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Shirin Faraji - Publications

Affiliations: 
2006-2010 Heidelberg University, Tiffin, OH, United States 
 2010-2012 University of Southern California, Los Angeles, CA, United States 
 2017- University of Groningen, Groningen, Netherlands 
Website:
https://www.rug.nl/research/zernike/news/newsitems/2017_faraji_start?lang=en
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34 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Menger MFSJ, Ou Q, Shao Y, Faraji S, Subotnik JE, Cofer-Shabica DV. Nature of Hops, Coordinates, and Detailed Balance for Nonadiabatic Simulations in the Condensed Phase. The Journal of Physical Chemistry. A. 127: 8427-8436. PMID 37782887 DOI: 10.1021/acs.jpca.3c03546  0.338
2023 Grigorenko BL, Polyakov IV, Khrenova MG, Giudetti G, Faraji S, Krylov AI, Nemukhin AV. Multiscale Simulations of the Covalent Inhibition of the SARS-CoV-2 Main Protease: Four Compounds and Three Reaction Mechanisms. Journal of the American Chemical Society. 145: 13204-13214. PMID 37294056 DOI: 10.1021/jacs.3c02229  0.588
2022 Cofer-Shabica DV, Menger MFSJ, Ou Q, Shao Y, Subotnik JE, Faraji S. INAQS, a Generic Interface for Nonadiabatic QM/MM Dynamics: Design, Implementation, and Validation for GROMACS/Q-CHEM simulations. Journal of Chemical Theory and Computation. PMID 35901266 DOI: 10.1021/acs.jctc.2c00204  0.343
2022 Giudetti G, Polyakov I, Grigorenko BL, Faraji S, Nemukhin AV, Krylov AI. How Reproducible Are QM/MM Simulations? Lessons from Computational Studies of the Covalent Inhibition of the SARS-CoV-2 Main Protease by Carmofur. Journal of Chemical Theory and Computation. PMID 35797455 DOI: 10.1021/acs.jctc.2c00286  0.642
2021 Bruininks BMH, Thie AS, Souza PCT, Wassenaar TA, Faraji S, Marrink SJ. Sequential Voxel-Based Leaflet Segmentation of Complex Lipid Morphologies. Journal of Chemical Theory and Computation. PMID 34609876 DOI: 10.1021/acs.jctc.1c00446  0.416
2021 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, ... ... Faraji S, et al. Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package. The Journal of Chemical Physics. 155: 084801. PMID 34470363 DOI: 10.1063/5.0055522  0.492
2020 Straatsma TP, Broer R, Faraji S, Havenith RWA, Suarez LEA, Kathir RK, Wibowo M, Graaf Cd. GronOR: Massively parallel and GPU-accelerated non-orthogonal configuration interaction for large molecular systems Journal of Chemical Physics. 152: 64111. PMID 32061226 DOI: 10.1063/1.5141358  0.372
2020 Mulks FF, Hashmi ASK, Faraji S. Sesquicarbene Complexes: Bonding at the Interface Between M–C Single Bonds and M═C Double Bonds Organometallics. 39: 1814-1823. DOI: 10.1021/Acs.Organomet.0C00102  0.7
2019 Ryerson JL, Zaykov A, Aguilar Suarez LE, Havenith RWA, Stepp BR, Dron PI, Kaleta J, Akdag A, Teat SJ, Magnera TF, Miller JR, Havlas Z, Broer R, Faraji S, Michl J, et al. Structure and photophysics of indigoids for singlet fission: Cibalackrot. The Journal of Chemical Physics. 151: 184903. PMID 31731849 DOI: 10.1063/1.5121863  0.38
2019 Moghaddam KG, de Vries AH, Marrink SJ, Faraji S. Binding of quinazolinones to c-KIT G-quadruplex; an interplay between hydrogen bonding and π-π stacking. Biophysical Chemistry. 253: 106220. PMID 31302375 DOI: 10.1016/J.Bpc.2019.106220  0.477
2019 Sen R, Dreuw A, Faraji S. Algebraic diagrammatic construction for the polarisation propagator in combination with effective fragment potentials. Physical Chemistry Chemical Physics : Pccp. PMID 30632554 DOI: 10.1039/C8Cp06527F  0.666
2019 Suarez LEA, Kathir RK, Siagri E, Havenith RWA, Faraji S. Determination of electronic couplings in the singlet fission process using a nonorthogonal configuration interaction approach Advances in Quantum Chemistry. 79: 263-287. DOI: 10.1016/Bs.Aiq.2019.05.004  0.39
2018 Faraji S, Matsika S, Krylov AI. Calculations of non-adiabatic couplings within equation-of-motion coupled-cluster framework: Theory, implementation, and validation against multi-reference methods. The Journal of Chemical Physics. 148: 044103. PMID 29390851 DOI: 10.1063/1.5009433  0.586
2018 Mulks FF, Faraji S, Rominger F, Dreuw A, Hashmi ASK. Highly Strained Organogold Complexes and Their Gold- or Rhodium-Catalyzed Isomerizations. Chemistry (Weinheim An Der Bergstrasse, Germany). 24: 71-76. PMID 28976042 DOI: 10.1002/Chem.201704652  0.722
2018 Straatsma TP, Broer R, Faraji S, Havenith RWA. GronOR Nonorthogonal Configuration Interaction Calculations at Exascale Annual Reports in Computational Chemistry. 14: 77-91. DOI: 10.1016/Bs.Arcc.2018.06.003  0.337
2017 Faraji S, Dreuw A. Insights into Light-driven DNA Repair by Photolyases: Challenges and Opportunities for Electronic Structure Theory. Photochemistry and Photobiology. 93: 37-50. PMID 27925218 DOI: 10.1111/Php.12679  0.657
2016 Faraji S, Zhong D, Dreuw A. Characterization of the Intermediate in and Identification of the Repair Mechanism of (6-4) Photolesions by Photolyases. Angewandte Chemie (International Ed. in English). PMID 26996356 DOI: 10.1002/Anie.201511950  0.654
2015 Faraji S, Krylov AI. On the Nature of an Extended Stokes Shift in the mPlum Fluorescent Protein. The Journal of Physical Chemistry. B. 119: 13052-62. PMID 26402581 DOI: 10.1021/Acs.Jpcb.5B07724  0.535
2015 Schelkle KM, Becht S, Faraji S, Petzoldt M, Müllen K, Buckup T, Dreuw A, Motzkus M, Hamburger M. Emission turn-on and solubility turn-off in conjugated polymers: one- and two-photon-induced removal of fluorescence-quenching solubilizing groups. Macromolecular Rapid Communications. 36: 31-7. PMID 25451983 DOI: 10.1002/Marc.201400562  0.607
2014 Faraji S, Dreuw A. Physicochemical mechanism of light-driven DNA repair by (6-4) photolyases Annual Review of Physical Chemistry. 65: 275-292. PMID 24364918 DOI: 10.1146/Annurev-Physchem-040513-103626  0.637
2014 Fletcher K, Dreuw A, Faraji S. Potential energy surfaces and approximate kinetic model for the excited state dynamics of Pigment Yellow 101 Computational and Theoretical Chemistry. 1040: 177-185. DOI: 10.1016/J.Comptc.2014.04.003  0.642
2013 Harbach PH, Schneider M, Faraji S, Dreuw A. Intermolecular Coulombic Decay in Biology: The Initial Electron Detachment from FADH(-) in DNA Photolyases. The Journal of Physical Chemistry Letters. 4: 943-9. PMID 26291360 DOI: 10.1021/Jz400104H  0.714
2013 Dreuw A, Faraji S. A quantum chemical perspective on (6-4) photolesion repair by photolyases Physical Chemistry Chemical Physics. 15: 19957-19969. PMID 24145385 DOI: 10.1039/C3Cp53313A  0.669
2013 Faraji S, Groenhof G, Dreuw A. Combined QM/MM investigation on the light-driven electron-induced repair of the (6-4) thymine dimer catalyzed by DNA photolyase Journal of Physical Chemistry B. 117: 10071-10079. PMID 23915283 DOI: 10.1021/Jp401662Z  0.67
2013 Faraji S, Wirz L, Dreuw A. Quantum chemical study of the enzymatic repair of T(6-4)C/C(6-4)T UV-photolesions by DNA photolyases Chemphyschem. 14: 2817-2824. PMID 23821498 DOI: 10.1002/Cphc.201300223  0.647
2013 Harbach PHP, Schneider M, Faraji S, Dreuw A. Intermolecular coulombic decay in biology: The initial electron detachment from FADH- in DNA photolyases Journal of Physical Chemistry Letters. 4: 943-949. DOI: 10.1021/jz400104h  0.649
2012 Faraji S, Köppel H. Multi-state vibronic interactions in the 1,2,3-trifluorobenzene radical cation. The Journal of Chemical Physics. 137: 22A531. PMID 23249068 DOI: 10.1063/1.4746159  0.708
2012 Meng Q, Faraji S, Vendrell O, Meyer HD. Full dimensional quantum-mechanical simulations for the vibronic dynamics of difluorobenzene radical cation isomers using the multilayer multiconfiguration time-dependent Hartree method. The Journal of Chemical Physics. 137: 134302. PMID 23039594 DOI: 10.1063/1.4755372  0.395
2012 Faraji S, Köppel H. Multi-state vibronic interactions in the 1,2,3-trifluorobenzene radical cation Journal of Chemical Physics. 137. DOI: 10.1063/1.4746159  0.33
2012 Faraji S, Dreuw A. Proton-transfer-steered mechanism of photolesion repair by (6-4)-photolyases Journal of Physical Chemistry Letters. 3: 227-230. DOI: 10.1021/Jz201587V  0.671
2011 Faraji S, Vazdar M, Reddy VS, Eckert-Maksic M, Lischka H, Köppel H. Ab initio quantum dynamical study of the multi-state nonadiabatic photodissociation of pyrrole Journal of Chemical Physics. 135. PMID 22029316 DOI: 10.1063/1.3651536  0.7
2008 Faraji S, Meyer HD, Köppel H. Multistate vibronic interactions in difluorobenzene radical cations. II. Quantum dynamical simulations. The Journal of Chemical Physics. 129: 074311. PMID 19044771 DOI: 10.1063/1.2958918  0.715
2008 Faraji S, Köppel H. Multistate vibronic interactions in difluorobenzene radical cations. I. Electronic structure calculations Journal of Chemical Physics. 129. PMID 19044770 DOI: 10.1063/1.2958915  0.708
2008 Faraji S, Köppel H, Eisfeld W, Mahapatra S. Towards a higher-order description of Jahn-Teller coupling effects in molecular spectroscopy: The over(A, ∼)2 E″ state of NO3 Chemical Physics. 347: 110-119. DOI: 10.1016/J.Chemphys.2007.10.006  0.746
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