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Title: Modeling Optical Spectra of Large Organic Systems Using Real-Time Propagation of Semiempirical Effective Hamiltonians

Abstract

We present an implementation of a time-dependent semiempirical method (INDO/S) in NWChem using real-time (RT) propagation to address, in principle, the entire spectrum of valence electronic excitations. Adopting this model, we study the UV/vis spectra of medium-sized systems such as P3B2 and f-coronene, and in addition much larger systems such as ubiquitin in the gas phase and the betanin chromophore in the presence of two explicit solvents (water and methanol). RT-INDO/S provides qualitatively and often quantitatively accurate results when compared with RT- TDDFT or experimental spectra. Even though we only consider the INDO/S Hamiltonian in this work, our implementation provides a framework for performing electron dynamics in large systems using semiempirical Hartree–Fock Hamiltonians in general.

Authors:
ORCiD logo [1];  [2]; ORCiD logo [1]; ORCiD logo [1];  [2]
  1. Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, United States
  2. Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99338, United States
Publication Date:
Research Org.:
Univ. of Minnesota, Minneapolis, MN (United States); Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES); USDOE Office of Science (SC), Advanced Scientific Computing Research (ASCR); USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1414779
Alternate Identifier(s):
OSTI ID: 1508253
Grant/Contract Number:  
SC0008666; AC05-76RL01830
Resource Type:
Journal Article: Published Article
Journal Name:
Journal of Chemical Theory and Computation
Additional Journal Information:
Journal Name: Journal of Chemical Theory and Computation Journal Volume: 13 Journal Issue: 9; Journal ID: ISSN 1549-9618
Publisher:
American Chemical Society
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY

Citation Formats

Ghosh, Soumen, Andersen, Amity, Gagliardi, Laura, Cramer, Christopher J., and Govind, Niranjan. Modeling Optical Spectra of Large Organic Systems Using Real-Time Propagation of Semiempirical Effective Hamiltonians. United States: N. p., 2017. Web. doi:10.1021/acs.jctc.7b00618.
Ghosh, Soumen, Andersen, Amity, Gagliardi, Laura, Cramer, Christopher J., & Govind, Niranjan. Modeling Optical Spectra of Large Organic Systems Using Real-Time Propagation of Semiempirical Effective Hamiltonians. United States. https://doi.org/10.1021/acs.jctc.7b00618
Ghosh, Soumen, Andersen, Amity, Gagliardi, Laura, Cramer, Christopher J., and Govind, Niranjan. 2017. "Modeling Optical Spectra of Large Organic Systems Using Real-Time Propagation of Semiempirical Effective Hamiltonians". United States. https://doi.org/10.1021/acs.jctc.7b00618.
@article{osti_1414779,
title = {Modeling Optical Spectra of Large Organic Systems Using Real-Time Propagation of Semiempirical Effective Hamiltonians},
author = {Ghosh, Soumen and Andersen, Amity and Gagliardi, Laura and Cramer, Christopher J. and Govind, Niranjan},
abstractNote = {We present an implementation of a time-dependent semiempirical method (INDO/S) in NWChem using real-time (RT) propagation to address, in principle, the entire spectrum of valence electronic excitations. Adopting this model, we study the UV/vis spectra of medium-sized systems such as P3B2 and f-coronene, and in addition much larger systems such as ubiquitin in the gas phase and the betanin chromophore in the presence of two explicit solvents (water and methanol). RT-INDO/S provides qualitatively and often quantitatively accurate results when compared with RT- TDDFT or experimental spectra. Even though we only consider the INDO/S Hamiltonian in this work, our implementation provides a framework for performing electron dynamics in large systems using semiempirical Hartree–Fock Hamiltonians in general.},
doi = {10.1021/acs.jctc.7b00618},
url = {https://www.osti.gov/biblio/1414779}, journal = {Journal of Chemical Theory and Computation},
issn = {1549-9618},
number = 9,
volume = 13,
place = {United States},
year = {Tue Sep 12 00:00:00 EDT 2017},
month = {Tue Sep 12 00:00:00 EDT 2017}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record at https://doi.org/10.1021/acs.jctc.7b00618

Citation Metrics:
Cited by: 14 works
Citation information provided by
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Works referenced in this record:

Elucidating Band-Selective Sensitization in Iron(II) Polypyridine-TiO 2 Assemblies
journal, July 2013


Real-time linear response for time-dependent density-functional theory
journal, November 2004


Intermediate neglect of differential overlap for spectroscopy: INDO/S
journal, January 2013


Exciton States of Dynamic DNA Double Helices:  Alternating dCdG Sequences
journal, August 2005


Optical Absorption and Band Gap Reduction in (Fe 1– x Cr x ) 2 O 3 Solid Solutions: A First-Principles Study
journal, November 2013


Approximate Self‐Consistent Molecular‐Orbital Theory. V. Intermediate Neglect of Differential Overlap
journal, September 1967


Applications of the random phase approximation with the INDO/S Hamiltonian: UVVIS spectra of free base porphin
journal, December 1990


Molecular dynamics implementation in MSINDO: Study of silicon clusters
journal, January 2004


A comprehensive study of the spectral and photophysical properties of arylthiophenes
journal, February 2008


DFTB+, a Sparse Matrix-Based Implementation of the DFTB Method
journal, July 2007


Quantum Mechanical Identification of Quadrupolar Plasmonic Excited States in Silver Nanorods
journal, November 2016


Computer Simulation of the Excited State Dynamics of Betaine-30 in Acetonitrile
journal, November 1999


Tetraammineruthenium(II) and -ruthenium(III) Complexes of o -Benzoquinone Diimine and Their Redox Series
journal, October 1997


Subpicosecond Dynamics of Metal-to-Ligand Charge-Transfer Excited States in Solvated [Ru(bpy) 3 ] 2+ Complexes
journal, July 2011


Quantum chemical modeling of structure and absorption spectra of the chromophore in green fluorescent proteins
journal, May 1998


Time-resolved spectroscopy of the singlet excited state of betanin in aqueous and alcoholic solutions
journal, January 2015


Functional properties of anthocyanins and betalains in plants, food, and in human nutrition
journal, January 2004


A computational investigation on singlet and triplet exciton couplings in acene molecular crystals
journal, January 2011


Black-Box, Real-Time Simulations of Transient Absorption Spectroscopy
journal, April 2016


Intramolecular Polarization Induces Electron–Hole Charge Separation in Light-Harvesting Molecular Triads
journal, December 2013


Near and Above Ionization Electronic Excitations with Non-Hermitian Real-Time Time-Dependent Density Functional Theory
journal, September 2013


Tight-binding approach to time-dependent density-functional response theory
journal, February 2001


Vibronic and Coherent Effects on Interfacial Electron Transfer Dynamics
journal, December 2015


Large-Scale Computations in Chemistry: A Bird’s Eye View of a Vibrant Field
journal, April 2015


Nonadiabatic Molecular Dynamics for Thousand Atom Systems: A Tight-Binding Approach toward PYXAID
journal, March 2016


Time-dependent configuration-interaction calculations of laser-pulse-driven many-electron dynamics: Controlled dipole switching in lithium cyanide
journal, August 2005


A new quantum method for electrostatic solvation energy of protein
journal, September 2006


Approximate Self‐Consistent Molecular Orbital Theory. III. CNDO Results for AB 2 and AB 3 Systems
journal, May 1966


Correction to Efficient Calculation of Electronic Absorption Spectra by Means of Intensity-Selected Time-Dependent Density Functional Tight Binding
journal, June 2017


Pigment Organization and Transfer of Electronic Excitation in the Photosynthetic Unit of Purple Bacteria
journal, May 1997


Electron transfer beyond the static picture: A TDDFT/TD-ZINDO study of a pentacene dimer
journal, December 2012


An intermediate neglect of differential overlap theory for transition metal complexes: Fe, Co and Cu chlorides
journal, January 1979


UV spectroscopy of entire proteins in the gas phase
journal, November 2010


Strong Interaction at the Perovskite/TiO 2 Interface Facilitates Ultrafast Photoinduced Charge Separation: A Nonadiabatic Molecular Dynamics Study
journal, February 2017


Calculation of molecular polarizabilities for large systems within the random phase approximation
journal, September 1987


An intermediate neglect of differential overlap technique for spectroscopy of transition-metal complexes. Ferrocene
journal, January 1980


A Semi‐Empirical Theory of the Electronic Spectra and Electronic Structure of Complex Unsaturated Molecules. II
journal, May 1953


Efficient Calculation of Electronic Absorption Spectra by Means of Intensity-Selected Time-Dependent Density Functional Tight Binding
journal, December 2014


Molecular dynamics with coupling to an external bath
journal, October 1984


Assessment of semiempirical methods for the computation of charge transfer in DNA π-stacks
journal, August 2006


Electron interaction in unsaturated hydrocarbons
journal, January 1953


Exact two-electron wave packet dynamics of H2 in an intense laser field: Formation of localized ionic states H+H−
journal, November 2000


INDO/X: A New Semiempirical Method for Excited States of Organic and Biological Molecules
journal, October 2014


Can optical spectroscopy directly elucidate the ground state of C20?
journal, February 2002


Propagators for the time-dependent Kohn–Sham equations
journal, August 2004


New Developments in Molecular Orbital Theory
journal, April 1951


Low-Spin versus High-Spin Ground State in Pseudo-Octahedral Iron Complexes
journal, May 2012


Effect of Solvation on Electron Detachment and Excitation Energies of a Green Fluorescent Protein Chromophore Variant
journal, May 2016


VISCANA:  Visualized Cluster Analysis of Protein−Ligand Interaction Based on the ab Initio Fragment Molecular Orbital Method for Virtual Ligand Screening
journal, January 2006


Range separated functionals in the density functional based tight-binding method: Formalism
journal, December 2011


Solvent and Intramolecular Effects on the Absorption Spectrum of Betaine-30
journal, February 2000


Efficient Algorithms for Estimating the Absorption Spectrum within Linear Response TDDFT
journal, October 2015


An intermediate neglect of differential overlap technique for actinide compounds
journal, January 1994


Approximate Self‐Consistent Molecular Orbital Theory. II. Calculations with Complete Neglect of Differential Overlap
journal, November 1965


Approximate Self‐Consistent Molecular Orbital Theory. I. Invariant Procedures
journal, November 1965


The missing term in effective pair potentials
journal, November 1987


P450 Enzymes: Their Structure, Reactivity, and Selectivity—Modeled by QM/MM Calculations
journal, February 2010


VMD: Visual molecular dynamics
journal, February 1996


Self—Consistent Molecular Orbital Methods. XII. Further Extensions of Gaussian—Type Basis Sets for Use in Molecular Orbital Studies of Organic Molecules
journal, March 1972


Elongation cutoff technique at Kohn-Sham level of theory: Elongation Cutoff Technique at KS Level of Theory
journal, March 2010


Photoinduced Electron-Transfer Processes along Molecular Wires Based on Phenylenevinylene Oligomers:  A Quantum-Chemical Insight
journal, March 2002


Electronic Excitations in Aggregates of Bacteriochlorophylls
journal, September 1998


Time-dependent local-density approximation in real time
journal, August 1996


Linker dependence of interfacial electron transfer rates in Fe(II)-polypyridine sensitized solar cells
journal, March 2015


Comparison of Real-Time and Linear-Response Time-Dependent Density Functional Theories for Molecular Chromophores Ranging from Sparse to High Densities of States
journal, February 2015


Modeling Fast Electron Dynamics with Real-Time Time-Dependent Density Functional Theory: Application to Small Molecules and Chromophores
journal, April 2011


Near-resonant absorption in the time-dependent self-consistent field and multiconfigurational self-consistent field approximations
journal, January 2001


The implementation of a self-consistent constricted variational density functional theory for the description of excited states
journal, March 2012


Excited State Absorption from Real-Time Time-Dependent Density Functional Theory
journal, August 2015


Solvent effects on optical properties of molecules: A combined time-dependent density functional theory/effective fragment potential approach
journal, October 2008


An Extended Hückel Theory. I. Hydrocarbons
journal, September 1963


An accurate and efficient scheme for propagating the time dependent Schrödinger equation
journal, November 1984


Analysis of Absorption Spectra of Zinc Porphyrin, Zinc m eso -Tetraphenylporphyrin, and Halogenated Derivatives
journal, September 2002


Inclusion of Rydberg orbitals in semiempirical calculations on excited states?
journal, January 2003


Betanin-A food colorant with biological activity
journal, October 2014


Electronic Absorption Spectra from MM and ab Initio QM/MM Molecular Dynamics: Environmental Effects on the Absorption Spectrum of Photoactive Yellow Protein
journal, September 2012


Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties
journal, September 1998


octopus: a tool for the application of time-dependent density functional theory
journal, September 2006


Analytic gradient for the adaptive frozen orbital bond detachment in the fragment molecular orbital method
journal, July 2009


Absorption Spectra of Estradiol and Tryptophan Constructed by the Statistical and Elongation Methods
journal, February 2009


SCC-DFTB: What Is the Proper Degree of Self-Consistency?
journal, July 2007


Density Matrix Analysis and Simulation of Electronic Excitations in Conjugated and Aggregated Molecules
journal, September 2002


Extended Hückel Tight-Binding Calculations of Electronic Resonances in Linear Chains of Gold Atoms and Clusters
journal, October 2010


Dimers of Dimers (DOD): A New Fragment-Based Method Applied to Large Water Clusters
journal, November 2013


NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations
journal, September 2010


Validation of the density-functional based tight-binding approximation method for the calculation of reaction energies and other data
journal, March 2005


Linear optical response of finite systems using multishift linear system solvers
journal, July 2014


An Efficient Local Molecular Dynamics Polymerization Simulation Combined with an Ab Initio MO Method
journal, March 2013


Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: Design and assessment of accuracy
journal, January 2005


Density‐functional thermochemistry. III. The role of exact exchange
journal, April 1993


Convergence of Excitation Energies in Mixed Quantum and Classical Solvent: Comparison of Continuum and Point Charge Models
journal, November 2016


Finite lifetime effects on the polarizability within time-dependent density-functional theory
journal, June 2005


Implementation of the time-dependent configuration-interaction singles method for atomic strong-field processes
journal, August 2010


Time-dependent Hartree-Fock theory of multiphoton ionization: Helium
journal, September 1987


The influence of polarization functions on molecular orbital hydrogenation energies
journal, January 1973


Modeling molecular effects on plasmon transport: Silver nanoparticles with tartrazine
journal, February 2011


Long-range correction for tight-binding TD-DFT
journal, October 2015


Tailoring approach for exploring electron densities and electrostatic potentials of molecular crystals
journal, January 2004


Visible Light Sensitization of TiO 2 Surfaces with Alq3 Complexes
journal, December 2009


Accurate Prediction of Band Gaps in Neutral Heterocyclic Conjugated Polymers
journal, November 2002


The Impact of Molecular Orientation on the Photovoltaic Properties of a Phthalocyanine/Fullerene Heterojunction
journal, April 2012


Quantum Dynamics Simulations of Interfacial Electron Transfer in Sensitized TiO 2 Semiconductors
journal, July 2003


Nonlinear response theory with relaxation: The first-order hyperpolarizability
journal, November 2005


Convergence of Computed Aqueous Absorption Spectra with Explicit Quantum Mechanical Solvent
journal, April 2017


Liouville–von Neumann molecular dynamics
journal, June 2009


Toward reliable density functional methods without adjustable parameters: The PBE0 model
journal, April 1999


Geometry Optimization of the Active Site of a Large System with the Fragment Molecular Orbital Method
journal, January 2011


An intermediate neglect of differential overlap technique for spectroscopy: Pyrrole and the azines
journal, January 1973


Two-component relativistic density functional method for computing nonsingular complex linear response of molecules based on the zeroth order regular approximation
journal, May 2009


Excited-State Absorption from Real-Time Time-Dependent Density Functional Theory: Optical Limiting in Zinc Phthalocyanine
journal, March 2016


Solvent-Induced Frequency Shifts: Configuration Interaction Singles Combined with the Effective Fragment Potential Method
journal, July 2010


Efficient Calculations of Molecular Linear Response Properties for Spectral Regions
journal, May 2014


Construction of tight-binding-like potentials on the basis of density-functional theory: Application to carbon
journal, May 1995


Conformation Dependence of DNA Exciton Parentage
journal, July 2009


Ab initio energies of nonconducting crystals by systematic fragmentation
journal, October 2007


Cyclometalated Fe(II) Complexes as Sensitizers in Dye-Sensitized Solar Cells
journal, December 2014


Excited-State Studies of Polyacenes: A Comparative Picture Using EOMCCSD, CR-EOMCCSD(T), Range-Separated (LR/RT)-TDDFT, TD-PM3, and TD-ZINDO
journal, October 2011


Solvent Effects on Electronic Excitations of an Organic Chromophore
journal, March 2016


Time-dependent quantum-mechanical methods for molecular dynamics
journal, April 1988


Triplet states via intermediate neglect of differential overlap: Benzene, pyridine and the diazines
journal, January 1976


Linear‐scaling semiempirical quantum calculations for macromolecules
journal, August 1996


A Nonadiabatic Excited State Molecular Mechanics/Extended Hückel Ehrenfest Method
journal, November 2016


Time-Dependent Extension of the Long-Range Corrected Density Functional Based Tight-Binding Method
journal, March 2017


A time-dependent semiempirical approach to determining excited states
journal, June 2010


A Semi‐Empirical Theory of the Electronic Spectra and Electronic Structure of Complex Unsaturated Molecules. I.
journal, March 1953


Tight-Binding Density Functional Theory:  An Approximate Kohn−Sham DFT Scheme
journal, July 2007


Nonadiabatic Molecular Dynamics with Tight-Binding Fragment Molecular Orbitals
journal, November 2016