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Items: 1 to 50 of 116

1.

Synthesis, spectroscopy and QM/MM simulations of a biomimetic ultrafast light-driven molecular motor.

Schapiro I, Gueye M, Paolino M, Fusi S, Marchand G, Haacke S, Martin ME, Huntress M, Vysotskiy VP, Veryazov V, Léonard J, Olivucci M.

Photochem Photobiol Sci. 2019 Jul 26. doi: 10.1039/c9pp00223e. [Epub ahead of print]

PMID:
31347633
2.

CpHMD-Then-QM/MM Identification of the Amino Acids Responsible for the Anabaena Sensory Rhodopsin pH-Dependent Electronic Absorption Spectrum.

Pieri E, Ledentu V, Sahlin M, Dehez F, Olivucci M, Ferré N.

J Chem Theory Comput. 2019 Aug 13;15(8):4535-4546. doi: 10.1021/acs.jctc.9b00221. Epub 2019 Jul 2.

PMID:
31264415
3.

Red-shifting mutation of light-driven sodium-pump rhodopsin.

Inoue K, Del Carmen Marín M, Tomida S, Nakamura R, Nakajima Y, Olivucci M, Kandori H.

Nat Commun. 2019 Apr 30;10(1):1993. doi: 10.1038/s41467-019-10000-x.

4.

Bile Acid Binding Protein Functionalization Leads to a Fully Synthetic Rhodopsin Mimic.

Pagano K, Paolino M, Fusi S, Zanirato V, Trapella C, Giuliani G, Cappelli A, Zanzoni S, Molinari H, Ragona L, Olivucci M.

J Phys Chem Lett. 2019 May 2;10(9):2235-2243. doi: 10.1021/acs.jpclett.9b00210. Epub 2019 Apr 22.

PMID:
30995409
5.

a-ARM: Automatic Rhodopsin Modeling with Chromophore Cavity Generation, Ionization State Selection, and External Counterion Placement.

Pedraza-González L, De Vico L, Marı N MADC, Fanelli F, Olivucci M.

J Chem Theory Comput. 2019 May 14;15(5):3134-3152. doi: 10.1021/acs.jctc.9b00061. Epub 2019 Apr 12.

PMID:
30916955
6.

Two-State, Three-Mode Parametrization of the Force Field of a Retinal Chromophore Model.

Marsili E, Farag MH, Yang X, De Vico L, Olivucci M.

J Phys Chem A. 2019 Mar 7;123(9):1710-1719. doi: 10.1021/acs.jpca.8b10010. Epub 2019 Feb 26.

PMID:
30753077
7.

Assessment of MC-PDFT Excitation Energies for a Set of QM/MM Models of Rhodopsins.

Marín MDC, De Vico L, Dong SS, Gagliardi L, Truhlar DG, Olivucci M.

J Chem Theory Comput. 2019 Mar 12;15(3):1915-1923. doi: 10.1021/acs.jctc.8b01069. Epub 2019 Feb 20.

PMID:
30721054
8.

Fluorescence Enhancement of a Microbial Rhodopsin via Electronic Reprogramming.

Marín MDC, Agathangelou D, Orozco-Gonzalez Y, Valentini A, Kato Y, Abe-Yoshizumi R, Kandori H, Choi A, Jung KH, Haacke S, Olivucci M.

J Am Chem Soc. 2019 Jan 9;141(1):262-271. doi: 10.1021/jacs.8b09311. Epub 2018 Dec 28.

9.

Electronic State Mixing Controls the Photoreactivity of a Rhodopsin with all- trans Chromophore Analogues.

Manathunga M, Yang X, Olivucci M.

J Phys Chem Lett. 2018 Nov 1;9(21):6350-6355. doi: 10.1021/acs.jpclett.8b02550. Epub 2018 Oct 23.

10.

A Comparative Study of Modern Homology Modeling Algorithms for Rhodopsin Structure Prediction.

Nikolaev DM, Shtyrov AA, Panov MS, Jamal A, Chakchir OB, Kochemirovsky VA, Olivucci M, Ryazantsev MN.

ACS Omega. 2018 Jul 31;3(7):7555-7566. doi: 10.1021/acsomega.8b00721. Epub 2018 Jul 9.

11.

Relationship between Excited State Lifetime and Isomerization Quantum Yield in Animal Rhodopsins: Beyond the One-Dimensional Landau-Zener Model.

El-Tahawy MMT, Nenov A, Weingart O, Olivucci M, Garavelli M.

J Phys Chem Lett. 2018 Jun 21;9(12):3315-3322. doi: 10.1021/acs.jpclett.8b01062. Epub 2018 Jun 6.

12.

Systematic Excited State Studies of Reversibly Switchable Fluorescent Proteins.

Smyrnova D, Marín MDC, Olivucci M, Ceulemans A.

J Chem Theory Comput. 2018 Jun 12;14(6):3163-3172. doi: 10.1021/acs.jctc.8b00050. Epub 2018 May 29.

PMID:
29772175
13.

Evidence for a vibrational phase-dependent isotope effect on the photochemistry of vision.

Schnedermann C, Yang X, Liebel M, Spillane KM, Lugtenburg J, Fernández I, Valentini A, Schapiro I, Olivucci M, Kukura P, Mathies RA.

Nat Chem. 2018 Apr;10(4):449-455. doi: 10.1038/s41557-018-0014-y. Epub 2018 Mar 19.

PMID:
29556051
14.

Effect of point mutations on the ultrafast photo-isomerization of Anabaena sensory rhodopsin.

Agathangelou D, Orozco-Gonzalez Y, Del Carmen Marín M, Roy PP, Brazard J, Kandori H, Jung KH, Léonard J, Buckup T, Ferré N, Olivucci M, Haacke S.

Faraday Discuss. 2018 Apr 17;207(0):55-75. doi: 10.1039/c7fd00200a.

PMID:
29388996
15.

Engineering the vibrational coherence of vision into a synthetic molecular device.

Gueye M, Manathunga M, Agathangelou D, Orozco Y, Paolino M, Fusi S, Haacke S, Olivucci M, Léonard J.

Nat Commun. 2018 Jan 22;9(1):313. doi: 10.1038/s41467-017-02668-w.

16.

An Average Solvent Electrostatic Configuration Protocol for QM/MM Free Energy Optimization: Implementation and Application to Rhodopsin Systems.

Orozco-Gonzalez Y, Manathunga M, Marín MDC, Agathangelou D, Jung KH, Melaccio F, Ferré N, Haacke S, Coutinho K, Canuto S, Olivucci M.

J Chem Theory Comput. 2017 Dec 12;13(12):6391-6404. doi: 10.1021/acs.jctc.7b00860. Epub 2017 Nov 21.

PMID:
29112449
17.

Theory and Simulation of the Ultrafast Double-Bond Isomerization of Biological Chromophores.

Gozem S, Luk HL, Schapiro I, Olivucci M.

Chem Rev. 2017 Nov 22;117(22):13502-13565. doi: 10.1021/acs.chemrev.7b00177. Epub 2017 Oct 30. Review.

PMID:
29083892
18.

Impact of Electronic State Mixing on the Photoisomerization Time Scale of the Retinal Chromophore.

Manathunga M, Yang X, Orozco-Gonzalez Y, Olivucci M.

J Phys Chem Lett. 2017 Oct 19;8(20):5222-5227. doi: 10.1021/acs.jpclett.7b02344. Epub 2017 Oct 11.

PMID:
28981285
19.

Optomechanical Control of Quantum Yield in Trans-Cis Ultrafast Photoisomerization of a Retinal Chromophore Model.

Valentini A, Rivero D, Zapata F, García-Iriepa C, Marazzi M, Palmeiro R, Fdez Galván I, Sampedro D, Olivucci M, Frutos LM.

Angew Chem Int Ed Engl. 2017 Mar 27;56(14):3842-3846. doi: 10.1002/anie.201611265. Epub 2017 Mar 2.

PMID:
28251753
20.

Modulation of thermal noise and spectral sensitivity in Lake Baikal cottoid fish rhodopsins.

Luk HL, Bhattacharyya N, Montisci F, Morrow JM, Melaccio F, Wada A, Sheves M, Fanelli F, Chang BS, Olivucci M.

Sci Rep. 2016 Dec 9;6:38425. doi: 10.1038/srep38425.

21.

Mechanism of excited state deactivation of indan-1-ylidene and fluoren-9-ylidene malononitriles.

Estrada LA, Francés-Monerris A, Schapiro I, Olivucci M, Roca-Sanjuán D.

Phys Chem Chem Phys. 2016 Dec 7;18(48):32786-32795.

PMID:
27878166
22.

Toward Automatic Rhodopsin Modeling as a Tool for High-Throughput Computational Photobiology.

Melaccio F, Del Carmen Marín M, Valentini A, Montisci F, Rinaldi S, Cherubini M, Yang X, Kato Y, Stenrup M, Orozco-Gonzalez Y, Ferré N, Luk HL, Kandori H, Olivucci M.

J Chem Theory Comput. 2016 Dec 13;12(12):6020-6034. Epub 2016 Nov 15.

PMID:
27779842
23.

Design, Synthesis, and Dynamics of a Green Fluorescent Protein Fluorophore Mimic with an Ultrafast Switching Function.

Paolino M, Gueye M, Pieri E, Manathunga M, Fusi S, Cappelli A, Latterini L, Pannacci D, Filatov M, Léonard J, Olivucci M.

J Am Chem Soc. 2016 Aug 10;138(31):9807-25. doi: 10.1021/jacs.5b10812. Epub 2016 Jul 29.

PMID:
27322488
24.

Space and Time Evolution of the Electrostatic Potential During the Activation of a Visual Pigment.

Melaccio F, Calimet N, Schapiro I, Valentini A, Cecchini M, Olivucci M.

J Phys Chem Lett. 2016 Jul 7;7(13):2563-7. doi: 10.1021/acs.jpclett.6b00977. Epub 2016 Jun 23.

PMID:
27322155
25.

Assessment of Approximate Coupled-Cluster and Algebraic-Diagrammatic-Construction Methods for Ground- and Excited-State Reaction Paths and the Conical-Intersection Seam of a Retinal-Chromophore Model.

Tuna D, Lefrancois D, Wolański Ł, Gozem S, Schapiro I, Andruniów T, Dreuw A, Olivucci M.

J Chem Theory Comput. 2015 Dec 8;11(12):5758-81. doi: 10.1021/acs.jctc.5b00022. Epub 2015 Nov 13.

PMID:
26642989
26.

Probing the Photodynamics of Rhodopsins with Reduced Retinal Chromophores.

Manathunga M, Yang X, Luk HL, Gozem S, Frutos LM, Valentini A, Ferrè N, Olivucci M.

J Chem Theory Comput. 2016 Feb 9;12(2):839-50. doi: 10.1021/acs.jctc.5b00945. Epub 2016 Jan 6.

PMID:
26640959
27.

Molecular bases for the selection of the chromophore of animal rhodopsins.

Luk HL, Melaccio F, Rinaldi S, Gozem S, Olivucci M.

Proc Natl Acad Sci U S A. 2015 Dec 15;112(50):15297-302. doi: 10.1073/pnas.1510262112. Epub 2015 Nov 25.

28.

Role of the Molecular Environment in Flavoprotein Color and Redox Tuning: QM Cluster versus QM/MM Modeling.

Udvarhelyi A, Olivucci M, Domratcheva T.

J Chem Theory Comput. 2015 Aug 11;11(8):3878-94. doi: 10.1021/acs.jctc.5b00197.

PMID:
26574469
29.

Molcas 8: New capabilities for multiconfigurational quantum chemical calculations across the periodic table.

Aquilante F, Autschbach J, Carlson RK, Chibotaru LF, Delcey MG, De Vico L, Fdez Galván I, Ferré N, Frutos LM, Gagliardi L, Garavelli M, Giussani A, Hoyer CE, Li Manni G, Lischka H, Ma D, Malmqvist PÅ, Müller T, Nenov A, Olivucci M, Pedersen TB, Peng D, Plasser F, Pritchard B, Reiher M, Rivalta I, Schapiro I, Segarra-Martí J, Stenrup M, Truhlar DG, Ungur L, Valentini A, Vancoillie S, Veryazov V, Vysotskiy VP, Weingart O, Zapata F, Lindh R.

J Comput Chem. 2016 Feb 15;37(5):506-41. doi: 10.1002/jcc.24221. Epub 2015 Nov 12.

PMID:
26561362
30.

Directionality of Double-Bond Photoisomerization Dynamics Induced by a Single Stereogenic Center.

Marchand G, Eng J, Schapiro I, Valentini A, Frutos LM, Pieri E, Olivucci M, Léonard J, Gindensperger E.

J Phys Chem Lett. 2015 Feb 19;6(4):599-604. doi: 10.1021/jz502644h. Epub 2015 Jan 29.

PMID:
26262473
31.

Quantum Monte Carlo Treatment of the Charge Transfer and Diradical Electronic Character in a Retinal Chromophore Minimal Model.

Zen A, Coccia E, Gozem S, Olivucci M, Guidoni L.

J Chem Theory Comput. 2015 Mar 10;11(3):992-1005.

32.

A surface hopping algorithm for nonadiabatic minimum energy path calculations.

Schapiro I, Roca-Sanjuán D, Lindh R, Olivucci M.

J Comput Chem. 2015 Feb 15;36(5):312-20. doi: 10.1002/jcc.23805. Epub 2015 Jan 6.

PMID:
25564760
33.

Initial excited-state dynamics of an N-alkylated indanylidene-pyrroline (NAIP) rhodopsin analog.

Schapiro I, Fusi S, Olivucci M, Andruniów T, Sasidharanpillai S, Loppnow GR.

J Phys Chem B. 2014 Oct 23;118(42):12243-50. doi: 10.1021/jp508060z. Epub 2014 Oct 10.

PMID:
25255466
34.

Shape of Multireference, Equation-of-Motion Coupled-Cluster, and Density Functional Theory Potential Energy Surfaces at a Conical Intersection.

Gozem S, Melaccio F, Valentini A, Filatov M, Huix-Rotllant M, Ferré N, Frutos LM, Angeli C, Krylov AI, Granovsky AA, Lindh R, Olivucci M.

J Chem Theory Comput. 2014 Aug 12;10(8):3074-84. doi: 10.1021/ct500154k. Epub 2014 Jun 11.

PMID:
26588278
35.

A conical intersection controls the deactivation of the bacterial luciferase fluorophore.

Gozem S, Mirzakulova E, Schapiro I, Melaccio F, Glusac KD, Olivucci M.

Angew Chem Int Ed Engl. 2014 Sep 8;53(37):9870-5. doi: 10.1002/anie.201404011. Epub 2014 Jul 14.

PMID:
25045117
36.

Learning from photobiology how to design molecular devices using a computer.

Gozem S, Melaccio F, Luk HL, Rinaldi S, Olivucci M.

Chem Soc Rev. 2014 Jun 21;43(12):4019-36. doi: 10.1039/c4cs00037d. Review.

PMID:
24811294
37.

Designing conical intersections for light-driven single molecule rotary motors: from precessional to axial motion.

Filatov M, Olivucci M.

J Org Chem. 2014 Apr 18;79(8):3587-600. doi: 10.1021/jo5004289. Epub 2014 Apr 7.

PMID:
24673424
38.

Comparison of the isomerization mechanisms of human melanopsin and invertebrate and vertebrate rhodopsins.

Rinaldi S, Melaccio F, Gozem S, Fanelli F, Olivucci M.

Proc Natl Acad Sci U S A. 2014 Feb 4;111(5):1714-9. doi: 10.1073/pnas.1309508111. Epub 2014 Jan 21.

39.

Mapping the Excited State Potential Energy Surface of a Retinal Chromophore Model with Multireference and Equation-of-Motion Coupled-Cluster Methods.

Gozem S, Melaccio F, Lindh R, Krylov AI, Granovsky AA, Angeli C, Olivucci M.

J Chem Theory Comput. 2013 Oct 8;9(10):4495-506. doi: 10.1021/ct400460h. Epub 2013 Sep 6.

PMID:
26589167
40.

Assessment of Density Functional Theory for Describing the Correlation Effects on the Ground and Excited State Potential Energy Surfaces of a Retinal Chromophore Model.

Huix-Rotllant M, Filatov M, Gozem S, Schapiro I, Olivucci M, Ferré N.

J Chem Theory Comput. 2013 Sep 10;9(9):3917-32. doi: 10.1021/ct4003465. Epub 2013 Aug 13.

PMID:
26592387
41.

Probing vibrationally mediated ultrafast excited-state reaction dynamics with multireference (CASPT2) trajectories.

El-Khoury PZ, Joseph S, Schapiro I, Gozem S, Olivucci M, Tarnovsky AN.

J Phys Chem A. 2013 Nov 7;117(44):11271-5. doi: 10.1021/jp408441w. Epub 2013 Oct 23.

PMID:
24001155
42.

Toward an understanding of the retinal chromophore in rhodopsin mimics.

Huntress MM, Gozem S, Malley KR, Jailaubekov AE, Vasileiou C, Vengris M, Geiger JH, Borhan B, Schapiro I, Larsen DS, Olivucci M.

J Phys Chem B. 2013 Sep 5;117(35):10053-70. doi: 10.1021/jp305935t. Epub 2013 Aug 26.

PMID:
23971945
43.

Effects of the protein environment on the spectral properties of tryptophan radicals in Pseudomonas aeruginosa azurin.

Bernini C, Andruniów T, Olivucci M, Pogni R, Basosi R, Sinicropi A.

J Am Chem Soc. 2013 Mar 27;135(12):4822-33. doi: 10.1021/ja400464n. Epub 2013 Mar 13.

PMID:
23458492
44.

Combined Self-Consistent-Field and Spin-Flip Tamm-Dancoff Density Functional Approach to Potential Energy Surfaces for Photochemistry.

Xu X, Gozem S, Olivucci M, Truhlar DG.

J Phys Chem Lett. 2013 Jan 17;4(2):253-8. doi: 10.1021/jz301935x. Epub 2012 Dec 31.

PMID:
26283430
45.

Conical Intersection and Potential Energy Surface Features of a Model Retinal Chromophore: Comparison of EOM-CC and Multireference Methods.

Gozem S, Krylov AI, Olivucci M.

J Chem Theory Comput. 2013 Jan 8;9(1):284-92. doi: 10.1021/ct300759z. Epub 2012 Nov 9.

PMID:
26589030
46.

Dynamic Electron Correlation Effects on the Ground State Potential Energy Surface of a Retinal Chromophore Model.

Gozem S, Huntress M, Schapiro I, Lindh R, Granovsky AA, Angeli C, Olivucci M.

J Chem Theory Comput. 2012 Nov 13;8(11):4069-80. doi: 10.1021/ct3003139. Epub 2012 Sep 24.

PMID:
26605574
47.

Mechanistic origin of the vibrational coherence accompanying the photoreaction of biomimetic molecular switches.

Léonard J, Schapiro I, Briand J, Fusi S, Paccani RR, Olivucci M, Haacke S.

Chemistry. 2012 Nov 26;18(48):15296-304. doi: 10.1002/chem.201201430. Epub 2012 Nov 6.

PMID:
23132675
48.

The molecular mechanism of thermal noise in rod photoreceptors.

Gozem S, Schapiro I, Ferré N, Olivucci M.

Science. 2012 Sep 7;337(6099):1225-8. doi: 10.1126/science.1220461.

49.

Origin of Fluorescence in 11-cis Locked Bovine Rhodopsin.

Laricheva EN, Gozem S, Rinaldi S, Melaccio F, Valentini A, Olivucci M.

J Chem Theory Comput. 2012 Aug 14;8(8):2559-63. doi: 10.1021/ct3002514. Epub 2012 Jul 31.

PMID:
26592102
50.

Quantum chemical modeling of rhodopsin mutants displaying switchable colors.

Melaccio F, Ferré N, Olivucci M.

Phys Chem Chem Phys. 2012 Sep 28;14(36):12485-95. doi: 10.1039/c2cp40940b. Epub 2012 Jun 14.

PMID:
22699180

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