Electronic Free Energy Surface of the Nitrogen Dimer Using First-Principles Finite Temperature Electronic Structure Methods
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37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
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Results for “nitrogen dimer”
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Effect of environmental screening and strain on optoelectronic properties of two-dimensional quantum defects
Point defects in hexagonal boron nitride (hBN) are promising candidates as single-photon emitters (SPEs) in nanophotonics and quantum information applications. The precise control of SPEs requires in-depth understanding of their optoelectronic properties. However, how the surrounding environment of host materials, including the number of layers, substrates, and strain, influences SPEs has not been fully understood. Here, in this work, we study the dielectric screening effect due to the number of layers and substrates, and the strain effect on the optical properties of carbon dimer and nitrogen vacancy defects in hBN from first-principles many-body perturbation theory. We report that environmental screening causes a lowering of the quasiparticle gap and exciton binding energy, leading to nearly constant optical excitation energy and exciton radiative lifetime. We explain the results with an analytical model starting from the Bethe–Salpeter equation Hamiltonian with Wannier basis. We also show that optical properties of quantum defects are largely tunable by strain with highly anisotropic response, in good agreement with experimental measurements. Our work clarifies the effect of environmental screening and strain on optoelectronic properties of quantum defects in two-dimensional insulators, facilitating future applications of SPEs and spin qubits in low-dimensional systems.
36 MATERIALS SCIENCE↗
Variational quantum eigensolver for approximate diagonalization of downfolded Hamiltonians using generalized unitary coupled cluster ansatz
In this paper we discuss the utilization of Variational Quantum Solver (VQE) and recently introduced Generalized Unitary Coupled Cluster (GUCC) formalism for the diagonalization of downfolded/effective Hamiltonians in active spaces. In addition to effective Hamiltonians defined by the downfolding of a subset of virtual orbitals we also consider their form defined by freezing core orbitals, which enables us to deal with larger systems. Furthermore, we also consider various solvers to identify solutions of the GUCC equations. We use N 2 , H 2 O, and C 2 H 4 , and benchmark systems to illustrate the performance of the combined framework.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Self-deactivation of water vapor - Role of the dimer
A phenomenological multiple-relaxation theory of the deactivation rate constant for the nu-2 (1 - 0) bending mode of water vapor is presented which incorporates the role not only of the excited monomer but also of the bound molecular complex, in particular the dimer. The deactivation takes place by means of three parallel processes: (1) collisional deexcitation of the excited monomer, (2) a two-step reaction involving association and spontaneous redissociation of an H2O collision complex, and (3) spontaneous dissociation of the stably bound H2O dimer. Oxygen, but not nitrogen or argon, serves as an effective chaperon for the formation of the activated complex. This observation explains the impurity dependence of the self-deactivation rate constant of water vapor. Analysis of an ultrasonic absorption peak based on the third process yields values for the standard entropy and enthalpy of dissociation of the stably bound H2O dimer.
Zuckerwar, A. J.↗
Insertion reactions and structural studies of [(NHC)CuH] 2 with nitrogen-based substrates
The stoichiometric and catalytic reactions of Cu-H dimers supported by N-heterocyclic carbenes (NHCs) have mainly focused on the insertions of aldehydes, ketones, CO 2 , and unsaturated hydrocarbons. Here we investigated the stoichiometric reactions of dimeric [(NHC)CuH] 2 (NHC = IPr*, 6Dipp) with unsaturated nitrogen-based substrates of PhN=NPh, N 3 Ad, pyrazine, and N 2 O. The spectroscopic and structural chacterizations of the resulting monomeric, two-coordinate Cu(I) complexes containing diphenyl hydrazido, triazenido, pyrazinyl, and hydroxide ligands are discussed. The hydrazido complex of (IPr*)Cu(NPh-NHPh) and triazenido complex of (IPr*)Cu(HNNNAd) are resistant to N—N bond cleavage and loss of N 2 , respectively, to form the corresponding amido complexes even when heated at 80 °C over several hours.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Initiating Molecular Growth in the Interstellar Medium via Dimeric Complexes of Observed Ions and Molecules
A feasible initiation step for particle growth in the interstellar medium (ISM) is simulated by means of ab quantum chemistry methods. The systems studied are dimer ions formed by pairing nitrogen containing small molecules known to exist in the ISM with ions of unsaturated hydrocarbons or vice versa. Complexation energies, structures of ensuing complexes and electronic excitation spectra of the encounter complexes are estimated using various quantum chemistry methods. Moller-Plesset perturbation theory (MP2, Z-averaged perturbation theory (ZAP2), coupled cluster singles and doubles with perturbative triples corrections (CCSD(T)), and density functional theory (DFT) methods (B3LYP) were employed along with the correlation consistent cc-pVTZ and aug-cc-pVTZ basis sets. Two types of complexes are predicted. One type of complex has electrostatic binding with moderate (7-20 kcal per mol) binding energies, that are nonetheless significantly stronger than typical van der Waals interactions between molecules of this size. The other type of complex develops strong covalent bonds between the fragments. Cyclic isomers of the nitrogen containing complexes are produced very easily by ion-molecule reactions. Some of these complexes show intense ultraviolet visible spectra for electronic transitions with large oscillator strengths at the B3LYP, omegaB97, and equations of motion coupled cluster (EOM-CCSD) levels. The open shell nitrogen containing carbonaceous complexes especially exhibit a large oscillator strength electronic transition in the visible region of the electromagnetic spectrum.
Bera, Partha P.↗
Proton-bound cluster ions in ion mobility spectrometry
Gaseous oxygen and nitrogen bases, both singly and as binary mixtures, have been introduced into ion mobility spectrometers to study the appearance of protonated molecules, and proton-bound dimers and trimers. At ambient temperature it was possible to simultaneously observe, following the introduction of molecule A, comparable intensities of peaks ascribable to the reactant ion (H2O)nH+, the protonated molecule AH+ and AH+ H2O, and the symmetrical proton bound dimer A2H+. Mass spectral identification confirmed the identifications and also showed that the majority of the protonated molecules were hydrated and that the proton-bound dimers were hydrated to a much lesser extent. No significant peaks ascribable to proton-bound trimers were obtained no matter how high the sample concentration. Binary mixtures containing molecules A and B, in some cases gave not only the peaks unique to the individual compounds but also peaks due to asymmetrical proton bound dimers AHB+. Such ions were always present in the spectra of mixtures of oxygen bases but were not observed for several mixtures of oxygen and nitrogen bases. The dimers, which were not observable, notable for their low hydrogen bond strengths, must have decomposed in their passage from the ion source to the detector, i.e. in a time less than approximately 5 ms. When the temperature was lowered to -20 degrees C, trimers, both homogeneous and mixed, were observed with mixtures of alcohols. The importance of hydrogen bond energy, and hence operating temperature, in determining the degree of solvation of the ions that will be observed in an ion mobility spectrometer is stressed. The possibility is discussed that a displacement reaction involving ambient water plays a role in the dissociation.
Non-NASA Center↗
Electrocatalytic Ammonia Oxidation by Pyridyl-Substituted Ferrocenes
Ammonia (NH 3 ) is a promising carbon-free fuel when prepared from sustainable resources. First-row transition metal electrocatalysts for ammonia oxidation are an enabling technology for sustainable energy production. We describe electrocatalytic ammonia oxidation using robust molecular complexes based on Earth-abundant iron. Electrochemical studies of ferrocenes with covalently attached pyridine arms reveal facile ammonia oxidation in DMSO (2.4 M NH 3 ) with modest overpotentials (η = 770–820 mV) and turnover frequencies (125–560 h –1 ). Experimental and computational studies indicate that the pendant pyridyl base serves as an H-bond acceptor with an N–H bond of ammonia that transfers a proton to the pyridine following oxidation by the attached ferrocenium moiety in a proton-coupled electron transfer (PCET) step. This generates an amidyl (•NH 2 ) radical stabilized via H-bonding to a pendant pyridinium moiety that rapidly dimerizes to hydrazine (H 2 N–NH 2 ), which is easily oxidized to nitrogen (N 2 ) at the glassy carbon working electrode. This report identifies a general strategy to oxidize ammonia via H-bonding to a base (B:), thereby activating [B···H-NH 2 ] toward PCET by a proximal oxidant to form [BH···NH 2 ] +/• radical cations, which are susceptible to dimerization to form easily oxidized hydrazine.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Reduction of a Heme Cofactor Initiates N -Nitroglycine Degradation by NnlA
Linear nitramines are potentially carcinogenic environmental contaminants. The NnlA enzyme from Variovorax sp. strain JS1663 degrades the nitramine N-nitroglycine (NNG)—a natural product produced by some bacteria—to glyoxylate and nitrite (NO 2 –). Ammonium (NH 4 +) was predicted as the third product of this reaction. A source of nonheme Fe II was shown to be required for initiation of NnlA activity. However, the role of this Fe II for NnlA activity was unclear. This work reveals that NnlA contains a b-type heme cofactor. Reduction of this heme—either by a nonheme iron source or dithionite—is required to initiate NnlA activity. Therefore, Fe II is not an essential substrate for holoenzyme activity. Our data show that reduced NnlA (Fe II -NnlA) catalyzes at least 100 turnovers and does not require O 2 . Finally, NH 4 + was verified as the third product, accounting for the complete nitrogen mass balance. Size exclusion chromatography showed that NnlA is a dimer in solution. Additionally, Fe II -NnlA is oxidized by O 2 and NO 2 – and stably binds carbon monoxide (CO) and nitric oxide (NO). These are characteristics shared with heme-binding PAS domains. Furthermore, a structural homology model of NnlA was generated using the PAS domain from Pseudomonas aeruginosa Aer2 as a template. The structural homology model suggested His 73 is the axial ligand of the NnlA heme. Site-directed mutagenesis of His 73 to alanine decreased the heme occupancy of NnlA and eliminated NNG activity, validating the homology model. We conclude that NnlA forms a homodimeric heme-binding PAS domain protein that requires reduction for initiation of the activity.
59 BASIC BIOLOGICAL SCIENCES↗
Crystal structure of vismodegib, C 19 H 14 Cl 2 N 2 O 3 S
The crystal structure of vismodegib has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional theory techniques. Vismodegib crystallizes in space group P2 1 /a (#14) with a = 16.92070(20), b = 10.20235(4), c = 12.16161(10) Å, β = 108.6802(3)°, V = 1988.873(9) Å 3 , and Z = 4. The crystal structure consists of corrugated layers of molecules parallel to the bc-plane. There is only one classical hydrogen bond in the structure, between the amide nitrogen atom and the N atom of the pyridine ring. Pairs of these hydrogen bonds link the molecules into dimers, with a graph set R2,2(14) > a > a. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).
36 MATERIALS SCIENCE↗
Structural insights into redox signal transduction mechanisms in the control of nitrogen fixation by the NifLA system
NifL is a conformationally dynamic flavoprotein responsible for regulating the activity of the σ 54 -dependent activator NifA to control the transcription of nitrogen fixation (nif) genes in response to intracellular oxygen, cellular energy, or nitrogen availability. The NifL-NifA two-component system is the master regulatory system for nitrogen fixation. NifL serves as a sensory protein, undergoing signal-dependent conformational changes that modulate its interaction with NifA, forming the NifL–NifA complex, which inhibits NifA activity in conditions unsuitable for nitrogen fixation. While NifL-NifA regulation is well understood, these conformationally flexible proteins have eluded previous attempts at structure determination. In work described here, we advance a structural model of the NifL dimer supported by a combination of scattering techniques and mass spectrometry (MS)-coupled structural analyses that report on the average structure in solution. Using a combination of small angle X-ray scattering-derived electron density maps and MS-coupled surface labeling, we investigate the conformational dynamics responsible for NifL oxygen and energy responses. Our results reveal conformational differences in the structure of NifL under reduced and oxidized conditions that provide the basis for a model for modulating NifLA complex formation in the regulation of nitrogen fixation in response to oxygen in the model diazotroph,Azotobacter vinelandii.
59 BASIC BIOLOGICAL SCIENCES↗
Nitrous oxide production via enzymatic nitroxyl from the nitrifying archaeon Nitrosopumilus maritimus
Ammonia oxidizing archaea (AOA) are among the most abundant microorganisms on earth and are known to be a major source of nitrous oxide (N 2 O) emissions, although biochemical origins of this N 2 O remain unknown. Enzymological details of AOA nitrogen metabolism are broadly unavailable. We report the recombinant expression, purification, and characterization of a multicopper oxidase, Nmar_1354, from the AOA Nitrosopumilus maritimus . We show that Nmar_1354 selectively produces nitroxyl (HNO) by coupling the oxidation of the obligate nitrification intermediate hydroxylamine (NH 2 OH) to dioxygen (O 2 ) reduction. This HNO undergoes several downstream reactions, although the major fates are production of N 2 via reaction with NH 2 OH and dimerization with itself to yield N 2 O. These results afford one plausible enzymatic origin for N 2 O release by AOA. Moreover, these results reveal a physiologically relevant enzymatic reaction for producing HNO, an enigmatic nitrogen oxide speculated to be operative in cellular signaling and in energy transduction.
Voland, Robert W. (ORCID:0000000201061257)↗
Ultrafast time-resolved x-ray absorption spectroscopy of ionized urea and its dimer through ab initio nonadiabatic dynamics
Investigating the early dynamics of chemical systems following ionization is essential for our understanding of radiation damage. However, experimental as well as theoretical investigations are very challenging due to the complex nature of these processes. Time-resolved x-ray absorption spectroscopy on a femtosecond timescale, in combination with appropriate simulations, is able to provide crucial insights into the ultrafast processes that occur upon ionization due to its element-specific probing nature. In this theoretical study, we investigate the ultrafast dynamics of valence-ionized states of urea and its dimer employing Tully's fewest switches surface hopping approach using Koopmans' theorem to describe the ionized system. We demonstrate that following valence ionization through a pump pulse, the time-resolved x-ray absorption spectra at the carbon, nitrogen, and oxygen K-edges reveal rich insights into the dynamics. Excited states of the ionized system give rise to time-delayed blueshifts in the x-ray absorption spectra as a result of electronic relaxation dynamics through nonadiabatic transitions. Moreover, our statistical analysis reveals specific structural dynamics in the molecule that induce time-dependent changes in the spectra. For the urea monomer, we elucidate the possibility to trace effects of specific molecular vibrations in the time-resolved x-ray absorption spectra. For the urea dimer, where ionization triggers a proton transfer reaction, we show how the x-ray absorption spectra can reveal specific details on the progress of proton transfer.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Submillimeter Spectra of Low Temperature Gases and Mixtures
Submillimeter absorption spectra of nitrogen, nitrogen-argon mixtures, and methane have been measured using temperatures and pressures near to those found in the atmospheres of Titan and Saturn. The experiments show the spectral signature of dimers which will likely appear in far-infrared spectra of Titan that will be obtained by the Composite Infrared Spectrometer (CIS) onboard the Cassini spacecraft. The recent CIRS spectrum of Jupiter shows far-infrared spectral lines of methane and the corresponding lines are observed in the laboratory. We are extending this work to lower frequencies using a new differential Michelson interferometer that operates over the frequency region 3-30 1/cm..
Wishnow, E. H.↗
Diversifying hierarchical ionic assembly by docking cations to anions as salt bridges
Here, we expand the diversity of building blocks available for ionic assembly by introducing tertiary (3°) ammonium cations into anion complexes. We use proton transfer between 3° amines and organo-phosphoric acids to generate H-bonding cations (R 3 NH + ) and anions (RHPO 4 – ) that co-assemble with cyanostar macrocycles into assemblies with 2:2:2 stoichiometry. At the heart is a supramolecular dimer where phosphate anions form salt bridges by H-bonding with cations. Unlike conventional 4° ammonium cations, 3,000 commercial amines provide diversity for high-throughput screening of 72 combinations (9 nitrogen bases and 8 acids), producing 13 privileged partners for quantitative assembly. Yields depend on the solvent and sterics of salt bridge formation. Ten more nitrogen bases connect to fluorophores (pyrene), photocatalysts (quinoline), drugs (Cipralex, Zytiga), and ionic liquids (imidazole). The synthesis and examination of 82 new salts exemplify how acid-base chemistry can open a pipeline to a diversity of building blocks for exploring hierarchical ionic assembly.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Nitrogen-induced absorption of oxygen in the Herzberg continuum
Total absorption of O2 induced by collisions with N2 has been measured at room temperature in the Hersberg continuum using a one meter normal incidence grating monochromator. The enhanced absorption is ascribed to the formation of O2-O2 and O2-N2 dimers. The interaction constants for these dimers are determined and utilized to investigate their effect on the absorption of solar radiation in the stratosphere.
Shardanand, MR.↗
Stratospheric ozone - Impact of human activity
The current knowledge of the chemistry of the stratosphere is reviewed, with particular consideration given to the measurements from the Atmospheric Trace Molecule Spectroscopy (ATMOS) experiment and from the Airborne Antarctic Ozone Experiment. Analysis of the ATMOS data at 30 deg N suggests that the current understanding of the contemporary-stratosphere chemistry at mid-latitudes is relatively complete, except for possible problems with the diurnal variations of N2O5 at low altitudes, and with ClNO3 at higher altitudes. Except for some difficulties with these two compounds, the data from ATMOS agree well with the gas phase models for nitrogen and chlorine species at 30 deg N in spring. It is emphasized that, in addition to the HOCl mechanism proposed by Solomon et al. (1986), the ClO-BrO scheme proposed by McElroy et al. (1986), and the ClO dimer mechanism introduced by Molina and Molina (1987), other processes exist that are responsible for ozone removal.
Mcelroy, Michael B.↗
A Cloud Algorithm Based on the O2-O2 477 nm Absorption Band Featuring an Advanced Spectral Fitting Method and the Use of Surface Geometry-Dependent Lambertian-Equivalent Reflectivity
We discuss a new cloud algorithm that retrieves an effective cloud pressure, also known as cloud optical centroid pressure (OCP), from oxygen dimer (O2-O2) absorption at 477nm after determining an effective cloud fraction (ECF) at 466nm, a wavelength not significantly affected by trace-gas absorption and rotational Raman scattering. The retrieved cloud products are intended for use as inputs to the operational nitrogen dioxide (NO2) retrieval algorithm for the Ozone Monitoring Instrument (OMI) flying on the Aura satellite. The cloud algorithm uses temperature-dependent O2-O2 cross sections and incorporates flexible spectral fitting techniques that account for specifics of the surface reflectivity. The fitting procedure derives O2-O2 slant column densities (SCDs) from radiances after O3, NO2, and H2O absorption features have been removed based on estimates of the amounts of these species from independent OMI algorithms. The cloud algorithm is based on the frequently used mixed Lambertian-equivalent reflectivity (MLER) concept. A geometry-dependent Lambertian-equivalent reflectivity (GLER), which is a proxy of surface bidirectional reflectance, is used for the ground reflectivity in our implementation of the MLER approach. The OCP is derived from a match of the measured O2-O2 SCD to that calculated with the MLER method. Temperature profiles needed for computation of vertical column densities are taken from the Global Modeling Initiative (GMI) model. We investigate the effect of using GLER instead of climatological LER on the retrieved ECF and OCP. For evaluation purposes, the retrieved ECFs and OCPs are compared with those from the operational OMI cloud product, which is also based on the same O2-O2 absorption band. Impacts of the application of the newly developed cloud algorithm to the OMI NO2 retrieval are discussed.
cloud fraction and pressure↗