@article{doi101021ja01639a090,
    author = "Huggins, Maurice L.",
    title = "Principles of Polymer Chemistry.",
    year = "1954",
    journal = "Journal of the American Chemical Society",
    url = "https://doi.org/10.1021/ja01639a090",
    doi = "10.1021/ja01639a090",
    openalex = "W2314659927"
}

@misc{goldberg1961chemistry9,
    author = "Goldberg, E. D",
    title = "Chemistry in the Oceans, in Sears, M., ed., Oceanography",
    year = "1961",
    howpublished = "Washington, D.C., American Association for the Advancement of Science, p. 583-597; Publication No. 67",
    note = "talkorigins\_source = {true}; raw\_reference = {Goldberg, E. D., 1961, Chemistry in the Oceans, in Sears, M., ed., Oceanography: Washington, D.C., American Association for the Advancement of Science, p. 583-597; Publication No. 67.}"
}

@book{calvin1969chemical3,
    author = "Calvin, M",
    title = "Chemical Evolution",
    year = "1969",
    publisher = "Oxford, Oxford University Press, 278 p",
    note = "talkorigins\_source = {true}; raw\_reference = {Calvin, M., 1969, Chemical Evolution: Oxford, Oxford University Press, 278 p.}"
}

@misc{dose1971the6,
    author = "Dose, K. and Zaki, L",
    title = "The peroxidatic and catalytic activity of hemoprotenoids",
    year = "1971",
    howpublished = "Z. Naturforsch, v. 26b, p. 144-148",
    note = "talkorigins\_source = {true}; raw\_reference = {Dose, K., and Zaki, L., 1971, The peroxidatic and catalytic activity of hemoprotenoids: Z. Naturforsch, v. 26b, p. 144-148.}"
}

@misc{fuller1974chemistry8,
    author = "Fuller, E. C",
    title = "Chemistry and Man's Environment",
    year = "1974",
    howpublished = "Boston, Houghton Mifflin",
    note = "talkorigins\_source = {true}; raw\_reference = {Fuller, E. C., 1974, Chemistry and Man's Environment: Boston, Houghton Mifflin.}"
}

@misc{schramm1974the11,
    author = "Schramm, D. N",
    title = "The Age of the Elements",
    year = "1974",
    howpublished = "Scientific American, v. 230, no. 1, p. 69-77",
    note = "talkorigins\_source = {true}; raw\_reference = {Schramm, D. N., 1974, The Age of the Elements: Scientific American, v. 230, no. 1, p. 69-77.}"
}

@book{aw1976chemical1,
    author = "Aw, S. E",
    title = "Chemical Evolution",
    year = "1976",
    publisher = "Singapore, University Education Press",
    note = "talkorigins\_source = {true}; raw\_reference = {Aw, S. E., 1976, Chemical Evolution: Singapore, University Education Press.}"
}

@misc{dickerson1976chemistry5,
    author = "Dickerson, R. E. and Geis, I",
    title = "Chemistry, Matter, and the Universe",
    year = "1976",
    howpublished = "Menlo Park, Ca., W.A. Benjamin",
    note = "talkorigins\_source = {true}; raw\_reference = {Dickerson, R. E., and Geis, I., 1976, Chemistry, Matter, and the Universe: Menlo Park, Ca., W.A. Benjamin.}"
}

@misc{dickerson1978chemical4,
    author = "Dickerson, R. E",
    title = "Chemical evolution and the origin of life",
    year = "1978",
    howpublished = "Scientific American, v. 239, no. 3, p. 70-108",
    note = "talkorigins\_source = {true}; raw\_reference = {Dickerson, R. E., 1978, Chemical evolution and the origin of life: Scientific American, v. 239, no. 3, p. 70-108.}"
}

@book{fox1980a7,
    author = "Fox, S. W. and Adachi, T. and Stillwell, W",
    title = "A quinone-assisted photoformation of energy-rich chemical bonds, in Veziroglu, T. N., ed., Solar Energy",
    year = "1980",
    publisher = "International Progress: New York, Pergamon Press, v. 2, p. 1056-1074",
    note = "talkorigins\_source = {true}; raw\_reference = {Fox, S. W., Adachi, T., and Stillwell, W., 1980, A quinone-assisted photoformation of energy-rich chemical bonds, in Veziroglu, T. N., ed., Solar Energy: International Progress: New York, Pergamon Press, v. 2, p. 1056-1074.}"
}

@misc{raloff1986is10,
    author = "Raloff, J",
    title = "Is There a Cosmic Chemistry of Life?",
    year = "1986",
    howpublished = "Science News, v. 130, p. 182",
    note = "talkorigins\_source = {true}; raw\_reference = {Raloff, J., 1986, Is There a Cosmic Chemistry of Life?: Science News, v. 130, p. 182.}"
}

@misc{brauman1988frontiers2,
    author = "Brauman, J. L",
    title = "Frontiers in Chemistry",
    year = "1988",
    howpublished = "Science, v. 240, no. 373",
    note = "talkorigins\_source = {true}; raw\_reference = {Brauman, J. L., 1988, Frontiers in Chemistry: Science, v. 240, no. 373.}"
}

@misc{waldrop1989catalytic12,
    author = "Waldrop, M. M",
    title = "Catalytic RNA Wins Chemistry Nobel",
    year = "1989",
    howpublished = "Science, v. 246, p. 325",
    note = "talkorigins\_source = {true}; raw\_reference = {Waldrop, M. M., 1989, Catalytic RNA Wins Chemistry Nobel: Science, v. 246, p. 325.}"
}

@article{doi105860choice273873,
    title = "Wonderful life: the Burgess Shale and the nature of history",
    year = "1990",
    journal = "Choice Reviews Online",
    abstract = "High in the Canadian Rockies is a small limestone quarry formed 530 million years ago called the Burgess Shale. It hold the remains of an ancient sea where dozens of strange creatures lived-a forgotten corner of evolution preserved in awesome detail. In this book Stephen Jay Gould explores what the Burgess Shale tells us about evolution and the nature of history.",
    url = "https://doi.org/10.5860/choice.27-3873",
    doi = "10.5860/choice.27-3873",
    openalex = "W1675572849"
}

@book{doi1010023527607439,
    author = "Lehn, J.-M.",
    title = "Supramolecular Chemistry",
    year = "1995",
    abstract = "Part 1 From molecular to supramolecular chemistry: concepts and language of supramolecular chemistry. Part 2 Molecular recognition: recognition, information, complementarity molecular receptors - design principles spherical recognition - cryptates of metal cations tetrahedral recognition by macrotricyclic cryptands recognition of ammonium ions and related substrates binding and recognition of neutral moelcules. Part 3 Anion co-ordination chemistry and the recognition of anionic substrates. Part 4 Coreceptor molecules and multiple recognition: dinuclear and polynuclear metal ion cryptates linear recognition of molecular length by ditopic coreceptors heterotopic coreceptors - cyclophane receptors, amphiphilic receptors, large molecular cage multiple recognition in metalloreceptors supramolecular dynamics. Part 5 Supramolecular reactivity and catalysis: catalysis by reactive macrocyclic cation receptor molecules catalysis by reactive anion receptor molecules catalysis with cyclophane type receptors supramolecular metallo-catalysis cocatalysis - catalysis of synthetic reactions biomolecular and abiotic catalysis. Part 6 Transport processes and carrier design: carrier-mediated transport cation-transport processes - cation carriers anion transport processes - anion carriers coupled transport processes electron-coupled transpoort in a redox gradient proton-coupled transport in a pH gradient light-coupled transport processes transfer via transmembrane channels. Part 7 From supermolecules to polymolecular assemblies: heterogeneous molecular recognition - supramolecular solid materials from endoreceptors to exoreceptors - molecular recognition at surfaces molecular and supramolecular morphogenesis supramolecular heterogeneous catalysis. Part 8 Molecular and supramolecular devices: molecular recognition, information and signals - semiochemistry supramolecular photochemistry - molecular and supramolecular photonic devices light conversion and energy transfer devices photosensitive molecular receptors photoinduced electron transfer in photoactive devices photoinduced reactions in supramolecular species non-linear optical properties of supramolecular species supramolecular effects in photochemical hole burning molecular and supramolecular electronic devices supramolecular electrochemistry electron conducting devices - molecular wires polarized molecular wires - rectifying devices modified and switchable molecular wires molecular magnetic devices molecular and supramolecular ionic devices tubular mesophases. (Part contents).",
    url = "https://doi.org/10.1002/3527607439",
    doi = "10.1002/3527607439",
    openalex = "W29179573"
}

@article{doi101096fasebj987768349,
    author = "Hanks, Steven K. and Hunter, Tony",
    title = "The eukaryotic protein kinase superfamily: kinase (catalytic) domain structure and classification 1",
    year = "1995",
    journal = "The FASEB Journal",
    abstract = "The eukaryotic protein kinases make up a large superfamily of homologous proteins. They are related by virtue of their kinase domains (also known as catalytic domains), which consist of ≈ 250‐300 amino acid residues. The kinase domains that define this group of enzymes contain 12 conserved subdomains that fold into a common catalytic core structure, as revealed by the 3‐dimensional structures of severed protein‐serine kinases. There are two main subdivisions within the superfamily: the protein‐serine/threonine kinases and the protein‐tyrosine kinases. A classification scheme can be founded on a kinase domain phylogeny, which reveals families of enzymes that have related substrate specificities and modes of regulation.—Hanks, S. K., Hunter, T. The eukaryotic protein kinase superfamily: kinase (catalytic) domain structure and classification. FASEB J. 9, 576‐596 (1995)",
    url = "https://doi.org/10.1096/fasebj.9.8.7768349",
    doi = "10.1096/fasebj.9.8.7768349",
    openalex = "W4295216797"
}

@article{doi105860choice332140,
    title = "Principles of polymer chemistry",
    year = "1995",
    journal = "Choice Reviews Online",
    url = "https://doi.org/10.5860/choice.33-2140",
    doi = "10.5860/choice.33-2140",
    openalex = "W1505352099"
}

@article{openalexw1875580551,
    author = "Hanks, Steven K. and Hunter, Tony",
    title = "Protein kinases 6. The eukaryotic protein kinase superfamily: kinase (catalytic) domain structure and classification.",
    year = "1995",
    journal = "PubMed",
    abstract = "The eukaryotic protein kinases make up a large superfamily of homologous proteins. They are related by virtue of their kinase domains (also known as catalytic domains), which consist of approximately 250-300 amino acid residues. The kinase domains that define this group of enzymes contain 12 conserved subdomains that fold into a common catalytic core structure, as revealed by the 3-dimensional structures of several protein-serine kinases. There are two main subdivisions within the superfamily: the protein-serine/threonine kinases and the protein-tyrosine kinases. A classification scheme can be founded on a kinase domain phylogeny, which reveals families of enzymes that have related substrate specificities and modes of regulation.",
    openalex = "W1875580551"
}

@article{doi105860choice354499,
    author = "Adamson, Arthur W.",
    title = "Physical chemistry of surfaces",
    year = "1998",
    journal = "Choice Reviews Online",
    abstract = "Capillarity. The Nature and Thermodynamics of Liquid Interfaces. Surface Films on Liquid Substrates. Electrical Aspects of Surface Chemistry. Long--Range Forces. Surfaces of Solids. Surfaces of Solids: Microscopy and Spectroscopy. The Formation of a New Phase--Nucleation and Crystal Growth. The Solid--Liquid Interface--Contact Angle. The Solid--Liquid Interface--Adsorption from Solution. Frication, Lubrication, and Adhesion. Wetting, Flotation, and Detergency. Emulsions, Foams, and Aerosols. Macromolecular Surface Films, Charged Films, and Langmuir--Blodgett Layers. The Solid--Gas Interface--General Considerations. Adsorption of Gases and Vapors on Solids. Chemisorption and Catalysis. Index.",
    url = "https://doi.org/10.5860/choice.35-4499",
    doi = "10.5860/choice.35-4499",
    openalex = "W2062070676"
}

@article{doi105860choice370940,
    title = "Advanced inorganic chemistry",
    year = "1999",
    journal = "Choice Reviews Online",
    abstract = "For more than a quarter century, Cotton and Wilkinson's Advanced Inorganic Chemistry has been the source that students and professional chemists have turned to for the background needed to understand current research literature in inorganic chemistry and aspects of organometallic chemistry. Like its predecessors, this updated Sixth Edition is organized around the periodic table of elements and provides a systematic treatment of the chemistry of all chemical elements and their compounds. It incorporates important recent developments with an emphasis on advances in the interpretation of structure, bonding, and reactivity.From the reviews of the Fifth Edition:* The first place to go when seeking general information about the chemistry of a particular element, especially when up-to-date, authoritative information is desired. -Journal of the American Chemical Society.* Every student with a serious interest in inorganic chemistry should have [this book]. -Journal of Chemical Education.* A mine of information... an invaluable guide. -Nature.* The standard by which all other inorganic chemistry books are judged.-Nouveau Journal de Chimie.* A masterly overview of the chemistry of the elements.-The Times of London Higher Education Supplement.* A bonanza of information on important results and developments which could otherwise easily be overlooked in the general deluge of publications. -Angewandte Chemie.",
    url = "https://doi.org/10.5860/choice.37-0940",
    doi = "10.5860/choice.37-0940",
    openalex = "W1523417784"
}

@article{doi101002jcc1056,
    author = "te Velde, G. and Bickelhaupt, F. Matthias and Baerends, Evert Jan and Guerra, Célia Fonseca and van Gisbergen, S. J. A. and Snijders, J. G. and Ziegler, Tom",
    title = "Chemistry with ADF",
    year = "2001",
    journal = "Journal of Computational Chemistry",
    abstract = "Abstract We present the theoretical and technical foundations of the Amsterdam Density Functional (ADF) program with a survey of the characteristics of the code (numerical integration, density fitting for the Coulomb potential, and STO basis functions). Recent developments enhance the efficiency of ADF (e.g., parallelization, near order‐N scaling, QM/MM) and its functionality (e.g., NMR chemical shifts, COSMO solvent effects, ZORA relativistic method, excitation energies, frequency‐dependent (hyper)polarizabilities, atomic VDD charges). In the Applications section we discuss the physical model of the electronic structure and the chemical bond, i.e., the Kohn–Sham molecular orbital (MO) theory, and illustrate the power of the Kohn–Sham MO model in conjunction with the ADF‐typical fragment approach to quantitatively understand and predict chemical phenomena. We review the “Activation‐strain TS interaction” (ATS) model of chemical reactivity as a conceptual framework for understanding how activation barriers of various types of (competing) reaction mechanisms arise and how they may be controlled, for example, in organic chemistry or homogeneous catalysis. Finally, we include a brief discussion of exemplary applications in the field of biochemistry (structure and bonding of DNA) and of time‐dependent density functional theory (TDDFT) to indicate how this development further reinforces the ADF tools for the analysis of chemical phenomena. © 2001 John Wiley \& Sons, Inc. J Comput Chem 22: 931–967, 2001",
    url = "https://doi.org/10.1002/jcc.1056",
    doi = "10.1002/jcc.1056",
    openalex = "W2150345533",
    references = "doi101021cr00088a005, doi101039p29930000799, doi1010631464304, doi1010631464913, doi101103physrev140a1133, doi101103physreva383098, doi101103physrevb338822, doi101103physrevb37785, doi101103physrevb466671, doi101103physrevb4849782, doi101139p80159"
}

@article{doi101021cr0307143,
    author = "Denisov, Ilia G. and Makris, Thomas M. and Sligar, Stephen G. and Schlichting, Ilme",
    title = "Structure and Chemistry of Cytochrome P450",
    year = "2005",
    journal = "Chemical Reviews",
    abstract = "The title to a seminar presentation by I. C. Gunsalus in 1973 was Oxygen: An essential toxin, referring to the complex \nrole that atmospheric dioxygen has in biology. The relatively simple function as terminal oxidant for aerobic life was dramatically \naugmented by Osamu Hayaishi with his identification of an enzyme that catalyzes the conversion of catechol to muconic acid by \noxidative cleavage.1 He named this biological catalyst pyrocatechase, which proved to be the landmark discovery of an enzyme \nthat incorporated atmospheric dioxygen into the carbon chain of the substrate, thereby initiating cleavage of the benzene ring. \nThis review of the oxygenase cytochrome P450 is dedicated to Dr. Hayaishi and his pioneering discovery in what is now the 50th anniversary of his work!\n\nWe now realize that Nature has found many ways to utilize atmospheric dioxygen to functionalize molecules through the use of a diverse \nset of cofactors. Flavin, non−heme iron, copper, and metalloporphyrin complexes have all been conscripted to metabolize atmospheric \ndioxygen in an oxygenase catalytic cycle, resulting in the incorporation of one or both oxygen atoms into a substrate. This review focuses \non one of the heme−containing classes, termed cytochrome P450s and abbreviated CYP. Although but one member in the large group of \noxygenases, the cytochrome P450s play a variety of critical roles in biology.\n\nMany members of the cytochrome P450 superfamily of hemoproteins are currently known, and the numbers continue to grow as more genomes \nare sequenced. There are almost 4000 identified P450 genes at the date of this writing, and they are collected and annotated in a variety \nof web sites, such as that maintained by Nelson (http://drnelson. utmem.edu/CytochromeP450.html). The cytochrome P450s have been found in \nall branches of the tree of life that catalogs the diversity of life forms. In the broadest terms, there are two main functional roles for \nthese oxygenases. One is the metabolism of xenobiotics (compounds exogenous to the organism) as a protective role of degradation or provision \nof polar handles for solubilization in preparation for excretion. A second broad functional role is in the biosynthesis of critical signaling \nmolecules used for control of development and homeostasis. In mammalian tissues the P450s play these roles through the metabolism of drugs \nand xenobiotics and the synthesis of steroid hormones and fat−soluble vitamin metabolism and the conversion of polyunsaturated fatty \nacids to biologically active molecules, respectively. Similar roles are fulfilled in plants (hormone biosynthesis and herbicide degradation) \nand insects (control of development via hormone biosynthesis or provision of insecticide resistance). For instance, plants have an unusually \nlarge number of P450 genes. A reason is their sessile nature: for example, plants defend themselves through breakdown of herbicides by \ncatalyzing the synthesis of a large number of secondary metabolites or by synthesizing defense molecules such as DIMBOA.2,3 In addition, \nthe biosynthesis of critical metabolic regulators is also often carried out by the cytochrome P450s.\n\nThe important metabolic role together with the unique chemistry and physical properties of the cytochrome P450s provide a strong attraction \nfor scientists in many disciplines. Relevance to human health was the initial focus of pharmacologists and toxicologists. The role of metal \ncenters and their associated unique spectral properties in the cytochrome P450s is a magnet for bioinorganic chemists and biophysicists. The \ndifficult conversion of unactivated hydrocarbons attracted the bioorganic chemist. With the genome revolution and insights into the complex \nprocess of transcriptional and translational regulation, biochemists and molecular biologists found exciting problems in the study of CYPs.\n\nA continuing challenge is to understand how the diverse set of substrate specificities and metabolic transformations are determined by the \nprecise nature of the heme−iron oxygen and protein structure. The structure and electronic configuration of the active oxygen \nintermediates which serve as efficient catalysts remains an area of active research. Complicating this richness in metabolic potential \nis the importance of genetic differences, including single nucleotide polymorphisms, which can alter the physiological responses of the \ncytochrome P450s. Thus, over the past five−plus decades one has seen the evolution from a whole−organ and animal pharmacology \napproach to a quest for the molecular details necessary for precise understanding of structure and function of the P450 systems in \nmaintaining cellular homeostasis. The P450s are now recognized to occupy a great variety of phylogenetically distributed isoform \nactivities, and these variations in metabolic profile and substrate specificity are ultimately dictated by the bioinorganic chemistry \nof heme iron and oxygen as controlled by the protein environment.\n\nWith the elucidation of precise structures for many P450 hemoproteins as well as the application of varied biochemical and biophysical \nmethodologies, this diverse class of oxygenases is beginning to yield its secrets. Much remains to be learned, however, as many of the \nfundamental chemical entities and catalytic details, though perhaps described in textbooks, are in fact still poorly understood. The \nfocus of this review is to place the current knowledge base of cytochrome P450 structure−function in context with the general \naspects of metalloenzyme function. In 2006 Dr. Hayaishi, the founder of this broad field of oxygen metabolism, will celebrate an \nimportant birthday. Hopefully, in reading this review, he will be struck with the outstanding progress that has been realized with \nthis one particular oxygenase and at the same time perhaps provide some important suggestions as to pathways for solving the remaining problems.4\n\nCytochrome P450 has benefited from the attention of inorganic, organic, and physical chemists since its discovery due to its unique \nspectral properties as well as its ability to efficiently catalyze a variety of difficult biotransformations. With the discovery of \nP450 involvement in steroid biosynthesis in the 1970s, joined with its central function in drug metabolism, with its role in a variety \nof other pharmaceutical applications, P450 became one of the most intensively investigated biochemical systems. Multiple monographs, \nprinted conference proceedings, and thematic books have been published as well as special Methods in Enzymology volumes, only a few \nof which can be referenced here.5−12\n\nThe cytochrome P450s became most known for their efficiency in hydroxylation of unactivated alkanes as only a select few oxygenases \npossess the requisite active oxygen state. With equal efficacy, P450s can carry out a wide variety of biotransformations. The list \nin ref 13 includes more than 20 different chemical reactions. Some more unusual reactions catalyzed by P450 were recently reviewed by Guengerich.14\n\nThe mechanism of P450 is a complex cascade of individual steps involving the interaction of protein redox partners and consumption of \nreducing equivalents, most commonly in the form of NAD(P)H. It is somewhat humbling that the earliest versions of the enzymatic cycle \npublished over 30 years ago had much of the important steps characterized by physical and chemical methods.15 Continual refinement has \nled to more detailed versions and the direct observation and structural characterization of new adducts of iron and oxygen. The current \nversion contains eight intermediates, including highly transient caged radical pairs, and has been reviewed from various perspectives.11,12,16−19\n\nWhile the basic concepts central to P450 catalysis were appreciated by early 1970, notable progress in the detailed understanding of these \nmechanisms has been made in the past decade. This has been possible due to the accumulation of exciting data generated through application \nof a wide set of new methodologies, including systematic directed mutagenesis, high−resolution X−ray crystal structure \ndetermination, multiparametric spectroscopic characterization of intermediates, isolation of critical steps using cryogenic or fast \nkinetic techniques, and many excellent quantum chemical and molecular dynamics computational studies. The current view of the oxygen \nactivation mechanisms, catalyzed by metal centers in heme enzymes (as well as in non−heme enzymes, which lie outside the scope \nof this review), ensures one with a much better opportunity to see the common mechanistic picture than was possible earlier.20 \nSuccessful mechanistic studies of other heme enzymes which use different forms of so−called 'active oxygen \nintermediates', such as peroxidases,21,22 heme oxygenases (HO),23−25 catalases,26 nitric oxide synthases \n(NOS),27,28 peroxygenases,29,30 provide a vision of a highly diverse cofactor. Mechanistic insight from each of these various \nsystems has provided important complementary insight into cytochrome P450 mechanism. A fundamental question remaining is how the \nprotein controls efficient performance of such different functions using similar highly reactive heme−oxygen complexes. The \ncomparison of similar reactive intermediates in different enzymes helps to distinguish between the essential features of each of the \nenzymes and so provides additional clues to the revelation of the active role of the protein in heme−enzyme catalysis. The \nrecent progress in isolation and cryogenic stabilization of some of these intermediates makes possible direct spectroscopic and \nstructural studies of this type.\n\nAn exhaustive review of all achievements in oxygen activation chemistry is clearly difficult, even if the field is limited to \nthe processes directly relevant to P450 catalysis. Discussion of the P450 cat",
    url = "https://doi.org/10.1021/cr0307143",
    doi = "10.1021/cr0307143",
    openalex = "W2077621515",
    references = "doi101016000926149500905j, doi1010160022328x88831036, doi101016c20090227140, doi101016s0021925820822443, doi101016s0021925820822455, doi101021ar50088a003, doi101021cr020628n, doi101021cr9500500, doi101146annurevbi47070178001343, openalexw2561553333"
}

@article{doi101098rstb20061904,
    author = "Wächtershäuser, Günter",
    title = "From volcanic origins of chemoautotrophic life to Bacteria, Archaea and Eukarya",
    year = "2006",
    journal = "Philosophical Transactions of the Royal Society B Biological Sciences",
    abstract = "The theory of a chemoautotrophic origin of life in a volcanic iron-sulphur world postulates a pioneer organism at sites of reducing volcanic exhalations. The pioneer organism is characterized by a composite structure with an inorganic substructure and an organic superstructure. Within the surfaces of the inorganic substructure iron, cobalt, nickel and other transition metal centres with sulphido, carbonyl and other ligands were catalytically active and promoted the growth of the organic superstructure through carbon fixation, driven by the reducing potential of the volcanic exhalations. This pioneer metabolism was reproductive by an autocatalytic feedback mechanism. Some organic products served as ligands for activating catalytic metal centres whence they arose. The unitary structure-function relationship of the pioneer organism later gave rise to two major strands of evolution: cellularization and emergence of the genetic machinery. This early phase of evolution ended with segregation of the domains Bacteria, Archaea and Eukarya from a rapidly evolving population of pre-cells. Thus, life started with an initial, direct, deterministic chemical mechanism of evolution giving rise to a later, indirect, stochastic, genetic mechanism of evolution and the upward evolution of life by increase of complexity is grounded ultimately in the synthetic redox chemistry of the pioneer organism.",
    url = "https://doi.org/10.1098/rstb.2006.1904",
    doi = "10.1098/rstb.2006.1904",
    openalex = "W2146529099",
    references = "doi101038191144a0, doi10103832096, doi10103835051550, doi101073pnas87124576, doi101093oso97801985029440010001, doi101111j155856461995tb04464x, doi101128mr5122212711987, doi1023072218271, doi1023072260026, doi1023072551371"
}

@article{doi101039b917103g,
    author = "Dreyer, Daniel R. and Park, Sungjin and Bielawski, Christopher W. and Ruoff, Rodney S.",
    title = "The chemistry of graphene oxide",
    year = "2009",
    journal = "Chemical Society Reviews",
    abstract = "The chemistry of graphene oxide is discussed in this critical review. Particular emphasis is directed toward the synthesis of graphene oxide, as well as its structure. Graphene oxide as a substrate for a variety of chemical transformations, including its reduction to graphene-like materials, is also discussed. This review will be of value to synthetic chemists interested in this emerging field of materials science, as well as those investigating applications of graphene who would find a more thorough treatment of the chemistry of graphene oxide useful in understanding the scope and limitations of current approaches which utilize this material (91 references).",
    url = "https://doi.org/10.1039/b917103g",
    doi = "10.1039/b917103g",
    openalex = "W2135479172",
    references = "doi101016jcarbon200702034, doi101021ja01269a023, doi101021ja01539a017, doi101021ja803688x, doi101021nl071822y, doi101038nature04969, doi101038nmat1849, doi101038nnano200958, doi101126science1102896, doi105860choice370940"
}

@article{doi101021ja405051f,
    author = "Reetz, Manfred T.",
    title = "Biocatalysis in Organic Chemistry and Biotechnology: Past, Present, and Future",
    year = "2013",
    journal = "Journal of the American Chemical Society",
    abstract = "Enzymes as catalysts in synthetic organic chemistry gained importance in the latter half of the 20th century, but nevertheless suffered from two major limitations. First, many enzymes were not accessible in large enough quantities for practical applications. The advent of recombinant DNA technology changed this dramatically in the late 1970s. Second, many enzymes showed a narrow substrate scope, often poor stereo- and/or regioselectivity and/or insufficient stability under operating conditions. With the development of directed evolution beginning in the 1990s and continuing to the present day, all of these problems can be addressed and generally solved. The present Perspective focuses on these and other developments which have popularized enzymes as part of the toolkit of synthetic organic chemists and biotechnologists. Included is a discussion of the scope and limitation of cascade reactions using enzyme mixtures in vitro and of metabolic engineering of pathways in cells as factories for the production of simple compounds such as biofuels and complex natural products. Future trends and problems are also highlighted, as is the discussion concerning biocatalysis versus nonbiological catalysis in synthetic organic chemistry. This Perspective does not constitute a comprehensive review, and therefore the author apologizes to those researchers whose work is not specifically treated here.",
    url = "https://doi.org/10.1021/ja405051f",
    doi = "10.1021/ja405051f",
    openalex = "W1976236461",
    references = "doi101146annurevbiochem030409143718"
}

@article{doi101038nmat3700,
    author = "Voiry, Damien and Yamaguchi, Hisato and Li, Junwen and Silva, Rafael and Alves, Diego C. B. and Fujita, Takeshi and Chen, Mingwei and Asefa, Tewodros and Shenoy, Vivek B. and Eda, Goki and Chhowalla, Manish",
    title = "Enhanced catalytic activity in strained chemically exfoliated WS2 nanosheets for hydrogen evolution",
    year = "2013",
    journal = "Nature Materials",
    url = "https://doi.org/10.1038/nmat3700",
    doi = "10.1038/nmat3700",
    openalex = "W2086270926"
}

@article{doi101073pnas1218525110,
    author = "McFall‐Ngai, Margaret and Hadfield, Michael G.‏ and Bosch, Thomas C. G. and Carey, Hannah V. and Domazet‐Lošo, Tomislav and Douglas, Angela E. and Dubilier, Nicole and Eberl, Gérard and Fukami, Tadashi and Gilbert, Scott F. and Hentschel, Ute and King, Nicole and Kjelleberg, Staffan and Knoll, Andrew H. and Kremer, Natacha and Mazmanian, Sarkis K. and Metcalf, Jessica L. and Nealson, Kenneth H. and Pierce, Naomi E. and Rawls, John F. and Reid, Ann and Ruby, Edward G. and Rumpho, Mary E. and Sanders, Jon G. and Tautz, Diethard and Wernegreen, Jennifer J.",
    title = "Animals in a bacterial world, a new imperative for the life sciences",
    year = "2013",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = "In the last two decades, the widespread application of genetic and genomic approaches has revealed a bacterial world astonishing in its ubiquity and diversity. This review examines how a growing knowledge of the vast range of animal-bacterial interactions, whether in shared ecosystems or intimate symbioses, is fundamentally altering our understanding of animal biology. Specifically, we highlight recent technological and intellectual advances that have changed our thinking about five questions: how have bacteria facilitated the origin and evolution of animals; how do animals and bacteria affect each other's genomes; how does normal animal development depend on bacterial partners; how is homeostasis maintained between animals and their symbionts; and how can ecological approaches deepen our understanding of the multiple levels of animal-bacterial interaction. As answers to these fundamental questions emerge, all biologists will be challenged to broaden their appreciation of these interactions and to include investigations of the relationships between and among bacteria and their animal partners as we seek a better understanding of the natural world.",
    url = "https://doi.org/10.1073/pnas.1218525110",
    doi = "10.1073/pnas.1218525110",
    openalex = "W1964306176",
    references = "doi1010384441022a, doi101038nature09922, doi101038nature11053, doi101038nature11234, doi101038nature11550, doi101038nri2515, doi101073pnas0407076101, doi101073pnas1002601107, doi101073pnas87124576, doi101126science1223813, doi101146annurevecolsys36102403114735, doi101146annurevmarine010908163834, doi1023073515363"
}

@article{doi101126science1230444,
    author = "Furukawa, Hiroyasu and Cordova, Kyle E. and O’Keeffe, M. and Yaghi, Omar M.",
    title = "The Chemistry and Applications of Metal-Organic Frameworks",
    year = "2013",
    journal = "Science",
    abstract = "Crystalline metal-organic frameworks (MOFs) are formed by reticular synthesis, which creates strong bonds between inorganic and organic units. Careful selection of MOF constituents can yield crystals of ultrahigh porosity and high thermal and chemical stability. These characteristics allow the interior of MOFs to be chemically altered for use in gas separation, gas storage, and catalysis, among other applications. The precision commonly exercised in their chemical modification and the ability to expand their metrics without changing the underlying topology have not been achieved with other solids. MOFs whose chemical composition and shape of building units can be multiply varied within a particular structure already exist and may lead to materials that offer a synergistic combination of properties.",
    url = "https://doi.org/10.1126/science.1230444",
    doi = "10.1126/science.1230444",
    openalex = "W2141939342",
    references = "doi101021cr300014x, doi101021ja8057953, doi101038229453c0, doi10103846248, doi101038nature01650, doi101039b807080f, doi101073pnas0602439103, doi101126science1067208, doi101126science1116275, doi101126science28354051148"
}

@book{doi101201b17118,
    author = "Haynes, W.M.",
    title = "CRC Handbook of Chemistry and Physics",
    year = "2014",
    abstract = "Proudly serving the scientific community for over a century, this 95th edition of the CRC Handbook of Chemistry and Physics is an update of a classic reference, mirroring the growth and direction of science. This venerable work continues to be the most accessed and respected scientific reference in the world. An authoritative resource consisting of",
    url = "https://doi.org/10.1201/b17118",
    doi = "10.1201/b17118",
    openalex = "W2132905138"
}

@article{doi101016jjmb201511010,
    author = "Furnham, Nicholas and Dawson, Natalie L. and Rahman, Syed Asad and Thornton, Janet M. and Orengo, Christine",
    title = "Large-Scale Analysis Exploring Evolution of Catalytic Machineries and Mechanisms in Enzyme Superfamilies",
    year = "2015",
    journal = "Journal of Molecular Biology",
    abstract = "Enzymes, as biological catalysts, form the basis of all forms of life. How these proteins have evolved their functions remains a fundamental question in biology. Over 100 years of detailed biochemistry studies, combined with the large volumes of sequence and protein structural data now available, means that we are able to perform large-scale analyses to address this question. Using a range of computational tools and resources, we have compiled information on all experimentally annotated changes in enzyme function within 379 structurally defined protein domain superfamilies, linking the changes observed in functions during evolution to changes in reaction chemistry. Many superfamilies show changes in function at some level, although one function often dominates one superfamily. We use quantitative measures of changes in reaction chemistry to reveal the various types of chemical changes occurring during evolution and to exemplify these by detailed examples. Additionally, we use structural information of the enzymes active site to examine how different superfamilies have changed their catalytic machinery during evolution. Some superfamilies have changed the reactions they perform without changing catalytic machinery. In others, large changes of enzyme function, in terms of both overall chemistry and substrate specificity, have been brought about by significant changes in catalytic machinery. Interestingly, in some superfamilies, relatives perform similar functions but with different catalytic machineries. This analysis highlights characteristics of functional evolution across a wide range of superfamilies, providing insights that will be useful in predicting the function of uncharacterised sequences and the design of new synthetic enzymes.",
    url = "https://doi.org/10.1016/j.jmb.2015.11.010",
    doi = "10.1016/j.jmb.2015.11.010",
    openalex = "W2204659374",
    references = "doi101002bip360221211, doi101006jmbi20014513, doi1010160022283689900843, doi101038nrg3744, doi101093bioinformaticsbtg412, doi101093nargkh028, doi101093nargkt1140, doi101093nargku947, doi101126science1123348, doi101146annurevbiochem030409143718"
}

@article{doi101038nmicrobiol201648,
    author = "Hug, Laura and Baker, Brett J. and Anantharaman, Karthik and Brown, Christopher T. and Probst, Alexander J. and Castelle, Cindy J. and Butterfield, Cristina N. and Hernsdorf, Alex W and Amano, Yuki and Ise, Kotaro and Suzuki, Yohey and Dudek, Natasha K. and Relman, David A. and Finstad, Kari and Amundson, Ronald and Thomas, Brian C. and Banfield, Jillian F.",
    title = "A new view of the tree of life",
    year = "2016",
    journal = "Nature Microbiology",
    abstract = "The tree of life is one of the most important organizing principles in biology(1). Gene surveys suggest the existence of an enormous number of branches(2), but even an approximation of the full scale of the tree has remained elusive. Recent depictions of the tree of life have focused either on the nature of deep evolutionary relationships(3-5) or on the known, well-classified diversity of life with an emphasis on eukaryotes(6). These approaches overlook the dramatic change in our understanding of life's diversity resulting from genomic sampling of previously unexamined environments. New methods to generate genome sequences illuminate the identity of organisms and their metabolic capacities, placing them in community and ecosystem contexts(7,8). Here, we use new genomic data from over 1,000 uncultivated and little known organisms, together with published sequences, to infer a dramatically expanded version of the tree of life, with Bacteria, Archaea and Eukarya included. The depiction is both a global overview and a snapshot of the diversity within each major lineage. The results reveal the dominance of bacterial diversification and underline the importance of organisms lacking isolated representatives, with substantial evolution concentrated in a major radiation of such organisms. This tree highlights major lineages currently underrepresented in biogeochemical models and identifies radiations that are probably important for future evolutionary analyses.",
    url = "https://doi.org/10.1038/nmicrobiol.2016.48",
    doi = "10.1038/nmicrobiol.2016.48",
    openalex = "W2315521535",
    references = "doi101038nature12352, doi101038nature14447, doi101038nature14486, doi101038nrmicro3330, doi101073pnas82206955, doi101073pnas87124576, doi101093bioinformaticsbtl446, doi101093bioinformaticsbts252, doi101093nargkh340, doi101093nargkm864, doi101093nargks808, doi101109gce20105676129, doi101126science7542800"
}

@article{doi101126scienceaah6219,
    author = "Kan, S. B. Jennifer and Lewis, Russell D. and Chen, Kai and Arnold, Frances H.",
    title = "Directed evolution of cytochrome c for carbon–silicon bond formation: Bringing silicon to life",
    year = "2016",
    journal = "Science",
    abstract = "Enzymes that catalyze carbon-silicon bond formation are unknown in nature, despite the natural abundance of both elements. Such enzymes would expand the catalytic repertoire of biology, enabling living systems to access chemical space previously only open to synthetic chemistry. We have discovered that heme proteins catalyze the formation of organosilicon compounds under physiological conditions via carbene insertion into silicon-hydrogen bonds. The reaction proceeds both in vitro and in vivo, accommodating a broad range of substrates with high chemo- and enantioselectivity. Using directed evolution, we enhanced the catalytic function of cytochrome c from Rhodothermus marinus to achieve more than 15-fold higher turnover than state-of-the-art synthetic catalysts. This carbon-silicon bond-forming biocatalyst offers an environmentally friendly and highly efficient route to producing enantiopure organosilicon molecules.",
    url = "https://doi.org/10.1126/science.aah6219",
    doi = "10.1126/science.aah6219",
    openalex = "W2554528613",
    references = "doi101146annurevbiochem030409143718"
}

@book{doi1012019781315380476,
    author = "Haynes, William M.",
    title = "CRC Handbook of Chemistry and Physics",
    year = "2016",
    abstract = "Proudly serving the scientific community for over a century, this 97th edition of the CRC Handbook of Chemistry and Physics is an update of a classic reference, mirroring the growth and direction of science. This venerable work continues to be the most accessed and respected scientific reference in the world. An authoritative resource consisting of tables of data and current international recommendations on nomenclature, symbols, and units, its usefulness spans not only the physical sciences but also related areas of biology, geology, and environmental science. The 97th edition of the Handbook includes 20 new or updated tables along with other updates and expansions. It is now also available as an eBook. This reference puts physical property data and mathematical formulas used in labs and classrooms every day within easy reach.",
    url = "https://doi.org/10.1201/9781315380476",
    doi = "10.1201/9781315380476",
    openalex = "W2964344211"
}

@article{doi101002anie201708408,
    author = "Arnold, Frances H.",
    title = "Directed Evolution: Bringing New Chemistry to Life",
    year = "2017",
    journal = "Angewandte Chemie International Edition",
    abstract = "Tailor-made: Discussed herein is the ability to adapt biology's mechanisms for innovation and optimization to solving problems in chemistry and engineering. The evolution of nature's enzymes can lead to the discovery of new reactivity, transformations not known in biology, and reactivity inaccessible by small-molecule catalysts.",
    url = "https://doi.org/10.1002/anie.201708408",
    doi = "10.1002/anie.201708408",
    openalex = "W2767044445"
}

@article{doi101016jgsf201707007,
    author = "Kitadai, N. and Maruyama, S.",
    title = "Origins of building blocks of life: A review",
    year = "2017",
    journal = "Geoscience Frontiers",
    abstract = "Abstract How and where did life on Earth originate? To date, various environments have been proposed as plausible sites for the origin of life. However, discussions have focused on a limited stage of chemical evolution, or emergence of a specific chemical function of proto-biological systems. It remains unclear what geochemical situations could drive all the stages of chemical evolution, ranging from condensation of simple inorganic compounds to the emergence of self-sustaining systems that were evolvable into modern biological ones. In this review, we summarize reported experimental and theoretical findings for prebiotic chemistry relevant to this topic, including availability of biologically essential elements (N and P) on the Hadean Earth, abiotic synthesis of life's building blocks (amino acids, peptides, ribose, nucleobases, fatty acids, nucleotides, and oligonucleotides), their polymerizations to bio-macromolecules (peptides and oligonucleotides), and emergence of biological functions of replication and compartmentalization. It is indicated from the overviews that completion of the chemical evolution requires at least eight reaction conditions of (1) reductive gas phase, (2) alkaline pH, (3) freezing temperature, (4) fresh water, (5) dry/dry-wet cycle, (6) coupling with high energy reactions, (7) heating-cooling cycle in water, and (8) extraterrestrial input of life's building blocks and reactive nutrients. The necessity of these mutually exclusive conditions clearly indicates that life's origin did not occur at a single setting; rather, it required highly diverse and dynamic environments that were connected with each other to allow intra-transportation of reaction products and reactants through fluid circulation. Future experimental research that mimics the conditions of the proposed model are expected to provide further constraints on the processes and mechanisms for the origin of life.",
    url = "https://doi.org/10.1016/j.gsf.2017.07.007",
    doi = "10.1016/J.GSF.2017.07.007",
    is_oa = "true",
    number = "4",
    pages = "1117-1153",
    semanticscholar_citation_count = "349",
    semanticscholar_id = "b0926c65e24d5418043226bdf1055eaf2178a79e",
    volume = "9"
}

@article{doi1010800026897620171333644,
    author = "Mardirossian, Narbe and Head‐Gordon, Martin",
    title = "Thirty years of density functional theory in computational chemistry: an overview and extensive assessment of 200 density functionals",
    year = "2017",
    journal = "Molecular Physics",
    abstract = "In the past 30 years, Kohn–Sham density functional theory has emerged as the most popular electronic structuremethod in computational chemistry. To assess the ever-increasing number of approximate exchange-correlation functionals, this review benchmarks a total of 200 density functionals on a molecular database (MGCDB84) of nearly 5000 data points. The database employed, provided as Supplemental Data, is comprised of 84 data-sets and contains non-covalent interactions, isomerisation energies, thermochemistry, and barrier heights. In addition, the evolution of nonempirical and semi-empirical density functional design is reviewed, and guidelines are provided for the proper and effective use of density functionals. The most promising functional considered is ωB97M-V, a range-separated hybrid meta-GGA with VV10 nonlocal correlation, designed using a combinatorial approach. From the local GGAs, B97-D3, revPBE-D3, and BLYP-D3 are recommended, while from the local meta-GGAs, B97M-rV is the leading choice, followed by MS1-D3 and M06-LD3. The best hybrid GGAs are ωB97X-V, ωB97X-D3, and ωB97X-D, while useful hybrid meta-GGAs (besides ωB97M-V) include ωM05-D, M06-2X-D3, and MN15. Ultimately, today’s state-of-the-art functionals are close to achieving the level of accuracy desired for a broad range of chemical applications, and the principal remaining limitations are associated with systems that exhibit significant selfinteraction/ delocalisation errors and/or strong correlation effects.",
    url = "https://doi.org/10.1080/00268976.2017.1333644",
    doi = "10.1080/00268976.2017.1333644",
    openalex = "W2639728117",
    references = "doi101007s002140070310x, doi10106312370993, doi101080002689762014952696"
}

@article{doi101021acschemrev8b00039,
    author = "Davidi, Dan and Longo, Liam M. and Jabłońska, Jagoda and Milo, Ron and Tawfik, Dan S.",
    title = "A Bird’s-Eye View of Enzyme Evolution: Chemical, Physicochemical, and Physiological Considerations",
    year = "2018",
    journal = "Chemical Reviews",
    abstract = {Enzymes catalyze a vast range of reactions. Their catalytic performances, mechanisms, global folds, and active-site architectures are also highly diverse, suggesting that enzymes are shaped by an entire range of physiological demands and evolutionary constraints, as well as by chemical and physicochemical constraints. We have attempted to identify signatures of these shaping demands and constraints. To this end, we describe a bird's-eye view of the enzyme space from two angles: evolution and chemistry. We examine various chemical reaction parameters that may have shaped the catalytic performances and active-site architectures of enzymes. We test and weigh these considerations against physiological and evolutionary factors. Although the catalytic properties of the "average" enzyme correlate with cellular metabolic demands and enzyme expression levels, at the level of individual enzymes, a multitude of physiological demands and constraints, combined with the coincidental nature of evolutionary processes, result in a complex picture. Indeed, neither reaction type (a chemical constraint) nor evolutionary origin alone can explain enzyme rates. Nevertheless, chemical constraints are apparent in the convergence of active-site architectures in independently evolved enzymes, although significant variations within an architecture are common.},
    url = "https://doi.org/10.1021/acs.chemrev.8b00039",
    doi = "10.1021/acs.chemrev.8b00039",
    openalex = "W2888107191",
    references = "doi101016jjmb201511010, doi101016jsbi201711007, doi101016s0969212601002209, doi101021bi2002289, doi101038msb201165, doi101038nbt1614, doi101038nchembio186, doi101038s4158901800432, doi101042bj1030514, doi101093nar27129, doi101093nar28127, doi101093nargkh081, doi101146annurevbiochem73011303074021"
}

@article{doi101126scienceaam5979,
    author = "Blount, Zachary D. and Lenski, Richard E. and Losos, Jonathan B.",
    title = "Contingency and determinism in evolution: Replaying life’s tape",
    year = "2018",
    journal = "Science",
    abstract = {Historical processes display some degree of "contingency," meaning their outcomes are sensitive to seemingly inconsequential events that can fundamentally change the future. Contingency is what makes historical outcomes unpredictable. Unlike many other natural phenomena, evolution is a historical process. Evolutionary change is often driven by the deterministic force of natural selection, but natural selection works upon variation that arises unpredictably through time by random mutation, and even beneficial mutations can be lost by chance through genetic drift. Moreover, evolution has taken place within a planetary environment with a particular history of its own. This tension between determinism and contingency makes evolutionary biology a kind of hybrid between science and history. While philosophers of science examine the nuances of contingency, biologists have performed many empirical studies of evolutionary repeatability and contingency. Here, we review the experimental and comparative evidence from these studies. Replicate populations in evolutionary "replay" experiments often show parallel changes, especially in overall performance, although idiosyncratic outcomes show that the particulars of a lineage's history can affect which of several evolutionary paths is taken. Comparative biologists have found many notable examples of convergent adaptation to similar conditions, but quantification of how frequently such convergence occurs is difficult. On balance, the evidence indicates that evolution tends to be surprisingly repeatable among closely related lineages, but disparate outcomes become more likely as the footprint of history grows deeper. Ongoing research on the structure of adaptive landscapes is providing additional insight into the interplay of fate and chance in the evolutionary process.},
    url = "https://doi.org/10.1126/science.aam5979",
    doi = "10.1126/science.aam5979",
    openalex = "W2900065583",
    references = "doi101016jtree201206001, doi101038nrg3483, doi101038nrg3744, doi101073pnas0508724103, doi101111j15585646201101289x"
}

@article{doi103390life8040046,
    author = "Li, Yamei and Kitadai, Norio and Nakamura, Ryuhei",
    title = "Chemical Diversity of Metal Sulfide Minerals and Its Implications for the Origin of Life",
    year = "2018",
    journal = "Life",
    abstract = {Prebiotic organic synthesis catalyzed by Earth-abundant metal sulfides is a key process for understanding the evolution of biochemistry from inorganic molecules, yet the catalytic functions of sulfides have remained poorly explored in the context of the origin of life. Past studies on prebiotic chemistry have mostly focused on a few types of metal sulfide catalysts, such as FeS or NiS, which form limited types of products with inferior activity and selectivity. To explore the potential of metal sulfides on catalyzing prebiotic chemical reactions, here, the chemical diversity (variations in chemical composition and phase structure) of 304 natural metal sulfide minerals in a mineralogy database was surveyed. Approaches to rationally predict the catalytic functions of metal sulfides are discussed based on advanced theories and analytical tools of electrocatalysis such as proton-coupled electron transfer, structural comparisons between enzymes and minerals, and in situ spectroscopy. To this end, we introduce a model of geoelectrochemistry driven prebiotic synthesis for chemical evolution, as it helps us to predict kinetics and selectivity of targeted prebiotic chemistry under "chemically messy conditions". We expect that combining the data-mining of mineral databases with experimental methods, theories, and machine-learning approaches developed in the field of electrocatalysis will facilitate the prediction and verification of catalytic performance under a wide range of pH and Eh conditions, and will aid in the rational screening of mineral catalysts involved in the origin of life.},
    url = "https://doi.org/10.3390/life8040046",
    doi = "10.3390/life8040046",
    openalex = "W2897794194",
    references = "doi101002adma201302685, doi101021cr068357u, doi101021ja0504690, doi101021ja404523s, doi101038nchem121, doi101038nmat3700, doi101038s415700160003, doi10106314812323, doi101126science1141483, doi101126scienceaas9100"
}

@article{doi101074jbcrev119006289,
    author = "Ribeiro, António J. M. and Tyzack, Jonathan D. and Borkakoti, Neera and Holliday, Gemma L. and Thornton, Janet M.",
    title = "A global analysis of function and conservation of catalytic residues in enzymes",
    year = "2019",
    journal = "Journal of Biological Chemistry",
    abstract = "The catalytic residues of an enzyme comprise the amino acids located in the active center responsible for accelerating the enzyme-catalyzed reaction. These residues lower the activation energy of reactions by performing several catalytic functions. Decades of enzymology research has established general themes regarding the roles of specific residues in these catalytic reactions, but it has been more difficult to explore these roles in a more systematic way. Here, we review the data on the catalytic residues of 648 enzymes, as annotated in the Mechanism and Catalytic Site Atlas (M-CSA), and compare our results with those in previous studies. We structured this analysis around three key properties of the catalytic residues: amino acid type, catalytic function, and sequence conservation in homologous proteins. As expected, we observed that catalysis is mostly accomplished by a small set of residues performing a limited number of catalytic functions. Catalytic residues are typically highly conserved, but to a smaller degree in homologues that perform different reactions or are nonenzymes (pseudoenzymes). Cross-analysis yielded further insights revealing which residues perform particular functions and how often. We obtained more detailed specificity rules for certain functions by identifying the chemical group upon which the residue acts. Finally, we show the mutation tolerance of the catalytic residues based on their roles. The characterization of the catalytic residues, their functions, and conservation, as presented here, is key to understanding the impact of mutations in evolution, disease, and enzyme design. The tools developed for this analysis are available at the M-CSA website and allow for user specific analysis of the same data.",
    url = "https://doi.org/10.1074/jbc.rev119.006289",
    doi = "10.1074/jbc.rev119.006289",
    openalex = "W2993164685",
    references = "doi101126scisignalaat9797"
}

@article{doi101126scisignalaav3810,
    author = "Kwon, Annie and Scott, Steven Thomas and Taujale, Rahil and Yeung, Wayland and Kochut, Krys J. and Eyers, Patrick A. and Kannan, Natarajan",
    title = "Tracing the origin and evolution of pseudokinases across the tree of life",
    year = "2019",
    journal = "Science Signaling",
    abstract = "Protein phosphorylation by eukaryotic protein kinases (ePKs) is a fundamental mechanism of cell signaling in all organisms. In model vertebrates, \textasciitilde 10\% of ePKs are classified as pseudokinases, which have amino acid changes within the catalytic machinery of the kinase domain that distinguish them from their canonical kinase counterparts. However, pseudokinases still regulate various signaling pathways, usually doing so in the absence of their own catalytic output. To investigate the prevalence, evolutionary relationships, and biological diversity of these pseudoenzymes, we performed a comprehensive analysis of putative pseudokinase sequences in available eukaryotic, bacterial, and archaeal proteomes. We found that pseudokinases are present across all domains of life, and we classified nearly 30,000 eukaryotic, 1500 bacterial, and 20 archaeal pseudokinase sequences into 86 pseudokinase families, including \textasciitilde 30 families that were previously unknown. We uncovered a rich variety of pseudokinases with notable expansions not only in animals but also in plants, fungi, and bacteria, where pseudokinases have previously received cursory attention. These expansions are accompanied by domain shuffling, which suggests roles for pseudokinases in plant innate immunity, plant-fungal interactions, and bacterial signaling. Mechanistically, the ancestral kinase fold has diverged in many distinct ways through the enrichment of unique sequence motifs to generate new families of pseudokinases in which the kinase domain is repurposed for noncanonical nucleotide binding or to stabilize unique, inactive kinase conformations. We further provide a collection of annotated pseudokinase sequences in the Protein Kinase Ontology (ProKinO) as a new mineable resource for the signaling community.",
    url = "https://doi.org/10.1126/scisignal.aav3810",
    doi = "10.1126/scisignal.aav3810",
    openalex = "W2941880204",
    references = "doi101038s4158901800432"
}

@article{doi101111febs15246,
    author = "Shrestha, Safal and Byrne, Dominic P. and Harris, John A. and Kannan, Natarajan and Eyers, Patrick A.",
    title = "Cataloguing the dead: breathing new life into pseudokinase research",
    year = "2020",
    journal = "FEBS Journal",
    abstract = "Pseudoenzymes are present within many, but not all, known enzyme families and lack one or more conserved canonical amino acids that help define their catalytically active counterparts. Recent findings in the pseudokinase field confirm that evolutionary repurposing of the structurally defined bilobal protein kinase fold permits distinct biological functions to emerge, many of which rely on conformational switching, as opposed to canonical catalysis. In this analysis, we evaluate progress in evaluating several members of the 'dark' pseudokinome that are pertinent to help drive this expanding field. Initially, we discuss how adaptions in erythropoietin-producing hepatocellular carcinoma (Eph) receptor tyrosine kinase domains resulted in two vertebrate pseudokinases, EphA10 and EphB6, in which co-evolving sequences generate new motifs that are likely to be important for both nucleotide binding and catalysis-independent signalling. Secondly, we discuss how conformationally flexible Tribbles pseudokinases, which have radiated in the complex vertebrates, control fundamental aspects of cell signalling that may be targetable with covalent small molecules. Finally, we show how species-level adaptions in the duplicated canonical kinase protein serine kinase histone (PSKH)1 sequence have led to the appearance of the pseudokinase PSKH2, whose physiological role remains mysterious. In conclusion, we show how the patterns we discover are selectively conserved within specific pseudokinases, and that when they are modelled alongside closely related canonical kinases, many are found to be located in functionally important regions of the conserved kinase fold. Interrogation of these patterns will be useful for future evaluation of these, and other, members of the unstudied human kinome.",
    url = "https://doi.org/10.1111/febs.15246",
    doi = "10.1111/febs.15246",
    openalex = "W3006367023",
    references = "doi101126scisignalaat9797"
}

@article{doi101007s00239020099884,
    author = "Goldman, Aaron D. and Kaçar, Betül",
    title = "Cofactors are Remnants of Life’s Origin and Early Evolution",
    year = "2021",
    journal = "Journal of Molecular Evolution",
    abstract = "The RNA World is one of the most widely accepted hypotheses explaining the origin of the genetic system used by all organisms today. It proposes that the tripartite system of DNA, RNA, and proteins was preceded by one consisting solely of RNA, which both stored genetic information and performed the molecular functions encoded by that genetic information. Current research into a potential RNA World revolves around the catalytic properties of RNA-based enzymes, or ribozymes. Well before the discovery of ribozymes, Harold White proposed that evidence for a precursor RNA world could be found within modern proteins in the form of coenzymes, the majority of which contain nucleobases or nucleoside moieties, such as Coenzyme A and S-adenosyl methionine, or are themselves nucleotides, such as ATP and NADH (a dinucleotide). These coenzymes, White suggested, had been the catalytic active sites of ancient ribozymes, which transitioned to their current forms after the surrounding ribozyme scaffolds had been replaced by protein apoenzymes during the evolution of translation. Since its proposal four decades ago, this groundbreaking hypothesis has garnered support from several different research disciplines and motivated similar hypotheses about other classes of cofactors, most notably iron-sulfur cluster cofactors as remnants of the geochemical setting of the origin of life. Evidence from prebiotic geochemistry, ribozyme biochemistry, and evolutionary biology, increasingly supports these hypotheses. Certain coenzymes and cofactors may bridge modern biology with the past and can thus provide insights into the elusive and poorly-recorded period of the origin and early evolution of life.",
    url = "https://doi.org/10.1007/s00239-020-09988-4",
    doi = "10.1007/s00239-020-09988-4",
    openalex = "W3127613891",
    references = "doi101038216029a0, doi103390life8040046"
}

@article{doi10106350055522,
    author = "Epifanovsky, Evgeny and Gilbert, Andrew T. B. and Feng, Xintian and Lee, Joonho and Mao, Yuezhi and Mardirossian, Narbe and Pokhilko, Pavel and White, Alec F. and Coons, Marc P. and Dempwolff, Adrian L. and Gan, Zhengting and Hait, Diptarka and Horn, Paul R. and Jacobson, Leif D. and Kaliman, Ilya and Kußmann, Jörg and Lange, Adrian W. and Lao, Ka Un and Levine, Daniel S. and Liu, Jie and McKenzie, Simon C. and Morrison, Adrian F. and Nanda, Kaushik and Plasser, Felix and Rehn, Dirk R. and Vidal, Marta L. and You, Zhi-Qiang and Zhu, Ying and Alam, Bushra and Albrecht, Benjamin and Aldossary, Abdulrahman and Alguire, Ethan and Andersen, Josefine H. and Athavale, Vishikh and Barton, Dennis L. and Begam, Khadiza and Behn, Andrew and Bellonzi, Nicole and Bernard, Yves and Berquist, Eric and Burton, Hugh G. A. and Carreras, Abel and Carter-Fenk, Kevin and Chakraborty, Romit and Chien, Alan D. and Closser, Kristina D. and Cofer-Shabica, D. Vale and Dasgupta, Saswata and de Wergifosse, Marc and Deng, Jia and Diedenhofen, Michael and Do, Hainam and Ehlert, Sebastian and Fang, Po-Tung and Fatehi, Shervin and Feng, Qingguo and Friedhoff, Triet and Gayvert, James R. and Ge, Qinghui and Gidofalvi, Gergely and Goldey, Matthew and Gomes, Joe and González‐Espinoza, Cristina E. and Gulania, Sahil and Gunina, Anastasia O. and Hanson‐Heine, Magnus W. D. and Harbach, Phillip H. P. and Hauser, Andreas and Herbst, Michael F. and Vera, Mario Hernández and Hodecker, Manuel and Holden, Zachary C. and Houck, Shannon E. and Huang, Xunkun and Hui, Kerwin and Huynh, Bang C. and Ivanov, Maxim and Jász, Ádám and Ji, Hyunjun and Jiang, Hanjie and Kaduk, Benjamin and Kähler, Sven and Khistyaev, Kirill and Kim, Jaehoon and Kis, Gergely and Klunzinger, Phil and Koczor-Benda, Zsuzsanna and Koh, Joong Hoon and Kosenkov, Dmytro and Koulias, Laura and Kowalczyk, Tim and Krauter, Caroline M. and Kue, Karl Y. and Kunitsa, Alexander A. and Kus, Thomas and Ladjánszki, István and Landau, Arie and Lawler, Keith V. and Lefrancois, Daniel and Lehtola, Susi",
    title = "Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package",
    year = "2021",
    journal = "The Journal of Chemical Physics",
    abstract = {This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange-correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear-electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an "open teamware" model and an increasingly modular design.},
    url = "https://doi.org/10.1063/5.0055522",
    doi = "10.1063/5.0055522",
    openalex = "W3193988690",
    references = "doi1010631441359, doi101080002689762014952696"
}

@article{doi101111tpj15782,
    author = "Yao, Shengbo and Liu, Yajun and Zhuang, Juhua and Zhao, Yue and Dai, Xinlong and Jiang, Changjuan and Wang, Zhihui and Jiang, Xiaolan and Zhang, Shuxiang and Qian, Yumei and Tai, Yuling and Wang, Yunsheng and Wang, Haiyan and Xie, De‐Yu and Gao, Liping and Xia, Tao",
    title = "Insights into acylation mechanisms: co‐expression of serine carboxypeptidase‐like acyltransferases and their non‐catalytic companion paralogs",
    year = "2022",
    journal = "The Plant Journal",
    abstract = "Serine carboxypeptidase-like acyltransferases (SCPL-ATs) play a vital role in the diversification of plant metabolites. Galloylated flavan-3-ols highly accumulate in tea (Camellia sinensis), grape (Vitis vinifera), and persimmon (Diospyros kaki). To date, the biosynthetic mechanism of these compounds remains unknown. Herein, we report that two SCPL-AT paralogs are involved in galloylation of flavan-3-ols: CsSCPL4, which contains the conserved catalytic triad S-D-H, and CsSCPL5, which has the alternative triad T-D-Y. Integrated data from transgenic plants, recombinant enzymes, and gene mutations showed that CsSCPL4 is a catalytic acyltransferase, while CsSCPL5 is a non-catalytic companion paralog (NCCP). Co-expression of CsSCPL4 and CsSCPL5 is likely responsible for the galloylation. Furthermore, pull-down and co-immunoprecipitation assays showed that CsSCPL4 and CsSCPL5 interact, increasing protein stability and promoting post-translational processing. Moreover, phylogenetic analyses revealed that their homologs co-exist in galloylated flavan-3-ol- or hydrolyzable tannin-rich plant species. Enzymatic assays further revealed the necessity of co-expression of those homologs for acyltransferase activity. Evolution analysis revealed that the mutations of the CsSCPL5 catalytic residues may have taken place about 10 million years ago. These findings show that the co-expression of SCPL-ATs and their NCCPs contributes to the acylation of flavan-3-ols in the plant kingdom.",
    url = "https://doi.org/10.1111/tpj.15782",
    doi = "10.1111/tpj.15782",
    openalex = "W4224217433",
    references = "doi101126scisignalaat9797"
}

@article{doi101021acsaccounts6c00037,
    author = "Gao, Ziqi and Zhang, Jinpeng and Wang, Jinyu and Wang, Jie",
    title = "Chemical Editing of Proteins: From a Specific Residue to Functional Domains.",
    year = "2026",
    journal = "Accounts of chemical research",
    abstract = {ConspectusThe remarkable complexity of life is supported by proteins, yet their functional diversity is constrained by the limited chemical alphabet of 20 canonical amino acids. Although nature partially overcomes this restriction through nongenetically encoded processes such as post-translational modifications or cofactors, these mechanisms are often difficult to predict, control and engineer. This limitation raises a fundamental question: can we programmably "chemically edit" proteins to generate new functions on demand? To address this challenge, our laboratory has been dedicated to advancing a "protein chemical editing" toolkit by integrating synthetic chemistry with protein engineering. This framework enables precise manipulation of proteins from individual residues to entire functional domains. We pursue two complementary strategies: genetic code expansion, which introduces unnatural amino acids (UAAs) as new chemical building blocks, and directed evolution platforms, which generate programmable protein-editing enzymes capable of rewriting protein sequences.In this Account, we outline a multiscale approach for protein chemical editing, spanning atomic-level control of active sites with photocaged amino acids, refinement of catalytic pockets using noncanonical residues, covalent stabilization of protein-protein interfaces through designer electrophile warheads, and domain-level editing enabled by evolved proteases.Prospectively, through the synergistic integration of chemical design, genetic encoding, and directed evolution, protein chemical editing unlocks a new level of control over biological function. This paradigm, which merges the precision of synthetic chemistry with the complexity of living systems, fundamentally transforms our capabilities from merely observing life to actively programming it, with profound implications for biomedicine and biotechnology.},
    url = "https://pubmed.ncbi.nlm.nih.gov/41973472/",
    doi = "10.1021/acs.accounts.6c00037",
    openalex = "W7154135829",
    pmid = "41973472",
    references = "doi101002anie200501023, doi101002anie201708408, doi101016jcell201706009, doi101021cr400477t, doi101038343767a0, doi10103835057062, doi101038nature18629, doi101038s41573020001358, doi101038s415860202188x, doi101146annurevbiochem052308105824"
}