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Edison X. Salazar, Maximilian F. S. J. Menger, Shirin Faraji (2024) Ultrafast Photoinduced Dynamics in 1,3-Cyclohexadiene: A Comparison of Trajectory Surface Hopping Schemes. J. Chem. Theory Comput. published https://pubs.acs.org/doi/10.1021/acs.jctc.4c00012

Vito F. Palmisano, Nuria Anguita-Ortiz, Shirin Faraji, Juan Jose Nogueira (2024) . Voltage Gated Ion Channels: Structure, Pharmacology and Photopharmacology. ChemPhysChem. e202400162. https://doi.org/10.1002/cphc.202400162

Palmisano, V. F., Agnorelli, C., Fagiolini, A., Erritzoe, D., Nutt, D., Faraji, S., & Nogueira, J. J. (2024). Membrane Permeation of Psychedelic Tryptamines by Dynamic Simulations. Biochemistry63(4), 419-428. https://doi.org/(...)/acs.biochem.3c00598


Huo, Y., Cangahuala, M. K. E., Zamudio-bayer, V., Goulart, M., Kubin, M., Timm, M., Lau, J. T., Issendorff, B. V., Hoekstra, R., Faraji, S., & Schlathölter, T. (2023). A comparative laboratory study of soft X-ray-induced ionization and fragmentation of five small PAH cations. The European Physical Journal D77(10), Article 181. https://doi.org/(...)d/s10053-023-00763-w

Huo, Y., Espinoza Cangahuala, M., Zamudio-Bayer, V., Goulart, M., Kubin, M., Timm, M., Lau, J. T., Issendorff, B. V., Hoekstra, R., Faraji, S., & Schlathölter, T. (2023). An X-ray spectroscopy study of structural stability of superhydrogenated pyrene derivatives. Monthly Notices of the Royal Astronomical Society523(1), 865-875. Article 11. https://doi.org/10.1093/mnras/stad1341

Landau, A., Eduardus, Behar, D., Wallach, E. R., Pašteka, L. F., Faraji, S., Borschevsky, A., & Shagam, Y. (2023). Chiral molecule candidates for trapped ion spectroscopy by ab initio calculations: From state preparation to parity violation. The Journal of Chemical Physics159(11), Article 114307. https://doi.org/10.1063/5.0163641

Palmisano, V. F., Faraji, S., & Nogueira, J. J. (2023). Effect of stacking interactions on charge transfer states in photoswitches interacting with ion channels. PPCP : Physical Chemistry Chemical Physics25(12), 8331-8335. https://doi.org/10.1039/d2cp05678j

Thie, A., Menger, M. F. S. J., & Faraji, S. (2023). HOAX: A hyperparameter optimisation algorithm explorer for neural networks. Molecular Physics121(9-10), Article e2172732. https://doi.org/(...)0268976.2023.2172732

Eduardus, E., Shagam, Y., Landau, A., Faraji, S., Schwerdtfeger, P., Borschevsky, A., & Pašteka, L. F. (2023). Large vibrationally induced parity violation effects in CHDBrI +. Chemical communications (Cambridge, England)59, 14579-14582. https://doi.org/10.1039/d3cc03787h

Grigorenko, B. L., Polyakov, I. V., Khrenova, M. G., Giudetti, G., Faraji, S., Krylov, A. I., & Nemukhin, A. V. (2023). Multiscale Simulations of the Covalent Inhibition of the SARS-CoV-2 Main Protease: Four Compounds and Three Reaction Mechanisms. Journal of the American Chemical Society145(24), 13204-13214. https://doi.org/10.1021/jacs.3c02229

Menger, M. F. S. J., Ou, Q., Shao, Y., Faraji, S., Subotnik, J. E., & Cofer-Shabica, D. V. (2023). Nature of Hops, Coordinates, and Detailed Balance for Nonadiabatic Simulations in the Condensed Phase. The journal of physical chemistry. A127(40), 8427-8436. https://doi.org/10.1021/acs.jpca.3c03546



Witek, J., Heindel, J. P., Guan, X., Leven, I., Hao, H., Naullage, P., LaCour, A., Sami, S., Menger, M. F. S. J., Cofer-Shabica, D. V., Berquist, E., Faraji, S., Epifanovsky, E., & Head-Gordon, T. (2023). M-Chem: a modular software package for molecular simulation that spans scientific domains. Molecular Physics121(9-10), Article e2129500. https://doi.org/(...)0268976.2022.2129500

Giudetti, G., Polyakov, I., Grigorenko, B. L., Faraji, S., Nemukhin, A. V., & Krylov, A. I. (2022). 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 Computation18(8), 5056–5067. https://doi.org/10.1021/acs.jctc.2c00286

Cofer-Shabica, D. V., Menger, M. F. S. J., Ou, Q., Shao, Y., Subotnik, J. E., & Faraji, S. (2022). INAQS, a Generic Interface for Nonadiabatic QM/MM Dynamics: Design, Implementation, and Validation for GROMACS/Q-CHEM simulations. Journal of Chemical Theory and Computation18(8), 4601-4614. https://doi.org/10.1021/acs.jctc.2c00204

Wang, X., Rathnachalam, S., Zamudio-Bayer, V., Bijlsma, K., Li, W., Hoekstra, R., Kubin, M., Timm, M., von Issendorff, B., Lau, J. T., Faraji, S., & Schlathölter, T. (2022). Intramolecular hydrogen transfer in DNA induced by site-selective resonant core excitation. PPCP : Physical Chemistry Chemical Physics24(13), 7815-7825. https://doi.org/10.1039/D1CP05741C

Salazar, E., Reinink, S., & Faraji, S. (2022). Providing theoretical insight into the role of symmetry in the photoisomerization mechanism of a non-symmetric dithienylethene photoswitch. PPCP : Physical Chemistry Chemical Physics24(19), 11592-11602. https://doi.org/10.1039/d2cp00550f

Huo, Y., Cangahuala, M. K. E., Goulart, M., Zamudio-Bayer, V., Kubin, M., Timm, M., Lau, J. T., Von Issendorff, B., Hoekstra, R., Faraji, S., & Schlathölter, T. (2022). Soft-x-ray spectroscopy of coronene plus and (coronene plus H) plus cations: The influence of hydrogenation on electronic structure and photofragmentation. Physical Review A - Atomic, Molecular, and Optical Physics106(6), Article 063104. https://doi.org/(...)/PhysRevA.106.063104

Toyoda, R., Hoang, N. V., Moghaddam, K. G., Crespi, S., Pooler, D. R. S., Faraji, S., Pshenichnikov, M. S., & Feringa, B. L. (2022). Synergistic interplay between photoisomerization and photoluminescence in a light-driven rotary molecular motor. Nature Communications13(1), Article 5765. https://doi.org/(...)8/s41467-022-33177-0


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 Physics23(5), 3552-3564. https://doi.org/10.1039/d0cp06140a

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 Physics23(26), 14113–14534. https://doi.org/10.1039/d1cp00298h

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, & Biophysical125(9), 2231–2240. https://doi.org/10.1021/acs.jpcb.0c10466

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 Computation17(8), 4946–4960. https://doi.org/10.1021/acs.jctc.1c00195

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 D75(5), Article 152. https://doi.org/(...)d/s10053-021-00155-y

Bruininks, B. M. H., Thie, A. S., Souza, P. C. T., Wassenaar, T. A., Faraji, S., & Marrink, S. J. (2021). Sequential Voxel-Based Leaflet Segmentation of Complex Lipid Morphologies. Journal of Chemical Theory and Computation17(12), 7873–7885. https://doi.org/10.1021/acs.jctc.1c00446

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 Physics20, 11900-11906. https://doi.org/10.1039/D1CP01014J

Epifanovsky, E., Gilbert, A. T. B., Feng, X., Lee, J., Mao, Y., Mardirossian, N., Pokhilko, P., White, A. F., Coons, M. P., Dempwolff, A. L., Gan, Z., Hait, D., Horn, P. R., Jacobson, L. D., Kaliman, I., Kussmann, J., Lange, A. W., Lao, K. U., Levine, D. S., ... Krylov, A. I. (2021). Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package. The Journal of Chemical Physics155(8), Article 084801. https://doi.org/10.1063/5.0055522

Barakat, F., Laref, A., Alterary, S., Faraji, S., & Alsalhi, M. (2021). Structural and optical behaviors of 2D-layered molybdenum disulfide thin film: Experimental and ab-initio insights. Journal of Materials Research and Technology14, 780-796. https://doi.org/(...)6/j.jmrt.2021.06.059

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 science33(3), Article 101389. https://doi.org/(...)/j.jksus.2021.101389

Romeo-Gella, F., Corral, I., & Faraji, S. (2021). Theoretical investigation of a novel xylene-based light-driven unidirectional molecular motor. The Journal of Chemical Physics154(6), Article 064111. https://doi.org/10.1063/5.0038281


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 Physics152(6), Article 064111. https://doi.org/10.1063/1.5141358

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 Chemistry11(15), 2749-2760. https://doi.org/10.1039/c9py01915d

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 development64(3-4), Article 8960361. https://doi.org/10.1147/JRD.2020.2965881

Menger, M. F. S. J., Ehrmaier, J., & Faraji, S. (2020). PySurf: A Framework for Database Accelerated Direct Dynamics. Journal of Chemical Theory and Computation16(12), 7681-7689. https://doi.org/10.1021/acs.jctc.0c00825

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. Organometallics39(10), 1814-1823. https://doi.org/(...)cs.organomet.0c00102

Suarez, L. E. A., Menger, M. F. S. J., & Faraji, S. (2020). Singlet fission in tetracene: An excited state analysis. Molecular Physics118(21-22), Article e1769870. https://doi.org/(...)0268976.2020.1769870

Barakat, F., Laref, A., AlSalhi, M., & Faraji, S. (2020). The impact of anion elements on the engineering of the electronic and optical characteristics of the two dimensional monolayer janus MoSSe for nanoelectronic device applications. Results in Physics18, Article 103284. https://doi.org/(...)6/j.rinp.2020.103284

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 Physics22(46), 26944-26954. https://doi.org/10.1039/d0cp04392c

Salazar, E., & Faraji, S. (2020). Theoretical study of cyclohexadiene/hexatriene photochemical interconversion using spin-Flip time-Dependent density functional theory. Molecular Physics118(19-20), Article 1764120. https://doi.org/(...)0268976.2020.1764120


Sen, R., Dreuw, A., & Faraji, S. (2019). Algebraic diagrammatic construction for the polarisation propagator in combination with effective fragment potentials. Physical Chemistry Chemical Physics21(7), 3683-3694. https://doi.org/10.1039/c8cp06527f

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 Chemistry253, Article 106220. https://doi.org/(...)16/j.bpc.2019.106220

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. https://doi.org/(...)6/bs.aiq.2019.05.004

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 Interfaces123(42), 25908-25914. https://doi.org/10.1021/acs.jpcc.9b05889

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 Physics151(18), Article 184903. https://doi.org/10.1063/1.5121863

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 Omega4(15), 16481-16492. https://doi.org/10.1021/acsomega.9b02126


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 Physics148(4), Article 044103. https://doi.org/10.1063/1.5009433

Straatsma, T. P., Broer, R., Faraji, S., & Havenith, R. W. A. (2018). GronOR Nonorthogonal Configuration Interaction Calculations at Exascale. Annual Reports in Computational Chemistry14, 77-91. https://doi.org/(...)/bs.arcc.2018.06.003

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. Chemistry24(1), 71-76. https://doi.org/10.1002/chem.201704652


Faraji, S., & Dreuw, A. (2017). Insights into Light-driven DNA Repair by Photolyases: Challenges and Opportunities for Electronic Structure Theory. Photochemistry and Photobiology93(1), 37-50. https://doi.org/10.1111/php.12679


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 Edition55(17), 5175-5178. https://doi.org/10.1002/anie.201511950


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 Communications36(1), 31-37. https://doi.org/10.1002/marc.201400562

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, & Biophysical119(41), 13052-13062. https://doi.org/10.1021/acs.jpcb.5b07724


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. https://doi.org/(...)yschem-040513-103626

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 Chemistry1040-1041, 177-185. https://doi.org/(...)j.comptc.2014.04.003


Dreuw, A., & Faraji, S. (2013). A quantum chemical perspective on (6-4) photolesion repair by photolyases. PPCP : Physical Chemistry Chemical Physics15(46), 19957-19969. https://doi.org/10.1039/c3cp53313a

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, & Biophysical117(35), 10071-10079. https://doi.org/10.1021/jp401662z

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 Letters4(6), 943-949. https://doi.org/10.1021/jz400104h

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. Chemphyschem14(12), 2817-2824. https://doi.org/10.1002/cphc.201300223


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 Physics137(13), Article 134302. https://doi.org/10.1063/1.4755372

Faraji, S., & Koeppel, H. (2012). Multi-state vibronic interactions in the 1,2,3-trifluorobenzene radical cation. Journal of Chemical Physics137(22), Article ARTN 22A531. https://doi.org/10.1063/1.4746159

Faraji, S., & Dreuw, A. (2012). Proton-Transfer-Steered Mechanism of Photo lesion Repair by (6-4)-Photolyases. The Journal of Physical Chemistry Letters3(2), 227-230. https://doi.org/10.1021/jz201587v


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 Physics135(15), Article 154310. https://doi.org/10.1063/1.3651536

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. https://doi.org/(...)/978-3-642-03432-9_9


Faraji, S., & Koeppel, H. (2008). Multistate vibronic interactions in difluorobenzene radical cations. I. Electronic structure calculations. Journal of Chemical Physics129(7), Article 074310. https://doi.org/10.1063/1.2958915

Faraji, S., Meyer, H.-D., & Koeppel, H. (2008). Multistate vibronic interactions in difluorobenzene radical cations. II. Quantum dynamical simulations. Journal of Chemical Physics129(7), Article 074311. https://doi.org/10.1063/1.2958918

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 chemie139(2), 89-100. https://doi.org/(...)07/s00706-007-0744-9

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 Physics347(1-3), 110-119. https://doi.org/(...)chemphys.2007.10.006