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Liu A, Zhang T, Hammes-Schiffer S, Li X. Multicomponent Cholesky Decomposition: Application to Nuclear-Electronic Orbital Theory. J Chem Theory Comput 2023; 19:6255-6262. [PMID: 37699735 DOI: 10.1021/acs.jctc.3c00686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
The Cholesky decomposition technique is commonly used to reduce the memory requirement for storing two-particle repulsion integrals in quantum chemistry calculations that use atomic orbital bases. However, when quantum methods use multicomponent bases, such as nuclear-electronic orbitals, additional challenges are introduced due to asymmetric two-particle integrals. This work proposes several multicomponent Cholesky decomposition methods for calculations using nuclear-electronic orbital density functional theory. To analyze the errors in different Cholesky decomposition components, benchmark calculations using water clusters are carried out. The largest benchmark calculation is a water cluster (H2O)27 where all 54 protons are treated quantum mechanically. This study provides energetic and complexity analyses to demonstrate the accuracy and performance of the proposed multicomponent Cholesky decomposition method.
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Affiliation(s)
- Aodong Liu
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Tianyuan Zhang
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | | | - Xiaosong Li
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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Iguchi A, Singh A, Bergmeister S, Azhagesan AA, Mizuse K, Fujii A, Tanuma H, Azuma T, Scheier P, Kuma S, Vilesov AF. Isolation and Infrared Spectroscopic Characterization of Hemibonded Water Dimer Cation in Superfluid Helium Nanodroplets. J Phys Chem Lett 2023; 14:8199-8204. [PMID: 37672355 PMCID: PMC10510431 DOI: 10.1021/acs.jpclett.3c02150] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 08/30/2023] [Indexed: 09/08/2023]
Abstract
The structure of the minimum unit of the radical cationic water clusters, the (H2O)2+ dimer, has attracted much attention because of its importance for the radiation chemistry of water. Previous spectroscopic studies indicated that the dimers have a proton-transferred structure (H3O+·OH), though the alternate metastable hemibonded structure (H2O·OH2)+ was also predicted based on theoretical calculations. Here, we produce (H2O)2+ dimers in superfluid helium nanodroplets and study their infrared spectra in the range of OH stretching vibrations. The observed spectra indicate the coexistence of the two structures in the droplets, supported by density functional theory calculations. This is the first spectroscopic identification of the hemibonded isomer of water radical cation dimers. The observation of the higher-energy isomer reveals efficient kinetic trapping for metastable ionic clusters due to the rapid cooling in helium droplets.
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Affiliation(s)
- Arisa Iguchi
- Department
of Physics, Tokyo Metropolitan University, Tokyo 192-0397, Japan
- Atomic,
Molecular, and Optical Physics Laboratory, RIKEN, Saitama 351-0198, Japan
| | - Amandeep Singh
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Stefan Bergmeister
- Institut
für Ionenphysik und Angewandte Physik, Universität Innsbruck, A-6020 Innsbruck, Austria
| | - Andrew A. Azhagesan
- Department
of Computer Science, University of Southern
California, Los Angeles, California 90089, United States
| | - Kenta Mizuse
- Department
of Chemistry, School of Science, Kitasato
University, Sagamihara, Kanagawa 252-0373, Japan
| | - Asuka Fujii
- Department
of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Hajime Tanuma
- Department
of Physics, Tokyo Metropolitan University, Tokyo 192-0397, Japan
| | - Toshiyuki Azuma
- Atomic,
Molecular, and Optical Physics Laboratory, RIKEN, Saitama 351-0198, Japan
| | - Paul Scheier
- Institut
für Ionenphysik und Angewandte Physik, Universität Innsbruck, A-6020 Innsbruck, Austria
| | - Susumu Kuma
- Atomic,
Molecular, and Optical Physics Laboratory, RIKEN, Saitama 351-0198, Japan
| | - Andrey F. Vilesov
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089, United States
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Perrella F, Coppola F, Rega N, Petrone A. An Expedited Route to Optical and Electronic Properties at Finite Temperature via Unsupervised Learning. Molecules 2023; 28:molecules28083411. [PMID: 37110644 PMCID: PMC10144358 DOI: 10.3390/molecules28083411] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 04/06/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
Electronic properties and absorption spectra are the grounds to investigate molecular electronic states and their interactions with the environment. Modeling and computations are required for the molecular understanding and design strategies of photo-active materials and sensors. However, the interpretation of such properties demands expensive computations and dealing with the interplay of electronic excited states with the conformational freedom of the chromophores in complex matrices (i.e., solvents, biomolecules, crystals) at finite temperature. Computational protocols combining time dependent density functional theory and ab initio molecular dynamics (MD) have become very powerful in this field, although they require still a large number of computations for a detailed reproduction of electronic properties, such as band shapes. Besides the ongoing research in more traditional computational chemistry fields, data analysis and machine learning methods have been increasingly employed as complementary approaches for efficient data exploration, prediction and model development, starting from the data resulting from MD simulations and electronic structure calculations. In this work, dataset reduction capabilities by unsupervised clustering techniques applied to MD trajectories are proposed and tested for the ab initio modeling of electronic absorption spectra of two challenging case studies: a non-covalent charge-transfer dimer and a ruthenium complex in solution at room temperature. The K-medoids clustering technique is applied and is proven to be able to reduce by ∼100 times the total cost of excited state calculations on an MD sampling with no loss in the accuracy and it also provides an easier understanding of the representative structures (medoids) to be analyzed on the molecular scale.
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Affiliation(s)
- Fulvio Perrella
- Scuola Superiore Meridionale, Largo San Marcellino 10, I-80138 Napoli, Italy
| | - Federico Coppola
- Scuola Superiore Meridionale, Largo San Marcellino 10, I-80138 Napoli, Italy
| | - Nadia Rega
- Scuola Superiore Meridionale, Largo San Marcellino 10, I-80138 Napoli, Italy
- Department of Chemical Sciences, University of Napoli Federico II, Complesso Universitario di M.S. Angelo, via Cintia 21, I-80126 Napoli, Italy
- Istituto Nazionale di Fisica Nucleare, Sezione di Napoli, Complesso Universitario di M.S. Angelo ed. 6, via Cintia 21, I-80126 Napoli, Italy
| | - Alessio Petrone
- Scuola Superiore Meridionale, Largo San Marcellino 10, I-80138 Napoli, Italy
- Department of Chemical Sciences, University of Napoli Federico II, Complesso Universitario di M.S. Angelo, via Cintia 21, I-80126 Napoli, Italy
- Istituto Nazionale di Fisica Nucleare, Sezione di Napoli, Complesso Universitario di M.S. Angelo ed. 6, via Cintia 21, I-80126 Napoli, Italy
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Shepard C, Kanai Y. Nonlinear electronic excitation in water under proton irradiation: a first principles study. Phys Chem Chem Phys 2022; 24:5598-5603. [PMID: 35175259 DOI: 10.1039/d1cp05313b] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nonlinear dynamics of electronic excitation bridge physical and physicochemical stages of water radiolysis under proton irradiation, a multi-scale physicochemical process that is fundamental to a wide range of technological and medical applications of high-energy protons. We study the spatial and temporal changes to the excited holes generated in this ionization event using first-principles theory simulation. A significant majority of holes are formed in the immediate vicinity of the irradiating proton paths, and these holes decay rapidly, while secondary excitations are simultaneously induced in regions farther away. While the hole population remains constant, the observed spatially spreading hole distribution cannot be described as concentration-dependent diffusion current. Compared to the primary excitation induced by the irradiating protons, the secondary excitation farther away is somewhat less energetic. The first-principles theory simulation here provides a detailed description of how the primary excitation by proton radiation precedes the formation of cationic holes, which undergo ultrafast chemical processes in water radiolysis.
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Affiliation(s)
- Christopher Shepard
- Department of Chemistry, University of North Carolina at Chapel Hill, NC, USA.
| | - Yosuke Kanai
- Department of Chemistry, University of North Carolina at Chapel Hill, NC, USA.
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Wong JC, Kanai Y. First Principles Dynamics Study of Excited Hole Relaxation in DNA. Chemphyschem 2021; 23:e202100521. [PMID: 34494706 DOI: 10.1002/cphc.202100521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/30/2021] [Indexed: 11/08/2022]
Abstract
A recent theoretical work showed that ion irradiation generates excited holes deep within the valence band of DNA. In this work, we investigate the excited hole relaxation toward HOMO using a first-principles computational method following such ionization events. The excited hole relaxation is found to depend significantly on the energetic position of the excited hole generated. The relaxation process is found to be an order of magnitude slower for holes that are generated deeper than 20 eV than those generated within 10 eV, where the probability for the initial ionization events is the highest. However, the excited holes that are generated in different spatial moieties such as DNA nucleotide bases and phosphate backbones do not show noticeable differences in terms of the relaxation time. Our work also shows that decoherence due to nuclei dynamics slows down the relaxation by a factor of two or more. At the same time, the relaxation time is found to be less than a couple of picoseconds, much shorter than typical timescales associated with chemical bond dissociation.
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Affiliation(s)
- Jian Cheng Wong
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Yosuke Kanai
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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Xu J, Chen D, Meng S. Probing Laser-Induced Plasma Generation in Liquid Water. J Am Chem Soc 2021; 143:10382-10388. [PMID: 34197710 DOI: 10.1021/jacs.1c04675] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Understanding photoexcitation dynamics in liquid water is of crucial significance for both fundamental scientific exploration and technological applications. Despite the observations of photoinduced macroscopic phenomena, the initial atomistic movements and associated energy transfer pathways immediately following laser irradiation are hard to track due to the extreme complexity of laser-water interaction and its ultrafast time scale. We explore the femtosecond evolution of liquid water upon intense photoexcitation based on nonadiabatic quantum dynamics simulations. Separate ionic and electronic dynamics were explicitly monitored with tremendous details unveiled on an unprecedented microscopic level. Water was found to undergo the two-step heating processes. The strong-field effects and electronic excitations dominate the first-stage heating and pressurization. Subsequent relaxation of ionic and electronic subsystems further increases the ionic temperature but releases the large internal pressure. The water molecules are stretched during the laser pulses, and the electronic excitations result in the proton transfers after laser pulses. Intense laser pulses violently excite liquid water, giving rise to severe molecular dissociation and plasma generation during the laser pulses. The laser-induced water plasma is characterized by a high fraction of free protons (∼50%), nonequilibrium ionic and electronic distributions, and a metallic electronic density of states.
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Affiliation(s)
- Jiyu Xu
- Beijing National Laboratory for Condensed Matter Physics and Institute of Physics, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
| | - Daqiang Chen
- Beijing National Laboratory for Condensed Matter Physics and Institute of Physics, Chinese Academy of Sciences, Beijing 100190, People's Republic of China.,School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Sheng Meng
- Beijing National Laboratory for Condensed Matter Physics and Institute of Physics, Chinese Academy of Sciences, Beijing 100190, People's Republic of China.,School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China.,Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, People's Republic of China
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Shao C, Xu J, Wang L. Branching and phase corrected surface hopping: A benchmark of nonadiabatic dynamics in multilevel systems. J Chem Phys 2021; 154:234109. [PMID: 34241240 DOI: 10.1063/5.0056224] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Since the seminal work of Tully [J. Chem. Phys. 93, 1061 (1990)], two-level scattering models have been extensively adopted as the standard benchmark systems to assess the performance of different trajectory surface hopping methods for nonadiabatic dynamics simulations. Here, we extend the branching and phase corrections to multilevel systems and combine them with both the traditional fewest switches surface hopping (FSSH) and its variant global flux surface hopping (GFSH) algorithms. To get a comprehensive evaluation of the proposed methods, we construct a series of more challenging and diverse three-level and four-level scattering models and use exact quantum solutions as references. Encouragingly, both FSSH and GFSH with the branching and phase corrections produce excellent and nearly identical results in all investigated systems, indicating that the new surface hopping methods are robust to describe multilevel problems and the reliability is insensitive to the definition of self-consistent hopping probabilities in the adiabatic representation. Furthermore, the branching correction is found to be especially important when dealing with strongly repulsive potential energy surfaces, which are common in realistic systems, thus promising for general applications.
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Affiliation(s)
- Cancan Shao
- Key Laboratory of Excited-State Materials of Zhejiang Province, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Jiabo Xu
- Key Laboratory of Excited-State Materials of Zhejiang Province, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Linjun Wang
- Key Laboratory of Excited-State Materials of Zhejiang Province, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
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