Chérif F. Matta

• PhD, HDR, FRSA, FRSB, FInstP, FRSC, FAAAS
• Professor and Department Chair at Mount Saint Vincent University

This approach to quantum crystallography ensures the satisfaction of three quantum conditions, namely, idempotency, hermiticity, and normalization of the one-body density matrix, simultaneously as the X-ray diffraction problem is solved to reproduce the observed structure factors. The variational theorem used to optimize energy will only hold true...

The electric potential across the inner mitochondrial membrane must be maintained within certain bounds for the proper functioning of the cell. A feedback control mechanism for the homeostasis of this membrane potential is proposed whereby an increase in the electric field decreases the rate-limiting steps of the electron transport chain (ETC). An...

Intriguing symmetries are uncovered regarding all magic squares of orders 3, 4, and 5, with 1, 880, and 275,305,224 distinct configurations, respectively. In analogy with the travelling salesman problem, the distributions of the total topological distances of the paths travelled by passing through all the vertices (matrix elements) only once and sp...

Mycobacteria are opportunistic intracellular pathogens that have plagued humans and other animals throughout history and still are today. They manipulate and hijack phagocytic cells of immune systems, enabling them to occupy this peculiar infection niche. Mycobacteria exploit a plethora of mechanisms to resist antimicrobials (e. g., waxy cell walls...

Quantum mechanical calculations are used to explore the thermodynamics of possible prebiotic synthesis of the building blocks of nucleic acids. Different combinations of D-ribofuranose (Ribf) and N-(2-aminoethyl)-glycine (AEG) (trifunctional connectors (TCs)); the nature of the Ribf, its anomeric form, and its ring puckering (conformation); and the...

Despite its amazing quantitative successes and contributions to revolutionary technologies, physics currently faces many unsolved mysteries ranging from the meaning of quantum mechanics to the nature of the dark energy that will determine the future of the Universe. It is clearly prohibitive for the general reader, and even the best informed physic...

Identification of molecular carriers for diffuse interstellar bands (DIBs) may stem in part from the determination of interrelated lines using the Apache Point Observatory Catalog of DIBs. However, Pearson correlations may be impacted by the number of interstellar clouds along the sightlines. The trend of extinction with distance was constrained us...

Enzymes are life’s catalysts par excellence. They are incredibly efficient and are mainly composed of protein—save prosthetic groups and/or nucleic acid components. They can enhance the rate of virtually all the chemical reactions within cells and by astronomical factors so much as to often limit reaction rates by diffusion, that is, the access of...

In this chapter, three case studies will be presented illustrating how to use electron localization-delocalization matrices (LDMs) analysis in the prediction of corrosion inhibitors’ activities. Furthermore, the analysis is shown to go beyond the mere prediction of activity to deepen our mechanistic understanding by uncovering the active molecular...

The electron density (ρ) is a scalar field that determines the chemical, physical, and biological properties of macroscopic matter as we know it. An atom, a molecule, an ion, a crystal, all have in common that they interact with their surroundings through their electron density distributions. All chemistry is a reflection of an underlying electroni...

In molecular chemistry, the terms localized/delocalized usually refer to electrons (atomic nuclei (exclusively protons) are rarely delocalized). Localized electrons are typically associated with a specific atom or pair of atoms; delocalized electrons are diffuse and spread out over several atomic nuclei. Typically, in an organic compound, electrons...

Insects are both humankind’s best friends and worst enemies. Modern agriculture could not survive without the presence of honeybees and other pollinators including mosquitoes. At the same time, mosquitoes are human’s worst enemy. They transmit the protozoan parasite that causes malaria and several viruses that cause dangerous infections such as den...

In previous chapters, we have demonstrated the extraction of chemical information from molecular structures via the use of Bader’s Quantum Theory of Atoms in Molecules (QTAIM) followed by the analysis of the electron localization-delocalization matrices by such methods as Principal Component Analysis (PCA) to predict useful properties.

Ismat Sumar of Saint Mary’s University, one of whom this book is dedicated, pioneered the first software implementation of an algorithm to automate the localization-delocalization matrices (LDMs) analysis of a series of molecules.

Principal Component Analysis (PCA) and one of its variants, Factor Analysis (FA), are dimensionality reduction statistical approaches that replace the original correlated variables in a data set with fewer new ones that are linear combinations of the old ones. These new fewer variables capture the majority of the variability in the original data se...

This book has been written with the practicing chemist in sight. It is not a book on theoretical chemistry but rather one that is primarily focused on making practical predictions starting from theoretical chemistry calculations.

A network is a set of objects connected in a pairwise fashion. Frequently, the word network and graph are used interchangeably, even though some authors stress that the network is a set of identifiable connected objects, while the objects connected in a graph are identical. In this monograph, the two terms are used interchangeably.

The electronic and optical properties of a NaLaS2 compound, doped with different concentrations of Se and Te atoms, are explored using periodic density functional theory calculations. The primary objective is to identify light-absorbing materials for use in photovoltaic applications. It is found that the dopant concentration can induce a crystallin...

Mitochondria are the central hub of ATP production in most eukaryotic cells. Cellular power (energy per unit time), which is primarily generated in these organelles, is crucial to our understanding of cell function in health and disease. We investigated the relation between a mitochondrion's power (metabolic rate) and host cell size by combining me...

Despite its amazing quantitative successes and contributions to revolutionary technologies, physics currently faces many unsolved mysteries ranging from the meaning of quantum mechanics to the nature of the dark energy that will determine the future of the universe. It is clearly prohibitive for the general reader, and even the best informed physic...

Mitochondria are the central hub of ATP production in most eukaryotic cells. Cellular power (energy per unit time), which is primarily generated in these organelles, is crucial to our understanding of cell function in health and disease. We investigated the relation between a mitochondrion's power (metabolic rate) and host cell size by combining me...

Niosome vesicles as potential nanocarriers for drug delivery systems have been in development since the mid-1980s. These vesicles form by self-assembly of cholesterol and nonionic surfactants in an aqueous phase. The aim of the present molecular dynamics (MD) simulation study is to determine how changes in the sterol side chain and ring affect the...

Present-day known predominance of the β- over the α-anomers in nucleosides and nucleotides emerges from a thermodynamic analysis of their assembly from their components, i.e. bases, sugars, and a phosphate group. Furthermore, the incorporation of uracil into RNA and thymine into DNA rather than the other way around is also predicted from the calcul...

This chapter explores the role played by the Quantum Theory of Atoms in Molecules (QTAIM) in the relation between molecular chemistry and quantum mechanics, in the conceptual framework of coarse graining. It is shown that the electron density is a coarse-grained magnitude when considered from the viewpoint of quantum mechanics. As a consequence, al...

An approach is developed for the fast calculation of the interacting quantum atoms energy decomposition (IQA) from the information contained in the first order reduced density matrix only. The proposed methodology utilizes an approximate exchange-correlation density from Density Matrix Functional Theory without the need to evaluate the correlation-...

The relatively new and expansive Apache Point Observatory Catalog of Optical Diffuse Interstellar Bands was analyzed to identify novel correlations between diffuse interstellar bands (DIBs) and optical reddening E ( B − V ), with a principal aim being to facilitate future identifications of the host molecular carriers. The following lines exhibit t...

The cover art is based on the Research Paper: ATP synthase: A moonlighting enzyme with unprecedented functions, https://doi.org/10.1039/D1CC06793A.

The cover image is based on the Research Article Two projector triple products in quantum crystallography by Cherif F Matta et al., https://doi.org/10.1002/qua.26838.

ATP synthase’s intrinsic molecular electrostatic potential (MESP) adds constructively to, and hence reinforces, the chemiosmotic voltage. This ATP synthase voltage represents a new free energy term that appears to have been overlooked. This term is at least roughly equal in order of magnitude and opposite in sign to the energy needed to be dissipat...

Experiments by Chrétien and coworkers suggest that mitochondria are 10°C hotter than their surroundings. Steady-state theoretical estimates place this difference at a maximum of 10^−5°C. This millionfold disagreement may be called the 'hot mitochondrion paradox'. It is suggested that every proton translocated via ATP synthase sparks a picosecond te...

Linus Pauling contributions span structural biology, chemistry in its broadest definition, quantum mechanical theory, valence bond theory, and even nuclear physics. A principal tool developed and used by Pauling is X-ray (and electron) diffraction. One possible extension of Pauling's oeuvre could be the “marriage” of crystallography and quantum mec...

The diffusion of molecular hydrogen, helium, and neon through a polyvinyl butyral (PVB) membrane is investigated by Molecular Dynamics (MD) simulations. An understanding of the mechanism of this diffusion is crucial to optimize the industrial conditions for the production of PVB with desired properties. In this work, a comparison of the radial dist...

Consider a projector matrix P, representing the first order reduced density matrix in a basis of orthonormal atom‐centric basis functions. A mathematical question arises, and that is, how to break P into its natural component kernel projector matrices, while preserving N‐representability of . The answer relies upon 2‐projector triple products, P′jP...

The electron density and the electron localization‐delocalization matrices (LDMs) are used to revisit the cyclooctetraene (COT) dimerization mechanism. The global minimum of a COT monomer (the tub geometry) exhibits a rare topological feature, giving rise, not to one, but to two ring critical points and a cage critical point necessary to satisfy th...

Crystal structures, electronic, and magnetic properties of RbCeX2 (X = S, Se, Te) crystals are investigated using periodic density functional theory (DFT) calculations under hydrostatic pressures up to 10 GPa. The ferromagnetic phase is slightly more stable than the anti-ferromagnetic one for all compounds and pressures. A pressure-induced transiti...

Linus Pauling contributions span structural biology, chemistry in its broadest definition, quantum mechanical theory, valence bond theory, and even nuclear physics. A principal tool developed and used by Pauling is Xray, and electron, diffraction. One possible extension of the Pauling oeuvre could be the marriage of crystallography and quantum mech...

Consider a projector matrix P, representing the first order reduced density matrix in a basis of orthonormal atom-centric basis functions. A mathematical question arises, and that is, how to break P into its natural component kernel projector matrices, while preserving N-representability of P. The answer relies upon 2- projector triple products, P'...

Observations from the Apache Point Observatory Catalog of Optical Diffuse Interstellar Bands (DIBs) were analysed to establish highly correlated pairs in terms of their equivalent widths (EWs) (r > 0.95), which importantly facilitate the identification of common carriers. A total of 154846 possible DIB pairs were originally examined, yet only those...

The Kato cusp condition involves a spherically-averaged derivative of the electron density with respect to distance from a given nucleus weighted by the electron density at this nucleus. This “Kato ratio” is shown analytically to vanish at all points of the electron density (and of the underlying external potential) that do not exhibit a singularit...

Recent experiments and thermodynamic arguments suggest that mitochondrial temperatures are higher than those of the cytoplasm. A “hot mitochondrion” calls for a closer examination of the energy balance that endows it with these claimed elevated temperatures. As a first step in this effort, we present here a semi-quantitative bookkeeping whereby, in...

Experiments by Chrétien and coworkers suggest that mitochondria are 10°C hotter than their surroundings. Steady-state theoretical estimates place this difference at a maximum of 10^−5°C. This millionfold disagreement may be called the 'hot mitochondrion paradox'. It is suggested that every proton translocated via ATP synthase sparks a picosecond te...

An elastic network model (ENM) represents a molecule as a matrix of pairwise atomic interactions. Rich in coded information, ENMs are hereby proposed as a novel tool for the prediction of the activity of series of molecules, with widely different chemical structures, but a common biological activity. The new approach is developed and tested using a...

Electric-field-mediated chemistry is an emerging topic that is rapidly growing and fanning out in many directions. It involves theoretical and experimental aspects, as well as intense interplay between them, including breakthrough achievements such as the proof-of-principle that a Diels–Alder reaction, which involves two simultaneous C–C bond makin...

Electric-field-mediated chemistry is an emerging topic that is rapidly growing and fanning out in many directions. It involves theoretical and experimental aspects, as well as intense interplay between them, including breakthrough achievements such as the proof-of-principle that a Diels–Alder reaction, which involves two simultaneous C–C bond makin...

A magic square is a square matrix whereby the sum of any row, column, or any one of the two principal diagonals is equal. A surrogate of this abstract mathematical construct, introduced in 2012 by Fahimi and Jaleh, is the “electrostatic potential (ESP)” that results from treating the matrix elements of the magic square as electric charges. The over...

Proton transfer (PT) reactions, in particular single (SPT), double (DPT) or multiple (MPT), are widespread phenomena in many branches of the life sciences. These reactions proceed through the transfer of the proton between donor and acceptor atoms, in some cases catalyzed by water molecules acting as a connector between these donor and acceptor ato...

Electronic structure and bonding properties of the Group 12 dications M2(2+) (M = Zn, Cd, Hg) are investigated and electron density-derived quantities are used to characterize the metastability of these species. Of particular interest are the complementary descriptions afforded by the Laplacian of the electron density and the one-electron Bohm qu...

Background: Chrétien and co-workers (PLOS Biology. 2018;16(1):e2003992) recently suggested that the mitochondrion might possibly be hotter than its surrounding (by as much as 10°C). Objectives: To examine the validity of this claim and review the possible implications and repercussion of such a claim-if true-on some aspects of mitochondrial biochem...

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Background: Chrétien and co-workers (PLOS Biology. 2018; 16 (1): e2003992) recently suggested that the mitochondrion might possibly be hotter than its surrounding (by as much as 10°C). Objectives: To examine the validity of this claim and review the possible implications and repercussion of such a claim – if true – on some aspects of mitochondrial...

The structural, magnetic, electronic, and elastic properties of magnetic semiconductors RbLnSe2 (Ln = Ce, Pr, Nd and Gd) are elucidated using density functional theory (DFT) using both large and small core pseudopotentials for the lanthanide atoms. Magnetic ordering is investigated using spin-polarized calculations, and the higher stability of ferr...

Atomic and molecular (bond) properties of a set of homo- (H 2 , N 2 , O 2 , F 2 , and Cl 2 ) and hetero-diatomic (HF, HCl, CO, and NO) molecules under intense external electric fields are studied in the context of quantum theory of atoms in molecules (QTAIM). Field-effects on basic QTAIM properties are elucidated. Atomic charges and energies are fo...

By moving away from the traditional reductionist reading of the quantum theory of atoms in molecules (QTAIM), 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 eme...

Alanine is used as a transfer standard dosimeter for gamma-ray and electron beam calibration. An important factor affecting its dosimetric response is humidity which can lead to errors in absorbed dose calculations. Ab initio molecular dynamics (MD) calculations were performed to determine the environmental effects on the electron paramagnetic reso...

The possibility and mechanism of water desalination using newly designed doped graphene sheets is reported. It is hereby demonstrated, through molecular dynamics (MD) simulations, that an electric field-assisted selective ion separation is possible using boron- and nitrogen-doped nano-porous graphene sheets. The sheets are shown to behave as nano-s...

Atomic and molecular (bond) properties of a set of homo- (H$_2$, N$_2$, O$_2$, F$_2$, and Cl$_2$) and hetero-diatomic (HF, HCl, CO, and NO) molecules under intense external electric fields are studied in the context of quantum theory of atoms in molecules (QTAIM). Field-effects on basic QTAIM properties are elucidated. Atomic charges and energies a...

The sources behind numerous key diffuse interstellar bands (DIBs) remain elusive, and thus evidence is presented here that a family of seven anionic hydrogen atomic clusters (H(-)2n+1, n = 1 to 7) are pertinent contributors. Configuration interaction calculations show hat these charge-induced dipole clusters are stable at temperatures characteristi...

The aqueous extract of the herb Phyllanthus orbicularis Kunth inhibits the mutagenicity of certain aromatic amines (mphenylendiamine (m-PDA), 4-aminobiphenyl (4-ABP), and 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP)). Meanwhile, the phenolic compound 2–6 di-sec-butylphenol (DSBP) was isolated from this plant’s extract. Computational evide...

New ternary and quaternary NaYS2(1–x)Te2x alloys (with x = 0, 0.33, 0.67, and 1) are proposed as promising candidates for photon energy conversion in photovoltaic applications. The effects of Te doping on crystal, spectral, and optical properties are studied within the framework of periodic density functional theory. Increasing Te content decreases...

Typical contemporary X‐ray crystallography delivers the geometries and, at best, the electron densities of molecules or periodic systems in the crystalline phase. Energies, electron momentum densities, and information relating to the pair density such as electron delocalization measures—all crucial to chemistry—are simply missed. Quantum crystallog...

About this Research Topic in Frontiers in Chemistry (IF=4.155) https://www.frontiersin.org/research-topics/9554/proton-transfer-processes-in-biological-reactions-a-computational-approach Proton transfer (PT) reactions, in particular single (SPT), double (DPT) or multiple (MPT), are widespread phenomena in many branches of the life sciences. These...

Запрошуємо Вас на науково-популярну лекцію ІВТ, що відбудеться у середу, 07 листопада 2018 р., о 14:30 в ауд. 01, факультету комп’ютерних наук та кібернетики. Доповідач: проф. Chérif F. Matta, Department of Chemistry & Physics Mount Saint Vincent University, Canada. Доповідь на тему: «The Kidney, the Mitochondrion, and Maxwell Demon – An Informa...

The double proton transfer reaction in the guanine–cytosine (GC) base pair is studied, using density functional theory, to understand the chances of mutations under the effect of uniform electric fields in the order of 10⁸ to 10⁹ V m–1. On the basis of potential energy surfaces, reaction Gibbs energies, equilibrium constants, imaginary frequencies,...

A tale of two worlds: The painting used for the frontispiece is F. Rasma's “Mehr Licht” from 1991. We are grateful to the artist for his permission to reproduce it here. “Mehr Licht!” (more light!) can be understood as the very human outcry for more insight, more understanding, more knowledge. It is said to be Johann Wolfgang von Goethe's last word...

The Kernel Energy Method (KEM) of Massa, Huang, and Karle is a many-body expansion method of predicting the energy and other quantum properties of large molecules from fragments thereof, called kernels. In this poster, atomic energies and their intra-atomic and inter-atomic contributions as defined by QTAIM and the Interacting Quantum Atoms method...

The effect of strong electric fields on the tautomerization of the adenine–thymine (AT) base pair in DNA is explored using density functional theory. It was found that the AT base pair is not likely to undergo a double proton transfer reaction even in the presence of electric fields ranging from 5.14 × 10⁸ to 5.14 × 10⁹ V m⁻¹. This conclusion holds...

An explanation is presented for the unusual conformations of some molecules that contain the C═C–C═C core, namely, butadienes, biphenyls, and styrenes. Small substituents often induce a synclinal conformation, which brings the substituents into close proximity, and sometimes, there is no anticlinal minimum at all. This would not be predicted from s...

Crystallography and quantum mechanics have always been tightly connected because reliable quantum mechanical models are needed to determine crystal structures. Due to this natural synergy, nowadays accurate distributions of electrons in space can be obtained from diffraction and scattering experiments. In the original definition of quantum crystall...

Long before the phrases “climate change” and “butterfly effect” were incorporated into the mainstream literature, these phrases appeared in an appropriate context almost verbatim in the first Chapter of a book entitled “The Emigrant” published in the mid-nineteenth century (in 1846) by Sir Francis Bond Head (1793–1875). Head was Upper Canada’s sixt...

Quantum crystallography (QCr) is a branch of crystallography aimed at obtaining the complete quantum mechanics of a crystal given its X-ray scattering data. The fundamental value of obtaining an electron density matrix that is N-representable is that it ensures consistency with an underlying properly antisymmetrized wavefunction, a requirement of q...

Extraction of the complete quantum mechanics from X-ray scattering data is the ultimate goal of quantum crystallography. This article delivers a perspective for that possibility. It is desirable to have a method for the conversion of X-ray diffraction data into an electron density that reflects the antisymmetry of an N-electron wave function. A for...

Maxwell’s demon makes observations and thereby collects information. As Brillouin points out such information is the negative of entropy (negentropy) and is the equivalent of a cost in energy. The energy cost of information can be quantified in the relationship E = kTln2, where k is the Boltzmann constant, T is the absolute temperature, and the fac...

Inspired by chemical graph theory (CGT), a matrix representation of molecules and reaction paths is presented within the framework of Bader's quantum theory of atoms in molecules (QTAIM). A molecule is viewed as a network of electron delocalization channels or highways (vertices) that connect every pair of atoms in the system and electron localizat...