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Hasecke L, Breitenbach M, Gimferrer M, Oswald R, Mata RA. Addressing Anharmonic Effects with Density-Fitted Multicomponent Density Functional Theory. J Phys Chem A 2025; 129:3560-3566. [PMID: 40193096 PMCID: PMC12010317 DOI: 10.1021/acs.jpca.5c00382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2025] [Revised: 03/04/2025] [Accepted: 03/12/2025] [Indexed: 04/18/2025]
Abstract
In this contribution we present the first local density-fitted multicomponent density functional theory implementation and assess its use for the calculation of anharmonic zero-point energies. Four challenging cases of molecular aggregates are reviewed: deprotonated formic acid trimer, diphenyl ether-tert-butyl alcohol conformers, anisole/methanol and anisole/2-naphtol dimers. These are all cases where a mismatch between the low-temperature computationally predicted minimum and the experimentally determined structure was observed. Through the use of nuclear-electronic orbital energies in the thermodynamic correction, the correct energetic ordering is recovered. For the smallest system, we compare our results to vibrational perturbation theory anharmonically corrected zero-point energy, with perfect agreement for the lower-lying conformers. The performance of the newly developed code and the density fitting errors are also analyzed. Overall, the new implementation shows a very good scaling with system size and the density fitting approximations exhibit a negligible impact.
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Affiliation(s)
- Lukas Hasecke
- Institute of Physical Chemistry, University of Göttingen, Tammannstrasse 6, 37077 Göttingen, Germany
| | - Maximilian Breitenbach
- Institute of Physical Chemistry, University of Göttingen, Tammannstrasse 6, 37077 Göttingen, Germany
| | - Martí Gimferrer
- Institute of Physical Chemistry, University of Göttingen, Tammannstrasse 6, 37077 Göttingen, Germany
| | - Rainer Oswald
- Institute of Physical Chemistry, University of Göttingen, Tammannstrasse 6, 37077 Göttingen, Germany
| | - Ricardo A. Mata
- Institute of Physical Chemistry, University of Göttingen, Tammannstrasse 6, 37077 Göttingen, Germany
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2
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Khan RU, Tonner-Zech R. Optimizing Computational Parameters for Nuclear Electronic Orbital Density Functional Theory: A Benchmark Study on Proton Affinities. J Comput Chem 2025; 46:e70082. [PMID: 40099631 PMCID: PMC11915487 DOI: 10.1002/jcc.70082] [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: 11/08/2024] [Revised: 02/27/2025] [Accepted: 03/01/2025] [Indexed: 03/20/2025]
Abstract
This study benchmarks the nuclear electronic orbital density functional theory (NEO-DFT) method for a set of molecules that is larger than in previous studies. The focus is on proton affinity predictions to assess the influences of computational parameters. NEO-DFT incorporates nuclear quantum effects for protons involved in protonation processes. Using a test set of 72 molecules with experimental proton affinities as reference, we evaluated various exchange-correlation functionals, finding that B3LYP-based functionals deliver the most accurate results. Among the tested functionals, CAM-B3LYP performs the best with an MAD value of 6.2 kJ/mol with respect to experimental data. In NEO-DFT, electron-proton correlation (epc) functionals were assessed, with LDA-type epc17-2 yielding comparable results to the GGA-type epc19 functional. Compared to traditional DFT (MAD value of 31.6 kJ/mol), which treats nuclei classically, NEO-DFT provides enhanced accuracy for proton affinities when electron-proton correlation is included. Regarding basis sets, the def2-QZVP electronic basis set achieved the highest accuracy with an MAD value of 5.0 kJ/mol, though at a higher computational cost compared to def2-TZVP and def2-SVP, while nuclear basis sets showed minimal impact on proton affinity accuracy and no consistent trend. Overall, this study demonstrates NEO-DFT's efficacy in addressing nuclear quantum effects for proton affinity predictions, providing guidance on optimal parameter selection for future NEO-DFT applications.
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Affiliation(s)
- Raza Ullah Khan
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Leipzig, Germany
| | - Ralf Tonner-Zech
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Leipzig, Germany
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3
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Liu Y, Wang Y, Guo G, Yang T, Liu Y, Gao H, Jiang T, Li X. Analysis of community older adult care facility construction and demand differentiation based on residential area and population attribute differences. Front Public Health 2025; 13:1495608. [PMID: 40013030 PMCID: PMC11860882 DOI: 10.3389/fpubh.2025.1495608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2024] [Accepted: 01/13/2025] [Indexed: 02/28/2025] Open
Abstract
Currently, China has fully entered an aging society. The construction and efficient utilization of community older adult care facilities have become urgent issues that need to be addressed. To explore the differences in the needs of older adult people in the community for older adult care services, this study selected three basic needs: life care, medical security, and cultural and entertainment, as the primary indicators of community older adult care needs. A community older adult care demand indicator system was constructed, which included three primary indicators and 11 secondary indicators. Based on the indicator system, a survey questionnaire was designed, and validity analysis was conducted using Kaiser Meyer Olkin test and Bartlett sphericity test. 490 survey questionnaires were distributed to 22 communities in Wuhan, and 447 valid questionnaires were collected, with a response rate of 91.22%. The results indicated that there were significant differences in the distribution of older adult population in different communities. Different types of residential areas and housing prices affected its construction and use. The demand for home-based older adult care services in communities varied significantly. Through analysis of variance, the type of residential area did not show significant differences in older adult bathing assistance, daytime care, mental comfort, sports activities, etc. (p > 0.05), while there were statistical differences in nighttime care, medical care, rehabilitation care, older adult canteens, chess and card entertainment, artistic activities, etc. (p < 0.05). No significant difference existed in different housing prices for daytime care, nighttime care, mental comfort, and fitness activities (p > 0.05), but there was statistical difference for rehabilitation care, medical care, chess and card entertainment, senior dining halls, and artistic activities (p < 0.05). According to logistic regression analysis, the income level, self-care ability, and education level had obvious impacts on their basic needs for life care, with OR values of 11.68, 2.621, and 1.792, respectively. This study can provide effective reference for building diversified community home-based older adult care service facilities.
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Affiliation(s)
- Yanzhe Liu
- Xiangya Hospital of Central South University, Changsha, China
| | - Yaolei Wang
- Xiangya Hospital of Central South University, Changsha, China
| | - Guiping Guo
- Xiangya School of Public Health, Central South University, Changsha, China
| | - Tubao Yang
- Xiangya School of Public Health, Central South University, Changsha, China
- Hunan Key Laboratory of Epidemiology, Changsha, China
| | - Yupeng Liu
- Xiangya Hospital of Central South University, Changsha, China
| | - Hongmei Gao
- Xiangya Hospital of Central South University, Changsha, China
| | - Tiejian Jiang
- Xiangya Hospital of Central South University, Changsha, China
| | - Xiangmin Li
- Xiangya Hospital of Central South University, Changsha, China
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4
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Amin S, Krishnamurty S, Ahmad Dar M, Joshi K. Size and Morphology Dependent Activity of Cu Clusters for CO 2 Activation and Reduction: A First Principles Investigation. Chemphyschem 2024; 25:e202400442. [PMID: 39261277 DOI: 10.1002/cphc.202400442] [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: 04/16/2024] [Revised: 08/28/2024] [Accepted: 09/05/2024] [Indexed: 09/13/2024]
Abstract
Various Cu-based materials in diverse forms have been investigated as efficient catalysts for electrochemical reduction of CO2; however, they suffer from issues such as higher over potential and poor selectivity. The activity and selectivity of CO2 electro reduction have been shown to change significantly when the surface morphology (steps, kinks, and edges) of these catalysts is altered. In light of this, size and morphology dependent activity of selected copper clusters, Cun (n=2-20) have been evaluated for the activation and reduction of CO2 molecule. The phase-space of these copper clusters is rich in conformations of distinct morphologies starting from planar, 2D geometries to prolate-shaped geometries and also high-symmetry structures. The binding efficiency and the activation of CO2 are highest for medium sized clusters (n=9-17) with prolate-morphologies as compared to small or larger sized CunCO2 clusters that are existing mainly as planar (triangular, tetragonal etc.) or highly-symmetric geometries (icosahedron, capped-icosahedron etc.), respectively. The best performing (prolate-shaped) CunCO2 conformations are quite fluxional and also they are thermally stable, as demonstrated by the molecular dynamics simulations. Furthermore, on these CunCO2 conformations, the step-by-step hydrogenation pathways of CO2 to produce value-added products like methanol, formic acid, and methane are exceptionally favorable and energy-efficient.
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Affiliation(s)
- Seerat Amin
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory (CSIR-NCL), Pune, 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sailaja Krishnamurty
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory (CSIR-NCL), Pune, 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Manzoor Ahmad Dar
- Department of Chemistry, Islamic University of Science and Technology, Awantipora, Jammu and Kashmir, 192122, India
| | - Krati Joshi
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory (CSIR-NCL), Pune, 411008, India
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Chow M, Reinhardt CR, Hammes-Schiffer S. Nuclear Quantum Effects in Quantum Mechanical/Molecular Mechanical Free Energy Simulations of Ribonucleotide Reductase. J Am Chem Soc 2024; 146:33258-33264. [PMID: 39566052 PMCID: PMC11625381 DOI: 10.1021/jacs.4c13955] [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: 11/22/2024]
Abstract
The enzyme ribonucleotide reductase plays a critical role in DNA synthesis and repair. Its mechanism requires long-range radical transfer through a series of proton-coupled electron transfer (PCET) steps. Nuclear quantum effects such as zero-point energy, proton delocalization, and hydrogen tunneling are known to be important in PCET. We present a strategy for efficiently incorporating nuclear quantum effects into multidimensional free energy surfaces and real-time dynamical simulations for condensed-phase systems such as enzymes. This strategy is based on the nuclear-electronic orbital (NEO) method, which treats specified protons quantum mechanically on the same level as the electrons. NEO density functional theory (NEO-DFT) is combined with the quantum mechanical/molecular mechanical finite temperature string method with umbrella sampling via a simple reweighting procedure. Application of this strategy to PCET between two tyrosines, Y731 and Y730, in ribonucleotide reductase illustrates that nuclear quantum effects could either raise or lower the free energy barrier, leading to a range of possible kinetic isotope effects. Real-time time-dependent DFT (RT-NEO-TDDFT) simulations highlight nuclear-electronic quantum dynamics. These approaches enable the incorporation of nuclear quantum effects into a wide range of chemically and biologically important processes.
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Affiliation(s)
- Mathew Chow
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Clorice R Reinhardt
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Sharon Hammes-Schiffer
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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Hasecke L, Mata RA. Local Electronic Correlation in Multicomponent Møller-Plesset Perturbation Theory. J Chem Theory Comput 2024; 20:9928-9938. [PMID: 39514695 PMCID: PMC11603598 DOI: 10.1021/acs.jctc.4c01059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Revised: 10/08/2024] [Accepted: 10/22/2024] [Indexed: 11/16/2024]
Abstract
We present in this contribution the first application of local correlation in the context of multicomponent methods. Multicomponent approaches allow for the targeted simulation of electrons together with other Fermions (most commonly protons) as quantum particles. These methods have become increasingly popular over the last years, particularly for the description of nuclear quantum effects (in strong hydrogen bonds, proton tunneling, and many more). However, most implementations are still based on canonical formulations of wave function theory, which we know for decades to be computationally inefficient for capturing dynamical correlation effects. Local correlation approaches, particularly with the use of pair natural orbitals (PNOs), enable asymptotically linear scaling of computational costs with very little impact on the overall accuracy. In this context, the efficient use of density fitting approximations in the integral calculation proves essential. We start by discussing our implementation of density-fitted NEO-MP2 and NEO-PNO-LMP2, upgrading the electronic correlation treatment up to PNO local coupled cluster level of theory. Several challenging examples are provided to benchmark the method in terms of accuracy as well as computational cost scaling. Following appropriate protocols, anharmonic corrections to localized X-H stretches can be applied routinely with little computational overhead.
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Affiliation(s)
- Lukas Hasecke
- Institute of Physical Chemistry, University of Göttingen, Tammannstrasse 6, 37077 Göttingen, Germany
| | - Ricardo A. Mata
- Institute of Physical Chemistry, University of Göttingen, Tammannstrasse 6, 37077 Göttingen, Germany
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Dickinson JA, Hammes-Schiffer S. Nonadiabatic Hydrogen Tunneling Dynamics for Multiple Proton Transfer Processes with Generalized Nuclear-Electronic Orbital Multistate Density Functional Theory. J Chem Theory Comput 2024. [PMID: 39259939 DOI: 10.1021/acs.jctc.4c00737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2024]
Abstract
Proton transfer and hydrogen tunneling play key roles in many processes of chemical and biological importance. The generalized nuclear-electronic orbital multistate density functional theory (NEO-MSDFT) method was developed in order to capture hydrogen tunneling effects in systems involving the transfer and tunneling of one or more protons. The generalized NEO-MSDFT method treats the transferring protons quantum mechanically on the same level as the electrons and obtains the delocalized vibronic states associated with hydrogen tunneling by mixing localized NEO-DFT states in a nonorthogonal configuration interaction scheme. Herein, we present the derivation and implementation of analytical gradients for the generalized NEO-MSDFT vibronic state energies and the nonadiabatic coupling vectors between these vibronic states. We use this methodology to perform adiabatic and nonadiabatic dynamics simulations of the double proton transfer reactions in the formic acid dimer and the heterodimer of formamidine and formic acid. The generalized NEO-MSDFT method is shown to capture the strongly coupled synchronous or asynchronous tunneling of the two protons in these processes. Inclusion of vibronically nonadiabatic effects is found to significantly impact the double proton transfer dynamics. This work lays the foundation for a variety of nonadiabatic dynamics simulations of multiple proton transfer systems, such as proton relays and hydrogen-bonding networks.
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Affiliation(s)
- Joseph A Dickinson
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Sharon Hammes-Schiffer
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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8
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Holzer C, Franzke YJ. Beyond Electrons: Correlation and Self-Energy in Multicomponent Density Functional Theory. Chemphyschem 2024; 25:e202400120. [PMID: 38456204 DOI: 10.1002/cphc.202400120] [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: 02/02/2024] [Revised: 03/07/2024] [Accepted: 03/08/2024] [Indexed: 03/09/2024]
Abstract
Post-Kohn-Sham methods are used to evaluate the ground-state correlation energy and the orbital self-energy of systems consisting of multiple flavors of different fermions. Starting from multicomponent density functional theory, suitable ways to arrive at the corresponding multicomponent random-phase approximation and the multicomponent Green's functionG W ${GW}$ approximation, including relativistic effects, are outlined. Given the importance of both of this methods in the development of modern Kohn-Sham density functional approximations, this work will provide a foundation to design advanced multicomponent density functional approximations. Additionally, theG W ${GW}$ quasiparticle energies are needed to study light-matter interactions with the Bethe-Salpeter equation.
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Affiliation(s)
- Christof Holzer
- Karlsruhe Institute of Technology (KIT), Institute of Theoretical Solid State Physics, Kaiserstraße 12, 76131, Karlsruhe, Germany
| | - Yannick J Franzke
- Friedrich Schiller University Jena, Otto Schott Institute of Materials Research, Löbdergraben 32, 07743, Jena, Germany
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9
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Hasecke L, Mata RA. Optimization of Quantum Nuclei Positions with the Adaptive Nuclear-Electronic Orbital Approach. J Phys Chem A 2024; 128:3205-3211. [PMID: 38619054 PMCID: PMC11056972 DOI: 10.1021/acs.jpca.4c00096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/08/2024] [Accepted: 03/08/2024] [Indexed: 04/16/2024]
Abstract
The use of multicomponent methods has become increasingly popular over the last years. Under this framework, nuclei (commonly protons) are treated quantum mechanically on the same footing as the electronic structure problem. Under the use of atomic-centered orbitals, this can lead to some complications as the ideal location of the nuclear basis centers must be optimized. In this contribution, we propose a straightforward approach to determine the position of such centers within the self-consistent cycle of a multicomponent calculation, making use of individual proton charge centroids. We test the method on model systems including the water dimer, a protonated water tetramer, and a porphine system. Comparing to numerical gradient calculations, the adaptive nuclear-electronic orbital (NEO) procedure is able to converge the basis centers to within a few cents of an Ångström and with less than 0.1 kcal/mol differences in absolute energies. This is achieved in one single calculation and with a small added computational effort of up to 80% compared to a regular NEO- self-consistent field run. An example application for the human transketolase proton wire is also provided.
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Affiliation(s)
- Lukas Hasecke
- Institute of Physical Chemistry, University
of Göttingen, Tammannstrasse 6, 37077 Göttingen, Germany
| | - Ricardo A. Mata
- Institute of Physical Chemistry, University
of Göttingen, Tammannstrasse 6, 37077 Göttingen, Germany
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