Literature DB >> 21663351

Reduction of the virtual space for coupled-cluster excitation energies of large molecules and embedded systems.

Robert Send1, Ville R I Kaila, Dage Sundholm.   

Abstract

We investigate how the reduction of the virtual space affects coupled-cluster excitation energies at the approximate singles and doubles coupled-cluster level (CC2). In this reduced-virtual-space (RVS) approach, all virtual orbitals above a certain energy threshold are omitted in the correlation calculation. The effects of the RVS approach are assessed by calculations on the two lowest excitation energies of 11 biochromophores using different sizes of the virtual space. Our set of biochromophores consists of common model systems for the chromophores of the photoactive yellow protein, the green fluorescent protein, and rhodopsin. The RVS calculations show that most of the high-lying virtual orbitals can be neglected without significantly affecting the accuracy of the obtained excitation energies. Omitting all virtual orbitals above 50 eV in the correlation calculation introduces errors in the excitation energies that are smaller than 0.1 eV. By using a RVS energy threshold of 50 eV, the CC2 calculations using triple-ζ basis sets (TZVP) on protonated Schiff base retinal are accelerated by a factor of 6. We demonstrate the applicability of the RVS approach by performing CC2/TZVP calculations on the lowest singlet excitation energy of a rhodopsin model consisting of 165 atoms using RVS thresholds between 20 eV and 120 eV. The calculations on the rhodopsin model show that the RVS errors determined in the gas-phase are a very good approximation to the RVS errors in the protein environment. The RVS approach thus renders purely quantum mechanical treatments of chromophores in protein environments feasible and offers an ab initio alternative to quantum mechanics/molecular mechanics separation schemes.
© 2011 American Institute of Physics

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Year:  2011        PMID: 21663351      PMCID: PMC3133567          DOI: 10.1063/1.3596729

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  30 in total

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Authors:  Mihály Kállay; Jürgen Gauss
Journal:  J Chem Phys       Date:  2004-11-15       Impact factor: 3.488

2.  S1 and S2 excited States of gas-phase Schiff-base retinal chromophores.

Authors:  I B Nielsen; L Lammich; L H Andersen
Journal:  Phys Rev Lett       Date:  2006-01-04       Impact factor: 9.161

3.  Density functional self-consistent quantum mechanics/molecular mechanics theory for linear and nonlinear molecular properties: Applications to solvated water and formaldehyde.

Authors:  Christian B Nielsen; Ove Christiansen; Kurt V Mikkelsen; Jacob Kongsted
Journal:  J Chem Phys       Date:  2007-04-21       Impact factor: 3.488

4.  Benchmarks for electronically excited states: time-dependent density functional theory and density functional theory based multireference configuration interaction.

Authors:  Mario R Silva-Junior; Marko Schreiber; Stephan P A Sauer; Walter Thiel
Journal:  J Chem Phys       Date:  2008-09-14       Impact factor: 3.488

5.  Computational studies of semiconductor quantum dots.

Authors:  Olli Lehtonen; Dage Sundholm; Tommy Vänskä
Journal:  Phys Chem Chem Phys       Date:  2008-07-09       Impact factor: 3.676

6.  Maximum locality in occupied and virtual orbital spaces using a least-change strategy.

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Journal:  J Chem Phys       Date:  2009-09-28       Impact factor: 3.488

7.  Molecular basis of visual excitation.

Authors:  G Wald
Journal:  Science       Date:  1968-10-11       Impact factor: 47.728

8.  Coupled-cluster and density functional theory studies of the electronic excitation spectra of trans-1,3-butadiene and trans-2-propeniminium.

Authors:  Olli Lehtonen; Dage Sundholm; Robert Send; Mikael P Johansson
Journal:  J Chem Phys       Date:  2009-07-14       Impact factor: 3.488

9.  Color tuning in short wavelength-sensitive human and mouse visual pigments: ab initio quantum mechanics/molecular mechanics studies.

Authors:  Ahmet Altun; Shozo Yokoyama; Keiji Morokuma
Journal:  J Phys Chem A       Date:  2009-10-29       Impact factor: 2.781

10.  Assessing Excited State Methods by Adiabatic Excitation Energies.

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Journal:  J Chem Theory Comput       Date:  2011-07-19       Impact factor: 6.006

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  8 in total

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Journal:  J Chem Phys       Date:  2017-06-07       Impact factor: 3.488

2.  Energetics and dynamics of a light-driven sodium-pumping rhodopsin.

Authors:  Carl-Mikael Suomivuori; Ana P Gamiz-Hernandez; Dage Sundholm; Ville R I Kaila
Journal:  Proc Natl Acad Sci U S A       Date:  2017-06-13       Impact factor: 11.205

3.  Computational and experimental studies of the electronic excitation spectra of EDTA and DTPA substituted tetraphenylporphyrins and their Lu complexes.

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Journal:  J Mol Model       Date:  2012-03-25       Impact factor: 1.810

4.  Benchmarking the Performance of Time-Dependent Density Functional Theory Methods on Biochromophores.

Authors:  Yihan Shao; Ye Mei; Dage Sundholm; Ville R I Kaila
Journal:  J Chem Theory Comput       Date:  2019-12-26       Impact factor: 6.006

Review 5.  Artificial Photosynthesis: Is Computation Ready for the Challenge Ahead?

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Journal:  Nanomaterials (Basel)       Date:  2021-01-24       Impact factor: 5.076

6.  Divergent Carbocatalytic Routes in Oxidative Coupling of Benzofused Heteroaryl Dimers: A Mechanistic Update.

Authors:  David S Casadio; Santeri Aikonen; Anna Lenarda; Martin Nieger; Tao Hu; Stefan Taubert; Dage Sundholm; Mikko Muuronen; Tom Wirtanen; Juho Helaja
Journal:  Chemistry       Date:  2021-02-18       Impact factor: 5.236

7.  Ultrafast carbon monoxide photolysis and heme spin-crossover in myoglobin via nonadiabatic quantum dynamics.

Authors:  Konstantin Falahati; Hiroyuki Tamura; Irene Burghardt; Miquel Huix-Rotllant
Journal:  Nat Commun       Date:  2018-10-29       Impact factor: 14.919

8.  QM/MM Benchmarking of Cyanobacteriochrome Slr1393g3 Absorption Spectra.

Authors:  Christian Wiebeler; Igor Schapiro
Journal:  Molecules       Date:  2019-05-03       Impact factor: 4.411

  8 in total

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