Submitted

[61] Lee, S.; Park, W.; Komarov, K.; Farmani, M.; Mironov, V.; Nakata, H.; Lashakripour, A.; Zeng, T.; Huix-Rotllant, M.; Choi, C.; Expanding Horizons in Quantum Chemical Studies: The Versatile Power of MRSF-TDDFT. (submitted) 2024.

[60] Bonfrate, S.; Park, W.; Trejo, D.; Ferré, N.; Choi, C.; Huix-Rotllant, M.; Assessment of free energies from electrostatic embedding density functional tight binding-based/molecular mechanics in periodic boundary conditions. (submitted) 2024.

[59] Fay, T.; Ferré, N.; Huix-Rotllant, M.; Efficient polarizable QM/MM using the direct reaction field Hamiltonian with electrostatic potential fitted multipole operators. (accepted) 2024. DOI: 10.48550/arXiv.2409.10483

[58] Barreiro-Lage, D.; Ledentu, V.; D'Ascenzi, J.; Huix-Rotllant, M.; Ferré, N.; Investigating the origin of Automatic Rhodopsin Modeling outliers using the microbial Gloeobacter rhodopsin as testbed. (submitted) 2024. DOI: 10.1021/acs.jpcb.4c05962

Accepted

[57] Park, W.; Oh, J.; Kim, J.; Lee, S.; Kim, J. H.; Huix-Rotllant, M.; Kim, D.; Choi, C.; Temperature Controlled Decay and Pendulum Dynamics of Green Fluorescent Protein (GFP) Chromophore. J. Chem. Phys. Lett. 2024. DOI: 10.1021/acs.jpclett.4c02761

[56] Mironov, V.; Komarov, K.; Li, J.; Gerasimov, I.; Nakata, H.; Mazaheri, M.; Ishimura, K.; Park, W.; Lashkaripour, A.; Oh, M.; Huix-Rotllant, M.; Lee, S.; Choi, C. H.; OpenQP: A Quantum Chemical Platform Featuring MRSF-TDDFT with an Emphasis on Open-source Ecosystem. J. Chem. Theor. Comput. (accepted) 2024. DOI: 10.1021/acs.jctc.4c01117

[55] Fall, A.; Tintori, G.; Rollet, M.; Zhao, Y.; Charles, L.; Berge-Lefranc, D.; Clément, J.-L.; Redon, S.; Gigmes, D.; Vanelle, P.; Huix-Rotllant, M.; Broggi, J. α-Trifluoromethylated Quinolines as Air-Stable and Safe PET-Donor for Radical Polymerizations. Macromol. Rapid Commun. (accepted) 2024. DOI: 10.1002/marc.202400710

[54] Park, W.; Lashakripour, A. ; Komarov, K. ; Lee, S. ; Huix-Rotllant, M. ; Choi, C. H. Toward Consistent Predictions of Core/Valence Ionization Potentials and Valence Excitation Energies by MRSF-TDDFT. J. Chem. Theor. Comput. 20, 5679-5694, 2024. DOI: 10.1021/acs.jctc.4c00640

[53] Alias-Rodríguez, M.; Huix-Rotllant, M. Control of the Iron-Tris(2,2’-Bipyridine) Light-Induced Excited-State Trapping via External Electromagnetic Fields. ChemPhysChem 25, e202400471, 2024. DOI: 10.1002/cphc.202400471

[52] Bonfrate, S.; Ferré, N.; Huix-Rotllant, M. Analytic Gradients for the Electrostatic Embedding QM/MM in Periodic Boundary Conditions Using Particle-Mesh Ewald Sums and Electrostatic Potential Fitted Charge Operators. J. Comp. Theor. Comput. 20, 4338–4349, 2024. DOI: 10.1021/acs.jctc.4c00201

[51] Barends, T. R. M.; Bhattacharyya, S.; Gorel, A.; Schiro, G.; Bacellar, C.; Cirelli, C.; Colletier, J.-P.; Foucar, L.; Grünbein, M. L.; Hartmann, E.; Hilpert, M.; Johnson, P. J. M.; Kloos, M.; Knopp, G.; Marekha, B.; Nass, K.; Kovacs, G. N.; Ozerov, D.; Stricker, M.; Weik, M.; Doak, R. B.; Shoeman, R. L.; Milne, C. J.; Huix-Rotllant, M.; Cammarata, M.; Schlichting, I. Influence of Pump Laser Fluence on Ultrafast Structural Changes in Myoglobin. Nature 626, 905–911, 2024. DOI: 10.1038/s41586-024-07032-9.

[50] Pieri, E.; Weingart, O.; Huix-Rotllant, M.; Ledentu, V.; Garavelli, M.; Ferré, N. Modeling PH-Dependent Biomolecular Photochemistry. Journal of Chemical Theory and Computation 20, 842–855, 2024. DOI: 10.1021/acs.jctc.3c00980.

[49] González-Sánchez, J. M.; Huix-Rotllant, M.; Brun, N.; Morin, J.; Demelas, C.; Durand, A.; Ravier, S.; Clément, J.-L.; Monod, A. Direct Formation of HONO through Aqueous-Phase Photolysis of Organic Nitrates. Atmospheric Chemistry and Physics 23, 15135–15147, 2023. DOI: 10.5194/acp-23-15135-2023.

[48] Barneschi, L.; Kaliakin, D.; Huix-Rotllant, M.; Ferré, N.; Filatov(Gulak), M.; Olivucci, M. Assessment of the Electron Correlation Treatment on the Quantum-Classical Dynamics of Retinal Protonated Schiff Base Models: XMS-CASPT2, RMS-CASPT2, and REKS Methods. Journal of Chemical Theory and Computation 19, 8189–8200, 2023. DOI: 10.1021/acs.jctc.3c00879.

[47] Komarov, K.; Park, W.; Lee, S.; Huix-Rotllant, M.; Choi, C. H. Doubly Tuned Exchange–Correlation Functionals for Mixed-Reference Spin-Flip Time-Dependent Density Functional Theory. Journal of Chemical Theory and Computation 19, 7671–7684, 2023. DOI: 10.1021/acs.jctc.3c00884.

[46] Cárdenas, G.; Ledentu, V.; Huix-Rotllant, M.; Olivucci, M.; Ferré, N. Automatic Rhodopsin Modeling with Multiple Protonation Microstates. The Journal of Physical Chemistry A 127, 9365–9380, 2023. DOI: 10.1021/acs.jpca.3c05413.

[45] Alías-Rodríguez, M.; Bonfrate, S.; Park, W.; Ferré, N.; Choi, C. H.; Huix-Rotllant, M. Solvent Effects and pH Dependence of the X-Ray Absorption Spectra of Proline from Electrostatic Embedding Quantum Mechanics / Molecular Mechanics and Mixed-Reference Spin-Flip Time-Dependent Density-Functional Theory. The Journal of Physical Chemistry A 127, 10382–10392, 2023. DOI: 10.1021/acs.jpca.3c05070.

[44] Alías-Rodríguez, M.; Bhattacharyya, S.; Huix-Rotllant, M. Ultrafast Spin Crossover Photochemical Mechanism in [Fe^II(2,2\prime-Bipyridine)₃]²⁺ Revealed by Quantum Dynamics. The Journal of Physical Chemistry Letters 8571–8576, 2023. DOI: 10.1021/acs.jpclett.3c02201.

[43] Manni, G. L.; Galván, I. Fdez.; Alavi, A.; Aleotti, F.; Aquilante, F.; Autschbach, J.; Avagliano, D.; Baiardi, A.; Bao, J. J.; Battaglia, S.; Birnoschi, L.; Blanco-González, A.; Bokarev, S. I.; Broer, R.; Cacciari, R.; Calio, P. B.; Carlson, R. K.; Couto, R. C.; Cerdán, L.; Chibotaru, L. F.; Chilton, N. F.; Church, J. R.; Conti, I.; Coriani, S.; Cuéllar-Zuquin, J.; Daoud, R. E.; Dattani, N.; Decleva, P.; de Graaf, C.; Delcey, M. G.; Vico, L. D.; Dobrautz, W.; Dong, S. S.; Feng, R.; Ferré, N.; Filatov(Gulak), M.; Gagliardi, L.; Garavelli, M.; González, L.; Guan, Y.; Guo, M.; Hennefarth, M. R.; Hermes, M. R.; Hoyer, C. E.; Huix-Rotllant, M.; Jaiswal, V. K.; Kaiser, A.; Kaliakin, D. S.; Khamesian, M.; King, D. S.; Kochetov, V.; Krośnicki, M.; Kumaar, A. A.; Larsson, E. D.; Lehtola, S.; Lepetit, M.-B.; Lischka, H.; Ríos, P. L.; Lundberg, M.; Ma, D.; Mai, S.; Marquetand, P.; Merritt, I. C. D.; Montorsi, F.; Mörchen, M.; Nenov, A.; Nguyen, V. H. A.; Nishimoto, Y.; Oakley, M. S.; Olivucci, M.; Oppel, M.; Padula, D.; Pandharkar, R.; Phung, Q. M.; Plasser, F.; Raggi, G.; Rebolini, E.; Reiher, M.; Rivalta, I.; Roca-Sanjuán, D.; Romig, T.; Safari, A. A.; Sánchez-Mansilla, A.; Sand, A. M.; Schapiro, I.; Scott, T. R.; Segarra-Martí, J.; Segatta, F.; Sergentu, D.-C.; Sharma, P.; Shepard, R.; Shu, Y.; Staab, J. K.; Straatsma, T. P.; Sørensen, L. K.; Tenorio, B. N. C.; Truhlar, D. G.; Ungur, L.; Vacher, M.; Veryazov, V.; Voß, T. A.; Weser, O.; Wu, D.; Yang, X.; Yarkony, D.; Zhou, C.; Zobel, J. P.; Lindh, R. The OpenMolcas Web: A Community-Driven Approach to Advancing Computational Chemistry. Journal of Chemical Theory and Computation 2023. DOI: 10.1021/acs.jctc.3c00182.

[42] Bonfrate, S.; Ferré, N.; Huix-Rotllant, M. An Efficient Electrostatic Embedding QM/MM Method Using Periodic Boundary Conditions Based on Particle-Mesh Ewald Sums and Electrostatic Potential Fitted Charge Operators. The Journal of Chemical Physics 158, 2023. DOI: 10.1063/5.0133646.

[41] Huix-Rotllant, M.; Schwinn, K.; Pomogaev, V.; Farmani, M.; Ferré, N.; Lee, S.; Choi, C. H. Photochemistry of Thymine in Solution and DNA Revealed by an Electrostatic Embedding QM/MM Combined with Mixed-Reference Spin-Flip TDDFT. Journal of Chemical Theory and Computation 19, 147–156, 2022. DOI: 10.1021/acs.jctc.2c01010.

[40] Barneschi, L.; Marsili, E.; Pedraza-González, L.; Padula, D.; Vico, L. D.; Kaliakin, D.; Blanco-González, A.; Ferré, N.; Huix-Rotllant, M.; Filatov, M.; Olivucci, M. On the Fluorescence Enhancement of Arch Neuronal Optogenetic Reporters. Nature Communications 13, 2022. DOI: 10.1038/s41467-022-33993-4.

[39] Filatov, M.; Paolino, M.; Pierron, R.; Cappelli, A.; Giorgi, G.; Léonard, J.; Huix-Rotllant, M.; Ferré, N.; Yang, X.; Kaliakin, D.; Blanco-González, A.; Olivucci, M. Towards the Engineering of a Photon-Only Two-Stroke Rotary Molecular Motor. Nature Communications 13, 2022. DOI: 10.1038/s41467-022-33695-x.

[38] Park, W.; Alías-Rodríguez, M.; Cho, D.; Lee, S.; Huix-Rotllant, M.; Choi, C. H. Mixed-Reference Spin-Flip Time-Dependent Density Functional Theory for Accurate X-Ray Absorption Spectroscopy. Journal of Chemical Theory and Computation 18, 6240–6250, 2022. DOI: 10.1021/acs.jctc.2c00746.

[37] Tissier, R.-C.; Rigaud, B.; Thureau, P.; Huix-Rotllant, M.; Jaber, M.; Ferré, N. Stressing the Differences in Alizarin and Purpurin Dyes through UV-Visible Light Absorption and ¹H-NMR Spectroscopies. Physical Chemistry Chemical Physics 2022. DOI: 10.1039/d2cp00520d.

[36] Alías-Rodríguez, M.; Huix-Rotllant, M.; de Graaf, C. Quantum Dynamics Simulations of the Thermal and Light-Induced High-Spin to Low-Spin Relaxation in Fe(Bpy)₃ and Fe(Mtz)₆. Faraday Discussions 2022. DOI: 10.1039/d2fd00027j.

[35] Alías-Rodríguez, M.; de Graaf, C.; Huix-Rotllant, M. Ultrafast Intersystem Crossing in Xanthone from Wavepacket Dynamics. Journal of the American Chemical Society 143, 21474–21477, 2021. DOI: 10.1021/jacs.1c07039.

[34] Huix-Rotllant, M. Photochemistry of Thymine in Protic Polar Nanomeric Droplets Using Electrostatic Embeding TD-DFT/MM. Molecules 26, 2021. DOI: 10.3390/molecules26196021.

[33] Park, W.; Lee, S.; Huix-Rotllant, M.; Filatov, M.; Choi, C. H. Impact of the Dynamic Electron Correlation on the Unusually Long Excited-State Lifetime of Thymine. The Journal of Physical Chemistry Letters 12, 4339–4346, 2021. DOI: 10.1021/acs.jpclett.1c00712.

[32] Huix-Rotllant, M.; Schwinn, K.; Ferré, N. Infrared Spectroscopy from Electrostatic Embedding QM/MM: Local Normal Mode Analysis of Infrared Spectra of Arabidopsis Thaliana Plant Cryptochrome. Phys. Chem. Chem. Phys. 23, 1666–1674, 2021. DOI: 10.1039/D0CP06070D.

[31] Huix-Rotllant, M.; Ferré, N. Analytic Energy, Gradient, and Hessian of Electrostatic Embedding QM/MM Based on Electrostatic Potential-Fitted Atomic Charges Scaling Linearly with the MM Subsystem Size. Journal of Chemical Theory and Computation 17, 538–548, 2021. DOI: 10.1021/acs.jctc.0c01075.

[30] Mondal, P.; Schwinn, K.; Huix-Rotllant, M. Impact of the Redox State of Flavin Chromophores on the UV–Vis Spectra, Redox and Acidity Constants and Electron Affinities. Journal of Photochemistry and Photobiology A: Chemistry 387, 112164, 2020. DOI: 10.1016/j.jphotochem.2019.112164.

[29] Schwinn, K.; Ferré, N.; Huix-Rotllant, M. Efficient Analytic Second Derivative of Electrostatic Embedding QM/MM Energy: Normal Mode Analysis of Plant Cryptochrome. Journal of Chemical Theory and Computation 16, 3816–3824, 2020. DOI: 10.1021/acs.jctc.9b01145.

[28] Schwinn, K.; Ferré, N.; Huix-Rotllant, M. UV-Visible Absorption Spectrum of FAD and Its Reduced Forms Embedded in Cryptochrome Protein. Phys. Chem. Chem. Phys. 12447–12455, 2020. DOI: 10.1039/D0CP01714K.

[27] Schwinn, K.; Ferré, N.; Huix-Rotllant, M. Analytic QM/MM Atomic Charge Derivatives Avoiding the Scaling of Coupled Perturbed Equations with the MM Subsystem Size. The Journal of Chemical Physics 151, 041102, 2019. DOI: 10.1063/1.5115125.

[26] Mondal, P.; Huix-Rotllant, M. Theoretical Insights into the Formation and Stability of Radical Oxygen Species in Cryptochrome. Phys. Chem. Chem. Phys. 8874–8882, 2019. DOI: 10.1039/C9CP00782B.

[25] Pieri, E.; Ledentu, V.; Huix-Rotllant, M.; Ferré, N. Sampling the Protonation States: The PH-Dependent UV Absorption Spectrum of a Polypeptide Dyad. Phys. Chem. Chem. Phys. 20, 23252–23261, 2018. DOI: 10.1039/C8CP03557A.

[24] Falahati, K.; Tamura, H.; Burghardt, I.; Huix-Rotllant, M. Ultrafast Carbon Monoxide Photolysis and Heme Spin-Crossover in Myoglobin via Nonadiabatic Quantum Dynamics. Nature Communications 9, 2018. DOI: 10.1038/s41467-018-06615-1.

[23] Falahati, K.; Hamerla, C.; Huix-Rotllant, M.; Burghardt, I. Ultrafast Photochemistry of Free-Base Porphyrin: A Theoretical Investigation of B → Q Internal Conversion Mediated by Dark States. Phys. Chem. Chem. Phys. 20, 12483–12492, 2018. DOI: 10.1039/C8CP00657A.

[22] Vayá, I.; Brazard, J.; Huix-Rotllant, M.; Thazhathveetil, A. K.; Lewis, F. D.; Gustavsson, T.; Burghardt, I.; Improta, R.; Markovitsi, D. High-Energy Long-Lived Mixed Frenkel–Charge-Transfer Excitons: From Double Stranded (AT)ₙ to Natural DNA. Chemistry – A European Journal 22, 4904–4914, 2016. DOI: 10.1002/chem.201504007.

[21] Huix-Rotllant, M.; Burghardt, I.; Ferré, N. Population of Triplet States in Acetophenone: A Quantum Dynamics Perspective. Comptes Rendus Chimie 19, 50–56, 2016. DOI: 10.1016/j.crci.2015.10.002.

[20] Huix-Rotllant, M.; Ferré, N. An Effective Procedure for Analyzing Molecular Vibrations in Terms of Local Fragment Modes. Journal of Chemical Theory and Computation 12, 4768–4777, 2016. DOI: 10.1021/acs.jctc.6b00514.

[19] Tamura, H.; Huix-Rotllant, M.; Burghardt, I.; Olivier, Y.; Beljonne, D. First-Principles Quantum Dynamics of Singlet Fission: Coherent versus Thermally Activated Mechanisms Governed by Molecular π Stacking. Physical Review Letters 115, 2015. DOI: 10.1103/physrevlett.115.107401.

[18] Huix-Rotllant, M.; Tamura, H.; Burghardt, I. Concurrent Effects of Delocalization and Internal Conversion Tune Charge Separation at Regioregular Polythiophene-Fullerene Heterojunctions. The Journal of Physical Chemistry Letters 6, 1702–1708, 2015. DOI: 10.1021/acs.jpclett.5b00336.

[17] Huix-Rotllant, M.; Brazard, J.; Improta, R.; Burghardt, I.; Markovitsi, D. Stabilization of Mixed Frenkel-Charge Transfer Excitons Extended Across Both Strands of Guanine-Cytosine DNA Duplexes. The Journal of Physical Chemistry Letters 6, 2247–2251, 2015. DOI: 10.1021/acs.jpclett.5b00813.

[16] Filatov, M.; Huix-Rotllant, M.; Burghardt, I. Ensemble Density Functional Theory Method Correctly Describes Bond Dissociation, Excited State Electron Transfer, and Double Excitations. The Journal of Chemical Physics 142, 2015. DOI: 10.1063/1.4919773.

[15] Huix-Rotllant, M.; Nikiforov, A.; Thiel, W.; Filatov, M. Description of Conical Intersections with Density Functional Methods; Density-Functional Methods for Excited States; Springer International Publishing, 2015; pp 445–476. DOI: 10.1007/128_2015_631.

[14] Casida, M. E.; Huix-Rotllant, M. Many-Body Perturbation Theory (MBPT) and Time-Dependent Density-Functional Theory (TD-DFT): MBPT Insights About What Is Missing In, and Corrections To, the TD-DFT Adiabatic Approximation; Density-Functional Methods for Excited States; Springer International Publishing, 2015; pp 1–60. DOI: 10.1007/128_2015_632.

[13] Huix-Rotllant, M.; Ferré, N. Triplet State Photochemistry and the Three-State Crossing of Acetophenone within Time-Dependent Density-Functional Theory. The Journal of Chemical Physics 140, 2014. DOI: 10.1063/1.4869802.

[12] Huix-Rotllant, M.; Ferré, N. Theoretical Study of the Photochemical Initiation in Nitroxide-Mediated Photopolymerization. The Journal of Physical Chemistry A 118, 4464–4470, 2014. DOI: 10.1021/jp501773n.

[11] Huix-Rotllant, M.; Dumont, E.; Ferré, N.; Monari, A. Photophysics of Acetophenone Interacting with DNA: Why the Road to Photosensitization Is Open. Photochemistry and Photobiology 91, 323–330, 2014. DOI: 10.1111/php.12395.

[10] Nikiforov, A.; Gamez, J. A.; Thiel, W.; Huix-Rotllant, M.; Filatov, M. Assessment of Approximate Computational Methods for Conical Intersections and Branching Plane Vectors in Organic Molecules. The Journal of Chemical Physics 141, 2014. DOI: 10.1063/1.4896372.

[9] Gozem, S.; Melaccio, F.; Valentini, A.; Filatov, M.; Huix-Rotllant, M.; Ferré, N.; Frutos, L. M.; Angeli, C.; Krylov, A. I.; Granovsky, A. A.; Lindh, R.; Olivucci, M. Shape of Multireference, Equation-of-Motion Coupled-Cluster, and Density Functional Theory Potential Energy Surfaces at a Conical Intersection. Journal of Chemical Theory and Computation 10, 3074–3084, 2014. DOI: 10.1021/ct500154k.

[8] Filatov, M.; Huix-Rotllant, M. Assessment of Density Functional Theory Based ΔSCF (Self-Consistent Field) and Linear Response Methods for Longest Wavelength Excited States of Extended π-Conjugated Molecular Systems. The Journal of Chemical Physics 141, 2014. DOI: 10.1063/1.4887087.

[7] Huix-Rotllant, M.; Filatov, M.; Gozem, S.; Schapiro, I.; Olivucci, M.; Ferré, N. Assessment of Density Functional Theory for Describing the Correlation Effects on the Ground and Excited State Potential Energy Surfaces of a Retinal Chromophore Model. Journal of Chemical Theory and Computation 9, 3917–3932, 2013. DOI: 10.1021/ct4003465.

[6] Huix-Rotllant, M.; Siri, D.; Ferré, N. Theoretical Study of the Photochemical Generation of Triplet Acetophenone. Physical Chemistry Chemical Physics 15, 19293, 2013. DOI: 10.1039/c3cp52703d.

[5] Casida, M. E.; Huix-Rotllant, M. Progress in Time-Dependent Density-Functional Theory. Annual Review of Physical Chemistry 63, 287–323, 2012. DOI: 10.1146/annurev-physchem-032511-143803.

[4] Huix-Rotllant, M.; Ipatov, A.; Rubio, A.; Casida, M. E. Assessment of Dressed Time-Dependent Density-Functional Theory for the Low-Lying Valence States of 28 Organic Chromophores. Chemical Physics 391, 120–129, 2011. DOI: 10.1016/j.chemphys.2011.03.019.

[3] Huix-Rotllant, M.; Natarajan, B.; Ipatov, A.; Wawire, C. M.; Deutsch, T.; Casida, M. E. Assessment of Noncollinear Spin-Flip Tamm–Dancoff Approximation Time-Dependent Density-Functional Theory for the Photochemical Ring-Opening of Oxirane. Physical Chemistry Chemical Physics 12, 12811, 2010. DOI: 10.1039/c0cp00273a.

[2] Huix-Rotllant, M.; Deka, A.; Matveev, A. V.; Bosko, S. I.; Moskaleva, L. V.; Rösch, N. Characterization of Optical Spectra of Interacting Systems: Application to Oxide-Supported Metal Clusters. International Journal of Quantum Chemistry 108, 2978–2990, 2008. DOI: 10.1002/qua.21853.

[1] Bonness, S.; Kirtman, B.; Huix, M.; Sanchez, A. J.; Luis, J. M. Simulation of Photoelectron Spectra with Anharmonicity Fully Included: Application to the \tildeXA²₂\leftarrow\tildeXA¹₁ Band of Furan. The Journal of Chemical Physics 125, 2006. DOI: 10.1063/1.2210479.

Book chapters

[1] Huix-Rotllant, M.; Ferré, N.; Barbatti, M. Time-Dependent Density Functional Theory: From Fundamentals to Non-Adiabatic Dynamics; González, L., Lindh, R., Eds.; Quantum Chemistry and Dynamics of Excited States: Methods and Applications; Wiley, 2020; pp 13–46. DOI: 10.1002/9781119417774.ch2.

Edition

[1] Density-Functional Methods for Excited States; Ferré, N., Filatov, M., Huix-Rotllant, M., Eds.; Springer International Publishing, 2016. DOI: 10.1007/978-3-319-22081-9.

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