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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Optimal Orbital Selection for Full Configuration Interaction (OptOrbFCI): Pursuing the Basis Set Limit under a Budget
Full configuration interaction (FCI) solvers are limited to small basis sets due to their expensive computational costs. An optimal orbital selection for FCI (OptOrbFCI) is proposed to boost the power of existing FCI solvers to pursue the basis set limit under a computational budget. The optimization problem coincides with that of the complete active space SCF method (CASSCF), while OptOrbFCI is algorithmically quite different. OptOrbFCI effectively finds an optimal rotation matrix via solving a constrained optimization problem directly to compress the orbitals of large basis sets to one with a manageable size, conducts FCI calculations only on rotated orbital sets, and produces a variational ground-state energy and its wave function. Coupled with coordinate descent full configuration interaction (CDFCI), we demonstrate the efficiency and accuracy of the method on the carbon dimer and nitrogen dimer under basis sets up to cc-pV5Z. We also benchmark the binding curve of the nitrogen dimer under the cc-pVQZ basis set with 28 selected orbitals, which provide consistently lower ground-state energies than the FCI results under the cc-pVDZ basis set. Furthermore, the dissociation energy in this case is found to be of higher accuracy.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
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↗
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↗
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↗
Nucleation of soot: experimental assessment of the role of polycyclic aromatic hydrocarbon (PAH) dimers
The irreversible dimerization of polycyclic aromatic hydrocarbons (PAHs) – typically pyrene (C 16 H 10 ) dimerization – is widely used in combustion chemistry models to describe the soot particle inception step. This study concerns itself with the detection and identification of dimers of flame-synthesized PAH radicals and closed-shell molecules and an experimental assessment of the role of these PAH dimers for the nucleation of soot. To this end, flame-generated species were extracted from an inverse co-flow flame of ethylene at atmospheric pressure and immediately diluted with excess nitrogen before the mixture was analyzed using flame-sampling tandem mass spectrometry with collision-induced fragmentation. Signal at m/z = 404.157 (C 32 H 20 ) and m/z = 452.157 (C 36 H 20 ) were detected and identified as dimers of closed-shell C 16 H 10 and C 18 H 10 monomers, respectively. A complex between a C 13 H 9 radical and a C 24 H 12 closed-shell PAH was observed at m/z = 465.164 (C 37 H 21 ). However, a rigorous analysis of the flame-sampled mass spectra as a function of the dilution ratio, defined as the ratio of the flow rates of the diluent nitrogen to the sampled gases, indicates that the observed dimers are not flame-born, but are produced in the sampling line. In agreement with theoretical considerations, this paper provides experimental evidence that pyrene dimers cannot be a key intermediate in particle inception at elevated flame temperatures.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
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↗
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↗
On the mechanism of intermolecular nitrogen-atom transfer from a lattice-isolated diruthenium nitride intermediate
Catalyst confinement within microporous media provides the opportunity to site isolate reactive intermediates, enforce intermolecular functionalization chemistry by co-localizing reactive intermediates and substrates in molecular-scale interstices, and harness non-covalent host–guest interactions to achieve selectivities that are complementary to those accessible in solution. As part of an ongoing program to develop synthetically useful nitrogen-atom transfer (NAT) catalysts, we have demonstrated intermolecular benzylic amination of toluene at a Ru 2 nitride intermediate confined within the interstices of a Ru2-based metal–organic framework (MOF), Ru 3 (btc) 2 X 3 (btc = 1,3,5-benzenetricarboxylate, i.e., Ru-HKUST-1 for X = Cl). Nitride confinement within the extended MOF lattice enabled intermolecular C–H functionalization of benzylic C–H bonds in preference to nitride dimerization, which was encountered with soluble molecular analogues. Detailed study of the kinetic isotope effects (KIEs, i.e., k H /k D ) of C–H amination, assayed both as intramolecular effects using partially labeled toluene and as intermolecular effects using a mixture of per-labeled and unlabeled toluene, provided evidence for restricted substrate mobility on the time scale of interstitial NAT. Analysis of these KIEs as a function of material mesoporosity provided approximate experimental values for functionalization in the absence of mass transport barriers. Here, we disclose a combined experimental and computational investigation of the mechanism of NAT from a Ru 2 nitride to the C–H bond of toluene. Computed kinetic isotope effects for a H-atom abstraction (HAA)/radical rebound (RR) mechanism are in good agreement with experimental data obtained for C–H amination at the rapid diffusion limit. These results provide the first detailed analysis of the mechanism of intermolecular NAT to a C–H bond, bolster the use of KIEs as a probe of confinement effects on NAT within MOF lattices, and provide mechanistic insights unavailable by experiment because rate-determining mass transport obscured the underlying chemical kinetics.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Crystal structure of a thermophilic fungal cyanase and its implications on the catalytic mechanism for bioremediation
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99 GENERAL AND MISCELLANEOUS↗
Molecular dissection of the glutamine synthetase-GlnR nitrogen regulatory circuitry in Gram-positive bacteria
How bacteria sense and respond to nitrogen levels are central questions in microbial physiology. In Gram-positive bacteria, nitrogen homeostasis is controlled by an operon encoding glutamine synthetase (GS), a dodecameric machine that assimilates ammonium into glutamine, and the GlnR repressor. GlnR detects nitrogen excess indirectly by binding glutamine-feedback-inhibited-GS (FBI-GS), which activates its transcription-repression function. The molecular mechanisms behind this regulatory circuitry, however, are unknown. Here we describe biochemical and structural analyses of GS and FBI-GS-GlnR complexes from pathogenic and non-pathogenic Gram-positive bacteria. The structures show FBI-GS binds the GlnR C-terminal domain within its active-site cavity, juxtaposing two GlnR monomers to form a DNA-binding-competent GlnR dimer. The FBI-GS-GlnR interaction stabilizes the inactive GS conformation. Strikingly, this interaction also favors a remarkable dodecamer to tetradecamer transition in some GS, breaking the paradigm that all bacterial GS are dodecamers. These data thus unveil unique structural mechanisms of transcription and enzymatic regulation.
59 BASIC BIOLOGICAL SCIENCES↗
Alternant Hydrocarbon Diradicals as Optically Addressable Molecular Qubits
High-spin molecules allow for bottom-up qubit design and are promising platforms for magnetic sensing and quantum information science. Optical addressability of molecular electron spins has also been proposed in first-row transition-metal complexes via optically detected magnetic resonance (ODMR) mechanisms analogous to the diamond-nitrogen-vacancy color center. However, significantly less progress has been made on the front of metal-free molecules, which can deliver lower costs and milder environmental impacts. At present, most luminescent open-shell organic molecules are π-diradicals, but such systems often suffer from poor ground-state open-shell characters necessary to realize a stable ground-state molecular qubit. In this work, we use alternancy symmetry to selectively minimize radical–radical interactions in the ground state, generating π-systems with high diradical characters. We call them m-dimers, referencing the need to covalently link two benzylic radicals at their meta carbon atoms for the desired symmetry. Through a detailed electronic structure analysis, we find that the excited states of alternant hydrocarbon m-diradicals contain important symmetries that can be used to construct ODMR mechanisms leading to ground-state spin polarization. Furthermore, the molecular parameters are set in the context of a tris(2,4,6-trichlorophenyl)methyl (TTM) radical dimer covalently tethered at the meta position, demonstrating the feasibility of alternant m-diradicals as molecular color centers.
Chemistry↗
Mechanical coupling in the nitrogenase complex
The enzyme nitrogenase reduces dinitrogen to ammonia utilizing electrons, protons, and energy obtained from the hydrolysis of ATP. Mo-dependent nitrogenase is a symmetric dimer, with each half comprising an ATP-dependent reductase, termed the Fe Protein, and a catalytic protein, known as the MoFe protein, which hosts the electron transfer P-cluster and the active-site metal cofactor (FeMo-co). A series of synchronized events for the electron transfer have been characterized experimentally, in which electron delivery is coupled to nucleotide hydrolysis and regulated by an intricate allosteric network. We report a graph theory analysis of the mechanical coupling in the nitrogenase complex as a key step to understanding the dynamics of allosteric regulation of nitrogen reduction. This analysis shows that regions near the active sites undergo large-scale, large-amplitude correlated motions that enable communications within each half and between the two halves of the complex. Computational predictions of mechanically regions were validated against an analysis of the solution phase dynamics of the nitrogenase complex via hydrogen-deuterium exchange. These regions include the P-loops and the switch regions in the Fe proteins, the loop containing the residue β-188Ser adjacent to the P-cluster in the MoFe protein, and the residues near the protein-protein interface. In particular, it is found that: (i) within each Fe protein, the switch regions I and II are coupled to the [4Fe-4S] cluster; (ii) within each half of the complex, the switch regions I and II are coupled to the loop containing β-188Ser; (iii) between the two halves of the complex, the regions near the nucleotide binding pockets of the two Fe proteins (in particular the P-loops, located over 130 Å apart) are also mechanically coupled. Notably, we found that residues next to the P-cluster (in particular the loop containing β-188Ser) are important for communication between the two halves.
59 BASIC BIOLOGICAL SCIENCES↗