It is argued that the conventional descriptions of chemical bonds as covalent, ionic, metallic, and Van der Waals are compromising the usefulness of quantum mechanics in the synthesis and design of new molecules and materials. Parallels are drawn between the state of chemistry now and when the idea that phlogiston was an element impeded the development of chemistry. Overcoming the current obstacles will require new methods to describe molecular structure and bonding, just as new concepts were needed before the phlogiston (...) theory could be set aside. (shrink)

For many decades, chemists regarded rigid models of molecular structure as representing structures of real molecules as their attributes. However, new experimental data required a new theoretical conceptualization. The rigid model has been replaced with a dynamic model in which molecular structure is changed under the influence of environmental conditions. The above case shows some problems connected with recognizing theoretical models as structural representations of real empirical systems. Owing to the fact that theoretical models of molecular structure obtain local interpretations (...) with a procedural character, they can be carriers of specific information about structures of real molecules. Finally, I argue that, although theoretical models can be well corroborated empirically, they cannot be treated as representations of real empirical systems but can play a very important role in experimental practice. (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)

What, precisely, is `salt'? It is a certainwhite, solid, crystalline, material, alsocalled sodium chloride. Does any of that solidwhite stuff exist in the sea? – Clearly not.One can make salt from sea water easily enough,but that fact does not establish thatsalt, as such, is present in brine. (Paper andink can be made into a novel – but no novelactually exists in a stack of blank paper witha vial of ink close by.) When salt dissolves inwater, what is present is no (...) longer `salt' butrather a collection of hydrated sodium cationsand chloride anions, neither of which isprecisely salt, nor is the collection. Theaqueous material in brine is also significantlydifferent from pure water. Salt may beconsidered to be present in seawater, but onlyin a more or less vague `potential' way.Actually, there is no salt in the sea. In bothancient and modern treatments of otherimportant chemical concepts, including thenotions of `element', related complication,especially polysemy (terms with multiplemeanings), also occurs.In a recent paper, Paul Needham discussed the(predicable) properties of chemical substances,phases, and solutions. He provided a valuablecharacterization of cases in which severalquantities occupy the same space. He alsoconcluded that solution properties are not`intensive', because solvent and solute do nothave parts in common. He tacitly assumed thatingredients are not altered by their inclusionin a solution. This may be the case in somespecial cases (deutero-benzene dissolved inbenzene, say) but is not true in general – andcertainly does not apply to the case of brine,which Needham used as an example – since theions that exist in the solution, and also theaqueous material there, are quite differentfrom the pure ingredients used in making thesolution. An adequate theory of wholes andparts (mereology) must take into account thatwhen individuals enter combinations ofinteresting sorts they no longer are the verysame individuals that existed prior to thecomposition. It appears that no such formaltheory now actually exists. (shrink)

In this paper, aspects of observable and non-observable based models are discussed. A survey of recent literature was done to show how using non-observable-based language carelessly may cause disagreement, even in professional research programs and incorrect assertions, even in prestigious journals. The relation between physical measurements and observables is discussed and it is shown that, in contrast to general belief, this relation may be complicated and not always straightforward. The decomposition of the system into basic subsystems (physical or conceptual) is (...) traced as the origin of non-observable-based languages. The possibility of defining new quantum mechanical observables for open quantum subsystems and of replacing them with non-observable-based concepts has been mentioned and the AIM theory is explained as an example. An account of some current non-observable-based models for molecular geometry is discussed and it is shown that not all non-observable-based languages possess the same effectiveness. In the end, the need to develop a clear chemical language is stressed. (shrink)

While the principal ideas of a systems theory for the molecular sciences have been introduced in part I (Reiher, 2003), illustrative examples for the ingredients of this systems chemistry are discussed in greater detail in this work. The potential wealth of systems chemistry is then demonstrated for a recently developed approach for the calculation of hydrogen bond energies in non-decomposable systems.

The issue of approximations is mostly neglected in the philosophy of science, and sometimes misinterpreted. The paper demonstrates that approximations are in fact in the core of some recent discussions in the philosophy of chemistry: on the shape of molecules, the Born-Oppenheimer approximation, the role of orbitals, and the physical explanation of the Periodic Table of Elements. The ontological and epistemological significance of approximations in the exact sciences is analyzed. The crucial role of approximations in generating qualitative images and comprehensible (...) models is emphasized. A complementarity relation between numerically 'exact' theories and explanatory approximate approaches is claimed. (shrink)