Publications
2024
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. Biochemistry,
63(4), 419-428. https://doi.org/10.1021/acs.biochem.3c00598
2023
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
D, 77(10), Article 181. https://doi.org/10.1140/epjd/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 Society,
523(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 Physics,
159(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 Physics, 25(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
Physics, 121(9-10), Article e2172732. https://doi.org/10.1080/00268976.2023.2172732
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 Society, 145(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. A, 127(40), 8427-8436. https://doi.org/10.1021/acs.jpca.3c03546
2022
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 Physics,
121(9-10), Article e2129500. https://doi.org/10.1080/00268976.2022.2129500
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
Computation, 18(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
Computation, 18(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 Physics, 24(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
Physics, 24(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 Physics,
106(6), Article 063104. https://doi.org/10.1103/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 Communications, 13(1),
Article 5765. https://doi.org/10.1038/s41467-022-33177-0
2021
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. 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 Physics, 23(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, & Biophysical,
125(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 Computation, 17(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
D, 75(5), Article 152. https://doi.org/10.1140/epjd/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
Computation, 17(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
Physics, 20, 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
Physics, 155(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 Technology, 14, 780-796. https://doi.org/10.1016/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 science, 33(3), Article
101389. https://doi.org/10.1016/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 Physics, 154(6), Article
064111. https://doi.org/10.1063/5.0038281
2020
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), 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
Chemistry, 11(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
development, 64(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 Computation, 16(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.
Organometallics, 39(10), 1814-1823.
https://doi.org/10.1021/acs.organomet.0c00102
Suarez,
L. E. A., Menger, M. F. S. J., &
Faraji, S. (2020). Singlet fission in tetracene: An
excited state analysis. Molecular
Physics, 118(21-22), Article e1769870. https://doi.org/10.1080/00268976.2020.1769870
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 Physics,
18, Article 103284. https://doi.org/10.1016/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 Physics, 22(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 Physics, 118(19-20),
Article 1764120. https://doi.org/10.1080/00268976.2020.1764120
2019
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. 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
Chemistry, 253, Article 106220. https://doi.org/10.1016/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/10.1016/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
Interfaces, 123(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 Physics, 151(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
Omega, 4(15), 16481-16492. https://doi.org/10.1021/acsomega.9b02126
2018
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), 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 Chemistry,
14, 77-91. https://doi.org/10.1016/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.
Chemistry, 24(1), 71-76. https://doi.org/10.1002/chem.201704652
2017
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. https://doi.org/10.1111/php.12679
2016
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. https://doi.org/10.1002/anie.201511950
2015
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. 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, & Biophysical,
119(41), 13052-13062. https://doi.org/10.1021/acs.jpcb.5b07724
2014
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/10.1146/annurev-physchem-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 Chemistry,
1040-1041, 177-185. https://doi.org/10.1016/j.comptc.2014.04.003
2013
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. 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, & Biophysical,
117(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 Letters,
4(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. Chemphyschem,
14(12), 2817-2824. https://doi.org/10.1002/cphc.201300223
2012
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), 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 Physics,
137(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 Letters,
3(2), 227-230. https://doi.org/10.1021/jz201587v
2011
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), 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.
2009
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/10.1007/978-3-642-03432-9_9
2008
Faraji,
S., & Koeppel, H. (2008). Multistate vibronic
interactions in difluorobenzene radical cations. I. Electronic
structure calculations. Journal of Chemical
Physics, 129(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
Physics, 129(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
chemie, 139(2), 89-100. https://doi.org/10.1007/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 Physics,
347(1-3), 110-119. https://doi.org/10.1016/j.chemphys.2007.10.006
Last modified: | 09 June 2023 8.36 p.m. |