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Items: 27

1.

Molecular Simulations with in-deMon2k QM/MM, a Tutorial-Review.

de la Lande A, Alvarez-Ibarra A, Hasnaoui K, Cailliez F, Wu X, Mineva T, Cuny J, Calaminici P, López-Sosa L, Geudtner G, Navizet I, Garcia Iriepa C, Salahub DR, Köster AM.

Molecules. 2019 Apr 26;24(9). pii: E1653. doi: 10.3390/molecules24091653. Review.

2.

Effect of Protein Conformation and AMP Protonation State on Fireflies' Bioluminescent Emission.

Garcia-Iriepa C, Navizet I.

Molecules. 2019 Apr 20;24(8). pii: E1565. doi: 10.3390/molecules24081565.

3.

The role of solvation models on the computed absorption and emission spectra: the case of fireflies oxyluciferin.

García-Iriepa C, Zemmouche M, Ponce-Vargas M, Navizet I.

Phys Chem Chem Phys. 2019 Feb 20;21(8):4613-4623. doi: 10.1039/c8cp07352j.

PMID:
30742153
4.

Beetle luciferases with naturally red- and blue-shifted emission.

Carrasco-López C, Ferreira JC, Lui NM, Schramm S, Berraud-Pache R, Navizet I, Panjikar S, Naumov P, Rabeh WM.

Life Sci Alliance. 2018 Aug 16;1(4):e201800072. doi: 10.26508/lsa.201800072. eCollection 2018 Aug.

5.

Modeling Chemical Reactions by QM/MM Calculations: The Case of the Tautomerization in Fireflies Bioluminescent Systems.

Berraud-Pache R, Garcia-Iriepa C, Navizet I.

Front Chem. 2018 Apr 17;6:116. doi: 10.3389/fchem.2018.00116. eCollection 2018.

6.

Rationalisation of the optical signatures of nor-dihydroxanthene-hemicyanine fused near-infrared fluorophores by first-principle tools.

Azarias C, Ponce-Vargas M, Navizet I, Fleurat-Lessard P, Romieu A, Le Guennic B, Richard JA, Jacquemin D.

Phys Chem Chem Phys. 2018 May 7;20(17):12120-12128. doi: 10.1039/c8cp01587b. Epub 2018 Apr 20.

PMID:
29676420
7.

QM/MM Study of the Formation of the Dioxetanone Ring in Fireflies through a Superoxide Ion.

Berraud-Pache R, Lindh R, Navizet I.

J Phys Chem B. 2018 May 24;122(20):5173-5182. doi: 10.1021/acs.jpcb.8b00642. Epub 2018 May 11.

PMID:
29659277
8.

Simulation and Analysis of the Spectroscopic Properties of Oxyluciferin and Its Analogues in Water.

García-Iriepa C, Gosset P, Berraud-Pache R, Zemmouche M, Taupier G, Dorkenoo KD, Didier P, Léonard J, Ferré N, Navizet I.

J Chem Theory Comput. 2018 Apr 10;14(4):2117-2126. doi: 10.1021/acs.jctc.7b01240. Epub 2018 Mar 16.

PMID:
29509419
9.

Chemi- and Bioluminescence of Cyclic Peroxides.

Vacher M, Fdez Galván I, Ding BW, Schramm S, Berraud-Pache R, Naumov P, Ferré N, Liu YJ, Navizet I, Roca-Sanjuán D, Baader WJ, Lindh R.

Chem Rev. 2018 Aug 8;118(15):6927-6974. doi: 10.1021/acs.chemrev.7b00649. Epub 2018 Mar 1. Review.

PMID:
29493234
10.

Mechanistic investigations of the 2-coumaranone chemiluminescence.

Schramm S, Navizet I, Prasad Karothu D, Oesau P, Bensmann V, Weiss D, Beckert R, Naumov P.

Phys Chem Chem Phys. 2017 Aug 30;19(34):22852-22859. doi: 10.1039/c7cp03425c.

PMID:
28812068
11.

QM/MM calculations on a newly synthesised oxyluciferin substrate: new insights into the conformational effect.

Berraud-Pache R, Navizet I.

Phys Chem Chem Phys. 2016 Oct 5;18(39):27460-27467.

PMID:
27711533
12.

The synthesis of a corrole analogue of aquacobalamin (vitamin B12a) and its ligand substitution reactions.

Zipp CF, Michael JP, Fernandes MA, Mathura S, Perry CB, Navizet I, Govender PP, Marques HM.

Inorg Chem. 2014 May 5;53(9):4418-29. doi: 10.1021/ic5000793. Epub 2014 Apr 10.

PMID:
24721109
13.

Hybrid QM/MM simulations of the obelin bioluminescence and fluorescence reveal an unexpected light emitter.

Chen S, Navizet I, Lindh R, Liu Y, Ferré N.

J Phys Chem B. 2014 Mar 20;118(11):2896-903. doi: 10.1021/jp412198w. Epub 2014 Mar 6.

PMID:
24601757
14.

The preparation of N-acetyl-Co(III)-microperoxidase-8 (NAcCoMP8) and its ligand substitution reactions: a comparison with aquacobalamin (vitamin B(12a)).

Mathura S, Sannasy D, de Sousa AS, Perry CB, Navizet I, Marques HM.

J Inorg Biochem. 2013 Jun;123:66-79. doi: 10.1016/j.jinorgbio.2013.03.001. Epub 2013 Mar 16.

PMID:
23563390
15.

DFT studies of trans and cis influences in the homolysis of the Co-C bond in models of the alkylcobalamins.

Govender PP, Navizet I, Perry CB, Marques HM.

J Phys Chem A. 2013 Apr 11;117(14):3057-68. doi: 10.1021/jp311788t. Epub 2013 Apr 2.

PMID:
23510290
16.

Are the bio- and chemiluminescence states of the firefly oxyluciferin the same as the fluorescence state?

Navizet I, Roca-Sanjuán D, Yue L, Liu YJ, Ferré N, Lindh R.

Photochem Photobiol. 2013 Mar-Apr;89(2):319-25. doi: 10.1111/php.12007. Epub 2012 Dec 17.

PMID:
23057607
17.

Chemiluminescence of Coelenterazine and Fluorescence of Coelenteramide: A Systematic Theoretical Study.

Chen SF, Navizet I, Roca-Sanjuán D, Lindh R, Liu YJ, Ferré N.

J Chem Theory Comput. 2012 Aug 14;8(8):2796-807. doi: 10.1021/ct300356j. Epub 2012 Jul 23.

PMID:
26592121
18.

cis influence in models of cobalt corrins by DFT and TD-DFT studies.

Navizet I, Perry CB, Govender PP, Marques HM.

J Phys Chem B. 2012 Aug 2;116(30):8836-45. doi: 10.1021/jp304007a. Epub 2012 Jul 13.

PMID:
22731781
19.

Photostability Mechanisms in Human γB-Crystallin: Role of the Tyrosine Corner Unveiled by Quantum Mechanics and Hybrid Quantum Mechanics/Molecular Mechanics Methodologies.

Marazzi M, Navizet I, Lindh R, Frutos LM.

J Chem Theory Comput. 2012 Apr 10;8(4):1351-9. doi: 10.1021/ct300114w. Epub 2012 Mar 27.

PMID:
26596750
20.

Chemiluminescence and Fluorescence States of a Small Model for Coelenteramide and Cypridina Oxyluciferin: A CASSCF/CASPT2 Study.

Roca-Sanjuán D, Delcey MG, Navizet I, Ferré N, Liu YJ, Lindh R.

J Chem Theory Comput. 2011 Dec 13;7(12):4060-9. doi: 10.1021/ct2004758. Epub 2011 Nov 11.

PMID:
26598351
21.

The chemistry of bioluminescence: an analysis of chemical functionalities.

Navizet I, Liu YJ, Ferré N, Roca-Sanjuán D, Lindh R.

Chemphyschem. 2011 Dec 9;12(17):3064-76. doi: 10.1002/cphc.201100504. Epub 2011 Oct 13. Review.

PMID:
21997887
22.

Systematic Theoretical Investigation on the Light Emitter of Firefly.

Chen SF, Liu YJ, Navizet I, Ferré N, Fang WH, Lindh R.

J Chem Theory Comput. 2011 Mar 8;7(3):798-803. doi: 10.1021/ct200045q. Epub 2011 Feb 16.

PMID:
26596309
23.

Color-tuning mechanism of firefly investigated by multi-configurational perturbation method.

Navizet I, Liu YJ, Ferré N, Xiao HY, Fang WH, Lindh R.

J Am Chem Soc. 2010 Jan 20;132(2):706-12. doi: 10.1021/ja908051h.

PMID:
20014859
24.

Electronic spectrum of the AlC(2) radical.

Chasovskikh E, Jochnowitz EB, Kim E, Maier JP, Navizet I.

J Phys Chem A. 2007 Nov 29;111(47):11986-9. Epub 2007 Oct 30.

PMID:
17966995
25.

Vibrations in the B4 rhombic structure.

Linguerri R, Navizet I, Rosmus P, Carter S, Maier JP.

J Chem Phys. 2005 Jan 15;122(3):34301.

PMID:
15740195
26.

Probing protein mechanics: residue-level properties and their use in defining domains.

Navizet I, Cailliez F, Lavery R.

Biophys J. 2004 Sep;87(3):1426-35.

27.

Myosin flexibility: structural domains and collective vibrations.

Navizet I, Lavery R, Jernigan RL.

Proteins. 2004 Feb 15;54(3):384-93.

PMID:
14747987

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