1
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Rana B, Hohenstein EG, Martínez TJ. Simulating the Excited-State Dynamics of Polaritons with Ab Initio Multiple Spawning. J Phys Chem A 2024; 128:139-151. [PMID: 38110364 DOI: 10.1021/acs.jpca.3c06607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Over the past decade, there has been a growth of interest in polaritonic chemistry, where the formation of hybrid light-matter states (polaritons) can alter the course of photochemical reactions. These hybrid states are created by strong coupling between molecules and photons in resonant optical cavities and can even occur in the absence of light when the molecule is strongly coupled with the electromagnetic fluctuations of the vacuum field. We present a first-principles model to simulate nonadiabatic dynamics of such polaritonic states inside optical cavities by leveraging graphical processing units (GPUs). Our first implementation of this model is specialized for a single molecule coupled to a single-photon mode confined inside the optical cavity but with any number of excited states computed using complete active space configuration interaction (CASCI) and a Jaynes-Cummings-type Hamiltonian. Using this model, we have simulated the excited-state dynamics of a single salicylideneaniline (SA) molecule strongly coupled to a cavity photon with the ab initio multiple spawning (AIMS) method. We demonstrate how the branching ratios of the photodeactivation pathways for this molecule can be manipulated by coupling to the cavity. We also show how one can stop the photoreaction from happening inside of an optical cavity. Finally, we also investigate cavity-based control of the ordering of two excited states (one optically bright and the other optically dark) inside a cavity for a set of molecules, where the dark and bright states are close in energy.
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Affiliation(s)
- Bhaskar Rana
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Edward G Hohenstein
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Todd J Martínez
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
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2
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Silfies MC, Mehmood A, Kowzan G, Hohenstein EG, Levine BG, Allison TK. Ultrafast internal conversion and photochromism in gas-phase salicylideneaniline. J Chem Phys 2023; 159:104304. [PMID: 37681695 DOI: 10.1063/5.0161238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 08/11/2023] [Indexed: 09/09/2023] Open
Abstract
Salicylideneaniline (SA) is an archetypal system for excited-state intramolecular proton transfer (ESIPT) in non-planar systems. Multiple channels for relaxation involving both the keto and enol forms have been proposed after excitation to S1 with near-UV light. Here, we present transient absorption measurements of hot gas-phase SA, jet-cooled SA, and SA in Ar clusters using cavity-enhanced transient absorption spectroscopy (CE-TAS). Assignment of the spectra is aided by simulated TAS spectra, computed by applying time-dependent complete active space configuration interaction (TD-CASCI) to structures drawn from nonadiabatic molecular dynamics simulations. We find prompt ESIPT in all conditions followed by the rapid generation of the trans keto metastable photochrome state and fluorescent keto state in parallel. Increasing the internal energy increases the photochrome yield and decreases the fluorescent yield and fluorescent state lifetime observed in TAS. In Ar clusters, internal conversion of SA is severely hindered, but the photochrome yield is unchanged. Taken together, these results are consistent with the photochrome being produced via the vibrationally excited keto population after ESIPT.
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Affiliation(s)
- Myles C Silfies
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, New York 11794, USA
| | - Arshad Mehmood
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, USA
- Institute for Advanced Computational Science, Stony Brook University, Stony Brook, New York 11794, USA
| | - Grzegorz Kowzan
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, USA
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Toruń, ul. Grudziadzka 5, 87-100 Toruń, Poland
| | | | - Benjamin G Levine
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, USA
- Institute for Advanced Computational Science, Stony Brook University, Stony Brook, New York 11794, USA
| | - Thomas K Allison
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, New York 11794, USA
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, USA
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3
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Hohenstein EG, Oumarou O, Al-Saadon R, Anselmetti GLR, Scheurer M, Gogolin C, Parrish RM. Efficient quantum analytic nuclear gradients with double factorization. J Chem Phys 2023; 158:114119. [PMID: 36948843 DOI: 10.1063/5.0137167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Abstract
Efficient representations of the Hamiltonian, such as double factorization, drastically reduce the circuit depth or the number of repetitions in error corrected and noisy intermediate-scale quantum (NISQ) algorithms for chemistry. We report a Lagrangian-based approach for evaluating relaxed one- and two-particle reduced density matrices from double factorized Hamiltonians, unlocking efficiency improvements in computing the nuclear gradient and related derivative properties. We demonstrate the accuracy and feasibility of our Lagrangian-based approach to recover all off-diagonal density matrix elements in classically simulated examples with up to 327 quantum and 18 470 total atoms in QM/MM simulations with modest-sized quantum active spaces. We show this in the context of the variational quantum eigensolver in case studies, such as transition state optimization, ab initio molecular dynamics simulation, and energy minimization of large molecular systems.
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4
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Cruzeiro VWD, Wang Y, Pieri E, Hohenstein EG, Martínez TJ. TeraChem protocol buffers (TCPB): Accelerating QM and QM/MM simulations with a client-server model. J Chem Phys 2023; 158:044801. [PMID: 36725506 DOI: 10.1063/5.0130886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The routine use of electronic structures in many chemical simulation applications calls for efficient and easy ways to access electronic structure programs. We describe how the graphics processing unit (GPU) accelerated electronic structure program TeraChem can be set up as an electronic structure server, to be easily accessed by third-party client programs. We exploit Google's protocol buffer framework for data serialization and communication. The client interface, called TeraChem protocol buffers (TCPB), has been designed for ease of use and compatibility with multiple programming languages, such as C++, Fortran, and Python. To demonstrate the ease of coupling third-party programs with electronic structures using TCPB, we have incorporated the TCPB client into Amber for quantum mechanics/molecular mechanics (QM/MM) simulations. The TCPB interface saves time with GPU initialization and I/O operations, achieving a speedup of more than 2× compared to a prior file-based implementation for a QM region with ∼250 basis functions. We demonstrate the practical application of TCPB by computing the free energy profile of p-hydroxybenzylidene-2,3-dimethylimidazolinone (p-HBDI-)-a model chromophore in green fluorescent proteins-on the first excited singlet state using Hamiltonian replica exchange for enhanced sampling. All calculations in this work have been performed with the non-commercial freely-available version of TeraChem, which is sufficient for many QM region sizes in common use.
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Affiliation(s)
| | - Yuanheng Wang
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA
| | - Elisa Pieri
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA
| | - Edward G Hohenstein
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA
| | - Todd J Martínez
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA
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5
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Wang Y, Seritan S, Lahana D, Ford JE, Valentini A, Hohenstein EG, Martínez TJ. InteraChem: Exploring Excited States in Virtual Reality with Ab Initio Interactive Molecular Dynamics. J Chem Theory Comput 2022; 18:3308-3317. [PMID: 35649124 DOI: 10.1021/acs.jctc.2c00005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
InteraChem is an ab initio interactive molecular dynamics (AI-IMD) visualizer that leverages recent advances in virtual reality hardware and software, as well as the graphical processing unit (GPU)-accelerated TeraChem electronic structure package, in order to render quantum chemistry in real time. We introduce the exploration of electronically excited states via AI-IMD using the floating occupation molecular orbital-complete active space configuration interaction method. The optimization tools in InteraChem enable identification of excited state minima as well as minimum energy conical intersections for further characterization of excited state chemistry in small- to medium-sized systems. We demonstrate that finite-temperature Hartree-Fock theory is an efficient method to perform ground state AI-IMD. InteraChem allows users to track electronic properties such as molecular orbitals and bond order in real time, resulting in an interactive visualization tool that aids in the interpretation of excited state chemistry data and makes quantum chemistry more accessible for both research and educational purposes.
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Affiliation(s)
- Yuanheng Wang
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Stefan Seritan
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Dean Lahana
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Jason E Ford
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Alessio Valentini
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Edward G Hohenstein
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Todd J Martínez
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
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6
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Hohenstein EG, Fales BS, Parrish RM, Martínez TJ. Rank-reduced coupled-cluster. III. Tensor hypercontraction of the doubles amplitudes. J Chem Phys 2022; 156:054102. [DOI: 10.1063/5.0077770] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Edward G. Hohenstein
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - B. Scott Fales
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | | | - Todd J. Martínez
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
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7
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Abstract
We have developed a graphical processing unit (GPU) accelerated implementation of our recently introduced rank-reduced coupled-cluster singles and doubles (RR-CCSD) method. RR-CCSD introduces a low-rank approximation of the doubles amplitudes. This is combined with a low-rank approximation of the electron repulsion integrals via Cholesky decomposition. The result of these two low-rank approximations is the replacement of the usual fourth-order CCSD tensors with products of second- and third-order tensors. In our implementation, only a single fourth-order tensor must be constructed as an intermediate during the solution of the amplitude equations. Owing in large part to the compression of the doubles amplitudes, the GPU-accelerated implementation shows excellent parallel efficiency (95% on eight GPUs). Our implementation can solve the RR-CCSD equations for up to 400 electrons and 1550 basis functions-roughly 50% larger than the largest canonical CCSD computations that have been performed on any hardware. In addition to increased scalability, the RR-CCSD computations are faster than the corresponding CCSD computations for all but the smallest molecules. We test the accuracy of RR-CCSD for a variety of chemical systems including up to 1000 basis functions and determine that accuracy to better than 0.1% error in the correlation energy can be achieved with roughly 95% compression of the ov space for the largest systems considered. We also demonstrate that conformational energies can be predicted to be within 0.1 kcal mol-1 with efficient compression applied to the wavefunction. Finally, we find that low-rank approximations of the CCSD doubles amplitudes used in the similarity transformation of the Hamiltonian prior to a conventional equation-of-motion CCSD computation will not introduce significant errors (on the order of a few hundredths of an electronvolt) into the resulting excitation energies.
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Affiliation(s)
- Edward G Hohenstein
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA
| | - Todd J Martínez
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA
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8
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Hohenstein EG, Yu JK, Bannwarth C, List NH, Paul AC, Folkestad SD, Koch H, Martínez TJ. Predictions of Pre-edge Features in Time-Resolved Near-Edge X-ray Absorption Fine Structure Spectroscopy from Hole-Hole Tamm-Dancoff-Approximated Density Functional Theory. J Chem Theory Comput 2021; 17:7120-7133. [PMID: 34623139 DOI: 10.1021/acs.jctc.1c00478] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Time-resolved near-edge X-ray absorption fine structure (TR-NEXAFS) spectroscopy is a powerful technique for studying photochemical reaction dynamics with femtosecond time resolution. In order to avoid ambiguity in TR-NEXAFS spectra from nonadiabatic dynamics simulations, core- and valence-excited states must be evaluated on equal footing and those valence states must also define the potential energy surfaces used in the nonadiabatic dynamics simulation. In this work, we demonstrate that hole-hole Tamm-Dancoff-approximated density functional theory (hh-TDA) is capable of directly simulating TR-NEXAFS spectroscopies. We apply hh-TDA to the excited-state dynamics of acrolein. We identify two pre-edge features in the oxygen K-edge TR-NEXAFS spectrum associated with the S2 (ππ*) and S1 (nπ*) excited states. We show that these features can be used to follow the internal conversion dynamics between the lowest three electronic states of acrolein. Due to the low, O(N2) apparent computational complexity of hh-TDA and our GPU-accelerated implementation, this method is promising for the simulation of pre-edge features in TR-NEXAFS spectra of large molecules and molecules in the condensed phase.
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Affiliation(s)
- Edward G Hohenstein
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Jimmy K Yu
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States.,Biophysics Program, Stanford University, Stanford, California 94305, United States
| | - Christoph Bannwarth
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Nanna Holmgaard List
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Alexander C Paul
- Department of Chemistry, Norwegian University of Science and Technology, NTNU, 7491 Trondheim, Norway
| | - Sarai D Folkestad
- Department of Chemistry, Norwegian University of Science and Technology, NTNU, 7491 Trondheim, Norway
| | - Henrik Koch
- Department of Chemistry, Norwegian University of Science and Technology, NTNU, 7491 Trondheim, Norway.,Scuola Normale Superiore, Piazza dei Cavaleri 7, 56126 Pisa, Italy
| | - Todd J Martínez
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
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9
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Yu JK, Bannwarth C, Liang R, Hohenstein EG, Martínez TJ. Nonadiabatic Dynamics Simulation of the Wavelength-Dependent Photochemistry of Azobenzene Excited to the nπ* and ππ* Excited States. J Am Chem Soc 2020; 142:20680-20690. [DOI: 10.1021/jacs.0c09056] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jimmy K. Yu
- Biophysics Program, Stanford University, Stanford, California 94305, United States
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Christoph Bannwarth
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Ruibin Liang
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Edward G. Hohenstein
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Todd J. Martínez
- Biophysics Program, Stanford University, Stanford, California 94305, United States
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
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10
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Yu JK, Bannwarth C, Hohenstein EG, Martínez TJ. Ab Initio Nonadiabatic Molecular Dynamics with Hole–Hole Tamm–Dancoff Approximated Density Functional Theory. J Chem Theory Comput 2020; 16:5499-5511. [DOI: 10.1021/acs.jctc.0c00644] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Jimmy K. Yu
- Biophysics Program, Stanford University, Stanford, California 94305, United States
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Christoph Bannwarth
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Edward G. Hohenstein
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Todd J. Martínez
- Biophysics Program, Stanford University, Stanford, California 94305, United States
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
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11
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Seritan S, Bannwarth C, Fales BS, Hohenstein EG, Isborn CM, Kokkila‐Schumacher SIL, Li X, Liu F, Luehr N, Snyder JW, Song C, Titov AV, Ufimtsev IS, Wang L, Martínez TJ. TeraChem
: A graphical processing unit
‐accelerated
electronic structure package for
large‐scale
ab initio molecular dynamics. WIREs Comput Mol Sci 2020. [DOI: 10.1002/wcms.1494] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Stefan Seritan
- Department of Chemistry and the PULSE Institute Stanford University Stanford California USA
- SLAC National Accelerator Laboratory Menlo Park California USA
| | - Christoph Bannwarth
- Department of Chemistry and the PULSE Institute Stanford University Stanford California USA
- SLAC National Accelerator Laboratory Menlo Park California USA
| | - Bryan S. Fales
- Department of Chemistry and the PULSE Institute Stanford University Stanford California USA
- SLAC National Accelerator Laboratory Menlo Park California USA
| | - Edward G. Hohenstein
- Department of Chemistry and the PULSE Institute Stanford University Stanford California USA
- SLAC National Accelerator Laboratory Menlo Park California USA
| | - Christine M. Isborn
- Department of Chemistry University of California Merced Merced California USA
| | | | - Xin Li
- Division of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health KTH Royal Institute of Technology Stockholm Sweden
| | - Fang Liu
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge Massachusetts USA
| | | | | | - Chenchen Song
- Department of Physics University of California Berkeley Berkeley California USA
- Molecular Foundry Lawrence Berkeley National Laboratory Berkeley California USA
| | | | - Ivan S. Ufimtsev
- Department of Structural Biology Stanford University School of Medicine Stanford California USA
| | - Lee‐Ping Wang
- Department of Chemistry University of California Davis Davis California USA
| | - Todd J. Martínez
- Department of Chemistry and the PULSE Institute Stanford University Stanford California USA
- SLAC National Accelerator Laboratory Menlo Park California USA
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12
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van den Berg JL, Neumann KI, Harrison JA, Weir H, Hohenstein EG, Martinez TJ, Zare RN. Strong, Nonresonant Radiation Enhances Cis- Trans Photoisomerization of Stilbene in Solution. J Phys Chem A 2020; 124:5999-6008. [PMID: 32585098 DOI: 10.1021/acs.jpca.0c02732] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Previously, it has been demonstrated that external electric fields may be used to exert control over chemical reactivity. In this study, the impact of a strong, nonresonant IR field (1064 nm) on the photoisomerization of cis-stilbene is investigated in cyclohexane solution. The design of a suitable reaction vessel for characterization of this effect is presented. The electric field supplied by the pulsed, near-IR radiation (εl = 4.5 × 107 V/cm) enhances the cis → trans photoisomerization yield at the red edge of the absorption spectrum (wavelengths between 337 and 340 nm). Within the microliter focal volume, up to 75% of all cis-stilbene molecules undergo isomerization to trans-stilbene in the strong electric-field environment, indicating a significant increase relative to the 35% yield of trans-stilbene under field-free conditions. This result correlates with a 1-3% enhancement in the trans-stilbene concentration throughout the bulk solution. Theoretical analysis suggests that the observed change is the result of dynamic Stark shifting of the ground and first excited states, leading to a significant redshift in cis-stilbene's absorption spectrum. The predicted increase in the absorption cross section in this range of excitation wavelengths is qualitatively consistent with the experimental increase in trans-stilbene production.
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Affiliation(s)
- Jana L van den Berg
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Kallie Ilene Neumann
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - John A Harrison
- Department of Chemistry, Stanford University, Stanford, California 94305, United States.,Chemistry, School of Natural and Computational Sciences, Massey University Auckland, Private Bag 102904, Auckland 4442, New Zealand
| | - Hayley Weir
- Department of Chemistry, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Edward G Hohenstein
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Todd J Martinez
- Department of Chemistry, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Richard N Zare
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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13
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Bannwarth C, Yu JK, Hohenstein EG, Martínez TJ. Hole-hole Tamm-Dancoff-approximated density functional theory: A highly efficient electronic structure method incorporating dynamic and static correlation. J Chem Phys 2020; 153:024110. [PMID: 32668944 DOI: 10.1063/5.0003985] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The study of photochemical reaction dynamics requires accurate as well as computationally efficient electronic structure methods for the ground and excited states. While time-dependent density functional theory (TDDFT) is not able to capture static correlation, complete active space self-consistent field methods neglect much of the dynamic correlation. Hence, inexpensive methods that encompass both static and dynamic electron correlation effects are of high interest. Here, we revisit hole-hole Tamm-Dancoff approximated (hh-TDA) density functional theory for this purpose. The hh-TDA method is the hole-hole counterpart to the more established particle-particle TDA (pp-TDA) method, both of which are derived from the particle-particle random phase approximation (pp-RPA). In hh-TDA, the N-electron electronic states are obtained through double annihilations starting from a doubly anionic (N+2 electron) reference state. In this way, hh-TDA treats ground and excited states on equal footing, thus allowing for conical intersections to be correctly described. The treatment of dynamic correlation is introduced through the use of commonly employed density functional approximations to the exchange-correlation potential. We show that hh-TDA is a promising candidate to efficiently treat the photochemistry of organic and biochemical systems that involve several low-lying excited states-particularly those with both low-lying ππ* and nπ* states where inclusion of dynamic correlation is essential to describe the relative energetics. In contrast to the existing literature on pp-TDA and pp-RPA, we employ a functional-dependent choice for the response kernel in pp- and hh-TDA, which closely resembles the response kernels occurring in linear response and collinear spin-flip TDDFT.
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Affiliation(s)
- Christoph Bannwarth
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA
| | - Jimmy K Yu
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA
| | - Edward G Hohenstein
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA
| | - Todd J Martínez
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA
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14
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Fales BS, Curtis ER, Johnson KG, Lahana D, Seritan S, Wang Y, Weir H, Martínez TJ, Hohenstein EG. Performance of Coupled-Cluster Singles and Doubles on Modern Stream Processing Architectures. J Chem Theory Comput 2020; 16:4021-4028. [PMID: 32567305 DOI: 10.1021/acs.jctc.0c00336] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We develop a new implementation of coupled-cluster singles and doubles (CCSD) optimized for the most recent graphical processing unit (GPU) hardware. We find that a single node with 8 NVIDIA V100 GPUs is capable of performing CCSD computations on roughly 100 atoms and 1300 basis functions in less than 1 day. Comparisons against massively parallel implementations of CCSD suggest that more than 64 CPU-based nodes (each with 16 cores) are required to match this performance.
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Affiliation(s)
- B Scott Fales
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Ethan R Curtis
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - K Grace Johnson
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Dean Lahana
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Stefan Seritan
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Yuanheng Wang
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Hayley Weir
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Todd J Martínez
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Edward G Hohenstein
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
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15
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Seritan S, Bannwarth C, Fales BS, Hohenstein EG, Kokkila-Schumacher SIL, Luehr N, Snyder JW, Song C, Titov AV, Ufimtsev IS, Martínez TJ. TeraChem: Accelerating electronic structure and ab initio molecular dynamics with graphical processing units. J Chem Phys 2020; 152:224110. [PMID: 32534542 PMCID: PMC7928072 DOI: 10.1063/5.0007615] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 05/19/2020] [Indexed: 11/15/2022] Open
Abstract
Developed over the past decade, TeraChem is an electronic structure and ab initio molecular dynamics software package designed from the ground up to leverage graphics processing units (GPUs) to perform large-scale ground and excited state quantum chemistry calculations in the gas and the condensed phase. TeraChem's speed stems from the reformulation of conventional electronic structure theories in terms of a set of individually optimized high-performance electronic structure operations (e.g., Coulomb and exchange matrix builds, one- and two-particle density matrix builds) and rank-reduction techniques (e.g., tensor hypercontraction). Recent efforts have encapsulated these core operations and provided language-agnostic interfaces. This greatly increases the accessibility and flexibility of TeraChem as a platform to develop new electronic structure methods on GPUs and provides clear optimization targets for emerging parallel computing architectures.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Ivan S. Ufimtsev
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, USA
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16
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Weir H, Williams M, Parrish RM, Hohenstein EG, Martínez TJ. Nonadiabatic Dynamics of Photoexcited cis-Stilbene Using Ab Initio Multiple Spawning. J Phys Chem B 2020; 124:5476-5487. [DOI: 10.1021/acs.jpcb.0c03344] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Hayley Weir
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Monika Williams
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Robert M. Parrish
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Edward G. Hohenstein
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Todd J. Martínez
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
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17
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Smith DGA, Burns LA, Simmonett AC, Parrish RM, Schieber MC, Galvelis R, Kraus P, Kruse H, Di Remigio R, Alenaizan A, James AM, Lehtola S, Misiewicz JP, Scheurer M, Shaw RA, Schriber JB, Xie Y, Glick ZL, Sirianni DA, O’Brien JS, Waldrop JM, Kumar A, Hohenstein EG, Pritchard BP, Brooks BR, Schaefer HF, Sokolov AY, Patkowski K, DePrince AE, Bozkaya U, King RA, Evangelista FA, Turney JM, Crawford TD, Sherrill CD. Psi4 1.4: Open-source software for high-throughput quantum chemistry. J Chem Phys 2020; 152:184108. [PMID: 32414239 PMCID: PMC7228781 DOI: 10.1063/5.0006002] [Citation(s) in RCA: 301] [Impact Index Per Article: 75.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 04/12/2020] [Indexed: 12/13/2022] Open
Abstract
PSI4 is a free and open-source ab initio electronic structure program providing implementations of Hartree-Fock, density functional theory, many-body perturbation theory, configuration interaction, density cumulant theory, symmetry-adapted perturbation theory, and coupled-cluster theory. Most of the methods are quite efficient, thanks to density fitting and multi-core parallelism. The program is a hybrid of C++ and Python, and calculations may be run with very simple text files or using the Python API, facilitating post-processing and complex workflows; method developers also have access to most of PSI4's core functionalities via Python. Job specification may be passed using The Molecular Sciences Software Institute (MolSSI) QCSCHEMA data format, facilitating interoperability. A rewrite of our top-level computation driver, and concomitant adoption of the MolSSI QCARCHIVE INFRASTRUCTURE project, makes the latest version of PSI4 well suited to distributed computation of large numbers of independent tasks. The project has fostered the development of independent software components that may be reused in other quantum chemistry programs.
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Affiliation(s)
| | - Lori A. Burns
- Center for Computational Molecular Science and
Technology, School of Chemistry and Biochemistry, School of Computational Science and
Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400,
USA
| | - Andrew C. Simmonett
- National Institutes of Health – National Heart,
Lung and Blood Institute, Laboratory of Computational Biology, Bethesda,
Maryland 20892, USA
| | - Robert M. Parrish
- Center for Computational Molecular Science and
Technology, School of Chemistry and Biochemistry, School of Computational Science and
Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400,
USA
| | - Matthew C. Schieber
- Center for Computational Molecular Science and
Technology, School of Chemistry and Biochemistry, School of Computational Science and
Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400,
USA
| | | | - Peter Kraus
- School of Molecular and Life Sciences, Curtin
University, Kent St., Bentley, Perth, Western Australia 6102,
Australia
| | - Holger Kruse
- Institute of Biophysics of the Czech Academy of
Sciences, Královopolská 135, 612 65 Brno, Czech
Republic
| | - Roberto Di Remigio
- Department of Chemistry, Centre for Theoretical
and Computational Chemistry, UiT, The Arctic University of Norway, N-9037
Tromsø, Norway
| | - Asem Alenaizan
- Center for Computational Molecular Science and
Technology, School of Chemistry and Biochemistry, School of Computational Science and
Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400,
USA
| | - Andrew M. James
- Department of Chemistry, Virginia
Tech, Blacksburg, Virginia 24061, USA
| | - Susi Lehtola
- Department of Chemistry, University of
Helsinki, P.O. Box 55 (A. I. Virtasen aukio 1), FI-00014 Helsinki,
Finland
| | - Jonathon P. Misiewicz
- Center for Computational Quantum Chemistry,
University of Georgia, Athens, Georgia 30602, USA
| | - Maximilian Scheurer
- Interdisciplinary Center for Scientific
Computing, Heidelberg University, D-69120 Heidelberg,
Germany
| | - Robert A. Shaw
- ARC Centre of Excellence in Exciton Science,
School of Science, RMIT University, Melbourne, VIC 3000,
Australia
| | - Jeffrey B. Schriber
- Center for Computational Molecular Science and
Technology, School of Chemistry and Biochemistry, School of Computational Science and
Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400,
USA
| | - Yi Xie
- Center for Computational Molecular Science and
Technology, School of Chemistry and Biochemistry, School of Computational Science and
Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400,
USA
| | - Zachary L. Glick
- Center for Computational Molecular Science and
Technology, School of Chemistry and Biochemistry, School of Computational Science and
Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400,
USA
| | - Dominic A. Sirianni
- Center for Computational Molecular Science and
Technology, School of Chemistry and Biochemistry, School of Computational Science and
Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400,
USA
| | - Joseph Senan O’Brien
- Center for Computational Molecular Science and
Technology, School of Chemistry and Biochemistry, School of Computational Science and
Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400,
USA
| | - Jonathan M. Waldrop
- Department of Chemistry and Biochemistry, Auburn
University, Auburn, Alabama 36849, USA
| | - Ashutosh Kumar
- Department of Chemistry, Virginia
Tech, Blacksburg, Virginia 24061, USA
| | - Edward G. Hohenstein
- SLAC National Accelerator Laboratory, Stanford
PULSE Institute, Menlo Park, California 94025,
USA
| | | | - Bernard R. Brooks
- National Institutes of Health – National Heart,
Lung and Blood Institute, Laboratory of Computational Biology, Bethesda,
Maryland 20892, USA
| | - Henry F. Schaefer
- Center for Computational Quantum Chemistry,
University of Georgia, Athens, Georgia 30602, USA
| | - Alexander Yu. Sokolov
- Department of Chemistry and Biochemistry, The
Ohio State University, Columbus, Ohio 43210, USA
| | - Konrad Patkowski
- Department of Chemistry and Biochemistry, Auburn
University, Auburn, Alabama 36849, USA
| | - A. Eugene DePrince
- Department of Chemistry and Biochemistry,
Florida State University, Tallahassee, Florida 32306-4390,
USA
| | - Uğur Bozkaya
- Department of Chemistry, Hacettepe
University, Ankara 06800, Turkey
| | - Rollin A. King
- Department of Chemistry, Bethel
University, St. Paul, Minnesota 55112, USA
| | | | - Justin M. Turney
- Center for Computational Quantum Chemistry,
University of Georgia, Athens, Georgia 30602, USA
| | | | - C. David Sherrill
- Center for Computational Molecular Science and
Technology, School of Chemistry and Biochemistry, School of Computational Science and
Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400,
USA
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18
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Hohenstein EG, Zhao Y, Parrish RM, Martínez TJ. Rank reduced coupled cluster theory. II. Equation-of-motion coupled-cluster singles and doubles. J Chem Phys 2019; 151:164121. [DOI: 10.1063/1.5121867] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Edward G. Hohenstein
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
- Department of Chemistry and Biochemistry, The City College of New York, New York, New York 10031, USA
- Ph.D. Program in Chemistry, The Graduate Center, City University of New York, New York, New York 10016, USA
| | - Yao Zhao
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
- Department of Chemistry and Biochemistry, The City College of New York, New York, New York 10031, USA
- Ph.D. Program in Chemistry, The Graduate Center, City University of New York, New York, New York 10016, USA
| | - Robert M. Parrish
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
- QCWare Corporation, Palo Alto, California 94301, USA
| | - Todd J. Martínez
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
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19
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Zhang X, Wilson JH, Lawson AJ, Hohenstein EG, Jans U. Stereoisomer specific reaction of hexabromocyclododecane with reduced sulfur species in aqueous solutions. Chemosphere 2019; 226:238-245. [PMID: 30928716 DOI: 10.1016/j.chemosphere.2019.03.134] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 03/14/2019] [Accepted: 03/19/2019] [Indexed: 06/09/2023]
Abstract
The individual degradation rates of the three dominant stereoisomers (α, β, γ) of hexabromocyclododecane (HBCDD) with bisulfide and polysulfides were investigated at pH 9 in methanol/water solutions at two different temperatures (25 °C and 40 °C). Under all conditions investigated, α-HBCDD reacts 10 to 20 times slower with bisulfide than β-HBCDD and γ-HBCDD. The difference in reactivity of HBCDD isomers can be explained by the different populations of stable conformers with large dihedral angle between the vicinal bromine atoms. It was also observed that the reaction of HBCDD with polysulfides is about six times faster than with bisulfide. The experiments performed in solvent mixtures with increased water content at 40 °C indicated that the reaction of HBCDD with bisulfide is faster with higher percentage of water. The much slower abiotic reaction of α-HBCDD compared to β-HBCDD and γ-HBCDD could potentially contribute to the fact that α-HBCDD is more persistent in the environment than γ-HBCDD. Only one isomer of tetrabromocyclododecene (TBCDe-5) was identified as a degradation product of the reaction of HBCDD with reduced sulfur species. TBCDe-5 itself reacts about ten times slower with bisulfide and twenty times slower with polysulfide than HBCDD. The study demonstrates that polysulfides and bisulfides can reduce HBCDD sufficiently in natural anoxic environments and the dominant pathway for the degradation of HBCDD by reduced sulfur species is very likely to be the reductive debromination of vicinal dibromides via concerted anti-elimination.
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Affiliation(s)
- Xianmiao Zhang
- Chemistry Program, The Graduate Center of the City University of New York, New York, NY, 10016, United States
| | - John H Wilson
- Department of Chemistry and Biochemistry, The City College of New York, CUNY, New York, NY, 10031, United States
| | - Ariel J Lawson
- Department of Chemistry and Biochemistry, The City College of New York, CUNY, New York, NY, 10031, United States
| | - Edward G Hohenstein
- Chemistry Program, The Graduate Center of the City University of New York, New York, NY, 10016, United States; Department of Chemistry and Biochemistry, The City College of New York, CUNY, New York, NY, 10031, United States
| | - Urs Jans
- Chemistry Program, The Graduate Center of the City University of New York, New York, NY, 10016, United States; Department of Chemistry and Biochemistry, The City College of New York, CUNY, New York, NY, 10031, United States.
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20
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Parrish RM, Hohenstein EG, McMahon PL, Martínez TJ. Quantum Computation of Electronic Transitions Using a Variational Quantum Eigensolver. Phys Rev Lett 2019; 122:230401. [PMID: 31298869 DOI: 10.1103/physrevlett.122.230401] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 04/10/2019] [Indexed: 06/10/2023]
Abstract
We develop an extension of the variational quantum eigensolver (VQE) algorithm-multistate contracted VQE (MC-VQE)-that allows for the efficient computation of the transition energies between the ground state and several low-lying excited states of a molecule, as well as the oscillator strengths associated with these transitions. We numerically simulate MC-VQE by computing the absorption spectrum of an ab initio exciton model of an 18-chromophore light-harvesting complex from purple photosynthetic bacteria.
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Affiliation(s)
- Robert M Parrish
- Department of Chemistry and the PULSE Institute, Stanford University, Stanford, California, 94305, USA
- SLAC National Accelerator Laboratory, Menlo Park, California, 94025, USA
- QC Ware Corporation, Palo Alto, California 94301, USA
| | - Edward G Hohenstein
- Department of Chemistry and the PULSE Institute, Stanford University, Stanford, California, 94305, USA
- SLAC National Accelerator Laboratory, Menlo Park, California, 94025, USA
| | - Peter L McMahon
- QC Ware Corporation, Palo Alto, California 94301, USA
- E. L. Ginzton Laboratory, Stanford University, Stanford, California, 94305, USA
| | - Todd J Martínez
- Department of Chemistry and the PULSE Institute, Stanford University, Stanford, California, 94305, USA
- SLAC National Accelerator Laboratory, Menlo Park, California, 94025, USA
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21
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Parrish RM, Zhao Y, Hohenstein EG, Martínez TJ. Rank reduced coupled cluster theory. I. Ground state energies and wavefunctions. J Chem Phys 2019; 150:164118. [DOI: 10.1063/1.5092505] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Robert M. Parrish
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Yao Zhao
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
- Department of Chemistry and Biochemistry, The City College of New York, New York, New York 10031, USA
- Ph.D. Program in Chemistry, The Graduate Center, City University of New York, New York, New York 10016, USA
| | - Edward G. Hohenstein
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
- Department of Chemistry and Biochemistry, The City College of New York, New York, New York 10031, USA
- Ph.D. Program in Chemistry, The Graduate Center, City University of New York, New York, New York 10016, USA
| | - Todd J. Martínez
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
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22
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Snyder JW, Fales BS, Hohenstein EG, Levine BG, Martínez TJ. A direct-compatible formulation of the coupled perturbed complete active space self-consistent field equations on graphical processing units. J Chem Phys 2018; 146:174113. [PMID: 28477593 DOI: 10.1063/1.4979844] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We recently developed an algorithm to compute response properties for the state-averaged complete active space self-consistent field method (SA-CASSCF) that capitalized on sparsity in the atomic orbital basis. Our original algorithm was limited to treating small to moderate sized active spaces, but the recent development of graphical processing unit (GPU) based direct-configuration interaction algorithms provides an opportunity to extend this to large active spaces. We present here a direct-compatible version of the coupled perturbed equations, enabling us to compute response properties for systems treated with arbitrary active spaces (subject to available memory and computation time). This work demonstrates that the computationally demanding portions of the SA-CASSCF method can be formulated in terms of seven fundamental operations, including Coulomb and exchange matrix builds and their derivatives, as well as, generalized one- and two-particle density matrix and σ vector constructions. As in our previous work, this algorithm exhibits low computational scaling and is accelerated by the use of GPUs, making possible optimizations and nonadiabatic dynamics on systems with O(1000) basis functions and O(100) atoms, respectively.
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Affiliation(s)
- James W Snyder
- Department of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, USA
| | - B Scott Fales
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
| | - Edward G Hohenstein
- Department of Chemistry and Biochemistry, The City College of New York, New York, New York 10031, USA
| | - Benjamin G Levine
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
| | - Todd J Martínez
- Department of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, USA
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23
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Pijeau S, Foster D, Hohenstein EG. Effect of Nonplanarity on Excited-State Proton Transfer and Internal Conversion in Salicylideneaniline. J Phys Chem A 2018; 122:5555-5562. [DOI: 10.1021/acs.jpca.8b02426] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Shiela Pijeau
- Department of Chemistry and Biochemistry, The City College of New York, New York, New York 10031, United States
| | - Donneille Foster
- Department of Chemistry and Biochemistry, The City College of New York, New York, New York 10031, United States
| | - Edward G. Hohenstein
- Department of Chemistry and Biochemistry, The City College of New York, New York, New York 10031, United States
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
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24
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Hollas D, Šištík L, Hohenstein EG, Martínez TJ, Slavíček P. Nonadiabatic Ab Initio Molecular Dynamics with the Floating Occupation Molecular Orbital-Complete Active Space Configuration Interaction Method. J Chem Theory Comput 2017; 14:339-350. [DOI: 10.1021/acs.jctc.7b00958] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Daniel Hollas
- Department
of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, 16628 Prague 6, Czech Republic
| | - Lukáš Šištík
- Department
of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, 16628 Prague 6, Czech Republic
| | - Edward G. Hohenstein
- Department
of Chemistry and Biochemistry, The City College of New York, New York, New York 10031, United States
- PhD
Program in Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
| | - Todd J. Martínez
- Department
of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Petr Slavíček
- Department
of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, 16628 Prague 6, Czech Republic
- J. Heyrovský Institute of Physical Chemistry, Dolejškova 3, 18223 Prague 8, Czech Republic
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25
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Fales BS, Shu Y, Levine BG, Hohenstein EG. Complete active space configuration interaction from state-averaged configuration interaction singles natural orbitals: Analytic first derivatives and derivative coupling vectors. J Chem Phys 2017; 147:094104. [DOI: 10.1063/1.5000476] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- B. Scott Fales
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
| | - Yinan Shu
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Benjamin G. Levine
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
| | - Edward G. Hohenstein
- Department of Chemistry and Biochemistry, City College of New York, New York, New York 10031, USA
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, USA
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26
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Pijeau S, Foster D, Hohenstein EG. Excited-State Dynamics of a Benzotriazole Photostabilizer: 2-(2′-Hydroxy-5′-methylphenyl)benzotriazole. J Phys Chem A 2017; 121:6377-6387. [DOI: 10.1021/acs.jpca.7b04504] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Shiela Pijeau
- Department
of Chemistry and Biochemistry, The City College of New York, New York, New York 10031, United States
| | - Donneille Foster
- Department
of Chemistry and Biochemistry, The City College of New York, New York, New York 10031, United States
| | - Edward G. Hohenstein
- Department
of Chemistry and Biochemistry, The City College of New York, New York, New York 10031, United States
- Ph.D.
Program in Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
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27
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Parrish RM, Burns LA, Smith DGA, Simmonett AC, DePrince AE, Hohenstein EG, Bozkaya U, Sokolov AY, Di Remigio R, Richard RM, Gonthier JF, James AM, McAlexander HR, Kumar A, Saitow M, Wang X, Pritchard BP, Verma P, Schaefer HF, Patkowski K, King RA, Valeev EF, Evangelista FA, Turney JM, Crawford TD, Sherrill CD. Psi4 1.1: An Open-Source Electronic Structure Program Emphasizing Automation, Advanced Libraries, and Interoperability. J Chem Theory Comput 2017; 13:3185-3197. [PMID: 28489372 PMCID: PMC7495355 DOI: 10.1021/acs.jctc.7b00174] [Citation(s) in RCA: 742] [Impact Index Per Article: 106.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Psi4 is an ab initio electronic structure program providing methods such as Hartree-Fock, density functional theory, configuration interaction, and coupled-cluster theory. The 1.1 release represents a major update meant to automate complex tasks, such as geometry optimization using complete-basis-set extrapolation or focal-point methods. Conversion of the top-level code to a Python module means that Psi4 can now be used in complex workflows alongside other Python tools. Several new features have been added with the aid of libraries providing easy access to techniques such as density fitting, Cholesky decomposition, and Laplace denominators. The build system has been completely rewritten to simplify interoperability with independent, reusable software components for quantum chemistry. Finally, a wide range of new theoretical methods and analyses have been added to the code base, including functional-group and open-shell symmetry adapted perturbation theory, density-fitted coupled cluster with frozen natural orbitals, orbital-optimized perturbation and coupled-cluster methods (e.g., OO-MP2 and OO-LCCD), density-fitted multiconfigurational self-consistent field, density cumulant functional theory, algebraic-diagrammatic construction excited states, improvements to the geometry optimizer, and the "X2C" approach to relativistic corrections, among many other improvements.
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Affiliation(s)
- Robert M Parrish
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
| | - Lori A Burns
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
| | - Daniel G A Smith
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
| | - Andrew C Simmonett
- National Institutes of Health , National Heart, Lung and Blood Institute, Laboratory of Computational Biology, 5635 Fishers Lane, T-900 Suite, Rockville, Maryland 20852, United States
| | - A Eugene DePrince
- Department of Chemistry and Biochemistry, Florida State University , Tallahassee, Florida 32306-4390, United States
| | - Edward G Hohenstein
- Department of Chemistry and Biochemistry, The City College of New York , New York, New York 10031, United States
| | - Uğur Bozkaya
- Department of Chemistry, Hacettepe University , Ankara 06800, Turkey
| | - Alexander Yu Sokolov
- Division of Chemistry and Chemical Engineering, California Institute of Technology , Pasadena, California 91125, United States
| | - Roberto Di Remigio
- Department of Chemistry, Centre for Theoretical and Computational Chemistry, UiT, The Arctic University of Norway , N-9037 Tromsø, Norway
| | - Ryan M Richard
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
| | - Jérôme F Gonthier
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
| | - Andrew M James
- Department of Chemistry, Virginia Tech , Blacksburg, Virginia 24061, United States
| | - Harley R McAlexander
- Department of Chemistry, Virginia Tech , Blacksburg, Virginia 24061, United States
| | - Ashutosh Kumar
- Department of Chemistry, Virginia Tech , Blacksburg, Virginia 24061, United States
| | - Masaaki Saitow
- Department of Chemistry and Research Center for Smart Molecules, Rikkyo University , 3-34-1 Nishi-ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Xiao Wang
- Department of Chemistry, Virginia Tech , Blacksburg, Virginia 24061, United States
| | - Benjamin P Pritchard
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
| | - Prakash Verma
- Department of Chemistry, Emory University , Atlanta, Georgia 30322, United States
| | - Henry F Schaefer
- Center for Computational Quantum Chemistry, University of Georgia , Athens, Georgia 30602, United States
| | - Konrad Patkowski
- Department of Chemistry and Biochemistry, Auburn University , Auburn, Alabama 36849, United States
| | - Rollin A King
- Department of Chemistry, Bethel University , St. Paul, Minnesota 55112, United States
| | - Edward F Valeev
- Department of Chemistry, Virginia Tech , Blacksburg, Virginia 24061, United States
| | | | - Justin M Turney
- Center for Computational Quantum Chemistry, University of Georgia , Athens, Georgia 30602, United States
| | - T Daniel Crawford
- Department of Chemistry, Virginia Tech , Blacksburg, Virginia 24061, United States
| | - C David Sherrill
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
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28
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Pijeau S, Foster D, Hohenstein EG. Excited-State Dynamics of 2-(2′-Hydroxyphenyl)benzothiazole: Ultrafast Proton Transfer and Internal Conversion. J Phys Chem A 2017; 121:4595-4605. [DOI: 10.1021/acs.jpca.7b01215] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Shiela Pijeau
- Department
of Chemistry and Biochemistry, The City College of New York, New York, New York 10031, United States
| | - Donneille Foster
- Department
of Chemistry and Biochemistry, The City College of New York, New York, New York 10031, United States
| | - Edward G. Hohenstein
- Department
of Chemistry and Biochemistry, The City College of New York, New York, New York 10031, United States
- Ph.D.
Program in Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
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29
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Pijeau S, Hohenstein EG. Improved Complete Active Space Configuration Interaction Energies with a Simple Correction from Density Functional Theory. J Chem Theory Comput 2017; 13:1130-1146. [DOI: 10.1021/acs.jctc.6b00893] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Shiela Pijeau
- Department
of Chemistry and Biochemistry, The City College of New York, New York, New York 10031, United States
| | - Edward G. Hohenstein
- Department
of Chemistry and Biochemistry, The City College of New York, New York, New York 10031, United States
- Ph.D.
Program in Chemistry, The City University of New York, New York, New York 10016, United States
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30
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Sisto A, Stross C, van der Kamp MW, O’Connor M, McIntosh-Smith S, Johnson GT, Hohenstein EG, Manby FR, Glowacki DR, Martinez TJ. Atomistic non-adiabatic dynamics of the LH2 complex with a GPU-accelerated ab initio exciton model. Phys Chem Chem Phys 2017; 19:14924-14936. [DOI: 10.1039/c7cp00492c] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We present GPU-accelerated ab initio molecular dynamics simulations of nonadiabatic dynamics in the LH2 complex in full atomistic detail.
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Affiliation(s)
- Aaron Sisto
- PULSE Institute and Department of Chemistry
- Stanford University
- Stanford
- USA
- SLAC National Accelerator Laboratory
| | - Clem Stross
- School of Chemistry
- University of Bristol
- Bristol
- UK
| | | | - Michael O’Connor
- School of Chemistry
- University of Bristol
- Bristol
- UK
- Department of Computer Science
| | | | - Graham T. Johnson
- California Institute for Quantitative Biosciences (QB3)
- University of California
- San Francisco
- USA
- Department of Bioengineering and Therapeutic Sciences
| | | | | | - David R. Glowacki
- School of Chemistry
- University of Bristol
- Bristol
- UK
- Department of Computer Science
| | - Todd J. Martinez
- PULSE Institute and Department of Chemistry
- Stanford University
- Stanford
- USA
- SLAC National Accelerator Laboratory
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31
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Hohenstein EG. Analytic formulation of derivative coupling vectors for complete active space configuration interaction wavefunctions with floating occupation molecular orbitals. J Chem Phys 2016; 145:174110. [DOI: 10.1063/1.4966235] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Edward G. Hohenstein
- Department of Chemistry and Biochemistry, The City College of New York, New York, New York 10031, USA and Ph.D. Program in Chemistry, The City University of New York, New York, New York 10016, USA
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32
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Parrish RM, Hohenstein EG, Martínez TJ. Comment on “Positive semidefinite tensor factorizations of the two-electron integral matrix for low-scaling ab initioelectronic structure” [J. Chem. Phys. 143, 064103 (2015)]. J Chem Phys 2016; 145:027101. [DOI: 10.1063/1.4955316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Robert M. Parrish
- Department of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, USA
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Edward G. Hohenstein
- Department of Chemistry and Biochemistry, City College of New York, New York, New York 10031, USA
| | - Todd J. Martínez
- Department of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, USA
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
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33
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Affiliation(s)
- Robert M. Parrish
- Department
of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Edward G. Hohenstein
- Department
of Chemistry and Biochemistry, The City College of New York, New York, New York 10031, United States
- Ph.D.
Program in Chemistry, The Graduate Center, City University of New York, New
York, New York 10016, United States
| | - Todd J. Martínez
- Department
of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
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34
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Hohenstein EG, Green MA, Kariev A, Naganathan S, Manning Cleveland M, Haines TH. “Anionic H-Bonds” Structure Two Simple Bilayers, One Natural. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.3100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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35
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Affiliation(s)
- Edward G. Hohenstein
- Department
of Chemistry and Biochemistry, The City College of New York, New York, New York 10031, United States
- Ph.D.
Program in Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
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36
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Carson BE, Parker TM, Hohenstein EG, Brizius GL, Komorner W, King RA, Collard DM, Sherrill CD. Competition Between π-π and C-H/π Interactions: A Comparison of the Structural and Electronic Properties of Alkoxy-Substituted 1,8-Bis((propyloxyphenyl)ethynyl)naphthalenes. Chemistry 2015; 21:19168-75. [PMID: 26568396 DOI: 10.1002/chem.201502363] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Indexed: 11/11/2022]
Abstract
The structural and electronic consequences of π-π and C-H/π interactions in two alkoxy-substituted 1,8-bis- ((propyloxyphenyl)ethynyl)naphthalenes are explored by using X-ray crystallography and electronic structure computations. The crystal structure of analogue 4, bearing an alkoxy side chain in the 4-position of each of the phenyl rings, adopts a π-stacked geometry, whereas analogue 8, bearing alkoxy groups at both the 2- and the 5-positions of each ring, has a geometry in which the rings are splayed away from a π-stacked arrangement. Symmetry-adapted perturbation theory analysis was performed on the two analogues to evaluate the interactions between the phenylethynyl arms in each molecule in terms of electrostatic, steric, polarization, and London dispersion components. The computations support the expectation that the π-stacked geometry of the alkoxyphenyl units in 4 is simply a consequence of maximizing π-π interactions. However, the splayed geometry of 8 results from a more subtle competition between different noncovalent interactions: this geometry provides a favorable anti-alignment of C-O bond dipoles, and two C-H/π interactions in which hydrogen atoms of the alkyl side chains interact favorably with the π electrons of the other phenyl ring. These favorable interactions overcome competing π-π interactions to give rise to a geometry in which the phenylethynyl substituents are in an offset, unstacked arrangement.
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Affiliation(s)
- Bradley E Carson
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Dr., Atlanta, GA 30332-0400 (USA), Fax: (+1) 404-894-7452
| | - Trent M Parker
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Dr., Atlanta, GA 30332-0400 (USA), Fax: (+1) 404-894-7452.,Center for Computational Molecular Science and Technology, Georgia Institute of Technology, 901 Atlantic Dr., Atlanta, GA 30332-0400 (USA)
| | - Edward G Hohenstein
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Dr., Atlanta, GA 30332-0400 (USA), Fax: (+1) 404-894-7452.,Center for Computational Molecular Science and Technology, Georgia Institute of Technology, 901 Atlantic Dr., Atlanta, GA 30332-0400 (USA)
| | - Glen L Brizius
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Dr., Atlanta, GA 30332-0400 (USA), Fax: (+1) 404-894-7452
| | - Whitney Komorner
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Dr., Atlanta, GA 30332-0400 (USA), Fax: (+1) 404-894-7452
| | - Rollin A King
- Department of Chemistry, Bethel University, St. Paul, MN 55112 (USA)
| | - David M Collard
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Dr., Atlanta, GA 30332-0400 (USA), Fax: (+1) 404-894-7452.
| | - C David Sherrill
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Dr., Atlanta, GA 30332-0400 (USA), Fax: (+1) 404-894-7452. .,Center for Computational Molecular Science and Technology, Georgia Institute of Technology, 901 Atlantic Dr., Atlanta, GA 30332-0400 (USA). .,School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, GA 30332 (USA).
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37
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Snyder JW, Hohenstein EG, Luehr N, Martínez TJ. An atomic orbital-based formulation of analytical gradients and nonadiabatic coupling vector elements for the state-averaged complete active space self-consistent field method on graphical processing units. J Chem Phys 2015; 143:154107. [DOI: 10.1063/1.4932613] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- James W. Snyder
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Edward G. Hohenstein
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Nathan Luehr
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Todd J. Martínez
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
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38
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Hohenstein EG, Bouduban MEF, Song C, Luehr N, Ufimtsev IS, Martínez TJ. Analytic first derivatives of floating occupation molecular orbital-complete active space configuration interaction on graphical processing units. J Chem Phys 2015; 143:014111. [DOI: 10.1063/1.4923259] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Edward G. Hohenstein
- Department of Chemistry and the PULSE Institute,
Stanford University, Stanford, California 94305,
USA
- SLAC National Accelerator Laboratory, Menlo Park, California 94025,
USA
| | - Marine E. F. Bouduban
- Department of Chemistry and the PULSE Institute,
Stanford University, Stanford, California 94305,
USA
- SLAC National Accelerator Laboratory, Menlo Park, California 94025,
USA
- Group for Photochemical Dynamics, Institute of Chemical
Sciences and Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Chenchen Song
- Department of Chemistry and the PULSE Institute,
Stanford University, Stanford, California 94305,
USA
- SLAC National Accelerator Laboratory, Menlo Park, California 94025,
USA
| | - Nathan Luehr
- Department of Chemistry and the PULSE Institute,
Stanford University, Stanford, California 94305,
USA
- SLAC National Accelerator Laboratory, Menlo Park, California 94025,
USA
| | - Ivan S. Ufimtsev
- Department of Chemistry and the PULSE Institute,
Stanford University, Stanford, California 94305,
USA
- SLAC National Accelerator Laboratory, Menlo Park, California 94025,
USA
| | - Todd J. Martínez
- Department of Chemistry and the PULSE Institute,
Stanford University, Stanford, California 94305,
USA
- SLAC National Accelerator Laboratory, Menlo Park, California 94025,
USA
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39
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Kokkila Schumacher SIL, Hohenstein EG, Parrish RM, Wang LP, Martínez TJ. Tensor Hypercontraction Second-Order Møller–Plesset Perturbation Theory: Grid Optimization and Reaction Energies. J Chem Theory Comput 2015; 11:3042-52. [DOI: 10.1021/acs.jctc.5b00272] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sara I. L. Kokkila Schumacher
- Department
of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Edward G. Hohenstein
- Department
of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
- Department
of Chemistry and Biochemistry, City College of New York, New York, New York 10031, United States
| | - Robert M. Parrish
- Center
for Computational Molecular Science and Technology, School of Chemistry
and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Lee-Ping Wang
- Department
of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Todd J. Martínez
- Department
of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
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40
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Hohenstein EG, Luehr N, Ufimtsev IS, Martínez TJ. An atomic orbital-based formulation of the complete active space self-consistent field method on graphical processing units. J Chem Phys 2015; 142:224103. [DOI: 10.1063/1.4921956] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Edward G. Hohenstein
- Department of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, USA
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Nathan Luehr
- Department of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, USA
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Ivan S. Ufimtsev
- Department of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, USA
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Todd J. Martínez
- Department of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, USA
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
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41
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Sigala PA, Ruben EA, Liu CW, Piccoli PMB, Hohenstein EG, Martínez TJ, Schultz AJ, Herschlag D. Determination of Hydrogen Bond Structure in Water versus Aprotic Environments To Test the Relationship Between Length and Stability. J Am Chem Soc 2015; 137:5730-40. [PMID: 25871450 DOI: 10.1021/ja512980h] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Hydrogen bonds profoundly influence the architecture and activity of biological macromolecules. Deep appreciation of hydrogen bond contributions to biomolecular function thus requires a detailed understanding of hydrogen bond structure and energetics and the relationship between these properties. Hydrogen bond formation energies (ΔGf) are enormously more favorable in aprotic solvents than in water, and two classes of contributing factors have been proposed to explain this energetic difference, focusing respectively on the isolated and hydrogen-bonded species: (I) water stabilizes the dissociated donor and acceptor groups much better than aprotic solvents, thereby reducing the driving force for hydrogen bond formation; and (II) water lengthens hydrogen bonds compared to aprotic environments, thereby decreasing the potential energy within the hydrogen bond. Each model has been proposed to provide a dominant contribution to ΔGf, but incisive tests that distinguish the importance of these contributions are lacking. Here we directly test the structural basis of model II. Neutron crystallography, NMR spectroscopy, and quantum mechanical calculations demonstrate that O-H···O hydrogen bonds in crystals, chloroform, acetone, and water have nearly identical lengths and very similar potential energy surfaces despite ΔGf differences >8 kcal/mol across these solvents. These results rule out a substantial contribution from solvent-dependent differences in hydrogen bond structure and potential energy after association (model II) and thus support the conclusion that differences in hydrogen bond ΔGf are predominantly determined by solvent interactions with the dissociated groups (model I). These findings advance our understanding of universal hydrogen-bonding interactions and have important implications for biology and engineering.
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Affiliation(s)
| | | | | | - Paula M B Piccoli
- §Intense Pulsed Neutron Source, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | | | | | - Arthur J Schultz
- §Intense Pulsed Neutron Source, Argonne National Laboratory, Argonne, Illinois 60439, United States
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42
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Shu Y, Hohenstein EG, Levine BG. Configuration interaction singles natural orbitals: An orbital basis for an efficient and size intensive multireference description of electronic excited states. J Chem Phys 2015; 142:024102. [DOI: 10.1063/1.4905124] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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43
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Flick JC, Kosenkov D, Hohenstein EG, Sherrill CD, Slipchenko LV. Erratum: Accurate Prediction of Noncovalent Interaction Energies with the Effective Fragment Potential Method: Comparison of Energy Components to Symmetry-Adapted Perturbation Theory for the S22 Test Set. J Chem Theory Comput 2014; 10:4759-60. [PMID: 26588163 DOI: 10.1021/ct500658b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Shao Y, Gan Z, Epifanovsky E, Gilbert AT, Wormit M, Kussmann J, Lange AW, Behn A, Deng J, Feng X, Ghosh D, Goldey M, Horn PR, Jacobson LD, Kaliman I, Khaliullin RZ, Kuś T, Landau A, Liu J, Proynov EI, Rhee YM, Richard RM, Rohrdanz MA, Steele RP, Sundstrom EJ, Woodcock HL, Zimmerman PM, Zuev D, Albrecht B, Alguire E, Austin B, Beran GJO, Bernard YA, Berquist E, Brandhorst K, Bravaya KB, Brown ST, Casanova D, Chang CM, Chen Y, Chien SH, Closser KD, Crittenden DL, Diedenhofen M, DiStasio RA, Do H, Dutoi AD, Edgar RG, Fatehi S, Fusti-Molnar L, Ghysels A, Golubeva-Zadorozhnaya A, Gomes J, Hanson-Heine MW, Harbach PH, Hauser AW, Hohenstein EG, Holden ZC, Jagau TC, Ji H, Kaduk B, Khistyaev K, Kim J, Kim J, King RA, Klunzinger P, Kosenkov D, Kowalczyk T, Krauter CM, Lao KU, Laurent AD, Lawler KV, Levchenko SV, Lin CY, Liu F, Livshits E, Lochan RC, Luenser A, Manohar P, Manzer SF, Mao SP, Mardirossian N, Marenich AV, Maurer SA, Mayhall NJ, Neuscamman E, Oana CM, Olivares-Amaya R, O’Neill DP, Parkhill JA, Perrine TM, Peverati R, Prociuk A, Rehn DR, Rosta E, Russ NJ, Sharada SM, Sharma S, Small DW, Sodt A, Stein T, Stück D, Su YC, Thom AJ, Tsuchimochi T, Vanovschi V, Vogt L, Vydrov O, Wang T, Watson MA, Wenzel J, White A, Williams CF, Yang J, Yeganeh S, Yost SR, You ZQ, Zhang IY, Zhang X, Zhao Y, Brooks BR, Chan GK, Chipman DM, Cramer CJ, Goddard WA, Gordon MS, Hehre WJ, Klamt A, Schaefer HF, Schmidt MW, Sherrill CD, Truhlar DG, Warshel A, Xu X, Aspuru-Guzik A, Baer R, Bell AT, Besley NA, Chai JD, Dreuw A, Dunietz BD, Furlani TR, Gwaltney SR, Hsu CP, Jung Y, Kong J, Lambrecht DS, Liang W, Ochsenfeld C, Rassolov VA, Slipchenko LV, Subotnik JE, Van Voorhis T, Herbert JM, Krylov AI, Gill PM, Head-Gordon M. Advances in molecular quantum chemistry contained in the Q-Chem 4 program package. Mol Phys 2014. [DOI: 10.1080/00268976.2014.952696] [Citation(s) in RCA: 1769] [Impact Index Per Article: 176.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Parrish RM, Hohenstein EG, Sherrill CD. Tractability gains in symmetry-adapted perturbation theory including coupled double excitations: CCD+ST(CCD) dispersion with natural orbital truncations. J Chem Phys 2014; 139:174102. [PMID: 24206282 DOI: 10.1063/1.4826520] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
This work focuses on efficient and accurate treatment of the intermolecular dispersion interaction using the CCD+ST(CCD) dispersion approach formulated by Williams et al. [J. Chem. Phys. 103, 4586 (1995)]. We apply natural orbital truncation techniques to the solution of the monomer coupled-cluster double (CCD) equations, yielding substantial accelerations in this computationally demanding portion of the SAPT2+(CCD), SAPT2+(3)(CCD), and SAPT2+3(CCD) analyses. It is shown that the wholly rate-limiting dimer-basis particle-particle ladder term can be computed in a reduced natural virtual space which is essentially the same size as the monomer-basis virtual space, with an error on the order of a few thousandths of 1 kcal mol(-1). Coupled with our existing natural orbital techniques for the perturbative triple excitation contributions [E. G. Hohenstein and C. D. Sherrill, J. Chem. Phys. 133, 104107 (2010)], this technique provides speedups of greater than an order of magnitude for the evaluation of the complete SAPT2+3(CCD) decomposition, with a total error of a few hundredths of 1 kcal mol(-1). The combined approach yields tractability gains of almost 2× in the system size, allowing for SAPT2+3(CCD)/aug-cc-pVTZ analysis to be performed for systems such as adenine-thymine for the first time. Natural orbital based SAPT2+3(CCD)/aug-cc-pVTZ results are presented for stacked and hydrogen-bonded configurations of uracil dimer and the adenine-thymine dimer.
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Affiliation(s)
- Robert M Parrish
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
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Parrish RM, Sherrill CD, Hohenstein EG, Kokkila SIL, Martínez TJ. Communication: Acceleration of coupled cluster singles and doubles via orbital-weighted least-squares tensor hypercontraction. J Chem Phys 2014; 140:181102. [DOI: 10.1063/1.4876016] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Parrish RM, Hohenstein EG, Schunck NF, Sherrill CD, Martínez TJ. Exact tensor hypercontraction: a universal technique for the resolution of matrix elements of local finite-range N-body potentials in many-body quantum problems. Phys Rev Lett 2013; 111:132505. [PMID: 24116775 DOI: 10.1103/physrevlett.111.132505] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2013] [Revised: 05/17/2013] [Indexed: 06/02/2023]
Abstract
Configuration-space matrix elements of N-body potentials arise naturally and ubiquitously in the Ritz-Galerkin solution of many-body quantum problems. For the common specialization of local, finite-range potentials, we develop the exact tensor hypercontraction method, which provides a quantized renormalization of the coordinate-space form of the N-body potential, allowing for a highly separable tensor factorization of the configuration-space matrix elements. This representation allows for substantial computational savings in chemical, atomic, and nuclear physics simulations, particularly with respect to difficult "exchangelike" contractions.
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Affiliation(s)
- Robert M Parrish
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
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Hohenstein EG, Kokkila SIL, Parrish RM, Martínez TJ. Tensor Hypercontraction Equation-of-Motion Second-Order Approximate Coupled Cluster: Electronic Excitation Energies in O(N4) Time. J Phys Chem B 2013; 117:12972-8. [DOI: 10.1021/jp4021905] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Edward G. Hohenstein
- Department
of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Sara I. L. Kokkila
- Department
of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Robert M. Parrish
- Center
for Computational Molecular Science and Technology, School of Chemistry
and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Todd J. Martínez
- Department
of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
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Parrish RM, Hohenstein EG, Martínez TJ, Sherrill CD. Discrete variable representation in electronic structure theory: Quadrature grids for least-squares tensor hypercontraction. J Chem Phys 2013; 138:194107. [DOI: 10.1063/1.4802773] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Hohenstein EG, Kokkila SIL, Parrish RM, Martínez TJ. Quartic scaling second-order approximate coupled cluster singles and doubles via tensor hypercontraction: THC-CC2. J Chem Phys 2013; 138:124111. [DOI: 10.1063/1.4795514] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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