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Hernández-Segura LI, Olvera-Rubalcava FA, Flores-Moreno R, Calaminici P, Köster AM. Exchange-correlation kernel for perturbation dependent auxiliary functions in auxiliary density perturbation theory. J Mol Model 2024; 30:302. [PMID: 39115689 PMCID: PMC11310252 DOI: 10.1007/s00894-024-06091-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 07/23/2024] [Indexed: 08/11/2024]
Abstract
CONTEXT Analytic exchange-correlation kernel formulations are of the outermost importance for density functional theory (DFT) perturbation calculations. In this paper, the working equation for the exchange-correlation kernel of the generalized gradient approximation (GGA) for perturbation dependent auxiliary functions is derived and discussed in the framework of auxiliary density functional theory (ADFT). The presented new formulation is extended to the unrestricted approach, too. A comprehensive discussion of the implementation of the GGA ADFT kernel, using either the native exchange-correlation functional implementations in deMon2k or the ones from the LibXC library, is given. Calculations with analytic exchange-correlation kernels are compared to their finite difference counterparts. The obtained results are in quantitative agreement. Nevertheless, analytic GGA ADFT kernel implementations show substantial improvement in the computational performance. Similar results are reported for analytic second derivatives of effective core potential (ECP) and model core potential (MCP) matrix elements when compared to their finite difference counterparts in molecular frequency analyses. METHOD All calculations are performed in the framework of ADFT as implemented in deMon2k. In the ADFT analytic frequency calculations, auxiliary density perturbation theory was used. The underlying two-center exchange-correlation kernel matrix elements are calculated by numerical integration either with analytic or finite difference kernel expressions. Validation calculations are performed with the VWN and PBE functionals employing DFT-optimized DZVP basis sets in conjunction with automatically generated GEN-A2 auxiliary density function sets. In the (Pt3Cu)n cluster benchmark calculations, the RPBE functional was used. For Pt atoms, the quasi-relativistic LANL2DZ effective core potential with the corresponding valence basis set was employed, whereas for Cu atoms, the all-electron DFT-optimized TZVP basis was applied. The auxiliary density was expanded by the automatically generated GEN-A2* auxiliary function set. We run all benchmark calculations in parallel on 24 cores.
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Affiliation(s)
- Luis I Hernández-Segura
- Chemistry Department, CINVESTAV, Av. Instituto Politecnico Nacional 2508, Col. San Pedro Zacatenco, Del. Gustavo A. Madero, Mexico City, C.P. 07360, Mexico.
| | - Flor A Olvera-Rubalcava
- Chemistry Department, CINVESTAV, Av. Instituto Politecnico Nacional 2508, Col. San Pedro Zacatenco, Del. Gustavo A. Madero, Mexico City, C.P. 07360, Mexico
| | - Roberto Flores-Moreno
- Departamento de Química, Universidad de Guadalajara, Blvd. Gral. Marcelino García Barragán 1421, Guadalajara, Jal., C.P. 44430, Mexico
| | - Patrizia Calaminici
- Chemistry Department, CINVESTAV, Av. Instituto Politecnico Nacional 2508, Col. San Pedro Zacatenco, Del. Gustavo A. Madero, Mexico City, C.P. 07360, Mexico
| | - Andreas M Köster
- Chemistry Department, CINVESTAV, Av. Instituto Politecnico Nacional 2508, Col. San Pedro Zacatenco, Del. Gustavo A. Madero, Mexico City, C.P. 07360, Mexico.
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Fontanini RE, Flores-Moreno R, Zúñiga-Gutiérrez BA, Kaya S, Katin KP, Maslov MM, Kochaev A. Semiempirical Approach to the Fukui Function Analysis of Uric Acid under Different pH Conditions. J Phys Chem A 2023; 127:8228-8237. [PMID: 37751600 DOI: 10.1021/acs.jpca.3c04695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Abstract
Analytic Fukui functions calculated at a first-principles level are combined with experimental pKa values and the calculation of tautomerization energies to obtain the effective regioselectivity of uric acid toward electron-transfer reactions under different pH conditions. Second-order electron binding energies are also computed to determine which of the tautomers is more likely to participate in the electron transfer. A comparison of vertical and adiabatic proton detachment energies allows us to conclude that tautomerization is not mediating deprotonation and that two monoanionic species are of comparable relevance. The main difference between these monoanionic species is the ring that has been deprotonated. Both monoanionic species are produced from a single neutral tautomer and mainly produce a single dianionic tautomer. As a method for the analysis of systems affected by pH such as uric acid, we propose to plot condensed Fukui functions versus pH, allowing us to draw the effect of pH on the regioselectivity of electron transfer in a single image.
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Affiliation(s)
- Roberto E Fontanini
- Departamento de Química, Universidad de Guadalajara, Blvd. Marcelino García Barragán 1421, Guadalajara Jal. C. P, 44430 Mexico
| | - Roberto Flores-Moreno
- Departamento de Química, Universidad de Guadalajara, Blvd. Marcelino García Barragán 1421, Guadalajara Jal. C. P, 44430 Mexico
| | - Bernardo A Zúñiga-Gutiérrez
- Departamento de Química, Universidad de Guadalajara, Blvd. Marcelino García Barragán 1421, Guadalajara Jal. C. P, 44430 Mexico
| | - Savas Kaya
- Sivas Cumhuriyet University, Health Services Vocational School, Department of Pharmacy, 58140 Sivas, Turkey
| | - Konstantin P Katin
- Laboratory of Computational Design of Nanostructures Nanodevices and Nanotechnologies, Research Institute for the Development of Scientific and Educational Potential of Youth, Aviatorov str. 14/55, Moscow 119620, Russia
- Nanoengineering in Electronics Spintronics and Photonics Institute, National Research Nuclear University "MEPhI", Kashirskoe Shosse 31, Moscow 115409, Russia
| | - Mikhail M Maslov
- Laboratory of Computational Design of Nanostructures Nanodevices and Nanotechnologies, Research Institute for the Development of Scientific and Educational Potential of Youth, Aviatorov str. 14/55, Moscow 119620, Russia
- Nanoengineering in Electronics Spintronics and Photonics Institute, National Research Nuclear University "MEPhI", Kashirskoe Shosse 31, Moscow 115409, Russia
| | - Aleksey Kochaev
- Laboratory of Computational Design of Nanostructures Nanodevices and Nanotechnologies, Research Institute for the Development of Scientific and Educational Potential of Youth, Aviatorov str. 14/55, Moscow 119620, Russia
- Research and Education Center "Silicon and Carbon Nanotechnologies", Ulyanovsk State University, 42 Leo Tolstoy Str, Ulyanovsk 432017, Russia
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Hernández-Segura LI, Köster AM. Efficient implementation of time-dependent auxiliary density functional theory. J Chem Phys 2023; 158:024108. [PMID: 36641386 DOI: 10.1063/5.0135263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The random phase approximation of time-dependent auxiliary density functional theory (TDADFT) is rederived from auxiliary density perturbation theory. Our exhaustive validation of TDADFT reveals an upshift of the excitation energies by ∼0.1 eV with respect to standard time-dependent density functional theory. For the computationally efficient implementation of TDADFT, floating point operation optimized three-center electron repulsion integral recurrence relations and their double asymptotic expansions are implemented into the Davidson solver. The computational efficiency of TDADFT is benchmarked with four sets of molecules comprising alkanes, fullerenes, DNA fragments, and zeolites. The results show that TDADFT has a computational scaling between 1.3 and 1.9 with respect to the number of basis functions, which is lower than the scaling of standard time-dependent density functional theory. Due to its computational simplifications, TDADFT is particularly well suited for Born-Oppenheimer molecular dynamics simulations. As illustrative examples, we present the temperature effects on the gas-phase absorption spectra of benzene, naphthalene, and anthracene.
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Affiliation(s)
- Luis I Hernández-Segura
- Departamento de Química, Cinvestav, Avenida Instituto Politécnico Nacional 2508, A.P. 14-740, CDMX C.P. 07360, Mexico
| | - Andreas M Köster
- Departamento de Química, Cinvestav, Avenida Instituto Politécnico Nacional 2508, A.P. 14-740, CDMX C.P. 07360, Mexico
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Pedroza-Montero JN, Calaminici P, Köster AM. First-principle polarizabilities of nanosystems from auxiliary density perturbation theory with MINRES. Theor Chem Acc 2022. [DOI: 10.1007/s00214-021-02864-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Mejia-Rodriguez D, Kunitsa A, Aprà E, Govind N. Scalable Molecular GW Calculations: Valence and Core Spectra. J Chem Theory Comput 2021; 17:7504-7517. [PMID: 34855381 DOI: 10.1021/acs.jctc.1c00738] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a scalable implementation of the GW approximation using Gaussian atomic orbitals to study the valence and core ionization spectroscopies of molecules. The implementation of the standard spectral decomposition approach to the screened-Coulomb interaction, as well as a contour-deformation method, is described. We have implemented both of these approaches using the robust variational fitting approximation to the four-center electron repulsion integrals. We have utilized the MINRES solver with the contour-deformation approach to reduce the computational scaling by 1 order of magnitude. A complex heuristic in the quasiparticle equation solver further allows a speed-up of the computation of core and semicore ionization energies. Benchmark tests using the GW100 and CORE65 data sets and the carbon 1s binding energy of the well-studied ethyl trifluoroacetate, or ESCA molecule, were performed to validate the accuracy of our implementation. We also demonstrate and discuss the parallel performance and computational scaling of our implementation using a range of water clusters of increasing size.
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Affiliation(s)
- Daniel Mejia-Rodriguez
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Alexander Kunitsa
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Edoardo Aprà
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Niranjan Govind
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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Flores-Moreno R, Cortes-Llamas SA, Pineda-Urbina K, Medel VM, Jayaprakash GK. Analytic Alchemical Derivatives for the Analysis of Differential Acidity Assisted by the h Function. J Phys Chem A 2021; 125:10463-10474. [PMID: 34812636 DOI: 10.1021/acs.jpca.1c07364] [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
Analytical calculation of alchemical derivatives based on auxiliary density perturbation theory is described, coded, and validated. For the case where the nucleus is a hydrogen atom and the nuclear charge is changed from 1 to 0, it turns out that a good estimate of the proton binding energies can be obtained very efficiently. First-order results correspond exactly to the molecular electrostatic potential evaluated at the hydrogen nucleus location (removing self-repulsion), in agreement with previously reported extensive studies. Therefore, the second-order results reported here are refinements in accuracy that finally allow a quantitative exploration of differential acidity. Furthermore, the recently reported h function is produced in its analytical form as a byproduct and local descriptor associated with the proton binding energy values found with this approach. In an example application, proton binding energies are computed for a family of imidazolium derivatives to demonstrate the capabilities and the stability of the method with respect to changes in basis set or exchange-correlation functional.
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Affiliation(s)
- Roberto Flores-Moreno
- Departamento de Química, Universidad de Guadalajara, Blvd. Marcelino García Barragán 1421, Col. Olímpica, 44430 Guadalajara, Jalisco, México
| | - Sara A Cortes-Llamas
- Departamento de Química, Universidad de Guadalajara, Blvd. Marcelino García Barragán 1421, Col. Olímpica, 44430 Guadalajara, Jalisco, México
| | - Kayim Pineda-Urbina
- Facultad de Ciencias Químicas, Universidad de Colima, Carretera Colima-Coquimatlan Km. 9, 28400 Coquimatlan, Colima, México
| | - Victor M Medel
- Departamento de Química, Universidad de Guadalajara, Blvd. Marcelino García Barragán 1421, Col. Olímpica, 44430 Guadalajara, Jalisco, México
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Delesma FA, Delgado-Venegas RI, Salahub DR, Del Campo JM, Pedroza-Montero JN, Calaminici P, Köster AM. Self-Consistent Auxiliary Density Perturbation Theory. J Chem Theory Comput 2021; 17:6934-6946. [PMID: 34709812 DOI: 10.1021/acs.jctc.1c00713] [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
The working equations for the extension of auxiliary density perturbation theory (ADPT) to hybrid functionals, employing the variational fitting of the Fock potential, are derived. The response equations in the resulting self-consistent ADPT (SC-ADPT) are solved iteratively with an adapted Eirola-Nevanlinna algorithm. As a result, a memory and CPU time efficient implementation of perturbation theory free of four-center electron repulsion integrals (ERIs) is obtained. Our validation calculations of SC-ADPT static and dynamic polarizabilities show quantitative agreement with corresponding coupled perturbed Hartree-Fock and Kohn-Sham results employing four-center ERIs. The comparison of SC-ADPT hybrid functional polarizabilities with coupled cluster reference calculations yield semiquantitative agreement. The presented systematic study of the dynamic polarizabilities of oligothiophenes shows that hybrid functionals can overcome the pathological misplacement of excitation poles by the local density and generalized gradient approximations. Good agreement with experimental dynamic polarizabilities for all studied oligothiophenes is achieved with range-separated hybrid functionals in the framework of SC-ADPT.
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Affiliation(s)
- Francisco A Delesma
- Departamento de Química, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Ciudad de México 07000, México.,Programa de Doctorado en Nanociencias y Nanotecnología, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Ciudad de México 07000, México
| | - Rogelio I Delgado-Venegas
- Department of Chemistry, Department of Physics and Astronomy CMS - Centre for Molecular Simulation, IQST - Institute for Quantum Science and Technology and Quantum Alberta, University of Calgary, 2500 University Drive N.W., Calgary, AB Canada T2N 1N4
| | - Dennis R Salahub
- Department of Chemistry, Department of Physics and Astronomy CMS - Centre for Molecular Simulation, IQST - Institute for Quantum Science and Technology and Quantum Alberta, University of Calgary, 2500 University Drive N.W., Calgary, AB Canada T2N 1N4
| | - Jorge M Del Campo
- Departamento de Física y Química Teórica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, México
| | - Jesús N Pedroza-Montero
- Departamento de Química, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Ciudad de México 07000, México.,Programa de Doctorado en Nanociencias y Nanotecnología, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Ciudad de México 07000, México
| | - Patrizia Calaminici
- Departamento de Química, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Ciudad de México 07000, México.,Programa de Doctorado en Nanociencias y Nanotecnología, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Ciudad de México 07000, México
| | - Andreas M Köster
- Departamento de Química, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Ciudad de México 07000, México.,Programa de Doctorado en Nanociencias y Nanotecnología, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Ciudad de México 07000, México
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Geudtner G. Parallelization of deMon2k: an overview. Theor Chem Acc 2021. [DOI: 10.1007/s00214-021-02786-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Delgado-Venegas RI, Calaminici P, Köster AM. Mixed second and third energy derivatives from auxiliary density perturbation theory. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1549339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
| | - Patrizia Calaminici
- Departamento de Química, CINVESTAV. Avenida Instituto Politécnico Nacional 2508, México D.F., México
| | - Andreas M. Köster
- Departamento de Química, CINVESTAV. Avenida Instituto Politécnico Nacional 2508, México D.F., México
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Delgado-Venegas RI, Mejía-Rodríguez D, Flores-Moreno R, Calaminici P, Köster AM. Analytic second derivatives from auxiliary density perturbation theory. J Chem Phys 2016; 145:224103. [PMID: 27984884 DOI: 10.1063/1.4971292] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Rogelio Isaac Delgado-Venegas
- Departamento de Química, CINVESTAV, Avenida Instituto Politécnico Nacional 2508, A.P. 14-740, México D.F. 07000, Mexico
| | - Daniel Mejía-Rodríguez
- Departamento de Química, CINVESTAV, Avenida Instituto Politécnico Nacional 2508, A.P. 14-740, México D.F. 07000, Mexico
| | - Roberto Flores-Moreno
- Departamento de Química, Universidad de Guadalajara, Boulevard Marcelino García Barragán 1421, Guadalajara, Jalisco 44430, Mexico
| | - Patrizia Calaminici
- Departamento de Química, CINVESTAV, Avenida Instituto Politécnico Nacional 2508, A.P. 14-740, México D.F. 07000, Mexico
| | - Andreas M. Köster
- Departamento de Química, CINVESTAV, Avenida Instituto Politécnico Nacional 2508, A.P. 14-740, México D.F. 07000, Mexico
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Zuniga-Gutierrez B, Köster AM. Analytical GGA exchange–correlation kernel calculation in auxiliary density functional theory. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1125026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
| | - Andreas M. Köster
- Departamento de Química, CINVESTAV, Avenida Instituto Politécnico Nacional 2508, México D.F., México
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