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Herbert JM. Visualizing and characterizing excited states from time-dependent density functional theory. Phys Chem Chem Phys 2024; 26:3755-3794. [PMID: 38226636 DOI: 10.1039/d3cp04226j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Abstract
Time-dependent density functional theory (TD-DFT) is the most widely-used electronic structure method for excited states, due to a favorable combination of low cost and semi-quantitative accuracy in many contexts, even if there are well recognized limitations. This Perspective describes various ways in which excited states from TD-DFT calculations can be visualized and analyzed, both qualitatively and quantitatively. This includes not just orbitals and densities but also well-defined statistical measures of electron-hole separation and of Frenkel-type exciton delocalization. Emphasis is placed on mathematical connections between methods that have often been discussed separately. Particular attention is paid to charge-transfer diagnostics, which provide indicators of when TD-DFT may not be trustworthy due to its categorical failure to describe long-range electron transfer. Measures of exciton size and charge separation that are directly connected to the underlying transition density are recommended over more ad hoc metrics for quantifying charge-transfer character.
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Affiliation(s)
- John M Herbert
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA.
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2
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Tolu D, Guillaumont D, de la Lande A. Irradiation of Plutonium Tributyl Phosphate Complexes by Ionizing Alpha Particles: A Computational Study. J Phys Chem A 2023; 127:7045-7057. [PMID: 37606197 DOI: 10.1021/acs.jpca.3c02117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
The PUREX solvent extraction process, widely used for recovering uranium and plutonium from spent nuclear fuel, utilizes an organic solvent composed of tributyl phosphate (TBP). The emission of ionizing particles such as alpha particles, resulting from the decay of plutonium, makes the organic solvent vulnerable to degradation. Here, we study the ultrashort time alpha irradiation of tributylphosphate (TBP) and Pu(NO3)4(TBP)2 complex formed in the PUREX process. Electron dynamics is propagated by Real-Time-Dependent Auxiliary Density Functional Theory (RT-TD-ADFT). We investigate the use of previously proposed absorption boundary conditions (ABC) in the molecular orbital space to treat secondary electron emission. Basis set and exchange correlation functional effects with ABC are reported as well as a detailed analysis of the ABC parametrization. Preliminary results on the water molecule and then on TBP show that the phenomenological nature of the ABC parameters necessitates selecting appropriate values for each system under study. Irradiation of free and complexed TBP shows an influence of the ligands on the variation of atomic charges on the femtosecond time scale. An accumulation of atomic charges in the alkyl chains of TBP is observed in the case where the nitrate groups are predominantly irradiated. In addition, we find that the Pu atom regains its electric charge very rapidly after being hit by the projectile, with the coordination sphere serving as an electron reservoir to preserve its formal redox state. This study paves the road toward a full understanding of the degradation of organic extracants employed in the nuclear industry.
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Affiliation(s)
- Damien Tolu
- CEA, DES, ISEC, DMRC, Université Montpellier, Marcoule, 30207 Bagnols sur Cèze, France
- Institut de Chimie Physique, CNRS, Université Paris Saclay, 15 Avenue Jean Perrin, Paris, 91405, France
| | - Dominique Guillaumont
- CEA, DES, ISEC, DMRC, Université Montpellier, Marcoule, 30207 Bagnols sur Cèze, France
| | - Aurélien de la Lande
- Institut de Chimie Physique, CNRS, Université Paris Saclay, 15 Avenue Jean Perrin, Paris, 91405, France
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3
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Li J, Zou Y, Li Z, Fu S, Lu Y, Li S, Zhu X, Zhang T. Modulating the Electronic Coordination Configuration and d-Band Center in Homo-Diatomic Fe 2N 6 Catalysts for Enhanced Peroxymonosulfate Activation. ACS APPLIED MATERIALS & INTERFACES 2022; 14:37865-37877. [PMID: 35971618 DOI: 10.1021/acsami.2c12036] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The electronic coordination configuration of metal active sites and the reaction mechanism were investigated by constructing homo-diatomic Fe sites for visible-light-assisted heterogeneous peroxymonosulfate (PMS) activation. A novel Fe2N6 catalyst was synthesized by selecting uniform pyridinic-N of graphitic carbon nitride (g-C3N4) as anchoring sites. The results demonstrated that homo-diatomic Fe sites modulated the d-band center and electron delocalization and thus enhanced the PMS activation kinetics (3.58 times vs single-atom Fe catalyst) with kobs of 0.111 min-1 owing to the synergistic effect between adjacent Fe atoms. New Fe-Fe coordination significantly decreased the contribution of the antibonding state in the Fe-O bond due to the coupling of the Fe-3d orbitals, which facilitated the O-O bond cleavage of the Fe2-HOO-SO3 complex with a reduced thermodynamic energy barrier of only -0.29 eV. This work provided comprehensive mechanistic insights into developing homo-diatomic catalysts governed by the coordination configuration and radical pathway for efficient heterogeneous PMS catalysis.
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Affiliation(s)
- Jie Li
- Department of Environmental Science and Engineering, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Yixiao Zou
- Department of Environmental Science and Engineering, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Zhifeng Li
- Department of Environmental Science and Engineering, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Shuhan Fu
- Department of Environmental Science and Engineering, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Yong Lu
- College of Mathematics and Physics, Beijing University of Chemical Technology, Beijing 10029, People's Republic of China
| | - Shangyi Li
- Department of Environmental Science and Engineering, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
- School of Environment, Tsinghua University, Beijing 100084, People's Republic of China
| | - Xiaobiao Zhu
- Department of Environmental Science and Engineering, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Tingting Zhang
- Department of Environmental Science and Engineering, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
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4
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Wozniak AP, Przybytek M, Lewenstein M, Moszynski R. Effects of electronic correlation on the high harmonic generation in helium: a time-dependent configuration interaction singles vs time-dependent full configuration interaction study. J Chem Phys 2022; 156:174106. [DOI: 10.1063/5.0087384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this paper, we investigate the effects of full electronic correlation on the high harmonic generation in the helium atom subjected to laser pulses of extremely high intensity. To do this, we perform real-time propagations of the helium atom wavefunction using quantum chemistry methods coupled to Gaussian basis sets. The calculations are done within the real-time time-dependent configuration interaction framework, at two levels of theory: time-dependent configuration interation with single excitations (TD-CIS, uncorrelated method) and time-dependent full configuration interaction (TD-FCI, fully correlated method). The electronic wavefunction is expanded in Dunning basis sets supplemented with functions adapted to describing highly excited and continuum states. We also compare the TD-CI results with grid-based propagations of the helium atom within the single-active-electron approximation. Our results show that when including the dynamical electron correlation, a noticeable improvement to the description of HHG can be achieved, in terms of e.g. a more constant intensity in the lower energy part of the harmonic plateau. However, such effects can be captured only if the basis set used suffices to reproduce the most basic features, such as the HHG cutoff position, at the uncorrelated level of theory.
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De Santis M, Vallet V, Gomes ASP. Environment Effects on X-Ray Absorption Spectra With Quantum Embedded Real-Time Time-Dependent Density Functional Theory Approaches. Front Chem 2022; 10:823246. [PMID: 35295974 PMCID: PMC8919347 DOI: 10.3389/fchem.2022.823246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 02/04/2022] [Indexed: 11/13/2022] Open
Abstract
In this work we implement the real-time time-dependent block-orthogonalized Manby-Miller embedding (rt-BOMME) approach alongside our previously developed real-time frozen density embedding time-dependent density functional theory (rt-TDDFT-in-DFT FDE) code, and investigate these methods’ performance in reproducing X-ray absorption spectra (XAS) obtained with standard rt-TDDFT simulations, for model systems comprised of solvated fluoride and chloride ions ([X@(H2O)8−, X = F, Cl). We observe that for ground-state quantities such as core orbital energies, the BOMME approach shows significantly better agreement with supermolecular results than FDE for the strongly interacting fluoride system, while for chloride the two embedding approaches show more similar results. For the excited states, we see that while FDE (constrained not to have the environment densities relaxed in the ground state) is in good agreement with the reference calculations for the region around the K and L1 edges, and is capable of reproducing the splitting of the 1s1 (n + 1)p1 final states (n + 1 being the lowest virtual p orbital of the halides), it by and large fails to properly reproduce the 1s1 (n + 2)p1 states and misses the electronic states arising from excitation to orbitals with important contributions from the solvent. The BOMME results, on the other hand, provide a faithful qualitative representation of the spectra in all energy regions considered, though its intrinsic approximation of employing a lower-accuracy exchange-correlation functional for the environment induces non-negligible shifts in peak positions for the excitations from the halide to the environment. Our results thus confirm that QM/QM embedding approaches are viable alternatives to standard real-time simulations of X-ray absorption spectra of species in complex or confined environments.
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6
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Coccia E, Luppi E. Time-dependent ab initioapproaches for high-harmonic generation spectroscopy. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2021; 34:073001. [PMID: 34731835 DOI: 10.1088/1361-648x/ac3608] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 11/03/2021] [Indexed: 06/13/2023]
Abstract
High-harmonic generation (HHG) is a nonlinear physical process used for the production of ultrashort pulses in XUV region, which are then used for investigating ultrafast phenomena in time-resolved spectroscopies. Moreover, HHG signal itself encodes information on electronic structure and dynamics of the target, possibly coupled to the nuclear degrees of freedom. Investigating HHG signal leads to HHG spectroscopy, which is applied to atoms, molecules, solids and recently also to liquids. Analysing the number of generated harmonics, their intensity and shape gives a detailed insight of, e.g., ionisation and recombination channels occurring in the strong-field dynamics. A number of valuable theoretical models has been developed over the years to explain and interpret HHG features, with the three-step model being the most known one. Originally, these models neglect the complexity of the propagating electronic wavefunction, by only using an approximated formulation of ground and continuum states. Many effects unravelled by HHG spectroscopy are instead due to electron correlation effects, quantum interference, and Rydberg-state contributions, which are all properly captured by anab initioelectronic-structure approach. In this review we have collected recent advances in modelling HHG by means ofab initiotime-dependent approaches relying on the propagation of the time-dependent Schrödinger equation (or derived equations) in presence of a very intense electromagnetic field. We limit ourselves to gas-phase atomic and molecular targets, and to solids. We focus on the various levels of theory employed for describing the electronic structure of the target, coupled with strong-field dynamics and ionisation approaches, and on the basis used to represent electronic states. Selected applications and perspectives for future developments are also given.
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Affiliation(s)
- Emanuele Coccia
- Dipartimento di Scienze Chimiche e Farmaceutiche, University of Trieste, via Giorgieri 1, 34127 Trieste, Italy
| | - Eleonora Luppi
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7616, Laboratoire de Chimie Théorique, F-75005 Paris, France
- CNRS, UMR 7616, Laboratoire de Chimie Théorique, F-75005 Paris, France
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Semmeq A, Badawi M, Dziurla MA, Ouaskit S, Monari A. Nucleic Acids under Stress: Understanding and Simulating Nucleobase Fragmentation Pathways. Chempluschem 2021; 86:1426-1435. [PMID: 34637193 DOI: 10.1002/cplu.202100323] [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: 07/18/2021] [Revised: 09/24/2021] [Indexed: 11/10/2022]
Abstract
The effects of radiations on nucleic acids and their constituents is widely studied across several research fields using different experimental and theoretical protocols. While a large number of studies were performed in this context, many fundamental physical and chemical effects are still being investigated, particularly involving the effect of the biological environment. As an example, the interpretation of experimental nucleic acid bases mass spectra, and hence inferring their reactivity in complex environment still poses great challenge. This Minireview summarizes recent theoretical advancements aiming to predict and interpret the reactivity of nucleic acid bases. We focus not only on the understanding of the inherent fragmentation pathways of isolated nucleobases but also on the modeling of a realistic nano-environments highlighting the importance of molecular dynamics simulations and the non-innocent role of the environment and also the possibility to open novel fragmentation pathways.
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Affiliation(s)
| | - Michael Badawi
- Université de Lorraine and CNRS, UMR 7019 LPCT, 54000, Nancy, France
| | | | - Said Ouaskit
- Laboratoire de Physique de la Matière Condensée, Faculté de Sciences Ben M'sick, University Hassan II of Casablanca, Morocco
| | - Antonio Monari
- Université de Lorraine and CNRS, UMR 7019 LPCT, 54000, Nancy, France
- Université de Paris and CNRS, ITODYS, 75006, Paris, France
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8
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Omar KA, Hasnaoui K, de la Lande A. First-Principles Simulations of Biological Molecules Subjected to Ionizing Radiation. Annu Rev Phys Chem 2021; 72:445-465. [PMID: 33878897 DOI: 10.1146/annurev-physchem-101419-013639] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Ionizing rays cause damage to genomes, proteins, and signaling pathways that normally regulate cell activity, with harmful consequences such as accelerated aging, tumors, and cancers but also with beneficial effects in the context of radiotherapies. While the great pace of research in the twentieth century led to the identification of the molecular mechanisms for chemical lesions on the building blocks of biomacromolecules, the last two decades have brought renewed questions, for example, regarding the formation of clustered damage or the rich chemistry involving the secondary electrons produced by radiolysis. Radiation chemistry is now meeting attosecond science, providing extraordinary opportunities to unravel the very first stages of biological matter radiolysis. This review provides an overview of the recent progress made in this direction, focusing mainly on the atto- to femto- to picosecond timescales. We review promising applications of time-dependent density functional theory in this context.
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Affiliation(s)
- Karwan Ali Omar
- Institut de Chimie Physique, CNRS UMR 8000, Université Paris-Saclay, 91405 Orsay, France; .,Department of Chemistry, College of Education, University of Sulaimani, 41005 Kurdistan, Iraq
| | - Karim Hasnaoui
- High Performance Computing User Support Team, Institut du Développement et des Ressources en Informatique Scientifique (IDRIS), 91403 Orsay, France.,Maison de la Simulation, CNRS, Commissariat à l'Energie Atomique et aux Énergies Alternatives (CEA), Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Aurélien de la Lande
- Institut de Chimie Physique, CNRS UMR 8000, Université Paris-Saclay, 91405 Orsay, France;
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9
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Tandiana R, Brun E, Sicard-Roselli C, Domin D, Van-Oanh NT, Clavaguéra C. Probing the structural properties of the water solvation shell around gold nanoparticles: A computational study. J Chem Phys 2021; 154:044706. [DOI: 10.1063/5.0037551] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Rika Tandiana
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, UMR8000, 91405 Orsay, France
| | - Emilie Brun
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, UMR8000, 91405 Orsay, France
| | - Cécile Sicard-Roselli
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, UMR8000, 91405 Orsay, France
| | - Dominik Domin
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, UMR8000, 91405 Orsay, France
| | - Nguyen-Thi Van-Oanh
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, UMR8000, 91405 Orsay, France
| | - Carine Clavaguéra
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, UMR8000, 91405 Orsay, France
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10
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Pauletti CF, Coccia E, Luppi E. Role of exchange and correlation in high-harmonic generation spectra of H 2, N 2, and CO 2: Real-time time-dependent electronic-structure approaches. J Chem Phys 2021; 154:014101. [PMID: 33412879 DOI: 10.1063/5.0033072] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
This study arises from the attempt to answer the following question: how different descriptions of electronic exchange and correlation affect the high-harmonic generation (HHG) spectroscopy of H2, N2, and CO2 molecules? We compare HHG spectra for H2, N2, and CO2 with different ab initio electronic structure methods: real-time time-dependent configuration interaction and real-time time-dependent density functional theory (RT-TDDFT) using truncated basis sets composed of correlated wave functions expanded on Gaussian basis sets. In the framework of RT-TDDFT, we employ Perdew-Burke-Ernzerhof (PBE) and long-range corrected Perdew-Burke-Ernzerhof (LC-ωPBE) functionals. We study HHG spectroscopy by disentangling the effect of electronic exchange and correlation. We first analyze the electronic exchange alone, and in the case of RT-TDDFT with LC-ωPBE, we use ω = 0.3 and ω = 0.4 to tune the percentage of long-range Hartree-Fock exchange and short-range exchange PBE. Then, we added the correlation as described by the PBE functional. All the methods give very similar HHG spectra, and they seem not to be particularly sensitive to the different description of exchange and correlation or to the correct asymptotic behavior of the Coulomb potential. Despite this general trend, some differences are found in the region connecting the cutoff and the background. Here, the harmonics can be resolved with different accuracy depending on the theoretical schemes used. We believe that the investigation of the molecular continuum and its coupling with strong fields merits further theoretical investigations in the near future.
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Affiliation(s)
| | - Emanuele Coccia
- Dipartimento di Scienze Chimiche e Farmaceutiche, Via Giorgieri 1, Trieste Italy
| | - Eleonora Luppi
- Laboratoire de Chimie Théorique, Sorbonne Université and CNRS, F-75005 Paris, France
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11
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Yang J, Pei Z, Deng J, Mao Y, Wu Q, Yang Z, Wang B, Aikens CM, Liang W, Shao Y. Analysis and visualization of energy densities. I. Insights from real-time time-dependent density functional theory simulations. Phys Chem Chem Phys 2020; 22:26838-26851. [PMID: 33170198 PMCID: PMC7722154 DOI: 10.1039/d0cp04206d] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this article, we report a scheme to analyze and visualize the energy density fluctuations during the real-time time-dependent density functional theory (RT-TDDFT) simulations. Using Ag4-N2 complexes as examples, it is shown that the grid-based Kohn-Sham energy density can be computed at each time step using a procedure from Nakai and coworkers. Then the instantaneous energy of each molecular fragment (such as Ag4 and N2) can be obtained by partitioning the Kohn-Sham energy densities using Becke or fragment-based Hirshfeld (FBH) scheme. A strong orientation-dependence is observed for the energy flow between the Ag4 cluster and a nearby N2 molecule in the RT-TDDFT simulations. Future applications of such an energy density analysis in electron dynamics simulations are discussed.
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Affiliation(s)
- Junjie Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Pkwy, Norman, OK 73019, USA.
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12
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Alvarez-Ibarra A, Parise A, Hasnaoui K, de la Lande A. The physical stage of radiolysis of solvated DNA by high-energy-transfer particles: insights from new first principles simulations. Phys Chem Chem Phys 2020; 22:7747-7758. [DOI: 10.1039/d0cp00165a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Electron dynamics simulations based on density functional theory are carried out on nanometric molecular systems to decipher the primary processes following irradiation of bio-macromolecules by high energy transfer charged particles.
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Affiliation(s)
| | - Angela Parise
- Université Paris-Saclay
- CNRS
- Institut de Chimie Physique UMR8000
- Orsay
- France
| | - Karim Hasnaoui
- Institut du Développement et des Ressources en Informatique Scientifique
- Rue John von Neumann
- Orsay
- France
- Maison de la Simulation
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Parise A, de la Lande A, Marino T, Russo N. Attosecond dynamics simulations of glycine irradiated by α-particle: Comment on "A never-ending story in the sky: The secrets of chemical evolution" by C. Puzzarini and V. Barone. Phys Life Rev 2019; 32:114-116. [PMID: 31451435 DOI: 10.1016/j.plrev.2019.08.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 08/19/2019] [Indexed: 11/16/2022]
Affiliation(s)
- Angela Parise
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Rende (CS), Italy; Laboratoire de Chimie Physique, Université Paris Sud, CNRS, Université Paris Saclay, 15 avenue Jean Perrin, F91405 Orsay, France
| | - Aurelien de la Lande
- Laboratoire de Chimie Physique, Université Paris Sud, CNRS, Université Paris Saclay, 15 avenue Jean Perrin, F91405 Orsay, France
| | - Tiziana Marino
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Rende (CS), Italy
| | - Nino Russo
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Rende (CS), Italy.
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14
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de la Lande A, Alvarez-Ibarra A, Hasnaoui K, Cailliez F, Wu X, Mineva T, Cuny J, Calaminici P, López-Sosa L, Geudtner G, Navizet I, Garcia Iriepa C, Salahub DR, Köster AM. Molecular Simulations with in-deMon2k QM/MM, a Tutorial-Review. Molecules 2019; 24:molecules24091653. [PMID: 31035516 PMCID: PMC6539060 DOI: 10.3390/molecules24091653] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/11/2019] [Accepted: 04/12/2019] [Indexed: 12/18/2022] Open
Abstract
deMon2k is a readily available program specialized in Density Functional Theory (DFT) simulations within the framework of Auxiliary DFT. This article is intended as a tutorial-review of the capabilities of the program for molecular simulations involving ground and excited electronic states. The program implements an additive QM/MM (quantum mechanics/molecular mechanics) module relying either on non-polarizable or polarizable force fields. QM/MM methodologies available in deMon2k include ground-state geometry optimizations, ground-state Born-Oppenheimer molecular dynamics simulations, Ehrenfest non-adiabatic molecular dynamics simulations, and attosecond electron dynamics. In addition several electric and magnetic properties can be computed with QM/MM. We review the framework implemented in the program, including the most recently implemented options (link atoms, implicit continuum for remote environments, metadynamics, etc.), together with six applicative examples. The applications involve (i) a reactivity study of a cyclic organic molecule in water; (ii) the establishment of free-energy profiles for nucleophilic-substitution reactions by the umbrella sampling method; (iii) the construction of two-dimensional free energy maps by metadynamics simulations; (iv) the simulation of UV-visible absorption spectra of a solvated chromophore molecule; (v) the simulation of a free energy profile for an electron transfer reaction within Marcus theory; and (vi) the simulation of fragmentation of a peptide after collision with a high-energy proton.
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Affiliation(s)
- Aurélien de la Lande
- Laboratoire de Chimie Physique, CNRS, Université Paris Sud, Université Paris Saclay, 15 avenue Jean Perrin, 91405 Orsay, France.
| | - Aurelio Alvarez-Ibarra
- Laboratoire de Chimie Physique, CNRS, Université Paris Sud, Université Paris Saclay, 15 avenue Jean Perrin, 91405 Orsay, France.
| | - Karim Hasnaoui
- Laboratoire de Chimie Physique, CNRS, Université Paris Sud, Université Paris Saclay, 15 avenue Jean Perrin, 91405 Orsay, France.
| | - Fabien Cailliez
- Laboratoire de Chimie Physique, CNRS, Université Paris Sud, Université Paris Saclay, 15 avenue Jean Perrin, 91405 Orsay, France.
| | - Xiaojing Wu
- Laboratoire de Chimie Physique, CNRS, Université Paris Sud, Université Paris Saclay, 15 avenue Jean Perrin, 91405 Orsay, France.
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, PSL University, 75005 Paris, France.
| | - Tzonka Mineva
- Matériaux Avancés pour la Catalyse et la Santé, UMR 5253 CNRS/UM/ENSCM, Institut Charles Gerhardt de Montpellier (ICGM) Montpellier CEDEX 5, 34090 Montpellier, France.
| | - Jérôme Cuny
- Laboratoire de Chimie et Physique Quantiques, IRSAMC, Université Paul Sabatier, 118 Route de Narbonne, 31062 Toulouse CEDEX 4, France.
| | - Patrizia Calaminici
- Programa de Doctorado en Nanociencias y Nanotecnología, CINVESTAV, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, Ciudad de México 07000, Mexico.
- Departamento de Química, CINVESTAV, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, Ciudad de México 07000, México.
| | - Luis López-Sosa
- Departamento de Química, CINVESTAV, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, Ciudad de México 07000, México.
| | - Gerald Geudtner
- Departamento de Química, CINVESTAV, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, Ciudad de México 07000, México.
| | - Isabelle Navizet
- Laboratoire Modélisation et Simulation Multi Échelle, Université Paris-Est, MSME, UMR 8208 CNRS, UPEM, 5 bd Descartes, 77454 Marne-la-Vallée, France.
| | - Cristina Garcia Iriepa
- Laboratoire Modélisation et Simulation Multi Échelle, Université Paris-Est, MSME, UMR 8208 CNRS, UPEM, 5 bd Descartes, 77454 Marne-la-Vallée, France.
| | - Dennis R Salahub
- Department of Chemistry, Centre for Molecular Simulation, Institute for Quantum Science and Technology and Quantum Alberta, University of Calgary, 2500 University Drive N.W., Calgary, AB T2N 1N4, Canada.
- College of Chemistry and Chemical Engineering, Henan University of Technology, No. 100, Lian Hua Street, High-Tech Development Zone, Zhengzhou 450001, China.
| | - Andreas M Köster
- Programa de Doctorado en Nanociencias y Nanotecnología, CINVESTAV, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, Ciudad de México 07000, Mexico.
- Departamento de Química, CINVESTAV, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, Ciudad de México 07000, México.
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