Two major energy-related problems confront the world in the
next 50 years. First, increased worldwide competition for
gradually depleting fossil fuel reserves (derived from past
photosynthesis) will lead to higher costs, both monetarily and politically. Second, atmospheric CO_2 levels are at their highest recorded level since records began. Further increases are predicted to produce large and uncontrollable impacts on the world climate. These projected impacts extend beyond climate to ocean acidification, because the ocean is a major sink for atmospheric CO2.1 Providing a future energy supply that is secure and CO_2-neutral will require switching to nonfossil energy sources such as wind, solar, nuclear, and geothermal energy and developing methods for transforming the energy produced by these new sources into forms that can be stored, transported, and used upon demand.

Frontiers, Opportunities, and Challenges in Biochemical and Chemical Catalysis of CO2 Fixation

In this contribution to the special software-centered issue, the ORCA program package is described. We start with a short historical perspective of how the project began and go on to discuss its current feature set. ORCA has grown into a rather comprehensive general-purpose package for theoretical research in all areas of chemistry and many neighboring disciplines such as materials sciences and biochemistry. ORCA features density functional theory, a range of wavefunction based correlation methods, semi-empirical methods, and even force-field methods. A range of solvation and embedding models is featured as well as a complete intrinsic to ORCA quantum mechanics/molecular mechanics engine. A specialty of ORCA always has been a focus on transition metals and spectroscopy as well as a focus on applicability of the implemented methods to "real-life" chemical applications involving systems with a few hundred atoms. In addition to being efficient, user friendly, and, to the largest extent possible, platform independent, ORCA features a number of methods that are either unique to ORCA or have been first implemented in the course of the ORCA development. Next to a range of spectroscopic and magnetic properties, the linear- or low-order single- and multi-reference local correlation methods based on pair natural orbitals (domain based local pair natural orbital methods) should be mentioned here. Consequently, ORCA is a widely used program in various areas of chemistry and spectroscopy with a current user base of over 22 000 registered users in academic research and in industry.

The ORCA quantum chemistry program package

Brian M. Hoffman,* Dmitriy Lukoyanov, Zhi-Yong Yang,† Dennis R. Dean,*,‡ and Lance C. Seefeldt*,† †Department of Chemistry and Biochemistry, Utah State University, 0300 Old Main Hill, Logan, Utah 84322, United States ‡Department of Biochemistry, Virginia Tech, 900 West Campus Drive, Blacksburg, Virginia 24061, United States Departments of Chemistry and Molecular Biosciences, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States

Mechanism of Nitrogen Fixation by Nitrogenase: The Next Stage

Structure/function relationships of [NiFe]- and [FeFe]-hydrogenases.

Ammonia is an important nutrient for the growth of plants. In industry, ammonia is produced by the energy expensive Haber–Bosch process where dihydrogen and dinitrogen form ammonia at a very high pressure and temperature. In principle one could also reduce dinitrogen upon addition of protons and electrons similar to the mechanism of ammonia production by nitrogenases. Recently, major breakthroughs have taken place in our understanding of biological fixation of dinitrogen, of molecular model systems that can reduce dinitrogen, and in the electrochemical reduction of dinitrogen at heterogeneous surfaces. Yet for efficient reduction of dinitrogen with protons and electrons major hurdles still have to be overcome. In this tutorial review we give an overview of the different catalytic systems, highlight the recent breakthroughs, pinpoint common grounds and discuss the bottlenecks and challenges in catalytic reduction of dinitrogen.

Challenges in reduction of dinitrogen by proton and electron transfer

Nitrogenase is a complex enzyme that catalyzes the reduction of dinitrogen to ammonia. Despite insight from structural and biochemical studies, its structure and mechanism await full characterization. An iron-molybdenum cofactor (FeMoco) is thought to be the site of dinitrogen reduction, but the identity of a central atom in this cofactor remains unknown. Fe Kβ x-ray emission spectroscopy (XES) of intact nitrogenase MoFe protein, isolated FeMoco, and the FeMoco-deficient nifB protein indicates that among the candidate atoms oxygen, nitrogen, and carbon, it is carbon that best fits the XES data. The experimental XES is supported by computational efforts, which show that oxidation and spin states do not affect the assignment of the central atom to C(4-). Identification of the central atom will drive further studies on its role in catalysis.

/pdf/x-ray-emission-spectroscopy-evidences-a-central-carbon-in-345zg912r8.pdf

X-ray Emission Spectroscopy Evidences a Central Carbon in the Nitrogenase Iron-Molybdenum Cofactor

The trace element molybdenum is essential for nearly all organisms and forms the catalytic centre of a large variety of enzymes such as nitrogenase, nitrate reductases, sulphite oxidase and xanthine oxidoreductases. Nature has developed two scaffolds holding molybdenum in place, the iron-molybdenum cofactor and pterin-based molybdenum cofactors. Despite the different structures and functions of molybdenum-dependent enzymes, there are important similarities, which we highlight here. The biosynthetic pathways leading to both types of cofactor have common mechanistic aspects relating to scaffold formation, metal activation and cofactor insertion into apoenzymes, and have served as an evolutionary 'toolbox' to mediate additional cellular functions in eukaryotic metabolism.

Molybdenum cofactors, enzymes and pathways

Vanadium nitrogenase not only reduces dinitrogen to ammonia but also reduces carbon monoxide to ethylene, ethane, and propane. The parallelism between the two reactions suggests a potential link in mechanism and evolution between the carbon and nitrogen cycles on Earth.

https://science.sciencemag.org/content/sci/329/5992/642.full.pdf

Vanadium Nitrogenase Reduces CO

The active site of nitrogenase, the M-cluster, is a metal-sulfur cluster containing a carbide at its core. Using radiolabeling experiments, we show that this carbide originates from the methyl group of S-adenosylmethionine (SAM) and that it is inserted into the M-cluster by the assembly protein NifB. Our SAM cleavage and deuterium substitution analyses suggest a similarity between the mechanism of carbon insertion by NifB and the proposed mechanism of RNA methylation by the radical SAM enzymes RlmN and Cfr, which involves methyl transfer from one SAM equivalent, followed by hydrogen atom abstraction from the methyl group by a 5′-deoxyadenosyl radical generated from a second SAM equivalent. This work is an initial step toward unraveling the importance of the interstitial carbide and providing insights into the nitrogenase mechanism.

/pdf/radical-sam-dependent-carbon-insertion-into-the-nitrogenase-3dsceq47v4.pdf

Radical SAM-dependent Carbon Insertion Into the Nitrogenase M-cluster

In a small-scale reaction, vanadium-dependent nitrogenase has previously been shown to catalyze reductive catenation of carbon monoxide (CO) to ethylene, ethane, propylene, and propane. Here, we report the identification of additional hydrocarbon products [α-butylene, n-butane, and methane (CH(4))] in a scaled-up reaction featuring 20 milligrams of vanadium-iron protein, the catalytic component of vanadium nitrogenase. Additionally, we show that the more common molybdenum-dependent nitrogenase can generate the same hydrocarbons from CO, although CH(4) was not detected. The identification of CO as a substrate for both molybdenum- and vanadium-nitrogenases strengthens the hypothesis that CO reduction is an evolutionary relic of the function of the nitrogenase family. Moreover, the comparison between the CO-reducing capacities of the two nitrogenases suggests that the identity of heterometal at the active cofactor site affects the efficiency and product distribution of this reaction.

/pdf/extending-the-carbon-chain-hydrocarbon-formation-catalyzed-1mmqctf208.pdf

Markus W. Ribbe

Papers

X-ray Emission Spectroscopy Evidences a Central Carbon in the Nitrogenase Iron-Molybdenum Cofactor

Molybdenum cofactors, enzymes and pathways

Vanadium Nitrogenase Reduces CO

Radical SAM-dependent Carbon Insertion Into the Nitrogenase M-cluster

Extending the Carbon Chain: Hydrocarbon Formation Catalyzed by Vanadium/Molybdenum Nitrogenases