Ksenia Bravaya | Profiles RNS

Ksenia Bravaya, PhD

Associate Professor

Boston University College of Arts and Sciences

Chemistry

PhD, Lomonosov Moscow State University
MSc, Lomonosov Moscow State University
BSc, Lomonosov Moscow State University

Websites

	Chemistry Faculty
	The Bravaya Group
	Google Scholar
	LinkedIn
	ResearchGate

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.

Member
Boston University
Evans Center for Interdisciplinary Biomedical Research

BU Research

SBIR Phase I: Algorithmic improvements in large scale polarizable QM/MM simulations
08/01/2022 - 07/31/2025 (Subcontract PI)
Q-Chem Inc. NIH NIGMS
5R44GM126804-03

Control of Energy Transport and Transduction in Photosynthetic Down-Conversion
09/15/2019 - 09/17/2023 (Multi-PI)
PI: Ksenia Bravaya, PhD
Department of Energy
DE-SC0020437

Alfred P. Sloan Research Fellowship for Ksenia Bravaya in Chemistry
09/15/2020 - 09/14/2022 (PI)
Alfred P. Sloan Foundation

Non-Hermitian Quantum Mechanics for Chemistry and Catalysis
01/18/2019 - 01/17/2022 (PI)
Department of Defense/ARO

LibCAP: An open source library for studying metastable electronic states in molecules
01/01/2020 - 12/31/2021 (Key Person / Mentor)
Virginia Polytechnic Institute & State University National Science Fdn
ACI-1547580

Metastable electronic states: electronic structure, dynamics, and chemistry
06/01/2017 - 05/31/2021 (PI)
National Science Foundation
CHE-1665276

Algorithmic improvements in large scale polarizable QM/MM simulations
01/01/2019 - 06/30/2019 (Subcontract PI)
Q-Chem Inc. NIH NIGMS
1R43GM126804-01A1

S212: Impl: The Molecular Sciences Software Institute
01/01/2018 - 06/30/2018 (Subcontract PI)
Virginia Polytechinic Institute and State University National Science Fdn
ACI-1547580

Title

Yr	Title	Project-Sub Proj	Pubs

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.

iCite Analysis Copy PMIDs To Clipboard

Mondal S, Bravaya KB. Complex potential energy surfaces with projected CAP technique: Vibrational excitation of N2. J Chem Phys. 2024 Jul 14; 161(2). PMID: 38984953

Gayvert JR, Bravaya KB. Application of Box and Voronoi CAPs for Metastable Electronic States in Molecular Clusters. J Phys Chem A. 2022 Aug 04; 126(30):5070-5078. PMID: 35881428

Gayvert JR, Bravaya KB. Projected CAP-EOM-CCSD method for electronic resonances. J Chem Phys. 2022 Mar 07; 156(9):094108. PMID: 35259909

Epifanovsky E, Gilbert ATB, Feng X, Lee J, Mao Y, Mardirossian N, Pokhilko P, White AF, Coons MP, Dempwolff AL, Gan Z, Hait D, Horn PR, Jacobson LD, Kaliman I, Kussmann J, Lange AW, Lao KU, Levine DS, Liu J, McKenzie SC, Morrison AF, Nanda KD, Plasser F, Rehn DR, Vidal ML, You ZQ, Zhu Y, Alam B, Albrecht BJ, Aldossary A, Alguire E, Andersen JH, Athavale V, Barton D, Begam K, Behn A, Bellonzi N, Bernard YA, Berquist EJ, Burton HGA, Carreras A, Carter-Fenk K, Chakraborty R, Chien AD, Closser KD, Cofer-Shabica V, Dasgupta S, de Wergifosse M, Deng J, Diedenhofen M, Do H, Ehlert S, Fang PT, Fatehi S, Feng Q, Friedhoff T, Gayvert J, Ge Q, Gidofalvi G, Goldey M, Gomes J, González-Espinoza CE, Gulania S, Gunina AO, Hanson-Heine MWD, Harbach PHP, Hauser A, Herbst MF, Hernández Vera M, Hodecker M, Holden ZC, Houck S, Huang X, Hui K, Huynh BC, Ivanov M, Jász Á, Ji H, Jiang H, Kaduk B, Kähler S, Khistyaev K, Kim J, Kis G, Klunzinger P, Koczor-Benda Z, Koh JH, Kosenkov D, Koulias L, Kowalczyk T, Krauter CM, Kue K, Kunitsa A, Kus T, Ladjánszki I, Landau A, Lawler KV, Lefrancois D, Lehtola S, Li RR, Li YP, Liang J, Liebenthal M, Lin HH, Lin YS, Liu F, Liu KY, Loipersberger M, Luenser A, Manjanath A, Manohar P, Mansoor E, Manzer SF, Mao SP, Marenich AV, Markovich T, Mason S, Maurer SA, McLaughlin PF, Menger MFSJ, Mewes JM, Mewes SA, Morgante P, Mullinax JW, Oosterbaan KJ, Paran G, Paul AC, Paul SK, Pavoševic F, Pei Z, Prager S, Proynov EI, Rák Á, Ramos-Cordoba E, Rana B, Rask AE, Rettig A, Richard RM, Rob F, Rossomme E, Scheele T, Scheurer M, Schneider M, Sergueev N, Sharada SM, Skomorowski W, Small DW, Stein CJ, Su YC, Sundstrom EJ, Tao Z, Thirman J, Tornai GJ, Tsuchimochi T, Tubman NM, Veccham SP, Vydrov O, Wenzel J, Witte J, Yamada A, Yao K, Yeganeh S, Yost SR, Zech A, Zhang IY, Zhang X, Zhang Y, Zuev D, Aspuru-Guzik A, Bell AT, Besley NA, Bravaya KB, Brooks BR, Casanova D, Chai JD, Coriani S, Cramer CJ, Cserey G, DePrince AE, DiStasio RA, Dreuw A, Dunietz BD, Furlani TR, Goddard WA, Hammes-Schiffer S, Head-Gordon T, Hehre WJ, Hsu CP, Jagau TC, Jung Y, Klamt A, Kong J, Lambrecht DS, Liang W, Mayhall NJ, McCurdy CW, Neaton JB, Ochsenfeld C, Parkhill JA, Peverati R, Rassolov VA, Shao Y, Slipchenko LV, Stauch T, Steele RP, Subotnik JE, Thom AJW, Tkatchenko A, Truhlar DG, Van Voorhis T, Wesolowski TA, Whaley KB, Woodcock HL, Zimmerman PM, Faraji S, Gill PMW, Head-Gordon M, Herbert JM, Krylov AI. Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package. J Chem Phys. 2021 Aug 28; 155(8):084801. PMID: 34470363; PMCID: PMC9984241; DOI: 10.1063/5.0055522;

Karnaukh EA, Bravaya KB. The redox potential of a heme cofactor in Nitrosomonas europaea cytochrome c peroxidase: a polarizable QM/MM study. Phys Chem Chem Phys. 2021 Aug 12; 23(31):16506-16515. PMID: 34017969; PMCID: PMC11178132; DOI: 10.1039/d0cp06632j;

Kim Y, Bui Y, Tazhigulov RN, Bravaya KB, Slipchenko LV. Effective Fragment Potentials for Flexible Molecules: Transferability of Parameters and Amino Acid Database. J Chem Theory Comput. 2020 Dec 08; 16(12):7735-7747. PMID: 33236635

Kumar T P R, Kocišek J, Bravaya K, Fedor J. Electron-induced vibrational excitation and dissociative electron attachment in methyl formate. Phys Chem Chem Phys. 2020 Jan 02; 22(2):518-524. PMID: 31829379

Tazhigulov RN, Gayvert JR, Wei M, Bravaya KB. eMap: A Web Application for Identifying and Visualizing Electron or Hole Hopping Pathways in Proteins. J Phys Chem B. 2019 08 15; 123(32):6946-6951. PMID: 31288524

Tazhigulov RN, Gurunathan PK, Kim Y, Slipchenko LV, Bravaya KB. Polarizable embedding for simulating redox potentials of biomolecules. Phys Chem Chem Phys. 2019 Jun 05; 21(22):11642-11650.View Related Profiles.

Allen, Karen
Bravaya, Ksenia

PMID: 31116217; PMCID: PMC6611676; DOI: 10.1039/c9cp01533g;

Li Z, Ryszka M, Dawley MM, Carmichael I, Bravaya KB, Ptasinska S. Dipole-Supported Electronic Resonances Mediate Electron-Induced Amide Bond Cleavage. Phys Rev Lett. 2019 Feb 22; 122(7):073002. PMID: 30848645

Showing 10 of 45 results. Show More

Lee MK, Bravaya KB, Coker DF. First-Principles Models for Biological Light-Harvesting: Phycobiliprotein Complexes from Cryptophyte Algae. J Am Chem Soc. 2017 06 14; 139(23):7803-7814.View Related Profiles.

Coker, David
Bravaya, Ksenia

PMID: 28521106

Jagau TC, Bravaya KB, Krylov AI. Extending Quantum Chemistry of Bound States to Electronic Resonances. Annu Rev Phys Chem. 2017 05 05; 68:525-553. PMID: 28463649

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; DOI: 10.1021/acs.chemrev.6b00238;

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; DOI: 10.1021/acs.jpclett.6b00893;

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; DOI: 10.1021/jacs.6b00092;

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; DOI: 10.1039/c5cp06476g;

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; DOI: 10.1063/1.4932100;

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; DOI: 10.1021/acs.jpclett.5b02017;

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; DOI: 10.1063/1.4914456;

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; DOI: 10.1021/acs.jpclett.5b00207;

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; DOI: 10.1021/jp5075219;

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; DOI: 10.1063/1.4885056;

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; PMCID: PMC4010289; DOI: 10.1021/jp500919a;

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; DOI: 10.1021/jz402482a;

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; DOI: 10.1021/jp406029p;

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; DOI: 10.1021/jp4028904;

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; DOI: 10.1063/1.4795750;

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; DOI: 10.1021/jz3011139;

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; DOI: 10.1021/ct300043e;

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; DOI: 10.1038/nchem.1298;

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; PMCID: PMC3310345; DOI: 10.1021/ja2114568;

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; DOI: 10.1063/1.3660350;

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; DOI: 10.1021/ar2001556;

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; DOI: 10.1021/jp2020269;

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; DOI: 10.1063/1.3516211;

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

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; DOI: 10.1021/jp1063726;

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; DOI: 10.1039/b921498d;

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; DOI: 10.1039/b919930f;

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; DOI: 10.1039/b914276b;

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; DOI: 10.1021/jp904660w;

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; DOI: 10.1021/jp804183w;

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

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

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; DOI: 10.1021/ct6000686;

This graph shows the total number of publications by year, by first, middle/unknown, or last author.

Bar chart showing 45 publications over 17 distinct years, with a maximum of 5 publications in 2011

Bar chart showing 45 publications over 17 distinct years, with a maximum of 5 publications in 2011

Year	Publications
2006	1
2007	2
2008	1
2009	2
2010	3
2011	5
2012	4
2013	4
2014	3
2015	4
2016	4
2017	2
2019	3
2020	2
2021	2
2022	2
2024	1

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