Electron redistribution is the cornerstone of our understanding of chemical reactivity. For the vast majority of organic reactions electrons are assumed to move in pairs providing explanatory mechanisms through the generation of intermediate structures. But for many transformations these discrete steps are idealized constructs, involving intermediates assumed but not empirically justified. This unitary perspective predicated on the curved arrow formalism has resulted in the scenario where for many organic transformations our supposed understanding far surpasses our growing knowledge. Reformulating (...) organic mechanisms to include single electron transfer as a component of, or an alternative to, the prevailing iconic descriptions can provide for a more empirically adequate mechanistic description. In addition using the language of SET presents an opportunity to unify mechanistic concepts under a common donor/acceptor framework. (shrink)

Focusing on computational studies of pericyclic reactions from the late twentieth century into the twenty-first century, this paper argues that computational diagnostics is a key methodological development that characterize the management and coordination of plural approximation methods in computational organic chemistry. Predictive divergence between semi-empirical and ab initio approximation methods in the study of pericyclic reactions has issued in epistemic dissent. This has resulted in the use of diagnostics to unpack computational greyboxes in order to critically assess the (...) effect of specific misrepresentations on predictive accuracy given that approximations and idealizations must be made to render computational models tractable. Furthermore, benchmarking is used to determine the applicability of approximation methods depending on how accurate the results need to be in a given research context. The epistemology of benchmarking consists of the co-generation of data sets in a hybrid computational–experimental form used to standardize computational methods but does not determine a unique quantitative method to be used across computational organic chemistry. (shrink)

Organic chemists have been able to develop a robust, theoretical understanding of the phenomena they study; however, the primary theoretical devices employed in this field are not mathematical equations or laws, as is the case in most other physical sciences. Instead it is the diagram, and in particular the structural formula, that carries the explanatory weight in the discipline. To understand how this is so, it is necessary to investigate both the nature of the diagrams employed in organic (...) chemistry and how these diagrams are used in the explanations of the discipline. I will begin this paper by describing and characterizing the roles of the most important sort of diagram used in organic chemistry. Next I will present a model of explanations in organic chemistry and describe how diagrams contribute to these explanations. This will be followed by two examples that will support my abstract account of the role of diagrams in the explanations of organic chemistry. (shrink)

This paper examines a facet of the rise of the Hughes-Ingold Theory of Nucleophilic Substitution in Organic Chemistry 1933-1942, arguing that the SN1/SN2 model of reaction mechanism used by Hughes and Ingold is an example of a fuzzy model. Many real world 'Fuzzy Logic' Controlling Devices gave better results compared to classical logic controlling devices in the period 1975-1985. I propose that the adoption of fuzzy principles in the Hughes-Ingold program 1933-1940 led to scientific advance at a time (...) when the rival programs, based on classical principles, had stalled owing to problems associated with the fuzziness of the data. I suggest also that there is an analogy between the success of second generation fuzzy logic controllers 1985-95 and the success of the successor Winstein model from 1956 onwards. (shrink)

Chemical visualizations and models are special kinds of situated, inductive arguments. In this paper, I examine several historical case studies—an archive of images from museums, special collections, and popular magazines—as examples of emergent practices of physical modeling as theoretical play which became the basis for molecular biology and structural chemistry. Specifically, I trace a legacy of visualization tools that starts with Archibald Scott Cooper and Friedrich Kekulé in the late 1800s, crystallizes as material manipulatives in Kekulé’s student Jacobus Henricus (...) Van’t Hoff and his folded paper “toys,” is legitimized in the California lab of Linus Pauling, and is glorified in the popular imaginary with James Watson and Francis Crick’s model of DNA. My tracing then follows several threads into contemporary modeling practices. I ultimately argue that modeling play, originally outside of the boundary of deductive, positivist science, is now an accepted mode of inductive reasoning in these related chemical fields. (shrink)

Organic chemists have been able to develop a robust, theoretical understanding of the phenomena they study; however, the primary theoretical devices employed in this field are not mathematical equations or laws, as is the case in most other physical sciences. Instead it is diagrams, and in particular structural formulas and potential energy diagrams, that carry the explanatory weight in the discipline. To understand how this is so, it is necessary to investigate both the nature of the diagrams employed in (...) organic chemistry and how these diagrams are used in the explanations of the discipline. I will begin this paper by characterizing some of the major ways that structural formulas used in organic chemistry. Next I will present a model of the explanations in organic chemistry and describe how both structural formulas and potential energy diagrams contribute to these explanations. This will be followed by several examples that support my abstract account of the role of diagrams in the explanations of organic chemistry. In particular, I will consider both the appeal to ‘hyperconjugation’ in the explanation of alkene stability and how the idea of ‘ring strain’ was developed to explain the relative stability of cyclic compounds. (shrink)

This paper characterizes the increase in ‘scientific understanding’ that resulted from the Ingold Revolution in organic chemistry. By describing both the sorts of explanations facilitated by Ingold’s Revolution and the sense in which organic chemistry was ‘unified’ by adopting these approaches to explanation, one can appreciate how this revolution led to a dramatic qualitative improvement in organic chemists’ understanding of the phenomena that they study. The explanatory unification responsible for this transformation in organic (...) class='Hi'>chemistry is contrasted with contemporary philosophical accounts of unification and its relationship to both scientific understanding and explanation. (shrink)

The foundations of modern organic chemistry were laid by the seminal work of Hughes and Ingold. The rise from being an interesting alternative hypothesis in 1933 to being the leading theory (outside the USA) in 1942 was achieved by a multiplicity of methods. This include:the construction of a new scientific notation, the rationalisation of some seemingly contradictory reported data, the refutation of the experimental work of one of their persistent critics, the use of conceptual arguments and also the (...) achievement of a score of successful predictions which exceeded the score of unsuccessful predictions. Within the USA it was felt that the Hughes/Ingold system, whilst representing a considerable advance, had achieved spectacular success in spite ofits attractively simple basic assumptions, and represented merely an interim stage on the way towards a more comprehensive theory. However,the flexible, simple notation was adopted without modification, leading to a change in the way practitioners of synthetic organic chemistry were, and still are, trained to think. In a conclusion the author claims that this historical episode does not lend any support to the philosophical position of Thomas Kuhn. (shrink)

During the 1930s and 1940s, American physical organic chemists employed electronic theories of reaction mechanisms to construct models offering explanations of organic reactions. But two molecular rearrangements presented enormous challenges to model construction. The Claisen and Cope rearrangements were predominantly inaccessible to experimental investigation and they confounded explanation in theoretical terms. Drawing on the idea that models can be autonomous agents in the production of scientific knowledge, I argue that one group of models in particular were functionally autonomous (...) from the Hughes–Ingold theory. Cope and Hardy’s models of the Claisen and Cope rearrangements were resources for the exploration of the Hughes–Ingold theory that otherwise lacked explanatory power. By generating ‘how-possibly’ explanations, these models explained how these rearrangements could happen rather than why they did happen. Furthermore, although these models were apparently closely connected to theory in terms of their construction, I argue that partial autonomy issued in extra-logical factors concerning the attitudes of American chemists to the Hughes–Ingold theory. And in the absence of a complete theoretical hegemony, a degree of consensus was reached concerning modelling the Claisen rearrangement mechanism.Keywords: Models; Explanation; Physical organic chemistry; Rearrangements. (shrink)

Organic chemistry provides fertile ground for scholars interested in understanding the role of non-linguistic representations in scientific thinking. In this discipline, it is not plausible to regard diagrams as simply heuristic aids for expressing or applying what is essentially a linguistic theory. Instead, it is more plausible to think of linguistic representation as supplementing theories whose principal expression is diagrammatic. Among the many sorts of diagrams employed by organic chemists, structural formulas are the most important. In this (...) paper, by examining two central episodes in the development of structural formulas—Kekulé’s proposal of a structure for benzene and Ingold’s explanation of dipole moments in terms of ‘mesomerism’—I investigate how the norms for the production and interpretation of structural formulas evolve in response to experimental results and theoretical developments. I conclude that one principal way in which structural formulas embody the theory of organic chemistry is through these evolving norms. (shrink)

Chemists take mechanisms to be an important way of explaining chemical change. I examine the usefulness of the mechanism approach in the recent philosophical literature in explicating the explanatory use of mechanisms by organic chemists. I argue that chemists consider a mechanism to be explanatory because it accounts for the “dynamic process of bringing about” (Tabery 2004 , 10) chemical change. For chemists, mechanisms are causal explanations based on interventions that show “how some possibilities depend on others” (Woodward 2003 (...) , 375). Only possibilities are achievable because chemists face a number of challenges when they explain by means of a mechanism. †To contact the author, please write to: Department of Philosophy, Smith College, Northampton, MA 01063; e‐mail: [email protected]. (shrink)

The paper illustrates how organic chemists dramatically altered their practices in the middle part of the twentieth century through the adoption of analytical instrumentation - such as ultraviolet and infrared absorption spectroscopy and nuclear magnetic resonance spectroscopy - through which the difficult process of structure determination for small molecules became routine. Changes in practice were manifested in two ways: in the use of these instruments in the development of 'rule-based' theories; and in an increased focus on synthesis, at the (...) expense of chemical analysis. These rule-based theories took the form of generalizations relating structure to chemical and physical properties, as measured by instrumentation. This 'Instrumental Revolution' in organic chemistry was two-fold: encompassing an embrace of new tools that provided unprecedented access to structures, and a new way of thinking about molecules and their reactivity in terms of shape and structure. These practices suggest the possibility of a change in the ontological status of chemical structures, brought about by the regular use of instruments. The career of Robert Burns Woodward (1917-1979) provides the central historical examples for the paper. Woodward was an organic chemist at Harvard from 1937 until the time of his death. In 1965, he won the Nobel Prize in Chemistry. (shrink)

In modern German ‘Anschauung’ is translated as intuition. But in Kant’s technical philosophical context, it means an intuition derived from previous visualizations of physical processes in the world of perceptions. The nineteenth century chemists’ predilection for Kantian Anschauung led them to develop an intuitive representation of what exists beyond the bounds of the senses. Molecular structure is one of the illuminating outcomes. (Ochiai 2021, pp. 1–51) This mental habit seems to be dominant among chemists even in the twentieth century, as (...) is illustrated by the electronic theory of organic chemistry and the frontier orbital theory as well. The former assumes that (1) bonds are paired electrons shared by bonded atoms—in fact, electrons in molecules are not localized in bonds; (2) the difference of electronegativities between bonded atoms causes electron drifts—expressed by the curly arrow—that result in bond formation or bond cleavage. The latter focuses on the orbitals that make the greatest contribution to the energy of a system undergoing electron delocalization, while the LCAO method says, as is suggested by the word Linear Combination of Atomic Orbitals, molecular orbitals should be constructed from all of the atomic orbitals that have the appropriate symmetry. In other words, every molecular orbital contributes to some extent to the electronic state of a molecule. The curly arrow in the electronic theory and the orbital lobe in the frontier orbital theory illustrate an intuitive character of these theories. Although both theories rely on such simple and qualitative models rather than mathematically rigid quantum mechanical calculations, they are successful in explaining, predicting, and designing chemical reactions. What makes these prima facie intuitive theories so successful? In this study we address this problem from a historical and philosophical as well as scientific point of view. The key to solve this problem is that they are concerned with only bond formation or bond cleavage, in which the localized-bond principle holds. (shrink)

Musks, the foundation of many perfumes, as well as other ingredients of perfumes, were critical objects of study for establishing theoretical concepts about large ring chemical compounds and polymerization in the 1920s and 1930s. Because fragrance chemistry has been underdeveloped in the historiography, doubtless partly because it has become associated with the feminine, this has been ignored in the historiography. This essay highlights the strategic importance of perfume research, looking in particular at the work of Leopold Ružičkač, 1939 Nobel (...) laureate in chemistry who had close ties to the fragrance industry, and Wallace Carothers at DuPont, whose well-known work on polymerization was intimately concerned with large ring compounds, including musk, and which indeed led to DuPont producing a synthetic musk in the 1930s. (shrink)

In this essay I consider whether the theory of organic chemistry is reducible to the theory of quantum chemistry. Using philosophical machinery developed by James Woodward, I characterize the understanding provided by both theories. Then I argue that there are systematic reasons to suspect that quantum chemistry is incapable of supporting some of the significant explanations, predictions, and applications underwritten by an understanding of theoretical organic chemistry. Consequently, even should quantum chemistry be ‘reducible (...) to’ quantum physics in some suitable sense, there are good reasons to doubt that many of the significant results of organic chemistry could be reproduced by quantum chemistry alone. (shrink)

Proclaiming Louis Pasteur as the “Founder of Stereochemistry”, the distinguished Scottish chemist, Crum Brown, addressing a late nineteenth-century audience of Edinburgh savants, drew attention—as Pasteur had incessantly done—to the intimate relationship between living organisms and the optical activity of compounds sustaining them. It seemed to Crum Brown “that we must go very much further down in the scale of animate existence than Buridan's ass, before we come to a being incapable of giving practical expression to a distinct preference for one (...) of two objects differing only in being one to the right and the other to the left”. Crum Brown's lecture must have been entertaining, but it was also motivated by a serious desire to do justice to a particular assertion of Pasteur—an assertion which had, moreover, been misunderstood and dismissed by no less a chemical genius than Wilhelm Ostwald. Writing at a time when the majority of his colleagues were stressing the resemblances between inorganic and organic compounds, Pasteur had insisted that he “could not point out the existence of any more profound distinction between the products formed under the influence of life and all others” than that “artificial products have … no molecular asymmetry”. Pasteur was obliged to concede that the chemist might produce enantiomorphic pairs of isomers, but without resorting to a manual separation of crystals he was powerless to imitate Nature's performance, powerless to fabricate by chemical means a separate optical isomer, divorced from its partner. Now it was not only Crum Brown who felt that chemists had brushed aside this proposition of Pasteur. In his 1898 Presidential Address to the chemical section of the British Association, Professor F. R. Japp also complained that the possible vitalistic implications of Pasteur's distinction between natural and artificial products had been misapprehended or tacitly ignored. (shrink)

Discussing the relationship of mathematics to chemistry is closely related to the emergence of physical chemistry and of quantum chemistry. We argue that, perhaps, the most significant issue that the 'mathematization of chemistry' has historically raised is not so much methodological, as it is philosophical: the discussion over the ontological status of theoretical entities which were introduced in the process. A systematic study of such an approach to the mathematization of chemistry may, perhaps, contribute to (...) the realist/antirealist debate. To this end, in this paper we briefly discuss Lewis' introduction of fugacity and activity to his chemical thermodynamics and more fully analyze the issues surrounding the appropriation of resonance by Linus Pauling into quantum chemistry, particularly as these issues arose in organic chemistry as discussed by George W. Wheland. (shrink)

Kant’s treatment of organic phenomena in the third _Critique_ is relatively well-known. Less known is that Schelling offered an original answer to the same problems in his early writings on the philosophy of nature. Even less known is the significance of his rethinking of the role of chemistry in his approach to organic phenomena. In this article, after outlining the problem of organic phenomena at the end of the eighteenth century, I reconstruct Schelling’s account of (...) class='Hi'>chemistry against the background of Kant’s theory of matter. I show that, while Schelling endorses Kant’s verdict that chemistry is not a proper science, he nevertheless assigns to it a far greater scope and explanatory power than Kant does. After that, I briefly sketch Schelling’s solution to the problem of organic phenomena while stressing the significance of his thinking about chemistry for this solution. (shrink)

Dissatisfied with the descriptive and speculative methods of evolutionary biology of his time, the physiologist Jacques Loeb , best known for his “engineering” approach to biology, reflected on the possibilities of artificially creating life in the laboratory. With the objective of experimentally tackling one of the crucial questions of organic evolution, i.e., the origin of life from inanimate matter, he rejected claims made by contemporary scientists of having produced artificial life through osmotic growth processes in inorganic salt solutions. According (...) to Loeb, the answer to the question of whether or not life could be created artificially had to come from macro-molecular chemistry, in particular from the research on the recently discovered DNA. He was convinced that a prerequisite for making living matter from inanimate substances was the chemical synthesis of nuclear material capable of self-replication. Moreover, Loeb, experimentally refuting some vitalistic explanations as well as colloidal chemists’ far-reaching claims that biologically relevant macromolecules follow colloidal rather than chemical laws, pioneered research on the physical and chemical explanations of biological phenomena. (shrink)

Teaching chemistry remains a profoundly challenging activity. This paper arises from reflection on the challenges of creating meaningful assessments. Herein a simple framework to assist in making more visible the different kinds of knowledge required for mastery of chemistry is described. Building from a realist foundation the purpose of this paper is to lay the intellectual scaffolding for the framework. By situating the framework theoretically, it is intended to highlight the value of engaging with philosophy for the project (...) of knowledge building in chemistry. Use of this framework has laid bare some significant limitations to the ways in which organic chemistry has been assessed. Making the visible to students aids in their engagement with knowledge and for a small minority has developed their understanding of science more generally. The framework provides a simple, easily usable tool for the evaluation of chemistry assessments. (shrink)