing a saturated, all-electron basis set. The characteristic geometry of methane adsorption on a carbon surface ("lander approach") arises due to bonding interactions of the adsorbent π-system with the proximal H-C bonds of methane, in addition to tetrel bonding between the antibonding orbital of the distal C-H bond and the central atom of the maquette (C, B, or N). The polarization of the electron density, structural deformations, and the comprehensive energetic analysis clearly indicate a ∼3 kJ mol-1 preference for methane binding on the N-substituted maquette. The B-substituted maquette showed a comparable or lower binding energy than the unsubstituted, pure C model, depending on the level of theory employed. The calculated thermodynamic results indicate a strategy for incorporating electron-enriched substitutions (e.g., N) into carbon materials as a way to increase methane storage capacity over electron-deficient (e.g., B) modifications. The thermochemical analysis was revised for establishing a conceptual agreement between the experimental isosteric heat of adsorption and the binding enthalpies from statistical thermodynamics principles.
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Affiliation(s)
- Rylan Rowsey
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Erin E Taylor
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Stephan Irle
- Computational Sciences & Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Nicholas P Stadie
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Robert K Szilagyi
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, Montana 59717, United States
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5
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DFT study on binding of single and double methane with aromatic hydrocarbons and graphene: stabilizing CH…HC interactions between two methane molecules. Struct Chem 2020. [DOI: 10.1007/s11224-020-01657-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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6
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Zhang Y, Lee WH, Seong JG, Bae JY, Zhuang Y, Feng S, Wan Y, Lee YM. Alicyclic segments upgrade hydrogen separation performance of intrinsically microporous polyimide membranes. J Memb Sci 2020. [DOI: 10.1016/j.memsci.2020.118363] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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7
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Patkowski K. Recent developments in symmetry‐adapted perturbation theory. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2019. [DOI: 10.1002/wcms.1452] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Konrad Patkowski
- Department of Chemistry and Biochemistry Auburn University Auburn Alabama
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8
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Saha B, Bhattacharyya PK. Density Functional Study on the Adsorption of 5-Membered N-Heterocycles on B/N/BN-Doped Graphene: Coronene as a Model System. ACS OMEGA 2018; 3:16753-16768. [PMID: 31458306 PMCID: PMC6643900 DOI: 10.1021/acsomega.8b02340] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 11/23/2018] [Indexed: 05/07/2023]
Abstract
Adsorption of seven 5-membered N-heterocycles on B/N/BN-doped graphene (with coronene as a model system) has been studied using density functional theory (DFT). The geometry of the complexes validated the involvement of both π···π stacking and N-H···π interaction in the adsorption process. The stability of the complexes is measured in terms of stabilization energy, and the results suggested that the complexes are stable enough (stabilization energies are in the range of 7.61-14.77 kcal mol-1). Studies confirmed the stability of complexes in the solvent phase too irrespective of the dielectric of the solvent. Dispersive force is the major mode of interaction in stabilizing the complexes. Natural bond orbital analysis indicated a small contribution from electrostatic and covalent interactions. Thermochemical analysis revealed that the complexation is exothermic in nature and favorable at a lower temperature. Adsorption of N-heterocycles exerts a nominal impact on the electronic properties of the undoped/doped graphene. The study presents a simple approach to introduce an arbitrary functionality to undoped/doped graphene by preserving its electronic properties.
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Affiliation(s)
- Bapan Saha
- Department
of Chemistry, Handique Girls’ College, Panbazar, Guwahati 781001, Assam, India
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9
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Vekeman J, G Cuesta I, Faginas-Lago N, Wilson J, Sánchez-Marín J, Sánchez de Merás A. Potential models for the simulation of methane adsorption on graphene: development and CCSD(T) benchmarks. Phys Chem Chem Phys 2018; 20:25518-25530. [PMID: 30277488 DOI: 10.1039/c8cp03652g] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Different force fields for the graphene-CH4 system are proposed including pseudo-atom and full atomistic models. Furthermore, different charge schemes are tested to evaluate the electrostatic interaction for the CH4 dimer. The interaction parameters are optimized by fitting to interaction energies at the DFT level, which were themselves benchmarked against CCSD(T) calculations. The potentials obtained with both the pseudo-atom and full atomistic approaches describe accurately enough the average interaction in the methane dimer as well as in the graphene-methane system. Moreover, the atom-atom potentials also correctly provide the energies associated with different orientations of the molecules. In the atomistic models, charge schemes including small charges allow for the adequate representation of the stability sequence of significant conformations of the methane dimer. Additionally, an intermediate charge of -0.63e on the carbon atom in methane leads to bond energies with errors of ca. 0.07 kcal mol-1 with respect to the CCSD(T) values for the methane dimer. For the graphene-methane interaction, the atom-atom potential model predicts an average interaction energy of 2.89 kcal mol-1, comparable to the experimental interaction energy of 3.00 kcal mol-1. Finally, the presented force fields were used to obtain self-diffusion coefficients that were checked against the experimental value found in the literature. The no-charge and Hirshfeld charge atom-atom models perform extremely well in this respect, while the cheapest potential considered, a pseudo-atom model without charges, still performs reasonably well.
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Affiliation(s)
- J Vekeman
- Instituto de Ciencia Molecular, Parc cientifico de la Universidad de Valencia, C/Catedrático José Beltrán 2, E-46980 Paterna, Spain.
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10
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Dutta NN, Patkowski K. Improving “Silver-Standard” Benchmark Interaction Energies with Bond Functions. J Chem Theory Comput 2018; 14:3053-3070. [DOI: 10.1021/acs.jctc.8b00204] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Narendra Nath Dutta
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Konrad Patkowski
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
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11
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Prasad VK, Otero-de-la-Roza A, DiLabio GA. Atom-Centered Potentials with Dispersion-Corrected Minimal-Basis-Set Hartree–Fock: An Efficient and Accurate Computational Approach for Large Molecular Systems. J Chem Theory Comput 2018; 14:726-738. [DOI: 10.1021/acs.jctc.7b01158] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Viki Kumar Prasad
- Department
of Chemistry, University of British Columbia, 3247 University Way, Kelowna, British Columbia, Canada V1V 1V7
| | - Alberto Otero-de-la-Roza
- Department
of Chemistry, University of British Columbia, 3247 University Way, Kelowna, British Columbia, Canada V1V 1V7
| | - Gino A. DiLabio
- Department
of Chemistry, University of British Columbia, 3247 University Way, Kelowna, British Columbia, Canada V1V 1V7
- Faculty
of Management, University of British Columbia, 1137 Alumni Avenue, Kelowna, British Columbia, Canada V1V 1V7
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12
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Armaković S, Armaković SJ, Tomić BT, Pillai RR, Panicker CY. Adsorption properties of graphene towards the ephedrine – A frequently used molecule in sport. COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2017.12.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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13
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Saha B, Bhattacharyya PK. B–Hb⋯π interaction in borane–graphene complexes: coronene as a case study. NEW J CHEM 2017. [DOI: 10.1039/c7nj00057j] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
N/B/BN doping in graphene enhances adsorption of boranes.
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14
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Sirianni DA, Burns LA, Sherrill CD. Comparison of Explicitly Correlated Methods for Computing High-Accuracy Benchmark Energies for Noncovalent Interactions. J Chem Theory Comput 2016; 13:86-99. [DOI: 10.1021/acs.jctc.6b00797] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dominic A. Sirianni
- Center for Computational
Molecular Science and Technology, School of Chemistry and Biochemistry,
School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Lori A. Burns
- Center for Computational
Molecular Science and Technology, School of Chemistry and Biochemistry,
School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - C. David Sherrill
- Center for Computational
Molecular Science and Technology, School of Chemistry and Biochemistry,
School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
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15
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Zhang O, Zou X, Li QH, Sun Z, Liu YD, Zhong RG. Experimental and Theoretical Investigation of Effects of Ethanol and Acetic Acid on Carcinogenic NDMA Formation in Simulated Gastric Fluid. J Phys Chem A 2016; 120:4505-13. [DOI: 10.1021/acs.jpca.6b02582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ou Zhang
- College of Life Science & Bioengineering, Beijing University of Technology, Beijing 100124, P. R. China
| | - Xuan Zou
- Department
of Stomatology, Chinese PLA 307 Hospital, Academy of Military Medical Sciences, Beijing, 100071, P. R. China
| | - Qi-Hong Li
- Department
of Stomatology, Chinese PLA 307 Hospital, Academy of Military Medical Sciences, Beijing, 100071, P. R. China
| | - Zhi Sun
- College of Life Science & Bioengineering, Beijing University of Technology, Beijing 100124, P. R. China
| | - Yong Dong Liu
- College of Life Science & Bioengineering, Beijing University of Technology, Beijing 100124, P. R. China
| | - Ru Gang Zhong
- College of Life Science & Bioengineering, Beijing University of Technology, Beijing 100124, P. R. China
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16
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Smith DGA, Burns LA, Patkowski K, Sherrill CD. Revised Damping Parameters for the D3 Dispersion Correction to Density Functional Theory. J Phys Chem Lett 2016; 7:2197-203. [PMID: 27203625 DOI: 10.1021/acs.jpclett.6b00780] [Citation(s) in RCA: 224] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Since the original fitting of Grimme's DFT-D3 damping parameters, the number and quality of benchmark interaction energies has increased significantly. Here, conventional benchmark sets, which focus on minimum-orientation radial curves at the expense of angular diversity, are augmented by new databases such as side chain-side chain interactions (SSI), which are composed of interactions gleaned from crystal data and contain no such minima-focused bias. Moreover, some existing databases such as S22×5 are extended to shorter intermolecular separations. This improved DFT-D3 training set provides a balanced description of distances, covers the entire range of interaction types, and at 1526 data points is far larger than the original training set of 130. The results are validated against a new collection of 6773 data points and demonstrate that the effect of refitting the damping parameters ranges from no change in accuracy (LC-ωPBE-D3) to an almost 2-fold decrease in average error (PBE-D3).
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Affiliation(s)
- Daniel G A Smith
- Department of Chemistry and Biochemistry, Auburn University , Auburn, Alabama 36849, United States
| | - Lori A Burns
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
| | - Konrad Patkowski
- Department of Chemistry and Biochemistry, Auburn University , Auburn, Alabama 36849, United States
| | - C David Sherrill
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry and School of Computational Science and Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
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17
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Rohini K, Sylvinson DMR, Swathi RS. Intercalation of HF, H2O, and NH3 Clusters within the Bilayers of Graphene and Graphene Oxide: Predictions from Coronene-Based Model Systems. J Phys Chem A 2015; 119:10935-45. [DOI: 10.1021/acs.jpca.5b05702] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- K. Rohini
- School
of Chemistry, Indian Institute of Science Education and Research-Thiruvananthapuram, Kerala, India 695016
| | - Daniel M. R. Sylvinson
- School
of Chemistry, Indian Institute of Science Education and Research-Thiruvananthapuram, Kerala, India 695016
| | - R. S. Swathi
- School
of Chemistry, Indian Institute of Science Education and Research-Thiruvananthapuram, Kerala, India 695016
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18
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Cazorla C. The role of density functional theory methods in the prediction of nanostructured gas-adsorbent materials. Coord Chem Rev 2015. [DOI: 10.1016/j.ccr.2015.05.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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19
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Kocman M, Jurečka P, Dubecký M, Otyepka M, Cho Y, Kim KS. Choosing a density functional for modeling adsorptive hydrogen storage: reference quantum mechanical calculations and a comparison of dispersion-corrected density functionals. Phys Chem Chem Phys 2015; 17:6423-32. [DOI: 10.1039/c4cp04354e] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Various dispersion-corrected density functionals are compared with high level QM data for several model complexes for adsorptive hydrogen storage.
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Affiliation(s)
- Mikuláš Kocman
- Regional Centre of Advanced Technologies and Materials
- Department of Physical Chemistry
- Faculty of Science
- Palacky University
- 77146 Olomouc
| | - Petr Jurečka
- Regional Centre of Advanced Technologies and Materials
- Department of Physical Chemistry
- Faculty of Science
- Palacky University
- 77146 Olomouc
| | - Matúš Dubecký
- Regional Centre of Advanced Technologies and Materials
- Department of Physical Chemistry
- Faculty of Science
- Palacky University
- 77146 Olomouc
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials
- Department of Physical Chemistry
- Faculty of Science
- Palacky University
- 77146 Olomouc
| | - Yeonchoo Cho
- Center for Superfunctional Materials
- Department of Chemistry and Department of Physics
- Pohang University of Science and Technology
- Pohang 790-784
- Korea
| | - Kwang S. Kim
- Center for Superfunctional Materials
- Department of Chemistry
- Ulsan National Institute of Science and Technology (UNIST)
- Ulsan 689-798
- Korea
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20
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Li S, Smith DGA, Patkowski K. An accurate benchmark description of the interactions between carbon dioxide and polyheterocyclic aromatic compounds containing nitrogen. Phys Chem Chem Phys 2015; 17:16560-74. [DOI: 10.1039/c5cp02365c] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We assessed the performance of a large variety of modern density functional theory approaches for the adsorption of carbon dioxide on molecular models of pyridinic N-doped graphene.
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Affiliation(s)
- Sicheng Li
- Department of Chemistry and Biochemistry
- Auburn University
- Auburn
- USA
| | | | - Konrad Patkowski
- Department of Chemistry and Biochemistry
- Auburn University
- Auburn
- USA
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21
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Zhao C, Li P, Smith MD, Pellechia PJ, Shimizu KD. Experimental Study of the Cooperativity of CH−π Interactions. Org Lett 2014; 16:3520-3. [DOI: 10.1021/ol5014729] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Chen Zhao
- Department
of Chemistry and
Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Ping Li
- Department
of Chemistry and
Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Mark D. Smith
- Department
of Chemistry and
Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Perry J. Pellechia
- Department
of Chemistry and
Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Ken D. Shimizu
- Department
of Chemistry and
Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
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22
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Hughes ZE, Tomásio SM, Walsh TR. Efficient simulations of the aqueous bio-interface of graphitic nanostructures with a polarisable model. NANOSCALE 2014; 6:5438-5448. [PMID: 24722915 DOI: 10.1039/c4nr00468j] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
To fully harness the enormous potential offered by interfaces between graphitic nanostructures and biomolecules, detailed connections between adsorbed conformations and adsorption behaviour are needed. To elucidate these links, a key approach, in partnership with experimental techniques, is molecular simulation. For this, a force-field (FF) that can appropriately capture the relevant physics and chemistry of these complex bio-interfaces, while allowing extensive conformational sampling, and also supporting inter-operability with known biological FFs, is a pivotal requirement. Here, we present and apply such a force-field, GRAPPA, designed to work with the CHARMM FF. GRAPPA is an efficiently implemented polarisable force-field, informed by extensive plane-wave DFT calculations using the revPBE-vdW-DF functional. GRAPPA adequately recovers the spatial and orientational structuring of the aqueous interface of graphene and carbon nanotubes, compared with more sophisticated approaches. We apply GRAPPA to determine the free energy of adsorption for a range of amino acids, identifying Trp, Tyr and Arg to have the strongest binding affinity and Asp to be a weak binder. The GRAPPA FF can be readily incorporated into mainstream simulation packages, and will enable large-scale polarisable biointerfacial simulations at graphitic interfaces, that will aid the development of biomolecule-mediated, solution-based graphene processing and self-assembly strategies.
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Affiliation(s)
- Zak E Hughes
- Institute for Frontier Materials, Deakin University, Geelong, Australia.
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23
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Ihm Y, Cooper VR, Gallego NC, Contescu CI, Morris JR. Microstructure-Dependent Gas Adsorption: Accurate Predictions of Methane Uptake in Nanoporous Carbons. J Chem Theory Comput 2013; 10:1-4. [DOI: 10.1021/ct400875n] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Yungok Ihm
- Department
of Materials Science and Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Valentino R. Cooper
- Materials
Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6069, United States
| | - Nidia C. Gallego
- Materials
Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6069, United States
| | - Cristian I. Contescu
- Materials
Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6069, United States
| | - James R. Morris
- Department
of Materials Science and Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
- Materials
Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6069, United States
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24
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Patkowski K. Basis set converged weak interaction energies from conventional and explicitly correlated coupled-cluster approach. J Chem Phys 2013; 138:154101. [DOI: 10.1063/1.4800981] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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25
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Lazar P, Karlický F, Jurečka P, Kocman M, Otyepková E, Šafářová K, Otyepka M. Adsorption of Small Organic Molecules on Graphene. J Am Chem Soc 2013; 135:6372-7. [DOI: 10.1021/ja403162r] [Citation(s) in RCA: 359] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Petr Lazar
- Regional Centre
of Advanced Technologies and Materials,
Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, 771 46 Olomouc,
Czech Republic
| | - František Karlický
- Regional Centre
of Advanced Technologies and Materials,
Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, 771 46 Olomouc,
Czech Republic
| | - Petr Jurečka
- Regional Centre
of Advanced Technologies and Materials,
Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, 771 46 Olomouc,
Czech Republic
| | - Mikuláš Kocman
- Regional Centre
of Advanced Technologies and Materials,
Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, 771 46 Olomouc,
Czech Republic
| | - Eva Otyepková
- Regional Centre
of Advanced Technologies and Materials,
Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, 771 46 Olomouc,
Czech Republic
| | - Klára Šafářová
- Regional Centre
of Advanced Technologies and Materials,
Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, 771 46 Olomouc,
Czech Republic
| | - Michal Otyepka
- Regional Centre
of Advanced Technologies and Materials,
Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, 771 46 Olomouc,
Czech Republic
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