Keywords: development of contemporary chemistry, complexity and inexhaustibility of matter, novelty, by-products, molecular structure, realism.
Let us try to sketch the developmental features of contemporary chemistry. Apparently, synthetic chemistry, both in its traditional fields, as well as in recent developments (e.g. dendrimer chemistry, inclusion compounds chemistry, etc.) forms a very big part of current chemical research. (Synthetic chemistry is a unique science in that it produces the objects it is interested in.). However, remarkable advances have taken place also in other branches of chemistry dealing with molecular reactivity (like photochemistry, electrochemistry, and, in a way, mass spectrometry), and in the field of reaction mechanisms. Furthermore, a huge number of analytical and physicochemical studies have appeared in the literature, either aiming at the explication of reaction mechanisms (identification of reaction intermediates, spectroscopic investigation of transition states, kinetic and isotopic labeling studies) or centered on specifically structural aspects (structure determination of complex natural compounds, description of structural features of unusual compounds, e.g. fullerenes, strained small ring systems, etc.).
Moreover, chemistry has demonstrated a remarkable capacity to describe phenomena in terms of molecular structure, to conceive facts in terms of molecular constitution and spatial arrangement of molecules. In fact, during the second half of this century advances in the understanding of molecular mechanisms of natural systems have been impressive. While one may give examples galore, suffice it to remember the discovery of the double-helix structure of DNA, through which the mechanism of transmission of hereditary characters has been explained, and the identification of the biochemical reactions that constitute the photosynthetic process. Undoubtedly, such an extensive comprehension of natural phenomena  has been possible thanks to the isolation and structure elucidation of molecules belonging to a great number of natural systems, molecules which (let us think, for example, of biomolecules) are often complex to a high degree.
Thus, the field of application of contemporary chemistry is wide, comprising different branches of biology, earth sciences, material sciences, and so on.
Naturally, at a given moment of history, the ability to explain facts in chemical terms is not unlimited: when, in very complex molecular aggregates, such as, for example, organelles, properties that are no longer explainable in chemical terms emerge from the whole of molecular interactions, a different scientific approach is needed. Such is possible thanks to the disciplines that are immediately higher than chemistry in the hierarchy of complex systems, i.e. cellular biology, pharmacology, genetics, physiology, etc.
A complete analysis of the historic, psychological, and methodological elements of the development of chemistry is beyond the scope of this paper. Undoubtedly, such elements are complex and not understandable only in terms of a utilitarian conception of science, according to which the growing need of society for new, useful materials would be the only raison d’être for chemical synthesis. As for the factors in the present stage of evolution of chemistry, I would just mention that the interaction with other sciences, i.e. physics and mathematics on the one hand, and biology and other natural sciences on the other, has indeed given a substantial boost to modern chemistry.
Several interesting philosophical issues of chemistry emanate from a
reflection on developmental aspects of modern chemistry. We have grouped
our considerations into three main themes. In Sect. I, we shall point out
how unexpected anomalies are the very essence of scientific research. They
form the way to get detailed descriptions of phenomena that take into account
more and more particulars, and thus lead to a deeper understanding of the
physical systems under study, more and more conforming to the inexhaustible,
abysmal complexity of the real, with its mysterious, original irreducibility.
On this ground, we shall consider from a chemical viewpoint the idea of
inexhaustibility, or bottomlessness, of the material being. We shall bear
in mind this idea in Sect. II, where the problem of formation of by-products
in chemical reactions will give us a clue to speak of the limits of human
capacity for scientifically understanding, or describing, certain aspects
of the physical world. In Sect. III, we shall propose arguments based on
the accomplishments and advances of modern chemistry for a realistic interpretation
of molecular structure.
Modern (Galilean) sciences rely on the application of experiments, conceived on the basis of explanatory hypotheses, through which, once he had placed a portion of matter under certain artificial conditions, the researcher ‘puts nature some questions’. Thus, he is able to know, as far as quantity and relation are concerned, aspects of reality, thanks to mathematics, which establishes relationships between quantities by means of equalities, inequalities, equations etc. Chemistry falls into this scheme, though it makes use of largely non-mathematical formal instruments (pivoted on the fundamental concept of molecular structure) which were conceived through a very long process, which was to a large extent autonomous and independent of physics.
On the basis of the experimental outcomes we note regularities, which we call laws, and elaborate models and theories, through which we are able, at least potentially, to reveal some aspects of the material systems under study. We formulate new explanatory hypotheses, thence devise experiments that can be applied to analogous systems, or even to systems with a higher degree of complexity. In this way the progress of a scientific discipline is realized, that is we know more and more aspects of the physical world.
We cannot scientifically investigate reality as such. Therefore, as stated above, we examine portions of reality, usually referred to as systems, which, as far as possible, we must define in an unambiguous manner, and which we think of as being discrete parts of the universe. In practice they are something much smaller and less complex compared with the objects and phenomena we experience in everyday life. The real is so complex that global scientific representations of too big or too complex portions of it are elusive.
According to the post-Newtonian view, the systems of the physical world belong to hierarchically ordered complexity levels. Upon perceiving reality on a rather fixed level of complexity every scientific discipline marks out a locus, from which the sensible, corporeal being is, at least in part, comprehensible by means of descriptions, models, or laws. That is to say, that the ‘sense of matter’ – as far as quantitative and relational aspects of a certain complexity level are concerned – is intelligible, its congruousness, its orderliness being recognized; i.e. form, proportion, and structure of this congruousness can be approximately determined.
Obviously, neither chemistry (or any of the other natural sciences), nor science as a whole can clarify a phenomenon completely:
If we regard the substantial growth of modern synthetic chemistry against the background of such a strict requirement of novelty, we may conclude that, from a chemical-structural viewpoint, reality is extremely rich in novelty. In fact, the prolonged exertion of chemical inquiry has not resulted in the reduction of chances of making new discoveries. On the contrary, the more compounds we prepare, the greater are our synthetic prospects; i.e., a ‘virtuous circle’ has set up resulting in an exponential growth of chemical synthesis. In consequence, on preparing and analyzing so many molecules, the architectural complexity of which is astonishing sometimes, modern chemistry has shown that matter can be subjected to a huge number of transformations, a process which seems to have unlimited possibilities. In other words, matter has an impressive and potentially infinite structural, hence functional, diversity.
Modern physics perceives the bottomlessness of matter concerning the immensity of the celestial body on the one hand, and concerning the apparently endless possibility of disassembling the structure of the sub-atomic world, on the other. Unlike that, chemistry (and molecular biology) perceives the deepness, the inexhaustibility of matter in terms of the potentially infinite number of substances, which could be prepared, and of the organizational complexity of its microscopic components. Let us think, for example, of the process of protein folding, which results from the complicated, puzzling interplay of intramolecular forces. Let us think, above all, of the astounding complexity of the organization of the cell at the molecular level. Though detailed, inclusive descriptions of the functioning of living organisms in molecular terms are elusive, we are able to know by intuition the marvelous order existing at the biological level of matter:
In brief: at one moment of history, science is a magmatic scenery, the irreversible development of which is affected by innumerable factors, among which are cultural, or even social and political factors.
That does not mean that scientific knowledge is totally produced by the social context. For that matter, I agree with Koyré, who, on the basis of a "sufficiently realistic conception of the scientific knowledge" (Strumia 1992, p. 131, my translation) attributes a certain degree of autonomy from external factors to the scientific enterprise.
On the whole, I think the advance of scientific knowledge may be metaphorically
compared to the exploration of an unknown, woody territory following interlacing
paths, rather than to a trip on long, straight asphalt roads. In both cases,
our possible movements are fixed, for we follow pre-existent routes. However,
in the first case we must from time to time choose one of the many possible
alternative itineraries, the choices being influenced by several factors.
As for the lack of epistemological grounds for condition ii), one may object that products formed in very low yield relate to reaction pathways of minor importance, precisely because low amounts of those products were formed. However, a statement like this again rests in part on prevailing cultural values (e.g. the idea of profit) and, what is more, there are indeed several strictly chemical arguments against it.
However, our ability to study products formed in lower and lower yields is limited. To whatever extent reactions may be scaled up in order to isolate by-products, however powerful our analytical instruments may become, there will presumably remain a fathomless depth of reactions due to the myriad of products formed in infinitesimal quantities, which we will not be able to say anything about. This kind of considerations might be cautiously generalized. Apart from cultural customs, prevailing opinions, etc., which may prevent us from observations that might improve our scientific understanding of the world, there is an intrinsic limitation of our human nature. For practical reasons we are not able to investigate extremely reduced systems properly at the chemical level, or to study phenomena whose dimensions are too minimal.
What is more, I think one cannot exclude the possibility that minimal
unfathomable structural elements generate, modify, or influence properties
of systems on a higher level of complexity, e.g. the macromolecular
or cellular level – provided that variations of these elements are adequately
amplified through ordered structures, so that minimal pieces of information
can be transmitted to higher levels and eventually turned into macroscopic
effects. In fact, organic and medicinal chemists often experience that
minor structural changes in molecules cause remarkable effects on chemical
reactivity and biological activity, respectively. Reasonings based on classical
chemical concepts, such as ‘steric hindrance’, ‘lipophilicity’, ‘bond polarization’,
‘electronegativity’, etc., do not always account for these effects.
Anyway, this should not be surprising, if we but keep in mind that certain
hormones are active, i.e. they produce physiological responses,
at 10-12 M concentrations! In brief, if
we are concerned with highly organized, complex systems, such as biological
systems, unfathomable structural elements may be no longer negligible.
It is worthwhile to pause upon the differences between the analytical procedures most commonly employed to investigate chemical structure. On the one hand, there are spectroscopic methods based on the absorption of radiant energy corresponding to the transition between distinct energy states, such as IR, NMR, and UV spectroscopy. On the other hand, there are mass spectrometry and elemental analysis based on principles which are completely different from those of absorption spectroscopy. Mass spectrometry utilizes the chemical processes, namely the formation of ions and their successive fragmentation (which is indirectly determined by measuring the molecular weight of the gaseous fragments), after the sample has been subjected to vaporization and electron impact (EI). In elemental analysis, which is also a degradative method, the sample is combusted and the resulting amounts of water, carbon dioxide (as well as other compounds, depending on which elements are present in the substance) are determined.
Among further analytical methods, we should at least mention the degradative method of structure deduction by means of reasoning based on chemical behavior. Though it has been supplanted by modern spectroscopy, it is historically significant. This method is exclusively grounded on chemical properties of substances. Chemists used it, not seldom brilliantly, in order to establish the structure of sometimes very complex natural compounds. In supporting the argument of the present Section, the results obtained by means of such degradative procedures have been confirmed by instrumental analysis.
As far as geometrical features and thermodynamic data (such as bond distances and angles, enthalpies of formation, conformational preferences, and so on) are concerned, theoretical calculations and the results coming from experimental approaches, such as NMR and IR spectroscopy, X-ray diffraction, etc. are often comparable. In brief, on applying different methods to the same system we obtain primary results that are unlike in kind or character (e.g. the ‘external’ appearance of a set of numbers from a computer calculation is quite different from, say, an X-ray map, which is in turn different from an NMR, or mass spectrum). Nonetheless, we can interpret these results to give structural representations that, in general, are consistent with each other.
Owing to the growth of synthetic chemistry, the structure of an impressive
number of molecules has been determined. The process of structure elucidation
takes place every day in the laboratories all over the world where classes
of molecules with totally different structural features are studied. Resulting
from such a huge analytical effort, there is, as it were, an overall congruity
of structural data.
As a consequence, today we are able to rationalize a variety of material
properties of substances in terms of molecular structure. For example,
we can explain how, in a series of homologous hydrocarbons, the melting
(or boiling) points vary according to molecular weight, or, in a series
of isomers, to the degree of branching; we can give a valid explanation
for the color of the sky, the antiknocking properties of globular molecules
like tetraethyllead, the difference between the macroscopic characteristics
(i.e. stretchability, elasticity, tensile strength, and softness
to the touch) of wool and silk. We also better and
better understand chemical reactivity, both by means of coarse, non-formalized
structural concepts, such as ‘steric hindrance’, ‘nucleophilicity’, etc.,
and by sophisticated computer modeling of transition states. Moreover,
as already mentioned in the Introduction, nowadays we are able to describe
and interpret a great many different natural processes consistently in
molecular terms, among which photosynthesis, transmission of hereditary
characters, aging of documents depending on the type of paper and ink,
In addition, the fact that analytical methods depending on totally different physical principles give results that converge at identical descriptions of molecular structure supports the steady consistency that the objects, we call ‘molecules’, have in responding to dissimilar actions done on them from the outside. In other words, molecules are not provisional appearances originating in the interaction between theory (and the experiments based on it) and matter. If it were so, one may reasonably suppose that experimental methods based on different principles give results not consistent with each other. The phenomenalistic conception of science leads one to believe that every observation is distorted "by a theory of the object that is to be observed, a theory on whose basis the experimental instrumentation is devised. As a consequence, that which one observes is not the real in itself, but the phenomenon resulting from the interaction between theory and fact. Carrying this idea to extremes Feyerabend conceives what we call an experimental fact as chiefly determined, in its informational content, by the theory that frames and interprets it. An experimental fact actually is a theoretical fact, since it can be conceived only through an observational language; if we changed this language, the fact would be no longer interpretable and comprehensible." (Strumia 1992, pp. 169-170, my translation, italics in the text). That is tantamount to saying that, according to the phenomenalistic theory, the material being is something undifferentiated, something easily moldable by the experiment. Accordingly, one could reasonably assume that different methods would give correspondingly different forms to the objects under examination, and this would result in incomparable, or even contradictory results. However, if we but consider the acquirements of contemporary chemical research (see above), it is much sounder to admit that matter possesses a real structure at the molecular level, a structure which a suitable chemical investigation, conceiving a veridical image of molecules, describes, albeit approximately.
I would like to remark on this last word; stating that matter possesses a real structure at the molecular level does not mean that actual molecules are somehow reducible to any of their structural models, for a model is after all only an abstract, simplified representation conceived mentally. Unavoidably, as H. Belloc once briefly stated, "consciousness [of matter] is not material." The whole truth of the physical objects called molecules is something fathomlessly complex, as is the reality of any physical object – if only owing to the fact that it is a portion of matter assembled in a complex way, the basic units of matter (the famous ‘atoms and quanta’) being themselves characterized by a remarkable and apparently elusive degree of complexity, as modern physics has indeed shown. As for molecules, they are not something ‘stiff’, but possess an ‘inward dynamism’. A molecule may be characterized as a system consisting of a dynamic equilibrium between a potentially infinite number of conformers, some of which energetically favored. A molecule may be also characterized by a set of distinct energy levels, so that changes in the environmental conditions (e.g., when energy is supplied from the outside) may result in transition from a rotational, vibrational, or electronic ground state to an excited state or even in a change of the energy levels. It is worthwhile remembering that the question of the validity of quantum descriptions of molecules based on Born-Oppenheimer theorem has been raised in connection with the dynamics of molecules.
We also ought to keep in mind that, unless we consider an ideal gas, i.e. an imaginary, abstract model, it is not possible to conceive of molecules as being isolated individual entities. Although a highly rarefied gas may be considered practically ideal, the interactions between its molecules being minimized, most of the systems chemical research deals with are in the liquid or solid state. In reality, an extremely rich organizational (hence functional) state at the microscopic level, resulting from the participation of molecules in the formation of quasi-molecular species, i.e. molecular aggregates formed through hydrogen bonds, van der Waals forces, etc., is characteristic of condensed matter. Hence, the idea of molecules as individual entities leads de facto to considerably simplified explanations of phenomena.
Clearly, molecular representations like structure formulas, but also pictographic representations including geometric details about angles and distances do not take into account, do not tell us anything about the aspects we have just surveyed: they only give a rather approximate description of a molecule. Nonetheless, as far as relational and quantitative aspects are concerned, they do say something about the ontology of molecules. In this regard, a metaphor, which has also been proposed by Del Re (1988), may be used: a photograph of a man (let us call him, say, Marco Bianchi) cannot define his personality, tell us the vicissitudes of his life, or reveal what percentage of his blood cells are red corpuscles. Yet, it would be absurd to deny that some real features of Mr. Bianchi are reproduced on it. Thus, the photograph is the vehicle for conveying true aspects of the personal reality of Marco Bianchi to our consciousness, the ‘amount of reality’ carried depending upon the quality of the photograph itself. Even a fuzzy photograph could still provide us information about Mr. Bianchi, for instance making us known of his height, build, etc.
This metaphor may also hint at the inconsistency of the claim that scientific
ideas are mere instruments of prediction, objective reality being not reflected
on them. If a friend of Marco Bianchi saw the Eiffel Tower standing out
against the background of our photo, he should infer that his friend had
visited Paris one day. Now, such an inference entails an act of identification,
that is, Marco Bianchi must be recognized in the photograph. In other words,
the correspondence, the assimilation between a portion of the physical
reality and the image obtained when that portion of reality is exposed
to the photographic process is granted. Interestingly, the verb ‘to recognize’
comes from the Latin word ‘recognoscere’, a word formed from the
root ‘gnosco’, ‘nosco’ (to come to know, know) by the addition
of the prefixes ‘re-’ (‘back’, ‘again’, ‘against’) and ‘co-’ (from
‘cum’, ‘with’). At least etymologically, recognition means that
one comes to know again.
 Of course, the understanding of natural phenomena in chemical terms is a process under constant refinement, for the molecular machinery to be examined is often highly complicated from a molecular-structural viewpoint. This is not surprising, given the complex nature of the overall processes to be achieved especially when biological processes are concerned. As for the chemical understanding of natural photosynthesis, for example, important advances in the comprehension of the two fundamental functions from the viewpoint of energy conversion, namely photo-induced charge separation, and energy migration in the so-called light harvesting antenna system, have been possible thanks to detailed structural information about reaction centers and antenna units. This kind of information has become available only in recent years; see the nice paper by Scandola et al. (1995).
 This will be the subject of a future paper.
 See Del Re 1994. For a general history of chemistry see, for instance, Leicester 1956; for a history of chemical theoretical thought see Solov’ev 1971.
 Suffice it to think, for example, of the neurobiological studies on memory (see Battaini and Govoni 1993). The very complex psychological and neuronal phenomena, of which learning and memory consist, are studied in terms of relatively simple synaptic events like long term potentiation (LTP) and depression (LTD). Also, one of the experimental models with which memory is studied is a marine snail called Aplysia Californica, whose nervous system consists of 20,000 neurons (human brain contains 1,000 billion neurons!)
 These themes are extensively treated in Strumia 1992.
 An interesting article by Bersanelli (1997) deals with the part the unforeseen event (l’imprevisto) plays in scientific discovery.
 This also applies to the other sciences of course.
 Cf. also Sect. III. 3.
 "Let us be aware that, however impossible it is to encounter such a thing as ‘raw datum’, our constitutive concepts had not emerged ex nihilo. They are the product of the active coping of our species with a reality irreducible to itself. Our ideas, at least our saner and more successful ones, bear always the impress both of ourselves and something beyond ourselves." (Sheehan 1981). See also Lorenz 1973 and Giussani 1997, pp. 23-33.
 As concerns chemistry, see the biochemical example of the digestion of the proteins in the gut, which is reported in the recent work by Akeroyd (1997). See also Del Re 1997, who has pointed out how the personal element is involved in scientific activity.
 As for this point, a telling (and pleasant to read) example is the discovery of radical deoxygenation (the reaction of Barton and McCombie); see Barton 1993, pp. 34-45. For another interesting example concerning benzodiazepines, see Sternbach 1977.
 This may also occur indirectly: though trivial per se, the preparation of a compound will be in fact published, if it forms part of a synthetic sequence of which some steps imply a novelty; or also, as usually happens in medicinal chemistry, when the novelty does not lie in synthetic aspects, but in the molecular description of the interaction between products and enzymes, receptor proteins, etc.
 See Schummer 1997. By the way, some chemists seem to guess at the thing: "The collection of reagents and reactions one can make use of, when planning a synthetic strategy, is now huge, and (often without any substantial justification) it continues to be enriched." (Rosini 1997, my translation).
 For example the isolation of several products in low yield enabled Moody and co-workers to elucidate reaction pathways of thermolysis of dienyl azides (Moody et al. 1985). Products formed in 1 % yield made possible the determination of the structure of a spiro dimer from methyl 2,3-Bis(chloromethy)thiophene-5-carboxylate possible (Takeshita et al. 1991). Davies and co-workers were able to rationalize the effect of the solvent on the rhodium(II)-catalyzed decomposition of vinyldiazomethanes in the presence of 1-methoxy-1-[(trimethylsilyl)oxy]buta-1,3 diene, leading to tropone derivatives, thanks to the observation of certain by-products (Davies et al. 1991).
 For example the palladium-catalyzed carbonylation and coupling of 1,2-dibromocyclopentene and aniline yields, among expected products, a dimer of the desired N-phenylimide derivative, the structure of which is unknown (Perry et al. 1991).
 For the role of analogy in the scientific knowledge see Del Re 1998, in particular sect. B.4; for a more extensive discussion see Strumia 1992, pp. 229-242.
 Here we shall not take into account the distinction, made by Schummer (1998), between structure formulas, to which the first part of our definition corresponds, and pictographic, geometrically detailed representations of molecules; although these two ways of describing molecular structure have a different linguistic significance, we shall assume that the two signs are different modes to look at the same object (cf. also the second part of footnote 25). This assumption seems to us a reasonable one, considering that, albeit a piece of information not stored in structure formulas, the geometrical characterization of a molecule presupposes an unambiguous spatial ordering of the parts which constitute the molecule itself, and this is precisely what structure formulas tell us. Moreover, on speaking of the possibility of a translation between the two languages, the author of the above paper, among other things, states that "the relative success of such translations […] gives at least some evidence of a common referential basis of the underlying theories of both type of representations."
 See for example Woolley 1978.
 EI has been the ionization method most commonly employed until now; however, many other ionization techniques are available today.
 The story of morphine structure elucidation provides a beautiful example in this regard; cf. Butora et al. 1998.
 Including both molecular orbital calculations (either ab intitio or semi-empirical methods) and the so-called molecular mechanics (or force fields calculations): again, methods which are theoretically different from one another, inasmuch as they make use of different mathematical models of molecular structure (though they all rest upon the classic notion of molecular structure, cf. the latter part of footnote 24).
 See for instance Bock et al. 1974 and Buyong Ma 1995. For a more specific example see Tontini et al. 1998. One may object, following for example Woolley 1978, that the kinds of quantum chemical calculations I consider here are in fact grounded on the classical theory of molecular structure, inasmuch as they make use of the Born-Oppenheimer separation of electronic and nuclear motion, hence they do not represent a ‘pure’ quantum mechanical approach to molecules. On the other hand, the above mentioned methods, inasmuch as theoretical, are in essence a kind of procedure different from empirical approaches, even if they all presuppose the classic notion of molecular structure as a common referential base. In fact, on the one hand we need only an algorithm to treat mathematical models of molecules computationally; on the other, a sample of substance is subjected to a physical action (data being subsequently treated according to theory, of course). It is on these grounds that I consider of interest the convergence of results mentioned in the text.
 Yet, occasionally, when applied to the same system, different methods, whose validity is unquestioned among the members of the chemical community, give responses apparently not reconcilable with each other. The determination of the microscopic structure of water is an interesting example (Benson & Siebert 1992; see also Bertagnolli 1992). With regard to apparently contradictory results, we might think to a town lying between two hills. Two completely different images of the same town will come into view from each of the two hilltops. If we took photographs from each hilltop and showed them to a stranger, he would say, perhaps, that those are views of two different towns, unless he is clever at finding common elements, which may be hidden through perspective phenomena.
 Chemically speaking, both materials are proteinaceous substances.
 The latter point may be related to the general ‘argument for the best explanation’, a type of reasoning used by some contemporary American philosophers of science (for an anthology covering inter alia some articles about this kind of argumentation see Leplin 1984). Interestingly, such an argument was first applied by Berzelius to chemistry, in that he reasoned that the law of multiple proportions would be a miracle without accepting Dalton’s atomism (J. Schummer, personal communication).
 Incidentally, starting from a reflection on the actual possibilities of synthetic chemistry, we have already come to a conclusion disproving such a conception of matter (cf. Sect. I.2).
 Cf. also the latter part of Sect. I.1
 Cf. Belloc 1992, sect. 3.ii.
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