Journal Articles

 

Journal Articles

(Items in blue are downloadable as pdf)

[93] A. Genoni, A.; Bučinský, L.; Claiser, N.; Contreras-Garcia, J.; Dittrich, B.; Dominiak, P. M.; Espinosa, E.; Gatti, C.; Giannozzi, P.; Gillet, M.; Jayatilaka, D.; Macchi, P.; Madsen, A. Ø.; Massa, L. J.; Matta, C. F.; Merz Jr., K. M.; Nakashima, P.; Ott, H.; Ryde, U.; Scherer, W.; Schwarz, K.; Sierka, M.; Grabowsky, S. (2017) “Quantum Crystallography: Current Developments and Future Perspectives”, Chemistry: A European Journal, in preparation.
[92] Macetti, G.; Gatti, C.; Boyd, R. J.; Matta, C. F. (2017). “A source function study of the electron density of DNA Watson-Crick base pairs in their neutral and ionized ground states”, Journal of Computational Chemistry, submitted.
[91] Matta, C. F. (2017). “Molecules as networks: A localization-delocalization matrices approach”, Theoretical and Computational Chemistry, submitted, in review. (Invited Viewpoint Article).
[90] Massa, L.; Matta, C. F. (2017). “Quantum Crystallography (QCr): Extraction of the complete quantum mechanics from X-ray scattering data”, Journal of Computational Chemistry, submitted, in review.
[89] Matta, C. F. (2017). “De la topogaphie de la densité électronique à une théorie quantique des atomes dans les molécules” [in French] (From the topography of the electron density to a quantum theory of atoms in molecules), Le BUP – Physique-Chimie (Bulletin de l’union des physiciens) 111, 825-845. (Chosen by the journal as “Article of the Month (Link)”).
[88] Matta, C. F. (2017). “A Path through Quantum Crystallography: A Short Tribute to Professor Lou Massa”, Structural Chemistry 28, 1279-1283.
[87] Matta, C. F. (2017). “On the connections between the quantum theory of atoms in molecules (QTAIM) and density functional theory (DFT): A letter from Richard F. W. Bader to Lou Massa”, Structural Chemistry 28, 1591-1597.
[86] Terrabuio, L. A.; da Silva, N. A.; Haiduke, R. L. A.; Matta, C. F. (2017). “Real Space Atomic Decomposition of Fundamental Properties of Carbon Monoxide in the Ground and Two Low-Lying Excited Electronic States”, Molecular Physics 115, 1955-1965. (INVITED – Special Issue: Bandrauk Festschrift).
[85] Matta, C. F. (2017). “El camino de enlace cuarenta años después de su descubrimiento: Una manifestación de los enlaces químicos en el espacio real” [in Spanish] (The bond path forty years after its discovery: A manifestation of chemical bonds in real space), Anales de Química (Spain) 113, 36-39.
[84] Rochette, E.; Bouchard, N.; Lavergne, J. L.; Matta, C. F.; Fontaine, F. G. (2016). “Spontaneous reduction of a hydroborane to generate a B-B single bond using a frustrated Lewis pair” Angewandte Chemie International Edition 55, 12722-12726.
[83] Matta, C. F. (2016). “Drawing a line under the chemical bond”, Chemistry World 13, (No. 10 (October)), 65.
[82] Terrabuio, L. A.; Haiduke, R. L. A.; Matta, C. F. (2016). “Difluorodiazirine (CF2N2): A comparative quantum mechanical study of the first triplet and first singlet excited states” Chemical Physics Letters 655-656, 92-102.
[81] Terrabuio, L. A.; Haiduke, R. L. A.; Matta, C. F. (2016). “Difluorodiazirine (CF2N2): A quantum mechanical study of the electron density and of the electrostatic potential in the ground- and first excited-electronic states” Theoretical Chemistry Accounts 135, 63.
[80] Terrabuio, L. A.; Teodoro, T. Q.; Matta, C. F.; Haiduke, R. L. A. (2016). “An investigation of non-nuclear attractors in heteronuclear diatomic systems” Journal of Physical Chemistry A 120, 1168-1174.
[79] Arabi, A. A.; Matta, C. F. (2016). “Bioisosteric groups in methylsquarate and carboxylic acid: The similarities of their electrostatic potentials and average electron densities” Future Medicinal Chemistry 8, 361-371.
[78] Rodríguez, J. I.; Matta, C. F.; Molina-Brito, B.; Götz A. W. (2016). “A QTAIM topological analysis of the P3HT-PCBM dimer” Chemical Physics Letters 644, 157-162.
[77] Sumar, I.; Cook, R.; Ayers, P. W.; Matta, C. F. (2016). “Aromaticity of rings-in-molecules (RIMs) from electron localization-delocalization matrices (LDMs)” Physica Scripta 91, 013001 (13 pp).
[76] Matta, C. F.; Sadjadi, S.; Braden, D. A.; Frenking, G. (2016). “The barrier to the methyl rotation in cis-2-butene and its isomerization energy to trans-2-butene revisited” Journal of Computational Chemistry 37, 143-154.
[75] Matta, C. F.; Massa, L. (2015). “The energy equivalence of information in the mitochondrion and the thermodynamic efficiency of ATP synthase” Biochemistry 54, 5376-5378.
[74] Huang, L.; Matta, C. F.; Massa, L. (2015). “The kernel energy method (KEM) delivers fast and accurate QTAIM electrostatic charge for atoms in large molecules” Structural Chemistry 26, 1433-1442.
[73] Sumar, I.; Cook, R.; Ayers, P. W.; Matta, C. F. (2015). “AIMLDM: A Program to Generate and Manipulate Electron Localization-Delocalization Matrices (LDMs)” Computational and Theoretical Chemistry 1070, 55-67.
[72] Lecomte, C.; Espinosa, E.; Matta, C. F. (2015). “On atom-atom “short contact” bonding interactions in crystals”; International Union of Crystallography Journal (IUCrJ) 2, 161–163.
[71] Huang, L.; Matta, C. F.; Wallace, S.; Massa, L.; Bernal, I. (2015). “A unique trapping by crystal forces of a hydronium cation displaying a transition state structure” Comptes Rendus Chimie 18, 511-515.
[70] Matta, C. F. (2014). “Modeling biophysical and biological properties from the characteristics of the molecular electron density, electron localization and delocalization, and electrostatic potential”; Journal of Computational Chemistry 35, 1165-1198.    [Click here for SUPPORTING INFORMATION]
[69] Timm, M.; Matta, C. F. (2014). “Primary retention following nuclear recoil in β-decay: Proposed synthesis of a metastable rare gas oxide (38ArO4) from (38ClO4) and the evolution of chemical bonding over the nuclear transmutation reaction path”; Applied Radiation and Isotopes 94, 206-215.
[68] Timm, M. J.; Matta, C. F.;* Massa, L.; Huang, L. (2014). “The localization-delocalization matrix and the electron density-weighted connectivity matrix of a finite graphene flake reconstructed from kernel fragments” Journal of Physical Chemistry A 118, 11304-11316.  [Click here for SUPPORTING INFORMATION].
[67] Sumar, I.; Ayers, P. W.; Matta, C. F. (2014). “Electron localization and delocalization matrices in the prediction of pKa‘s and UV-wavelengths of maximum absorbance of p-benzoic acids and the definition of super-atoms in molecules” Chemical Physics Letters 612, 190-197.  [Click here for SUPPORTING INFORMATION].
[66] Matta, C. F. (2014). “Localization-delocalization matrices: a molecular fingerprinting tool of potential utility in computational medicinal chemistry”, Future Medicinal Chemistry 6, 1475-1479.
[65] Huang, L.; Matta, C. F.; Massa, L. (2014). “A graphene flake under external electric fields reconstructed from field-perturbed kernels”; Carbon 76, 310-320.
[64] Dittrich, B.; Matta, C. F. (2014). “Contributions of charge-density research to medicinal chemistry”; International Union of Crystallography Journal (IUCrJ) 1, 457-469.
[63] Sowlati-Hashjin, S.; Matta, C. F. (2013) “The chemical bond in external electric fields. energies, geometries, and vibrational Stark shifts in diatomic molecules”; Journal of Chemical Physics 139, 144101 (1-14).[Click here for SUPPORTING INFORMATION]
[62] Matta, C. F.; Sowlati-Hashjin, S.; Bandrauk, A. D. (2013). “Dipole moment surfaces of the CH4 + •X → CH3• + HX (X = F, Cl) reactions from atomic dipole moment surfaces, and the origins of the sharp extrema of the dipole moments near the transition states; Journal of Physical Chemistry A 117, 7468-7483.
[61] Sadjadi, S.; Matta, C. F.; Hamilton, I. P. (2013). “Chemical bonding in groups 10, 11, and 12 transition metal homodimers: An electron density study”, Canadian Journal of Chemistry 91, 583-590.
[60] Bensasson, R.; Sowlati-Hashjin, S.; Zoete, V.; Dauzonne, D.; Matta, C. F. (2013). “Physicochemical properties of exogenous molecules correlated with their biological efficacy as protectors against carcinogenesis and inflammation”, International Reviews in Physical Chemistry 32, 393-434.
[59] Groves, B. R.; Crawford, S. M.; Lundrigan, T.;   S. Sowlati-Hashjin; Matta, C. F.; Thompson, A. (2013). “Improved synthesis and chemical manipulation of the simplest F-BODIPY framework”, Chemical Communications 49, 816-818.
[58] Matta, C. F. (2013). “Philosophical aspects and implications of the quantum theory of atoms in molecules (QTAIM)”, Foundations of Chemistry 15, 245-251.
[57] Bader, R. F. W.; Matta, C. F. (2013). “Atoms in molecules as non-overlapping, bounded, space-filling open quantum systems”, Foundations of Chemistry 15, 253-276.
[56] Bendeif, E.-E.; Matta, C. F.; Stradiotto, M.; Fertey, P.; Lecomte, C. (2012). “Can a formally zwitterionic rhodium(I) complex emulate the charge density of a cationic rhodium(I) complex? A combined synchrotron X-ray and theoretical charge density study”, Inorganic Chemistry 51, 3754-3769.[Click here for SUPPORTING INFORMATION]
[55] Wallace, S.; Huang, L.; Matta, C. F.; Massa, L.; Bernal, (2012). I. “New structures of hydronium cation clusters”, Comptes Rendus Chimie 15, 700-707.
[54] Matta, C. F.; Huang, L.; Massa, L. (2012). “Local intense cellular electric fields and their relevance in the computational modeling of biochemical reactions”, Future Medicinal Chemistry 4, 1873-1875.
[53] Arabi, A. A.; Matta, C. F. (2011). “Effects of external electric fields on double proton transfer kinetics in the formic acid dimer”, Physical Chemistry Chemical Physics (PCCP) 13, 13738-13748.
[52] Matta, C. F.; Sichinga, M.; Ayers, P. W. (2011). “Information theoretic properties from the quantum theory of atoms in molecules” Chemical Physics Letters 514, 379-383.
[51] Sadjadi, A.; Matta, C. F.; Lemke, K.; Hamilton, I. P. (2011). “Relativistic-consistent electron densities of the coinage metal clusters M2, M4, M42-, M4Na2 (M = Cu, Ag, Au): A QTAIM Study” Journal of Physical Chemistry A 115, 13024–13035.
[50] Bohorquez, H.; Boyd, R. J.; Matta, C. F. (2011). Molecular model with quantum mechanical bonding information, Journal of Physical Chemistry A 115, 12991–12997.
[49] Matta, C. F.; Huang, L.; Massa, L. (2011). “The characterization of a trihydrogen bond on the basis of the topology of the electron density”, Journal of Physical Chemistry A 115, 12451–12458.
[48] Huang, L.; Matta, C. F.; Massa, L. (2011). “Ion induced dipole clusters Hn (3 ≤ n-odd ≤ 13): Density functional theory calculations of structure and energy”, Journal of Physical Chemistry A 115, 12445–12450.
[47] Matta, C. F.; Arabi, A. A. (2011). “Electron density descriptors as predictors in quantitative structure-to-activity/property-relationships (QSAR/QSPR)”, Future Medicinal Chemistry 3, 969-994.
[46] Cukrowski, I.; Matta, C. F. (2011). “Protonation sequence of linear aliphatic polyamines from intramolecular atomic energies and charges”, Computational and Theoretical Chemistry 966, 213-219.
[45] Huang, L.; Bohorquez, H.; Matta, C. F.; Massa, L. (2011). “The kernel energy method: Application to graphene and extended aromatics”, International Journal of Quantum Chemistry 111, 4150–4157.
[44] Matta, C. F.; Massa, L., Keith T. A. (2011). “Richard F. W. Bader: A True Pioneer”, Journal of Physical Chemistry A 115, 12427-12431.
[43] Matta, C. F.; Massa, L. (2011). “Subsystem quantum mechanics and in-silico medicinal and biological chemistry”, Future Medicinal Chemistry 3, 1971–1974.
[42] Matta, C. F.; Massa, L; Gubskaya, V. A.; Knoll, E. (2011) “Can one take the logarithm or the sine of a dimensioned quantity or a unit? Dimensional analysis involving transcendental functions”, Journal of Chemical Education 88, 67–70.
[41] Cukrowski, I; Matta, C. F. (2010). “Hydrogen-hydrogen bonding: A stabilizing interaction in strained chelating rings of metal complexes in aqueous phase”, Chemical Physics Letters 499 66–69.
[40] Walker, V. E. J.; Castillo, N.; Matta, C. F.; Boyd, R. J. (2010) “The effect of multiplicity on the size of iron (II) and the structure of iron (II) porphyrins”, Journal of Physical Chemistry A 114, 10315–10319.
[39] Matta, C. F.; Arabi, A. A.; Weaver, D. F. (2010). “The bioisosteric similarity of the tetrazole and carboxylate anions: Clues from the topologies of the electrostatic potential and of the electron density”, European Journal of Medicinal Chemistry 45, 1868–1872.
[38] Matta, C. F. (2010). “How dependent are molecular and atomic properties on the electronic structure method? Comparison of Hartree-Fock, DFT, and MP2 on a biologically-relevant set of molecules”, Journal of Computational Chemistry 31, 1297-1311.[Click here for SUPPORTING INFORMATION]
[37] Bohórquez, H. J.; Matta, C. F.; Boyd, R. J. (2010). “The localized electron detector as an ab initio representation of molecular structures”, International Journal of Quantum Chemistry 110, 2418-2425.
[36] Arabi, A. A.; Matta, C. F. (2009). “Where is electronic energy stored in an adenosine triphosphate?”, Journal of Physical Chemistry A 113, 3360-3368.
[35] Matta, C. F.; Arabi, A., Keith, T. A. (2007). “Atomic contributions to the dissociation energy of the P-O(H) Bond in hydrogen phosphate anion (HPO42-): Disentangling the effect of Mg2+”, Journal of Physical Chemistry A 111, 8864-8872.
[34] Taylor, A.; Matta, C. F.; Boyd, R. J. (2007). “The hydrated electron as a pseudo-atom in cavity-bound water clusters”, Journal of Chemical Theory and Computation 3, 1054-1063.
[33] Hernández-Trujillo, J.; Matta C. F. (2007). “Hydrogen-hydrogen bonding in biphenyl revisited”, Structural Chemistry 18, 849-857.
[32] Wolstenholme, D.; Matta, C. F.; Cameron, T. S. (2007). “Experimental and theoretical charge density study of a highly twisted polycyclic aromatic hydrocarbon: 4-Methyl-[4]helicene”, Journal of Physical Chemistry A 111, 8803-8813.
[31] Matta, C. F., Castillo, N., Boyd, R. J. (2006). “Atomic contributions to bond dissociation energies in aliphatic hydrocarbons”, Journal of Chemical Physics 125, 204103-(1-13).
[30] Zhurova, E. A.; Matta, C. F.; Wu, N.; Chen, Y.-S., Pinkerton, A. A. (2006). “Experimental and theoretical electron density study of estrone”, Journal of the American Chemical Society 128, 8849-8861.
[29] Bandrauk, A. D.; Sedik, E. S.; Matta, C. F. (2006). “Laser control of reaction paths in ion-molecule reactions”, Molecular Physics 104, 95-102.
[28] Matta, C. F.; Castillo, N.; Boyd, R. J. (2006). “Extended weak bonding interactions in DNA: pi-stacking (base-base), base-backbone, and backbone-backbone interactions”, Journal of Physical Chemistry B 110, 563-578.
[27] Matta, C. F.; Bader, R. F. W. (2006). “An experimentalist’s reply to ‘What is an atom in a molecule?’ ”, Journal of Physical Chemistry A 110, 6365-6371.
[26] Dobrin, S.; Harikumar, K. R.; Matta, C. F.; Polanyi, J. C. (2005). “An STM study of the localized atomic reaction of 1,2 and 1,4-dibromoxylene at Si(111) 7×7”, Surface Science 580, 39-50.
[25] Matta, C. F.; Castillo, N.; Boyd, R. J. (2005). “Characterization of a closed-shell fluorine-fluorine bonding interaction in aromatic compounds on the basis of the electron density”, Journal of Physical Chemistry A 109, 3669-3681.
[24] Castillo, N.; Matta, C. F.; Boyd, R. J. (2005). “Fluorine-fluorine spin-spin coupling constants: Correlations with the delocalization index and with the internuclear separation”, Journal of Chemical Information and Modeling 45, 354-359.
[23] Castillo, N., Matta, C. F., Boyd, R. J. (2005). “The first example of a cage critical point in a single ring: A novel twisted α-helical ring topology”, Chemical Physics Letters 409, 265-269.
[22] Matta, C. F.; Polanyi, J. C. (2004). “Effect of adatom-to-adatom separation on the reactivity of dihalobenzenes at Si(111)7´7 surfaces: chemistry on a peg-board”, Philosophical Transactions of the Royal Society of London 362, 1185-1194 (10).
[21] Bandrauk, A. D.; Sedik, E. S.; Matta, C. F. (2004) “Effect of absolute laser phase on reaction paths in laser-induced chemical reactions”, Journal of Chemical Physics 121, 7764-7775.
[20] Bader, R. F. W.; Matta, C. F.; Cortés-Guzmán, F. (2004). “Where to draw the line in defining a molecular structure”, Organometallics 23, 6253-6263.
[19] Bader, R. F. W; Matta, C. F. (2004). “Atomic charges are measurable quantum expectation values: A rebuttal of criticisms of QTAIM charges“, Journal of Physical Chemistry A 108, 8385-8394.
[18] Matta, C. F.; Hernández-Trujillo, J.; Tang, T.-H.; and Bader, R. F. W. (2003). “Hydrogen-hydrogen bonding: a stabilizing interaction in molecules and crystals”, Chemistry – A European Journal 9, 1940-1951.
[17] Matta, C. F. and Hernández-Trujillo, J. (2003). “Bonding in polycyclic aromatic hydrocarbons in terms of the electron density and of the electron pair density”, Journal of Physical Chemistry A 107, 7496-7504.
[16] Wang, Y.-G.; Matta, C. F.; Werstiuk, N. H. (2003). “Comparison of localization and delocalization indices obtained with Hartree-Fock and conventional correlated methods: Effect of Coulomb correlation”, Journal of Computational Chemistry 24, 1720-1729.
[15] Matta, C. F. and Bader, R. F. W. (2003). “Atoms-in-molecules study of the genetically-encoded amino acids. III. Bond and atomic properties and their correlations with experiment including mutation-induced changes in protein stability and genetic coding”, Proteins: Structure, Function, and Genetics 52, 360-399.
[14] Matta, C. F. (2003). “Application of the quantum theory of atoms in molecules to selected physicochemical and biophysical problems: focus on correlation with experiment”, Journal of Computational Chemistry 24, 453-462.
[13] Matta, C. F.; Cow, C. N.; and Harrison, P. H. M. (2003). “Twisted amides: x-ray crystallographic and theoretical study of two acylated glycolurils with aromatic substituents” Journal of Molecular Structure 660, 81-97.
[12] Matta, C. F.; Hernández-Trujillo, J.; and Bader, R. F. W. (2002). “Proton spin-spin coupling and electron delocalization”, Journal of Physical Chemistry A 106, 7369-7375.
[11] Matta, C. F. and Bader, R. F. W. (2002). “Atoms-in-molecules study of the genetically- encoded amino acids. II. Computational study of molecular geometries”, Proteins: Structure, Function, and Genetics 48, 519-538.
[10] Matta, C. F. and Gillespie, R. J. (2002). “Understanding and interpreting molecular electron density distributions”, Journal of Chemical Education 79, 1141-1152.
[9] Matta, C. F. (2001). “Theoretical reconstruction of the electron density of large molecules from fragments determined as proper open quantum systems: The properties of morphine, the oripavine PEO, and enkephalins”, The Journal of Physical Chemistry A 105, 11088-11101.
[8] Bader, R. F. W. and Matta, C. F. (2001). “Properties of atoms in crystals: dielectric polarization”, International Journal of Quantum Chemistry 85, 592-607.
[7] Bader, R. F. W.; Matta, C. F. (2001). “Bonding to titanium”, Inorganic Chemistry 40, 5603-5611.
[6] Duspara, P. A.; Matta, C. F.; Jenkins, S. I.; and Harrison, P. H. M. (2001). “Twisted amides: Synthesis and structure of 1,6-dipivaloyl-3,4,7,8-tetramethyl-2,5-dithioglycoluril”, Organic Letters 3, 495-498.
[5] Gillespie, R. J. and Matta, C. F. (2001). “Teaching the VSEPR model and electron densities”, Chemistry Education: Research and Practice In Europe 2, 73-90.
[4] Matta, C. F. and Bader, R. F. W. (2000). “An atoms-in-molecules study of the genetically-encoded amino acids. I. Effects of conformation and of tautomerization on geometric, atomic, and bond properties”, Proteins: Structure, Function, and Genetics 40, 310-329.
[3] Matta, C. F.; Cow, C. C., Sun, S.; Britten, J. F.; and Harrison, P. H. M. (2000). “Twisted amides: Crystal and optimized structures, and molecular geometry analysis of 1-acetyl-3,4,7,8-tetramethylglycoluril and1,6-diacetyl-3,4,7,8-tetramethyl-glycoluril”, Journal of Molecular Structure 523, 241-255.
[2] Sun, S.; Britten, J. F.; Cow, C. C.; Matta, C. F.; and Harrison, P. H. M. (1998). “The crystal structure of 3,4,7,8-tetramethylglycoluril”, Canadian Journal of Chemistry 76, 301-306.
[1] Matta, C. F. (1991). “L’effet tunnel : quelques applications”, Bulletin de l’Union des physiciens (BUP) 85 (No. 734), 737-749. (in French).

 

 



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