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First-Principles Characterization of the Elusive I Fluorescent State and the Structural Evolution of Retinal Protonated Schiff Base in Bacteriorhodopsin
The conversion of light energy into work is essential to life on earth. Bacteriorhodopsin (bR), a light-activated proton pump in Archae, has served for many years as a model system for the study of this process in photoactive proteins. Upon absorption of a photon, its chromophore, the retinal protonated Schiff base (RPSB), isomerizes from its native all-trans form to a 13-cis form and pumps a proton out of the cell in a process that is coupled to eventual ATP synthesis. Despite numerous time-resolved spectroscopic studies over the years, the details of the photodynamics of bR on the excited state, particularly the characterization of the I fluorescent state, the time-resolved reaction mechanism, and the role of the counterion cluster of RPSB, remain uncertain. Here, in this work, we use ab initio multiple spawning (AIMS) with spin-restricted ensemble Kohn–Sham (REKS) theory to simulate the nonadiabatic dynamics of the ultrafast photoreaction in bR. The excited state dynamics can be partitioned into three distinct phases: (1) relaxation away from the Franck–Condon region dominated by changes in retinal bond length alternation, (2) dwell time on the excited state in the I fluorescent state featuring an untwisted, bond length inverted RPSB, and (3) rapid torsional evolution to the conical intersection after overcoming a small excited state barrier. We fully characterize the I fluorescent state and the excited state barrier that hinders direct evolution to the conical intersection following photoexcitation. We also find that photoisomerization is accompanied by weakening of the interaction between RPSB and its counterion cluster. However, in contradiction with a recent time-resolved X-ray experiment, hydrogen bond cleavage is not necessary to reproduce the observed photoisomerization dynamics.
Deconvoluting XPS Spectra of La-Containing Perovskites from First-Principles
Perovskite-based oxides are used in electrochemical CO 2 and H 2 O reduction in electrochemical cells due to their compositional versatility, redox properties and stability. However limited knowledge exists on the mechanisms driving these processes. Toward this understanding, herein we probe the core level binding energy shifts of water-derived adspecies (H, O, OH, H 2 O) as well as the adsorption of CO 2 on LaCoO 3 and LaNiO 3 and we correlate the simulated peaks with experimental Temperature Programmed X-ray Photoelectron Spectroscopy (TPXPS) results. We find the strong adsorption of such chemical species can affect the antiferromagnetic ordering of LaNiO 3 . The adsorption of such adspecies is further quantified through Bader and differential charge analyses. We find the higher O 1s core level binding energy peak for both LaCoO 3 and LaNiO 3 corresponds to adsorption of water-related species and CO 2 , while the lower energy peak is due to lattice oxygen. We further correlate these DFT-based core level O 1s binding energies with the TPXPS measurements to quantify the decrease of the O 1s contribution due to desorption of adsorbates and the apparent increase of the lattice oxygen (both bulk and surface) with temperature. Finally, we quantify the influence of adsorbates on the La 4d, Co 2p and the Ni 3p core level binding energy shifts. This work demonstrates how theoretically generated XPS data can be utilized to predict species-specific binding energy shifts to assist in the deconvolution of the experimental results.
Molecular Fingerprints of Ice Surfaces in Sum Frequency Generation Spectra: A First-Principles Machine Learning Study
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First-Principles Prediction of Intermediate Products in the Decomposition of Metal Amidoboranes
The non-volatile products remaining after the thermal decomposition of metal amidoboranes ([M]n+[NH2BH3] - , M = alkali or alkaline metal atom) are amorphous and incompletely characterized increasing the complexity of devising regeneration strategies for these potential hydrogen storage materials. Utilizing the combined prototype electrostatic ground state search (PEGS) and density-functional theory (DFT) methodology (PEGS+DFT), we have searched for crystal structures of possible intermediate phases with [NHBH2] - , [NBH] - , [N3H2B3H3] - , and polymer-M[NHBH2] anion groups in the decomposition of lithium amidoborane (LiAB) and calcium amidoborane (CaAB). All these potential reaction products are calculated to be significantly endothermic, in contrast to the experimentally measured nearly thermo neutral values [3 to 5 kJ/(mol H2) in LiAB and 3.5 kJ/(mol H2) in CaAB] suggesting that there are alternative products formed. The dianion group [NHBHNHBH3] 2- has recently been suggested to form in the decomposition of a calcium amidoborane complex in solution. In LiAB and CaAB, we use PEGS+DFT calculations to predict intermediate metal-dianion compounds, and the static H2 release enthalpy is 27.4 kJ/(mol H2) in LiAB and 27.3 kJ/(mol H2) in CaAB, respectively. Introducing vibrational effects by phonon calculations, the enthalpies are shifted down by a roughly constant amount, _25 kJ/(mol H2) at 0 K and _22 kJ/(mol H2) at 300 K. Thus, our theoretical H2 release enthalpies agree with the experimentally measured nearly thermo-neutral data in the decomposition of LiAB and CaAB. This agreement supports the existence of the dianion phases as products in the decomposition of metal amidoboranes. Then, using the dianion compound as an intermediate in the decomposition of MAB, we further study the stability trends of a series of MAB (M=Li, Na, K, Ca), and find that the reaction enthalpies generally obey the following trend: The amidoborane becomes more stable, i.e., MAB stability increases as the metal cation moves down in the periodic table along a given column (LiAB>NaAB>KAB), or as metal cation moves to the left along a given row (KAB>CaAB). T.A. acknowledges the Fuel Cell Technology Program at USDOE, Office of Energy Efficiency and Renewable Energy. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.
Dissociative Binding of Carboxylic Acid Ligand on Nanoceria Surface in Aqueous Solution: A Joint in Situ Spectroscopic Characterization and First-Principles Study
Carboxylic acid is a common ligand anchoring group to functionalize nanoparticle surfaces. Its binding structures and mechanisms as a function of the oxidation states of metal oxide nanoparticle surfaces are not well characterized experimentally. We present an in situ sum frequency generation vibrational spectroscopy (SFG-VS) study on the binding of deuterated acetic acid on ceria nanoparticles in the aqueous solution. In the SFG experiment, ceria nanoparticles were deposited on the flat surface of a CaF2 hemisphere in contact with acetic acid solutions. While the ceria nanoparticle deprotonated the acetic acid, the CaF2 surface could not. Thus, the binding of the deprotonated acetic acid on ceria can be selectively probed. SFG spectra revealed that the binding modes of the carboxylate group depend on the oxidation states of the ceria surfaces. SFG polarization analysis suggested that the bidentate chelating and bridging binding modes co-exist on the reduced ceria surfaces, while the oxidized ceria surfaces are dominated by the bidentate bridging mode. The direct spectroscopic evidence helps to clarify the binding structures and mechanisms on the ceria nanoparticles. Furthermore, the middle-infrared (IR) transparent CaF2 and its chemical inertness make CaF2 and similar substrate materials good candidates for direct SFG-VS measurement of nanoparticle surface reactions and binding chem-istry.
Insights into the Mechanism of Fe(II) Adsorption and Oxidation at Fe-Clay Mineral Surfaces from First-Principles Calculations
Interfacial reactivity of redox-active iron-bearing mineral surfaces plays a crucial role in many environmental processes including biogeochemical cycling of various elements and contaminants. Herein, we apply density-functional-theory (DFT) calculations to provide atomistic insights into the heterogeneous reaction between aqueous Fe(II) and the Fe-bearing clay mineral nontronite Fe2Si4O10(OH)2 by studying its adsorption mechanism and interfacial Fe(II)-Fe(III) electron transfer (ET) at edge and basal surfaces. We find that edge-bound Fe(II) adsorption complexes at different surface sites (ferrinol, silanol and mixed) may coexist on both (010) and (110) edge facets, with complexes at ferrinol FeO(H) sites being the most energetically favorable and coupled to proton transfer. Calculation of the ET activation energy suggests that interfacial ET into dioctahedral Fe(III) sheets is probable at the clay edges and occurs predominantly but not exclusively through the complexes adsorbed at ferrinol sites and might also involve mixed sites. No clear evidence is found for complexes on basal surface that are compatible with ET through the basal sheet despite this experimentally hypothesized ET interface. This study suggests a strong pH-dependence of Fe(II) surface complexation at basal versus edge facets and highlights the importance of the protonation state of bridging ligands and proton coupled electron transfer to facilitate ET into Fe-rich clay minerals.
Optical Absorption and Band Gap Reduction in (Fe 1– x Cr x ) 2 O 3 Solid Solutions: A First-Principles Study
We provide a detailed theoretical analysis of the character of optical transitions and band gap reduction in (Fe1-xCrx)2O3 solid solutions using extensive periodic model and embedded cluster calculations. Optical absorption bands for x = 0.0, 0.5, and 1.0 are assigned on the basis of timedependent density functional theory (TDDFT) calculations. A band-gap reduction of as much as 0.7 eV with respect to that of pure α-Fe2O3 is found. This result can be attributed to predominantly two effects: (i) the higher valence band edge for x ≈ 0.5, as compared to those in pure α-Fe2O3 and α-Cr2O3, and, (ii) the appearance of Cr α Fe d–d transitions in the solid solutions. Broadening of the valence band due to hybridization of the O 2p states with Fe and Cr 3d states also contributes to band gap reduction.
Calculation from First Principles of Intramolecular Golden-Rule Rate Constants for Photo-Induced Electron Transfer in Molecular Donor–Acceptor Systems
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New Insights into the Structure of the C-Terminated beta-Mo2C (001) Surface from First-Principles Calculations
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First-Principles Mechanistic Analysis of Dimethyl Ether Electro-Oxidation on Monometallic Single-Crystal Surfaces
Dimethyl ether is an attractive alternative to petroleum fuels due to its physical properties, comparable energy density to methanol and ethanol, and minimal deleterious environmental/toxicological effects. For direct fuel cells, it has a number of advantages over other prominent fuels, including easier storage with respect to hydrogen, lower toxicity and crossover when compared to methanol, and more facile complete oxidation as compared to ethanol (which includes a relatively difficult to break C–C bond). However, the dimethyl ether electro-oxidation reaction is poorly understood, hindering the development of improved electrocatalysts. Using periodic, self-consistent (PW91-GGA) density functional theory calculations, we evaluate the thermochemistry of dimethyl ether (DME) electro-oxidation, at the elementary step level, on 12 model, closed-packed facets of pure transition metals: Au, Ag, Cu, Pt, Pd, Ni, Ir, Rh, Co, Os, Ru, and Re. From the calculated thermochemistry, we determine the most probable reaction paths on each of these surfaces, focusing on Pt as a model system. Our results predict two key electro-oxidation peaks. At lower potentials, there is a peak corresponding to partial oxidation of DME to CO (and other surface poisoning species) or complete oxidation to CO 2 via formic acid as a key intermediate. A second, higher-potential peak is due to complete oxidation of adsorbed CO (and other surface poisoning species) to CO 2 . Assuming the catalysts remain in their metallic state during the DME electro-oxidation process, our results suggest that the onset potential of the surfaces increases in the order Cu < Ni < Os < Rh < Ir < Co < Ru < Pt < Ag < Pd < Re < Au. Using our results, we construct a theoretical phase diagram showing predicted catalyst activity based on two key reactivity descriptors, the free energies of adsorbed CO and OH. Here, we compare all results to methanol electro-oxidation to understand key mechanistic differences and their impacts on optimal catalyst design for direct DME fuel cells.
Strain-induced phase and oxygen-vacancy stability in ionic interfaces from first-principles calculations
Understanding interfacial chemistry is becoming crucial in materials design for heterointerfaces. Using density functional theory, we elucidate the effect of strained interfaces on phase and oxygen-vacancy stability for CeO2 | ZrO2, ThO2 | ZrO2 and CeO2 | ThO2 interfaces. The calculations show that ZrO2 transforms from cubic fluorite to the orthorhombic columbite under tensile strain providing evidence of a previous experimental speculation of an unrecognized ZrO2 phase. We also show that oxygen vacancies could be preferably stabilized on either side of the interface by manipulating strain. We predict that they are stable in tensile-strain, and unstable in compressivestrained materials.
Electrocatalytic Oxidation of Ammonia on Transition-Metal Surfaces: A First-Principles Study
Here, we investigate the catalytic electro-oxidation of ammonia on model close-packed surfaces of Au, Ag, Cu, Pd, Pt, Ni, Ir, Co, Rh, Ru, Os, and Re to derive insights for the reaction mechanism and evaluate the catalysts based on their energy efficiency and activity in the context of their application in fuel cells. Two mechanisms, which are differentiated by their N–N bond formation step, are compared: (1) a mechanism proposed by Gerischer and Mauerer, whereby the N–N bond formation occurs between hydrogenated NH x adsorbed species, and (2) a mechanism in which N–N bond formation occurs between N adatoms. The results of our study show that the mechanism proposed by Gerischer and Mauerer is kinetically preferred and that the formation of N adatoms poisons the surface of the catalyst. On the basis of a simple Sabatier analysis, we predict that Pt is the most active monometallic catalyst followed by Ir and Cu, whereas all other metal surfaces studied here have significantly lower activity. We conclude by outlining some design principles for bimetallic alloy catalysts for NH 3 electro-oxidation.
First-Principles Study of Redox End Members in Lithium-Sulfur Batteries
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Li–O 2 Kinetic Overpotentials: Tafel Plots from Experiment and First-Principles Theory
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Accurate Amorphous Silica Surface Models from First-Principles Thermodynamics of Surface Dehydroxylation
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Quantitative Current-Voltage Characteristics in Molecular Junctions from First Principles
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Accurate first-principles structures and energies of diversely bonded systems from an efficient density functional
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