Advances in methods and algorithms in a modern quantum chemistry program package

Shao, Yihan; Molnar, Laszlo Fusti; Jung, Yousung; Kussmann, Jörg; Ochsenfeld, Christian; Brown, Shawn T.; Gilbert, Andrew T. B.; Slipchenko, Lyudmila V.; Levchenko, Sergey V.; O’Neill, Darragh P.; DiStasio, Robert A.; Lochan, Rohini C.; Wang, Tao; Beran, Gregory J. O.; Besley, Nicholas A.; Herbert, John M.; Lin, Ching Yeh; Voorhis, Troy Van; Chien, Siu Hung; Sodt, Alex; Steele, Ryan P.; Rassolov, Vitaly A.; Maslen, Paul E.; Korambath, Prakashan; Adamson, Ross D.; Austin, Brian; Baker, Jon; Byrd, Edward F. C.; Dachsel, Holger; Doerksen, Robert J.; Dreuw, Andreas; Dunietz, Barry D.; Dutoi, Anthony D.; Furlani, Thomas R.; Gwaltney, Steven R.; Heyden, Andreas; Hirata, So; Hsu, Chao‐Ping; Kedziora, Gary S.; Khalliulin, Rustam Z.; Klunzinger, Phil; Lee, Aaron M.; Lee, Michael S.; Liang, WanZhen; Lotan, Itay; Nair, Nikhil U.; Peters, Baron; Proynov, Emil; Pieniazek, Piotr A.; Rhee, Young Min; Ritchie, Jim; Rosta, Edina; Sherrill, C. David; Simmonett, Andrew C.; Subotnik, Joseph E.; Woodcock, H. Lee; Zhang, Weimin; Bell, Alexis T.; Chakraborty, Arup; Chipman, Daniel M.; Keil, Frerich J.; Warshel, Arieh; Hehre, Warren J.; Schaefer, Henry F.; Kong, Jing; Krylov, Anna I.; Gill, Peter M. W.; Head‐Gordon, Martin

doi:10.1039/b517914a

Cited by 2,649 publications

(2,053 citation statements)

References 232 publications

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“…Treating the first and third terms of equation 3 with HF exchange and the remaining terms with DFT exchange leads to the following functional All calculations are performed with the Q-Chem software package, 49 and graphical representation of the spectra is achieved by representing each of the transitions by a Gaussian function with a full width at half maximum of 0.7 eV.…”

Section: Methodsmentioning

confidence: 99%

Quantum Chemical Calculations of X-ray Emission Spectroscopy

Wadey

Besley

2014

J. Chem. Theory Comput.

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110

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The calculation of X-ray emission spectroscopy with equation of motion coupled cluster theory (EOM-CCSD), time dependent density functional theory (TDDFT) and resolution of the identity single excitation configuration interaction with second order perturbation theory (RI-CIS(D)) is studied. These methods can be applied to calculate X-ray emission transitions by using a reference determinant with a core-hole, and they provide a convenient approach to compute the X-ray emission spectroscopy of large systems since all of the required states can be obtained within a single calculation removing the need to perform a separate calculation for each state. For all of the methods, basis sets with the inclusion of additional basis functions to describe core orbitals are necessary, particularly when studying transitions involving the 1s orbitals of heavier nuclei. EOM-CCSD predicts accurate transition energies when compared with experiment, however, its application to larger systems is restricted by its computational cost and difficulty in converging the CCSD equations for a core-hole reference determinant, which become increasing problematic as the size of the system studied increases. While RI-CIS(D)gives accurate transition energies for small molecules containing first row nuclei, its application to larger systems is limited by the CIS states providing a poor zeroth order reference for perturbation theory which leads to very large errors in the computed transition energies for some states. TDDFT with standard exchange-correlation functionals predicts transition energies that are much larger than experiment. Optimization of a hybrid and short-range corrected functional to predict the X-ray emission transitions results in much closer agreement with EOM-CCSD. The most accurate exchange-correlation functional identified is a modified B3LYP hybrid functional with 66% Hartree-Fock exchange, denoted B 66 LYP, which predicts X-ray emission spectra for a range of molecules including fluorobenzene, nitrobenzene, acetone, dimethyl sulfoxide and CF 3 Cl in good agreement with experiment.

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Section: Methodsmentioning

confidence: 99%

Quantum Chemical Calculations of X-ray Emission Spectroscopy

Wadey

Besley

2014

J. Chem. Theory Comput.

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110

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“…The temperature was fixed at 300 K. Then, the Q y excitation energies were computed for the syn and the anti monomers with the 4 fs time step. The TDDFT calculations were performed using the Q-CHEM quantum chemistry package [58] with the 6-31G basis set and the long-range corrected hybrid functional of Becke [59]. Finally, the results were interpolated to 2 fs time steps.…”

Section: Site Energy and Excitonic Coupling Calculationsmentioning

confidence: 99%

Theoretical characterization of excitation energy transfer in chlorosome light-harvesting antennae from green sulfur bacteria

et al. 2014

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We present a theoretical study of excitation dynamics in the chlorosome antenna complex of green photosynthetic bacteria based on a recently proposed model for the molecular assembly. Our model for the excitation energy transfer (EET) throughout the antenna combines a stochastic time propagation of the excitonic wave function with molecular dynamics simulations of the supramolecular structure, and electronic structure calculations of the excited states. We characterized the optical properties of the chlorosome with absorption, circular dichroism and fluorescence polarization anisotropy decay spectra. The simulation results for the excitation dynamics reveal a detailed picture of the EET in the chlorosome. Coherent energy transfer is significant only for the first 50 fs after the initial excitation, and the wavelike motion of the exciton is completely damped at 100 fs. Characteristic time constants of incoherent energy transfer, subsequently, vary from 1 ps to several tens of ps. We assign the time scales of the EET to specific physical processes by comparing our results with the data obtained from time-resolved spectroscopy experiments.

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“…Further calculations using the SRSC basis set for copper in conjunction with the 6-311++G** basis set for other atom types are also reported. All DFT and TDDFT calculations were performed using the Q-CHEM 31 software package, while Molpro 32 was used for the MRCI calculations.…”

Section: Computational Detailsmentioning

confidence: 99%

Theoretical Study of the Electronic Spectra of Small Molecules That Incorporate Analogues of the Copper–Cysteine Bond

Besley

2012

J. Phys. Chem. A

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The copper-sulphur bond which binds cysteinate to the metal centre is a key factor in the spectroscopy of blue copper proteins. We present theoretical calculations describing the electronically excited states of small molecules, including CuSH, CuSCH 3 , (CH 3 ) 2 SCuSH, (imidazole)-CuSH and (imidazole) 2 -CuSH, derived from the active site of blue copper proteins that contain the copper-sulphur bond in order to identify small molecular systems that have electronic structure that is analogous to the active site of the proteins. Both neutral and cationic forms are studied, since these represent the reduced and oxidised forms of the protein, respectively. For CuSH and CuSH + , excitation energies from time-dependent density functional theory with the B97-1 exchange-correlation functional agree well with the available experimental data and multireference configuration interaction calculations. For the positive ions, the singly occupied molecular orbital is formed from an antibonding combination of a 3d orbital on copper and a 3p p orbital on sulphur, which is analogous to the protein. This leads several of the molecules to have qualitatively similar electronic spectra to the proteins. For the neutral molecules, changes in the nature of the low lying virtual orbitals leads the predicted electronic spectra to vary substantially between the different molecules. In particular, addition of a ligand bonded directly to copper results in the low-lying excited states observed in CuSH and CuSCH 3 to be absent or shifted to higher energies.

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Advances in methods and algorithms in a modern quantum chemistry program package

Cited by 2,649 publications

References 232 publications

Quantum Chemical Calculations of X-ray Emission Spectroscopy

Quantum Chemical Calculations of X-ray Emission Spectroscopy

Theoretical characterization of excitation energy transfer in chlorosome light-harvesting antennae from green sulfur bacteria

Theoretical Study of the Electronic Spectra of Small Molecules That Incorporate Analogues of the Copper–Cysteine Bond

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