Energetics Of Protonation Research Articles

A unicellular cyanobacterium relies on sodium energetics to fix N2

Diazotrophic cyanobacteria can fix nitrogen gas (N2) but are usually scarce in nitrogen-limited coastal waters, which poses an apparent ecological paradox. One hypothesis is that high salinities (> 10 g/L NaCl) may inhibit cyanobacterial N2 fixation. However, here we show that N2 fixation in a unicellular coastal cyanobacterium exclusively depends on sodium ions and is inhibited at low NaCl concentrations (< 4 g/L). In the absence of Na+, cells of Cyanothece sp. ATCC 51142 (recently reclassified as Crocosphaera subtropica) upregulate the expression of nifHDK genes and synthesise a higher amount of nitrogenase, but do not fix N2 and do not grow. We find that the loss of N2-fixing ability in the absence of Na+ is due to insufficient ATP supply. Additional experiments suggest that N2 fixation in this organism is driven by sodium energetics and mixed-acid fermentation, rather than proton energetics and aerobic respiration, even though cells were cultured aerobically. Further work is needed to clarify the underlying mechanisms and whether our findings are relevant to other coastal cyanobacteria.

Electrocatalytic nitrite reduction to ammonia on isolated bismuth alloyed ruthenium

Electrochemical reduction of NO2− to NH3 (NO2−RR) is recognized as an appealing approach for achieving renewable NH3 synthesis and waste NO2− removal. Herein, we report isolated Bi alloyed Ru (Bi1Ru) as an efficient NO2−RR catalyst. Theoretical calculations and in situ electrochemical measurements reveal the creation of Bi1-Ru dual sites which can remarkably promote NO2− activation and suppress proton adsorption, while accelerating the NO2−RR protonation energetics to render a high NO2−-to-NH3 conversion efficiency. Remarkably, Bi1Ru assembled in a flow cell delivers an NH3 yield rate of 1901.4 μmol h−1 cm−2 and an NH3-Faradaic efficiency of 94.3% at an industrial-level current density of 324.3 mA cm−2. This study offers new perspectives for designing and constructing p-block single-atom alloys as robust and high-current-density NO2−RR catalysts toward the ammonia electrosynthesis.

P-Block Antimony-Copper Single-Atom Alloys for Selective Nitrite Electroreduction to Ammonia.

Electrocatalytic reduction of NO2- to NH3 (NO2RR) offers an effective method for alleviating NO2- pollution and generating valuable NH3. Herein, a p-block single-atom alloy, namely, isolated Sb alloyed in a Cu substrate (Sb1Cu), is explored as a durable and high-current-density NO2RR catalyst. As revealed by the theoretical calculations and operando spectroscopic measurements, we demonstrate that Sb1 incorporation can not only hamper the competing hydrogen evolution reaction but also optimize the d-band center of Sb1Cu and intermediate adsorption energies to boost the protonation energetics of NO2--to-NH3 conversion. Consequently, Sb1Cu integrated in a flow cell achieves an outstanding NH3 yield rate of 2529.4 μmol h-1 cm-2 and FENH3 of 95.9% at a high current density of 424.2 mA cm-2, as well as a high durability for 100 h of electrolysis.

Pd1Cu Single-Atom Alloys for High-Current-Density and Durable NO-to-NH3 Electroreduction.

Electrochemical reduction of NO to NH3 (NORR) offers a prospective method for efficient NH3 electrosynthesis. Herein, we first design single-atom Pd-alloyed Cu (Pd1Cu) as an efficient and robust NORR catalyst at industrial-level current densities (>0.2 A cm-2). Operando spectroscopic characterizations and theoretical computations unveil that Pd1 strongly electronically couples its adjacent two Cu atoms (Pd1Cu2) to enhance the NO activation while promoting the NO-to-NH3 protonation energetics and suppressing the competitive hydrogen evolution. Consequently, the flow cell assembled with Pd1Cu exhibits an unprecedented NH3 yield rate of 1341.3 μmol h-1 cm-2 and NH3-Faradaic efficiency of 85.5% at an industrial-level current density of 210.3 mA cm-2, together with an excellent long-term durability for 200 h of electrolysis, representing one of the highest NORR performances on record.

Multireference Protonation Energetics of a Dimeric Model of Nitrogenase Iron-Sulfur Clusters.

Characterizing the electronic structure of the iron-sulfur clusters in nitrogenase is necessary to understand their role in the nitrogen fixation process. One challenging task is to determine the protonation state of the intermediates in the nitrogen fixing cycle. Here, we use a dimeric iron-sulfur model to study relative energies of protonation at C, S, or Fe. Using a composite method based on coupled cluster and density matrix renormalization group energetics, we converge the relative energies of four protonated configurations with respect to basis set and correlation level. We find that accurate relative energies require large basis sets as well as a proper treatment of multireference and relativistic effects. We have also tested ten density functional approximations for these systems. Most of them give large errors in their relative energies. The best performing functional in this system is B3LYP, which gives mean absolute and maximum deviations of only 10 and 13 kJ/mol with respect to our correlated wave function estimates, respectively, comparable to the uncertainty in our correlated estimates. Our work provides benchmark results for the calibration of new approximate electronic structure methods and density functionals for these problems.

Atomically Dispersed Sn Confined in FeS2 for Nitrate‐to‐Ammonia Electroreduction

AbstractElectrocatalytic NO3− reduction to NH3 (NO3RR) is an efficient strategy to simultaneously mitigate NO3− contamination and produce sustainable NH3. Herein, atomically dispersed Sn confined in FeS2 (Sn‐FeS2) is reported as an effective and robust NO3RR catalyst, achieving a maximum NH3‐Faradaic efficiency of 96.7% with a corresponding NH3 yield rate of 15.8 mg h−1 cm−2, along with an excellent catalytic stability. Atomic coordination characterizations of Sn‐FeS2 unravel that single‐atomic Sn bonds with the surrounding Fe atoms to construct the unique p‐d hybridized Sn‐Fe pair sites. Combining theoretical investigations and operando spectroscopic measurements unveil that Sn‐Fe pair sites can synergistically promote the NO3− activation and N═O bond dissociation, accelerate the protonation energetics of NO3−‐to‐NH3 pathway and suppress the competing hydrogen evolution, eventually drastically enhancing the NO3RR activity and selectivity.

Mo single-atom catalyst boosts nitrite electroreduction for ammonia synthesis

Electrocatalytic nitrite reduction to ammonia (NO2RR) presents an efficient approach for both wastewater treatment and powerful ammonia electrosynthesis. However, the activity and selectivity of NO2RR are limited by its complex six−electron transfer process and competitive hydrogen evolution. Herein, Mo single atoms anchored on a zirconium dioxide substrate (Mo1–ZrO2) are first explored as a highly selective and active catalyst for the NO2RR, exhibiting a maximum NH3−Faraday efficiency of 94.83% with a corresponding ammonia yield rate of 346.92 μmol h−1 cm−2 at −0.7 V vs. RHE. Theoretical calculations reveal that the isolated Mo sites can effectively activate nitrite, enhance nitrite−to−ammonia protonation energetics and prohibit competitive hydrogen evolution, thus leading to the remarkably enhanced selectivity and activity of Mo1–ZrO2 for the NO2RR.

On energetics of proton and electron transfer of selected phenol derivatives: Theoretical investigation of radical and oxonium cations

AbstractIn this paper, the systematic theoretical study of phenol and 36 compounds representing various ortho, meta and para‐substituted (R‐PhOH) phenols is presented. The hydroxyl group acidity is a characteristic feature of phenol which can be modified using substitution of phenyl ring. The proton‐coupled electron transfer was investigated for parent neutral phenols, R‐PhOH, their cation radicals, R‐PhOH+•, and oxonium cations, R‐PhOH2+. Density functional theory calculations were combined with solvent continuum model for water and dimethyl sulfoxide environment. For aqueous solution, the Pourbaix diagrams (electrochemical potential vs. pH) were constructed from the theoretically predicted acidity constants and electrochemical standard potentials. From the thermodynamic point of view, the obtained theoretical results allow the estimation of the thermodynamically preferred process and alternative reaction pathways of phenolic derivatives in very acidic media.

Vanadium Diboride (VB2) for NO Electroreduction to NH3.

We report VB2 as an efficient electrocatalyst for NO-to-NH3 electroreduction (NORR), showing the highest NH3-Faradaic efficiency of 89.6% with the corresponding NH3 yield rate of 198.3 μmol h-1 cm-2 at -0.5 V vs RHE. Theoretical calculations demonstrate that B sites of VB2 act as the key active centers which can facilitate the NORR protonation energetics and inhibit the competitive hydrogen evolution, boosting both NORR activity and selectivity.

Self-Tandem Electrocatalytic NO Reduction to NH3 on a W Single-Atom Catalyst.

We design single-atom W confined in MoO3-x amorphous nanosheets (W1/MoO3-x) comprising W1-O5 motifs as a highly active and durable NORR catalyst. Theoretical and operando spectroscopic investigations reveal the dual functions of W1-O5 motifs to (1) facilitate the activation and protonation of NO molecules and (2) promote H2O dissociation while suppressing *H dimerization to increase the proton supply, eventually resulting in a self-tandem NORR mechanism of W1/MoO3-x to greatly accelerate the protonation energetics of the NO-to-NH3 pathway. As a result, W1/MoO3-x exhibits the highest NH3-Faradaic efficiency of 91.2% and NH3 yield rate of 308.6 μmol h-1 cm-2, surpassing that of most previously reported NORR catalysts.

Single‐Atom Bi Alloyed Pd Metallene for Nitrate Electroreduction to Ammonia

AbstractElectrochemical reduction of nitrate to ammonia (NO3RR) holds a great promise for attaining both NH3electrosynthesis and wastewater purification. Herein, single‐atom Bi alloyed Pd metallene (Bi1Pd) is reported as a highly effective NO3RR catalyst, showing a near 100% NH3‐Faradaic efficiency with the corresponding NH3yield of 33.8 mg h−1 cm−2at −0.6 V versus RHE, surpassing those of almost all ever reported NO3RR catalysts. In‐depth theoretical and operando spectroscopic investigations unveil that single‐atom Bi electronically couples with its neighboring Pd atoms to synergistically activate NO3−and destabilize *NO on Bi1Pd, leading to the reduced energy barrier of the potential‐determining step (*NO→*NOH) and enhanced protonation energetics of NO3−‐to‐NH3pathway.

Electrocatalytic NO Reduction to NH3 on Mo2C Nanosheets.

Electrocatalytic reduction of NO to NH3 (NORR) emerges as a promising route for achieving harmful NO treatment and sustainable NH3 generation. In this work, we first report that Mo2C is an active and selective NORR catalyst. The developed Mo2C nanosheets deliver a high NH3 yield rate of 122.7 μmol h-1 cm-2 with an NH3 Faradaic efficiency of 86.3% at -0.4 V. Theoretical computations unveil that the surface-terminated Mo atoms on Mo2C can effectively activate NO, promote protonation energetics, and suppress proton adsorption, resulting in high NORR activity and selectivity of Mo2C.

Incorporation of protons and hydroxide species in BaZrO3 and BaCeO3

We calculate the energetics of protonation in proton-conducting oxides, as well as defect concentrations and mobility under electrolysis conditions.

Determinants of Directionality and Efficiency of the ATP Synthase Fo Motor at Atomic Resolution.

Fo subcomplex of ATP synthase is a membrane-embedded rotary motor that converts proton motive force into mechanical energy. Despite a rapid increase in the number of high-resolution structures, the mechanism of tight coupling between proton transport and motion of the rotary c-ring remains elusive. Here, using extensive all-atom free energy simulations, we show how the motor’s directionality naturally arises from the interplay between intraprotein interactions and energetics of protonation of the c-ring. Notably, our calculations reveal that the strictly conserved arginine in the a-subunit (R176) serves as a jack-of-all-trades: it dictates the direction of rotation, controls the protonation state of the proton-release site, and separates the two proton-access half-channels. Therefore, arginine is necessary to avoid slippage between the proton flux and the mechanical output and guarantees highly efficient energy conversion. We also provide mechanistic explanations for the reported defective mutations of R176, reconciling the structural information on the Fo motor with previous functional and single-molecule data.

Generalizable Trends in Electrochemical Protonation Barriers.

Predicting activation energies for reaction steps is essential for modeling catalytic processes, but accurate barrier simulations often require considerable computational expense, especially for electrochemical reactions. Given the challenges of barrier computations and the growing promise of electrochemical routes for various processes, generalizable energetic trends in electrochemistry can significantly aid in analyzing reaction networks and building microkinetic models. Herein, we employ density functional theory and machine learning nudged elastic band models to simulate electrochemical protonation of *C, *N, and *O monatomic adsorbates from hydronium on a series of transition metal surfaces. We observe a consistent trend of decreasing protonation reaction energies yet increasing activation barriers from *O to *N to *C. Analysis of bond orders and reaction pathways provides insight into the origin of the observed trends in protonation energetics. We hypothesize that these results are relevant for polyatomic adsorbates, which can simplify analysis of reaction mechanisms and inform catalyst design.

Statistical analysis of C-H activation by oxo complexes supports diverse thermodynamic control over reactivity.

Transition metal oxo species are key intermediates for the activation of strong C–H bonds. As such, there has been interest in understanding which structural or electronic parameters of metal oxo complexes determine their reactivity. Factors such as ground state thermodynamics, spin state, steric environment, oxygen radical character, and asynchronicity have all been cited as key contributors, yet there is no consensus on when each of these parameters is significant or the relative magnitude of their effects. Herein, we present a thorough statistical analysis of parameters that have been proposed to influence transition metal oxo mediated C–H activation. We used density functional theory (DFT) to compute parameters for transition metal oxo complexes and analyzed their ability to explain and predict an extensive data set of experimentally determined reaction barriers. We found that, in general, only thermodynamic parameters play a statistically significant role. Notably, however, there are independent and significant contributions from the oxidation potential and basicity of the oxo complexes which suggest a more complicated thermodynamic picture than what has been shown previously.

Gas-Phase Deprotonation of Benzhydryl Cations: Carbene Basicity, Multiplicity, and Rearrangements.

Many fundamental properties of carbenes, particularly basicity, remain poorly understood. Herein, an experimental and computational examination of the deprotonation of a series of benzhydryl cations has been undertaken. These studies represent the first attempt at providing experimental values for diarylcarbene basicities. Pathways to deprotonation, including whether the singlet or triplet carbene is formed, are probed. Because diarylcarbenes are expected to be among the strongest organic bases known, assessing the energetics of protonation of these species is of fundamental importance for a wide range of chemical processes.

Solvent effect on the energetics of proton coupled electron transfer in guanine-cytosine pair in chloroform by mixed explicit and implicit solvation models

The Watson-Crick hydrogen bonded pair formed by deoxyguanosine and deoxycytidine (GC) in chloroform has been analysed by classical Molecular Dynamics simulations, which shows the existence of several fairly stable solute/solvent hydrogen bonds. Time-Dependent Density Functional Theory (TD-DFT) calculations with M052X functional, including solvation effect by a mixed continuum/discrete model, show that solvent stabilizes G → C Charge Transfer excited states (CTGC). The Proton Transfer (PT) processes that can occur in CTGC have been mapped by TD-DFT combining State Specific and Linear Response implementations of the Polarizable Continuum Model. For the first time, the effect of explicit solute/solvent interactions on the PT is considered by studying models containing up to three CHCl3 molecules. Our study shows that PT from the N1 atom of G to the N3 of C is exoergonic also in solution but, at variance with what observed in gas-phase, a stable minimum is predicted for CTGC state in chloroform.

Voltammetric Perspectives on the Acidity Scale and H+/H2 Process in Ionic Liquid Media.

Nonhaloaluminate ionic liquids (ILs) have received considerable attention as alternatives to molecular solvents in diverse applications spanning the fields of physical, chemical, and biological science. One important and often overlooked aspect of the implementation of these designer solvents is how the properties of the IL formulation affect (electro)chemical reactivity. This aspect is emphasized herein, where recent (voltammetric) studies on the energetics of proton (H+) transfer and electrode reaction mechanisms of the H+/H2 process in IL media are highlighted and discussed. The energetics of proton transfer, quantified using the p Ka (minus logarithm of acidity equilibrium constant, Ka) formalism, is strongly governed by the constituent IL anion, and to a lesser extent, the IL cation. The H+/H2 process, a model inner-sphere reaction, also displays electrochemical characteristics that are strongly IL-dependent. Overall, these studies highlight the need to carry out systematic investigations to resolve IL structure and function relationships in order to realize the potential of these diverse and versatile solvents.

Exceptionally High Proton and Lithium Cation Gas-Phase Basicity of the Anti-Diabetic Drug Metformin.

Substituted biguanides are known for their biological effect, and a few of them are used as drugs, the most prominent example being metformin (1,1-dimethylbiguanide, IUPAC name: N,N-dimethylimidodicarbonimidic diamide). Because of the presence of hydrogen atoms at the amino groups, biguanides exhibit a multiple tautomerism. This aspect of their structures was examined in detail for unsubstituted biguanide and metformin in the gas phase. At the density functional theory (DFT) level {essentially B3LYP/6-311+G(d,p)}, the most stable structures correspond to the conjugated, push-pull, system (NR2)(NH2)C═N-C(═NH)NH2 (R = H, CH3), further stabilized by an internal hydrogen bond. The structural and energetic aspects of protonation and lithium cation adduct formation of biguanide and metformin was examined at the same level of theory. The gas-phase protonation energetics reveal that the more stable tautomer is protonated at the terminal imino C═NH site, still with an internal hydrogen bond maintaining the structure of the neutral system. The calculated proton affinity and gas-phase basicity of the two molecules reach the domain of superbasicity. By contrast, the lithium cation prefers to bind the less stable, not fully conjugated, tautomer (NR2)C(═NH)-NH-C(═NH)NH2 of biguanides, in which the two C═NH groups are separated by NH. This less stable form of biguanides binds Li+ as a bidentate ligand, in agreement with what was reported in the literature for other metal cations in the solid phase. The quantitative assessment of resonance in biguanide, in metformin and in their protonated forms, using the HOMED and HOMA indices, reveals an increase in electron delocalization upon protonation. On the contrary, the most stable lithium cation adducts are less conjugated than the stable neutral biguanides, because the metal cation is better coordinated by the not-fully conjugated bidentate tautomer.