1
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Chen MS, Mao Y, Snider A, Gupta P, Montoya-Castillo A, Zuehlsdorff TJ, Isborn CM, Markland TE. Elucidating the Role of Hydrogen Bonding in the Optical Spectroscopy of the Solvated Green Fluorescent Protein Chromophore: Using Machine Learning to Establish the Importance of High-Level Electronic Structure. J Phys Chem Lett 2023; 14:6610-6619. [PMID: 37459252 DOI: 10.1021/acs.jpclett.3c01444] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
Hydrogen bonding interactions with chromophores in chemical and biological environments play a key role in determining their electronic absorption and relaxation processes, which are manifested in their linear and multidimensional optical spectra. For chromophores in the condensed phase, the large number of atoms needed to simulate the environment has traditionally prohibited the use of high-level excited-state electronic structure methods. By leveraging transfer learning, we show how to construct machine-learned models to accurately predict the high-level excitation energies of a chromophore in solution from only 400 high-level calculations. We show that when the electronic excitations of the green fluorescent protein chromophore in water are treated using EOM-CCSD embedded in a DFT description of the solvent the optical spectrum is correctly captured and that this improvement arises from correctly treating the coupling of the electronic transition to electric fields, which leads to a larger response upon hydrogen bonding between the chromophore and water.
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Affiliation(s)
- Michael S Chen
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Yuezhi Mao
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Andrew Snider
- Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Prachi Gupta
- Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Andrés Montoya-Castillo
- Department of Chemistry, University of Colorado, Boulder, Boulder, Colorado 80309, United States
| | - Tim J Zuehlsdorff
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, United States
| | - Christine M Isborn
- Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Thomas E Markland
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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2
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Ranka K, Isborn CM. Size-dependent errors in real-time electron density propagation. J Chem Phys 2023; 158:2887545. [PMID: 37125706 DOI: 10.1063/5.0142515] [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] [Received: 01/14/2023] [Accepted: 04/14/2023] [Indexed: 05/02/2023] Open
Abstract
Real-time (RT) electron density propagation with time-dependent density functional theory (TDDFT) or Hartree-Fock (TDHF) is one of the most popular methods to model the charge transfer in molecules and materials. However, both RT-TDHF and RT-TDDFT within the adiabatic approximation are known to produce inaccurate evolution of the electron density away from the ground state in model systems, leading to large errors in charge transfer and erroneous shifting of peaks in absorption spectra. Given the poor performance of these methods with small model systems and the widespread use of the methods with larger molecular and material systems, here we bridge the gap in our understanding of these methods and examine the size-dependence of errors in RT density propagation. We analyze the performance of RT density propagation for systems of increasing size during the application of a continuous resonant field to induce Rabi-like oscillations, during charge-transfer dynamics, and for peak shifting in simulated absorption spectra. We find that the errors in the electron dynamics are indeed size dependent for these phenomena, with the largest system producing the results most aligned with those expected from linear response theory. The results suggest that although the RT-TDHF and RT-TDDFT methods may produce severe errors for model systems, the errors in charge transfer and resonantly driven electron dynamics may be much less significant for more realistic, large-scale molecules and materials.
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Affiliation(s)
- Karnamohit Ranka
- Chemistry and Biochemistry, University of California Merced, Merced, California 95343, USA
| | - Christine M Isborn
- Chemistry and Biochemistry, University of California Merced, Merced, California 95343, USA
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3
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Han B, Isborn CM, Shi L. Incorporating Polarization and Charge Transfer into a Point-Charge Model for Water Using Machine Learning. J Phys Chem Lett 2023; 14:3869-3877. [PMID: 37067482 DOI: 10.1021/acs.jpclett.3c00036] [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: 06/19/2023]
Abstract
Rigid nonpolarizable water models with fixed point charges have been widely employed in molecular dynamics simulations due to their efficiency and reasonable accuracy for the potential energy surface. However, the dipole moment surface of water is not necessarily well-described by the same fixed charges, leading to failure in reproducing dipole-related properties. Here, we developed a machine-learning model trained against electronic structure data to assign point charges for water, and the resulting dipole moment surface significantly improved the predictions of the dielectric constant and the low-frequency IR spectrum of liquid water. Our analysis reveals that within our atom-centered point-charge description of the dipole moment surface, the intermolecular charge transfer is the major source of the peak intensity at 200 cm-1, whereas the intramolecular polarization controls the enhancement of the dielectric constant. The effects of exact Hartree-Fock exchange in the hybrid density functional on these properties are also discussed.
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Affiliation(s)
- Bowen Han
- Chemistry and Biochemistry, University of California, Merced, California 95343, United States
| | - Christine M Isborn
- Chemistry and Biochemistry, University of California, Merced, California 95343, United States
| | - Liang Shi
- Chemistry and Biochemistry, University of California, Merced, California 95343, United States
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4
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Abou Taka A, Lu SY, Gowland D, Zuehlsdorff TJ, Corzo HH, Pribram-Jones A, Shi L, Hratchian HP, Isborn CM. Comparison of Linear Response Theory, Projected Initial Maximum Overlap Method, and Molecular Dynamics-Based Vibronic Spectra: The Case of Methylene Blue. J Chem Theory Comput 2022; 18:3039-3051. [PMID: 35472264 DOI: 10.1021/acs.jctc.1c01127] [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: 11/28/2022]
Abstract
The simulation of optical spectra is essential to molecular characterization and, in many cases, critical for interpreting experimental spectra. The most common method for simulating vibronic absorption spectra relies on the geometry optimization and computation of normal modes for ground and excited electronic states. In this report, we show that the utilization of such a procedure within an adiabatic linear response (LR) theory framework may lead to state mixings and a breakdown of the Born-Oppenheimer approximation, resulting in a poor description of absorption spectra. In contrast, computing excited states via a self-consistent field method in conjunction with a maximum overlap model produces states that are not subject to such mixings. We show that this latter method produces vibronic spectra much more aligned with vertical gradient and molecular dynamics (MD) trajectory-based approaches. For the methylene blue chromophore, we compare vibronic absorption spectra computed with the following: an adiabatic Hessian approach with LR theory-optimized structures and normal modes, a vertical gradient procedure, the Hessian and normal modes of maximum overlap method-optimized structures, and excitation energy time-correlation functions generated from an MD trajectory. Because of mixing between the bright S1 and dark S2 surfaces near the S1 minimum, computing the adiabatic Hessian with LR theory and time-dependent density functional theory with the B3LYP density functional predicts a large vibronic shoulder for the absorption spectrum that is not present for any of the other methods. Spectral densities are analyzed and we compare the behavior of the key normal mode that in LR theory strongly couples to the optical excitation while showing S1/S2 state mixings. Overall, our study provides a note of caution in computing vibronic spectra using the excited-state adiabatic Hessian of LR theory-optimized structures and also showcases three alternatives that are less sensitive to adiabatic state mixing effects.
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Affiliation(s)
- Ali Abou Taka
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Shao-Yu Lu
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Duncan Gowland
- Department of Physics, King's College London, London WC2R 2LS, United Kingdom
| | - Tim J Zuehlsdorff
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, United States
| | - Hector H Corzo
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Aurora Pribram-Jones
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Liang Shi
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Hrant P Hratchian
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Christine M Isborn
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
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5
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Gupta P, Bhat HS, Ranka K, Isborn CM. Statistical Learning for Predicting Density‐Matrix Based Electron Dynamics. Stat (Int Stat Inst) 2021. [DOI: 10.1002/sta4.439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Prachi Gupta
- Chemistry and Biochemistry University of California Merced CA USA
- Applied Mathematics University of California Merced CA USA
| | - Harish S. Bhat
- Applied Mathematics University of California Merced CA USA
| | - Karnamohit Ranka
- Chemistry and Biochemistry University of California Merced CA USA
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6
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Lu SY, Zuehlsdorff TJ, Hong H, Aguirre VP, Isborn CM, Shi L. The Influence of Electronic Polarization on Nonlinear Optical Spectroscopy. J Phys Chem B 2021; 125:12214-12227. [PMID: 34726915 DOI: 10.1021/acs.jpcb.1c05914] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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
The environment surrounding a chromophore can dramatically affect the energy absorption and relaxation process, as manifested in optical spectra. Simulations of nonlinear optical spectroscopy, such as two-dimensional electronic spectroscopy (2DES) and transient absorption (TA), will be influenced by the computational model of the environment. We here compare a fixed point charge molecular mechanics model and a quantum mechanical (QM) model of the environment in computed 2DES and TA spectra of Nile red in water and the chromophore of photoactive yellow protein (PYP) in water and protein environments. In addition to simulating these nonlinear optical spectra, we directly juxtapose the computed excitation energy correlation function to the dynamic Stokes shift function often used to analyze environment dynamics. Overall, we find that for the three systems studied here the mutual electronic polarization provided by the QM environment manifests in broader 2DES signals, as well as a larger reorganization energy and a larger static Stokes shift due to stronger coupling between the chromophore and the environment.
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Affiliation(s)
- Shao-Yu Lu
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Tim J Zuehlsdorff
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, United States
| | - Hanbo Hong
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Vincent P Aguirre
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Christine M Isborn
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Liang Shi
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
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7
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Dunnett AJ, Gowland D, Isborn CM, Chin AW, Zuehlsdorff TJ. Influence of non-adiabatic effects on linear absorption spectra in the condensed phase: Methylene blue. J Chem Phys 2021; 155:144112. [PMID: 34654312 DOI: 10.1063/5.0062950] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Modeling linear absorption spectra of solvated chromophores is highly challenging as contributions are present both from coupling of the electronic states to nuclear vibrations and from solute-solvent interactions. In systems where excited states intersect in the Condon region, significant non-adiabatic contributions to absorption line shapes can also be observed. Here, we introduce a robust approach to model linear absorption spectra accounting for both environmental and non-adiabatic effects from first principles. This model parameterizes a linear vibronic coupling (LVC) Hamiltonian directly from energy gap fluctuations calculated along molecular dynamics (MD) trajectories of the chromophore in solution, accounting for both anharmonicity in the potential and direct solute-solvent interactions. The resulting system dynamics described by the LVC Hamiltonian are solved exactly using the thermalized time-evolving density operator with orthogonal polynomials algorithm (T-TEDOPA). The approach is applied to the linear absorption spectrum of methylene blue in water. We show that the strong shoulder in the experimental spectrum is caused by vibrationally driven population transfer between the bright S1 and the dark S2 states. The treatment of the solvent environment is one of many factors that strongly influence the population transfer and line shape; accurate modeling can only be achieved through the use of explicit quantum mechanical solvation. The efficiency of T-TEDOPA, combined with LVC Hamiltonian parameterizations from MD, leads to an attractive method for describing a large variety of systems in complex environments from first principles.
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Affiliation(s)
- Angus J Dunnett
- Sorbonne Université, CNRS, Institut des NanoSciences de Paris, 4 place Jussieu, 75005 Paris, France
| | - Duncan Gowland
- Department of Physics, King's College London, London WC2R 2LS, United Kingdom
| | - Christine M Isborn
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA
| | - Alex W Chin
- Sorbonne Université, CNRS, Institut des NanoSciences de Paris, 4 place Jussieu, 75005 Paris, France
| | - Tim J Zuehlsdorff
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
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8
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Zuehlsdorff TJ, Shedge SV, Lu SY, Hong H, Aguirre VP, Shi L, Isborn CM. Vibronic and Environmental Effects in Simulations of Optical Spectroscopy. Annu Rev Phys Chem 2021; 72:165-188. [DOI: 10.1146/annurev-physchem-090419-051350] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Including both environmental and vibronic effects is important for accurate simulation of optical spectra, but combining these effects remains computationally challenging. We outline two approaches that consider both the explicit atomistic environment and the vibronic transitions. Both phenomena are responsible for spectral shapes in linear spectroscopy and the electronic evolution measured in nonlinear spectroscopy. The first approach utilizes snapshots of chromophore-environment configurations for which chromophore normal modes are determined. We outline various approximations for this static approach that assumes harmonic potentials and ignores dynamic system-environment coupling. The second approach obtains excitation energies for a series of time-correlated snapshots. This dynamic approach relies on the accurate truncation of the cumulant expansion but treats the dynamics of the chromophore and the environment on equal footing. Both approaches show significant potential for making strides toward more accurate optical spectroscopy simulations of complex condensed phase systems.
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Affiliation(s)
- Tim J. Zuehlsdorff
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
| | - Sapana V. Shedge
- Department of Chemistry and Chemical Biology, University of California, Merced, California 95343, USA
| | - Shao-Yu Lu
- Department of Chemistry and Chemical Biology, University of California, Merced, California 95343, USA
| | - Hanbo Hong
- Department of Chemistry and Chemical Biology, University of California, Merced, California 95343, USA
| | - Vincent P. Aguirre
- Department of Chemistry and Chemical Biology, University of California, Merced, California 95343, USA
| | - Liang Shi
- Department of Chemistry and Chemical Biology, University of California, Merced, California 95343, USA
| | - Christine M. Isborn
- Department of Chemistry and Chemical Biology, University of California, Merced, California 95343, USA
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9
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Shedge SV, Zuehlsdorff TJ, Khanna A, Conley S, Isborn CM. Explicit environmental and vibronic effects in simulations of linear and nonlinear optical spectroscopy. J Chem Phys 2021; 154:084116. [PMID: 33639769 DOI: 10.1063/5.0038196] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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
Accurately simulating the linear and nonlinear electronic spectra of condensed phase systems and accounting for all physical phenomena contributing to spectral line shapes presents a significant challenge. Vibronic transitions can be captured through a harmonic model generated from the normal modes of a chromophore, but it is challenging to also include the effects of specific chromophore-environment interactions within such a model. We work to overcome this limitation by combining approaches to account for both explicit environment interactions and vibronic couplings for simulating both linear and nonlinear optical spectra. We present and show results for three approaches of varying computational cost for combining ensemble sampling of chromophore-environment configurations with Franck-Condon line shapes for simulating linear spectra. We present two analogous approaches for nonlinear spectra. Simulated absorption spectra and two-dimensional electronic spectra (2DES) are presented for the Nile red chromophore in different solvent environments. Employing an average Franck-Condon or 2DES line shape appears to be a promising method for simulating linear and nonlinear spectroscopy for a chromophore in the condensed phase.
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Affiliation(s)
- Sapana V Shedge
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA
| | - Tim J Zuehlsdorff
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
| | - Ajay Khanna
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA
| | - Stacey Conley
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA
| | - Christine M Isborn
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA
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10
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Abstract
Partial atomic charges provide an intuitive and efficient way to describe the charge distribution and the resulting intermolecular electrostatic interactions in liquid water. Many charge models exist and it is unclear which model provides the best assignment of partial atomic charges in response to the local molecular environment. In this work, we systematically scrutinize various electronic structure methods and charge models (Mulliken, natural population analysis, CHelpG, RESP, Hirshfeld, Iterative Hirshfeld, and Bader) by evaluating their performance in predicting the dipole moments of isolated water, water clusters, and liquid water as well as charge transfer in the water dimer and liquid water. Although none of the seven charge models is capable of fully capturing the dipole moment increase from isolated water (1.85 D) to liquid water (about 2.9 D), the Iterative Hirshfeld method performs best for liquid water, reproducing its experimental average molecular dipole moment, yielding a reasonable amount of intermolecular charge transfer, and showing modest sensitivity to the local water environment. The performance of the charge model is dependent on the choice of the density functional and the quantum treatment of the environment. The computed molecular dipole moment of water generally increases with the percentage of the exact Hartree-Fock exchange in the functional, whereas the amount of charge transfer between molecules decreases. For liquid water, including two full solvation shells of surrounding water molecules (within about 5.5 Å of the central water) in the quantum chemical calculation converges the charges of the central water molecule. Our final pragmatic quantum chemical charge-assigning protocol for liquid water is the Iterative Hirshfeld method with M06-HF/aug-cc-pVDZ and a quantum region cutoff radius of 5.5 Å.
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Affiliation(s)
- Bowen Han
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
| | - Christine M Isborn
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
| | - Liang Shi
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
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11
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Chen MS, Zuehlsdorff TJ, Morawietz T, Isborn CM, Markland TE. Exploiting Machine Learning to Efficiently Predict Multidimensional Optical Spectra in Complex Environments. J Phys Chem Lett 2020; 11:7559-7568. [PMID: 32808797 DOI: 10.1021/acs.jpclett.0c02168] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The excited-state dynamics of chromophores in complex environments determine a range of vital biological and energy capture processes. Time-resolved, multidimensional optical spectroscopies provide a key tool to investigate these processes. Although theory has the potential to decode these spectra in terms of the electronic and atomistic dynamics, the need for large numbers of excited-state electronic structure calculations severely limits first-principles predictions of multidimensional optical spectra for chromophores in the condensed phase. Here, we leverage the locality of chromophore excitations to develop machine learning models to predict the excited-state energy gap of chromophores in complex environments for efficiently constructing linear and multidimensional optical spectra. By analyzing the performance of these models, which span a hierarchy of physical approximations, across a range of chromophore-environment interaction strengths, we provide strategies for the construction of machine learning models that greatly accelerate the calculation of multidimensional optical spectra from first principles.
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Affiliation(s)
- Michael S Chen
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Tim J Zuehlsdorff
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
| | - Tobias Morawietz
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Christine M Isborn
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
| | - Thomas E Markland
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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12
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Zuehlsdorff TJ, Hong H, Shi L, Isborn CM. Nonlinear spectroscopy in the condensed phase: The role of Duschinsky rotations and third order cumulant contributions. J Chem Phys 2020; 153:044127. [PMID: 32752702 DOI: 10.1063/5.0013739] [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: 12/28/2022] Open
Abstract
First-principles modeling of nonlinear optical spectra in the condensed phase is highly challenging because both environment and vibronic interactions can play a large role in determining spectral shapes and excited state dynamics. Here, we compute two dimensional electronic spectroscopy (2DES) signals based on a cumulant expansion of the energy gap fluctuation operator, with specific focus on analyzing mode mixing effects introduced by the Duschinsky rotation and the role of the third order term in the cumulant expansion for both model and realistic condensed phase systems. We show that for a harmonic model system, the third order cumulant correction captures effects introduced by a mismatch in curvatures of ground and excited state potential energy surfaces, as well as effects of mode mixing. We also demonstrate that 2DES signals can be accurately reconstructed from purely classical correlation functions using quantum correction factors. We then compute nonlinear optical spectra for the Nile red and methylene blue chromophores in solution, assessing the third order cumulant contribution for realistic systems. We show that the third order cumulant correction is strongly dependent on the treatment of the solvent environment, revealing the interplay between environmental polarization and the electronic-vibrational coupling.
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Affiliation(s)
- Tim J Zuehlsdorff
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA
| | - Hanbo Hong
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA
| | - Liang Shi
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA
| | - Christine M Isborn
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA
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13
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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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14
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Isborn CM. The link between electrolytes and metals. Science 2020; 368:1056-1057. [PMID: 32499427 DOI: 10.1126/science.abb9717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Christine M Isborn
- Chemistry and Chemical Biology, University of California Merced, Merced, CA 95343, USA.
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15
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Kocherzhenko AA, Shedge SV, Germaux PF, Heidarian M, Isborn CM. Excitonic Hamiltonians for Calculating Optical Absorption Spectra and Optoelectronic Properties of Molecular Aggregates and Solids. J Vis Exp 2020. [PMID: 32538916 DOI: 10.3791/60598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Rational design of disordered molecular aggregates and solids for optoelectronic applications relies on our ability to predict the properties of such materials using theoretical and computational methods. However, large molecular systems where disorder is too significant to be considered in the perturbative limit cannot be described using either first principles quantum chemistry or band theory. Multiscale modeling is a promising approach to understanding and optimizing the optoelectronic properties of such systems. It uses first-principles quantum chemical methods to calculate the properties of individual molecules, then constructs model Hamiltonians of molecular aggregates or bulk materials based on these calculations. In this paper, we present a protocol for constructing a tight-binding Hamiltonian that represents the excited states of a molecular material in the basis of Frenckel excitons: electron-hole pairs that are localized on individual molecules that make up the material. The Hamiltonian parametrization proposed here accounts for excitonic couplings between molecules, as well as for electrostatic polarization of the electron density on a molecule by the charge distribution on surrounding molecules. Such model Hamiltonians can be used to calculate optical absorption spectra and other optoelectronic properties of molecular aggregates and solids.
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Affiliation(s)
| | - Sapana V Shedge
- Department of Chemistry and Chemical Biology, University of California, Merced
| | - Pauline F Germaux
- Department of Chemistry and Biochemistry, California State University, East Bay
| | - Mohammad Heidarian
- Department of Chemistry and Biochemistry, California State University, East Bay
| | - Christine M Isborn
- Department of Chemistry and Chemical Biology, University of California, Merced
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16
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Long MP, Alland S, Martin ME, Isborn CM. Molecular dynamics simulations of alkaline earth metal ions binding to DNA reveal ion size and hydration effects. Phys Chem Chem Phys 2020; 22:5584-5596. [DOI: 10.1039/c9cp06844a] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Classical molecular dynamics simulations reveal size-dependent trends of alkaline earth metal ions binding to DNA are due to ion size and hydration behavior.
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Affiliation(s)
| | - Serra Alland
- Department of Chemistry and Biochemistry
- University of Central Arkansas
- Arkansas 72035
- USA
| | - Madison E. Martin
- Department of Chemistry and Biochemistry
- University of Central Arkansas
- Arkansas 72035
- USA
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17
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Affiliation(s)
- Tim J. Zuehlsdorff
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
| | - Hanbo Hong
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
| | - Liang Shi
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
| | - Christine M. Isborn
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
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18
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Zuehlsdorff TJ, Montoya-Castillo A, Napoli JA, Markland TE, Isborn CM. Optical spectra in the condensed phase: Capturing anharmonic and vibronic features using dynamic and static approaches. J Chem Phys 2019; 151:074111. [PMID: 31438704 DOI: 10.1063/1.5114818] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Simulating optical spectra in the condensed phase remains a challenge for theory due to the need to capture spectral signatures arising from anharmonicity and dynamical effects, such as vibronic progressions and asymmetry. As such, numerous simulation methods have been developed that invoke different approximations and vary in their ability to capture different physical regimes. Here, we use several models of chromophores in the condensed phase and ab initio molecular dynamics simulations to rigorously assess the applicability of methods to simulate optical absorption spectra. Specifically, we focus on the ensemble scheme, which can address anharmonic potential energy surfaces but relies on the applicability of extreme nuclear-electronic time scale separation; the Franck-Condon method, which includes dynamical effects but generally only at the harmonic level; and the recently introduced ensemble zero-temperature Franck-Condon approach, which straddles these limits. We also devote particular attention to the performance of methods derived from a cumulant expansion of the energy gap fluctuations and test the ability to approximate the requisite time correlation functions using classical dynamics with quantum correction factors. These results provide insights as to when these methods are applicable and able to capture the features of condensed phase spectra qualitatively and, in some cases, quantitatively across a range of regimes.
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Affiliation(s)
- Tim J Zuehlsdorff
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA
| | | | - Joseph A Napoli
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Thomas E Markland
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Christine M Isborn
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA
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19
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Shedge SV, Zuehlsdorff TJ, Servis MJ, Clark AE, Isborn CM. Effect of Ions on the Optical Absorption Spectra of Aqueously Solvated Chromophores. J Phys Chem A 2019; 123:6175-6184. [DOI: 10.1021/acs.jpca.9b03163] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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)
- Sapana V. Shedge
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
| | - Tim J. Zuehlsdorff
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
| | - Michael J. Servis
- Department of Chemistry and the Material Science and Engineering Program, Washington State University, Pullman, Washington 99164, United States
| | - Aurora E. Clark
- Department of Chemistry and the Material Science and Engineering Program, Washington State University, Pullman, Washington 99164, United States
- Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, Washington 99164, United States
| | - Christine M. Isborn
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
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20
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Zuehlsdorff TJ, Napoli JA, Milanese JM, Markland TE, Isborn CM. Unraveling electronic absorption spectra using nuclear quantum effects: Photoactive yellow protein and green fluorescent protein chromophores in water. J Chem Phys 2018; 149:024107. [PMID: 30007372 DOI: 10.1063/1.5025517] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Many physical phenomena must be accounted for to accurately model solution-phase optical spectral line shapes, from the sampling of chromophore-solvent configurations to the electronic-vibrational transitions leading to vibronic fine structure. Here we thoroughly explore the role of nuclear quantum effects, direct and indirect solvent effects, and vibronic effects in the computation of the optical spectrum of the aqueously solvated anionic chromophores of green fluorescent protein and photoactive yellow protein. By analyzing the chromophore and solvent configurations, the distributions of vertical excitation energies, the absorption spectra computed within the ensemble approach, and the absorption spectra computed within the ensemble plus zero-temperature Franck-Condon approach, we show how solvent, nuclear quantum effects, and vibronic transitions alter the optical absorption spectra. We find that including nuclear quantum effects in the sampling of chromophore-solvent configurations using ab initio path integral molecular dynamics simulations leads to improved spectral shapes through three mechanisms. The three mechanisms that lead to line shape broadening and a better description of the high-energy tail are softening of heavy atom bonds in the chromophore that couple to the optically bright state, widening the distribution of vertical excitation energies from more diverse solvation environments, and redistributing spectral weight from the 0-0 vibronic transition to higher energy vibronic transitions when computing the Franck-Condon spectrum in a frozen solvent pocket. The absorption spectra computed using the combined ensemble plus zero-temperature Franck-Condon approach yield significant improvements in spectral shape and width compared to the spectra computed with the ensemble approach. Using the combined approach with configurations sampled from path integral molecular dynamics trajectories presents a significant step forward in accurately modeling the absorption spectra of aqueously solvated chromophores.
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Affiliation(s)
- Tim J Zuehlsdorff
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA
| | - Joseph A Napoli
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Joel M Milanese
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA
| | - Thomas E Markland
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Christine M Isborn
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA
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21
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Zuehlsdorff TJ, Isborn CM. Combining the ensemble and Franck-Condon approaches for calculating spectral shapes of molecules in solution. J Chem Phys 2018; 148:024110. [PMID: 29331131 DOI: 10.1063/1.5006043] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [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 correct treatment of vibronic effects is vital for the modeling of absorption spectra of many solvated dyes. Vibronic spectra for small dyes in solution can be easily computed within the Franck-Condon approximation using an implicit solvent model. However, implicit solvent models neglect specific solute-solvent interactions on the electronic excited state. On the other hand, a straightforward way to account for solute-solvent interactions and temperature-dependent broadening is by computing vertical excitation energies obtained from an ensemble of solute-solvent conformations. Ensemble approaches usually do not account for vibronic transitions and thus often produce spectral shapes in poor agreement with experiment. We address these shortcomings by combining zero-temperature vibronic fine structure with vertical excitations computed for a room-temperature ensemble of solute-solvent configurations. In this combined approach, all temperature-dependent broadening is treated classically through the sampling of configurations and quantum mechanical vibronic contributions are included as a zero-temperature correction to each vertical transition. In our calculation of the vertical excitations, significant regions of the solvent environment are treated fully quantum mechanically to account for solute-solvent polarization and charge-transfer. For the Franck-Condon calculations, a small amount of frozen explicit solvent is considered in order to capture solvent effects on the vibronic shape function. We test the proposed method by comparing calculated and experimental absorption spectra of Nile red and the green fluorescent protein chromophore in polar and non-polar solvents. For systems with strong solute-solvent interactions, the combined approach yields significant improvements over the ensemble approach. For systems with weak to moderate solute-solvent interactions, both the high-energy vibronic tail and the width of the spectra are in excellent agreement with experiments.
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Affiliation(s)
- T J Zuehlsdorff
- School of Natural Sciences, University of California Merced, N. Lake Road, Merced, California 95344, USA
| | - C M Isborn
- School of Natural Sciences, University of California Merced, N. Lake Road, Merced, California 95344, USA
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22
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Affiliation(s)
| | - Christine M. Isborn
- Chemistry
and Chemical Biology, University of California Merced, Merced, California 95343, United States
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23
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Kocherzhenko AA, Sosa Vazquez XA, Milanese JM, Isborn CM. Absorption Spectra for Disordered Aggregates of Chromophores Using the Exciton Model. J Chem Theory Comput 2017; 13:3787-3801. [DOI: 10.1021/acs.jctc.7b00477] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [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)
- Aleksey A. Kocherzhenko
- Department of Chemistry and
Chemical Biology, University of California, Merced, California 95343, United States
| | - Xochitl A. Sosa Vazquez
- Department of Chemistry and
Chemical Biology, University of California, Merced, California 95343, United States
| | - Joel M. Milanese
- Department of Chemistry and
Chemical Biology, University of California, Merced, California 95343, United States
| | - Christine M. Isborn
- Department of Chemistry and
Chemical Biology, University of California, Merced, California 95343, United States
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24
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Milanese JM, Provorse MR, Alameda E, Isborn CM. Convergence of Computed Aqueous Absorption Spectra with Explicit Quantum Mechanical Solvent. J Chem Theory Comput 2017; 13:2159-2171. [DOI: 10.1021/acs.jctc.7b00159] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joel M. Milanese
- Chemistry and Chemical Biology, University of California at Merced, Merced, California 95343, United States
| | - Makenzie R. Provorse
- Chemistry and Chemical Biology, University of California at Merced, Merced, California 95343, United States
| | - Enrique Alameda
- Chemistry and Chemical Biology, University of California at Merced, Merced, California 95343, United States
| | - Christine M. Isborn
- Chemistry and Chemical Biology, University of California at Merced, Merced, California 95343, United States
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25
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Provorse MR, Peev T, Xiong C, Isborn CM. Correction to “Convergence of Excitation Energies in Mixed Quantum and Classical Solvent: Comparison of Continuum and Point Charge Models”. J Phys Chem B 2017; 121:2372. [DOI: 10.1021/acs.jpcb.7b02004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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26
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Provorse MR, Peev T, Xiong C, Isborn CM. Convergence of Excitation Energies in Mixed Quantum and Classical Solvent: Comparison of Continuum and Point Charge Models. J Phys Chem B 2016; 120:12148-12159. [DOI: 10.1021/acs.jpcb.6b09176] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [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)
- Makenzie R. Provorse
- Chemistry and Chemical Biology, University of California at Merced, Merced, California 95343, United States
| | - Thomas Peev
- Chemistry and Chemical Biology, University of California at Merced, Merced, California 95343, United States
| | - Chou Xiong
- Chemistry and Chemical Biology, University of California at Merced, Merced, California 95343, United States
| | - Christine M. Isborn
- Chemistry and Chemical Biology, University of California at Merced, Merced, California 95343, United States
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27
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Sosa Vazquez XA, Isborn CM. Size-dependent error of the density functional theory ionization potential in vacuum and solution. J Chem Phys 2015; 143:244105. [DOI: 10.1063/1.4937417] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [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)
- Xochitl A. Sosa Vazquez
- Chemistry and Chemical Biology, School of Natural Sciences, University of California, Merced, 5200 North Lake Road, Merced, California 95343, USA
| | - Christine M. Isborn
- Chemistry and Chemical Biology, School of Natural Sciences, University of California, Merced, 5200 North Lake Road, Merced, California 95343, USA
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28
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Affiliation(s)
- Makenzie R. Provorse
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
| | - Bradley F. Habenicht
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
| | - Christine M. Isborn
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
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29
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Whittleton SR, Sosa Vazquez XA, Isborn CM, Johnson ER. Density-functional errors in ionization potential with increasing system size. J Chem Phys 2015; 142:184106. [DOI: 10.1063/1.4920947] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [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)
- Sarah R. Whittleton
- Chemistry and Chemical Biology, School of Natural Sciences, University of California, Merced, 5200 North Lake Road, Merced, California 95343, USA
| | - Xochitl A. Sosa Vazquez
- Chemistry and Chemical Biology, School of Natural Sciences, University of California, Merced, 5200 North Lake Road, Merced, California 95343, USA
| | - Christine M. Isborn
- Chemistry and Chemical Biology, School of Natural Sciences, University of California, Merced, 5200 North Lake Road, Merced, California 95343, USA
| | - Erin R. Johnson
- Chemistry and Chemical Biology, School of Natural Sciences, University of California, Merced, 5200 North Lake Road, Merced, California 95343, USA
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, Halifax, Nova Scotia B3H 4R2, Canada
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30
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Habenicht BF, Tani NP, Provorse MR, Isborn CM. Two-electron Rabi oscillations in real-time time-dependent density-functional theory. J Chem Phys 2014; 141:184112. [DOI: 10.1063/1.4900514] [Citation(s) in RCA: 33] [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: 11/14/2022] Open
Affiliation(s)
- Bradley F. Habenicht
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA
| | - Noriyuki P. Tani
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA
| | - Makenzie R. Provorse
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA
| | - Christine M. Isborn
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA
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31
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Garrett K, Sosa Vazquez X, Egri SB, Wilmer J, Johnson LE, Robinson BH, Isborn CM. Optimum Exchange for Calculation of Excitation Energies and Hyperpolarizabilities of Organic Electro-optic Chromophores. J Chem Theory Comput 2014; 10:3821-31. [DOI: 10.1021/ct500528z] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Kerry Garrett
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - XochitlA Sosa Vazquez
- Chemistry
and Chemical Biology, University of California Merced, Merced, California 95343, United States
| | - Shawn B. Egri
- Department
of Chemistry, University of Vermont, Burlington, Vermont 05405, United States
| | - Jacob Wilmer
- Chemistry
and Chemical Biology, University of California Merced, Merced, California 95343, United States
| | - Lewis E. Johnson
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Bruce H. Robinson
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Christine M. Isborn
- Chemistry
and Chemical Biology, University of California Merced, Merced, California 95343, United States
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32
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Isborn CM, Mar BD, Curchod BFE, Tavernelli I, Martínez TJ. The Charge Transfer Problem in Density Functional Theory Calculations of Aqueously Solvated Molecules. J Phys Chem B 2013; 117:12189-201. [DOI: 10.1021/jp4058274] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Christine M. Isborn
- Chemistry
and Chemical Biology, University of California Merced, Merced, California 95343, United States
| | - Brendan D. Mar
- PULSE
Institute and Department of Chemistry, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Basile F. E. Curchod
- Laboratory
of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Ivano Tavernelli
- Laboratory
of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Todd J. Martínez
- PULSE
Institute and Department of Chemistry, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
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33
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Isborn CM, Götz AW, Clark MA, Walker RC, Martínez TJ. Electronic Absorption Spectra from MM and ab initio QM/MM Molecular Dynamics: Environmental Effects on the Absorption Spectrum of Photoactive Yellow Protein. J Chem Theory Comput 2012; 8:5092-5106. [PMID: 23476156 PMCID: PMC3590007 DOI: 10.1021/ct3006826] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We describe a new interface of the GPU parallelized TeraChem electronic structure package and the Amber molecular dynamics package for quantum mechanical (QM) and mixed QM and molecular mechanical (MM) molecular dynamics simulations. This QM/MM interface is used for computation of the absorption spectra of the photoactive yellow protein (PYP) chromophore in vacuum, aqueous solution, and protein environments. The computed excitation energies of PYP require a very large QM region (hundreds of atoms) covalently bonded to the chromophore in order to achieve agreement with calculations that treat the entire protein quantum mechanically. We also show that 40 or more surrounding water molecules must be included in the QM region in order to obtain converged excitation energies of the solvated PYP chromophore. These results indicate that large QM regions (with hundreds of atoms) are a necessity in QM/MM calculations.
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Affiliation(s)
- Christine M. Isborn
- PULSE Institute and Department of Chemistry, Stanford University, Stanford, CA 94305
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Andreas W. Götz
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093
| | - Matthew A. Clark
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093
| | - Ross C. Walker
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Todd J. Martínez
- PULSE Institute and Department of Chemistry, Stanford University, Stanford, CA 94305
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025
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Ding F, Liang W, Chapman CT, Isborn CM, Li X. On the gauge invariance of nonperturbative electronic dynamics using the time-dependent Hartree-Fock and time-dependent Kohn-Sham. J Chem Phys 2011; 135:164101. [DOI: 10.1063/1.3655675] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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35
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Isborn CM, Luehr N, Ufimtsev IS, Martínez TJ. Excited-State Electronic Structure with Configuration Interaction Singles and Tamm-Dancoff Time-Dependent Density Functional Theory on Graphical Processing Units. J Chem Theory Comput 2011; 7:1814-1823. [PMID: 21687784 PMCID: PMC3114462 DOI: 10.1021/ct200030k] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Indexed: 12/12/2022]
Abstract
Excited-state calculations are implemented in a development version of the GPU-based TeraChem software package using the configuration interaction singles (CIS) and adiabatic linear response Tamm–Dancoff time-dependent density functional theory (TDA-TDDFT) methods. The speedup of the CIS and TDDFT methods using GPU-based electron repulsion integrals and density functional quadrature integration allows full ab initio excited-state calculations on molecules of unprecedented size. CIS/6-31G and TD-BLYP/6-31G benchmark timings are presented for a range of systems, including four generations of oligothiophene dendrimers, photoactive yellow protein (PYP), and the PYP chromophore solvated with 900 quantum mechanical water molecules. The effects of double and single precision integration are discussed, and mixed precision GPU integration is shown to give extremely good numerical accuracy for both CIS and TDDFT excitation energies (excitation energies within 0.0005 eV of extended double precision CPU results).
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36
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Fischer SA, Isborn CM, Prezhdo OV. Excited states and optical absorption of small semiconducting clusters: Dopants, defects and charging. Chem Sci 2011. [DOI: 10.1039/c0sc00626b] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
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37
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Liang W, Isborn CM, Lindsay A, Li X, Smith SM, Levis RJ. Time-Dependent Density Functional Theory Calculations of Ehrenfest Dynamics of Laser Controlled Dissociation of NO+: Pulse Length and Sequential Multiple Single-Photon Processes. J Phys Chem A 2010; 114:6201-6. [DOI: 10.1021/jp102013b] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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38
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Liang W, Isborn CM, Li X. Obtaining Hartree–Fock and density functional theory doubly excited states with Car–Parrinello density matrix search. J Chem Phys 2009; 131:204101. [DOI: 10.1063/1.3266564] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [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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39
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Affiliation(s)
- Christine M. Isborn
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700
| | - Xiaosong Li
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700
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40
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Liang W, Isborn CM, Li X. Laser-Controlled Dissociation of C2H22+: Ehrenfest Dynamics Using Time-Dependent Density Functional Theory. J Phys Chem A 2009; 113:3463-9. [DOI: 10.1021/jp811431u] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Wenkel Liang
- University of Washington, Department of Chemistry, Box 351700, Seattle, Washington 98195-1700
| | - Christine M. Isborn
- University of Washington, Department of Chemistry, Box 351700, Seattle, Washington 98195-1700
| | - Xiaosong Li
- University of Washington, Department of Chemistry, Box 351700, Seattle, Washington 98195-1700
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41
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Tretiak S, Isborn CM, Niklasson AMN, Challacombe M. Representation independent algorithms for molecular response calculations in time-dependent self-consistent field theories. J Chem Phys 2009; 130:054111. [DOI: 10.1063/1.3068658] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [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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42
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Isborn CM, Li X. Modeling the doubly excited state with time-dependent Hartree–Fock and density functional theories. J Chem Phys 2008; 129:204107. [DOI: 10.1063/1.3020336] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
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43
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Abstract
B3LYP/6-31G(d) calculations find that cubanes, persubstituted with NO2 or BF2 groups, are predicted to undergo near-barrierless, internal disrotations. However, as a consequence of the intrinsically higher energies of eclipsed conformations for threefold than for twofold rotors, the threshold mechanisms for octamethyl-, octakis(trifluoromethyl)-, octakis(trichloromethyl)-, octakis(tribromomethyl)-, octasilylcubane, and octakis(trichlorosilyl)cubane are calculated to be mono- or conrotation. The cubanes with the larger substituents are predicted to be O-symmetric, resolvable, and thus optically active.
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Affiliation(s)
- David A Hrovat
- Department of Chemistry and the Center for Advanced Scientific Computing and Modeling, Univeristy of North Texas, 1155 Union Circle, #305070, Denton, Texas 76203-5017, USA
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Davies JA, Elangovan A, Sullivan PA, Olbricht BC, Bale DH, Ewy TR, Isborn CM, Eichinger BE, Robinson BH, Reid PJ, Li X, Dalton LR. Rational Enhancement of Second-Order Nonlinearity: Bis-(4-methoxyphenyl)hetero-aryl-amino Donor-Based Chromophores: Design, Synthesis, and Electrooptic Activity. J Am Chem Soc 2008; 130:10565-75. [DOI: 10.1021/ja8007424] [Citation(s) in RCA: 170] [Impact Index Per Article: 10.6] [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)
- Joshua A. Davies
- Department of Chemistry, University of Washington, 109 Bagley Hall, Box 351700, Seattle, Washington 98195
| | - Arumugasamy Elangovan
- Department of Chemistry, University of Washington, 109 Bagley Hall, Box 351700, Seattle, Washington 98195
| | - Philip A. Sullivan
- Department of Chemistry, University of Washington, 109 Bagley Hall, Box 351700, Seattle, Washington 98195
| | - Benjamin C. Olbricht
- Department of Chemistry, University of Washington, 109 Bagley Hall, Box 351700, Seattle, Washington 98195
| | - Denise H. Bale
- Department of Chemistry, University of Washington, 109 Bagley Hall, Box 351700, Seattle, Washington 98195
| | - Todd R. Ewy
- Department of Chemistry, University of Washington, 109 Bagley Hall, Box 351700, Seattle, Washington 98195
| | - Christine M. Isborn
- Department of Chemistry, University of Washington, 109 Bagley Hall, Box 351700, Seattle, Washington 98195
| | - Bruce E. Eichinger
- Department of Chemistry, University of Washington, 109 Bagley Hall, Box 351700, Seattle, Washington 98195
| | - Bruce H. Robinson
- Department of Chemistry, University of Washington, 109 Bagley Hall, Box 351700, Seattle, Washington 98195
| | - Philip J. Reid
- Department of Chemistry, University of Washington, 109 Bagley Hall, Box 351700, Seattle, Washington 98195
| | - Xiaosong Li
- Department of Chemistry, University of Washington, 109 Bagley Hall, Box 351700, Seattle, Washington 98195
| | - Larry R. Dalton
- Department of Chemistry, University of Washington, 109 Bagley Hall, Box 351700, Seattle, Washington 98195
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Isborn CM, Davidson ER, Robinson BH. Ab initio diradical/zwitterionic polarizabilities and hyperpolarizabilities in twisted double bonds. J Phys Chem A 2007; 110:7189-96. [PMID: 16737270 DOI: 10.1021/jp056580+] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We investigated the nature of the ground state and static response properties (mu, alpha, and beta) for a promising class of twisted pi-electron system nonlinear optical chromophores at the HF, B3LYP, MP2, and CASSCF levels. We report results for a substituted twisted ethylene and a larger tictoid analogue. Previous work has reported only a zwitterionic character for such tictoid species, however, (14,13) CASSCF calculations predict a ground-state diradical. At the HF, B3LYP, MP2, and (14,13) CASSCF levels, the values of beta are orders of magnitude smaller than those predicted by semiempirical methods.
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Affiliation(s)
- Christine M Isborn
- Department of Chemistry, University of Washington, Seattle, 98195-1700, USA
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Isborn CM, Li X, Tully JC. Time-dependent density functional theory Ehrenfest dynamics: Collisions between atomic oxygen and graphite clusters. J Chem Phys 2007; 126:134307. [PMID: 17430032 DOI: 10.1063/1.2713391] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.4] [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
An ab initio direct Ehrenfest dynamics method with time-dependent density functional theory is introduced and applied to collisions of 5 eV oxygen atoms and ions with graphite clusters. Collisions at three different sites are simulated. Kinetic energy transfer from the atomic oxygen to graphite local vibrations is observed and electron-nuclear coupling resulting in electronic excitation within the graphite surface as well as alteration of the atomic charge is first reported in this paper. The three oxygen species studied, O(3P), O-(2P), and O+(4S), deposit different amounts of energy to the surface, with the highest degree of damage to the pi conjugation of the cluster produced by the atomic oxygen cation. Memory of the initial charge state is not lost as the atom approaches, in contrast to the usual assumption.
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Affiliation(s)
- Christine M Isborn
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, USA
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Isborn CM, Leclercq A, Vila FD, Dalton LR, Brédas JL, Eichinger BE, Robinson BH. Comparison of Static First Hyperpolarizabilities Calculated with Various Quantum Mechanical Methods. J Phys Chem A 2007; 111:1319-27. [PMID: 17256825 DOI: 10.1021/jp064096g] [Citation(s) in RCA: 112] [Impact Index Per Article: 6.6] [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
The prediction of nonlinear electro-optic (EO) behavior of molecules with quantum methods is the first step in the development of organic-based electro-optic devices. Typical EO molecules may require calculations with several hundred electrons, which prevents all but the fastest methods (semiempirical and density functional theory (DFT)) from being used for EO estimation. To test the reliability of these methods, we compare dipole moments, polarizabilities, and first-order hyperpolarizabilities for a wide range of structures of experimental interest with Hartree-Fock (HF), intermediate neglect of differential overlap (INDO), and DFT methods. The relative merits of molecules are consistently predictable with every method.
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Affiliation(s)
- C M Isborn
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, USA
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Abstract
Aromatic Möbius [4n]annulenes with 4n pi electrons, originally conceived by Heilbronner, are characterized computationally. These (CH)(12), (CH)(16), and (CH)(20) minima have nearly equal C-C bond lengths, small twist angles around the rings, and magnetic properties (NICS, nucleus-independent chemical shifts--see above at various positions in [16]annulene--and magnetic susceptibility exaltations) indicating significantly diatropic ring currents. The Möbius forms are not the most stable isomers but may contribute significantly to the chemistry of these annulenes. [structure: see text]
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Affiliation(s)
- Claire Castro
- Department of Chemistry, University of San Francisco, 2130 Fulton Street, San Francisco, CA 94117, USA.
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