I argue that molecules may not have structure in isolation. I support this by investigating how quantum models identify structure for isolated molecules. Specifically, I distinguish between two sets of models: those that identify structure in isolation and those that do not. The former identify structure because they presuppose structural information about the target system via the Born- Oppenheimer approximation. However, it is an idealisation to assume structure in isolation because there is no empirical evidence of this. In fact, whenever (...) structure is empirically examined it is always partially determined by factors that are absent in isolation. Together with the growing empirical evidence that isolated molecules behave in non-classical ways, this shows that the quantum models that do not identify structure are more faithful representations of isolated molecules. (shrink)

Many standard philosophical accounts of scientific practice fail to distinguish between modeling and other types of theory construction. This failure is unfortunate because there are important contrasts among the goals, procedures, and representations employed by modelers and other kinds of theorists. We can see some of these differences intuitively when we reflect on the methods of theorists such as Vito Volterra and Linus Pauling on the one hand, and Charles Darwin and Dimitri Mendeleev on the other. Much of Volterra's and (...) Pauling's work involved modeling; much of Darwin's and Mendeleev's did not. In order to capture this distinction, I consider two examples of theory construction in detail: Volterra's treatment of post-WWI fishery dynamics and Mendeleev's construction of the periodic system. I argue that modeling can be distinguished from other forms of theorizing by the procedures modelers use to represent and to study real-world phenomena: indirect representation and analysis. This differentiation between modelers and non-modelers is one component of the larger project of understanding the practice of modeling, its distinctive features, and the strategies of abstraction and idealization it employs. (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)

This paper combines naturalized metaphysics and a philosophical reflection on a recently evolving interdisciplinary branch of quantum chemistry, ab initio molecular dynamics. Bridging the gaps among chemistry, physics, and computer science, this cutting-edge research field explores the structure and dynamics of complex molecular many-body systems through computer simulations. These simulations are allegedly crafted solely by the laws of fundamental physics, and are explicitly designed to capture nature as closely as possible. The models and algorithms employed, however, involve many approximations and (...) significant degrees of idealization of their target systems. Therefore, for philosophers of science the pivotal question of whether relying only on the fundamental laws of physics supports a reductionist or realist stance arises. One conceivable answer to this question is that the irreducible approximations and idealizations support rather anti-realist positions. After reviewing an influential attitude in the philosophy of computer simulations and the debate concerning scientific realism, I offer a fair interpretation of such ab initio modelling in quantum chemistry within a naturalistic metaphysical framework that gives rise to a specific type of ontic structural realism. (shrink)

This article considers two important traditions concerning the chemical elements. The first is the meaning of the term “element” including the distinctions between element as basic substance, as simple substance and as combined simple substance. In addition to briefly tracing the historical development of these distinctions, I make comments on the recent attempts to clarify the fundamental notion of element as basic substance for which I believe the term “element” is best reserved. This discussion has focused on the writings of (...) Fritz Paneth which are here analyzed from a new perspective. The other tradition concerns the reduction of chemistry to quantum mechanics and an understanding of chemical elements through their microscopic components such as protons, neutrons and electrons. I claim that the use of electronic configurations has still not yet settled the question of the placement of several elements and discuss an alternative criterion based on maximizing triads of elements. I also point out another possible limitation to the reductive approach, namely the failure, up to now, to obtain a derivation of the Madelung rule. Mention is made of some recent similarity studies which could be used to clarify the nature of ‘elements’. Although it has been suggested that the notion of element as basic substance should be considered in terms of fundamental particles like protons and electrons, I resist this move and conclude that the quantum mechanical tradition has not had much impact on the question of what is an element which remains an essentially philosophical issue. (shrink)

Application of Einstein special theory of relativity in chemistry seems to be superfluous; energies are too low. The average velocity of electron in hydrogen atom is 1/135 c, making its actual mass only 26,6 ppm bigger than the rest mass. However, for heavier elements relativistic effects have to be taken into account and, more, many phenomena cannot be explained without ascribing new mass to electrons, in accordance with Einstein theory. In this paper such phenomena are described: color of metallic gold (...) and Bi and Pb compounds, contraction of Ln-X bond of lanthanide trihalides, voltage of lead-acid and Zn/HgO battery, and the shape of gold clusters. Besides, essentials of Einstein theory and quantum chemistry were problems concerning the validity of Lavoisier law. (shrink)

Usually within the context of computer simulations in quantum chemistry practices, there is a distinction between ab initio and semi-empirical methods. Related to this, a controversy within the scientific and philosophical communities came about regarding the superiority of the ab initio methods due to their theoretical rigor. In this article we re-evaluate the condition of the semi-empirical simulations in this area of research. We examine some of the aspects of this debate that have been considered in philosophy and provide additional (...) elements to the analysis. (shrink)

The recent exchange on the quantum justification of the Periodic System of the Elements in this Journal between Scerri [Foundations of Chemistry 6: 93–116, 2004] and Friedrich [Foundations of Chemistry 6: 117–132, 2004] is supplemented by some methodological comments.

This paper aims to show that there is a lot of philosophy in the philosophy of chemistry—not only in the problems and questions specific to chemistry, which this science brings up in philosophical discussions, but also in the topics of wider interest like reductionism and emergence, for which chemistry proves to be an ideal case study. The fact that chemical entities and properties are amenable to a quantitative understanding, to measurement and experiment to a greater extent than those in psychology (...) or biology, makes chemistry an ideal case study for those interested in reductionism and emergence. (shrink)

The aim of the present paper is to analyze the problem of the relationship between chemistry and physics, by focusing on the widely discussed case of the atomic orbitals. We will begin by remembering the difference between the physical and the chemical interpretation of the concept of orbital. Then, we will refer to the claim made in 1999 that atomic orbitals have been directly imaged for the first time. On this basis, we will analyze the problem from a new approach, (...) by comparing the concept of orbital used in physics with the concept of orbital used in chemistry. Such an analysis will allow us to argue for an ontological pluralism that admits the coexistence of different ontologies without priorities or metaphysical privileges. From this philosophical framework, the concepts of chemical orbital and physical orbital correspond to two different ontologies. As a consequence, chemical orbitals are real entities belonging to the ontology of molecular chemistry, and can be observed like any other entity not belonging to the quantum mechanical ontology. DOI:10.5007/1808-1711.2010v14n3p309. (shrink)

I propose that a sociological and historical examination of nanotechnologists can contribute more to an understanding of nanotechnology than an ontological definition. Nanotechnology emerged from the convergent evolution of numerous "technical knowledge communities"-networks of tightly-interconnected people who operate between disciplines and individual research groups. I demonstrate this proposition by sketching the co-evolution of computational chemistry and computational nanotechnology. Computational chemistry arose in the 1950s but eventually segregated into an ab initio, basic research, physics-oriented flavor and an industry-oriented, molecular modeling and (...) visualization, biochemical flavor. Computational nanotechnology arose in the 1990s as a synthesis of these two subgroups, infused by people and practices from computational materials science, engineering, computer science, and elsewhere. I show that to understand the aims and outcomes of computational nanotechnology-and nanotechnology more generally-we need to understand relationships between different, but related, nano knowledge communities and their dependence on particular practices, artifacts, and theories. (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)

A personal account is presented for the present status of mathematical chemistry, with emphasis on non-numerical applications. These use mainly graph-theoretical concepts. Most computational chemical applications involve quantum chemistry and are therefore largely reducible to physics, while discrete mathematical applications often do not. A survey is provided for opinions and definitions of mathematical chemistry, and then for journals, books and book series, as well as symposia of mathematical chemistry.

The analysis of the concept of orbital allows us to argue that—in opposition to a recent position in philosophy of science—it is impossible to defend the autonomy of the chemical reality in regard to physical reality, appealing to the idea that there is a conceptual rupture among a chemical interpretation and a quantuminterpretation of the concept. This is the case because there are not two different interpretations of the concept of orbital. On the contrary, the concept involved in structural chemistry (...) and in quantum chemistry comes from quantum mechanics.El análisis del concepto de orbital permite argumentar—en oposición a una propuesta reciente en filosofía de la química—que no es posible defender la autonomía ontológica de la realidad química respecto de la física, sobre la base de una ruptura conceptual entre una interpretación química del concepto y otra propia de la mecánica cuántica. Esto es así porque no existen tales interpretaciones distintas del concepto de orbital, sino que, por el contrario, este concepto en química cuántica y en química estructural proviene de la mecánica cuántica. (shrink)

The past decade or so has witnessed an increase in the number of philosophical discussions about emergence and reduction in science. However, many of these discussions (though not all) remain too abstract and theoretical, and are wanting with respect to concrete examples taken from the sciences. This dissertation studies the topics of reduction and emergence in the context of a case study. I focus on the case of chemistry and investigate how emergentism can help us secure the autonomy of this (...) discipline in relation to the underlying microphysics. I develop an account of emergence (called functional emergence) that is, I argue, capable of answering the question of why we have chemistry instead of just applied quantum mechanics. I argue that functionally emergent properties in chemistry -- properties that are defined by their behaviour, not by some shared microphysical constituent -- can help us defend the autonomy of chemistry; they allow for the existence of sui generis chemical regularities, which can be used in sui generis chemical explanations. Functional emergence generates difficulties for some accounts of inter-theoretic reduction, but unlike other theories of emergence it is compatible with weaker forms of reductionism. (shrink)

In robustness analysis, hypotheses are supported to the extent that a result proves robust, and a result is robust to the extent that we detect it in diverse ways. But what precise sense of diversity is at work here? In this paper, I show that the formal explications of evidential diversity most often appealed to in work on robustness – which all draw in one way or another on probabilistic independence – fail to shed light on the notion of diversity (...) relevant to robustness analysis. I close by briefly outlining a promising alternative approach inspired by Horwich’s (1982) eliminative account of evidential diversity. (shrink)