scholarly journals Quantum chemistry reveals the thermodynamic principles of redox biochemistry

2018 ◽  
Author(s):  
Adrian Jinich ◽  
Avi Flamholz ◽  
Haniu Ren ◽  
Sung-Jin Kim ◽  
Benjamin Sanchez-Lengeling ◽  
...  
Keyword(s):  
Quantum Chemistry ◽  
Material Flow ◽  
Redox Reactions ◽  
Redox Potentials ◽  
Accurate Calculation ◽  
Cellular Redox ◽  
Cellular Energy ◽  
Reduction Potentials ◽  
And Function ◽  
Electron Carriers

AbstractThermodynamics dictates the structure and function of metabolism. Redox reactions drive cellular energy and material flow. Hence, accurately quantifying the thermodynamics of redox reactions should reveal key design principles that shape cellular metabolism. However, only a limited number of redox potentials have been measured experimentally, and mostly with inconsistent, poorly-reported experimental setups. Here, we develop a quantum chemistry approach for the calculation of redox potentials of biochemical reactions. We demonstrate that our method predicts experimentally measured potentials with unparalleled accuracy. We calculate the reduction potentials of all redox pairs that can be generated from biochemically relevant compounds and highlight fundamental thermodynamic trends that define cellular redox biochemistry. We further use the calculated potentials to address the question of why NAD/NADP are used as the primary cellular electron carriers, demonstrating how their physiological redox range specifically fits the reactions of central metabolism and minimizes the concentration of reactive carbonyls. The use of quantum chemistry tools, as demonstrated in this study, can revolutionize our understanding of key biochemical phenomena by enabling fast and accurate calculation of large datasets of thermodynamic values.

scholarly journals A mixed quantum chemistry/machine learning approach for the fast and accurate prediction of biochemical redox potentials and its large-scale application to 315,000 redox reactions

2018 ◽  
Author(s):  
Adrian Jinich ◽  
Benjamin Sanchez-Lengeling ◽  
Haniu Ren ◽  
Rebecca Harman ◽  
Alán Aspuru-Guzik
Keyword(s):  
Machine Learning ◽  
Quantum Chemistry ◽  
Redox Reactions ◽  
Large Scale ◽  
Computational Cost ◽  
Accurate Method ◽  
Redox Potentials ◽  
Quantum Chemistry Calculations ◽  
Quantitative Understanding ◽  
Semi Empirical

AbstractA quantitative understanding of the thermodynamics of biochemical reactions is essential for accurately modeling metabolism. The group contribution method (GCM) is one of the most widely used approaches to estimating standard Gibbs energies and redox potentials of reactions for which no experimental measurements exist. Previous work has shown that quantum chemical predictions of biochemical thermodynamics are a promising approach to overcome the limitations of GCM. However, the quantum chemistry approach is significantly more expensive. Here we use a combination of quantum chemistry and machine learning to obtain a fast and accurate method for predicting the thermodynamics of biochemical redox reactions. We focus on predicting the redox potentials of carbonyl functional group reductions to alcohols and amines, two of the most ubiquitous carbon redox transformations in biology. Our method relies on semi-empirical quantum chemistry calculations calibrated with Gaussian Process (GP) regression against available experimental data. Our approach results in higher predictive power than the GCM at a low computational cost. We design and implement a network expansion algorithm that iteratively reduces and oxidizes a set of natural seed metabolites, and demonstrate the high-throughput applicability of our method by predicting the standard potentials of more than 315,000 redox reactions involving approximately 70,000 compounds. Additionally, we developed a novel fingerprint-based framework for detecting molecular environment motifs that are enriched or depleted across different regions of the redox potential landscape. We provide open access to all source code and data generated.

scholarly journals Endothelium as a Source and Target of H2S to Improve Its Trophism and Function

Antioxidants ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 486
Author(s):  
Valerio Ciccone ◽  
Shirley Genah ◽  
Lucia Morbidelli
Keyword(s):  
Endothelial Dysfunction ◽  
Vessel Wall ◽  
Redox Reactions ◽  
Single Layer ◽  
Fine Tuning ◽  
Therapeutic Approaches ◽  
Impaired Wound Healing ◽  
Blood Fluidity ◽  
And Function ◽  
And Control

The vascular endothelium consists of a single layer of squamous endothelial cells (ECs) lining the inner surface of blood vessels. Nowadays, it is no longer considered as a simple barrier between the blood and vessel wall, but a central hub to control blood flow homeostasis and fulfill tissue metabolic demands by furnishing oxygen and nutrients. The endothelium regulates the proper functioning of vessels and microcirculation, in terms of tone control, blood fluidity, and fine tuning of inflammatory and redox reactions within the vessel wall and in surrounding tissues. This multiplicity of effects is due to the ability of ECs to produce, process, and release key modulators. Among these, gasotransmitters such as nitric oxide (NO) and hydrogen sulfide (H2S) are very active molecules constitutively produced by endotheliocytes for the maintenance and control of vascular physiological functions, while their impairment is responsible for endothelial dysfunction and cardiovascular disorders such as hypertension, atherosclerosis, and impaired wound healing and vascularization due to diabetes, infections, and ischemia. Upregulation of H2S producing enzymes and administration of H2S donors can be considered as innovative therapeutic approaches to improve EC biology and function, to revert endothelial dysfunction or to prevent cardiovascular disease progression. This review will focus on the beneficial autocrine/paracrine properties of H2S on ECs and the state of the art on H2S potentiating drugs and tools.

scholarly journals Unveiling Extreme Photoreduction Potentials of Donor-Acceptor Cyanoarenes to Access Aryl Radicals from Aryl Chlorides

2021 ◽  
Author(s):  
Jinhui Xu ◽  
Jilei Cao ◽  
Xiangyang Wu ◽  
Han Wang ◽  
Xiaona Yang ◽  
...  
Keyword(s):  
Limited Range ◽  
Redox Potentials ◽  
Aryl Chlorides ◽  
Aryl Radicals ◽  
Reduction Potentials ◽  
Anion Form ◽  
Donor Acceptor ◽  
High Reduction ◽  
Very High ◽  
Excited Radical

Since the seminal work of Zhang in 2016, donor-acceptor cyanoarene-based fluorophores, such as 1,2,3,5-tetrakis(carbazol-9-yl)-4,6-dicyanobenzene (4CzIPN), have been widely applied in photoredox catalysis, and used as excellent metal-free alternatives to noble metal Ir- and Ru-based photocatalysts. However, all the reported photoredox reactions involving this chromophore family are based on harnessing the energy from a single visible light photon, with a limited range of redox potentials from -1.92 V to +1.79 V. Here, we document the unprecedented discovery that this family of fluorophores can undergo consecutive photoinduced electron transfer (ConPET) to achieve very high reduction potentials. One of the newly synthesized catalysts, 2,4,5-tri(9H-carbazol-9-yl)-6-(ethyl(phenyl)amino)isophthalonitrile (3CzEPAIPN), possesses a long-lived (12.95 ns) excited radical anion form, 3CzEPAIPN<sup>•</sup><sup>−</sup>*, which can be used to activate reductively recalcitrant aryl chlorides (E<sub>red </sub>≈ -1.9 to -2.9 V) under mild conditions. The resultant aryl radicals can be engaged in synthetically valuable aromatic C-B, C-P, and C-C bond formation to furnish arylboronates, arylphosphonium salts, arylphosphonates, and spirocyclic cyclohexadienes, respectively.

Substance and Function

2020 ◽  
pp. 188-203
Author(s):  
Jean-Pierre Llored
Keyword(s):  
Quantum Chemistry ◽  
Philosophy Of Science ◽  
Periodic Table ◽  
Functional Role ◽  
Functional Approach ◽  
Different Types ◽  
And Function

This paper aims to analyze the two aspects of elements, material and conceptual, in order to further understand the functional role played by elements in chemistry. First, we will refer to how Mendeleev gradually built his periodic table. Second, we will both highlight and reflect upon the functional role of elements in chemistry. In doing so, we will refer in particular to Cassirer’s philosophy of science. In conclusion, we propose that a functional approach is important for understanding current chemical practice, especially in nanochemistry and quantum chemistry. This approach also contributes to the analysis of different types of mereology that coexist in chemistry today.

scholarly journals Electrochemical, Spectroscopic, and Computational Investigations on Redox Reactions of Selenium Species on Galena Surfaces

Minerals ◽  
2019 ◽  
Vol 9 (7) ◽  
pp. 437 ◽  
Author(s):  
Peter Cook ◽  
YoungJae Kim ◽  
Ke Yuan ◽  
Maria C. Marcano ◽  
Udo Becker
Keyword(s):  
Photoelectron Spectroscopy ◽  
Redox Reactions ◽  
Redox Potentials ◽  
Free Energies ◽  
Cathodic Peak ◽  
Redox Transformation ◽  
Hydrogen Electrode ◽  
Midpoint Potential ◽  
Ph Conditions ◽  
Cv Measurements

Despite previous studies investigating selenium (Se) redox reactions in the presence of semiconducting minerals, Se redox reactions mediated by galena (PbS) are poorly understood. In this study, the redox chemistry of Se on galena is investigated over a range of environmentally relevant Eh and pH conditions (+0.3 to −0.6 V vs. standard hydrogen electrode, SHE; pH 4.6) using a combination of electrochemical, spectroscopic, and computational approaches. Cyclic voltammetry (CV) measurements reveal one anodic/cathodic peak pair at a midpoint potential of +30 mV (vs. SHE) that represents reduction and oxidation between HSeO3− and H2Se/HSe−. Two peak pairs with midpoint potentials of −400 and −520 mV represent the redox transformation from Se(0) to HSe− and H2Se species, respectively. The changes in Gibbs free energies of adsorption of Se species on galena surfaces as a function of Se oxidation state were modeled using quantum-mechanical calculations and the resulting electrochemical peak shifts are (−0.17 eV for HSeO3−/H2Se, −0.07 eV for HSeO3−/HSe−, 0.15 eV for Se(0)/HSe−, and −0.15 eV for Se(0)/H2Se). These shifts explain deviation between Nernstian equilibrium redox potentials and observed midpoint potentials. X-ray photoelectron spectroscopy (XPS) analysis reveals the formation of Se(0) potentials below −100 mV and Se(0) and Se(−II) species at potentials below −400 mV.

Synthesis and hydrolysis of gas-phase lanthanide and actinide oxide nitrate complexes: a correspondence to trivalent metal ion redox potentials and ionization energies

2015 ◽  
Vol 17 (15) ◽  
pp. 9942-9950 ◽  
Author(s):  
Ana F. Lucena ◽  
Célia Lourenço ◽  
Maria C. Michelini ◽  
Philip X. Rutkowski ◽  
José M. Carretas ◽  
...  
Keyword(s):  
Gas Phase ◽  
Metal Ion ◽  
Oxidation States ◽  
Redox Potentials ◽  
Trivalent Metal ◽  
Ionization Energies ◽  
Reduction Potentials ◽  
Hydrolysis Of ◽  
Nitrate Complexes

Gas-phase hydrolysis of lanthanide/actinide MO3(NO3)3−ions relates to the stabilities of the MIVoxidation states, which correlate with IV/III solution reduction potentials and 4th ionization energies.

scholarly journals Photochromic coenzyme Q derivatives: switching redox potentials with light

2017 ◽  
Vol 8 (9) ◽  
pp. 6474-6483 ◽  
Author(s):  
Nadja A. Simeth ◽  
Andrea C. Kneuttinger ◽  
Reinhard Sterner ◽  
Burkhard König
Keyword(s):  
Redox Reactions ◽  
Coenzyme Q ◽  
Redox Potentials ◽  
Isolated Mitochondria

A photochromic coenzyme Q derivative could be activated through irradiation with orange light and initiate redox reactions with Hantzsch ester and on isolated mitochondria.

A Critical Evaluation of the Redox Properties of Uranium, Neptunium and Plutonium Ions in Acidic Aqueous Solutions

1999 ◽  
Vol 71 (9) ◽  
pp. 1771-1807 ◽  
Author(s):  
Sorin Kihara ◽  
Zenko Yoshida ◽  
Hisao Aoyagi ◽  
Kohji Maeda ◽  
Osamu Shirai ◽  
...  
Keyword(s):  
Aqueous Solutions ◽  
Redox Reactions ◽  
Critical Evaluation ◽  
Redox Properties ◽  
Redox Processes ◽  
Redox Potentials ◽  
Electrode Processes ◽  
Reversible Redox ◽  
Reduction Mechanisms ◽  
Current Potential

Standard redox potentials, E0s, and redox processes of U, Np and Pu ions in acidic aqueous solutions are reviewed and evaluated critically. The E0sof reversible redox processes, MO22+/MO2+ and M4+/M3+ (M: U, Np or Pu) adopted are those proposed mainly by Riglet et al. on the basis of the precise correction of formal potentials, E0's, according to the improved theoretical approach to estimate the activity coefficient. Electrode processes of the U, Np and Pu ions are discussed in terms of current-potential curves, measured so far by polarography, voltammetry or flow coulometry. Special attention is payed to the irreversible MO2+/M4+ reactions. Disproportionation reactions of MO2+ are also discussed. New substances are introduced as intermediates during reductions of MO2+ to M4+ or disproportionations of MO2+.CONTENTSIntroductionStandard redox potentials for uranium, neptunium and plutonium ions in acidic aqueous solutions2.1 Evaluation of E0 from E0' determined by electrochemical measurements2.2 Temperature dependence of E0Redox reactions of uranium, neptunium and plutonium in acidic aqueous solutions investigated by polarography or voltammetry3.1 Uranium3.2 Neptunium3.3 Plutonium3.4 Disproportionation of NpO2+, PuO2+, Np4+ and Pu4+3.5 Reduction of MO2+ and reduction intermediatesRedox reactions of uranium, neptunium and plutonium in acidic aqueous solutions investigated by flow coulometry4.1 Electrode processes of the uranium, neptunium and plutonium ions investigated by flow coulometry at the column electrode at the column electrode4.2 Disproportionation of MO2+ during the electrolysis by flow coulometry4.3 Reduction mechanisms of MO2+ (M = Np or Pu) and reduction intermediates investigated by flow coulometryConclusionsList of abbreviationsAppendixReferences

Photoswitching of Redox Potentials and Spectroscopic Properties in the UV/vis Region

2005 ◽  
Vol 60 (1) ◽  
pp. 75-82 ◽  
Author(s):  
Nedko Drebov ◽  
Nikolai Tyutyulkov ◽  
Stojan Karabunarliev ◽  
Fritz Dietz
Keyword(s):  
Spectroscopic Properties ◽  
Visible Spectral Region ◽  
Redox Potentials ◽  
Electron Systems ◽  
Excitation Energies ◽  
Reduction Potentials ◽  
Open Ring ◽  
Wavelength Absorption ◽  
Donor Acceptor ◽  
Ct Transitions

The photoswitching of optical and electrochemical properties of di-donor, di-acceptor and donor-acceptor substituted photochromic tetrahydropyrene - [2,2]metacyclophanene and dihydropyrene - [2,2]metacyclophanediene systems has been studied theoretically. A switching of the halfwave oxidation and reduction potentials should be possible in the case of bis(pyridinium) and bis(hydroxyphenyl) substituted systems. Because of the relatively great perturbation of the planarity of the π-electron systems by large torsion of the substituents out of the π-electron structure of the photochromic system and the stair-like structure of the ring-opened isomer, relatively large excitation energies for CT transitions have been calculated with the AM1-CI procedure. The ring-closed structures should absorb in the visible spectral region, and the open-ring isomers should have a longest-wavelength absorption in the UV region.

Sign in / Sign up

Export Citation Format

Share Document