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Research Zernike (ZIAM) Theoretical Chemistry Faraji Group



Palmisano, V. F., Gómez-Rodellar, C., Pollak, H., Cárdenas, G., Corry, B., Faraji, S., & Nogueira, J. J. (2021). Binding of azobenzene and p-diaminoazobenzene to the human voltage-gated sodium channel Nav1.4. PPCP : Physical Chemistry Chemical Physics, 23(5), 3552-3564.
Aguilar Suarez, L. E., de Graaf, C., & Faraji, S. (2021). Influence of the crystal packing in singlet fission: One step beyond the gas phase approximation. PPCP : Physical Chemistry Chemical Physics, 23(26), 14113–14534.
Rathnachalam, S., Menger, M. F. S. J., & Faraji, S. (2021). Influence of the Environment on Shaping the Absorption of Monomeric Infrared Fluorescent Proteins. The Journal of Physical Chemistry. B: Materials, Surfaces, Interfaces, & Biophysical, 125(9), 2231–2240.
Sami, S., Menger, M. F. S. J., Faraji, S., Broer, R., & Havenith, R. W. A. (2021). Q-Force: Quantum Mechanically Augmented Molecular Force Fields. Journal of Chemical Theory and Computation, 17(8), 4946–4960.
Zettergren, H., Domaracka, A., Schlathölter, T., Bolognesi, P., Díaz-Tendero, S., Łabuda, M., Tosic, S., Maclot, S., Johnsson, P., Steber, A., Tikhonov, D., Castrovilli, M. C., Avaldi, L., Bari, S., Milosavljević, A. R., Palacios, A., Faraji, S., Piekarski, D. G., Rousseau, P., ... Petrignani, A. (2021). Roadmap on dynamics of molecules and clusters in the gas phase. The European Physical Journal D, 75(5), [152].
Wang, X., Rathnachalam, S., Bijlsma, K., Li, W., Hoekstra, R., Kubin, M., Timm, M., von Issendorff, B., Zamudio-Bayer, V., Lau, J. T., Faraji, S., & Schlathölter, T. (2021). Site-selective soft X-ray absorption as a tool to study protonation and electronic structure of gas-phase DNA. PCCP : Physical Chemistry Chemical Physics, 20, 11900-11906.
Barakat, F., AlSalhi, M. S., Prasad, S., Alterary, S., Faraji, S., & Laref, A. (2021). Synthesis of nanocomposite films based on conjugated oligomer-2D layered MoS2 as potential candidate for optoelectronic devices. Journal of king saud university science, 33(3), [101389].
Romeo-Gella, F., Corral, I., & Faraji, S. (2021). Theoretical investigation of a novel xylene-based light-driven unidirectional molecular motor. The Journal of Chemical Physics, 154(6), [064111].


Suarez, L. E. A., Menger, M. F. S. J., & Faraji, S. (2021). Singlet fission in tetracene: An excited state analysis. Molecular Physics, 118(21-22), [e1769870].
Straatsma, T. P., Broer, R., Faraji, S., Havenith, R. W. A., Suarez, L. E. A., Kathir, R. K., Wibowo, M., & de Graaf, C. (2020). GronOR: Massively parallel and GPU-accelerated non-orthogonal configuration interaction for large molecular systems. The Journal of Chemical Physics, 152(6), [064111].
Golkaram, M., Portale, G., Mulder, P., Maniar, D., Faraji, S., & Loos, K. (2020). Order-disorder transition in supramolecular polymer combs/brushes with polymeric side chains. Polymer Chemistry, 11(15), 2749-2760.
Luo, L., Straatsma, T. P., Suarez, L. E. A., Broer, R., Bykov, D., D'Azevedo, E. F., Faraji, S. S., Gottiparthi, K. C., de Graaf, C., Harris, J. A., Havenith, R. W. A., Jensen, H. J. A., Joubert, W., Kathir, R. K., Larkin, J., Li, Y. W., Lyakh, D., Messer, O. E. B., Norman, M. R., ... Wibowo, M. (2020). Pre-exascale accelerated application development: The ORNL Summit experience. Ibm journal of research and development, 64(3-4), [8960361].
Menger, M. F. S. J., Ehrmaier, J., & Faraji, S. (2020). PySurf: A Framework for Database Accelerated Direct Dynamics. Journal of Chemical Theory and Computation, 16(12), 7681-7689.
Mulks, F. F., Hashmi, A. S. K., & Faraji, S. (2020). Sesquicarbene Complexes: Bonding at the Interface Between M-C Single Bonds and M=C Double Bonds. Organometallics, 39(10), 1814-1823.
Barakat, F., Laref, A., AlSalhi, M., & Faraji, S. (2020). The impact of anion elements on the engineering of the electronic and T optical characteristics of the two dimensional monolayer janus MoSSe for nanoelectronic device applications. Results in Physics, 18, [103284].
Gholamjani Moghaddam, K., Giudetti, G., Sipma, W., & Faraji, S. (2020). Theoretical insights into the effect of size and substitution patterns of azobenzene derivatives on the DNA G-quadruplex. PPCP : Physical Chemistry Chemical Physics, 22(46), 26944-26954.
Salazar, E., & Faraji, S. (2020). Theoretical study of cyclohexadiene/hexatriene photochemical interconversion using spin-Flip time-Dependent density functional theory. Molecular Physics, 118(19-20), [1764120].


Sen, R., Dreuw, A., & Faraji, S. (2019). Algebraic diagrammatic construction for the polarisation propagator in combination with effective fragment potentials. Physical Chemistry Chemical Physics, 21(7), 3683-3694.
Gholamjani Moghaddam, K., de Vries, A., Marrink, S. J., & Faraji, S. (2019). Binding of quinazolinones to c-KIT G-quadruplex; an interplay between hydrogen bonding and π-π stacking. Biophysical Chemistry, 253, [106220].
Aguilar Suarez, L. E., Kathir, R. K., Siagri, E., Havenith, R. W. A., & Faraji, S. (2019). Determination of electronic couplings in the singlet fission process using a nonorthogonal configuration interaction approach. Adv. in Quantum Chem., 79, 263-287.
Kumar, S., Soni, S., Leach, I., Faraji, S., Feringa, B. L., Rudolf, P., & Chiechi, R. C. (2019). Eliminating Fatigue in Surface-Bound Spiropyrans. The Journal of Physical Chemistry. C: Nanomaterials and Interfaces, 123(42), 25908-25914.
Ryerson, J. L., Zaykov, A., Aguilar Suarez, L. E., Havenith, R. W. A., Stepp, B. R., Dron, P. I., Kaleta, J., Akdag, A., Teat, S. J., Magnera, T. F., Miller, J. R., Havlas, Z., Broer, R., Faraji, S., Michl, J., & Johnson, J. C. (2019). Structure and photophysics of indigoids for singlet fission: Cibalackrot. The Journal of Chemical Physics, 151(18), [184903].
Golkaram, M., Boetje, L., Dong, J., Aguilar Suarez, L., Fodor, C., Maniar, D., van Ruymbeke, E., Faraji, S., Portale, G., & Loos, K. (2019). Supramolecular Mimic for Bottlebrush Polymers in Bulk. ACS Omega, 4(15), 16481-16492.


Faraji, S., Matsika, S., & Krylov, A. I. (2018). Calculations of non-adiabatic couplings within equation-of-motion coupled-cluster framework: Theory, implementation, and validation against multi-reference methods. Journal of Chemical Physics, 148(4), [044103].
Straatsma, T. P., Broer, R., Faraji, S., & Havenith, R. W. A. (2018). GronOR Nonorthogonal Configuration Interaction Calculations at Exascale. Annual Reports in Computational Chemistry, 14, 77-91.
Mulks, F. F., Faraji, S., Rominger, F., Dreuw, A., & Hashmi, A. S. K. (2018). Highly Strained Organogold Complexes and Their Gold- or Rhodium-Catalyzed Isomerizations. Chemistry, 24(1), 71-76.


Faraji, S., & Dreuw, A. (2017). Insights into Light-driven DNA Repair by Photolyases: Challenges and Opportunities for Electronic Structure Theory. Photochemistry and Photobiology, 93(1), 37-50.


Faraji, S., Zhong, D., & Dreuw, A. (2016). Characterization of the Intermediate in and Identification of the Repair Mechanism of (6-4) Photolesions by Photolyases. Angewandte Chemie - International Edition, 55(17), 5175-5178.


Schelkle, K. M., Becht, S., Faraji, S., Petzoldt, M., Muellen, K., Buckup, T., Dreuw, A., Motzkus, M., & Hamburger, M. (2015). 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(1), 31-37.
Faraji, S., & Krylov, A. I. (2015). On the Nature of an Extended Stokes Shift in the mPlum Fluorescent Protein. The Journal of Physical Chemistry. B: Materials, Surfaces, Interfaces, & Biophysical, 119(41), 13052-13062.


Faraji, S., & Dreuw, A. (2014). Physicochemical Mechanism of Light-Driven DNA Repair by (6-4) Photolyases. In MA. Johnson, & TJ. Martinez (Eds.), ANNUAL REVIEW OF PHYSICAL CHEMISTRY, VOL 65 (Vol. 65, pp. 275-292). (Annual Review of Physical Chemistry; Vol. 65). Annual Reviews.
Fletcher, K., Dreuw, A., & Faraji, S. (2014). Potential energy surfaces and approximate kinetic model for the excited state dynamics of Pigment Yellow 101. Computational and Theoretical Chemistry, 1040-1041, 177-185.


Dreuw, A., & Faraji, S. (2013). A quantum chemical perspective on (6-4) photolesion repair by photolyases. PPCP : Physical Chemistry Chemical Physics, 15(46), 19957-19969.
Faraji, S., Groenhof, G., & Dreuw, A. (2013). Combined QM/MM Investigation on the Light-Driven Electron-Induced Repair of the (6-4) Thymine Dimer Catalyzed by DNA Photolyase. The Journal of Physical Chemistry. B: Materials, Surfaces, Interfaces, & Biophysical, 117(35), 10071-10079.
Harbach, P. H. P., Schneider, M., Faraji, S., & Dreuw, A. (2013). Intermolecular Coulombic Decay in Biology: The Initial Electron Detachment from FADH(-) in DNA Photolyases. The Journal of Physical Chemistry Letters, 4(6), 943-949.
Faraji, S., Wirz, L., & Dreuw, A. (2013). Quantum Chemical Study of the Enzymatic Repair of T(6-4)C/C(6-4)T UV-Photolesions by DNA Photolyases. Chemphyschem, 14(12), 2817-2824.


Meng, Q., Faraji, S., Vendrell, O., & Meyer, H-D. (2012). Full dimensional quantum-mechanical simulations for the vibronic dynamics of difluorobenzene radical cation isomers using the multilayer multiconfiguration time-dependent Hartree method. Journal of Chemical Physics, 137(13), [134302].
Faraji, S., & Koeppel, H. (2012). Multi-state vibronic interactions in the 1,2,3-trifluorobenzene radical cation. Journal of Chemical Physics, 137(22), [ARTN 22A531].
Faraji, S., & Dreuw, A. (2012). Proton-Transfer-Steered Mechanism of Photo lesion Repair by (6-4)-Photolyases. The Journal of Physical Chemistry Letters, 3(2), 227-230.


Faraji, S., Vazdar, M., Reddy, V. S., Eckert-Maksic, M., Lischka, H., & Koeppel, H. (2011). Ab initio quantum dynamical study of the multi-state nonadiabatic photodissociation of pyrrole. Journal of Chemical Physics, 135(15), [154310].
Faraji, S., Gomez-Carasco, S., & Köppel, H. (2011). Multi-State Vibronic Dynamics and Multiple Conical Intersections. In W. Domcke, D. R. Yarkony, & H. Köppel (Eds.), Conical Intersections: Theory, Computation and Experiment (Vol. 17, pp. 249-300). Word Scientific, Advanced series in physical chemistry.


Faraji, S., Gindensperger, E., & Köppel, H. (2009). Multi-Mode Jahn-Teller and Pseudo-Jahn-Teller Eects in Benzenoid Cations. In H. Köppel, D. R. Yarkony, & H. Barentzen (Eds.), The Jahn-Teller Efffect: Fundamentals and Implications for Physics and Chemistry (Vol. 97, pp. 239-276). (Springer Series in Chemical Physics; Vol. 97). Springer Verlag.


Faraji, S., & Koeppel, H. (2008). Multistate vibronic interactions in difluorobenzene radical cations. I. Electronic structure calculations. Journal of Chemical Physics, 129(7), [074310].
Faraji, S., Meyer, H-D., & Koeppel, H. (2008). Multistate vibronic interactions in difluorobenzene radical cations. II. Quantum dynamical simulations. Journal of Chemical Physics, 129(7), [074311].
Hashemianzadeh, S. M., Faraji, S., Amin, A. H., & Ketabi, S. (2008). Theoretical study of the interactions between isolated DNA bases and various groups IA and IIA metal ions by Ab initio calculations. Monatshefte fur chemie, 139(2), 89-100.
Faraji, S., Koeppel, H., Eisfeld, W., & Mahapatra, S. (2008). Towards a higher-order description of Jahn-Teller coupling effects in molecular spectroscopy: The (A)over-tilde(2)E '' state of NO3. Chemical Physics, 347(1-3), 110-119.
Last modified:06 March 2017 4.30 p.m.