Chérif F. Matta

Chérif F. Matta
Mount Saint Vincent University

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)
Article
Full-text available
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...
Article
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-...
Cover Page
Full-text available
The cover art is based on the Research Paper: ATP synthase: A moonlighting enzyme with unprecedented functions, https://doi.org/10.1039/D1CC06793A.
Article
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.
Preprint
Full-text available
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...
Article
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...
Article
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...
Article
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...
Article
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...
Article
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...
Article
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...
Preprint
Full-text available
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...
Preprint
Full-text available
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'...
Article
Full-text available
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...
Article
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...
Article
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...
Preprint
Full-text available
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...
Article
Full-text available
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...
Article
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...
Presentation
Full-text available
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...
Article
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...
Article
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...
Article
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
Article
Full-text available
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...
Article
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...
Article
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
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...
Article
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...
Preprint
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...
Preprint
Full-text available
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...
Article
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...
Article
Full-text available
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...
Article
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...
Presentation
Full-text available
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...
Poster
Full-text available
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...
Article
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,...
Article
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...
Poster
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...
Article
Full-text available
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...
Article
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...
Article
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...
Article
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...
Article
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...
Article
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...
Article
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...
Article
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...
Article
Full-text available
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...
Article
Full-text available
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...
Chapter
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...
Article
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)....
Article
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...
Article
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...
Article
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...
Chapter
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...
Article
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...
Article
Full-text available
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...
Article
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...
Article
Full-text available
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...
Article
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...
Article
Full-text available
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...
Article
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...
Article
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...
Article
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...
Article
Full-text available
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...