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Journal Articles

Interaction at a distance: Xenon migration in Mb

Haydar Taylan Turan, Eric Boittier, Markus Meuwly
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 125103 (2023)
https://doi.org/10.1063/5.0124502
Published: March 2023
View article titled, Interaction at a distance: Xenon migration in Mb
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Includes: Supplementary data
Journal Articles

Spin–orbit coupling corrections for the GFN-xTB method

Gautam Jha, Thomas Heine
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 044120 (2023)
https://doi.org/10.1063/5.0129071
Published: January 2023
View article titled, Spin–orbit coupling corrections for the GFN-xTB method
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Includes: Supplementary data
Journal Articles

Time-resolved spectroscopic mapping of vibrational energy flow in proteins: Understanding thermal diffusion at the nanoscale

Yasuhisa Mizutani, Misao Mizuno
Journal: The Journal of Chemical Physics
J. Chem. Phys. 157, 240901 (2022)
https://doi.org/10.1063/5.0116734
Published: December 2022
View article titled, Time-resolved spectroscopic mapping of vibrational energy flow in proteins: Understanding thermal diffusion at the nanoscale
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Journal Articles

A retrospective on statistical mechanical models for hemoglobin allostery

William A. Eaton
Journal: The Journal of Chemical Physics
J. Chem. Phys. 157, 184104 (2022)
https://doi.org/10.1063/5.0127585
Published: November 2022
View article titled, A retrospective on statistical mechanical models for hemoglobin allostery
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Journal Articles

Efficient simulation of resonance Raman spectra with tight-binding approximations to density functional theory

Sahar Ashtari-Jafari, Zahra Jamshidi, Lucas Visscher
Journal: The Journal of Chemical Physics
J. Chem. Phys. 157, 084104 (2022)
https://doi.org/10.1063/5.0107220
Published: August 2022
View article titled, Efficient simulation of resonance Raman spectra with tight-binding approximations to density functional theory
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Journal Articles

High suitability of tryptophan residues as a spectroscopic thermometer for local temperature in proteins under nonequilibrium conditions

Satoshi Yamashita, Misao Mizuno, Yasuhisa Mizutani
Journal: The Journal of Chemical Physics
J. Chem. Phys. 156, 075101 (2022)
https://doi.org/10.1063/5.0079797
Published: February 2022
View article titled, High suitability of tryptophan residues as a spectroscopic thermometer for local temperature in proteins under nonequilibrium conditions
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Includes: Supplementary data
Journal Articles

Calculation of CYP450 protein–ligand binding and dissociation free energy paths

Kuan-Hsuan Su, Chin-Teng Wu, Shang-Wei Lin, Seiji Mori, Wei-Min Liu, Hsiao-Ching Yang
Journal: The Journal of Chemical Physics
J. Chem. Phys. 155, 025101 (2021)
https://doi.org/10.1063/5.0046169
Published: July 2021
View article titled, Calculation of CYP450 protein–ligand binding and dissociation free energy paths
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Includes: Supplementary data
Journal Articles

Lessons from combined experimental and theoretical examination of the FTIR and 2D-IR spectroelectrochemistry of the amide I region of cytochrome c

Youssef El Khoury, Guillaume Le Breton, Ana. V. Cunha, Thomas L. C. Jansen, Luuk J. G. W. van Wilderen, Jens Bredenbeck
Journal: The Journal of Chemical Physics
J. Chem. Phys. 154, 124201 (2021)
https://doi.org/10.1063/5.0039969
Published: March 2021
View article titled, Lessons from combined experimental and theoretical examination of the FTIR and 2D-IR spectroelectrochemistry of the amide I region of cytochrome <em>c</em>
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Includes: Supplementary data
Journal Articles

The importance of exact exchange—A methodological investigation of NO reduction in heme–copper oxidases

Margareta R. A. Blomberg
Journal: The Journal of Chemical Physics
J. Chem. Phys. 154, 055103 (2021)
https://doi.org/10.1063/5.0035634
Published: February 2021
View article titled, The importance of exact exchange—A methodological investigation of NO reduction in heme–copper oxidases
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Includes: Supplementary data
Journal Articles

Electron transfer pathways from quantum dynamics simulations

F. N. Pedron, F. Issoglio, D. A. Estrin, D. A. Scherlis
Journal: The Journal of Chemical Physics
J. Chem. Phys. 153, 225102 (2020)
https://doi.org/10.1063/5.0023577
Published: December 2020
View article titled, Electron transfer pathways from quantum dynamics simulations
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Includes: Supplementary data
Journal Articles

Exact semi-classical light–matter interaction operator applied to two-photon processes with strong relativistic effects

Mickaël G. Delcey, Rafael Carvalho Couto, Lasse Kragh Sørensen, Ignacio Fdez. Galván, Meiyuan Guo, Roland Lindh, Marcus Lundberg
Journal: The Journal of Chemical Physics
J. Chem. Phys. 153, 024114 (2020)
https://doi.org/10.1063/5.0007833
Published: July 2020
View article titled, Exact semi-classical light–matter interaction operator applied to two-photon processes with strong relativistic effects
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Includes: Supplementary data
Journal Articles

Ultrafast molecular photophysics in the deep-ultraviolet

Majed Chergui
Journal: The Journal of Chemical Physics
J. Chem. Phys. 150, 070901 (2019)
https://doi.org/10.1063/1.5082644
Published: February 2019
View article titled, Ultrafast molecular photophysics in the deep-ultraviolet
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Journal Articles

Photoinduced transport in an H64Q neuroglobin antidote for carbon monoxide poisoning

J. Rydzewski, W. Nowak
Journal: The Journal of Chemical Physics
J. Chem. Phys. 148, 115101 (2018)
https://doi.org/10.1063/1.5013659
Published: March 2018
View article titled, Photoinduced transport in an H64Q neuroglobin antidote for carbon monoxide poisoning
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Includes: Supplementary data
Journal Articles

Perspective: Two-dimensional resonance Raman spectroscopy

Brian P. Molesky, Zhenkun Guo, Thomas P. Cheshire, Andrew M. Moran
Journal: The Journal of Chemical Physics
J. Chem. Phys. 145, 180901 (2016)
https://doi.org/10.1063/1.4966194
Published: November 2016
View article titled, Perspective: Two-dimensional resonance Raman spectroscopy
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Journal Articles

Mixed quantum-classical simulations of the vibrational relaxation of photolyzed carbon monoxide in a hemoprotein

Alexander Schubert, Cyril Falvo, Christoph Meier
Journal: The Journal of Chemical Physics
J. Chem. Phys. 145, 054108 (2016)
https://doi.org/10.1063/1.4959859
Published: August 2016
View article titled, Mixed quantum-classical simulations of the vibrational relaxation of photolyzed carbon monoxide in a hemoprotein
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Journal Articles

Two-dimensional resonance Raman spectroscopy of oxygen- and water-ligated myoglobins

Brian P. Molesky, Zhenkun Guo, Thomas P. Cheshire, Andrew M. Moran
Journal: The Journal of Chemical Physics
J. Chem. Phys. 145, 034203 (2016)
https://doi.org/10.1063/1.4958625
Published: July 2016
View article titled, Two-dimensional resonance Raman spectroscopy of oxygen- and water-ligated myoglobins
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Includes: Supplementary data
Journal Articles

Influence of mutations at the proximal histidine position on the Fe–O2 bond in hemoglobin from density functional theory

Guido Todde, Sven Hovmöller, Aatto Laaksonen
Journal: The Journal of Chemical Physics
J. Chem. Phys. 144, 095101 (2016)
https://doi.org/10.1063/1.4942614
Published: March 2016
View article titled, Influence of mutations at the proximal histidine position on the Fe–O<sub>2</sub> bond in hemoglobin from density functional theory
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Journal Articles

On the application of the MARTINI coarse-grained model to immersion of a protein in a phospholipid bilayer

Ghulam Mustafa, Prajwal P. Nandekar, Xiaofeng Yu, Rebecca C. Wade
Journal: The Journal of Chemical Physics
J. Chem. Phys. 143, 243139 (2015)
https://doi.org/10.1063/1.4936909
Published: December 2015
View article titled, On the application of the MARTINI coarse-grained model to immersion of a protein in a phospholipid bilayer
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Includes: Supplementary data
Journal Articles

Memetic algorithms for ligand expulsion from protein cavities

J. Rydzewski, W. Nowak
Journal: The Journal of Chemical Physics
J. Chem. Phys. 143, 124101 (2015)
https://doi.org/10.1063/1.4931181
Published: September 2015
View article titled, Memetic algorithms for ligand expulsion from protein cavities
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Journal Articles

Reproducing kernel potential energy surfaces in biomolecular simulations: Nitric oxide binding to myoglobin

Maksym Soloviov, Markus Meuwly
Journal: The Journal of Chemical Physics
J. Chem. Phys. 143, 105103 (2015)
https://doi.org/10.1063/1.4929527
Published: September 2015
View article titled, Reproducing kernel potential energy surfaces in biomolecular simulations: Nitric oxide binding to myoglobin
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