Chemical Explanation

This paper is a study of a distinctively chemical notion of possibility. This is the notion of possibility that occurs in chemical discourses when chemists speak of the possibility or impossibility of achieving a given result through chemical means. This notion pertains to the possibility of processes, not of compounds, so it differs from the kind of chemical possibility mentioned in Wittgenstein's Philosophical Investigations or the kinds discussed in the literature on Putnam's Twin Earth argument. I argue that this process-oriented (...) notion of possibility cannot be reduced in a simple way to physical possibility, and that standard possible worlds semantics does not allow a natural analysis of this notion. I suggest an extension of possible worlds semantics that may overcome this limitation. I finish by pointing out some open questions about chemical possibility. (shrink)

The periodic table represents and organizes all known chemical elements on the basis of their properties. While the importance of this table in chemistry is uncontroversial, the role that it plays in scientific reasoning remains heavily disputed. Many philosophers deny the explanatory role of the table and insist that it is “merely” classificatory The structure of scientific theories, University of Illinois Press, Illinois, 1977; Scerri in Erkenntnis 47:229–243, 1997). In particular, it has been claimed that the table does not figure (...) in causal explanation because it “does not reveal causal structure”. This paper provides an analysis of what it means to say that a scientific figure reveals causal structure and it argues that the modern periodic table does just this. It also clarifies why these “merely” classificatory claims have seemed so compelling–this is because these claims often focus on the earliest periodic tables, which lack the causal structure present in modern versions. (shrink)

I apply James Woodward’s interventionist theory of causation to organic chemistry, modelling three different ways that chemists are able to manipulate the reaction conditions in order to control the outcome of a reaction. These consist in manipulations to the reaction kinetics, thermodynamics, and whether the kinetics or thermodynamics predominates. It is possible to construct interventionist causal models of all of these kinds of manipulation, and therefore to account for them using Woodward’s theory. However, I show that there is an alternate, (...) more illuminating way of thinking about the third kind of reaction control, according to which chemists are thought of as manipulating which causal system is instantiated. I show that our ability to manipulate which system is instantiated is an important part of our ability to control the world, as is therefore especially relevant to interventionism. Thus, considering examples from organic chemistry leads to the identification of an important extension to Woodward’s theory. Finally, this investigation into reaction control in organic chemistry also has a more general implication: it suggests that interventionism results in a version of pragmatism about causation. (shrink)

This article examines a scientific controversy that raged for twenty years in physical organic chemistry during the second half of the twentieth century. After explaining what was at stake in the non-classical ion debate, I attempt—by examining the methodological reflections of some of the participants—a partial explanation of what sustained this controversy, particularly during its early stages. Instead of suggesting a breakdown of scientific method or the unavoidable historical contingency of scientific development, the endurance of this controversy instead reveals the (...) heuristic and pragmatic character of many of the explanations and predictions generated by theoretical organic chemistry. The results in this case are used to suggest a new role for the study of scientific controversies in revealing the economics of scientific inquiry. 1 Introduction2 The Non-classical Ion Debate3 Models for the 2-Norbornyl System4 Soft Theories and Reasoning by Analogy5 Scientific Controversy and the Non-classical Ion Debate6 Conclusion. (shrink)

The paper is aimed at defining reduction, oxidation, and redox reactions based both on the oxidation number and charge changes in reacting species. It is rationalized that the processes of oxidation and reduction, usually occurring simultaneously, can occur also as independent processes. It is explained that in balancing chemical equations of redox reactions the “gain” or “loss” of electrons should be understood as changes in oxidation number. A formal expressions “+n e−” and “−n e−” represent in reality a decrease and (...) increase in oxidation number by n units, respectively. (shrink)

Chemistry and physics are two sciences that are hard to connect. Yet there is significant overlap in their aims, methods, and theoretical approaches. In this book, the reduction of chemistry to physics is defended from the viewpoint of a naturalised Nagelian reduction, which is based on a close reading of Nagel's original text. This naturalised notion of reduction is capable of characterising the inter-theory relationships between theories of chemistry and theories of physics. The reconsideration of reduction also leads to a (...) new characterisation of chemical theories. This book is primarily aimed at philosophers of chemistry and chemists with an interest in philosophy, but is also of interest to the general philosopher of science. (shrink)

Machine generated contents note: -- Preface -- Acknowledgments -- Introduction, by Michael Weisberg and Jeffrey Kovac. -- 1 Trying to Understand, Making Bonds, by Roald Hoffmann -- Part 1: Chemical Reasoning and Explanation -- 2. Why Buy That Theory?, by Roald Hoffmann. -- 3. What Might Philosophy of Science Look Like If Chemists Built It?, by Roald Hoffmann -- 4. Unstable, by Roald Hoffmann -- 5. Nearly Circular Reasoning, by Roald Hoffmann -- 6. Ockham's Razor and Chemistry, by Roald Hoffmann, (...) Vladimir I. Minkin, and Barry K. Carpenter -- 7. Qualitative Thinking in the Age of Modern Computational Chemistry, or What Lionel Salem Knows, by Roald Hoffmann -- 8. Narrative, by Roald Hoffmann -- 9. Learning from Molecules in Distress, by Roald Hoffmann and Henning Hopf -- 10. Why Think Up New Molecules? by Roald Hoffmann -- 11. Protean, by Roald Hoffmann and Pierre Laszlo -- 12. How Should Chemists Think? by Roald Hoffmann -- Part 2: Writing and Communicating in Chemistry -- 13. Under the Surface of the Chemical Article, by Roald Hoffmann -- 14. Representation in Chemistry, by Roald Hoffmann and Pierre Laszlo -- 15.. The Say of Things, by Roald Hoffmann and Pierre Laszlo -- 16. How Symbolic and Iconic Languages Bridge the Two Worlds of the Chemist: A Case Study from Contemporary Bioorganic Chemistry, by Emily R. Grosholz and Roald Hoffmann -- 17 How Nice to Be an Outsider, by Roald Hoffmann -- 18. The Metaphor, Unchained, by Roald Hoffmann, -- Part 3: Art and Science -- 19. Art in Science? by Roald Hoffmann -- 20. Science and Crafts by Roald Hoffmann -- 21. Molecular Beauty, by Roald Hoffmann -- Part 4 Chemical Education -- 22. Teach to Search by Roald Hoffmann -- 23. Some Heretical Thoughts on What Our Students Are Telling Us, by Roald Hoffmann and Brian P. Coppola -- 24 Very Specific Teaching Strategies, and Why They Work, by Roald Hoffmann and Saundra Y. McGuire -- Part 5 Ethics in Science -- 25. Mind the Shade, by Roald Hoffmann -- 26. Science and Ethics: A Marriage of Necessity and Choice for this Millennium," by Roald Hoffmann -- 27. Honesty to the Singular Object, by Roald Hoffmann -- 28. The Material and Spiritual Rationales Are Inseparable, by Roald Hoffmann -- Index. (shrink)

This treatise presents thoughts on the divide that exists in chemistry between those who seek their understanding within a universe wherein the laws of physics apply and those who prefer alternative universes wherein the laws are suspended or ‘bent’ to suit preconceived ideas. The former approach is embodied in the quantum theory of atoms in molecules (QTAIM), a theory based upon the properties of a system’s observable distribution of charge. Science is experimental observation followed by appeal to theory that, upon (...) occasion, leads to new experiments. This is the path that led to the development of the molecular structure hypothesis—that a molecule is a collection atoms with characteristic properties linked by a network of bonds that impart a structure—a concept forged in the crucible of nineteenth century experimental chemistry. One hundred and fifty years of experimental chemistry underlie the realization that the properties of some total system are the sum of its atomic contributions. The concept of a functional group, consisting of a single atom or a linked set of atoms, with characteristic additive properties forms the cornerstone of chemical thinking of both molecules and crystals and Dalton’s atomic hypothesis has emerged as the operational theory of chemistry. We recognize the presence of a functional group in a given system and predict its effect upon the static, reactive and spectroscopic properties of the system in terms of the characteristic properties assigned to that group. QTAM gives physical substance to the concept of a functional group. (shrink)

Heisenberg’s explanation of how two coupled oscillators exchange energy represented a dramatic success for his new matrix mechanics. As matrix mechanics transmuted into wave mechanics, resulting in what Heisenberg himself described as …an extraordinary broadening and enrichment of the formalism of the quantum theory , the term resonance also experienced a corresponding evolution. Heitler and London’s seminal application of wave mechanics to explain the quantum origins of the covalent bond, combined with Pauling’s characterization of the effect, introduced resonance into the (...) chemical lexicon. As the Valence Bond approach gave way to a soon-to-be dominant Molecular Orbital method, our understanding of the term resonance, as it might apply to our understanding the chemical bond, has also changed. (shrink)

After Heitler and London published their pioneering work on the application of quantum mechanics to chemistry in 1927, it became an almost unquestioned dogma that chemistry would soon disappear as a discipline of its own rights. Reductionism felt victorious in the hope of analytically describing the chemical bond and the structure of molecules. The old quantum theory has already produced a widely applied model for the structure of atoms and the explanation of the periodic system. This paper will show two (...) examples of the entry of quantum physics into more classical fields of chemistry: inorganic chemistry and physical chemistry. Due to their professional networking, George Hevesy and Michael Polanyi found their ways to Niels Bohr and Fritz London, respectively, to cooperate in solving together some problems of classical chemistry. Their works on rare earth elements and adsorption theory throws light to the application of quantum physics outside the reductionist areas. They support the heuristic and persuasive value of quantum thinking in the 1920–1930s. Looking at Polanyi’s later oeuvre, his experience with adsorption theory could be a starting point of his non-justificationist philosophy. (shrink)

The philosophical significance of Dmitri Mendeleev’s successful predictions of the properties of gallium and scandium vis a vis the acceptance of the Periodic Table 1874–1886 has been debated recently. This author presents evidence that De Boisbaudran and Cleve both respectively predicted the possible existence of gallium and scandium, but on the basis of the old TRIAD methodology. This suggests that these successful Mendeleev predictions were therefore not independent corroboration of the concept of the Periodic System. Instead the significantly independent predictive (...) successes for Mendeleev’s system were the determination of the atomic weight of the known element uranium as 240 instead of the previously accepted 120 in 1874 and the isolation of germanium by Winkler in 1886. (shrink)

structure of a laboratory report (generalized from Italian, Chinese and US sources), we distill a fifth flavor, the givens, whose flip side is the freedoms or tangibles of an experiment. (Stated in terms of computer science, we are trying to find inputs and outputs, but these turn out to be surprisingly vague in chemistry.) Then, in the service of a white-boxing ethos (which sounds less severe than ‘anti black-boxing’), we establish a movable boundary between givens and tangibles, with implications for (...) ‘ontological attitudes’ and for the future of chemistry. Next, in revisiting a 2002 exchange between Schummer and Laszlo, which might be paraphrased as the chemist-as-philosopher versus chemist-as-artisan, we apply a second kind of sliding scale which seems to harmonize the discussion. Finally, on a possibly quixotic note, we look briefly at a third kind of sliding scale, now aimed squarely at ontology itself. For illustrative purposes, we adopt an atomocentric viewpoint (as distinct from atomistic), and assign it the provisional name ‘Fuzzy CH4 Ontology’. (shrink)

Mulliken proposed an Aufbauprinzip for the molecules on the basis of molecular spectroscopy while establishing, point by point, his concept of molecular orbit. It is the concept of electronic state which becomes the lever for his attribution of electronic configurations to a molecule. In 1932, the concept of orbit was transmuted into that of the molecular orbital to integrate the probabilistic approach of Born and to achieve quantitative accuracy. On the basis of the quantum works of Hund, Wigner, Lennard-Jones and (...) group theory, he suggested the fragment method to establish the characteristics of molecular orbital for polyatomic molecules. These developments make it possible to bring elements of thought on the relation between a molecular whole and its parts . An operational realism combined with the second law of thermodynamics can pave the way for interesting tracks in the mereological study of chemical systems. (shrink)

In the last years there has been a great improvement in the development of computational methods for combinatorial chemistry applied to drug discovery. This approach to drug discovery is sometimes called a “rational way” to manage a well known phenomenon in chemistry: serendipity discoveries. Traditionally, serendipity discoveries are understood as accidental findings made when the discoverer is in quest for something else. This ‘traditional’ pattern of serendipity appears to be a good characterization of discoveries where “luck” plays a key role. (...) In this sense, some initial failures in combinatorial chemistry are frequently attributed to a naïf appropriation of a “serendipity model” for discovery (a “serendipity mistake”). In this paper we try to evaluate this statement by criticizing its foundations. It will be suggested that the notion of serendipity has different aspects and that the criticism to the first attempts could be understood as a “serendipity mistake.” We will suggest that “serendipity” strategies, a kind of blind search, can be seen sometimes as a “genuine part” of scientific practice. A discussion will ensue about how this characterization can give us a better understanding of some aspects of serendipity discoveries. (shrink)

Next SectionOne of the indisputable signs of the progress made in organic chemistry over the last two hundred years is the increased ability of chemists to manipulate, control, and design chemical reactions. The technological expertise manifest in contemporary synthetic organic chemistry is, at least in part, due to developments in the theory of organic chemistry. By appealing to a notable chemist's attempts to articulate and codify the heuristics of synthetic design, this paper investigates how understanding theoretical organic chemistry facilitates progress (...) in synthetic organic chemistry. The picture that emerges of how the applications of organic chemistry are grounded in its theory is contrasted with both standard and some more contemporary philosophical accounts of the applications of science. IntroductionTotal Synthesis as Applied ScienceUnderstanding Organic ChemistryThe Heuristics of Synthetic DesignAn Example: LongifoleneConclusion. (shrink)

In this paper I expand Eric Scerri’s notion of Popper’s naturalised approach to reduction in chemistry and investigate what its consequences might be. I will argue that Popper’s naturalised approach to reduction has a number of interesting consequences when applied to the reduction of chemistry to physics. One of them is that it prompts us to look at a ‘bootstrap’ approach to quantum chemistry, which is based on specific quantum theoretical theorems and practical considerations that turn quantum ‘theory’ into quantum (...) ‘chemistry’ proper. This approach allows us to investigate some of the principles that drive theory formation in quantum chemistry. These ‘enabling theorems’ place certain limits on the explanatory latitude enjoyed by quantum chemists, and form a first step into establishing the relationship between chemistry and physics in more detail. (shrink)

Although chemical phenomena are primarily associated with electrons in atoms, ions, and molecules, the masses, charges, spins, and other properties of the nuclei in these species contribute significantly as well. Isotopes, for instance, have proven invaluable in chemistry, in particular the elucidation of reaction mechanisms. Elements with unstable nuclei, for example carbon-14 undergoing beta decay, have enriched chemistry and many other scientific disciplines. The nuclei of all elements have a much more subtle and largely unknown effect on chemical phenomena. All (...) nuclei are innately chiral and, because electrons can penetrate nuclei, all atoms and molecules are likewise chiral. This article describes in considerable detail the discovery of chiral nuclei, how this unusual chirality may influence the chemical behavior of atoms and molecules, and how atomic chirality may have been responsible for the synthesis of optically active molecules in the pre-biotic world. (shrink)

The concept developed in relation to Atman as infrasonic bio-mechanical oscillatorwill be used to delineate the physicochemical nature of thoughts and ideas. The insight available in the Upanishads, the Brahma Sutras, the Vishnu Sahasranaama and LalitaSahasranaama will be used to further and advance the understanding of mechanical, biochemical and electro-chemical nature of human thoughts and ideas. The conceptual clarity about these mental processes will be presented. A pictorial diagram of nature and forms of energy transformations involved in thought processes and (...) idea generations will be given. Implications and application of this insight to the disciplines of physiological psychology and mind-machine modeling will be hinted. (shrink)

The usefulness of isoelectronic series (same number of total electrons and atoms and of valence electrons) across Periods is often overlooked. Here we show the ubiquitousness of isoelectronic sets by means of matrices, arrays, and sequential series. Some of these series have not previously been identified. In addition, we recommend the use of the term valence-isoelectronic for species which differ in the number of core electrons and pseudo-isoelectronic for matching (n) and (n + 10) species.

Many theories require empirical patches or ad hoc assumptions to work properly in application to chemistry. Some examples include the Bohr quantum theory of atomic spectra, the Pauli exclusion principle, the Marcus theory of the rate-equilibrium correlation, Kekule’s hypothesis of bond oscillation in benzene, and the quantum calculation of reaction pathways. Often the proposed refinements do not grow out of the original theory but are devised and added ad hoc. This brings into question the goal of constructing theories derived from (...) first principles and the concept of ranking the merit of theories according to their freedom from empirical contamination. (shrink)

Because most chemical reactions, by definition, cannot avoid breaking of bonds, weakly bonded species exist fleetingly in almost every chemical change. Historically, chemical quantum mechanics was aimed at explaining the nature of strong bonds. The theory involved a number of approximations to the full solution of the Schrödinger equation. The study of non‐Kekulé molecules provides an opportunity to test whether modern quantum chemical computations are competent to deal with the nature of molecules with very weak bonds. †To contact the author, (...) please write to: Department of Chemistry, Yale University, New Haven, CT: 06520‐8107; e‐mail: jerome.berson@yale.edu. (shrink)

This is the third of a series of essays on the development and reception of Wilhelm Ostwald’s energetics. The first essay described the chemical origins of Ostwald’s interest in the energy concept and his motivations for seeking a comprehensive science of energy. The second essay and the present one discuss his various attempts, beginning in 1891 and extending over almost 3 years, to develop a consistent and coherent energetic theory. A final essay will consider reactions to this work and Ostwald’s (...) replies, and will also seek to evaluate his program of research. Ostwald’s project—to reconstruct physics and chemistry “as a pure energetics”—is worth attending to for several reasons: first, because Ostwald did ground-breaking work in chemistry (he was awarded a Nobel Prize in 1909 for his studies in catalysis and rates of reaction); second, because an important school of physical chemistry formed around him at Leipzig, a school that promoted his ideas; and, finally, because he was a prominent and vigorous participant in debates at the end of the nineteenth century concerning the proper course of physical theory. (shrink)

The project of chemistry to classify substances and develop techniques for their transformation into other substances rests on assumptions about the means by which compounds are constituted and reconstituted. Robert Boyle not only proposed empirical tests for a metaphysics of material corpuscules, but also a principle for designing experimental procedures in line with that metaphysics. Later chemists added activity concepts to the repertoire. The logic of activity explanations in modern times involves hierarchies of activity concepts, transitions between levels through non-dispositional (...) groundings. Such hierarchies terminate in powerful particulars, such as elementary charged particles. Do these have a fundamental place in the most recent accounts of molecular architecture, stabilities and transformations? However, a close study of the contemporary chemistry of substances transforming reactions discloses a hybrid metaphysics, making use of both the Boylean corpuscles and Faradayan fields. This is illustrated by an analysis of the metaphysics inherent in John Polanyi’s use of “chemoluminescence” to follow the formation of products in chemical reactions. A brief sketch of a resolution of the tension between the two metaphysical schemes is drawn from Niels Bohr’s radical metaphysics extended from the quantum realm proper to chemistry (and perhaps beyond). (shrink)

In this article I sketch G. N. Lewis’s views on chemical bonding and Linus Pauling’s attempt to preserve Lewis’s insights within a quantum‐mechanical theory of the bond. I then set out two broad conceptions of the chemical bond, the structural and the energetic views, which differ on the extent in which they preserve anything like the classical chemical bond in the modern quantum‐mechanical understanding of molecular structure. †To contact the author, please write to: Department of Philosophy, Durham University, 50 Old (...) Elvet, Durham DH1 3HN, UK; e‐mail: r.f.hendry@durham.ac.uk. (shrink)

This paper surveys some ways in which the chemical realm can be described and outlined in terms of the concept of supervenience. The particular contours of general chemical theory provide a ready basis for interpretation of determination, covariance, and nonreduction—the characteristic metaphysical facets of the supervenience relation—in mutual terms. Building on this, the extent to which chemically characterized properties and entities can be described in terms of a supervenience-scaffolded structure represents a particularly vivid application that philosophers in general interested in (...) supervenience would do well to attend to. In addition, the model of chemical supervenience given here can be used as a rubric on which to decide on issues already raised by philosophers of chemistry. (shrink)

We present some ideas on logical process descriptions, using relations from the DIO (Drug Interaction Ontology) as examples and explaining how these relations can be naturally decomposed in terms of more basic structured logical process descriptions using terms from linear logic. In our view, the process descriptions are able to clarify the usual relational descriptions of DIO. In particular, we discuss the use of logical process descriptions in proving linear logical theorems. Among the types of reasoning supported by DIO one (...) can distinguish both (1) basic reasoning about general structures in reality and (2) the domain-specific reasoning of experts. We here propose a clarification of this important distinction between (realist) reasoning on the basis of an ontology and rule-based inferences on the basis of an expert’s view. (shrink)

Despite the currently perceived urgent need among contemporary philosophers of chemistry for adjudicating between two rival metaphysical conceptual frameworks—is chemistry primarily a science of substances or processes?—this essay argues that neither provides us with what we need in our attempts to explain and comprehend chemical operations and phenomena. First, I show the concept of a chemical property can survive the abandoning of the metaphysical framework of substance. While this abandonment means that we will need to give up essential properties, contingent (...) properties can give us all the stability we need to account for chemical continuity as well as change. I then go on to show that this attention to clusters of contingent properties does not force us into the arms of an alternative process metaphysical framework either. Finally, I sketch a view I call particularism with respect to chemical properties on analogy with moral particularism. I conclude by sketching some of the implications for the field of philosophy of chemistry of my proposal that we abandon our interest in the metaphysical question of what chemistry is primarily about in favor of a broadly scientific particularism with respect to kinds and properties. (shrink)

This is the second of a series of essays on the development and reception of Wilhelm Ostwald’s energetics. The first essay described the chemical origins of Ostwald’s interest in the energy concept and his motivations for seeking a comprehensive science of energy. The present essay and the next discuss his various attempts, beginning in 1891 and extending over almost 3 years, to develop a consistent and coherent energetic theory. A final essay will consider reactions to this work and Ostwald’s replies, (...) and will also seek to evaluate his program of research. Ostwald’s project – to reconstruct physics and chemistry “as a pure energetics” – is worth attending to for several reasons: first, because Ostwald did ground-breaking work in chemistry (he was awarded a Nobel Prize in 1909 for his studies in catalysis and rates of reaction); second, because an important school of physical chemistry formed around him at Leipzig, a school that promoted his ideas; and, finally, because he was a prominent and vigorous participant in debates at the end of the nineteenth century concerning the proper course of physical theory. (shrink)

In this paper, domain-specificity is presented as an understudied problem in chemical education. This argument is unpacked by drawing from two bodies of literature: learning of science and epistemology of science, both themes that have cognitive as well as philosophical undertones. The wider context is students’ engagement in scientific inquiry, an important goal for science education and one that has not been well executed in everyday classrooms. The focus on science learning illustrates the role of domain specificity in scientific reasoning. (...) The discussion on epistemology of science presents ideas from the emerging field of philosophy of chemistry to highlight the much neglected area of epistemology in chemical education. Domain-specificity is exemplified in the context of chemical laws, in particular the Periodic Law. The applications of the discussion for chemical education are explored in relation to argumentation, itself an epistemologically grounded discourse pattern in science. The overall implications include the need for reconceptualization of the nature of teaching and learning in chemistry to include more particular epistemological aspects of chemistry. (shrink)

Had more philosophers of science come from chemistry, their thinking would have been different. I begin by looking at a typical chemical paper, in which making something is the leitmotif, and conjecture/refutation is pretty much irrelevant. What in fact might have been, might be, different? The realism of chemists is reinforced by their remarkable ability to transform matter; they buy into reductionism where it serves them, but make no real use of it. Incommensurability is taken without a blink, and actually (...) serves. The preeminence of synthesis in chemistry could have led philosophers of science to take more seriously questions of aesthetics within science, and to find a place in aesthetics for utility. The necessary motion twixt macroscopic and microscopic views of matter in modern chemistry leads to the coexistence of symbolic and iconic representations. And in another way to the deliberate, creative violation of categories. (shrink)

Similarities in properties among pairs of metallic elements and their compounds in the lower-right quadrant of the Periodic Table have been named the ‘Knight’s Move’ relationship. Here, we have undertaken a systematic study of the only two ‘double-pairs’ of ‘Knight’s Move’ elements within this region: copper-indium/indium-bismuth and zinc-tin/tin-polonium, focussing on: metal melting points; formulas and properties of compounds; and melting points of halides and chalcogenides. On the basis of these comparisons, we conclude that the systematic evidence for ‘Knight’s Move’ relationships (...) derives from similarities in formulas and properties of matching pairs of compounds in the same oxidation state. Physical properties, such as melting points, do not provide consistent patterns and trends and hence should not be considered as a common characteristic of this relationship. (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)

Thought experiments in the history of science display a striking asymmetry between chemistry and physics, namely that chemistry seems to lack well-known examples, whereas physics presents many famous examples. This asymmetry, I argue, is not independent data concerning the chemistry/physics distinction. The laws of chemistry such as the periodic table are incurably special, in that they make testable predictions only for a very restricted range of physical conditions in the universe which are necessarily conditioned by the contingences of chemical investigation. (...) The argument depends on how ‚thought experiment’ is construed. Here, several recent accounts of thought experiments are surveyed to help formulate what I call ‚crucial’ thought experiments. These have a historical role in helping to judge between hypotheses in physics, but are not helpful in chemistry past or present. (shrink)

Enzymes are protein catalysts of extraordinary efficiency, capable of bringing about rate enhancements of their biochemical reactions that can approach factors of 1020. Theories of enzyme catalysis, which seek to explain the means by which enzymes effect catalytic transformation of the substrate molecules on which they work, have evolved over the past century from the “lock-and-key” model proposed by Emil Fischer in 1894 to models that explicitly rely on transition state theory to the most recent theories that strive to provide (...) accounts that stress the essential role of protein dynamics. In this paper, I attempt to construct a metaphysical framework within which these new models of enzyme catalysis can be developed. This framework is constructed from key doctrines of process thought, which gives ontologic priority to becoming over being, as well as tenets of a process philosophy of chemistry, which stresses environmentally responsive molecular transformation. Enzyme catalysis can now be seen not as enzyme acting on its substrate, but rather as enzyme and substrate entering into a relation which allows them to traverse the reaction coordinate as an ontologic unity. (shrink)

The "usual story" regarding molecular chemistry is that it is roughly an application of quantum mechanics. That is to say, quantum mechanics supplies everything necessary and sufficient, both ontologically and epistemologically, to reduce molecular chemistry to quantum mechanics. This is a reductive story, to be sure, but a key explanatory element of molecular chemistry, namely molecular structure, is absent from the quantum realm. On the other hand, typical characterizations of emergence, such as the unpredictability or inexplicability of molecular structure based (...) on quantum mechanics, do not characterize the relationship between molecular chemistry and quantum mechanics well either. A different scheme for characterizing reduction and emergence is proposed that accommodates the relationship between quantum mechanics and molecular chemistry and some initial objections to the scheme are considered. (shrink)

In contrast to the conventional homogeneous kinetics, there is no conception of a simple reaction in the solid-state reaction kinetics. The geometric-probabilistic phenomenology currently in use is not adequate for describing the interplay between the chemical mechanism and the observed kinetic behaviour. An attempt is made to formulate a conception of simple reaction in the solid state as a basis for constructing kinetic models of involved reactions.

In the philosophy of chemistry a view is developed according to which laws of nature and scientific theories are peculiar in chemistry. This view was criticized in an earlier issue of the Foundations of Chemistry (Vihalemm, Foundation of Chemistry 5(1): 7–22, 2003) referring to an essay by Maureen and John Christie (Christie and Christie, in N. Bushan and S. Rosenfeld (Eds.), Of Minds and Molecules: New Philosophical Perspectives on Chemistry. Oxford University Press, New York, 2000, pp. 34–50). This criticism was (...) responded by the Christies (Christie and Christie, Foundations of Chemistry 5(2): 165–177, 2003). In the present article the debate is continued. The main issues which need to be elucidated in order to carry the analysis forward are pointed out and discussed. The relevance of a theoretical model of science for the philosophy of chemistry is stressed. (shrink)

Magnani, Lorenzo (2001), Abduction, Reason, and Science: Processes of Discovery and Explanation. New York: Kluwer Academic/ Plenum Publishers. Magnani. Lorenzo, and Nancy Nersessian (eds.) (2002), Model-Based Reasoning: Technology, Science, Values. New York: Kluwer Academic/ Plenum Publishers. Joseph E. Earley, Sr. (ed.), Chemical Explanation: Characteristics, Development, Autonomy, Annals of the New York Academy of Sciences, vol. 988. New York Academy of Sciences (2003), 370 pp., $130.00 (cloth).

In this paper I investigate two views of theoretical explanation in quantum chemistry, advocated by John Clarke Slater and Charles Coulson. Slater argued for quantum‐mechanical rigor, and the primacy of fundamental principles in models of chemical bonding. Coulson emphasized systematic explanatory power within chemistry, and continuity with existing chemical explanations. I relate these views to the epistemic contexts of their disciplines.

Chemistry deals with substances and their transformations. School chemistry provides a picture of this in terms of small balls called atoms and ball-and-stick structures called molecules which, despite its crudity, has been taken to justifiably reflect a reductionist conception of macroscopic concepts like the chemical substances and chemical reactions. But with the recent interest in chemistry within the philosophy of science, an extensive and determined criticism has developed of the idea that the macroscopic world has been, or is likely to (...) be, reduced to microscopic theory. From this perspective, it is of interest to see macroscopic ontology treated autonomously. I try to take a first few steps towards spelling this out. It involves recognising entities falling into two broad categories: continuants-things which can have different properties at different times — and processes — things whose temporal parts may have different features, but which themselves stand in contrast to continuants in this respect. The character of each and their interrelations depends on their mereological structure of parts, the exploration of which is one of the prime purposes of the paper. (shrink)

I consider a way the concept of causation could be excised from chemical practice, suggested by Kitcher's view that causes are just a subset of unifying patterns which play a particular psychological role for us. Kitcherian chemistry is at first blush well equipped to handle explanatory tasks. However, it would force chemists to accept certain unifying patterns as explanatory, which they do not think are at all explanatory. This might head off some descriptive lines of enquiry and damage prospects for (...) the identification of potentially larger‐scale explanations. More important than this, to chemists, it could put them off from finding the explanatory patterns that are true—true because they get at the real structure of the chemical phenomena in the world. (shrink)

Traditional nomological accounts of scientific explanation have assumed that a good scientific explanation consists in the derivation of the explanandum’s description from theory (plus antecedent conditions). But in more recent philosophy of science the adequacy of this approach has been challenged, because the relation between theory and phenomena in actual scientific practice turns out to be more intricate. This critique is here examined for an explanatory paradigm that was groundbreaking for 20th century physics and chemistry (and their interrelation): Bohr’s first (...) model of the atom and its explanatory relevance for the spectrum of hydrogen. First, the model itself is analysed with respect to the principles and assumptions that enter into its premises. Thereafter, the origin of the model’s explanandum is investigated. It can be shown that the explained “phenomenon” is itself the product of a host of modelling accomplishments that stem from an experimental tradition related to 19th century chemistry, viz. spectroscopy. The relation between theory and phenomenon is thus mediated in a twofold way: by (Bohr’s) theoretical model and a phenomenological model from spectroscopy. In the final section of the paper an account is outlined that nevertheless permits us to acknowledge this important physico-chemical achievement as a case of (nomological) explanation. (shrink)

This essay addresses issues concerningexplanation by exploring how explanatorystructures function within contemporarychemistry. Three examples are discussed:explanations of the behavior of gases using theideal gas law, explanations of trends inchemical properties using the periodic table,and explanations of molecular geometry usingdiagrammatic orbital schemes. In each case,the general explanatory structure, rather thanparticular explanations, occupies center stagein the analysis. It is argued that thisquasi-empirical investigation may be morefruitful than previous analyses that attempt toisolate the essential features of individualexplanations. There are two reasons for thisconclusion, (...) each discussed in some detail. First, the traditional analyses rely on highlyprecarious reasoning. Second, empiricallygrounded investigations provide a more naturalconnection to the core aim of analyses ofexplanation, namely to provide a rationale forthe widely expressed preference for explanatorytheories in science. (shrink)

This essay explores the connection between representation and explanation in the sciences. I suggest that scientific representation schemes be viewed as pragmatic tools for acquiring the sort of articulated awareness that is the hallmark of nontrivial knowledge. Crystal field theory in chemistry illustrates this perspective. Certain representations achieve the status of being paradigmatically explanatory, thereby shaping models of intelligibility. In turn, these explanatory preferences serve largely to define and differentiate disciplinary communities by implicitly endorsing particular epistemic aims and values. In (...) this way, the pragmatic nature of explanatory discourse effectively grants its intellectual utility. (shrink)