scholarly journals Role of the Perfluoro Effect in the Selective Photochemical Isomerization of Hexafluorobenzene

2021 ◽  
Author(s):  
Jordan Cox ◽  
Mike Kellogg ◽  
Matthew Bain ◽  
Stephen E. Bradforth ◽  
Steven Lopez
Keyword(s):  
Reaction Pathway ◽  
Stokes Shift ◽  
Vibronic Coupling ◽  
Absorption Bands ◽  
Time Resolved ◽  
Photochemical Isomerization ◽  
Dynamics Simulations ◽  
Highly Strained ◽  
Holistic Description

Hexafluorobenzene and many of its derivatives exhibit a chemoselective photochemical isomerization, resulting in highly-strained, Dewar-type bicyclohexenes. While the changes in absorption and emission associated with benzene hexafluorination have been attributed to the socalled “perfluoro effect,” the resulting electronic structure and photochemical reactivity of hexafluorobenzene are still unclear. We now use a combination of ultrafast time-resolved spectroscopy, multiconfigurational computations, and non-adiabatic dynamics simulations to develop a holistic description of the absorption, emission, and photochemical dynamics of the 4πelectrocyclic ring-closing of hexafluorobenzene and the fluorination effect along the reaction coordinate. Our calculations suggest that the electron-withdrawing fluorine substituents induce a vibronic coupling between the lowest-energy 1B2u (ππ*) and 1E1g (πσ*) excited states by selectively stabilizing the σ-type states. The vibronic coupling occurs along vibrational modes of e2u symmetry which distorts the excited-state minimum geometry resulting in the experimentally broad, featureless absorption bands, and a ~100 nm Stokes shift in fluorescence– in stark contrast to benzene. Finally, the vibronic coupling is shown to simultaneously destabilize the reaction pathway towards hexafluoro-benzvalene and promote molecular vibrations along the 4π ring-closing pathway, resulting in the chemoselectivity for hexafluoro-Dewar-benzene.

scholarly journals Role of the Perfluoro Effect in the Selective Photochemical Isomerization of Hexafluorobenzene

2021 ◽  
Author(s):  
Jordan Cox ◽  
Mike Kellogg ◽  
Matthew Bain ◽  
Stephen E. Bradforth ◽  
Steven Lopez
Keyword(s):  
Reaction Pathway ◽  
Stokes Shift ◽  
Vibronic Coupling ◽  
Absorption Bands ◽  
Time Resolved ◽  
Photochemical Isomerization ◽  
Dynamics Simulations ◽  
Highly Strained ◽  
Holistic Description

Hexafluorobenzene and many of its derivatives exhibit a chemoselective photochemical isomerization, resulting in highly-strained, Dewar-type bicyclohexenes. While the changes in absorption and emission associated with benzene hexafluorination have been attributed to the socalled “perfluoro effect,” the resulting electronic structure and photochemical reactivity of hexafluorobenzene are still unclear. We now use a combination of ultrafast time-resolved spectroscopy, multiconfigurational computations, and non-adiabatic dynamics simulations to develop a holistic description of the absorption, emission, and photochemical dynamics of the 4πelectrocyclic ring-closing of hexafluorobenzene and the fluorination effect along the reaction coordinate. Our calculations suggest that the electron-withdrawing fluorine substituents induce a vibronic coupling between the lowest-energy 1B2u (ππ*) and 1E1g (πσ*) excited states by selectively stabilizing the σ-type states. The vibronic coupling occurs along vibrational modes of e2u symmetry which distorts the excited-state minimum geometry resulting in the experimentally broad, featureless absorption bands, and a ~100 nm Stokes shift in fluorescence– in stark contrast to benzene. Finally, the vibronic coupling is shown to simultaneously destabilize the reaction pathway towards hexafluoro-benzvalene and promote molecular vibrations along the 4π ring-closing pathway, resulting in the chemoselectivity for hexafluoro-Dewar-benzene.

scholarly journals Role of the Perfluoro Effect in the Selective Photochemical Isomerization of Hexafluorobenzene

2021 ◽  
Author(s):  
Jordan Cox ◽  
Mike Kellogg ◽  
Matthew Bain ◽  
Stephen E. Bradforth ◽  
Steven Lopez
Keyword(s):  
Reaction Pathway ◽  
Stokes Shift ◽  
Vibronic Coupling ◽  
Absorption Bands ◽  
Time Resolved ◽  
Photochemical Isomerization ◽  
Dynamics Simulations ◽  
Highly Strained ◽  
Holistic Description

Hexafluorobenzene and many of its derivatives exhibit a chemoselective photochemical isomerization, resulting in highly-strained, Dewar-type bicyclohexenes. While the changes in absorption and emission associated with benzene hexafluorination have been attributed to the socalled “perfluoro effect,” the resulting electronic structure and photochemical reactivity of hexafluorobenzene are still unclear. We now use a combination of ultrafast time-resolved spectroscopy, multiconfigurational computations, and non-adiabatic dynamics simulations to develop a holistic description of the absorption, emission, and photochemical dynamics of the 4πelectrocyclic ring-closing of hexafluorobenzene and the fluorination effect along the reaction coordinate. Our calculations suggest that the electron-withdrawing fluorine substituents induce a vibronic coupling between the lowest-energy 1B2u (ππ*) and 1E1g (πσ*) excited states by selectively stabilizing the σ-type states. The vibronic coupling occurs along vibrational modes of e2u symmetry which distorts the excited-state minimum geometry resulting in the experimentally broad, featureless absorption bands, and a ~100 nm Stokes shift in fluorescence– in stark contrast to benzene. Finally, the vibronic coupling is shown to simultaneously destabilize the reaction pathway towards hexafluoro-benzvalene and promote molecular vibrations along the 4π ring-closing pathway, resulting in the chemoselectivity for hexafluoro-Dewar-benzene.

scholarly journals Role of the Perfluoro Effect in the Selective Photochemical Isomerization of Hexafluorobenzene

2021 ◽  
Author(s):  
Jordan Cox ◽  
Mike Kellogg ◽  
Matthew Bain ◽  
Stephen E. Bradforth ◽  
Steven Lopez
Keyword(s):  
Reaction Pathway ◽  
Stokes Shift ◽  
Vibronic Coupling ◽  
Absorption Bands ◽  
Time Resolved ◽  
Photochemical Isomerization ◽  
Dynamics Simulations ◽  
Highly Strained ◽  
Holistic Description

Hexafluorobenzene and many of its derivatives exhibit a chemoselective photochemical isomerization, resulting in highly-strained, Dewar-type bicyclohexenes. While the changes in absorption and emission associated with benzene hexafluorination have been attributed to the socalled “perfluoro effect,” the resulting electronic structure and photochemical reactivity of hexafluorobenzene are still unclear. We now use a combination of ultrafast time-resolved spectroscopy, multiconfigurational computations, and non-adiabatic dynamics simulations to develop a holistic description of the absorption, emission, and photochemical dynamics of the 4πelectrocyclic ring-closing of hexafluorobenzene and the fluorination effect along the reaction coordinate. Our calculations suggest that the electron-withdrawing fluorine substituents induce a vibronic coupling between the lowest-energy 1B2u (ππ*) and 1E1g (πσ*) excited states by selectively stabilizing the σ-type states. The vibronic coupling occurs along vibrational modes of e2u symmetry which distorts the excited-state minimum geometry resulting in the experimentally broad, featureless absorption bands, and a ~100 nm Stokes shift in fluorescence– in stark contrast to benzene. Finally, the vibronic coupling is shown to simultaneously destabilize the reaction pathway towards hexafluoro-benzvalene and promote molecular vibrations along the 4π ring-closing pathway, resulting in the chemoselectivity for hexafluoro-Dewar-benzene.

scholarly journals The role of ultrafast magnon generation in the magnetization dynamics of rare-earth metals

2020 ◽  
Vol 6 (39) ◽  
pp. eabb1601 ◽  
Author(s):  
B. Frietsch ◽  
A. Donges ◽  
R. Carley ◽  
M. Teichmann ◽  
J. Bowlan ◽  
...  
Keyword(s):  
Rare Earth ◽  
Spin Dynamics ◽  
Magnetic Moments ◽  
Rare Earth Metals ◽  
Ultrafast Dynamics ◽  
Magnetization Dynamics ◽  
Time Resolved ◽  
Spin Lattice ◽  
Dynamics Simulations

Ultrafast demagnetization of rare-earth metals is distinct from that of 3d ferromagnets, as rare-earth magnetism is dominated by localized 4f electrons that cannot be directly excited by an optical laser pulse. Their demagnetization must involve excitation of magnons, driven either through exchange coupling between the 5d6s-itinerant and 4f-localized electrons or by coupling of 4f spins to lattice excitations. Here, we disentangle the ultrafast dynamics of 5d6s and 4f magnetic moments in terbium metal by time-resolved photoemission spectroscopy. We show that the demagnetization time of the Tb 4f magnetic moments of 400 fs is set by 4f spin–lattice coupling. This is experimentally evidenced by a comparison to ferromagnetic gadolinium and supported by orbital-resolved spin dynamics simulations. Our findings establish coupling of the 4f spins to the lattice via the orbital momentum as an essential mechanism driving magnetization dynamics via ultrafast magnon generation in technically relevant materials with strong magnetic anisotropy.

scholarly journals Temporary Intermediates of L-Trp Along the Reaction Pathway of Human Indoleamine 2,3-Dioxygenase 1 and Identification of an Exo Site

2021 ◽  
Vol 14 ◽  
pp. 117864692110529
Author(s):  
Manon Mirgaux ◽  
Laurence Leherte ◽  
Johan Wouters
Keyword(s):  
Molecular Dynamics ◽  
Reaction Mechanism ◽  
Crystal Structures ◽  
Protein Dynamics ◽  
Active Site ◽  
Reaction Pathway ◽  
Small Unit ◽  
Indoleamine 2,3 Dioxygenase ◽  
Dynamics Simulations

Protein dynamics governs most of the fundamental processes in the human body. Particularly, the dynamics of loops located near an active site can be involved in the positioning of the substrate and the reaction mechanism. The understanding of the functioning of dynamic loops is therefore a challenge, and often requires the use of a multi-disciplinary approach mixing, for example, crystallographic experiments and molecular dynamics simulations. In the present work, the dynamic behavior of the JK-loop of the human indoleamine 2,3-dioxygenase 1 hemoprotein, a target for immunotherapy, is investigated. To overcome the lack of knowledge on this dynamism, the study reported here is based on 3 crystal structures presenting different conformations of the loop, completed with molecular dynamics trajectories and MM-GBSA analyses, in order to trace the reaction pathway of the enzyme. In addition, the crystal structures identify an exo site in the small unit of the enzyme, that is populated redundantly by the substrate or the product of the reaction. The role of this newer reported exo site still needs to be investigated.

scholarly journals Protonation of Glutamate 208 Induces the Release of Agmatine in an Outward-facing Conformation of an Arginine/Agmatine Antiporter

2011 ◽  
Vol 286 (22) ◽  
pp. 19693-19701 ◽  
Author(s):  
Elia Zomot ◽  
Ivet Bahar
Keyword(s):  
Binding Pocket ◽  
Substrate Binding Pocket ◽  
Time Resolved ◽  
Extracellular Region ◽  
Acidic Conditions ◽  
Using Data ◽  
Dynamics Simulations ◽  
The Impact ◽  
First Time

Virulent enteric pathogens have developed several systems that maintain intracellular pH to survive extreme acidic conditions. One such mechanism is the exchange of arginine (Arg+) from the extracellular region with its intracellular decarboxylated form, agmatine (Agm2+). The net result of this process is the export of a virtual proton from the cytoplasm per antiport cycle. Crystal structures of the arginine/agmatine antiporter from Escherichia coli, AdiC, have been recently resolved in both the apo and Arg+-bound outward-facing conformations, which permit us to assess for the first time the time-resolved mechanisms of interactions that enable the specific antiporter functionality of AdiC. Using data from ∼1 μs of molecular dynamics simulations, we show that the protonation of Glu-208 selectively causes the dissociation and release of Agm2+, but not Arg+, to the cell exterior. The impact of Glu-208 protonation is transmitted to the substrate binding pocket via the reorientation of Ile-205 carbonyl group at the irregular portion of transmembrane (TM) helix 6. This effect, which takes place only in the subunits where Agm2+ is released, invites attention to the functional role of the unwound portion of TM helices (TM6 Trp-202–Glu-208 in AdiC) in facilitating substrate translocation, reminiscent of the behavior observed in structurally similar Na+-coupled transporters.

Structural dynamics of P-type ATPase ion pumps

2019 ◽  
Vol 47 (5) ◽  
pp. 1247-1257 ◽  
Author(s):  
Mateusz Dyla ◽  
Sara Basse Hansen ◽  
Poul Nissen ◽  
Magnus Kjaergaard
Keyword(s):  
Structural Dynamics ◽  
Single Molecule ◽  
New Technologies ◽  
Atp Hydrolysis ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Time Resolved ◽  
Dynamics Simulations ◽  
Types Of Information ◽  
P Type

Abstract P-type ATPases transport ions across biological membranes against concentration gradients and are essential for all cells. They use the energy from ATP hydrolysis to propel large intramolecular movements, which drive vectorial transport of ions. Tight coordination of the motions of the pump is required to couple the two spatially distant processes of ion binding and ATP hydrolysis. Here, we review our current understanding of the structural dynamics of P-type ATPases, focusing primarily on Ca2+ pumps. We integrate different types of information that report on structural dynamics, primarily time-resolved fluorescence experiments including single-molecule Förster resonance energy transfer and molecular dynamics simulations, and interpret them in the framework provided by the numerous crystal structures of sarco/endoplasmic reticulum Ca2+-ATPase. We discuss the challenges in characterizing the dynamics of membrane pumps, and the likely impact of new technologies on the field.

The Role of Hydrophobicity in the Stability and pH-Switchability of (RXDX)4 and Coumarin-RXDX Conjugate β-Sheets

2020 ◽  
Author(s):  
Ryan Weber ◽  
Martin McCullagh
Keyword(s):  
Biological Imaging ◽  
Ph Sensing ◽  
Hydrophobic Residue ◽  
Ideal Candidate ◽  
Self Assembling ◽  
Sensing Applications ◽  
Β Sheets ◽  
The Stability ◽  
Dynamics Simulations

<p>pH-switchable, self-assembling materials are of interest in biological imaging and sensing applications. Here we propose that combining the pH-switchability of RXDX (X=Ala, Val, Leu, Ile, Phe) peptides and the optical properties of coumarin creates an ideal candidate for these materials. This suggestion is tested with a thorough set of all-atom molecular dynamics simulations. We first investigate the dependence of pH-switchabiliy on the identity of the hydrophobic residue, X, in the bare (RXDX)<sub>4</sub> systems. Increasing the hydrophobicity stabilizes the fiber which, in turn, reduces the pH-switchabilty of the system. This behavior is found to be somewhat transferable to systems in which a single hydrophobic residue is replaced with a coumarin containing amino acid. In this case, conjugates with X=Ala are found to be unstable and both pHs while conjugates with X=Val, Leu, Ile and Phe are found to form stable β-sheets at least at neutral pH. The (RFDF)<sub>4</sub>-coumarin conjugate is found to have the largest relative entropy value of 0.884 +/- 0.001 between neutral and acidic coumarin ordering distributions. Thus, we posit that coumarin-(RFDF)<sub>4</sub> containing peptide sequences are ideal candidates for pH-sensing bioelectronic materials.</p>

A Paramedic Treatment for Modeling Explicitly Solvated Chemical Reaction Mechanisms

2018 ◽  
Author(s):  
Yasemin Basdogan ◽  
John Keith
Keyword(s):  
Reaction Mechanism ◽  
Chemical Reaction ◽  
Reaction Mechanisms ◽  
Reaction Pathway ◽  
Optimization Procedure ◽  
Cost Effective ◽  
Chemical Reaction Mechanisms ◽  
Solvent Molecules ◽  
Dynamics Simulations ◽  
Mbh Reaction

<div> <div> <div> <p>We report a static quantum chemistry modeling treatment to study how solvent molecules affect chemical reaction mechanisms without dynamics simulations. This modeling scheme uses a global optimization procedure to identify low energy intermediate states with different numbers of explicit solvent molecules and then the growing string method to locate sequential transition states along a reaction pathway. Testing this approach on the acid-catalyzed Morita-Baylis-Hillman (MBH) reaction in methanol, we found a reaction mechanism that is consistent with both recent experiments and computationally intensive dynamics simulations with explicit solvation. In doing so, we explain unphysical pitfalls that obfuscate computational modeling that uses microsolvated reaction intermediates. This new paramedic approach can promisingly capture essential physical chemistry of the complicated and multistep MBH reaction mechanism, and the energy profiles found with this model appear reasonably insensitive to the level of theory used for energy calculations. Thus, it should be a useful and computationally cost-effective approach for modeling solvent mediated reaction mechanisms when dynamics simulations are not possible. </p> </div> </div> </div>

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