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Topics in molecular organization and engineering

From Geometrical Molecules to Topological Molecules: A Quantum Mechanical View

Paul G. Mezey

Published Jan 1, 1988• 9 citations
Publisher
DOI
10.1007/978-94-009-2851-0_2

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Abstract The classical concept of molecular structure (namely, a set of atoms with a well‐defined geometrical arrangement in space) originated well before the advent of quantum theory, and, contrary to widespread views, these two conceptual schemes (classical molecular structure and quantum theory) are not easy to reconcile. We begin with a preliminary discussion of molecular structure in terms of space and time correlations in the framework of quantum theory. Then we summarize the salient features of some critical views raised‐during recent years (essentially by Woolley) concerning the concept of molecular structure. The essential claim of this viewpoint is that “molecular structure” is not an intrinsic attribute of an isolated molecule, and appears rather as an effect of the environment (other molecules? vacuum electromagnetic field, according to quantum electrodynamics?). Afterwards, we discuss these issues in detail: we show that it is necessary to distinguish between a “quantum” or “potential” structure (which may be deduced in a straightforward way from the quantum treatment of the molecule), and the “classical” molecular structure (according to which the molecule is considered as a set of rotating and vibrating material points, corresponding to the atoms); we briefly discuss some aspects of the Born–Oppenheimer approximation. From our discussion, we deduce that the “classical structure” concept is indeed non‐trivial from a purely quantum‐mechanical point of view; in actual fact, it is related to the problem of the “classical limit” of quantum mechanics, and it appears that, at the present time, none of these classical concepts and behaviours is convincingly derivable from a strict quantum mechanical basis. Finally, we consider these same problems from the point of view of stochastic electrodynamics (SED), which is one of the stochastic models for microphysics proposed so far as a possible alternative or extension of usual quantum theory. In the framework of such a theory, the “classical limit” and, in particular, the “classical molecular structure” no longer poses a problem, but aside from these satisfactory qualitative aspects, several quantitative failures of SED prevent us from accepting it, at least in its present state, as a genuine physical alternative to quantum theory. We therefore conclude that “classical molecular structure”, and classical concepts in general, remain an open problem in the framework of present‐day quantum physics.

Israel Journal of Chemistry•Jan 1, 1980•88 citations
The Chiral-Induced Spin Selectivity (CISS) effect—where electrons are filtered by their spin when passing through chiral molecules—presents a major puzzle in quantum biology. Conventional theories often rely on assumed strong internal electric fields. We propose a radical alternative based on Superfluid Vacuum Topological-Geometric Dynamics (SV-TGD): CISS is a macroscopic hydrodynamic sieving process. In this view, an electron is a microscopic vortex carrying circulation, and a chiral molecule acts as a "rifled barrel" that imposes a helical vortex field on the vacuum fluid. Spin-matched electrons flow smoothly; spin-mismatched ones are deflected by a transverse Magnus force. This purely mechanical picture yields testable predictions and stems from a deeper identity: the Lorentz force is mathematically equivalent to the Magnus force in a fluid vacuum.
Abstract This study introduces a geometric framework to explain how quantum particles, specifically protons, move through energy barriers in biological molecules like DNA. Rather than viewing this tunneling as a purely random event, we propose that it is governed by the structural complexity of the surrounding molecular environment. By treating the energy landscape as a geometric shape, we demonstrate that the environment acts as a regulator that either facilitates or hinders the movement of protons between genetic base pairs. We applied this model to compare the two primary building blocks of the DNA ladder: the Guanine-Cytosine (G-C) and Adenine-Thymine (A-T) pairs. Our findings reveal that the G-C pair possesses a structural configuration that makes proton movement significantly more likely compared to the A-T pair. This difference provides a clear physical explanation for why certain parts of our genetic code are more prone to spontaneous changes, or tautomeric shifts, which can lead to mutations. Furthermore, the research explores how the DNA molecule interacts with its surrounding cellular noise (e.g. water molecules and proteins). We find that the proton behaves in a hybrid manner (at times acting like a coherent wave that exists in multiple places at once), and at other times like a solid particle trapped by its environment. This dual behavior suggests that life operates at a delicate balance between quantum mechanical effects and classical stability.
Abstract The classical concept of molecular structure (namely, a set of atoms with a well‐defined geometrical arrangement in space) originated well before the advent of quantum theory, and, contrary to widespread views, these two conceptual schemes (classical molecular structure and quantum theory) are not easy to reconcile. We begin with a preliminary discussion of molecular structure in terms of space and time correlations in the framework of quantum theory. Then we summarize the salient features of some critical views raised‐during recent years (essentially by Woolley) concerning the concept of molecular structure. The essential claim of this viewpoint is that “molecular structure” is not an intrinsic attribute of an isolated molecule, and appears rather as an effect of the environment (other molecules? vacuum electromagnetic field, according to quantum electrodynamics?). Afterwards, we discuss these issues in detail: we show that it is necessary to distinguish between a “quantum” or “potential” structure (which may be deduced in a straightforward way from the quantum treatment of the molecule), and the “classical” molecular structure (according to which the molecule is considered as a set of rotating and vibrating material points, corresponding to the atoms); we briefly discuss some aspects of the Born–Oppenheimer approximation. From our discussion, we deduce that the “classical structure” concept is indeed non‐trivial from a purely quantum‐mechanical point of view; in actual fact, it is related to the problem of the “classical limit” of quantum mechanics, and it appears that, at the present time, none of these classical concepts and behaviours is convincingly derivable from a strict quantum mechanical basis. Finally, we consider these same problems from the point of view of stochastic electrodynamics (SED), which is one of the stochastic models for microphysics proposed so far as a possible alternative or extension of usual quantum theory. In the framework of such a theory, the “classical limit” and, in particular, the “classical molecular structure” no longer poses a problem, but aside from these satisfactory qualitative aspects, several quantitative failures of SED prevent us from accepting it, at least in its present state, as a genuine physical alternative to quantum theory. We therefore conclude that “classical molecular structure”, and classical concepts in general, remain an open problem in the framework of present‐day quantum physics.