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Dong J, Qiu J, Bai X, Wang Z, Xiao B, Wang L. SPADE 1.0: A Simulation Package for Non-Adiabatic Dynamics in Extended Systems. J Chem Theory Comput 2025; 21:3300-3320. [PMID: 40126212 DOI: 10.1021/acs.jctc.4c01642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2025]
Abstract
Nonadiabatic molecular dynamics (NAMD) simulations are crucial for revealing the underlying mechanisms of photochemical and photophysical processes. Typical NAMD simulation software packages rely on on-the-fly ab initio electronic structure and nonadiabatic coupling calculations, and thus become challenging when dealing with large complex systems. We here introduce a new Simulation Package for non-Adiabatic Dynamics in Extended systems (SPADE), which is designed to address the limitations of traditional surface hopping methods in dealing with these problems. By design, SPADE enables the users to define arbitrary quasi-diabatic Hamiltonians through parametrized functions and incorporates a variety of algorithms (e.g., global flux hopping probabilities, complex crossing and decoherence corrections), which can realize efficient and reliable NAMD simulations without using nonadiabatic couplings at all. All the employed methods and expressions for diabatic Hamiltonian matrix elements can be flexibly set through the input files. SPADE is mainly written in Fortran based on a modular design and has a great capacity for further implementation of new methods. SPADE can be used to simulate both model and atomistic systems as long as proper Hamiltonians are provided. As demonstrations, a series of representative models are studied to show the main features and capabilities.
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Affiliation(s)
- Jiawei Dong
- Zhejiang Key Laboratory of Excited-State Energy Conversion and Energy Storage, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Jing Qiu
- Zhejiang Key Laboratory of Excited-State Energy Conversion and Energy Storage, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Xin Bai
- Zhejiang Key Laboratory of Excited-State Energy Conversion and Energy Storage, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Zedong Wang
- Zhejiang Key Laboratory of Excited-State Energy Conversion and Energy Storage, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Bingyang Xiao
- Zhejiang Key Laboratory of Excited-State Energy Conversion and Energy Storage, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Linjun Wang
- Zhejiang Key Laboratory of Excited-State Energy Conversion and Energy Storage, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
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Freixas VM, Malone W, Li X, Song H, Negrin-Yuvero H, Pérez-Castillo R, White A, Gibson TR, Makhov DV, Shalashilin DV, Zhang Y, Fedik N, Kulichenko M, Messerly R, Mohanam LN, Sharifzadeh S, Bastida A, Mukamel S, Fernandez-Alberti S, Tretiak S. NEXMD v2.0 Software Package for Nonadiabatic Excited State Molecular Dynamics Simulations. J Chem Theory Comput 2023; 19:5356-5368. [PMID: 37506288 DOI: 10.1021/acs.jctc.3c00583] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
We present NEXMD version 2.0, the second release of the NEXMD (Nonadiabatic EXcited-state Molecular Dynamics) software package. Across a variety of new features, NEXMD v2.0 incorporates new implementations of two hybrid quantum-classical dynamics methods, namely, Ehrenfest dynamics (EHR) and the Ab-Initio Multiple Cloning sampling technique for Multiconfigurational Ehrenfest quantum dynamics (MCE-AIMC or simply AIMC), which are alternative options to the previously implemented trajectory surface hopping (TSH) method. To illustrate these methodologies, we outline a direct comparison of these three hybrid quantum-classical dynamics methods as implemented in the same NEXMD framework, discussing their weaknesses and strengths, using the modeled photodynamics of a polyphenylene ethylene dendrimer building block as a representative example. We also describe the expanded normal-mode analysis and constraints for both the ground and excited states, newly implemented in the NEXMD v2.0 framework, which allow for a deeper analysis of the main vibrational motions involved in vibronic dynamics. Overall, NEXMD v2.0 expands the range of applications of NEXMD to a larger variety of multichromophore organic molecules and photophysical processes involving quantum coherences and persistent couplings between electronic excited states and nuclear velocity.
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Affiliation(s)
- Victor M Freixas
- Departments of Chemistry and Physics and Astronomy, University of California, Irvine, California 92697-2025, United States
| | - Walter Malone
- Department of Physics, Tuskegee University, Tuskegee, Alabama 36088, United States
| | - Xinyang Li
- Theoretical Division, Center for Nonlinear Studies (CNLS), and Center for Integrated Nanotechnologies (CINT), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Huajing Song
- Theoretical Division, Center for Nonlinear Studies (CNLS), and Center for Integrated Nanotechnologies (CINT), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Hassiel Negrin-Yuvero
- Departamento de Ciencia y Tecnologia, Universidad Nacional de Quilmes/CONICET, B1876BXD Bernal, Argentina
| | - Royle Pérez-Castillo
- Departamento de Ciencia y Tecnologia, Universidad Nacional de Quilmes/CONICET, B1876BXD Bernal, Argentina
| | - Alexander White
- Theoretical Division, Center for Nonlinear Studies (CNLS), and Center for Integrated Nanotechnologies (CINT), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Tammie R Gibson
- Theoretical Division, Center for Nonlinear Studies (CNLS), and Center for Integrated Nanotechnologies (CINT), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Dmitry V Makhov
- School of Chemistry, University of Leeds, Leeds LS2 9JT, United Kingdom
- School of Mathematics, University of Bristol, Bristol BS8 1TW, United Kingdom
| | | | - Yu Zhang
- Theoretical Division, Center for Nonlinear Studies (CNLS), and Center for Integrated Nanotechnologies (CINT), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Nikita Fedik
- Theoretical Division, Center for Nonlinear Studies (CNLS), and Center for Integrated Nanotechnologies (CINT), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Maksim Kulichenko
- Theoretical Division, Center for Nonlinear Studies (CNLS), and Center for Integrated Nanotechnologies (CINT), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Richard Messerly
- Theoretical Division, Center for Nonlinear Studies (CNLS), and Center for Integrated Nanotechnologies (CINT), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Luke Nambi Mohanam
- Department of Electrical and Computer Engineering, College of Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Sahar Sharifzadeh
- Department of Electrical and Computer Engineering, College of Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Adolfo Bastida
- Departamento de Química Física, Universidad de Murcia, Murcia 30100, Spain
| | - Shaul Mukamel
- Departments of Chemistry and Physics and Astronomy, University of California, Irvine, California 92697-2025, United States
| | | | - Sergei Tretiak
- Theoretical Division, Center for Nonlinear Studies (CNLS), and Center for Integrated Nanotechnologies (CINT), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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Lystrom L, Shukla M, Sun W, Kilina S. Extending Fluorescence of meso-Aryldipyrrin Indium(III) Complexes to Near-Infrared Regions via Electron Withdrawing or π-Expansive Aryl Substituents. J Phys Chem Lett 2021; 12:8009-8015. [PMID: 34433275 DOI: 10.1021/acs.jpclett.1c02150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The absorption and fluorescence spectra of 14 In(III) dipyrrin-based complexes are studied using time-dependent density functional theory (TDDFT). Calculations confirm that both heteroatom substitution of oxygen (N2O2-type) by nitrogen (N4-type) in dipyrrin ligand and functionalization at the meso-position by aromatic rings with strong electron-withdrawing (EW) substituents or extended π-conjugation are efficient tools in extending the fluorescence spectra of In(III) complexes to the near-infrared (NIR) region of 750-960 nm and in red-shifting the lowest absorption band to 560-630 nm. For all complexes, the emissive singlet state has π-π* character with a small addition of intraligand charge transfer (ILCT) contributing from the meso-aryl substituents to the dipyrrin ligand. Stronger EW nitro group on the meso-phenyl or meso-aryl group with extended π-conjugation induces red-shifted electronic absorption and fluorescence. More tetrahedral geometry of the complexes with N4-type ligands leads to less intensive but more red-shifted fluorescence to NIR, compared to the corresponding complexes with N2O2-type ligands that have a more planar geometry.
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Affiliation(s)
- Levi Lystrom
- Environmental Laboratory, U.S. Army Engineer Research and Development Center, Vicksburg, Mississippi 39180, United States
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee 37830, United States
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Manoj Shukla
- Environmental Laboratory, U.S. Army Engineer Research and Development Center, Vicksburg, Mississippi 39180, United States
| | - Wenfang Sun
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Svetlana Kilina
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, United States
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Malone W, Nebgen B, White A, Zhang Y, Song H, Bjorgaard JA, Sifain AE, Rodriguez-Hernandez B, Freixas VM, Fernandez-Alberti S, Roitberg AE, Nelson TR, Tretiak S. NEXMD Software Package for Nonadiabatic Excited State Molecular Dynamics Simulations. J Chem Theory Comput 2020; 16:5771-5783. [DOI: 10.1021/acs.jctc.0c00248] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Walter Malone
- Physics and Chemistry of Materials, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Benjamin Nebgen
- Physics and Chemistry of Materials, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Alexander White
- Physics and Chemistry of Materials, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Yu Zhang
- Physics and Chemistry of Materials, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Huajing Song
- Physics and Chemistry of Materials, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Josiah A. Bjorgaard
- Physics and Chemistry of Materials, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Andrew E. Sifain
- U.S. Army Research Laboratory, Aberdeen Proving Ground, Aberdeen, Maryland 21005, United States
| | | | - Victor M. Freixas
- Universidad Nacional de Quilmes/CONICET, Roque Saenz Peña 352, B1876BXD Bernal, Argentina
| | | | - Adrian E. Roitberg
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Tammie R. Nelson
- Physics and Chemistry of Materials, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Sergei Tretiak
- Physics and Chemistry of Materials, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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Lystrom L, Tamukong P, Mihaylov D, Kilina S. Phonon-Driven Energy Relaxation in PbS/CdS and PbSe/CdSe Core/Shell Quantum Dots. J Phys Chem Lett 2020; 11:4269-4278. [PMID: 32354213 DOI: 10.1021/acs.jpclett.0c00845] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We study the impact of the chemical composition on phonon-mediated exciton relaxation in the core/shell quantum dots (QDs), with 1 nm core made of PbX and the monolayer shell made of CdX, where X = S and Se. For this, time-domain nonadiabatic molecular dynamics (NAMD) based on density functional theory (DFT) and surface hopping techniques are applied. Simulations reveal twice faster energy relaxation in PbS/CdS than PbSe/CdSe because of dominant couplings to higher-energy optical phonons in structures with sulfur anions. For both QDs, the long-living intermediate states associated with the core-shell interface govern the dynamics. Therefore, a simple exponential model is not appropriate, and the four-state irreversible kinetic model is suggested instead, predicting 0.9 and 0.5 ps relaxation rates in PbSe/CdSe and PbS/CdS QDs, respectively. Thus, 2 nm PdSe/CdSe QDs with a single monolayer shell exhibit the phonon-mediated relaxation time sufficient for carrier multiplications to outpace energy dissipation and benefit the solar conversion efficiency.
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Affiliation(s)
- Levi Lystrom
- Chemistry & Biochemistry Department, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Patrick Tamukong
- School of Medicine & Health Sciences, University of North Dakota, Grand Forks, North Dakota 58202, United States
| | - Deyan Mihaylov
- Laboratory for Laser Energetics, University of Rochester, Rochester, New York 14623, United States
| | - Svetlana Kilina
- Chemistry & Biochemistry Department, North Dakota State University, Fargo, North Dakota 58108, United States
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6
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Zhang Y, Li L, Tretiak S, Nelson T. Nonadiabatic Excited-State Molecular Dynamics for Open-Shell Systems. J Chem Theory Comput 2020; 16:2053-2064. [DOI: 10.1021/acs.jctc.9b00928] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Yu Zhang
- Physics and Chemistry of Materials, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Linqiu Li
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Sergei Tretiak
- Physics and Chemistry of Materials, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Tammie Nelson
- Physics and Chemistry of Materials, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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Nelson TR, White AJ, Bjorgaard JA, Sifain AE, Zhang Y, Nebgen B, Fernandez-Alberti S, Mozyrsky D, Roitberg AE, Tretiak S. Non-adiabatic Excited-State Molecular Dynamics: Theory and Applications for Modeling Photophysics in Extended Molecular Materials. Chem Rev 2020; 120:2215-2287. [PMID: 32040312 DOI: 10.1021/acs.chemrev.9b00447] [Citation(s) in RCA: 251] [Impact Index Per Article: 50.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Optically active molecular materials, such as organic conjugated polymers and biological systems, are characterized by strong coupling between electronic and vibrational degrees of freedom. Typically, simulations must go beyond the Born-Oppenheimer approximation to account for non-adiabatic coupling between excited states. Indeed, non-adiabatic dynamics is commonly associated with exciton dynamics and photophysics involving charge and energy transfer, as well as exciton dissociation and charge recombination. Understanding the photoinduced dynamics in such materials is vital to providing an accurate description of exciton formation, evolution, and decay. This interdisciplinary field has matured significantly over the past decades. Formulation of new theoretical frameworks, development of more efficient and accurate computational algorithms, and evolution of high-performance computer hardware has extended these simulations to very large molecular systems with hundreds of atoms, including numerous studies of organic semiconductors and biomolecules. In this Review, we will describe recent theoretical advances including treatment of electronic decoherence in surface-hopping methods, the role of solvent effects, trivial unavoided crossings, analysis of data based on transition densities, and efficient computational implementations of these numerical methods. We also emphasize newly developed semiclassical approaches, based on the Gaussian approximation, which retain phase and width information to account for significant decoherence and interference effects while maintaining the high efficiency of surface-hopping approaches. The above developments have been employed to successfully describe photophysics in a variety of molecular materials.
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Affiliation(s)
- Tammie R Nelson
- Theoretical Division , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , United States
| | - Alexander J White
- Theoretical Division , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , United States
| | - Josiah A Bjorgaard
- Theoretical Division , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , United States
| | - Andrew E Sifain
- Theoretical Division , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , United States.,U.S. Army Research Laboratory , Aberdeen Proving Ground , Maryland 21005 , United States
| | - Yu Zhang
- Theoretical Division , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , United States
| | - Benjamin Nebgen
- Theoretical Division , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , United States
| | | | - Dmitry Mozyrsky
- Theoretical Division , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , United States
| | - Adrian E Roitberg
- Department of Chemistry , University of Florida , Gainesville , Florida 32611 , United States
| | - Sergei Tretiak
- Theoretical Division , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , United States
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