76
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Xu X, Gozem S, Olivucci M, Truhlar DG. Combined Self-Consistent-Field and Spin-Flip Tamm-Dancoff Density Functional Approach to Potential Energy Surfaces for Photochemistry. J Phys Chem Lett 2013; 4:253-258. [PMID: 26283430 DOI: 10.1021/jz301935x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We present a new approach to calculating potential energy surfaces for photochemical reactions by combining self-consistent-field calculations for single-reference ground and excited states with symmetry-corrected spin-flip Tamm-Dancoff approximation calculations for multireference electronic states. The method is illustrated by an application with the M05-2X exchange-correlation functional to cis-trans isomerization of the penta-2,4-dieniminium cation, which is a model (with three conjugated double bonds) of the protonated Schiff base of retinal. We find good agreement with multireference configuration interaction-plus-quadruples (MRCISD+Q) wave function calculations along three key paths in the strong-interaction region of the ground and first excited singlet states.
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Léonard J, Polli D, Cerullo G, Olivucci M, Haacke S. Influence of the Chemical Design on the Coherent Photoisomerization of Biomimetic Molecular Switches. EPJ WEB OF CONFERENCES 2013. [DOI: 10.1051/epjconf/20134105006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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78
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Léonard J, Schapiro I, Briand J, Fusi S, Paccani RR, Olivucci M, Haacke S. Cover Picture: Mechanistic Origin of the Vibrational Coherence Accompanying the Photoreaction of Biomimetic Molecular Switches (Chem. Eur. J. 48/2012). Chemistry 2012. [DOI: 10.1002/chem.201290204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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79
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Gozem S, Krylov AI, Olivucci M. Conical Intersection and Potential Energy Surface Features of a Model Retinal Chromophore: Comparison of EOM-CC and Multireference Methods. J Chem Theory Comput 2012; 9:284-92. [DOI: 10.1021/ct300759z] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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80
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Léonard J, Schapiro I, Briand J, Fusi S, Paccani RR, Olivucci M, Haacke S. Mechanistic Origin of the Vibrational Coherence Accompanying the Photoreaction of Biomimetic Molecular Switches. Chemistry 2012; 18:15296-304. [DOI: 10.1002/chem.201201430] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Revised: 08/29/2012] [Indexed: 11/08/2022]
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81
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Gozem S, Huntress M, Schapiro I, Lindh R, Granovsky AA, Angeli C, Olivucci M. Dynamic Electron Correlation Effects on the Ground State Potential Energy Surface of a Retinal Chromophore Model. J Chem Theory Comput 2012; 8:4069-80. [DOI: 10.1021/ct3003139] [Citation(s) in RCA: 129] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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82
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Gozem S, Schapiro I, Ferre N, Olivucci M. The Molecular Mechanism of Thermal Noise in Rod Photoreceptors. Science 2012; 337:1225-8. [DOI: 10.1126/science.1220461] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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83
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Laricheva EN, Gozem S, Rinaldi S, Melaccio F, Valentini A, Olivucci M. Origin of Fluorescence in 11-cis Locked Bovine Rhodopsin. J Chem Theory Comput 2012; 8:2559-63. [DOI: 10.1021/ct3002514] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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84
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Dunkelberger AD, Kieda RD, Shin JY, Rossi Paccani R, Fusi S, Olivucci M, Fleming Crim F. Photoisomerization and Relaxation Dynamics of a Structurally Modified Biomimetic Photoswitch. J Phys Chem A 2012; 116:3527-33. [DOI: 10.1021/jp300153a] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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85
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Rossi Paccani R, Donati D, Fusi S, Latterini L, Farina G, Zanirato V, Olivucci M. Toward a stable α-cycloalkyl amino acid with a photoswitchable cationic side chain. J Org Chem 2012; 77:1738-48. [PMID: 22239068 DOI: 10.1021/jo2022263] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The N-alkylated indanylidenepyrroline (NAIP) Schiff base 3 is an unnatural α-amino acid precursor potentially useful for the preparation of semisynthetic peptides and proteins incorporating charged side chains whose structure can be modulated via Z/E photoisomerization. Here we report that the heteroallylic protons of 3 led to partial loss of ethanol accompanied by formation of the novel heterocyclic system 4 during attempted deprotection. We also show that the same protons catalyze the thermal isomerization of 3, making the light-driven conformational control concept ineffective for times longer than a few hours. These problems are not present in the previously unreported compound 5 where the acidic methyl group is replaced by an H atom. Therefore, 5, rather than 3, constitutes a promising prototype for the design of building blocks capable to modulate the electrostatic potential of a protein in specific locations via light irradiation.
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Melaccio F, Ferré N, Olivucci M. Quantum chemical modeling of rhodopsin mutants displaying switchable colors. Phys Chem Chem Phys 2012; 14:12485-95. [DOI: 10.1039/c2cp40940b] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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87
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Réhault J, Zanirato V, Olivucci M, Helbing J. Linear dichroism amplification: adapting a long-known technique for ultrasensitive femtosecond IR spectroscopy. J Chem Phys 2011; 134:124516. [PMID: 21456685 DOI: 10.1063/1.3572334] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We demonstrate strong amplification of polarization-sensitive transient IR signals using a pseudo-null crossed polarizer technique first proposed by Keston and Lospalluto [Fed. Proc. 10, 207 (1951)] and applied for nanosecond flash photolysis in the visible by Che et al. [Chem. Phys. Lett. 224, 145 (1994)]. We adapted the technique to ultrafast pulsed laser spectroscopy in the infrared using photoelastic modulators, which allow us to measure amplified linear dichroism at kilohertz repetition rates. The method was applied to a photoswitch of the N-alkylated Schiff base family in order to demonstrate its potential of strongly enhancing sensitivity and signal to noise in ultrafast transient IR experiments, to simplify spectra and to determine intramolecular transition dipole orientations.
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88
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Zhou D, Mirzakulova E, Khatmullin R, Schapiro I, Olivucci M, Glusac KD. Fast Excited-State Deactivation in N(5)-Ethyl-4a-hydroxyflavin Pseudobase. J Phys Chem B 2011; 115:7136-43. [DOI: 10.1021/jp201903h] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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89
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Grilj J, Laricheva EN, Olivucci M, Vauthey E. Fluoreszenz von Radikalionen in flüssiger Phase: der Fall Wursters Blau. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201100015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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90
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Grilj J, Laricheva EN, Olivucci M, Vauthey E. Fluorescence of Radical Ions in Liquid Solution: Wurster’s Blue as a Case Study. Angew Chem Int Ed Engl 2011; 50:4496-8. [DOI: 10.1002/anie.201100015] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2011] [Indexed: 11/11/2022]
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91
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Schapiro I, Ryazantsev MN, Frutos LM, Ferré N, Lindh R, Olivucci M. The Ultrafast Photoisomerizations of Rhodopsin and Bathorhodopsin Are Modulated by Bond Length Alternation and HOOP Driven Electronic Effects. J Am Chem Soc 2011; 133:3354-64. [DOI: 10.1021/ja1056196] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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92
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Schapiro I, Melaccio F, Laricheva EN, Olivucci M. Using the computer to understand the chemistry of conical intersections. Photochem Photobiol Sci 2011; 10:867-86. [DOI: 10.1039/c0pp00290a] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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93
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Melloni A, Rossi Paccani R, Donati D, Zanirato V, Sinicropi A, Parisi ML, Martin E, Ryazantsev M, Ding WJ, Frutos LM, Basosi R, Fusi S, Latterini L, Ferré N, Olivucci M. Modeling, preparation, and characterization of a dipole moment switch driven by Z/E photoisomerization. J Am Chem Soc 2010; 132:9310-9. [PMID: 20568762 DOI: 10.1021/ja906733q] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report the results of a multidisciplinary research effort where the methods of computational photochemistry and retrosynthetic analysis/synthesis have contributed to the preparation of a novel N-alkylated indanylidene-pyrroline Schiff base featuring an exocyclic double bond and a permanent zwitterionic head. We show that, due to its large dipole moment and efficient photoisomerization, such a system may constitute the prototype of a novel generation of electrostatic switches achieving a reversible light-induced dipole moment change on the order of 30 D. The modeling of a peptide fragment incorporating the zwitterionic head into a conformationally rigid side chain shows that the switch can effectively modulate the fluorescence of a tryptophan probe.
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94
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El-Khoury PZ, George L, Kalume A, Schapiro I, Olivucci M, Tarnovsky AN, Reid SA. Matrix isolation and computational studies of the CF2I radical. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.07.032] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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95
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Nau WM, Greiner G, Rau H, Olivucci M, Robb MA. Discrimination between hydrogen atom and proton abstraction in the quenching of n, π* singlet-excited states by protic solvents. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/bbpc.19981020330] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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96
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Briand J, Bräm O, Réhault J, Léonard J, Cannizzo A, Chergui M, Zanirato V, Olivucci M, Helbing J, Haacke S. Coherent ultrafast torsional motion and isomerization of a biomimetic dipolar photoswitch. Phys Chem Chem Phys 2010; 12:3178-87. [PMID: 20237707 DOI: 10.1039/b918603d] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Femtosecond fluorescence up-conversion, UV-Vis and IR transient absorption spectroscopy are used to study the photo-isomerization dynamics of a new type of zwitterionic photoswitch based on a N-alkylated indanylidene pyrroline Schiff base framework (ZW-NAIP). The system is biomimetic, as it mimics the photophysics of retinal, in coupling excited state charge translocation and isomerization. While the fluorescence lifetime is 140 fs, excited state absorption persists over 230 fs in the form of a vibrational wavepacket according to twisting of the isomerizing double bond. After a short "dark" time window in the UV-visible spectra, which we associate with the passage through a conical intersection (CI), the wavepacket appears on the ground state potential energy surface, as evidenced by the transient mid-IR data. This allows for a precise timing of the photoreaction all the way from the initial Franck-Condon region, through the CI and into both ground state isomers, until incoherent vibrational relaxation dominates the dynamics. The photo-reaction dynamics remarkably follow those observed for retinal in rhodopsin, with the additional benefit that in ZW-NAIP the conformational change reverses the zwitterion dipole moment direction. Last, the pronounced low-frequency coherences make these molecules ideal systems for investigating wavepacket dynamics in the vicinity of a CI and for coherent control experiments.
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97
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Schapiro I, Ryazantsev MN, Ding WJ, Huntress MM, Melaccio F, Andruniow T, Olivucci M. Computational Photobiology and Beyond. Aust J Chem 2010. [DOI: 10.1071/ch09563] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In this paper we review the results of a group of computational studies of the spectroscopy and photochemistry of light-responsive proteins. We focus on the use of quantum mechanics/molecular mechanics protocols based on a multiconfigurational quantum chemical treatment. More specifically, we discuss the use, limitations, and application of the ab initio CASPT2//CASSCF protocol that, presently, constitutes the method of choice for the investigation of excited state organic molecules, most notably, biological chromophores and fluorophores. At the end of this Review we will also see how the computational investigation of the visual photoreceptor rhodopsin is providing the basis for the design of light-driven artificial molecular devices.
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98
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Pistolesi S, Sinicropi A, Pogni R, Basosi R, Ferré N, Olivucci M. Modeling the Fluorescence of Protein-Embedded Tryptophans with ab Initio Multiconfigurational Quantum Chemistry: The Limiting Cases of Parvalbumin and Monellin. J Phys Chem B 2009; 113:16082-90. [DOI: 10.1021/jp9080993] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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99
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Andruniów T, Olivucci M. How Does the Relocation of Internal Water Affect Resonance Raman Spectra of Rhodopsin? An Insight from CASSCF/Amber Calculations. J Chem Theory Comput 2009; 5:3096-104. [DOI: 10.1021/ct900071c] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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100
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El-Khoury PZ, Tarnovsky AN, Schapiro I, Ryazantsev MN, Olivucci M. Structure of the Photochemical Reaction Path Populated via Promotion of CF2I2 into Its First Excited State. J Phys Chem A 2009; 113:10767-71. [DOI: 10.1021/jp902873h] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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