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Last Name

Ksenia Bravaya, PhD

TitleAssistant Professor
InstitutionBoston University College of Arts and Sciences
DepartmentChemistry
Address590 Commonwealth Avenue
Boston MA 02215
Phone(617) 353-2082
Fax(617) 353-6466
 Research Expertise & Professional Interests
The Bravaya research group investigates challenging electronic structure phenomena in biomolecules and systems relevant for materials, which include photoinduced processes, autoionizing electronic states, and magnetic field effects. To this end, we use and develop high-level electronic structure methods targeting processes involving multiple electronic states, chemistry of open-shell species in magnetic fields, and electronically excited and metastable systems.

Autoionizing electronic states – Electronic states metastable with respect to electron detachment are Scientific Image -2ubiquitous in highly energetic environment, are common as excited states of anions, and play important role in condensed phases processes, e.g. DNA damage by secondary electrons. We develop methods combining accurate electronic structure techniques (for example EOM-CC) and theories for description of resonances position and lifetimes (complex scaling and complex-absorbing potential).

Avian birds magnetoreception (electronic structure of cryptochromes) – Cryptochromes are a diverse class of flavoproteins involved in a variety of biological processes, e.g. circadian clock regulation, Scientific Image -1phototropism. An intriguing question concerning these protoreceptors is their possible involvement in a light-dependent magnetoreception in insects and animals. Using computational chemistry tools we will explore the mechanism of cryptochromes photoactivation and analyze the effect of the Earth’s magnetic field on their photophysics. To this aim, we are interested in developing ab initio techniques for perturbative treatment of spin-spin, spin-orbit, and hyperfine interactions based on the EOM-CC family of methods.

 Publications
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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  1. Acharya A, Bogdanov AM, Grigorenko BL, Bravaya KB, Nemukhin AV, Lukyanov KA, Krylov AI. Photoinduced Chemistry in Fluorescent Proteins: Curse or Blessing? Chem Rev. 2017 Jan 25; 117(2):758-795. PMID: 27754659.
    View in: PubMed
  2. Tazhigulov RN, Bravaya KB. Free Energies of Redox Half-Reactions from First-Principles Calculations. J Phys Chem Lett. 2016 Jul 07; 7(13):2490-5. PMID: 27295124.
    View in: PubMed
  3. Bogdanov AM, Acharya A, Titelmayer AV, Mamontova AV, Bravaya KB, Kolomeisky AB, Lukyanov KA, Krylov AI. Turning On and Off Photoinduced Electron Transfer in Fluorescent Proteins by p-Stacking, Halide Binding, and Tyr145 Mutations. J Am Chem Soc. 2016 Apr 13; 138(14):4807-17. PMID: 26999576.
    View in: PubMed
  4. Kunitsa AA, Bravaya KB. Electronic structure of the para-benzoquinone radical anion revisited. Phys Chem Chem Phys. 2016 Feb 7; 18(5):3454-62. PMID: 26750380.
    View in: PubMed
  5. Zuev D, Jagau TC, Bravaya KB, Epifanovsky E, Shao Y, Sundstrom E, Head-Gordon M, Krylov AI. Erratum: "Complex absorbing potentials within EOM-CC family of methods: Theory, implementation, and benchmarks" [J. Chem. Phys. 141, 024102 (2014)]. J Chem Phys. 2015 Oct 14; 143(14):149901. PMID: 26472400.
    View in: PubMed
  6. Jagau TC, Zuev D, Bravaya KB, Epifanovsky E, Krylov AI. Correction to "A Fresh Look at Resonances and Complex Absorbing Potentials: Density Matrix-Based Approach". J Phys Chem Lett. 2015 Oct 1; 6(19):3866. PMID: 26722883.
    View in: PubMed
  7. Yoder BL, Bravaya KB, Bodi A, West AH, Sztáray B, Signorell R. Barrierless proton transfer across weak CH?O hydrogen bonds in dimethyl ether dimer. J Chem Phys. 2015 Mar 21; 142(11):114303. PMID: 25796245.
    View in: PubMed
  8. Kunitsa AA, Bravaya KB. First-Principles Calculations of the Energy and Width of the (2)A(u) Shape Resonance in p-Benzoquinone: A Gateway State for Electron Transfer. J Phys Chem Lett. 2015 Mar 19; 6(6):1053-8. PMID: 26262869.
    View in: PubMed
  9. Mironov VA, Bravaya KB, Nemukhin AV. Role of zwitterions in kindling fluorescent protein photochemistry. J Phys Chem B. 2015 Feb 12; 119(6):2467-74. PMID: 25365115.
    View in: PubMed
  10. Zuev D, Jagau TC, Bravaya KB, Epifanovsky E, Shao Y, Sundstrom E, Head-Gordon M, Krylov AI. Complex absorbing potentials within EOM-CC family of methods: theory, implementation, and benchmarks. J Chem Phys. 2014 Jul 14; 141(2):024102. PMID: 25027994.
    View in: PubMed
  11. Vegh RB, Bravaya KB, Bloch DA, Bommarius AS, Tolbert LM, Verkhovsky M, Krylov AI, Solntsev KM. Chromophore photoreduction in red fluorescent proteins is responsible for bleaching and phototoxicity. J Phys Chem B. 2014 May 1; 118(17):4527-34. PMID: 24712386.
    View in: PubMed
  12. Jagau TC, Zuev D, Bravaya KB, Epifanovsky E, Krylov AI. A Fresh Look at Resonances and Complex Absorbing Potentials: Density Matrix-Based Approach. J Phys Chem Lett. 2014 Jan 16; 5(2):310-5. PMID: 26270705.
    View in: PubMed
  13. Khistyaev K, Golan A, Bravaya KB, Orms N, Krylov AI, Ahmed M. Proton transfer in nucleobases is mediated by water. J Phys Chem A. 2013 Aug 8; 117(31):6789-97. PMID: 23805987.
    View in: PubMed
  14. Bravaya KB, Krylov AI. On the photodetachment from the green fluorescent protein chromophore. J Phys Chem A. 2013 Nov 21; 117(46):11815-22. PMID: 23662849.
    View in: PubMed
  15. Bravaya KB, Zuev D, Epifanovsky E, Krylov AI. Complex-scaled equation-of-motion coupled-cluster method with single and double substitutions for autoionizing excited states: theory, implementation, and examples. J Chem Phys. 2013 Mar 28; 138(12):124106. PMID: 23556708.
    View in: PubMed
  16. Bravaya KB, Epifanovsky E, Krylov AI. Four Bases Score a Run: Ab Initio Calculations Quantify a Cooperative Effect of H-Bonding and p-Stacking on the Ionization Energy of Adenine in the AATT Tetramer. J Phys Chem Lett. 2012 Sep 20; 3(18):2726-32. PMID: 26295899.
    View in: PubMed
  17. Grigorenko BL, Nemukhin AV, Morozov DI, Polyakov IV, Bravaya KB, Krylov AI. Toward Molecular-Level Characterization of Photoinduced Decarboxylation of the Green Fluorescent Protein: Accessibility of the Charge-Transfer States. J Chem Theory Comput. 2012 Jun 12; 8(6):1912-20. PMID: 26593825.
    View in: PubMed
  18. Golan A, Bravaya KB, Kudirka R, Kostko O, Leone SR, Krylov AI, Ahmed M. Ionization of dimethyluracil dimers leads to facile proton transfer in the absence of hydrogen bonds. Nat Chem. 2012 Apr; 4(4):323-9. PMID: 22437719.
    View in: PubMed
  19. Bravaya KB, Subach OM, Korovina N, Verkhusha VV, Krylov AI. Insight into the common mechanism of the chromophore formation in the red fluorescent proteins: the elusive blue intermediate revealed. J Am Chem Soc. 2012 Feb 8; 134(5):2807-14. PMID: 22239269.
    View in: PubMed
  20. Zuev D, Bravaya KB, Makarova MV, Krylov AI. Effect of microhydration on the electronic structure of the chromophores of the photoactive yellow and green fluorescent proteins. J Chem Phys. 2011 Nov 21; 135(19):194304. PMID: 22112079.
    View in: PubMed
  21. Bravaya KB, Grigorenko BL, Nemukhin AV, Krylov AI. Quantum chemistry behind bioimaging: insights from ab initio studies of fluorescent proteins and their chromophores. Acc Chem Res. 2012 Feb 21; 45(2):265-75. PMID: 21882809.
    View in: PubMed
  22. Bravaya KB, Khrenova MG, Grigorenko BL, Nemukhin AV, Krylov AI. Effect of protein environment on electronically excited and ionized states of the green fluorescent protein chromophore. J Phys Chem B. 2011 Jun 30; 115(25):8296-303. PMID: 21591720.
    View in: PubMed
  23. Zuev D, Bravaya KB, Crawford TD, Lindh R, Krylov AI. Electronic structure of the two isomers of the anionic form of p-coumaric acid chromophore. J Chem Phys. 2011 Jan 21; 134(3):034310. PMID: 21261356.
    View in: PubMed
  24. Khistyaev K, Bravaya KB, Kamarchik E, Kostko O, Ahmed M, Krylov AI. The effect of microhydration on ionization energies of thymine. Faraday Discuss. 2011; 150:313-30; discussion 391-418. PMID: 22457954.
    View in: PubMed
  25. Bravaya KB, Kostko O, Dolgikh S, Landau A, Ahmed M, Krylov AI. Electronic structure and spectroscopy of nucleic acid bases: ionization energies, ionization-induced structural changes, and photoelectron spectra. J Phys Chem A. 2010 Nov 25; 114(46):12305-17. PMID: 21038927.
    View in: PubMed
  26. Kostko O, Bravaya K, Krylov A, Ahmed M. Ionization of cytosine monomer and dimer studied by VUV photoionization and electronic structure calculations. Phys Chem Chem Phys. 2010 Mar 28; 12(12):2860-72. PMID: 20449376.
    View in: PubMed
  27. Bravaya KB, Kostko O, Ahmed M, Krylov AI. The effect of pi-stacking, H-bonding, and electrostatic interactions on the ionization energies of nucleic acid bases: adenine-adenine, thymine-thymine and adenine-thymine dimers. Phys Chem Chem Phys. 2010 Mar 14; 12(10):2292-307. PMID: 20449342.
    View in: PubMed
  28. Rajput J, Rahbek DB, Andersen LH, Rocha-Rinza T, Christiansen O, Bravaya KB, Erokhin AV, Bochenkova AV, Solntsev KM, Dong J, Kowalik J, Tolbert LM, Petersen MA, Nielsen MB. Photoabsorption studies of neutral green fluorescent protein model chromophores in vacuo. Phys Chem Chem Phys. 2009 Nov 21; 11(43):9996-10002. PMID: 19865751.
    View in: PubMed
  29. Rocha-Rinza T, Christiansen O, Rajput J, Gopalan A, Rahbek DB, Andersen LH, Bochenkova AV, Granovsky AA, Bravaya KB, Nemukhin AV, Christiansen KL, Nielsen MB. Gas phase absorption studies of photoactive yellow protein chromophore derivatives. J Phys Chem A. 2009 Aug 27; 113(34):9442-9. PMID: 19642665.
    View in: PubMed
  30. Bravaya KB, Bochenkova AV, Granovsky AA, Savitsky AP, Nemukhin AV. Modeling photoabsorption of the asFP595 chromophore. J Phys Chem A. 2008 Sep 18; 112(37):8804-10. PMID: 18729441.
    View in: PubMed
  31. Bravaya K, Bochenkova A, Granovsky A, Nemukhin A. An opsin shift in rhodopsin: retinal S0-S1 excitation in protein, in solution, and in the gas phase. J Am Chem Soc. 2007 Oct 31; 129(43):13035-42. PMID: 17924622.
    View in: PubMed
  32. Kessel L, Nielsen IB, Bochenkova AV, Bravaya KB, Andersen LH. Gas-phase spectroscopy of protonated 3-OH kynurenine and argpyrimidine. comparison of experimental results to theoretical modeling. J Phys Chem A. 2007 Oct 25; 111(42):10537-43. PMID: 17914773.
    View in: PubMed
  33. Bravaya K, Bochenkova A, Grigorenko B, Topol I, Burt S, Nemukhin A. Molecular Modeling the Reaction Mechanism of Serine-Carboxyl Peptidases. J Chem Theory Comput. 2006 Jul; 2(4):1168-75. PMID: 26633073.
    View in: PubMed
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