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Journal Articles

Anisotropic dynamics of an interfacial enzyme active site observed using tethered substrate analogs and ultrafast 2D IR spectroscopy

Tayler D. Hill, Sunil Basnet, Hannah H. Lepird, Blaze W. Rightnowar, Sean D. Moran
Journal: The Journal of Chemical Physics
J. Chem. Phys. 159, 165101 (2023)
https://doi.org/10.1063/5.0167991
Published: October 2023
View article titled, Anisotropic dynamics of an interfacial enzyme active site observed using tethered substrate analogs and ultrafast 2D IR spectroscopy
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Includes: Supplementary data
Journal Articles

Amide isomerization pathways: Electronic and structural background of protonation- and deprotonation-mediated cis-trans interconversions

Ádám A. Kelemen, András Perczel, Dániel Horváth, Imre Jákli
Journal: The Journal of Chemical Physics
J. Chem. Phys. 159, 154301 (2023)
https://doi.org/10.1063/5.0165772
Published: October 2023
View article titled, Amide isomerization pathways: Electronic and structural background of protonation- and deprotonation-mediated <em>cis-trans</em> interconversions
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Includes: Supplementary data
Journal Articles

Kinetic isotope effect study of N-6 methyladenosine chemical demethylation in bicarbonate-activated peroxide system

Fangya Li, Ying Wang, Jianyu Zhang
Journal: The Journal of Chemical Physics
J. Chem. Phys. 159, 124103 (2023)
https://doi.org/10.1063/5.0169285
Published: September 2023
View article titled, Kinetic isotope effect study of N-6 methyladenosine chemical demethylation in bicarbonate-activated peroxide system
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Includes: Supplementary data
Journal Articles

Protein–ligand interactions from a quantum fragmentation perspective: The case of the SARS-CoV-2 main protease interacting with α-ketoamide inhibitors

Luigi Genovese, William Dawson, Takahito Nakajima, Viviana Cristiglio, Valérie Vallet, Michel Masella
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 214121 (2023)
https://doi.org/10.1063/5.0148064
Published: June 2023
View article titled, Protein–ligand interactions from a quantum fragmentation perspective: The case of the SARS-CoV-2 main protease interacting with <em>α</em>-ketoamide inhibitors
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Includes: Supplementary data
Journal Articles

Allosteric communication between ACE2 active site and binding interface with SARS-CoV-2

Mauro L. Mugnai, D. Thirumalai
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 215102 (2023)
https://doi.org/10.1063/5.0137654
Published: June 2023
View article titled, Allosteric communication between ACE2 active site and binding interface with SARS-CoV-2
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Includes: Supplementary data
Journal Articles

Quantum chemical descriptors based on semiempirical methods for large biomolecules

Igor B. Grillo, Gabriel A. Urquiza-Carvalho, Gerd B. Rocha
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 201001 (2023)
https://doi.org/10.1063/5.0132687
Published: May 2023
View article titled, Quantum chemical descriptors based on semiempirical methods for large biomolecules
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Journal Articles

An ultrafast phototrigger of the Trp5CN–Trp motif in a β-hairpin peptide

Qin Zhang, Zhongneng Zhou, Bodan Deng, Bingyao Wang, Xiu-Wen Kang, Jinquan Chen, Bei Ding, Dongping Zhong
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 201102 (2023)
https://doi.org/10.1063/5.0143384
Published: May 2023
View article titled, An ultrafast phototrigger of the Trp<sub>5CN</sub>–Trp motif in a <em>β</em>-hairpin peptide
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Includes: Supplementary data
Journal Articles

Allosteric regulation of β-reaction stage I in tryptophan synthase upon the α-ligand binding

Shingo Ito, Kiyoshi Yagi, Yuji Sugita
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 115101 (2023)
https://doi.org/10.1063/5.0134117
Published: March 2023
View article titled, Allosteric regulation of β-reaction stage I in tryptophan synthase upon the α-ligand binding
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Includes: Supplementary data
Journal Articles

Model reduction for the Chemical Master Equation: An information-theoretic approach

Kaan Öcal, Guido Sanguinetti, Ramon Grima
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 114113 (2023)
https://doi.org/10.1063/5.0131445
Published: March 2023
View article titled, Model reduction for the Chemical Master Equation: An information-theoretic approach
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Journal Articles

Emergence of allostery through reorganization of protein residue network architecture

Riya Samanta, Neel Sanghvi, Dorothy Beckett, Silvina Matysiak
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 085104 (2023)
https://doi.org/10.1063/5.0136010
Published: February 2023
View article titled, Emergence of allostery through reorganization of protein residue network architecture
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Includes: Supplementary data
Journal Articles

Evaluating the active site-substrate interplay between x-ray crystal structure and molecular dynamics in chorismate mutase

Thomas J. Summers, Reza Hemmati, Justin E. Miller, Donatus A. Agbaglo, Qianyi Cheng, Nathan J. DeYonker
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 065101 (2023)
https://doi.org/10.1063/5.0127106
Published: February 2023
View article titled, Evaluating the active site-substrate interplay between x-ray crystal structure and molecular dynamics in chorismate mutase
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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

Geometrically driven aggregation of unsymmetrical dielectric particles

Daniel A. Olaya-Muñoz, Juan P. Hernández-Ortiz, Monica Olvera de la Cruz
Journal: The Journal of Chemical Physics
J. Chem. Phys. 157, 204104 (2022)
https://doi.org/10.1063/5.0127112
Published: November 2022
View article titled, Geometrically driven aggregation of unsymmetrical dielectric particles
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Journal Articles

Polarizable MD and QM/MM investigation of acrylamide-based leads to target the main protease of SARS-CoV-2

Jorge Nochebuena, G. Andrés Cisneros
Journal: The Journal of Chemical Physics
J. Chem. Phys. 157, 185101 (2022)
https://doi.org/10.1063/5.0123698
Published: November 2022
View article titled, Polarizable MD and QM/MM investigation of acrylamide-based leads to target the main protease of SARS-CoV-2
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Includes: Supplementary data
Journal Articles

Reduction pathway of glutaredoxin 1 investigated with QM/MM molecular dynamics using a neural network correction

Julian Böser, Tomáš Kubař, Marcus Elstner, Denis Maag
Journal: The Journal of Chemical Physics
J. Chem. Phys. 157, 154104 (2022)
https://doi.org/10.1063/5.0123089
Published: October 2022
View article titled, Reduction pathway of glutaredoxin 1 investigated with QM/MM molecular dynamics using a neural network correction
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Includes: Supplementary data
Journal Articles

SH—It happens: S–H bonds as intrinsic 2D-IR labels in proteins

E. Deniz, J. M. Schmidt-Engler, K. Ulrich, M. Oberle, G. Wille, J. Bredenbeck
Journal: The Journal of Chemical Physics
J. Chem. Phys. 157, 135102 (2022)
https://doi.org/10.1063/5.0107057
Published: October 2022
View article titled, SH—It happens: S–H bonds as intrinsic 2D-IR labels in proteins
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Includes: Supplementary data
Journal Articles

Time-correlation functions for odd Langevin systems

Kento Yasuda, Kenta Ishimoto, Akira Kobayashi, Li-Shing Lin, Isamu Sou, Yuto Hosaka, Shigeyuki Komura
Journal: The Journal of Chemical Physics
J. Chem. Phys. 157, 095101 (2022)
https://doi.org/10.1063/5.0095969
Published: September 2022
View article titled, Time-correlation functions for odd Langevin systems
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Journal Articles

Free-energy transduction in chemical reaction networks: From enzymes to metabolism

Artur Wachtel, Riccardo Rao, Massimiliano Esposito
Journal: The Journal of Chemical Physics
J. Chem. Phys. 157, 024109 (2022)
https://doi.org/10.1063/5.0091035
Published: July 2022
View article titled, Free-energy transduction in chemical reaction networks: From enzymes to metabolism
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Journal Articles

Xanthophyll-cycle based model of the rapid photoprotection of Nannochloropsis in response to regular and irregular light/dark sequences

Audrey H. Short, Thomas P. Fay, Thien Crisanto, Johanna Hall, Collin J. Steen, Krishna K. Niyogi, David T. Limmer, Graham R. Fleming
Journal: The Journal of Chemical Physics
J. Chem. Phys. 156, 205102 (2022)
https://doi.org/10.1063/5.0089335
Published: May 2022
View article titled, Xanthophyll-cycle based model of the rapid photoprotection of <em>Nannochloropsis</em> in response to regular and irregular light/dark sequences
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Journal Articles

Biotin-painted proteins have thermodynamic stability switched by kinetic folding routes

Frederico Campos Freitas, Michelli Maldonado, Antonio Bento Oliveira Junior, José Nelson Onuchic, Ronaldo Junio de Oliveira
Journal: The Journal of Chemical Physics
J. Chem. Phys. 156, 195101 (2022)
https://doi.org/10.1063/5.0083875
Published: May 2022
View article titled, Biotin-painted proteins have thermodynamic stability switched by kinetic folding routes
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Includes: Supplementary data