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Article ; Online: Quantitative Account of the Bonding Properties of a Rubredoxin Model Complex [Fe(SCH

Tzeli, Demeter / Raugei, Simone / Xantheas, Sotiris S

Journal of chemical theory and computation

2021 Volume 17, Issue 10, Page(s) 6080–6091

Abstract: Iron-sulfur clusters play important roles in biology as parts of electron-transfer chains and catalytic cofactors. Here, we report a detailed computational analysis of a structural model of the simplest natural iron-sulfur cluster of rubredoxin and its ... ...

Abstract	Iron-sulfur clusters play important roles in biology as parts of electron-transfer chains and catalytic cofactors. Here, we report a detailed computational analysis of a structural model of the simplest natural iron-sulfur cluster of rubredoxin and its cationic counterparts. Specifically, we investigated adiabatic reduction energies, dissociation energies, and bonding properties of the low-lying electronic states of the complexes [Fe(SCH
Language	English
Publishing date	2021-09-21
Publishing country	United States
Document type	Journal Article
ISSN	1549-9626
ISSN (online)	1549-9626
DOI	10.1021/acs.jctc.1c00485
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Article ; Online: Protonation of Serine in Gas and Condensed and Microsolvated States in Aqueous Solution.

Johnson, Samantha I / Baer, Marcel D / Raugei, Simone

The journal of physical chemistry. A

2021 Volume 126, Issue 1, Page(s) 44–52

Abstract: Identification of molecules and elucidation of their chemical structure are ubiquitous problems in chemistry. Mass spectrometry (MS) can be used due to its sensitivity and versatility. For detection to occur, analytes must be ionized and transferred to ... ...

Abstract	Identification of molecules and elucidation of their chemical structure are ubiquitous problems in chemistry. Mass spectrometry (MS) can be used due to its sensitivity and versatility. For detection to occur, analytes must be ionized and transferred to the gas phase. Soft ionization processes such as electrospray ionization are popular; however, resulting microsolvated phases can alter the chemistry of analytes and therefore detection and identification. To understand these processes, we use computational methods to probe the ionization propensity of serine in the gas phase, aqueous microsolvated clusters, and aqueous solution. We show that the tautomeric form of serine is altered by the presence of water, as five water molecules can stabilize the zwitterionic tautomer. Inclusion of cosolutes such as ions can stabilize the zwitterion with as few as one or two water molecules present. We demonstrate that ionization propensity, as measured by gas phase bacisity, can increase by over 100 kJ/mol when placed in a small water-serine cluster, showing the sensitivity of the chemistry of microsolvated analytes. Finally, detailed analysis reveals that small droplets (less than seven water molecules) are extremely sensitive to addition of further water molecules. Beyond this limit, structural and electronic properties change little with droplet size.
MeSH term(s)	Ions ; Serine ; Water
Chemical Substances	Ions ; Water (059QF0KO0R) ; Serine (452VLY9402)
Language	English
Publishing date	2021-12-23
Publishing country	United States
Document type	Journal Article
ISSN	1520-5215
ISSN (online)	1520-5215
DOI	10.1021/acs.jpca.1c08795
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Article ; Online: Atomistic insight on structure and dynamics of spinach acyl carrier protein with substrate length.

Baer, Marcel D / Shanklin, John / Raugei, Simone

Biophysical journal

2021 Volume 120, Issue 17, Page(s) 3841–3853

Abstract: The plant acyl-acyl carrier protein (ACP) desaturases are a family of soluble enzymes that convert saturated fatty acyl-ACPs into their cis-monounsaturated equivalents in an oxygen-dependent reaction. These enzymes play a key role in biosynthesis of ... ...

Abstract	The plant acyl-acyl carrier protein (ACP) desaturases are a family of soluble enzymes that convert saturated fatty acyl-ACPs into their cis-monounsaturated equivalents in an oxygen-dependent reaction. These enzymes play a key role in biosynthesis of monounsaturated fatty acids in plants. ACPs are central proteins in fatty acid biosynthesis that deliver acyl chains to desaturases. They have been reported to show a varying degree of local dynamics and structural variability depending on the acyl chain size. It has been suggested that substrate-specific changes in ACP structure and dynamics have a crucial impact on the desaturase enzymatic activity. Using molecular dynamics simulations, we investigated the intrinsic solution structure and dynamics of ACP from spinach with four different acyl chains: capric (C
MeSH term(s)	Acyl Carrier Protein ; Fatty Acids ; Fatty Acids, Monounsaturated ; Spinacia oleracea
Chemical Substances	Acyl Carrier Protein ; Fatty Acids ; Fatty Acids, Monounsaturated
Language	English
Publishing date	2021-02-23
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2020.12.036
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Article ; Online: Molecular mechanism of trehalose 6-phosphate inhibition of the plant metabolic sensor kinase SnRK1.

Blanford, Jantana / Zhai, Zhiyang / Baer, Marcel D / Guo, Gongrui / Liu, Hui / Liu, Qun / Raugei, Simone / Shanklin, John

Science advances

2024 Volume 10, Issue 20, Page(s) eadn0895

Abstract: SUCROSE-NON-FERMENTING1-RELATED PROTEIN KINASE1 (SnRK1), a central plant metabolic sensor kinase, phosphorylates its target proteins, triggering a global shift from anabolism to catabolism. Molecular modeling revealed that upon binding of KIN10 to ... ...

Abstract	SUCROSE-NON-FERMENTING1-RELATED PROTEIN KINASE1 (SnRK1), a central plant metabolic sensor kinase, phosphorylates its target proteins, triggering a global shift from anabolism to catabolism. Molecular modeling revealed that upon binding of KIN10 to GEMINIVIRUS REP-INTERACTING KINASE1 (GRIK1), KIN10's activation T-loop reorients into GRIK1's active site, enabling its phosphorylation and activation. Trehalose 6-phosphate (T6P) is a proxy for cellular sugar status and a potent inhibitor of SnRK1. T6P binds to KIN10, a SnRK1 catalytic subunit, weakening its affinity for GRIK1. Here, we investigate the molecular details of T6P inhibition of KIN10. Molecular dynamics simulations and in vitro phosphorylation assays identified and validated the T6P binding site on KIN10. Under high-sugar conditions, T6P binds to KIN10, blocking the reorientation of its activation loop and preventing its phosphorylation and activation by GRIK1. Under these conditions, SnRK1 maintains only basal activity levels, minimizing phosphorylation of its target proteins, thereby facilitating a general shift from catabolism to anabolism.
MeSH term(s)	Sugar Phosphates/metabolism ; Trehalose/analogs & derivatives ; Trehalose/metabolism ; Protein Serine-Threonine Kinases/metabolism ; Phosphorylation ; Arabidopsis Proteins/metabolism ; Arabidopsis Proteins/genetics ; Arabidopsis Proteins/antagonists & inhibitors ; Arabidopsis Proteins/chemistry ; Molecular Dynamics Simulation ; Protein Binding ; Arabidopsis/metabolism ; Binding Sites ; Transcription Factors
Chemical Substances	trehalose-6-phosphate ; SnRK1 protein, Arabidopsis ; KIN10 protein, Arabidopsis
Language	English
Publishing date	2024-05-17
Publishing country	United States
Document type	Journal Article
ZDB-ID	2810933-8
ISSN	2375-2548 ; 2375-2548
ISSN (online)	2375-2548
ISSN	2375-2548
DOI	10.1126/sciadv.adn0895
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Article: Multilevel Computational Studies Reveal the Importance of Axial Ligand for Oxygen Reduction Reaction on Fe–N–C Materials

Hutchison, Phillips / Rice, Peter S. / Warburton, Robert E. / Raugei, Simone / Hammes-Schiffer, Sharon

Journal of the American Chemical Society. 2022 Aug. 24, v. 144, no. 36

2022

Abstract: The systematic improvement of Fe–N–C materials for fuel cell applications has proven challenging, due in part to an incomplete atomistic understanding of the oxygen reduction reaction (ORR) under electrochemical conditions. Herein, a multilevel ... ...

Abstract	The systematic improvement of Fe–N–C materials for fuel cell applications has proven challenging, due in part to an incomplete atomistic understanding of the oxygen reduction reaction (ORR) under electrochemical conditions. Herein, a multilevel computational approach, which combines ab initio molecular dynamics simulations and constant potential density functional theory calculations, is used to assess proton-coupled electron transfer (PCET) processes and adsorption thermodynamics of key ORR intermediates. These calculations indicate that the potential-limiting step for ORR on Fe–N–C materials is the formation of the Feᴵᴵᴵ–OOH intermediate. They also show that an active site model with a water molecule axially ligated to the iron center throughout the catalytic cycle produces results that are consistent with the experimental measurements. In particular, reliable prediction of the ORR onset potential and the Fe(III/II) redox potential associated with the conversion of Feᴵᴵᴵ–OH to Feᴵᴵ and desorbed H₂O requires an axial H₂O co-adsorbed to the iron center. The observation of a five-coordinate rather than four-coordinate active site has significant implications for the thermodynamics and mechanism of ORR. These findings highlight the importance of solvent–substrate interactions and surface charge effects for understanding the PCET reaction mechanisms and transition-metal redox couples under realistic electrochemical conditions.
Keywords	active sites ; adsorption ; density functional theory ; electrochemistry ; electron transfer ; fuel cells ; ligands ; models ; molecular dynamics ; prediction ; redox potential ; thermodynamics
Language	English
Dates of publication	2022-0824
Size	p. 16524-16534.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/jacs.2c05779
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Article: Molecular Catalysts with Diphosphine Ligands Containing Pendant Amines

Wiedner, Eric S. / Appel, Aaron M. / Raugei, Simone / Shaw, Wendy J. / Bullock, R. Morris

Chemical reviews. 2022 May 31, v. 122, no. 14

2022

Abstract: Pendant amines play an invaluable role in chemical reactivity, especially for molecular catalysts based on earth-abundant metals. As inspired by [FeFe]-hydrogenases, which contain a pendant amine positioned for cooperative bifunctionality, synthetic ... ...

Abstract	Pendant amines play an invaluable role in chemical reactivity, especially for molecular catalysts based on earth-abundant metals. As inspired by [FeFe]-hydrogenases, which contain a pendant amine positioned for cooperative bifunctionality, synthetic catalysts have been developed to emulate this multifunctionality through incorporation of a pendant amine in the second coordination sphere. Cyclic diphosphine ligands containing two amines serve as the basis for a class of catalysts that have been extensively studied and used to demonstrate the impact of a pendant base. These 1,5-diaza-3,7-diphosphacyclooctanes, now often referred to as “P₂N₂” ligands, have profound effects on the reactivity of many catalysts. The resulting [Ni(Pᴿ₂Nᴿ′₂)₂]²⁺ complexes are electrocatalysts for both the oxidation and production of H₂. Achieving the optimal benefit of the pendant amine requires that it has suitable basicity and is properly positioned relative to the metal center. In addition to the catalytic efficacy demonstrated with [Ni(Pᴿ₂Nᴿ′₂)₂]²⁺ complexes for the oxidation and production of H₂, catalysts with diphosphine ligands containing pendant amines have also been demonstrated for several metals for many different reactions, both in solution and immobilized on surfaces. The impact of pendant amines in catalyst design continues to expand.
Keywords	catalysts ; ligands ; oxidation
Language	English
Dates of publication	2022-0531
Size	p. 12427-12474.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	207949-5
ISSN	1520-6890 ; 0009-2665
ISSN (online)	1520-6890
ISSN	0009-2665
DOI	10.1021/acs.chemrev.1c01001
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Article ; Online: Catalytic bias in oxidation-reduction catalysis.

Mulder, David W / Peters, John W / Raugei, Simone

Chemical communications (Cambridge, England)

2020 Volume 57, Issue 6, Page(s) 713–720

Abstract: Cataytic bias refers to the propensity of a reaction catalyst to effect a different rate acceleration in one direction versus the other in a chemical reaction under non-equilibrium conditions. In biocatalysis, the inherent bias of an enzyme is often ... ...

Abstract	Cataytic bias refers to the propensity of a reaction catalyst to effect a different rate acceleration in one direction versus the other in a chemical reaction under non-equilibrium conditions. In biocatalysis, the inherent bias of an enzyme is often advantagous to augment the innate thermodynamics of a reaction to promote efficiency and fidelity in the coordination of catabolic and anabolic pathways. In industrial chemical catalysis a directional cataltyic bias is a sought after property in facilitating the engineering of systems that couple catalysis with harvest and storage of for example fine chemicals or energy compounds. Interestingly, there is little information about catalytic bias in biocatalysis likely in large part due to difficulties in developing tractible assays sensitive enough to study detailed kinetics. For oxidation-reduction reactions, colorimetric redox indicators exist in a range of reduction potentials to provide a mechanism to study both directions of reactions in a fairly facile manner. The current short review attempts to define catalytic bias conceptually and to develop model systems for defining the parameters that control catalytic bias in enzyme catalyzed oxidation-reduction catalysis.
Language	English
Publishing date	2020-12-24
Publishing country	England
Document type	Journal Article
ZDB-ID	1472881-3
ISSN	1364-548X ; 1359-7345 ; 0009-241X
ISSN (online)	1364-548X
ISSN	1359-7345 ; 0009-241X
DOI	10.1039/d0cc07062a
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Article ; Online: Modeling Absolute Redox Potentials of Ferrocene in the Condensed Phase.

Makoś, Małgorzata Zofia / Gurunathan, Pradeep Kumar / Raugei, Simone / Kowalski, Karol / Glezakou, Vassiliki-Alexandra / Rousseau, Roger

The journal of physical chemistry letters

2022 Volume 13, Issue 42, Page(s) 10005–10010

Abstract: Absolute thermodynamic quantities for critical chemical reactions are needed to determine the role of solvents and reactive environments in catalysis and electrocatalysis. Theoretical methods can provide such quantification but are often hindered by the ... ...

Abstract	Absolute thermodynamic quantities for critical chemical reactions are needed to determine the role of solvents and reactive environments in catalysis and electrocatalysis. Theoretical methods can provide such quantification but are often hindered by the innate complexity of electron correlation and dynamic relaxation of solvent environments. We present and validate a protocol for calculating the redox potentials of the ferrocene/ferrocenium redox pair in acetonitrile. Equation-of-motion and effective fragment potential (EFP) methods are used to characterize the adiabatic and vertical ionization potentials as well as the electron affinity processes. We benchmark molecular mechanics against the EFP model to show the differences in the ferrocene electronic polarizability in two redox states. Our best estimate of the redox potential (4.94 eV) agrees well with the experimental value (4.93 eV). This demonstrates the ability of modern computational methods to predict absolute redox potentials quantitatively and to quantify the correlation of dynamic effects, which underlie their origin.
MeSH term(s)	Metallocenes ; Solvents/chemistry ; Oxidation-Reduction ; Acetonitriles
Chemical Substances	ferrocene (U96PKG90JQ) ; Metallocenes ; Solvents ; Acetonitriles
Language	English
Publishing date	2022-10-20
Publishing country	United States
Document type	Journal Article
ISSN	1948-7185
ISSN (online)	1948-7185
DOI	10.1021/acs.jpclett.2c02447
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Article ; Online: Multilevel Computational Studies Reveal the Importance of Axial Ligand for Oxygen Reduction Reaction on Fe-N-C Materials.

Hutchison, Phillips / Rice, Peter S / Warburton, Robert E / Raugei, Simone / Hammes-Schiffer, Sharon

Journal of the American Chemical Society

2022 Volume 144, Issue 36, Page(s) 16524–16534

Abstract: The systematic improvement of Fe-N-C materials for fuel cell applications has proven challenging, due in part to an incomplete atomistic understanding of the oxygen reduction reaction (ORR) under electrochemical conditions. Herein, a multilevel ... ...

Abstract	The systematic improvement of Fe-N-C materials for fuel cell applications has proven challenging, due in part to an incomplete atomistic understanding of the oxygen reduction reaction (ORR) under electrochemical conditions. Herein, a multilevel computational approach, which combines ab initio molecular dynamics simulations and constant potential density functional theory calculations, is used to assess proton-coupled electron transfer (PCET) processes and adsorption thermodynamics of key ORR intermediates. These calculations indicate that the potential-limiting step for ORR on Fe-N-C materials is the formation of the Fe
MeSH term(s)	Ferric Compounds/chemistry ; Iron/chemistry ; Ligands ; Oxidation-Reduction ; Oxygen/chemistry
Chemical Substances	Ferric Compounds ; Ligands ; Iron (E1UOL152H7) ; Oxygen (S88TT14065)
Language	English
Publishing date	2022-08-24
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/jacs.2c05779
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Article ; Online: Molecular Catalysts with Diphosphine Ligands Containing Pendant Amines.

Wiedner, Eric S / Appel, Aaron M / Raugei, Simone / Shaw, Wendy J / Bullock, R Morris

Chemical reviews

2022 Volume 122, Issue 14, Page(s) 12427–12474

Abstract	Pendant amines play an invaluable role in chemical reactivity, especially for molecular catalysts based on earth-abundant metals. As inspired by [FeFe]-hydrogenases, which contain a pendant amine positioned for cooperative bifunctionality, synthetic catalysts have been developed to emulate this multifunctionality through incorporation of a pendant amine in the second coordination sphere. Cyclic diphosphine ligands containing two amines serve as the basis for a class of catalysts that have been extensively studied and used to demonstrate the impact of a pendant base. These 1,5-diaza-3,7-diphosphacyclooctanes, now often referred to as "P
MeSH term(s)	Amines/chemistry ; Catalysis ; Hydrogen/chemistry ; Hydrogenase/chemistry ; Ligands
Chemical Substances	Amines ; Ligands ; Hydrogen (7YNJ3PO35Z) ; Hydrogenase (EC 1.12.7.2)
Language	English
Publishing date	2022-05-31
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	207949-5
ISSN	1520-6890 ; 0009-2665
ISSN (online)	1520-6890
ISSN	0009-2665
DOI	10.1021/acs.chemrev.1c01001
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