Computation of Reaction Mechanisms and Dynamics in Photobiology

Olsen, Seth; Toniolo, Alessandro; Ko, Chaehyuk; Manohar, Leslie; Lamothe, Kristina; Martı́nez, Todd J.

doi:10.1016/s1380-7323(05)80024-x

Cited by 12 publications

(17 citation statements)

References 100 publications

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“…In particular, increasing the bond order of the methylene′s double bond upon electronic excitation should lead to the internal rotation barrier decreasing and facilitate internal conversion and benefit the trans-cis chromophore isomerization. The importance of calculating the sections of the potential energy surfaces, the minimum energy pathways along the angular coordinates near the bridging fragment, and the conical intersection points for the chromophore molecule in the isolated state and in solution upon the gradually increasing complexity of the quantum chemistry approaches [ 57 , 60 , 61 , 69 , 72 , 91 , 101 ] is underlined. Since such calculations with an explicit consideration of the role of the protein matrix on the photophysical properties of the chromophore are too complicated, several modeling results [ 21 , 22 ] obtained with molecular mechanics methods are distinguished (in particular, those that formulated the role of sterical hindrance for the internal conversion of the chromophore).…”

Section: Discussionmentioning

confidence: 99%

Computer Modeling of the Structure and Spectra of Fluorescent Proteins

2009

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Fluorescent proteins from the family of green fluorescent proteins are intensively used as biomarkers in living systems. The chromophore group based on the hydroxybenzylidene-imidazoline molecule, which is formed in nature from three amino-acid residues inside the protein globule and well shielded from external media, is responsible for light absorption and fluorescence. Along with the intense experimental studies of the properties of fluorescent proteins and their chromophores by biochemical, X-ray, and spectroscopic tools, in recent years, computer modeling has been used to characterize their properties and spectra. We present in this review the most interesting results of the molecular modeling of the structural parameters and optical and vibrational spectra of the chromophorecontaining domains of fluorescent proteins by methods of quantum chemistry, molecular dynamics, and combined quantum-mechanical-molecular-mechanical approaches. The main emphasis is on the correlation of theoretical and experimental data and on the predictive power of modeling, which may be useful for creating new, efficient biomarkers.

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Section: Discussionmentioning

confidence: 99%

Computer Modeling of the Structure and Spectra of Fluorescent Proteins

2009

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“…The TD DFT method is known to give poor results in situations such as electron transfer or Rydberg state30 and also to strongly depend on the energy functional used. High accuracy methods as CASPT2 are usually to be preferred.…”

Section: Methods and Computational Detailsmentioning

confidence: 99%

Relation between pH, structure, and absorption spectrum of Cerulean: A study by molecular dynamics and TD DFT calculations

et al. 2009

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Molecular dynamics (MD) and quantum mechanical calculations of the Cerulean green fluorescent protein (a variant of enhanced cyan fluorescent protein ECFP) at pH 5.0 and 8.0 are presented, addressing two questions arising from experimental results (Malo et al., Biochemistry 2007;46:9865-9873): the origin of the blue shift of absorption spectrum when the pH is decreased from 8.0 to 5.0, and the lateral chain orientation of the key residue Asp148. We demonstrate that the blue shift is reproduced assuming that a rotation around the single bond of the exocyclic ring of the chromophore takes place when the pH changes from 5.0 to 8.0. We find that Asp148 is protonated and inside the barrel at pH 5.0 in agreement with crystallographic data. However, the hydrogen bond pattern of Asp148 is different in simulations of the solvated protein and in the crystal structure. This difference is explained by a partial closing of the cleft between strands 6 and 7 in MD simulations. This study provides also a structure at pH 8.0: the Asp148 carboxylate group is exposed to the solvent and the chromophore is stabilized in the trans conformation by a tighter hydrogen bond network. This work gives some insight into the relationship between the pH and the chromophore conformation and suggests an interpretation of the very similar fluorescent properties of ECFP and ECFP/H148D. Proteins 2010. (c) 2009 Wiley-Liss, Inc.

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“…Simulations of ultrafast photoisomerization have a long history, dating as far back as the simulations of the primary step in the vision process49 in the 1970s. Significant progress has been made on this front since then (e.g., Refs 50–5450, 54, 55 can have significant dynamical effects.…”

Section: Dynamical Effects In Ultrafast Reactionsmentioning

confidence: 99%

Polyaniline–nylon 6 composite nanowires prepared by emulsion polymerization and electrospinning process

Hong¹,

Kang²

2005

J of Applied Polymer Sci

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Polyaniline (PANI) nanoparticles doped with the dodecylbenzene sulfonic acid (DBSA) were prepared and these nanoparticles were electrospun with nylon 6 as matrix material into fiber web. Depending on the contents and concentrations of PANI and nylon 6, either nylon 6 nanofibers (ϳ96 nm) or PANI-nylon 6 composite nanofibers (ϳ12 nm) were obtained. The electrical conductivity of PANI(DBSA)-nylon 6 electrospun fiber web was lower than that of PANI(DBSA)-nylon 6 film because of the low crystallinity of the PANI(DBSA)-nylon 6 composite electrospun fiber web. However, it showed that the PANI-nylon 6 composite nanofibers would have applications as the nanowires for connecting the microelectromechanical system (MEMS).

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Computation of Reaction Mechanisms and Dynamics in Photobiology

Cited by 12 publications

References 100 publications

Computer Modeling of the Structure and Spectra of Fluorescent Proteins

Computer Modeling of the Structure and Spectra of Fluorescent Proteins

Relation between pH, structure, and absorption spectrum of Cerulean: A study by molecular dynamics and TD DFT calculations

Polyaniline–nylon 6 composite nanowires prepared by emulsion polymerization and electrospinning process

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