Simulating Redox Potentials of Biomolecules: the Case of Cryptochrome 1 from Arabidopsis thaliana

2019 ◽  
Author(s):  
Ruslan N. Tazhigulov ◽  
Pradeep Kumar Gurunathan ◽  
Yongbin Kim ◽  
Lyudmila V. Slipchenko ◽  
Ksenia B. Bravaya
Keyword(s):  
Arabidopsis Thaliana ◽  
Redox Potential ◽  
Long Range ◽  
Electrostatic Interactions ◽  
Theoretical Estimate ◽  
Theoretical Description ◽  
Redox Potentials ◽  
Redox Active ◽  
Solvent Polarization ◽  
Cryptochrome 1

Redox reactions play a key role in various biological processes, including photosynthesis and respiration. Quantitative and predictive computational characterization of redox events is therefore highly desirable for enriching our knowledge on mechanistic features of biological redox-active macromolecules. Here, we present the results of computational studies of the redox potential of flavin adenine dinucleotide (FAD) in cryptochrome 1 from <i>Arabidopsis thaliana</i> (Cry1At). The special attention is paid to fundamental aspects of the theoretical description such as the effects of environment polarization and of the long-range electrostatic interactions on the computed energetic parameters. Environment (protein and the solvent) polarization is shown to be crucial for accurate estimates of the redox potential: hybrid quantum-classical results with and without account for environment polarization differ by 1.4 V. Long-range electrostatic interactions are shown to contribute significantly to the computed redox potential value even at the distances far beyond the protein outer surface. The theoretical estimate (0.07 V) of the midpoint reduction potential of FAD in Cry1At is reported for the first time and is in good agreement with available experimental data.

Simulating Redox Potentials of Biomolecules: the Case of Cryptochrome 1 from Arabidopsis thaliana

2019 ◽  
Author(s):  
Ruslan N. Tazhigulov ◽  
Pradeep Kumar Gurunathan ◽  
Yongbin Kim ◽  
Lyudmila V. Slipchenko ◽  
Ksenia B. Bravaya
Keyword(s):  
Arabidopsis Thaliana ◽  
Redox Potential ◽  
Long Range ◽  
Electrostatic Interactions ◽  
Theoretical Estimate ◽  
Theoretical Description ◽  
Redox Potentials ◽  
Redox Active ◽  
Solvent Polarization ◽  
Cryptochrome 1

Redox reactions play a key role in various biological processes, including photosynthesis and respiration. Quantitative and predictive computational characterization of redox events is therefore highly desirable for enriching our knowledge on mechanistic features of biological redox-active macromolecules. Here, we present the results of computational studies of the redox potential of flavin adenine dinucleotide (FAD) in cryptochrome 1 from <i>Arabidopsis thaliana</i> (Cry1At). The special attention is paid to fundamental aspects of the theoretical description such as the effects of environment polarization and of the long-range electrostatic interactions on the computed energetic parameters. Environment (protein and the solvent) polarization is shown to be crucial for accurate estimates of the redox potential: hybrid quantum-classical results with and without account for environment polarization differ by 1.4 V. Long-range electrostatic interactions are shown to contribute significantly to the computed redox potential value even at the distances far beyond the protein outer surface. The theoretical estimate (0.07 V) of the midpoint reduction potential of FAD in Cry1At is reported for the first time and is in good agreement with available experimental data.

scholarly journals Polarizable embedding for simulating redox potentials of biomolecules

2019 ◽  
Vol 21 (22) ◽  
pp. 11642-11650 ◽  
Author(s):  
Ruslan N. Tazhigulov ◽  
Pradeep Kumar Gurunathan ◽  
Yongbin Kim ◽  
Lyudmila V. Slipchenko ◽  
Ksenia B. Bravaya
Keyword(s):  
Long Range ◽  
Electrostatic Interactions ◽  
Theoretical Description ◽  
Biological Macromolecules ◽  
Classical Approach ◽  
Redox Potentials ◽  
Computational Protocol ◽  
Polarizable Embedding

We present a computational protocol exploiting polarizable embedding hybrid quantum-classical approach and resulting in accurate estimates of redox potentials of biological macromolecules. A special attention is paid to fundamental aspects of the theoretical description such as the effects of environment polarization and of the long-range electrostatic interactions on the computed energetic parameters.

On the chemical consequences of long-range interactions in chiral systems

1975 ◽  
Vol 28 (6) ◽  
pp. 1161 ◽  
Author(s):  
PE Schipper
Keyword(s):  
Long Range ◽  
Electrostatic Interactions ◽  
Intermolecular Forces ◽  
Statistical Thermodynamic ◽  
Thermodynamic Quantities ◽  
Redox Potentials ◽  
Chiral Molecules ◽  
Long Range Interactions ◽  
Three Stages ◽  
Chiral Systems

The chemical manifestations of discrimination in long-range (non- contact) interactions of chiral molecules are analysed in three stages. A simple thermodynamic model is used to establish a method of presenting experimental data (such as differences in racemization rates, solubilities and redox potentials of pure enantiomers in non- associating chiral media) in terms of well defined thermodynamic discriminations. The thermodynamic quantities are then related directly to discriminations in intermolecular interactions through a statistical thermodynamic treatment. Estimates of the discrimination in intermolecular forces from experimental thermodynamic data suggest that only electrostatic interactions are sufficiently large to account for the experimentally observed values of the discrimination.

scholarly journals Geothrix fermentans Secretes Two Different Redox-Active Compounds To Utilize Electron Acceptors across a Wide Range of Redox Potentials

2012 ◽  
Vol 78 (19) ◽  
pp. 6987-6995 ◽  
Author(s):  
Misha G. Mehta-Kolte ◽  
Daniel R. Bond
Keyword(s):  
Electron Transfer ◽  
Redox Potential ◽  
Electron Acceptor ◽  
Extracellular Electron Transfer ◽  
Redox Potentials ◽  
Active Compounds ◽  
Content Type ◽  
Electron Shuttles ◽  
Redox Active ◽  
Geothrix Fermentans

ABSTRACTThe current understanding of dissimilatory metal reduction is based primarily on isolates from the proteobacterial generaGeobacterandShewanella. However, environments undergoing active Fe(III) reduction often harbor less-well-studied phyla that are equally abundant. In this work, electrochemical techniques were used to analyze respiratory electron transfer by the only known Fe(III)-reducing representative of theAcidobacteria,Geothrix fermentans. In contrast to previously characterized metal-reducing bacteria, which typically reach maximal rates of respiration at electron acceptor potentials of 0 V versus standard hydrogen electrode (SHE),G. fermentansrequired potentials as high as 0.55 V to respire at its maximum rate. In addition,G. fermentanssecreted two different soluble redox-active electron shuttles with separate redox potentials (−0.2 V and 0.3 V). The compound with the lower midpoint potential, responsible for 20 to 30% of electron transfer activity, was riboflavin. The behavior of the higher-potential compound was consistent with hydrophilic UV-fluorescent molecules previously found inG. fermentanssupernatants. Both electron shuttles were also produced when cultures were grown with Fe(III), but not when fumarate was the electron acceptor. This study reveals thatGeothrixis able to take advantage of higher-redox-potential environments, demonstrates that secretion of flavin-based shuttles is not confined toShewanella, and points to the existence of high-potential-redox-active compounds involved in extracellular electron transfer. Based on differences between the respiratory strategies ofGeothrixandGeobacter, these two groups of bacteria could exist in distinctive environmental niches defined by redox potential.

scholarly journals Redox potentials along the redox-active low-barrier H-bonds in electron transfer pathways

2020 ◽  
Vol 22 (44) ◽  
pp. 25467-25473 ◽  
Author(s):  
Keisuke Saito ◽  
Manoj Mandal ◽  
Hiroshi Ishikita
Keyword(s):  
Electron Transfer ◽  
Proton Transfer ◽  
Redox Potential ◽  
Driving Force ◽  
Electronic Coupling ◽  
Redox Potentials ◽  
Redox Active ◽  
Electron Transfer Pathways

Local proton transfer along redox-active low-barrier H-bonds can alter the driving force or electronic coupling for electron transfer, as the redox potential values depend on the H+ position in low-barrier H-bonds.

Theoretical Exploration of 2,2’-Bipyridines as Electro-Active Compounds in Flow Batteries

2019 ◽  
Author(s):  
Mariano Sánchez-Castellanos ◽  
Martha M. Flores-Leonar ◽  
Zaahel Mata-Pinzón ◽  
Humberto G. Laguna ◽  
Karl García-Ruiz ◽  
...  
Keyword(s):  
Redox Potential ◽  
Active Material ◽  
Chemical Properties ◽  
Small Subset ◽  
Solubility In Water ◽  
Protonation Reaction ◽  
Redox Active ◽  
Physico Chemical ◽  
Pka Value ◽  
Flow Batteries

Compounds from the 2,2’-bipyridine molecular family were investigated for use as redox-active materials in organic flow batteries. For 156 2,2’-bipyridine derivatives reported in the academic literature, we calculated the redox potential, the pKa for the first protonation reaction, and the solubility in aqueous solutions. Using experimental data on a small subset of derivatives, we were able to calibrate our calculations. We find that functionalization with electron-withdrawing groups leads to an increase of the redox potential and to an increase of the molecular acidity (as expressed in a reduction of the pKa value for the first protonation step). Furthermore, calculations of solubility in water indicate that some of the studied derivatives have adequate solubility for flow battery applications. Based on an analysis of the physico-chemical properties of the 156 studied compounds, we down-select five molecules with carbonyl- and nitro-based functional groups, whose parameters are especially promising for potential application as negative redox-active material inorganic flow batteries.

Theoretical Exploration of 2,2’-Bipyridines as Electro-Active Compounds in Flow Batteries

2019 ◽  
Author(s):  
Mariano Sánchez-Castellanos ◽  
Martha M. Flores-Leonar ◽  
Zaahel Mata-Pinzón ◽  
Humberto G. Laguna ◽  
Karl García-Ruiz ◽  
...  
Keyword(s):  
Redox Potential ◽  
Active Material ◽  
Chemical Properties ◽  
Small Subset ◽  
Solubility In Water ◽  
Protonation Reaction ◽  
Redox Active ◽  
Physico Chemical ◽  
Pka Value ◽  
Flow Batteries

Compounds from the 2,2’-bipyridine molecular family were investigated for use as redox-active materials in organic flow batteries. For 156 2,2’-bipyridine derivatives reported in the academic literature, we calculated the redox potential, the pKa for the first protonation reaction, and the solubility in aqueous solutions. Using experimental data on a small subset of derivatives, we were able to calibrate our calculations. We find that functionalization with electron-withdrawing groups leads to an increase of the redox potential and to an increase of the molecular acidity (as expressed in a reduction of the pKa value for the first protonation step). Furthermore, calculations of solubility in water indicate that some of the studied derivatives have adequate solubility for flow battery applications. Based on an analysis of the physico-chemical properties of the 156 studied compounds, we down-select five molecules with carbonyl- and nitro-based functional groups, whose parameters are especially promising for potential application as negative redox-active material inorganic flow batteries.

scholarly journals Insight to Microbial Fe(III) Reduction Mediated by Redox-Active Humic Acids with Varied Redox Potentials

2021 ◽  
Vol 18 (13) ◽  
pp. 6807
Author(s):  
Jingtao Duan ◽  
Zhiyuan Xu ◽  
Zhen Yang ◽  
Jie Jiang
Keyword(s):  
Molecular Weight ◽  
Electron Transfer ◽  
Humic Acids ◽  
Weight Fraction ◽  
Electrochemical Analysis ◽  
Microbial Reduction ◽  
Redox Potentials ◽  
Groundwater Environment ◽  
Redox Active ◽  
Different Molecular Weight

Redox-active humic acids (HA) are ubiquitous in terrestrial and aquatic systems and are involved in numerous electron transfer reactions affecting biogeochemical processes and fates of pollutants in soil environments. Redox-active contaminants are trapped in soil micropores (<2 nm) that have limited access to microbes and HA. Therefore, the contaminants whose molecular structure and properties are not damaged accumulate in the soil micropores and become potential pollution sources. Electron transfer capacities (ETC) of HA reflecting redox activities of low molecular weight fraction (LMWF, <2.5) HA can be detected by an electrochemical method, which is related to redox potentials (Eh) in soil and aquatic environments. Nevertheless, electron accepting capacities (EAC) and electron donating capacities (EDC) of these LMWF HA at different Eh are still unknown. EDC and EAC of different molecular weight HA at different Eh were analyzed using electrochemical methods. EAC of LMWF at −0.59 V was 12 times higher than that at −0.49 V, while EAC increased to 2.6 times when the Eh decreased from −0.59 V to −0.69 V. Afterward, LMWF can act as a shuttle to stimulate microbial Fe(III) reduction processes in microbial reduction experiments. Additionally, EAC by electrochemical analysis at a range of −0.49–−0.59 V was comparable to total calculated ETC of different molecular weight fractions of HA by microbial reduction. Therefore, it is indicated that redox-active functional groups that can be reduced at Eh range of −0.49–−0.59 are available to microbial reduction. This finding contributes to a novel perspective in the protection and remediation of the groundwater environment in the biogeochemistry process.

scholarly journals Role of redox-inactive metals in controlling the redox potential of heterometallic manganese–oxido clusters

2021 ◽  
Author(s):  
Keisuke Saito ◽  
Minesato Nakagawa ◽  
Manoj Mandal ◽  
Hiroshi Ishikita
Keyword(s):  
Photosystem Ii ◽  
Redox Potential ◽  
Quantum Chemical Calculations ◽  
Catalytic Reaction ◽  
Quantum Chemical ◽  
Ionic Radius ◽  
Redox Potentials ◽  
Oxygen Evolving ◽  
Highest Occupied Molecular Orbitals

AbstractPhotosystem II (PSII) contains Ca2+, which is essential to the oxygen-evolving activity of the catalytic Mn4CaO5 complex. Replacement of Ca2+ with other redox-inactive metals results in a loss/decrease of oxygen-evolving activity. To investigate the role of Ca2+ in this catalytic reaction, we investigate artificial Mn3[M]O2 clusters redox-inactive metals  [M] ([M]  = Mg2+, Ca2+, Zn2+, Sr2+, and Y3+), which were synthesized by Tsui et al. (Nat Chem 5:293, 2013). The experimentally measured redox potentials (Em) of these clusters are best described by the energy of their highest occupied molecular orbitals. Quantum chemical calculations showed that the valence of metals predominantly affects Em(MnIII/IV), whereas the ionic radius of metals affects Em(MnIII/IV) only slightly.

scholarly journals Distinguishing magnetic and electrostatic interactions by a Kelvin probe force microscopy–magnetic force microscopy combination

2011 ◽  
Vol 2 ◽  
pp. 552-560 ◽  
Author(s):  
Miriam Jaafar ◽  
Oscar Iglesias-Freire ◽  
Luis Serrano-Ramón ◽  
Manuel Ricardo Ibarra ◽  
Jose Maria de Teresa ◽  
...  
Keyword(s):  
Long Range ◽  
Electrostatic Interaction ◽  
Electrostatic Interactions ◽  
Magnetic Force Microscopy ◽  
Magnetic Force ◽  
Superparamagnetic Nanoparticles ◽  
Kelvin Probe Force Microscopy ◽  
Magnetic Interactions ◽  
Kelvin Probe ◽  
Force Microscopy

The most outstanding feature of scanning force microscopy (SFM) is its capability to detect various different short and long range interactions. In particular, magnetic force microscopy (MFM) is used to characterize the domain configuration in ferromagnetic materials such as thin films grown by physical techniques or ferromagnetic nanostructures. It is a usual procedure to separate the topography and the magnetic signal by scanning at a lift distance of 25–50 nm such that the long range tip–sample interactions dominate. Nowadays, MFM is becoming a valuable technique to detect weak magnetic fields arising from low dimensional complex systems such as organic nanomagnets, superparamagnetic nanoparticles, carbon-based materials, etc. In all these cases, the magnetic nanocomponents and the substrate supporting them present quite different electronic behavior, i.e., they exhibit large surface potential differences causing heterogeneous electrostatic interaction between the tip and the sample that could be interpreted as a magnetic interaction. To distinguish clearly the origin of the tip–sample forces we propose to use a combination of Kelvin probe force microscopy (KPFM) and MFM. The KPFM technique allows us to compensate in real time the electrostatic forces between the tip and the sample by minimizing the electrostatic contribution to the frequency shift signal. This is a great challenge in samples with low magnetic moment. In this work we studied an array of Co nanostructures that exhibit high electrostatic interaction with the MFM tip. Thanks to the use of the KPFM/MFM system we were able to separate the electric and magnetic interactions between the tip and the sample.

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