. Computational chemistry grew in a new era of “desktop modeling,” which coincided with a growing demand for modeling software, especially from the pharmaceutical industry. Parameterization of models in computational chemistry is an arduous enterprise, and we argue that this activity leads, in this specific context, to tensions among scientists regarding the epistemic opacity transparency of parameterized methods and the software implementing them. We relate one flame war from the Computational Chemistry mailing List in order to assess in detail the (...) relationships between modeling methods, parameterization, software and the various forms of their enclosure or disclosure. Our claim is that parameterization issues are an important and often neglected source of epistemic opacity and that this opacity is entangled in methods and software alike. Models and software must be addressed together to understand the epistemological tensions at stake. (shrink)

El propósito del presente trabajo consiste en abordar la pregunta por la ontología de la química cuántica. Para ello nos concentraremos en el concepto de enlace químico desde la perspectiva de los dos enfoques a través de los cuales la ecuación de Schrödinger se aplica a los sistemas químicos moleculares: la teoría del enlace de valencia (EV) y la teoría del orbital molecular (OM). Sobre la base de la presentación de ambos enfoques y su comparación, señalaremos que, a pesar de (...) su denominación tradicional, no pueden considerarse estrictamente como teorías científicas, sino que se ajustan mejor a la noción de modelo; en particular, son modelos que incorporan conceptos y leyes tanto del ámbito de la mecánica cuántica como del de la química estructural. Estas consideraciones nos permitirán argumentar que la química cuántica no posee un referente ontológico autónomo, sino que se trata de un ámbito científico cuya vigencia descansa sobre su éxito práctico en el cálculo y la predicción. Finalmente, indicaremos de qué modo los enfoques EV y OM del enlace químico abren una nueva perspectiva respecto de la noción misma de modelo en ciencias empíricas. (shrink)

The dissemination of models across disciplinary lines has become a phenomenon of interest to philosophers of science. To account for this phenomenon, philosophers have invented two units of analysis. The first identifies to the thing that transfers, model templates. The second identifies the thing to which transferable templates apply, landing zones. There exists a dynamic between the thing that is transferred and the thing to which transferrable templates apply. The use of a transferable template in a new domain requires reconception (...) of domain-specific phenomena. This paper examines two cases of model transfer, the use of the ideal gas law in biology by R.A. Fisher and the use of the virial theorem in chemistry by Richard Bader. These two stories of model transfer in biology and chemistry indicate a dimension to conceptual progress related to this dynamic. Using discourse on model transfer affords philosophers a novel approach for depicting the invention of, for instance, chemical concepts and resulting disputes. (shrink)

Today, the lipid bilayer structure is nearly ubiquitous, taken for granted in even the most rudimentary introductions to cell biology. Yet the image of the lipid bilayer, built out of lipids with heads and tails, went from having obscure origins deep in colloid chemical theory in 1924 to being “obvious to any competent physical chemist” by 1935. This chapter examines how this schematic, strictly heuristic explanation of the idea of molecular orientation was developed within colloid physical chemistry, and how the (...) image was transformed into a reflection of the reality and agency of lipid molecules in the biological microworld. Whereas in physical and colloid chemistry these images considered secondary to instrumental measurement and mathematical modeling of surface phenomena, in biology the manipulable image of the lipid on paper became an essential tool for the molecularization of the cell. (shrink)

The theoretical solid-state physicist Walter Kohn was awarded one-half of the 1998 Nobel Prize in Chemistry for his mid-1960s creation of an approach to the many-particle problem in quantum mechanics called density functional theory (DFT). In its exact form, DFT establishes that the total charge density of any system of electrons and nuclei provides all the information needed for a complete description of that system. This was a breakthrough for the study of atoms, molecules, gases, liquids, and solids. Before DFT, (...) it was thought that knowledge of the vastly more complicated many-electron wave function was essential for a complete description of such systems. Today, 50 years after its introduction, DFT (in one of its approximate forms) is the method of choice used by most scientists to calculate the physical properties of materials of all kinds. In this paper, I present a biographical essay of Kohn’s educational experiences and professional career up to and including the creation of DFT. My account begins with Kohn’s student years in Austria, England, and Canada during World War II and continues with his graduate and postgraduate training at Harvard University and Niels Bohr’s Institute for Theoretical Physics in Copenhagen. I then study the research choices he made during the first 10 years of his career (when he was a faculty member at the Carnegie Institute of Technology and a frequent visitor to the Bell Telephone Laboratories) in the context of the theoretical solid-state physics agenda of the late 1950s and early 1960s. Subsequent sections discuss his move to the University of California, San Diego, identify the research issue which led directly to DFT, and analyze the two foundational papers of the theory. The paper concludes with an explanation of how the chemists came to award “their” Nobel Prize to the physicist Kohn and a discussion of why he was unusually well suited to create the theory in the first place. (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)

This paper argues that a significant focus in computational organic chemistry, alongside the construction and deployment of models, is the “deconstruction” of computational models. This practice has arisen in response to difficulties and controversies resulting from the use of plural methods and computational models to study organic reaction mechanisms. Diagnostic controllability is the capacity of cognitive agents to gain epistemic access to grey-boxed computational models, to identify and explain the impact of specific idealizations on results, and to demonstrate the applicability (...) of computational methods to target systems. (shrink)

This paper first queries what type of concept of emergence, if any, could be connected with the different chemical activities subsumed under the label ‘quantum chemistry’. In line with Roald Hoffmann, we propose a ‘rotation to research laboratory’ in order to point out how practitioners hold a molecular whole, its parts, and the surroundings together within their various methods when exploring chemical transformation. We then identify some requisite contents that a concept of emergence must incorporate in order to be coherent (...) from the standpoint of the scientific practices involved. In this respect, we finally propose a relational form of emergence which pays attention to the constitutive role of the modes of intervention and to the co-definition of the levels of organization. No metaphysical distinction between the higher and basic levels of organization is supposed, but only a plurality of modes of access. Moreover, these modes of access are not construed as mere ways of revealing intrinsic patterns of organization but, on the contrary, are considered to be active elements on which the constitution of those patterns depends. What is at stake in this paper is therefore not an ontological form of emergence but an agnostic one which fits what chemists do in their daily work. (shrink)

Harold Kincaid in Individualism and the Unity of Science postulates a model of unity-without-reduction in order to accurately describe the relation between individualism and macroeconomics. I present this model and apply it to the description of the relation between chemistry and quantum mechanics. I argue that, when it comes to the description of molecular structure, chemistry and quantum mechanics are unified in Kincaid’s sense. Specifically, the two disciplines contribute to the formation of a unified body of knowledge with respect to (...) molecular structure. (shrink)