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The chemist’s concept of molecular structure

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Abstract

The concept of molecular structure is fundamental to the practice and understanding of chemistry, but the meaning of this term has evolved and is still evolving. The Born–Oppenheimer separation of electronic and nuclear motions lies at the heart of most modern quantum chemical models of molecular structure. While this separation introduces a great computational and practical simplification, it is neither essential to the conceptual formulation of molecular structure nor universally valid. Going beyond the Born–Oppenheimer approximation introduces new paradigms, bringing fresh insight into the chemistry of fluxional molecules, proteins, superconductors and macroscopic dielectrics, thus opening up new avenues for exploration. But it requires that our ideas of molecular structure need to evolve beyond simple ball-and-stick-type models.

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Notes

  1. Brown (2003a, b) has argued that molecular structure models should be seen as metaphors that reflect our conceptualization of chemistry and the manifestation of subconscious forms of understanding in the process of scientific reasoning.

  2. Structure can be quantified by structure factors, inter-particle distribution functions or pair correlation functions. Thus the two-particle density is given by:

    $$ \gamma ({\text{r}},\text{r}^{\prime}) = \int {{\text{dr}}_{3} \int {{\text{dr}}_{4} \ldots \int {{\text{dr}}_{\text{N}} \Uppsi *({\text{r}},\text{r}^{\prime},{\text{r}}_{3} ,{\text{r}}_{4} , \ldots {\text{r}}_{\text{N}} ) \Uppsi ({\text{r}}_{3} ,{\text{r}}_{4} , \ldots {\text{r}}_{\text{N}} )} } } $$

    where ψ(r, r′, r3, r4, … rN) is the quantum wave function as a function of the coordinates of all particles in the system, ψ* its complex conjugate and the integrals run over the coordinates of all particles but two. The two-particle density can further be integrated over angular coordinates to give the radial distribution function, a function of a single distance. See Fig. 2 for illustrative examples.

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  1. Department of Chemistry & Biological Chemistry, Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA

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Sukumar, N. The chemist’s concept of molecular structure. Found Chem 11, 7–20 (2009). https://doi.org/10.1007/s10698-008-9060-7

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