{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,31]],"date-time":"2026-08-31T23:17:00Z","timestamp":1788218220368,"version":"build-2803163510"},"reference-count":162,"publisher":"American Chemical Society (ACS)","issue":"16","license":[{"start":{"date-parts":[[2026,8,13]],"date-time":"2026-08-13T00:00:00Z","timestamp":1786579200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["2102619"],"award-info":[{"award-number":["2102619"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000165","name":"Division of Chemistry","doi-asserted-by":"publisher","award":["2047667"],"award-info":[{"award-number":["2047667"]}],"id":[{"id":"10.13039\/100000165","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100021856","name":"Ministero dell'Universit? e della Ricerca","doi-asserted-by":"publisher","award":["2022K3AY2K"],"award-info":[{"award-number":["2022K3AY2K"]}],"id":[{"id":"10.13039\/501100021856","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100021856","name":"Ministero dell'Universit? e della Ricerca","doi-asserted-by":"publisher","award":["CN00000041 CN3"],"award-info":[{"award-number":["CN00000041 CN3"]}],"id":[{"id":"10.13039\/501100021856","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,8,25]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Redox enzymes play an essential role in nature and in biotechnological applications such as (photo)biocatalysis and biosensing. Understanding how a protein\u2019s sequence and structure tune its redox potential is very valuable for engineering proteins with tailored (photo)redox properties. Since protein redox potential measurements are laborious, reliable redox potential computations present an attractive alternative. However, redox calculations come with their own set of challenges, such as ensuring adequate sampling and accurate force fields. Dealing with charge-changing states introduces additional challenges to theory and requires special considerations in the model setup. Here, we report a protocol for computing the change in the proton-coupled one-electron redox potential associated with a D63N charge-changing mutation in a prototypal flavoprotein, Desulfovibrio vulgaris flavodoxin. An automated average protein electrostatic configuration protocol, APEC-F 2.0, was used to construct hybrid quantum mechanics\/molecular mechanics (QM\/MM) models. These models were used for subsequent alchemical free energy simulations in which a charged surface aspartate residue was gradually converted to an isosteric but neutral asparagine (D63N) over 40 \u03bb windows. A thermodynamic cycle was employed to calculate the redox potential of the mutant relative to the wild-type reference. This calculation was repeated for the same D63N mutation using models prepared under slightly different conditions, focusing primarily on factors that affect the electrostatic environment in the system. Factors tested include (1) the effect of including extra salt ions in the model solution, (2) different protocols to balance the disappearing negative charge associated with the alchemical D63N mutation, and (3) the effect of accounting for the kinetic energy terms in the free energy protocol due to alchemical morphing of the atomic masses. The results indicate that such apparently minor details may have a considerable effect on the random and systematic errors obtained from the free energy simulations. The best models were shown to reproduce the experimental shift in the redox potential due to the D63N mutation with an accuracy of 0.3 kcal\/mol. The associated error for this shift is 1.3 kcal\/mol, calculated as the total standard deviation of triplicate simulations for each of the oxidized and reduced neutral semiquinone states of flavin. The addition of salt ions in the simulations and the proper treatment of charge-conserving coalchemical counterions in particular are found to be paramount, since less accurate models led to errors more than double the magnitude compared to the best protocol. The sources of those errors are discussed and often found to be associated with medium-range electrostatics due to missing or inaccurate second solvation\/ionic shells around the mutation site.<\/jats:p>","DOI":"10.1021\/acs.jctc.6c01142","type":"journal-article","created":{"date-parts":[[2026,8,13]],"date-time":"2026-08-13T16:02:45Z","timestamp":1786636965000},"page":"8682-8699","source":"Crossref","is-referenced-by-count":0,"title":["Toward Relative\nRedox Potential Predictions in Flavoproteins:\nTreatment of a Charge-Changing Mutation in Alchemical Free Energy\nSimulations"],"prefix":"10.1021","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7553-5662","authenticated-orcid":true,"given":"Sarah","family":"Elhajj","sequence":"first","affiliation":[{"name":"Georgia State University , , , ,","place":["Atlanta, Georgia, United States, 30302"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jacopo","family":"D\u2019Ascenzi","sequence":"additional","affiliation":[{"name":"Universita di Siena , , Via A. Moro 2 , ,","place":["Siena, Italy, 53100"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8247-209X","authenticated-orcid":true,"given":"Massimo","family":"Olivucci","sequence":"additional","affiliation":[{"name":"Universita di Siena , , Via A. Moro 2 , ,","place":["Siena, Italy, 53100"]},{"name":"Bowling Green State University , , , ,","place":["Bowling Green, Ohio, United States, 43403"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6429-2853","authenticated-orcid":true,"given":"Samer","family":"Gozem","sequence":"additional","affiliation":[{"name":"Georgia State University , , , ,","place":["Atlanta, Georgia, United States, 30302"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,8,13]]},"reference":[{"key":"2026083118574352200_cit1","doi-asserted-by":"publisher","first-page":"801","DOI":"10.1021\/acs.chemrev.7b00203","article-title":"Role of biocatalysis\nin sustainable chemistry","volume":"118","author":"Sheldon","year":"2018","journal-title":"Chem. Rev."},{"key":"2026083118574352200_cit2","doi-asserted-by":"publisher","first-page":"665","DOI":"10.1126\/science.adt7268","article-title":"De novo design of porphyrin-containing\nproteins as\nefficient and stereoselective catalysts","volume":"388","author":"Hou","year":"2025","journal-title":"Science"},{"key":"2026083118574352200_cit3","doi-asserted-by":"publisher","first-page":"7294","DOI":"10.1021\/acs.jpca.6b08405","article-title":"Improved flavin-based\ncatalytic photooxidation of alcohols through intersystem crossing\nrate enhancement","volume":"120","author":"Korvinson","year":"2016","journal-title":"J. Phys. Chem. A"},{"key":"2026083118574352200_cit4","doi-asserted-by":"publisher","first-page":"11642","DOI":"10.1039\/C9CP01533G","article-title":"Polarizable embedding\nfor simulating redox potentials\nof biomolecules","volume":"21","author":"Tazhigulov","year":"2019","journal-title":"Phys. Chem. Chem. Phys."},{"key":"2026083118574352200_cit5","doi-asserted-by":"publisher","first-page":"409","DOI":"10.1002\/anie.201910300","article-title":"Electrochemistry broadens the scope\nof flavin photocatalysis: photoelectrocatalytic oxidation of unactivated\nalcohols","volume":"59","author":"Zhang","year":"2020","journal-title":"Angew. Chem., Int. Ed."},{"key":"2026083118574352200_cit6","doi-asserted-by":"publisher","first-page":"6825","DOI":"10.1021\/acs.orglett.1c02391","article-title":"Amide bond\nformation via aerobic photooxidative coupling of aldehydes with amines\ncatalyzed by a riboflavin derivative","volume":"23","author":"Hassan Tolba","year":"2021","journal-title":"Org. Lett."},{"key":"2026083118574352200_cit7","doi-asserted-by":"publisher","first-page":"4721","DOI":"10.1021\/jacs.1c13285","article-title":"Reduced molecular flavins\nas single-electron reductants\nafter photoexcitation","volume":"144","author":"Foja","year":"2022","journal-title":"J. Am. Chem. Soc."},{"key":"2026083118574352200_cit8","doi-asserted-by":"publisher","first-page":"1446","DOI":"10.1021\/acs.accounts.4c00129","article-title":"From ground-state\nto excited-state activation modes:\nflavin-dependent \u201cene\u201d-reductases catalyzed non-natural\nradical reactions","volume":"57","author":"Fu","year":"2024","journal-title":"Acc. Chem. Res."},{"key":"2026083118574352200_cit9","doi-asserted-by":"publisher","first-page":"20694","DOI":"10.1021\/acscatal.5c07431","article-title":"Beyond Flavoproteins:\nToward the\nIndustrialization of Photobiocatalysis","volume":"15","author":"East","year":"2025","journal-title":"ACS\nCatal."},{"key":"2026083118574352200_cit10","doi-asserted-by":"publisher","first-page":"41639","DOI":"10.1021\/jacs.5c12802","article-title":"Molecular Origins of Simultaneous Chemo-, Enantio-,\nand Substrate Selectivity in Non-Natural Photoenzymatic Radical Reactions","volume":"147","author":"Curtolo","year":"2025","journal-title":"J. Am. Chem. Soc."},{"key":"2026083118574352200_cit11","doi-asserted-by":"publisher","DOI":"10.1016\/j.chempr.2024.09.017","article-title":"Engineering a photoenzyme to use red light","volume":"11","author":"Carceller","year":"2025","journal-title":"Chem"},{"key":"2026083118574352200_cit12","doi-asserted-by":"publisher","first-page":"31725","DOI":"10.1074\/jbc.M112.391896","article-title":"Redox modulation\nof flavin and tyrosine determines photoinduced proton-coupled electron\ntransfer and photoactivation of BLUF photoreceptors","volume":"287","author":"Mathes","year":"2012","journal-title":"J. Biol. Chem."},{"key":"2026083118574352200_cit13","doi-asserted-by":"publisher","first-page":"4380","DOI":"10.1021\/acs.jpclett.6b02075","article-title":"Photoadduct formation from the FMN\nsinglet excited state in the LOV2 domain of Chlamydomonas reinhardtii\nphototropin","volume":"7","author":"Zhu","year":"2016","journal-title":"J. Phys. Chem. Lett."},{"key":"2026083118574352200_cit14","doi-asserted-by":"publisher","first-page":"2256","DOI":"10.1002\/cbic.200700304","article-title":"Redox properties of LOV domains:\nchemical versus photochemical reduction, and influence on the photocycle","volume":"8","author":"No\u0308ll","year":"2007","journal-title":"ChemBioChem"},{"key":"2026083118574352200_cit15","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-017-13420-1","article-title":"Electron transfer pathways in a light,\noxygen, voltage (LOV) protein devoid of the photoactive cysteine","volume":"7","author":"Kopka","year":"2017","journal-title":"Sci. Rep."},{"key":"2026083118574352200_cit16","doi-asserted-by":"publisher","first-page":"14638","DOI":"10.1021\/jacs.7b07849","article-title":"Photoactivation\nof the BLUF protein PixD probed by\nthe site-specific incorporation of fluorotyrosine residues","volume":"139","author":"Gil","year":"2017","journal-title":"J. Am. Chem. Soc."},{"key":"2026083118574352200_cit17","doi-asserted-by":"publisher","first-page":"1480","DOI":"10.1073\/pnas.1621393114","article-title":"Role of active site conformational changes in photocycle\nactivation of the AppA BLUF photoreceptor","volume":"114","author":"Goyal","year":"2017","journal-title":"Proc.\nNatl. Acad. Sci. U.S.A."},{"key":"2026083118574352200_cit18","doi-asserted-by":"publisher","first-page":"1147","DOI":"10.1021\/ja510550g","article-title":"Solvent driving force\nensures fast formation of a persistent and well-separated radical\npair in plant cryptochrome","volume":"137","author":"Lu\u0308demann","year":"2015","journal-title":"J. Am. Chem. Soc."},{"key":"2026083118574352200_cit19","doi-asserted-by":"publisher","first-page":"13331","DOI":"10.1039\/D1SC03000K","article-title":"From crystallographic\ndata to the\nsolution structure of photoreceptors: the case of the AppA BLUF domain","volume":"12","author":"Hashem","year":"2021","journal-title":"Chem. Sci."},{"key":"2026083118574352200_cit20","doi-asserted-by":"publisher","first-page":"2752","DOI":"10.1021\/acschembio.0c00543","article-title":"Unraveling the mechanism of a LOV domain optogenetic sensor: A glutamine\nlever induces unfolding of the J\u03b1 helix","volume":"15","author":"Iuliano","year":"2020","journal-title":"ACS Chem. Biol."},{"key":"2026083118574352200_cit21","doi-asserted-by":"publisher","first-page":"3069","DOI":"10.1021\/acs.jpcb.3c06245","article-title":"Redox Properties of\nFlavin in BLUF and LOV Photoreceptor\nProteins from Hybrid QM\/MM Molecular Dynamics Simulation","volume":"128","author":"K\u0131l\u0131c\u0327","year":"2024","journal-title":"J. Phys. Chem. B"},{"key":"2026083118574352200_cit22","doi-asserted-by":"publisher","DOI":"10.1038\/s42004-025-01647-3","article-title":"The ionic and protonation states of flavin control\nthe activation\nand recovery of Drosophila cryptochrome","volume":"8","author":"Xie","year":"2025","journal-title":"Commun.\nChem."},{"key":"2026083118574352200_cit23","doi-asserted-by":"publisher","first-page":"4368","DOI":"10.1021\/jacs.5b10533","article-title":"Single hydrogen\nbond donation from flavin N5 to proximal asparagine ensures FAD reduction\nin DNA photolyase","volume":"138","author":"Wijaya","year":"2016","journal-title":"J. Am. Chem. Soc."},{"key":"2026083118574352200_cit24","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1016\/j.febslet.2010.11.035","article-title":"On the\nmidpoint potential of the FAD chromophore in a BLUF-domain containing\nphotoreceptor protein","volume":"585","author":"Arents","year":"2011","journal-title":"FEBS Lett."},{"key":"2026083118574352200_cit25","doi-asserted-by":"publisher","first-page":"5346","DOI":"10.1021\/ja1097379","article-title":"Modulation of the photocycle\nof a LOV domain photoreceptor by the hydrogen-bonding network","volume":"133","author":"Raffelberg","year":"2011","journal-title":"J. Am. Chem. Soc."},{"key":"2026083118574352200_cit26","doi-asserted-by":"publisher","first-page":"1172","DOI":"10.1038\/s41586-025-09971-3","article-title":"Quantum spin resonance in engineered proteins\nfor multimodal sensing","volume":"649","author":"Abrahams","year":"2026","journal-title":"Nature"},{"key":"2026083118574352200_cit27","doi-asserted-by":"publisher","DOI":"10.1016\/j.eurpolymj.2020.110055","article-title":"Riboflavin-induced metal-free ATRP\nof (meth) acrylates","volume":"140","author":"Zaborniak","year":"2020","journal-title":"Eur. Polym. J."},{"key":"2026083118574352200_cit28","doi-asserted-by":"publisher","first-page":"12927","DOI":"10.1021\/acs.jpcc.5c03226","article-title":"COOCH3-Modified Flavin as a Heavy-Atom-Free\nSensitizer for Efficient Photocatalytic Oxidative Coupling of Benzylic\nAmines","volume":"129","author":"Guo","year":"2025","journal-title":"J. Phys. Chem. C"},{"key":"2026083118574352200_cit29","doi-asserted-by":"publisher","first-page":"12551","DOI":"10.1039\/D6CP00754F","article-title":"Carboxyl-functionalized\nflavin as efficient heavy-atom-free\ntriplet photosensitizers: A Theoretical Investigation","volume":"28","author":"Guo","year":"2026","journal-title":"Phys. Chem. Chem. Phys."},{"key":"2026083118574352200_cit30","doi-asserted-by":"publisher","first-page":"734","DOI":"10.1016\/j.copbio.2010.08.011","article-title":"Beyond directed\nevolutionsemi-rational protein engineering and design","volume":"21","author":"Lutz","year":"2010","journal-title":"Curr. Opin. Biotechnol."},{"key":"2026083118574352200_cit31","doi-asserted-by":"publisher","first-page":"46","DOI":"10.1016\/j.tibtech.2009.10.001","article-title":"Enzyme engineering\nfor enantioselectivity:\nfrom trial-and-error to rational design?","volume":"28","author":"Otten","year":"2010","journal-title":"Trends\nBiotechnol."},{"key":"2026083118574352200_cit32","doi-asserted-by":"publisher","first-page":"2251","DOI":"10.1021\/ja972992n","article-title":"Linear free energy substituent effect on flavin redox\nchemistry","volume":"120","author":"Hasford","year":"1998","journal-title":"J. Am. Chem. Soc."},{"key":"2026083118574352200_cit33","doi-asserted-by":"publisher","first-page":"3517","DOI":"10.1021\/ja994204v","article-title":"Model systems\nfor flavoenzyme activity.\nThe role of N (3)- H hydrogen bonding in flavin redox processes","volume":"122","author":"Cuello","year":"2000","journal-title":"J. Am. Chem. Soc."},{"key":"2026083118574352200_cit34","doi-asserted-by":"publisher","first-page":"915","DOI":"10.1002\/ejoc.201403275","article-title":"Artificial\nflavin systems for chemoselective and stereoselective oxidations","volume":"2015","author":"Cibulka","year":"2015","journal-title":"Eur. J. Org. Chem."},{"key":"2026083118574352200_cit35","doi-asserted-by":"publisher","first-page":"9209","DOI":"10.1002\/chem.201600207","article-title":"Flavin derivatives with tailored redox properties:\nsynthesis, characterization, and electrochemical behavior","volume":"22","author":"Korma\u0301nyos","year":"2016","journal-title":"Chem. - Eur. J."},{"key":"2026083118574352200_cit36","doi-asserted-by":"publisher","DOI":"10.1016\/j.jphotochem.2019.112164","article-title":"Impact of the redox state of flavin\nchromophores on the UV\u2013vis spectra, redox and acidity constants\nand electron affinities","volume":"387","author":"Mondal","year":"2020","journal-title":"J. Photochem. Photobiol.,\nA"},{"key":"2026083118574352200_cit37","doi-asserted-by":"publisher","DOI":"10.1002\/cbic.202200144","article-title":"Broadening\nthe Scope of the Flavin-Tag\nMethod by Improving Flavin Incorporation and Incorporating Flavin\nAnalogs","volume":"23","author":"Tong","year":"2022","journal-title":"ChemBioChem"},{"key":"2026083118574352200_cit38","doi-asserted-by":"publisher","DOI":"10.1002\/chem.202502897","article-title":"Deazaalloxazines-Flavin\nDerivatives That Provide Reductive Photoredox Catalysis with Inert\nSubstrates","volume":"31","author":"Weisheitelova\u0301","year":"2025","journal-title":"Chem. - Eur. J."},{"key":"2026083118574352200_cit39","doi-asserted-by":"publisher","DOI":"10.1016\/j.electacta.2025.147520","article-title":"Redox properties of flavin derivatives:\nA Comparative study","volume":"543","author":"S\u030cimkova\u0301","year":"2025","journal-title":"Electrochim. Acta"},{"key":"2026083118574352200_cit40","doi-asserted-by":"publisher","first-page":"11255","DOI":"10.1039\/D5SC01630D","article-title":"Introduction\nof flavin anions into photoredox catalysis: acid-base equilibria of\nlumichrome allow photoreductions with an anion of an elusive 10-unsubstituted\nisoalloxazine","volume":"16","author":"Pruka\u0142a","year":"2025","journal-title":"Chem. Sci."},{"key":"2026083118574352200_cit41","doi-asserted-by":"publisher","DOI":"10.3390\/molecules31091400","article-title":"C 5-alkyl and C 5-aryl\nSubstituted 5-Deazaflavin as Sensitizers for Photodehalogenation of\nAryl Halides","volume":"31","author":"Guo","year":"2026","journal-title":"Molecules"},{"key":"2026083118574352200_cit42","doi-asserted-by":"publisher","first-page":"786","DOI":"10.1021\/acs.biochem.5c00803","article-title":"The Reductive\nPower of Flavin Mononucleotide Does Not\nDictate the Product Profile of the Nitroreductase, NfsA","volume":"65","author":"Cheema","year":"2026","journal-title":"Biochemistry"},{"key":"2026083118574352200_cit43","doi-asserted-by":"publisher","first-page":"3344","DOI":"10.1021\/acs.jpcb.6b01512","article-title":"Photophysics of the\nLOV-based fluorescent protein variant iLOV-Q489K determined by simulation\nand experiment","volume":"120","author":"Davari","year":"2016","journal-title":"J. Phys. Chem. B"},{"key":"2026083118574352200_cit44","doi-asserted-by":"publisher","DOI":"10.1002\/pro.4851","article-title":"Two distinct\nmechanisms of flavoprotein spectral tuning\nrevealed by low-temperature and time-dependent spectroscopy","volume":"33","author":"Nikolaev","year":"2024","journal-title":"Protein Sci."},{"key":"2026083118574352200_cit45","doi-asserted-by":"publisher","first-page":"143","DOI":"10.1016\/j.bbrc.2021.06.046","article-title":"High-resolution structure\nof a naturally red-shifted LOV domain","volume":"567","author":"Goncharov","year":"2021","journal-title":"Biochem.\nBiophys. Res. Commun."},{"key":"2026083118574352200_cit46","doi-asserted-by":"publisher","DOI":"10.1016\/j.jbc.2021.100662","article-title":"The molecular basis\nof spectral tuning in blue-and red-shifted flavin-binding fluorescent\nproteins","volume":"296","author":"Ro\u0308llen","year":"2021","journal-title":"J. Biol. Chem."},{"key":"2026083118574352200_cit47","doi-asserted-by":"publisher","DOI":"10.3390\/cryst10040256","article-title":"Effects of proline substitutions\non the thermostable LOV domain from Chloroflexus aggregans","volume":"10","author":"Remeeva","year":"2020","journal-title":"Crystals"},{"key":"2026083118574352200_cit48","doi-asserted-by":"publisher","first-page":"1005","DOI":"10.1002\/prot.26078","article-title":"Insights into\nthe mechanisms of light-oxygen-voltage domain color tuning from a\nset of high-resolution X-ray structures","volume":"89","author":"Remeeva","year":"2021","journal-title":"Proteins:\nStruct., Funct., Bioinf."},{"key":"2026083118574352200_cit49","doi-asserted-by":"crossref","unstructured":"Nikolaev, A.; Markeeva, E.; Maksimov, E. G.; Yudenko, A.; Tropina, E. V.; Boldyrev, K. N.; Nikolaeva, Y.; Cherepanov, D. A.; Kovalev, K.; Yang, Y.; et al.\n          Discovery of excited\nstate proton transfer in flavin-based fluorescent protein with large\nStokes shift\n          bioRxiv\n          2025\n          10.1101\/2025.06.07.658458.","DOI":"10.1101\/2025.06.07.658458"},{"key":"2026083118574352200_cit50","doi-asserted-by":"publisher","first-page":"5549","DOI":"10.1021\/ct500830a","article-title":"Assessment of Franck-Condon\nmethods\nfor computing vibrationally broadened UV\u2013vis absorption spectra\nof flavin derivatives: Riboflavin, roseoflavin, and 5-thioflavin","volume":"10","author":"Karasulu","year":"2014","journal-title":"J. Chem. Theory Comput."},{"key":"2026083118574352200_cit51","doi-asserted-by":"publisher","first-page":"3878","DOI":"10.1021\/acs.jctc.5b00197","article-title":"Role of the molecular environment\nin flavoprotein color and redox tuning: QM cluster versus QM\/MM modeling","volume":"11","author":"Udvarhelyi","year":"2015","journal-title":"J. Chem. Theory Comput."},{"key":"2026083118574352200_cit52","doi-asserted-by":"publisher","first-page":"5176","DOI":"10.1021\/acs.jpcb.5b01299","article-title":"Theoretical\ncharacterization of the\nflavin-based fluorescent protein iLOV and its Q489K mutant","volume":"119","author":"Khrenova","year":"2015","journal-title":"J. Phys. Chem. B"},{"key":"2026083118574352200_cit53","doi-asserted-by":"publisher","first-page":"10018","DOI":"10.1021\/acs.jpcb.7b07533","article-title":"Mutants of the flavoprotein\niLOV\nas prospective red-shifted fluorescent markers","volume":"121","author":"Khrenova","year":"2017","journal-title":"J. Phys. Chem. B"},{"key":"2026083118574352200_cit54","doi-asserted-by":"publisher","first-page":"16526","DOI":"10.1039\/C9CP02230A","article-title":"Electronic spectra\nof flavin in different\nredox and protonation states: a computational perspective on the effect\nof the electrostatic environment","volume":"21","author":"Kabir","year":"2019","journal-title":"Phys. Chem.\nChem. Phys."},{"key":"2026083118574352200_cit55","doi-asserted-by":"publisher","first-page":"1768","DOI":"10.1021\/acs.jpcb.0c10834","article-title":"Computational investigation\nof structural and spectroscopic properties of LOV-based proteins with\nimproved fluorescence","volume":"125","author":"Cardoso Ramos","year":"2021","journal-title":"J. Phys. Chem. B"},{"key":"2026083118574352200_cit56","doi-asserted-by":"publisher","first-page":"1301","DOI":"10.1021\/acs.jpcb.2c06475","article-title":"Alternative\nstrategy for spectral tuning of flavin-binding fluorescent proteins","volume":"127","author":"Kabir","year":"2023","journal-title":"J. Phys. Chem. B"},{"key":"2026083118574352200_cit57","doi-asserted-by":"publisher","DOI":"10.1002\/pro.4958","article-title":"Reengineering of a flavin-binding fluorescent protein\nusing ProteinMPNN","volume":"33","author":"Nikolaev","year":"2024","journal-title":"Protein Sci."},{"key":"2026083118574352200_cit58","doi-asserted-by":"publisher","first-page":"15111","DOI":"10.1021\/bi0483256","article-title":"Role of neighboring FMN side chains\nin the modulation of flavin reduction potentials and in the energetics\nof the FMN: apoprotein interaction in Anabaena flavodoxin","volume":"43","author":"Nogue\u0301s","year":"2004","journal-title":"Biochemistry"},{"key":"2026083118574352200_cit59","doi-asserted-by":"publisher","first-page":"15789","DOI":"10.1021\/ja036940b","article-title":"Model systems for\nflavoenzyme activity: relationships between cofactor structure, binding\nand redox properties","volume":"125","author":"Legrand","year":"2003","journal-title":"J. Am. Chem. Soc."},{"key":"2026083118574352200_cit60","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1016\/S0166-1280(02)00719-4","article-title":"Flavin reduction\npotential tuning by substitution and\nbending","volume":"623","author":"Walsh","year":"2003","journal-title":"J. Mol. Struct.: THEOCHEM"},{"key":"2026083118574352200_cit61","doi-asserted-by":"publisher","first-page":"14907","DOI":"10.1021\/jp108024b","article-title":"Improved density functional description\nof the electrochemistry and structure- property descriptors of substituted\nflavins","volume":"114","author":"North","year":"2010","journal-title":"J. Phys. Chem. B"},{"key":"2026083118574352200_cit62","doi-asserted-by":"publisher","first-page":"7762","DOI":"10.1039\/C9SC00942F","article-title":"Spectroscopic, thermodynamic and\ncomputational evidence\nof the locations of the FADs in the nitrogen fixation-associated electron\ntransfer flavoprotein","volume":"10","author":"Mohamed-Raseek","year":"2019","journal-title":"Chem. Sci."},{"key":"2026083118574352200_cit63","doi-asserted-by":"publisher","DOI":"10.1002\/cphc.202300091","article-title":"One-and Two-Electron\nReductions in\nMiniSOG and their Implication in Catalysis","volume":"24","author":"Azpitarte","year":"2023","journal-title":"ChemPhysChem"},{"key":"2026083118574352200_cit64","doi-asserted-by":"publisher","first-page":"661","DOI":"10.1021\/acs.jpcb.2c07266","article-title":"Flavin\nCharge Redistribution upon Optical Excitation Is Independent of Solvent\nPolarity","volume":"127","author":"Van Galen","year":"2023","journal-title":"J. Phys. Chem. B"},{"key":"2026083118574352200_cit65","doi-asserted-by":"publisher","first-page":"530","DOI":"10.1039\/D4CB00056K","article-title":"Reduction midpoint potential of a\nparadigm light-oxygen-voltage receptor and its modulation by methionine\nresidues","volume":"5","author":"de Fuentes","year":"2024","journal-title":"RSC Chem. Biol."},{"key":"2026083118574352200_cit66","doi-asserted-by":"publisher","DOI":"10.1016\/j.jbc.2024.107122","article-title":"Structure, dynamics, and redox reactivity\nof an all-purpose flavodoxin","volume":"300","author":"Khan","year":"2024","journal-title":"J. Biol. Chem."},{"key":"2026083118574352200_cit67","doi-asserted-by":"publisher","first-page":"5057","DOI":"10.1021\/jacs.5c16043","article-title":"Measurement\nand Control of Crossed\nPotentials in a Flavoprotein","volume":"148","author":"Jones","year":"2026","journal-title":"J. Am. Chem. Soc."},{"key":"2026083118574352200_cit68","doi-asserted-by":"publisher","first-page":"3862","DOI":"10.1021\/acs.chemrev.7b00707","article-title":"Flavin-based electron\nbifurcation, a new mechanism\nof biological energy coupling","volume":"118","author":"Buckel","year":"2018","journal-title":"Chem. Rev."},{"key":"2026083118574352200_cit69","doi-asserted-by":"publisher","DOI":"10.1016\/j.jbc.2022.102606","article-title":"Unusual reactivity\nof a flavin in a bifurcating electron-transferring flavoprotein leads\nto flavin modification and a charge-transfer complex","volume":"298","author":"Mohamed-Raseek","year":"2022","journal-title":"J. Biol. Chem."},{"key":"2026083118574352200_cit70","doi-asserted-by":"publisher","DOI":"10.1016\/j.jbc.2023.104762","article-title":"Noncovalent\ninteractions that tune the reactivities of the flavins in bifurcating\nelectron transferring flavoprotein","volume":"299","author":"Gonza\u0301lez-Viegas","year":"2023","journal-title":"J. Biol.\nChem."},{"key":"2026083118574352200_cit71","doi-asserted-by":"publisher","first-page":"1689","DOI":"10.1021\/jacsau.4c01219","article-title":"Electrochemical\nObservation and pH Dependence of All Three Expected Redox Couples\nin an Extremophilic Bifurcating Electron Transfer Flavoprotein with\nFused Subunits","volume":"5","author":"Das","year":"2025","journal-title":"JACS Au"},{"key":"2026083118574352200_cit72","doi-asserted-by":"publisher","first-page":"655","DOI":"10.1038\/nchembio.2348","article-title":"Mechanistic\ninsights into energy conservation\nby flavin-based electron bifurcation","volume":"13","author":"Lubner","year":"2017","journal-title":"Nat. Chem.\nBiol."},{"key":"2026083118574352200_cit73","doi-asserted-by":"publisher","DOI":"10.1063\/5.0287415","article-title":"An automated QM\/MM average protein\nelectrostatic configuration approach for flavoproteins: APEC-F 2.0","volume":"163","author":"Elhajj","year":"2025","journal-title":"J. Chem. Phys."},{"key":"2026083118574352200_cit74","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.70229","article-title":"Extensive TDDFT Benchmark\nStudy of the Resonance Raman\nSpectra of Lumiflavin","volume":"46","author":"Andrikopoulos","year":"2025","journal-title":"J. Comput. Chem."},{"key":"2026083118574352200_cit75","doi-asserted-by":"publisher","DOI":"10.1002\/wcms.1541","article-title":"Understanding flavin electronic structure\nand spectra","volume":"12","author":"Kar","year":"2022","journal-title":"WIREs Comput. Mol. Sci."},{"key":"2026083118574352200_cit76","doi-asserted-by":"publisher","first-page":"9751","DOI":"10.1021\/acs.jpcb.9b07250","article-title":"Microscopic picture of the solvent reorganization during\nelectron transfer to flavin in water","volume":"123","author":"K\u0131l\u0131c\u0327","year":"2019","journal-title":"J. Phys.\nChem. B"},{"key":"2026083118574352200_cit77","doi-asserted-by":"publisher","DOI":"10.1021\/ed081p596","article-title":"Molecular modeling\nof environmentally important processes: Reduction potentials","volume":"81","author":"Truhlar","year":"2004","journal-title":"J. Chem. Educ."},{"key":"2026083118574352200_cit78","doi-asserted-by":"publisher","first-page":"5729","DOI":"10.1021\/jp071526+","article-title":"Combined quantum mechanical\nand molecular mechanical simulations of one-and two-electron reduction\npotentials of flavin cofactor in water, medium-chain acyl-CoA dehydrogenase,\nand cholesterol oxidase","volume":"111","author":"Bhattacharyya","year":"2007","journal-title":"J. Phys. Chem. A"},{"key":"2026083118574352200_cit79","doi-asserted-by":"publisher","first-page":"112","DOI":"10.1016\/j.theochem.2008.01.029","article-title":"Theoretical study of\nreduction potentials of substituted flavins","volume":"856","author":"Li","year":"2008","journal-title":"J. Mol. Struct.: THEOCHEM"},{"key":"2026083118574352200_cit80","doi-asserted-by":"publisher","first-page":"2490","DOI":"10.1021\/acs.jpclett.6b00893","article-title":"Free energies of\nredox half-reactions from first-principles\ncalculations","volume":"7","author":"Tazhigulov","year":"2016","journal-title":"J. Phys. Chem. Lett."},{"key":"2026083118574352200_cit81","doi-asserted-by":"publisher","first-page":"6227","DOI":"10.1021\/acs.jctc.4c00602","article-title":"First and Second Reductions\nin an Aprotic Solvent: Comparing Computational\nand Experimental One-Electron Reduction Potentials for 345 Quinones","volume":"20","author":"Elhajj","year":"2024","journal-title":"J. Chem. Theory Comput."},{"key":"2026083118574352200_cit82","doi-asserted-by":"publisher","first-page":"11951","DOI":"10.1021\/acs.jctc.5c00976","article-title":"Prediction of the aqueous\nredox properties\nof functionalized quinones using a new QM\/MM variational formulation","volume":"21","author":"Labat","year":"2025","journal-title":"J. Chem. Theory Comput."},{"key":"2026083118574352200_cit83","doi-asserted-by":"publisher","first-page":"1259","DOI":"10.1021\/bi962180o","article-title":"Control of oxidation-\nreduction potentials\nin flavodoxin from Clostridium beijerinckii: The role of conformation\nchanges","volume":"36","author":"Ludwig","year":"1997","journal-title":"Biochemistry"},{"key":"2026083118574352200_cit84","doi-asserted-by":"publisher","first-page":"3183","DOI":"10.1021\/bi00010a007","article-title":"Electrostatic Effects\nof Surface Acidic Amino Acid\nResidues on the Oxidation-Reduction Potentials of the Flavodoxin from\nDesulfovibrio vulgaris (Hildenborough)","volume":"34","author":"Zhou","year":"1995","journal-title":"Biochemistry"},{"key":"2026083118574352200_cit85","doi-asserted-by":"publisher","first-page":"8686","DOI":"10.1021\/bi010571j","article-title":"Role of hydrogen\nbonding interactions to N (3) H of\nthe flavin mononucleotide cofactor in the modulation of the redox\npotentials of the Clostridium beijerinckii flavodoxin","volume":"40","author":"Bradley","year":"2001","journal-title":"Biochemistry"},{"key":"2026083118574352200_cit86","doi-asserted-by":"publisher","first-page":"9668","DOI":"10.1021\/bi980770b","article-title":"Role of Methionine 56 in the Control of the Oxidation-\nReduction Potentials of the Clostridium beijerinckii Flavodoxin: Effects\nof Substitutions by Aliphatic Amino Acids and Evidence for a Role\nof Sulfur- Flavin Interactions","volume":"37","author":"Druhan","year":"1998","journal-title":"Biochemistry"},{"key":"2026083118574352200_cit87","doi-asserted-by":"publisher","first-page":"3050","DOI":"10.1063\/1.449208","article-title":"Monte Carlo\nsimulation of differences in free energies\nof hydration","volume":"83","author":"Jorgensen","year":"1985","journal-title":"J. Chem. Phys."},{"key":"2026083118574352200_cit88","doi-asserted-by":"publisher","first-page":"564","DOI":"10.1126\/science.3576184","article-title":"Free energy calculations\nby computer simulation","volume":"236","author":"Bash","year":"1987","journal-title":"Science"},{"key":"2026083118574352200_cit89","doi-asserted-by":"publisher","first-page":"12782","DOI":"10.1021\/jp056623m","article-title":"Decomposition of the solvation free\nenergies of deoxyribonucleoside triphosphates using the free energy\nperturbation method","volume":"110","author":"Bren","year":"2006","journal-title":"J. Phys. Chem. B"},{"key":"2026083118574352200_cit90","doi-asserted-by":"publisher","first-page":"16567","DOI":"10.1021\/jp048502c","article-title":"Hydration of amino\nacid side chains: Nonpolar and electrostatic contributions\ncalculated from staged molecular dynamics free energy simulations\nwith explicit water molecules","volume":"108","author":"Deng","year":"2004","journal-title":"J. Phys. Chem.\nB"},{"key":"2026083118574352200_cit91","doi-asserted-by":"publisher","first-page":"919","DOI":"10.1021\/ct800445x","article-title":"Computations of absolute solvation\nfree energies of small molecules using explicit and implicit solvent\nmodel","volume":"5","author":"Shivakumar","year":"2009","journal-title":"J. Chem. Theory Comput."},{"key":"2026083118574352200_cit92","doi-asserted-by":"publisher","first-page":"9196","DOI":"10.1021\/acs.jcim.5c01563","article-title":"Efficient Free Energies from a Simplified\nElectrostatic Embedding QM\/MM Approach Based on Electrostatic Potential\nFitted Operators","volume":"65","author":"Bonfrate","year":"2025","journal-title":"J. Chem. Inf. Model."},{"key":"2026083118574352200_cit93","doi-asserted-by":"publisher","first-page":"2911","DOI":"10.1021\/acs.jcim.7b00564","article-title":"Relative binding\nfree energy calculations\nin drug discovery: recent advances and practical considerations","volume":"57","author":"Cournia","year":"2017","journal-title":"J. Chem. Inf. Model."},{"key":"2026083118574352200_cit94","doi-asserted-by":"publisher","first-page":"5649","DOI":"10.1021\/ja00197a022","article-title":"Free energy perturbation\nsimulations\nof the inhibition of thermolysin: prediction of the free energy of\nbinding of a new inhibitor","volume":"111","author":"Merz","year":"1989","journal-title":"J. Am. Chem. Soc."},{"key":"2026083118574352200_cit95","doi-asserted-by":"publisher","first-page":"921","DOI":"10.1088\/0034-4885\/62\/6\/202","article-title":"Ligand-receptor\ninteractions","volume":"62","author":"Bongrand","year":"1999","journal-title":"Rep. Prog. Phys."},{"key":"2026083118574352200_cit96","doi-asserted-by":"publisher","first-page":"7683","DOI":"10.1021\/ja0377908","article-title":"Standard free energy\nof releasing a localized water\nmolecule from the binding pockets of proteins: double-decoupling method","volume":"126","author":"Hamelberg","year":"2004","journal-title":"J. Am. Chem. Soc."},{"key":"2026083118574352200_cit97","doi-asserted-by":"publisher","first-page":"15813","DOI":"10.1021\/jp805529z","article-title":"Single mutation induced H3N2 hemagglutinin antibody\nneutralization: a free energy perturbation study","volume":"112","author":"Zhou","year":"2008","journal-title":"J. Phys. Chem. B"},{"key":"2026083118574352200_cit98","doi-asserted-by":"publisher","first-page":"547","DOI":"10.1016\/S0022-2836(02)00880-X","article-title":"Binding free energy differences in a TCR-peptide-MHC\ncomplex induced by a peptide mutation: a simulation analysis","volume":"324","author":"Michielin","year":"2002","journal-title":"J. Mol. Biol."},{"key":"2026083118574352200_cit99","doi-asserted-by":"publisher","first-page":"210","DOI":"10.1021\/acs.jctc.6b00979","article-title":"Rapid,\naccurate, precise, and reliable\nrelative free energy prediction using ensemble based thermodynamic\nintegration","volume":"13","author":"Bhati","year":"2017","journal-title":"J. Chem. Theory Comput."},{"key":"2026083118574352200_cit100","doi-asserted-by":"publisher","DOI":"10.33011\/livecoms.2.1.18378","article-title":"Best practices\nfor alchemical free energy calculations [article v1. 0]","volume":"2","author":"Mey","year":"2020","journal-title":"Living J. Comput. Mol. Sci."},{"key":"2026083118574352200_cit101","doi-asserted-by":"publisher","first-page":"8682","DOI":"10.1063\/1.459255","article-title":"Investigation of the free energy\nfunctions for electron transfer reactions","volume":"93","author":"King","year":"1990","journal-title":"J.\nChem. Phys."},{"key":"2026083118574352200_cit102","doi-asserted-by":"publisher","first-page":"16506","DOI":"10.1039\/D0CP06632J","article-title":"The redox\npotential of a heme cofactor\nin Nitrosomonas europaea cytochrome c peroxidase: A polarizable QM\/MM\nstudy","volume":"23","author":"Karnaukh","year":"2021","journal-title":"Phys. Chem. Chem. Phys."},{"key":"2026083118574352200_cit103","doi-asserted-by":"publisher","first-page":"7465","DOI":"10.1021\/acs.jpcb.5c01121","article-title":"Effects of\nconformational\nsampling on computing redox properties using linear response approach","volume":"129","author":"Maity","year":"2025","journal-title":"J. Phys. Chem. B"},{"key":"2026083118574352200_cit104","doi-asserted-by":"publisher","first-page":"1420","DOI":"10.1063\/1.1740409","article-title":"High-temperature equation of state by a perturbation\nmethod. I. Nonpolar gases","volume":"22","author":"Zwanzig","year":"1954","journal-title":"J. Chem. Phys."},{"key":"2026083118574352200_cit105","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1146\/annurev-biophys-062722-093258","article-title":"Free energy methods for the description\nof molecular\nprocesses","volume":"52","author":"Chipot","year":"2023","journal-title":"Annu. Rev. Biophys."},{"key":"2026083118574352200_cit106","doi-asserted-by":"publisher","first-page":"8643","DOI":"10.1021\/jp034286g","article-title":"Free energy\nperturbation calculations\nwith combined QM\/MM potentials complications, simplifications, and\napplications to redox potential calculations","volume":"107","author":"Li","year":"2003","journal-title":"J. Phys. Chem. B"},{"key":"2026083118574352200_cit107","doi-asserted-by":"publisher","first-page":"4131","DOI":"10.1021\/acs.jcim.1c00215","article-title":"FEPrepare: a web-based\ntool for automating the setup\nof relative binding free energy calculations","volume":"61","author":"Zavitsanou","year":"2021","journal-title":"J. Chem. Inf. Model."},{"key":"2026083118574352200_cit108","doi-asserted-by":"publisher","DOI":"10.3390\/molecules27031077","article-title":"Theoretical\nmodeling of redox potentials of biomolecules","volume":"27","author":"Chen","year":"2022","journal-title":"Molecules"},{"key":"2026083118574352200_cit109","doi-asserted-by":"publisher","first-page":"334","DOI":"10.1021\/acs.jctc.5c01656","article-title":"Reliable Redox-Potential Simulations\nof Proteins","volume":"22","author":"Stier","year":"2026","journal-title":"J. Chem. Theory Comput."},{"key":"2026083118574352200_cit110","doi-asserted-by":"crossref","unstructured":"Aeck, M.; de la Lande, A.; Clavague\u0301ra, C.; Cailliez, F.\n          AMOEBA polarizable\natomic multipole forcefield parameters for flavins\n          2026\n          https:\/\/chemrxiv.org\/doi\/pdf\/10.26434\/chemrxiv.15003242\/v1.\nChemRxiv.","DOI":"10.26434\/chemrxiv.15003242\/v1"},{"key":"2026083118574352200_cit111","doi-asserted-by":"publisher","first-page":"5876","DOI":"10.1063\/1.455539","article-title":"Free energy\nof ionic hydration: Analysis\nof a thermodynamic integration technique to evaluate free energy differences\nby molecular dynamics simulations","volume":"89","author":"Straatsma","year":"1988","journal-title":"J. Chem.\nPhys."},{"key":"2026083118574352200_cit112","doi-asserted-by":"publisher","first-page":"13053","DOI":"10.1021\/jp803859j","article-title":"Calculating\nChemically Accurate Redox\nPotentials for Engineered Flavoproteins from Classical Molecular Dynamics\nFree Energy Simulations","volume":"112","author":"Sattelle","year":"2008","journal-title":"J. Phys. Chem. A"},{"key":"2026083118574352200_cit113","doi-asserted-by":"publisher","DOI":"10.3390\/molecules28166016","article-title":"Assessing\nthe Performance of Non-Equilibrium Thermodynamic Integration in Flavodoxin\nRedox Potential Estimation","volume":"28","author":"Silvestri","year":"2023","journal-title":"Molecules"},{"key":"2026083118574352200_cit114","doi-asserted-by":"publisher","DOI":"10.1103\/PhysRevLett.78.2690","article-title":"Nonequilibrium equality for free\nenergy differences","volume":"78","author":"Jarzynski","year":"1997","journal-title":"Phys. Rev. Lett."},{"key":"2026083118574352200_cit115","doi-asserted-by":"publisher","DOI":"10.1103\/PhysRevE.56.5018","article-title":"Equilibrium free-energy differences\nfrom nonequilibrium\nmeasurements: A master-equation approach","volume":"56","author":"Jarzynski","year":"1997","journal-title":"Phys.\nRev. E"},{"key":"2026083118574352200_cit116","doi-asserted-by":"publisher","first-page":"1481","DOI":"10.1023\/A:1023208217925","article-title":"Nonequilibrium measurements of free\nenergy differences\nfor microscopically reversible Markovian systems","volume":"90","author":"Crooks","year":"1998","journal-title":"J. Stat. Phys."},{"key":"2026083118574352200_cit117","doi-asserted-by":"publisher","first-page":"25240","DOI":"10.1074\/jbc.M702788200","article-title":"Influence of the protein environment on the redox potentials\nof flavodoxins from Clostridium beijerinckii","volume":"282","author":"Ishikita","year":"2007","journal-title":"J. Biol. Chem."},{"key":"2026083118574352200_cit118","doi-asserted-by":"publisher","first-page":"4394","DOI":"10.1021\/bi702151k","article-title":"Redox potential difference between Desulfovibrio vulgaris\nand Clostridium beijerinckii flavodoxins","volume":"47","author":"Ishikita","year":"2008","journal-title":"Biochemistry"},{"key":"2026083118574352200_cit119","doi-asserted-by":"publisher","first-page":"10219","DOI":"10.1021\/bi00496a010","article-title":"pKa\u2019s of ionizable\ngroups\nin proteins: atomic detail from a continuum electrostatic model","volume":"29","author":"Bashford","year":"1990","journal-title":"Biochemistry"},{"key":"2026083118574352200_cit120","doi-asserted-by":"publisher","first-page":"5885","DOI":"10.1021\/acs.jctc.1c00221","article-title":"Free Energy\nComputation for an Isomerizing Chromophore in a Molecular Cavity via\nthe Average Solvent Electrostatic Configuration Model: Applications\nin Rhodopsin and Rhodopsin-Mimicking Systems","volume":"17","author":"Nikolaev","year":"2021","journal-title":"J. Chem. Theory Comput."},{"key":"2026083118574352200_cit121","doi-asserted-by":"publisher","first-page":"914","DOI":"10.1021\/acs.jctc.3c00757","article-title":"Guidelines for Free-Energy Calculations\nInvolving Charge Changes","volume":"20","author":"Petrov","year":"2024","journal-title":"J. Chem. Theory Comput."},{"key":"2026083118574352200_cit122","doi-asserted-by":"publisher","first-page":"331","DOI":"10.1016\/S0009-2614(02)00343-3","article-title":"Approximate\nelectrostatic\ninteraction operator for QM\/MM calculations","volume":"356","author":"Ferre\u0301","year":"2002","journal-title":"Chem. Phys. Lett."},{"key":"2026083118574352200_cit123","doi-asserted-by":"publisher","first-page":"18398","DOI":"10.1039\/D5SC02960K","article-title":"The influence of\nprotein electrostatics on potential inversion in flavoproteins","volume":"16","author":"Singh","year":"2025","journal-title":"Chem. Sci."},{"key":"2026083118574352200_cit124","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","article-title":"VMD: visual molecular\ndynamics","volume":"14","author":"Humphrey","year":"1996","journal-title":"J. Mol. Graphics"},{"key":"2026083118574352200_cit125","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1016\/j.softx.2015.06.001","article-title":"GROMACS: High\nperformance\nmolecular simulations through multi-level parallelism from laptops\nto supercomputers","volume":"1-2","author":"Abraham","year":"2015","journal-title":"SoftwareX"},{"key":"2026083118574352200_cit126","doi-asserted-by":"publisher","first-page":"712","DOI":"10.1002\/prot.21123","article-title":"Comparison\nof multiple Amber force\nfields and development of improved protein backbone parameters","volume":"65","author":"Hornak","year":"2006","journal-title":"Proteins: Struct., Funct., Bioinf."},{"key":"2026083118574352200_cit127","doi-asserted-by":"publisher","first-page":"1463","DOI":"10.1002\/(SICI)1096-987X(199709)18:12&lt;1463::AID-JCC4&gt;3.0.CO;2-H","article-title":"LINCS: A linear constraint solver for molecular simulations","volume":"18","author":"Hess","year":"1997","journal-title":"J. Comput. Chem."},{"key":"2026083118574352200_cit128","doi-asserted-by":"publisher","first-page":"116","DOI":"10.1021\/ct700200b","article-title":"P-LINCS: A parallel linear constraint\nsolver for molecular simulation","volume":"4","author":"Hess","year":"2008","journal-title":"J. Chem. Theory\nComput."},{"key":"2026083118574352200_cit129","doi-asserted-by":"publisher","first-page":"10089","DOI":"10.1063\/1.464397","article-title":"Particle\nmesh Ewald: An N log (N) method for Ewald sums in large systems","volume":"98","author":"Darden","year":"1993","journal-title":"J. Chem. Phys."},{"key":"2026083118574352200_cit130","doi-asserted-by":"publisher","first-page":"8577","DOI":"10.1063\/1.470117","article-title":"A smooth particle\nmesh Ewald method","volume":"103","author":"Essmann","year":"1995","journal-title":"J. Chem. Phys."},{"key":"2026083118574352200_cit131","doi-asserted-by":"publisher","first-page":"348","DOI":"10.1002\/jcc.23804","article-title":"pmx: Automated\nprotein structure and topology generation for alchemical perturbations","volume":"36","author":"Gapsys","year":"2015","journal-title":"J. Comput. Chem."},{"key":"2026083118574352200_cit132","doi-asserted-by":"publisher","first-page":"2309","DOI":"10.1016\/j.bpj.2010.01.051","article-title":"Protein Thermostability Calculations\nUsing Alchemical Free Energy Simulations","volume":"98","author":"Seeliger","year":"2010","journal-title":"Biophys.\nJ."},{"key":"2026083118574352200_cit133","doi-asserted-by":"publisher","first-page":"4403","DOI":"10.1021\/acs.jctc.0c01328","article-title":"Dummy Atoms in Alchemical\nFree Energy Calculations","volume":"17","author":"Fleck","year":"2021","journal-title":"J. Chem. Theory Comput."},{"key":"2026083118574352200_cit134","doi-asserted-by":"publisher","first-page":"1487","DOI":"10.1021\/j100056a020","article-title":"A Comparison of Alternative Approaches\nto Free Energy\nCalculations","volume":"98","author":"Pearlman","year":"1994","journal-title":"J. Phys. Chem. A"},{"key":"2026083118574352200_cit135","first-page":"271","volume-title":"Biomolecular Simulations","author":"Shirts","year":"2012"},{"key":"2026083118574352200_cit136","doi-asserted-by":"publisher","DOI":"10.1063\/1.2799191","article-title":"Nonlinear\nscaling\nschemes for Lennard-Jones interactions in free energy calculations","volume":"127","author":"Steinbrecher","year":"2007","journal-title":"J. Chem. Phys."},{"key":"2026083118574352200_cit137","unstructured":"Lemkul, J. A.\n          \n          Gromacs Tutorial\n          2025\n          http:\/\/www.mdtutorials.com\/gmx\/free_energy\/index.html. [Online;\naccessed 26-June-2025]."},{"key":"2026083118574352200_cit138","doi-asserted-by":"publisher","DOI":"10.33011\/livecoms.1.1.5068","article-title":"From proteins to perturbed\nHamiltonians: a suite of\ntutorials for the GROMACS-2018 molecular simulation package [article\nv1. 0]","volume":"1","author":"Lemkul","year":"2018","journal-title":"Living J. Comput. Mol. Sci."},{"key":"2026083118574352200_cit139","doi-asserted-by":"publisher","first-page":"9418","DOI":"10.1021\/acs.jpcb.4c04901","article-title":"Introductory tutorials for simulating protein dynamics\nwith GROMACS","volume":"128","author":"Lemkul","year":"2024","journal-title":"J. Phys. Chem. B"},{"key":"2026083118574352200_cit140","doi-asserted-by":"publisher","first-page":"3023","DOI":"10.1021\/acs.jcim.2c00348","article-title":"Alchemical Free Energy\nCalculations\nto Investigate Protein\u2500Protein Interactions: the Case of the\nCDC42\/PAK1 Complex","volume":"62","author":"La Serra","year":"2022","journal-title":"J. Chem. Inf. Model."},{"key":"2026083118574352200_cit141","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2023.168187","article-title":"Free Energy\nPerturbation Calculations\nof Mutation Effects on SARS-CoV-2 RBD::ACE2 Binding Affinity","volume":"435","author":"Sergeeva","year":"2023","journal-title":"J. Mol. Biol."},{"key":"2026083118574352200_cit142","doi-asserted-by":"publisher","first-page":"1481","DOI":"10.1016\/j.jmb.2019.02.003","article-title":"Relative Binding\nAffinity Prediction of Charge-Changing Sequence Mutations with FEP\nin Protein\u2500Protein Interfaces","volume":"431","author":"Clark","year":"2019","journal-title":"J. Mol.\nBiol."},{"key":"2026083118574352200_cit143","doi-asserted-by":"publisher","first-page":"7846","DOI":"10.1021\/acs.jctc.3c00842","article-title":"Comparison of Equilibrium and Nonequilibrium\nApproaches for Relative Binding Free Energy Predictions","volume":"19","author":"Wan","year":"2023","journal-title":"J. Chem. Theory Comput."},{"key":"2026083118574352200_cit144","doi-asserted-by":"publisher","first-page":"6127","DOI":"10.1021\/acs.jctc.8b00391","article-title":"Avoiding false positive\nconclusions in molecular simulation: the importance of replicas","volume":"14","author":"Knapp","year":"2018","journal-title":"J. Chem. Theory Comput."},{"key":"2026083118574352200_cit145","doi-asserted-by":"publisher","first-page":"6959","DOI":"10.1021\/acs.jcim.3c01654","article-title":"Ensemble-Based\nApproaches\nEnsure Reliability and Reproducibility","volume":"63","author":"Wan","year":"2023","journal-title":"J. Chem.\nInf. Model."},{"key":"2026083118574352200_cit146","doi-asserted-by":"publisher","first-page":"3227","DOI":"10.1021\/acs.jcim.3c00599","article-title":"Guidelines for\nreporting molecular dynamics simulations in JCIM publications","volume":"63","author":"Soares","year":"2023","journal-title":"J. Chem. Inf. Model."},{"key":"2026083118574352200_cit147","volume-title":"Amber 2024","author":"Case","year":"2024"},{"key":"2026083118574352200_cit148","doi-asserted-by":"publisher","first-page":"381","DOI":"10.1021\/ct400626b","article-title":"Quantifying Artifacts in Ewald Simulations of Inhomogeneous\nSystems with a Net Charge","volume":"10","author":"Hub","year":"2014","journal-title":"J. Chem. Theory Comput."},{"key":"2026083118574352200_cit149","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1016\/0021-9991(76)90078-4","article-title":"Efficient estimation of free energy\ndifferences from\nMonte Carlo data","volume":"22","author":"Bennett","year":"1976","journal-title":"J. Comput. Phys."},{"key":"2026083118574352200_cit150","unstructured":"\u201cIs gmx bar reading dH\/dl for masses?\u201d\nGROMACS User\nDiscussion post\n          2026\n          https:\/\/gromacs.bioexcel.eu\/t\/is-gmx-bar-reading-dh-dl-for-masses\/10316\/9. Accessed: June 06, 2026."},{"key":"2026083118574352200_cit151","doi-asserted-by":"publisher","first-page":"3253","DOI":"10.1002\/jcc.21909","article-title":"Soft-core potentials\nin thermodynamic integration: Comparing one-and two-step transformations","volume":"32","author":"Steinbrecher","year":"2011","journal-title":"J. Comput. Chem."},{"key":"2026083118574352200_cit152","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0335829","article-title":"Benchmarking free\nenergy calculations: Analysis of single and double mutations across\ntwo simulation software platforms for two protein systems","volume":"21","author":"Gupta","year":"2026","journal-title":"PLoS One"},{"key":"2026083118574352200_cit153","doi-asserted-by":"publisher","first-page":"7806","DOI":"10.1021\/acs.jctc.4c00806","article-title":"Automated\nAdaptive Absolute Binding Free Energy Calculations","volume":"20","author":"Clark","year":"2024","journal-title":"J. Chem. Theory Comput."},{"key":"2026083118574352200_cit154","first-page":"185","article-title":"The theory\nof electrolytes. I. Lowering of freezing point and related\nphenomena","volume":"24","author":"Debye","year":"1923","journal-title":"Phys. Z."},{"key":"2026083118574352200_cit155","doi-asserted-by":"publisher","first-page":"115","DOI":"10.1002\/jcc.20156","article-title":"Incorporating\nthe effect of ionic strength in free energy calculations using explicit\nions","volume":"26","author":"Donnini","year":"2005","journal-title":"J. Comput. Chem."},{"key":"2026083118574352200_cit156","doi-asserted-by":"publisher","first-page":"8384","DOI":"10.1021\/acs.jpclett.1c02173","article-title":"Ionic atmosphere\neffect on the absorption spectrum of a flavoprotein: a reminder to\nconsider solution ions","volume":"12","author":"Dratch","year":"2021","journal-title":"J. Phys. Chem. Lett."},{"key":"2026083118574352200_cit157","doi-asserted-by":"publisher","first-page":"2373","DOI":"10.1021\/ct300220p","article-title":"New soft-core\npotential\nfunction for molecular dynamics based alchemical free energy calculations","volume":"8","author":"Gapsys","year":"2012","journal-title":"J. Chem. Theory Comput."},{"key":"2026083118574352200_cit158","doi-asserted-by":"publisher","first-page":"3469","DOI":"10.1002\/prot.23125","article-title":"Simulating electrostatic energies\nin proteins: Perspectives and some recent studies of pKas, redox,\nand other crucial functional properties","volume":"79","author":"Warshel","year":"2011","journal-title":"Proteins:\nStruct., Funct., Bioinf."},{"key":"2026083118574352200_cit159","doi-asserted-by":"publisher","first-page":"11919","DOI":"10.1063\/1.1755656","article-title":"Accelerated molecular\ndynamics: a promising and efficient simulation method for biomolecules","volume":"120","author":"Hamelberg","year":"2004","journal-title":"J. Chem. Phys."},{"key":"2026083118574352200_cit160","doi-asserted-by":"publisher","first-page":"2677","DOI":"10.1021\/ct500090q","article-title":"Improved reweighting of accelerated\nmolecular dynamics simulations for free energy calculation","volume":"10","author":"Miao","year":"2014","journal-title":"J. Chem. Theory Comput."},{"key":"2026083118574352200_cit161","doi-asserted-by":"publisher","first-page":"4748","DOI":"10.1021\/acs.jcim.2c00858","article-title":"Machine learning for\nefficient prediction of protein redox potential: The flavoproteins\ncase","volume":"62","author":"Galuzzi","year":"2022","journal-title":"J. Chem. Inf. Model."},{"key":"2026083118574352200_cit162","doi-asserted-by":"publisher","first-page":"6747","DOI":"10.1021\/acs.jctc.4c00715","article-title":"Machine learning\napproach\nto vertical energy gap in redox processes","volume":"20","author":"Sarangi","year":"2024","journal-title":"J.\nChem. Theory Comput."}],"container-title":["Journal of Chemical Theory\nand Computation"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jctc.6c01142","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/jctcce\/article-pdf\/22\/16\/8682\/66532787\/acs.jctc.6c01142.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/jctcce\/article-pdf\/22\/16\/8682\/66532787\/acs.jctc.6c01142.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,31]],"date-time":"2026-08-31T22:57:50Z","timestamp":1788217070000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/jctcce\/article\/22\/16\/8682\/5254644\/Toward-Relative-Redox-Potential-Predictions-in"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,13]]},"references-count":162,"journal-issue":{"issue":"16","published-online":{"date-parts":[[2026,8,13]]},"published-print":{"date-parts":[[2026,8,25]]}},"URL":"https:\/\/doi.org\/10.1021\/acs.jctc.6c01142","relation":{},"ISSN":["1549-9618","1549-9626"],"issn-type":[{"value":"1549-9618","type":"print"},{"value":"1549-9626","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,13]]}}}