# Chérif F. MattaMount Saint Vincent University

Chérif F. Matta

PhD, HDR, FRSA, FRSB, FInstP, FRSC, FAAAS

## About

178

Publications

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Introduction

My Research Group's work is in theoretical, quantum, and computational chemistry and biophysics. We introduced electron localization-delocalization matrices (LDMs) and use them to monitor chemical properties and reactivity. We explore the structure and reactivity of molecules in external (static) electric fields and also in laser pulses. With a focus on mitochondrial ATP synthase, we seek a deeper understanding of the mitochondrion, the "powerhouse" of eukaryotic cells. (http://www.cmatta.ca/).

## Publications

Publications (178)

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...

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 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...

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...

This article has been withdrawn at the request of the authors. The Publisher apologizes for any inconvenience this may cause.
The full Elsevier Policy on Article Withdrawal can be found at https://www.elsevier.com/about/our-business/policies/article-withdrawal

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...

A 31-year-old letter from Professor Richard F. W. Bader to Professor Lou Massa outlining the connections between the quantum theory of atoms in molecules (QTAIM) and density functional theory (DFT) especially with regard to the first Hohenberg-Kohn theorem is brought to light. This connection has not often been the topic of such a focused review by...

Professor Lou Massa’s contributions since the late 1960s to the founding of the field now known as “Quantum Crystallography” (QCr) are briefly described. The term itself has been coined in 1995 by L. Huang, L. Massa, and J. Karle (1985 Nobel Laureate in Chemistry). Originally, QCr referred to the Clinton-Massa’s iterative approach that, for the fir...

It occurs that the kidney, an organ, and the mitochondrion, an organelle, are both physical realizations of a Maxwell demon. To understand how this occurs, a detailed analysis of the operation of the demon construct and of organ and organelle is given. The focus of attention in this chapter is upon the energetic cost of gathering information, as oc...

The properties of carbon monoxide in its ground and two lowest lying excited states are investigated by conventional and time-dependent (TD) density functional theory (DFT). The dipole moment is decomposed into atomic polarisation (AP) and inter-atomic charge transfer (CT) contributions according to the quantum theory of atoms in molecules (QTAIM)....

The ansa-aminohydroborane 1-NMe2 -2-(BH2 )C6 H4 crystallizes in an unprecedented type of dimer containing a B-H bond activated by one FLP moiety. Upon mild heating and without the use of any catalyst, this molecule liberates one equivalent of hydrogen to generate a diborane molecule. The synthesis and structural characterization of these new compou...

The ansa-aminohydroborane 1-NMe2-2-(BH2)C6H4 crystallizes in an unprecedented type of dimer containing a B−H bond activated by one FLP moiety. Upon mild heating and without the use of any catalyst, this molecule liberates one equivalent of hydrogen to generate a diborane molecule. The synthesis and structural characterization of these new compounds...

3,3-Difluorodiazirine is a precursor of difluorocarbene radical (:CF2) which is used in organic synthesis and photo affinity labelling. This molecule possesses no dipole moment in the ground electronic state (S0) but has a significant dipole moment (of magnitude > 0.97 D) in both its first (triplet, T1) and second (singlet S1) excited states. These...

Chemical graph theory (CGT) starts by defining matrices that represent the molecular graph then proceed to extract numbering-independent matrix invariants to be used as molecular descriptors in empirical quantitative structure to activity (or property) relationships (QSAR/QSPR). Two proposed matrix representations of molecular structure are present...

Background:
The bioisosterism in -CO2H and -C4HO3 is exploited using the quantum theory of atoms in molecules and molecular electrostatic potentials (ESP).
Results & discussion:
Bioisosteres in methylsquarate and acetic acid, in the neutral/anionic forms, have average electron densities that differ by less than 2% (i.e., ∼0.01 atomic units) whil...

The difluorocarbene radical (:CF2), used in organic synthesis and in photoaffinity labeling, can be generated by the pyrolytic or photolytic decomposition of 3,3-difluorodiazirine (CF2N2, DFD). DFD possesses no dipole moment in the ground electronic state S
0 but has an experimental dipole of 1.5 ± 0.2 debye (D) in its first singlet excited state S...

Non-nuclear attractors (NNAs) are observed in the electron density of a variety of systems but the factors governing their appearance and their contribution to the system's properties remain a mystery. The NNA occurring in homo- and hetero-nuclear diatomics of main group elements with atomic numbers up to Z=38 is investigated computationally (at th...

A new and powerful molecular descriptor termed the LDM (localization-delocalization matrix) has recently been proposed as a molecular fingerprinting tool and has been shown to yield robust quantitative-structure-to-activity/property-relationships (QSAR/QSPR). An LDM lists the average number of electrons localized within an atom in a molecule along...

In order to cast some light onto the nature of the chemical bonding between a 8-unit oligomer of the poly(3-hexylthiophene) (P3HT) and the fullerene derivative [6,6]-phenyl-C61-butyric acid methyl ester (PCBM) in the two stables isomers reported recently [I. Gutiérrez-González, B. Molina-Brito, A.W. Götz, F.L. Castillo-Alvarado, J.I. Rodríguez, Che...

We respond to the two questions posed by Weinhold, Schleyer, and McKee (WSM) in their study of cis-2-butene (Weinhold et al., J Comput Chem 2014, 35, 1499), in which they solicit explanations for the relative conformational energies of this molecule in terms of the Quantum Theory of Atoms in Molecules (QTAIM). WSM requested answers to the questions...

The kernel energy method (KEM) is a soft scaling fragment quantum chemical calculation method that proved very useful for the estimation of ab initio energies of very large biological molecules. In this approach, a large molecule is broken into computationally tractable pieces (kernels), which reduces the otherwise rapidly rising computational diff...

Half a century ago, Johnson and Knudsen resolved the puzzle of the apparent low efficiency of the kidney (~0.5%) compared to most other bodily organs (~40%) by taking into account the entropic cost of ion sorting, the principal function of this organ. Similarly, it shown that the efficiency of energy transduction of the chemiosmotic proton-motive f...

A merging of Chemical Graph Theory (CGT) with the Quantum Theory of Atoms in Molecules (QTAIM) has recently been proposed through the usage of the "localization-delocalization matrices" (LDMs). An LDM of a molecule composed of n atoms lists the complete set of localization indices as its diagonal elements while the delocalization indices divided by...

Professor Dunitz questions the usefulness of ascribing crystalline structural stability to individual atom-atom intermolecular interactions viewed as bonding (hence stabilizing) whenever linked by a bond path. An alternative view is expressed in the present essay that articulates the validity and usefulness of the bond path concept in a crystallogr...