The quantum theory of atoms in molecules (QTAIM) uses physics to define an atom and its contribution to observable properties in a given system. It does so using the electron density and its flow in a magnetic field, the current density. These are the two fields that Schrödinger said should be used to explain and understand the properties of matter. It is the purpose of this paper to show how QTAIM bridges the conceptual gulf that separates the observations (...) of chemistry from the realm of physics and do so in a manner that is both rigorous and conceptually simple. Since QTAIM employs real measurable fields, it enables one to present the findings of complex quantum mechanical calculations in a pictorial manner that isolates the essential physics. The time has arrived for a sea change in our attempts to predict and classify the observations of chemistry, time to replace the use of simplified and arbitrary models with the full predictive power of physics, as applied to an atom in a molecule. (shrink)

In this paper I discuss some consequences and manifestations of a mereology of structured wholes in chemistry, with particular reference to the concept of atoms in molecules.

By moving away from the traditional reductionist reading of the quantum theory of atoms in molecules, in this paper we analyze the role played by QTAIM in the relationship between molecular chemistry and quantum mechanics from an emergentist perspective. In particular, we show that such a relationship involves two steps: an intra-domain emergence and an inter-domain emergence. Intra-domain emergence, internal to quantum mechanics, results from the fact that the electron density, from which all the other QTAIM’s concepts are (...) defined, arises from the wavefunction as a coarse-grained magnitude. Inter-domain emergence involves an analogical link, a mapping, between QTAIM’s entities, such as topological atoms and bond paths, and the entities that populate the molecular-chemistry domain, such as chemical atoms and chemical bonds. (shrink)

The problem of the reduction of chemistry to physics has been traditionally addressed in terms of classical structural chemistry and standard quantum mechanics. In this work, we will study the problem from the perspective of the Quantum Theory of Atoms in Molecules, proposed by Richard Bader in the nineties. The purpose of this article is to unveil the role of QTAIM in the inter-theoretical relations between chemistry and physics. We argue that, although the QTAIM solves two relevant obstacles (...) to reduction by providing a rigorous definition of chemical bond and of atoms in a molecule, it appeals to concepts that are unacceptable in the quantum–mechanical context. Therefore, the QTAIM fails to provide the desired reduction. On the other hand, we will show that the QTAIM is more similar to Bohmian mechanics and that the basic elements of both theories are closely related. (shrink)

It is with great delight that I have accepted the unexpected invitation to edit this two part special issue of Foundations of Chemistry dedicated to the philosophical aspects and implications of the quantum theory of atoms in molecules (QTAIM) (Bader 1990). This theory has been primarily the oeuvre of Richard F. W. Bader (1931–2012), one of his most significant (but not the only significant) contributions to chemistry. Bader’s contributions have been summarized in a tribute (Matta et al. 2011) (...) that appeared in a recent Festschrift of The Journal of Physical Chemistry A (2011). This special issue of Foundations is neither a duplication, a complement, or an afterthought to that Festchrift, nor is it intended as another tribute to this great scientist, as deserving as he may be, instead it serves an entirely different purpose. This issue is focused principally on the epistemology and ontology of the science of QTAIM. The sort of questions that are addressed in, or that should emerge from. (shrink)

The concepts of atoms and bonds in molecules which appeared in chemistry during the nineteenth century are unavoidable to explain the structure and the reactivity of the matter at a chemical level of understanding. Although they can be criticized from a strict reductionist point of view, because neither atoms nor bonds are observable in the sense of quantum mechanics, the topological and statistical interpretative approaches of quantum chemistry (quantum theory of atoms in molecules, electron localization (...) function and maximum probability domain) provide consistent definitions which accommodate chemistry and quantum mechanics. (shrink)

To be, or not to be, that is the question…In his wonderful Facts and Mysteries, Martinus Veltman terminates a section with an anecdote: “When quarks were not immediately discovered after the introduction by Gell-Mann he took to calling them symbolic, saying they were indices. In the early seventies I met him at CERN and he again said something in that spirit. I then jumped up, coming down with some impact that made the floor tremble, and asked him: Do I look (...) like a heap of indices? This visibly rattled him, and indeed after that he no more advocated this vision, at least not as far as I know” (see page 240 in Veltman 2003). Although it is probable that Murray Gell-Mann, the inventor of quarks, has changed his mind regarding the reality of his symbols after this tough conversation, even later in the start of eighties the reality of quarks, as basic constituents of protons and neutrons, was a matter of disputes and exchanges (Shrader-Frechette 1982a, b; Albright 1982; Gruender 1982). A g. (shrink)

Insights into the history of chemistry Content Type Journal Article DOI 10.1007/s11016-010-9482-4 Authors Peter J. Ramberg, Truman State University, 100 E. Normal, Kirksville, MO 63501, USA Journal Metascience Online ISSN 1467-9981 Print ISSN 0815-0796.

Jean Perrin’s proof in the early-twentieth century of the reality of atoms and molecules is often taken as an exemplary form of robustness reasoning, where an empirical result receives validation if it is generated using multiple experimental approaches. In this article, I describe in detail Perrin’s style of reasoning, and locate both qualitative and quantitative forms of argumentation. Particularly, I argue that his quantitative style of reasoning has mistakenly been viewed as a form of robustness reasoning, whereas I (...) believe it is something different, what I call ‘calibration’. From this perspective, I re-evaluate recent interpretations of Perrin provided by Stathis Psillos, Peter Achinstein, Alan Chalmers, and Bas van Fraassen, all of whom read Perrin as a robustness reasoner, though not necessarily in the same sort of way. I then argue that by viewing Perrin as a ‘calibration’ reasoner we gain a better understanding of why he believes himself to have established the reality of atoms and molecules. To conclude, I provide an alternative and more productive understanding of the basis of the dispute between realists and anti-realists. _1_ Introduction _2_ Perrin’s Reasoning: The Qualitative Argument _3_ Perrin’s Reasoning: The Quantitative Argument _4_ Perrin’s Realism _5_ Psillos, Achinstein, Chalmers, and van Fraassen on Understanding Perrin _6_ Conclusion. (shrink)

This paper develops an approach to the scientific realism debate that has three main features. First, our approach admits multiple criteria of reality, i.e., criteria that, if satisfied, warrant belief in the reality of hypothetical entities. Second, our approach is experiment-based in the sense that it focuses on criteria that are satisfied by experiments as opposed to theories. Third, our approach is local in the sense that it focuses on the reality of particular kinds of entities. We apply this approach (...) to a case that many philosophers have debated, namely, Jean Perrin’s work on atoms and molecules. We provide a novel account by arguing that Perrin’s work warranted a minimal belief in the reality of atoms and molecules as unobservable, discrete particles by satisfying a criterion of reality that we call experimental determination of number per unit. By doing so, he confirmed Avogadro’s hypothesis, but he did not confirm other key constituents of the atomic theories involved. We argue that our account of Perrin’s work is preferable to several other accounts, and we use this as a reason in support of our approach to the realism debate more generally. (shrink)

Research into learners' ideas aboutscience suggests that school and collegestudents often hold alternative conceptionsabout `the atom'. This paper discusses whylearners acquire ideas about atoms which areincompatible with the modern scientificunderstanding. It is suggested that learners'alternative ideas derive – at least in part –from the way ideas about atoms are presented inthe school and college curriculum. Inparticular, it is argued that the atomicconcept met in science education is anincoherent hybrid of historical models, andthat this explains why learners commonlyattribute to (...) atoms properties (such as beingthe constituent particles of all substances, orof being indivisible and conserved inreactions) that more correctly belong to otherentities (such as molecules or sub-atomicparticles). Bachelard suggested that archaicscientific ideas act as `epistemologicalobstacles', and here it is argued thatanachronistic notions of the atom survive inthe chemistry curriculum. These conceptualfossils encourage learners to develop an`atomic ontology' (granting atoms `ontologicalpriority' in the molecular model of matter); tomake the `assumption of initial atomicity' whenconsidering chemical reactions; and to developan explanatory framework to rationalisechemical reactions which is based on thedesirability of full electron shells. Theseideas then act as impediments to thedevelopment of a modern chemical perspective onthe structure of matter, and an appreciation ofthe nature of chemical changes at the molecularlevel. (shrink)

Atoms and molecules are particular kinds of restricted n-body systems, which generally behave as quasi-separable, unlike other n-body systems, e.g., Newtonian ones. The Coulomb repulsion and the Pauli exclusion principle in atoms and molecules are responsible for that separability. Additionally, chemical bonds, especially covalent bonds, enhance the separability of molecules. Independent particle models do not describe atoms and molecules since first-order energy corrections are high. However, these corrections obtained by the first-order perturbation or (...) mean-field strongly converge, implying a one-electron effective potential description. Consequently, stable states of atoms and molecules can be reasonably described by one-electron effective potentials, which strongly differ from other n-body problems. We discuss the peculiarities of the correlation motion of generic systems in the context of the four fundamental forces. In particular, we have shown that the two components (attraction and repulsion) of the electromagnetic force confer a relatively low correlation motion to atoms and molecules. We discuss the physical and chemical nature of atoms and molecules, comparing the degrees of separability between different systems. For example, the separability of Newtonian systems is generally possible in particular classes of restricted systems due to relative mass differences. However, for atoms and molecules, the separability is much broader. (shrink)

A novel non-classical mereological concept built up by blending the Metaphysics of Xavier Zubiri and the Quantum Theory of Atoms in Molecules of R. F. W. Bader is proposed. It is argued that this philosophical concept is necessary to properly account for what happens in a chemical reaction. From the topology of the gradient of the laplacian of the electronic charge density, \\) within the QTAIM framework, different “atomic graphs” are found for each atom depending on the molecular (...) context, reflecting how the whole molecule affects each atom. In this way, the whole molecular system imposes certain geometry onto each atom, and every atom exhibits different ontological modality. On the Metaphysical side, for X. Zubiri real things are system of different notes. The physical essence is the subsystem of essential notes with a coherence unity. Every note is grounded on the essence. The unity of the system is present somehow in every note-of beforehand, and every essential note-of turns towards the other. The essence determines the position of each note within the system, and hence is the grounding for modality of the notes. By conflating both “theories” and taking the atoms as essential notes, we propose the concept of “Molecule in atoms-of” or “atoms-of in Molecules”. Within the course of a chemical reaction the atoms-of modified their “of” as required by the new molecular unity being formed, and eventually change their modality. The validity to the Zubiri’s statements, is attained by evaluating necessity and possibility in a set-up of finite accessible “possible worlds”. (shrink)

The issue of shifting scales between the microscopic and the macroscopic dimensions is a recurrent one in the history of science, and in particular the history of microscopy. But it took on new dimensions in the context of early twentieth-century microscophysics, with the progressive realisation that the physical laws governing the macroscopic world were not always adequate for describing the sub-microscopic one. The paper focuses on the researches of Jean Perrin in the 1900s, in particular his use of Brownian motion (...) to produce evidence of the existence of atoms and in favour of the kinetic theory. His results were described by many contemporaries, and subsequently by historians, as the first direct proof of atomic and molecular reality. The paper examines the different strategies developed by Perrin for bridging the macro and sub-microphysical realms and making the latter accessible to the senses; even though neither atoms nor molecules were ever actually seen, and in fact very few visual representations were shown and published in connection with these experiments. This case provides a good example of how visualizing, representing and convincing could be interwoven in the production of evidence about the sub-microphysical realm circa 1900.Keywords: Jean Perrin; Brownian motion; Ultramicroscope; Evidence; Atom; Atomism. (shrink)

The human sensory experience of submolecular phenomena is only possible through complex technological mediations that include not just magnifications, but also manipulations of time and translations from one sense to another. In my creative moving image project Wildly Oscillating Molecules, I develop strategies for using an atomic force microscope (AFM) as a cinematographic instrument, specifically using its tactile mechanisms to generate video. Using the AFM over four years to generate experimental moving image installations, I examine my physical and psychological (...) experiences of this nanoscientific instrumentation. Although referred to by the philosopher of technology Don Ihde, the AFM's style of technological mediation has not been subjectively explored. Working to engage with an infinitesimal scale, the AFM has a unique style of spatial and temporal mediation that can be manipulated through the post-production and exhibition practices of the moving image. Wildly Oscillating Molecules provides insight into how the AFM influences human spatial and temporal perception of nanoscale phenomena and provides a new framework with which to analyse nanoscientific imaging practices. Understanding the nuances of technological mediation encourages science artists working with submolecular phenomena to adopt, evolve or transform properties of technological mediation when presenting their work to an audience. (shrink)

This paper suggests that the cases made for atoms and the aether in nineteenth-century physical science were analogous, with the implication that the case for the atom was less than compelling, since there is no aether. It is argued that atoms did not play a productive role in nineteenth-century chemistry any more than the aether did in physics. Atoms and molecules did eventually find an indispensable home in chemistry but by the time that they did so (...) they were different kinds of entities to those figuring in the speculations of those natural philosophers who were atomists. Advances in nineteenth-century chemistry were a precondition for rather than the result of the productive introduction of atoms into chemistry. (shrink)

In this pedagogical communication after demonstrating the legitimacy for using the quantum theory of atoms in molecules (QTAIM) to non-Coulombic systems, Hookean H2 +/H3 2+ species are used for AIM analysis. In these systems, in contrast to their Coulombic counterparts, electron density is atom-like and instead of expected two/three topological atoms, just a single topological atom emerges. This observation is used to demonstrate that what is really “seen” by the topological analysis of electron densities is the clustering (...) of electrons. The very trait of monotonic decay of electron density around the “centers” of clustering guarantees the appearance of topological atoms as basin of attraction of the gradient vector field of the electron density. Although observations with Hookean molecules may seem disappointing at first glance, a careful reasoning points to the fact that the QTAIM methodology is extendable to novel domains, by a knowledge of the morphology of underlying densities, beyond the typical Coulombic systems. (shrink)

Although chemical phenomena are primarily associated with electrons in atoms, ions, and molecules, the masses, charges, spins, and other properties of the nuclei in these species contribute significantly as well. Isotopes, for instance, have proven invaluable in chemistry, in particular the elucidation of reaction mechanisms. Elements with unstable nuclei, for example carbon-14 undergoing beta decay, have enriched chemistry and many other scientific disciplines. The nuclei of all elements have a much more subtle and largely unknown effect on chemical (...) phenomena. All nuclei are innately chiral and, because electrons can penetrate nuclei, all atoms and molecules are likewise chiral. This article describes in considerable detail the discovery of chiral nuclei, how this unusual chirality may influence the chemical behavior of atoms and molecules, and how atomic chirality may have been responsible for the synthesis of optically active molecules in the pre-biotic world. (shrink)

There have been occasions when the publication of a particular book has had a singular impact on the conceptual world of the chemist. Sometimes the publication occurs near the beginning of a major change in discourse, and sometimes more near the end. Jean Perrin published Les Atomes in 1913 as the culmination of a century-long controversy over the size and physical reality of atoms and molecules. After its publication almost all chemists and physicists agreed that atoms and (...) molecules of the size we currently understand to be appropriate are real physical objects. The story of the background, development, publication, content and response to Les Atomes forms the text of this paper. The content of Les Atomes is also the basis for extended reflection on the philosophical significance of the work of Jean Perrin. (shrink)

Slater’s method is an integral part of the undergraduate experience. In actuality, Slater’s method is part of an atomic model and not simply a set of rules. Slater’s rules are a simple means for computing the effective nuclear charge experienced by an orbital. These rules are based on the shell-like structure of the Slater atom in which outer shell electrons are incapable of shielding inner electrons. Slater’s model provides a qualitative description of the valence electrons in multi-electron atoms with (...) tremendous ease. The model is useful for explaining atomic properties such as ionisation energy, electron affinity and atomic radius qualitatively. Slater’s rules also correctly reproduce the Madelung rule of filling and the ionisation sequence (4s before 3d); however, these rules are not able to reproduce the anomalous configurations of atoms such as Cr and Cu. It is found that the atomic properties that Slater’s model reproduces are all related to the exponential decay factor of the Slater orbital. We find—from estimating the polarity of a diatomic molecule using a simple model—that molecular polarity is related to the difference in the exponential decay factors of the valence orbitals of the two atoms, implying that the decay factor acts as the electronegativity of the atom. (shrink)

This treatise presents thoughts on the divide that exists in chemistry between those who seek their understanding within a universe wherein the laws of physics apply and those who prefer alternative universes wherein the laws are suspended or ‘bent’ to suit preconceived ideas. The former approach is embodied in the quantum theory of atoms in molecules (QTAIM), a theory based upon the properties of a system’s observable distribution of charge. Science is experimental observation followed by appeal to theory (...) that, upon occasion, leads to new experiments. This is the path that led to the development of the molecular structure hypothesis—that a molecule is a collection atoms with characteristic properties linked by a network of bonds that impart a structure—a concept forged in the crucible of nineteenth century experimental chemistry. One hundred and fifty years of experimental chemistry underlie the realization that the properties of some total system are the sum of its atomic contributions. The concept of a functional group, consisting of a single atom or a linked set of atoms, with characteristic additive properties forms the cornerstone of chemical thinking of both molecules and crystals and Dalton’s atomic hypothesis has emerged as the operational theory of chemistry. We recognize the presence of a functional group in a given system and predict its effect upon the static, reactive and spectroscopic properties of the system in terms of the characteristic properties assigned to that group. QTAM gives physical substance to the concept of a functional group. (shrink)

This paper aims to cast light on the reasons that explain the shift of opinion—from scepticism to realism—concerning the reality of atoms and molecules in the beginning of the twentieth century, in light of Jean Perrin’s theoretical and experimental work on the Brownian movement. The story told has some rather interesting repercussions for the rationality of accepting the reality of explanatory posits. Section 2 presents the key philosophical debate concerning the role and status of explanatory hypotheses c. 1900, (...) focusing on the work of Duhem, Stallo, Ostwald, Poincaré and Boltzmann. Section 3 examines in detail Perrin’s theoretical account of the molecular origins of Brownian motion, reconstructs the structure and explains the strength of Perrin’s argument for the reality of molecules. Section 4 draws three important lessons for the current debate over scientific realism. (shrink)

Electronegativity is an important physico-chemical concept to study the chemical structure and reactivity. Although, the conundrum related to measurement of electronegativity still persists. In view of this fact, a simple yet rigorous scale of electronegativity, invoking an inverse relationship with atomic nucleophilicity index, has been proposed for 103 elements of the periodic table. The computed data follows periodicity distinctly satisfying all the sine qua non of a standard scale of electronegativity. Further, electronegativity values display a sound similarity with the standard (...) electronegativity scales validating the suitability of the proposed model. Molecular electronegativities of some polyatomic molecules have also been calculated using the proposed scale of electronegativity.Graphic. (shrink)

The Periodic Table has the column of the noble gas atoms (He, Ne, Ar, Kr, Xe, Rn) as one of its main pillars. Indeed the inert chemical nature of their closed shell structure is so striking that it is sometimes extended to all such structures. Is it true however that any closed shell, say a closed d-subshell will denote a lack of chemical activity? Take the noble metals for instance, so renowned for their catalytic capacity. Platinum has 10 electrons (...) in its valence shell which makes one of its excited states to be a closed 5d10–6s0 state. Surely this state would not be expected to be crucial to the catalytic activity of platinum, or would it? Or take palladium whose ground state is precisely the 4d10–5s0 state, should we expect that an isolated Pd atom at near zero-point temperature would attack a closed-shell hydrogen molecule efficiently? We shall here show that this is precisely the case; the closed-shell excited states of nickel and platinum are indeed crucial, through symmetry avoided crossings, for their reactivity. Other valuable catalysts as ruthenium depend on their excited states with maximal d-shell occupancy for their activity. The most notable confirmation of this new finding; that closed d-shells are vital to the catalytic activity of noble metals however, is the case of palladium whose closed-shell ground state is indeed capable of attacking hydrogen and hydrocarbon molecules even at temperatures well below 10 K as was predicted theoretically and immediately confirmed experimentally. (shrink)

This paper distinguishes in Maxwell’s thought between “atomic molecules” and “ultimate atoms,” and arrives at a set of properties that characterize each type of atom. It concludes that Maxwell is a mathematical atomist, an approach that entails the notion that although it is impossible to observe the ultimate atoms as free particles, we can nevertheless study them as mathematical observables, on the caveat that mathematical formalism remains tied to phenomenalism and to theoretical interpretations of such phenomena as, (...) for example, mass and force variations, gravitational pull, gas diffusion and viscosity, and heat conduction. (shrink)

J. H. van 't Hoff's 1874 Dutch pamphlet, in which he proposed the spatial arrangement of atoms in a molecule, is one of the most significant documents in the history of chemistry. This essay presents a new narrative of Van 't Hoff's early life and places the appearance of the pamphlet within the context of the 'second golden age' of Dutch science. We argue that the combination of the reformed educational system in The Netherlands, the emergence of graphical molecular (...) modelling within the theoretical and practical culture of chemistry during the 1860s and 1870s, as well as Van 't Hoff's own personal research trajectory, formed the background to his unprecedented attribution of spatial meaning to the traditional concept of atomic 'arrangement'. We also present a new English translation of the pamphlet, for we have found that the existing translation, published by G. M. Richardson in 1901, contains many errors, changes and omissions. The new version offers a more accurate rendition in English of Van 't Hoff's style and argument. (shrink)

Recently, the author of this paper and his research team have extended the orthodox quantum theory of atoms in molecules (QTAIM) to a novel paradigm called the two-component QTAIM (TC-QTAIM). This extended framework enables one to incorporate nuclear dynamics into the AIM analysis as well as performing AIM analysis of the exotic species; positronic and muonic species are a few examples. In present paper, this framework has been reviewed, providing some computational examples with particular emphasis on origins and (...) applications, in a non-technical language. The main questions, enigmas and basic ideas that finally yielded the TC-QTAIM are considered in chronological order to help the reader comprehend the intuition behind the math. Finally, it is demonstrated that the TC-QTAIM and its more refined versions are able to tackle problems inaccessible to the orthodox QTAIM. (shrink)

Biomolecules and particularly proteins and DNA exhibit some mysterious features that cannot find satisfactory explanation by quantum mechanical modes of atoms. One of them, known as a Levinthal’s paradox, is the ability to preserve their complex three-dimensional structure in appropriate environments. Another one is that they possess some unknown energy mechanism. The Basic Structures of Matter Supergravitation Unified Theory (BSM-SG) allows uncovering the real physical structures of the elementary particles and their spatial arrangement in atomic nuclei. The resulting physical (...) models of the atoms are characterized by the same interaction energies as the quantum mechanical models, while the structure of the elementary particles influence their spatial arrangement in the nuclei. The resulting atomic models with fully identifiable parameters and angular positions of the quantum orbits permit studying the physical conditions behind the structural and bonding restrictions of the atoms connected in molecules. A new method for a theoretical analysis of biomolecules is proposed. The analysis of a DNA molecule leads to formulation of hypotheses about the energy storage mechanism in DNA and its role in the cell cycle synchronization. This permits shedding a light on the DNA feature known as a C-value paradox. The analysis of a tRNA molecule leads to formulation of a hypothesis about a binary decoding mechanism behind the 20 flavors of the complex aminoacyle-tRNA synthetases - tRNA, known as a paradox. (shrink)

Shortly before his death, Richard Bader commented in this Journal on the dichotomy that exists within chemistry and between chemists. We believe that the dichotomy results from different goals and objectives inherent in the chemical disciplines. At one extreme are designers who synthesize new molecules with interesting properties. For these chemists, the rationale underpinning molecular synthesis is far less important than the end product—the molecules themselves. At the other extreme are the chemists who seek a fundamental understanding of (...) molecular properties. We suggest that the Quantum Theory of Atoms in Molecules, by virtue of the rich hierarchical structure inherent in the theory, offers a bridge through which to unite these two groups. However, if there is to be reconciliation, it falls to the theorists to develop “quantum mechanically” correct tools and concepts useful to the synthetic and applied chemist. (shrink)

I present a response to Vollmer's review of the book Of Minds and Molecules, and especially her comments on my own article therein. This provides an opportunity to discuss two central ideas in the philosophy of chemistry. These are the distinction between elements as simple substances (element-1) and elements as basic substances (element-2) and Paneth's proposed intermediate position for philosophy of chemistry. The response also discusses the question of isotopes in relationship to the nature of the elements and their (...) classification as well as the philosophical status of atomic orbitals. (shrink)

The story of how Perrin’s experimental work established the reality of atoms and molecules has been a staple in (realist) philosophy of science writings (Wesley Salmon, Clark Glymour, Peter Achinstein, Penelope Maddy, …). I’ll argue that how this story is told distorts both what the work was and its significance, and draw morals for the understanding of how theories can be or fail to be empirically grounded.

It is argued that some elusive “entropic” characteristics of chemical bonds, e.g., bond multiplicities (orders), which connect the bonded atoms in molecules, can be probed using quantities and techniques of Information Theory (IT). This complementary perspective increases our insight and understanding of the molecular electronic structure. The specific IT tools for detecting effects of chemical bonds and predicting their entropic multiplicities in molecules are summarized. Alternative information densities, including measures of the local entropy deficiency or its displacement (...) relative to the system atomic promolecule, and the nonadditive Fisher information in the atomic orbital resolution(called contragradience) are used to diagnose the bonding patterns in illustrative diatomic and polyatomic molecules. The elements of the orbital communication theory of the chemical bond are briefly summarized and illustrated for the simplest case of the two-orbital model. The information-cascade perspective also suggests a novel, indirect mechanism of the orbital interactions in molecular systems, through “bridges” (orbital intermediates), in addition to the familiar direct chemical bonds realized through “space”, as a result of the orbital constructive interference in the subspace of the occupied molecular orbitals. Some implications of these two sources of chemical bonds in propellanes, π-electron systems and polymers are examined. The current–density concept associated with the wave-function phase is introduced and the relevant phase-continuity equation is discussed. For the first time, the quantum generalizations of the classical measures of the information content, functionals of the probability distribution alone, are introduced to distinguish systems with the same electron density, but differing in their current(phase) composition. The corresponding information/entropy sources are identified in the associated continuity equations. (shrink)

A theory, analogous with the kinetic theory of heat, is described, in which the role of heat is shared by all the phenomena of extra-atomic physics, including quantum electrodynamics, gravitation, and relativistic mass. The role of the randomly moving molecules, as a mechanical model, is taken for all of these by a single model, consisting of a turbulent, dissipationless liquid, the motion of which conforms to Newtonian mechanics. This model is capable of supporting spherical standing waves which are taken (...) to represent elementary particles. The mechanical counterparts of the physical equations are close approximations to those of the model. (shrink)

The story of how Perrin’s experimental work established the reality of atoms and molecules has been a staple in (realist) philosophy of science writings (Wesley Salmon, Clark Glymour, Peter Achinstein, Penelope Maddy, …). I’ll argue that how this story is told distorts both what the work was and its significance, and draw morals for the understanding of how theories can be or fail to be empirically grounded.

According to the BSM- Supergravitation Unified Theory (BSM-SG), the energy is indispensable feature of matter, while the matter possesses hierarchical levels of organization from a simple to complex forms, with appearance of fields at some levels. Therefore, the energy also follows these levels. At the fundamental level, where the primary energy source exists, the matter is in its primordial form, where two super-dense fundamental particles (FP) exist in a classical pure empty space (not a physical vacuum). They are associated with (...) the Planck scale parameters of frequency and distance and interact by Supergravitational forces. These forces are inverse proportional to the cube of distance at pure empty space and they are based on frequency interactions. Since the two FPs have different intrinsic frequencies, the SG forces appear different for interactions between the like and unlike FPs and may change the sign. This primordial form of matter exists in the super-heavy black holes located in the center of each well formed galaxy. The next upper level of matter organization includes the underlying structure of the physical vacuum, called a Cosmic Lattice, and the structure of elementary particles. They have common substructure elements obtained by specific crystallization process preceding the formation of the observable galaxies. The Cosmic Lattice, forming a space known as a physical vacuum, is responsible for the existence and propagation of the physical fields: electrical, magnetic, Newtonian gravity and inertia. The energy of physical vacuum is in two forms: Static (enormous) and Dynamic (weak). The Static energy is directly related to the Newtonian mass by the Einstein equation E = mc^2 and it is a primary source of the nuclear energy. The Dynamic energy is responsible for the existence of the electric and magnetic fields, the constant speed of light and the quantum mechanical properties of the physical vacuum. The next upper energy level is the dynamical energy of excited atoms and molecules. At this level a hidden energy wells exit, such as the internal energy of the electron and the internal energy of atoms with more than one electron. The next upper energy level is at some organic molecules and particularly in the biomolecules that contain ring atomic structures. In such a structure, some quantum states are not emitted immediately, but rotating in the ring. While in organic molecules the energy stored in such a ring is released by a chemical process, in the long chain molecule of proteins in the living organism the stored energy can be released simultaneously by triggering. A huge number of atomic rings are contained in the DNA strands. The release of the energy stored in DNA, for example, is an avalanche process that causes an emission of entangled photons possessing a strong penetrating capability. A sequence of entangled photons emitted by DNA should carry the genetic information encoded by the cordons. This mechanism, predicted in BSM-SG theory, is very important for intercommunication between the cells of the living organism. The next upper level of energy organization may exist in the brain. The brain is an organ of a most abundant number of atomic rings, while its tissue environment might permit complex energy interactions. The human brain contains billions of atomic rings. The next hypothetical upper level of energy organization is an information field, physically existed outside, but connected with the living brain. It corresponds to a specific field known as aura, while the possibility of its existence is still not accepted by the main stream science. The problem is that this field could not be detected by the currently existing technical means used for EM communications. The BSM-SG predicts that this field might differ from the EM field we use for communication, but it is a subject of a further theoretical development that must be supported by experiments using specifically designed technical means. According to the BSM-SG theory, the energy conversion from the primary energy source to the complex levels of matter and field organization is a permanent syntropic process based on complex resonance interactions. (shrink)

Natural selection of specific protobiomonomers during abiogenic development of the prototype genetic code is hindered by the diversity of structural, spatial, and rotational isomers that have identical elemental composition and molecular mass (M), but can vary significantly in their physicochemical characteristics, such as the melting temperature Tm, the Tm:M ratio, and the solubility in water, due to different positions of atoms in the molecule. These parameters differ between cis- and trans-isomers of dicarboxylic acids, spatial monosaccharide isomers, and structural isomers (...) of α-, β-, and γ-amino acids. The stable planar heterocyclic molecules of the major nucleobases comprise four (C, H, N, O) or three (C, H, N) elements and contain a single –C=C bond and two nitrogen atoms in each heterocycle involved in C–N and C=N bonds. They exist as isomeric resonance hybrids of single and double bonds and as a mixture of tautomer forms due to the presence of –C=O and/or –NH2 side groups. They are thermostable, insoluble in water, and exhibit solid-state stability, which is of central importance for DNA molecules as carriers of genetic information. In M–Tm diagrams, proteinogenic amino acids and the corresponding codons are distributed fairly regularly relative to the distinct clusters of purine and pyrimidine bases, reflecting the correspondence between codons and amino acids that was established in different periods of genetic code development. The body of data on the evolution of the genetic code system indicates that the elemental composition and molecular structure of protobiomonomers, and their M, Tm, photostability, and aqueous solubility determined their selection in the emergence of the standard genetic code. (shrink)

This work utilizes examples from chemical sciences to present fundamentals of dialectics and synergetics. The laws of dialectics remain appropriate at the level of atoms, at the level of molecules, at the level of the reactions, and at the level of ideas. The law of the unity and conflict of opposites is seen, for instance, in the relationships between the ionization energy and electron affinity of atoms, between the forward and back reactions, as well as in the (...) differentiation and integration between the various areas of chemistry. The law of the passage of quantitative changes into qualitative changes describes the transformation properties of the compounds when the number and arrangement of atoms in the molecule undergoes changes. According to this law, the development is accompanied by breaks and jumps. This paper suggests equations for the description of these relationships. The law of the negation of the negation is manifested in the Periodic Law, in the evolution of ideas about the mutual transformation of chemical elements, in the development the concept of triads of elements, etc. Small changes in the conventional Periodic Table on the basis of previously rejected versions allow reflecting secondary and additional periodicity. Synergetics, similarly to dialectics, is dedicated to the studies of general laws of evolution. Synergetics includes highly advanced and specified ideas of dialectics. The cornerstone of synergetics is the principles of self-organization and nonlinearity. Mathematical development of these concepts was substantially facilitated by considering oscillating chemical reactions as an example. These reactions are quite complex and therefore provide adequate models for self-organization. Oscillations may exist only upon execution of specific thermodynamic, mathematical, and chemical conditions. Mechanisms of several oscillatory reactions are briefly reviewed. The construction of novel biomimetic or smart materials based on oscillating reactions is described. (shrink)

In ‘Location and Perdurance’ (2010), I argued that there are no compelling mereological or sortal grounds requiring the perdurantist to distinguish the molecule Abel from the atom Abel in Gilmore’s original case (2007). The remaining issue Gilmore originally raised concerned the ‘mass history’ of Adam and Abel, the distribution of ‘their’ mass over spacetime. My response to this issue was to admit that mass histories needed to be relativised to a way of partitioning the location of Adam/Abel, but that did (...) not amount to relativising any fundamental natural intrinsic properties—the latter are all had unrelativised, and (so most perdurantists would say). (shrink)

The hypothesis that the particular linear tracks appearing in the measurement of a spherically-emitting radioactive source in a cloud chamber are determined by the positions of atoms or molecules inside the chamber is further explored in the framework of a recently established one-dimensional model. In this model, meshes of localized spins 1/2 play the role of the cloud-chamber atoms and the spherical wave is replaced by a linear superposition of two wave packets moving from the origin to (...) the left and to the right, evolving deterministically according to the Schrödinger equation. We first revisit these results using a time-dependent approach, where the wave packets impinge on a symmetric two-sided detector. We discuss the evolution of the wave function in the configuration space and stress the interest of a non-symmetric detector in a quantum-measurement perspective. Next we use a time-independent approach to study the scattering of a plane wave on a single-sided detector. Preliminary results are obtained, analytically for the single-spin case and numerically for up to 8 spins. They show that the spin-excitation probabilities are sometimes very sensitive to the parameters of the model, which corroborates the idea that the measurement result could be determined by the atom positions. The possible origin of decoherence and entropy increase in future models is finally discussed. (shrink)

Introduction -- Quantum information: basic relevant concepts and applications -- Theory -- Part I. Atomic processes -- Coulombic entanglement: one-step single photoionization of atoms -- Coulombic entanglement: one-step double photoinonization of atoms -- Coulombic entanglement: two-step double photoinonization of atoms -- Fine-structure entanglement: bipartite states of flying particlees with rest mass different from zero -- Bipartite states and flying electronic qubits -- Part II. Molecular processes -- One-step double photoionization of molecules -- Two-step double photoionization of (...) molecules -- Part III. Miscellaneous -- Conclusions and prospectives. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Teleology in Natural Theology and Theology of Nature:Classical Theism, Science-Oriented Panentheism, and Process TheismMariusz Tabaczek, O.P.IntroductionThe world is full of teleological dimensions. When we search for them, we can easily see that virtually any of the main aspects of our world can be taken as a particular case of teleology. Although this holds especially for living beings, the physicochemical world also exhibits many directional features that acquire a special (...) meaning when seen as necessary conditions for the existence of living beings. Directionality indicates the existence of tendencies toward goals, which is the hallmark of natural teleology.... It is not difficult to find examples of directionality and cooperativity. If we begin with the most elementary components of the world, we find out that subatomic particles and the four basic interactions behave according to well-known specific patterns and collaborate to build up successive levels of organization—atoms, molecules, macromolecules, and the bigger inorganic and organic beings. The entire construction of our world is the result of the deployment of tendencies that collaborate to make up unitary systems.1If Mariano Artigas is right in his assertion—and many seem to agree that he is2—it seems reasonable to ask about the ways in which the notion of [End Page 1179] teleology may inspire theology, especially in the context of the ongoing dialogue between science and theology. We may think about at least two possible answers to this question, in reference to two related, yet distinctive strategies pursued in theological reflection, (1) the approach of natural theology and (2) the approach of theology of nature. What brings them together is their close attention to nature and our attempts to understand it. Avoiding theological and spiritual escapism and dismissive detachment from nature and natural phenomena, both natural theology and theology of nature point toward their ultimate grounding in God. While doing so, both approaches strive to remain free from the errors of panpsychism, vitalism, and pantheism, thus enabling nature to be natural, available to a thorough and meaningful analysis and description at the level of the research pursued by natural sciences and philosophy of nature and of science. What differentiates these theological approaches are their starting and ending points.Natural theology departs from the observation of natural phenomena. In a search for their ultimate explanation, in reference to philosophy of nature and metaphysics, it arrives at the theological conclusion that only the existence of God offers a satisfying and conclusive answer to the human search for understanding and meaning of the reality that surrounds us. Consequently, one may say that natural phenomena, or at least some of their most fundamental aspects such as teleology, can be used as a basis for arguing in favor of the existence of God.The advantage of such an approach—notes Ian Barbour—is that "it starts from scientific data on which we might expect agreement despite cultural and religious differences."3 However, taken alone, it may reduce the notion of God to the God of philosophers, the unmoved mover, [End Page 1180] or even a deistic Creator, remote and not engaged in his relation to the created reality. Moreover, although we know many examples of people who actually did go through a conversion and discovered the existence of God following the path of natural theology, one might ask whether at least some of the arguments developed within it do not presuppose God's existence as rhetorical exercises for the expression of religious faith, compromising thus its principal commitment.In contrast to natural theology, theology of nature begins with a firm belief in God, based on historical revelation—codified in the Scriptures and reflected upon within theological Tradition—and religious experience (personal and communal). It applies this perspective as an explanatory tool, providing a definitive answer to the questions of origin and ultimate fulfillment of natural phenomena observed in the universe. Hence, while it would be rather strange to claim that the existence of God proves the existence of the natural world—which is better known to us (quoad nos) than the principles of theology—we may still argue that, from the point of view of theology of nature, our knowledge... (shrink)

Electronegativity, described by Linus Pauling described as “The power of an atom in a molecule to attract electrons to itself” (Pauling in The nature of the chemical bond, 3rd edn, Cornell University Press, Ithaca, p 88, 1960), is used to predict bond polarity. There are dozens of methods for empirically quantifying electronegativity including: the original thermochemical technique (Pauling in J Am Chem Soc 54:3570–3582, 1932), numerical averaging of the ionisation potential and electron affinity (Mulliken in J Chem Phys 2:782–784, 1934), (...) effective nuclear charge and covalent radius analysis (Sanderson in J Chem Phys 23:2467, 1955) and the averaged successive ionisation energies of an element’s valence electrons (Martynov and Batsanov in Zhurnal Neorganicheskoi Khimii 5:3171–3175, 1980), etc. Indeed, there are such strong correlations between numerous atomic parameters—physical and chemical—that the term “electronegativity” integrates them into a single dimensionless number between 0.78 and 4.00 that can be used to predict/describe/model much of an element’s physical character and chemical behaviour. The design of the common and popular medium form of the periodic table is in large part determined by four quantum numbers and four associated rules. However, adding electronegativity completes the construction so that it displays the multi-parameter periodic law operating in two dimensions, down the groups and across the periods, with minimal ambiguity. (shrink)