BOOKS
1.
Matta, C. F.,
(Ed.) (2010), Quantum Biochemistry: Electronic Structure and
Biological
Activity (Vol. 1 and 2), Wiley-VCH, Weinheim. (978 pages).
2. Matta, C.
F.
and Boyd, R. J., Eds. (2007), The Quantum Theory of Atoms in
Molecules: From
Solid State to DNA and Drug Design, Wiley-VCH, Weinheim, (567
pages).
3.
Matta
C. F. (2009), The Response of
Molecular Charge Density Distributions to Changes in the External
Potential,
HDR Dissertation (Habilitation à diriger des recherches), Université
Henri
Poincaré (Nancy-1), Nancy, France (223 pages).
4.
Matta,
C. F. (2002), Applications of the
Quantum Theory of Atoms in Molecules to Chemical and Biochemical
Problems,PhD Thesis, McMaster University,
Hamilton, Canada. (323 pages).
5.
Matta,
C. F. (2010) “Reflections on Quantum Biochemistry: From Context to
Contents”
in: Matta, C. F. (Ed.) Quantum
Biochemistry: Electronic Structure and Biological Activity (Vol. 1),
Wiley-VCH, Weinheim (pp. XI-L).
6.
Bohórquez,
H. J.; Cárdenas, C.; Matta, C. F.; Boyd, R. J.; Patarroyo, M. E. (2010)
“Methods in biocomputational chemistry: A lesson from the amino acids”,
Chapter
13 in: Matta, C.F. (Ed.) Quantum
Biochemistry: Electronic Structure and Biological Activity (Vol. 1),
Wiley-VCH,
Weinheim (pp.403-422).
7.
Matta,
C. F. (2010) “From atoms in amino acids to the genetic code and protein
stability, and backwards”, Chapter 14 in: Matta, C. F. (Ed.) Quantum
Biochemistry: Electronic
Structure and Biological Activity (Vol. 1), Wiley-VCH, Weinheim
(pp.
423-472).
8.
Arabi,
A. A.; Matta, C. F. (2010) “Energy richness of ATP in terms of atomic
energies:
A first step”, Chapter 15 in: Matta, C. F. (Ed.) Quantum
Biochemistry: Electronic Structure and Biological Activity
(Vol. 1), Wiley-VCH, Weinheim (pp. 473-498).
9.
Massa, L.; Matta, C.
F.;
Yonath, A.; Karle, J. (2010) “Quantum transition state for peptide bond
formation in the ribosome”, Chapter 16 in: Matta,
C. F. (Ed.) Quantum Biochemistry:
Electronic Structure and Biological Activity (Vol. 2), Wiley-VCH,
Weinheim
(pp. 501-516).
10. Matta, C. F.;
Boyd, R.
J. (2007). “Introduction to the quantum theory of atoms in molecules”,
Chapter
1 in: Matta, C. F. and Boyd, R. J. (Eds.) Quantum
Theory of Atoms in Molecules: From Solid State to DNA and Drug Design,
Wiley-VCH, pp.1-34.
11. Matta, C. F.
(2006).
"Hydrogen¾hydrogen bonding: The non-electrostatic limit
of closed-shell interaction between two hydrogen atoms. A critical
review", Chapter 9 in: Grabowski S. (Ed.): Hydrogen
Bonding - New Insight, (Challenges and Advances
in Computational Chemistry and PhysicsSeries),
Springer, pp. 337-375.
12. Matta
C. F. (2005) “Computational chemistry: A powerful and inexpensive tool
for
basic and applied research in the life sciences”, Chapter 23 in:
Serageldin, I. and Persley, G. J.
(Eds.) Discovery to Delivery: BioVision Alexandria 2004 (Proceedings of the World Biological Forum),
CABI Publishing, pp. 261-272.
13. Bader,
R. F. W.; Matta, C. F.; and Martín, F. J. (2003). “Atoms in
medicinal
chemistry”, in: Chapter 7 in: Alber, F. and Carloni, P. (Eds.) Medicinal Quantum Chemistry (Methods
and Principles in Medicinal Chemistry
Series), Wiley-VCH, Weinheim, pp. 201-232.
REFEREED ARTICLES/PAPERS
Submitted/In
Review
14. 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,
submitted.
15. Cukrowski, I;
Matta, C.
F. (2010). “Hydrogen-hydrogen bonding: A stabilizing interaction in
strained
chelating rings of metal complexes in aqueous phase”, Chemical
Communications (ChemComm), submitted.
16. Huang,
L.; Bohorquez, H.; Matta, C. F.; Massa, L. (2010). “The Kernel
Energy
Method: Application to Graphene and Extended Aromatics”, Journal
of Chemical Physics 132, submitted.
Accepted/Published
17. Matta, C. F.; Massa, L;
Gubskaya, V. A.;
Knoll, E. (2010) “Can you take the log of a dimension or unit?
dimensional
analysis involving transcendental functions”, Journal of
Chemical Education 87, accepted for publication.
18. 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 Chemistry45, 1868–1872.
19. 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 Chemistry31, 1297-1311.
20. 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 (accepted, in
press).
21. Arabi,
A. A.; Matta, C. F. (2009). “Where is electronic energy stored in an
adenosine triphosphate?”, Journal of
Physical Chemistry A113, 3360-3368.
22. 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 A111,
8864-8872.
23. 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 Computation3, 1054-1063.
24. Hernández-Trujillo,
J.;
Matta C. F. (2007). “Hydrogen-hydrogen bonding in biphenyl revisited”, Structural Chemistry18, 849-857.
25. 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 A111, 8803-8813.
26. 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).
27. 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.
28. Bandrauk, A. D.;
Sedik,
E. S.; Matta, C. F. (2006). “Laser Control of Reaction Paths in
Ion-Molecule
Reactions”, Molecular Physics,
104, 95-102.
29. 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 B110,
563-578.
30. 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.
31. 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) 7x7”, Surface Science580, 39-50.
32. 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.
33. 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.
34. 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.
35. Matta,
C. F.; Polanyi, J. C. (2004). “Effect of adatom-to-adatom separation on
the
reactivity of dihalobenzenes at Si(111)7x7 surfaces: chemistry on a
peg-board”, Philosophical Transactions of
the Royal Society of London.362, 1185-1194 (10).
36.
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.
37. 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.
38. 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 A108,
8385-8394.
39. 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
Journal9, 1940-1951.
40. 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 A107,
7496-7504.
41.
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 Chemistry24,
1720-1729.
42. 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 Genetics52,
360-399.
43.
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
Chemistry24, 453-462. (Invited
Review, Special Issue on Electron
Densities and Electrostatic Potentials).
44.
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 Structure660,
81-97.
45. 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.
46. 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
Genetics48, 519-538.
47.
Matta,
C. F. and Gillespie, R. J. (2002). “Understanding and interpreting
molecular
electron density distributions”, Journal
of Chemical Education79,
1141-1152.
48. 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 A105,
11088-11101.
49. Bader, R. F. W.
and
Matta, C. F. (2001). “Properties of atoms in crystals: dielectric
polarization”, International Journal
of Quantum Chemistry85,
592-607.
50. Bader,
R. F. W.; Matta, C. F. (2001). “Bonding to titanium”, Inorganic
Chemistry40,
5603-5611.
51.
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
Letters3,
495-498.
52.
Gillespie, R. J. and Matta, C. F. (2001).
“Teaching the
VSEPR model and electron densities”, Chemistry
Education: Research and Practice In Europe2,
73-90.
53.
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.
54. 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.
55. 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 Chemistry76, 301-306.
56. Matta, C. F.
(2001). QCPE 0801. FRAGDIP:Program to
calculate functional group contributions to the molecular dipole moment.
57. Matta, C. F.
(2001). QCPE 0802.AIMDELOC:Program to calculate electron localization
and delocalization indices.
EXTENDED
ABSTRACTS (Non-refereed)
58. Matta, C. F., Massa, L. (2008) “An Electron Density Study of the
Mechanism of Peptide Bond Formation in the Ribosome”, 236th American Chemical Society (ACS)National Meeting
and Exposition, Philadelphia,
Pennsylvania, USA.
59. Feng,
X.; Matta, C. F.; Ban, F.; Stuart Grossert, J.; Weaver, D. F. (2006)
“Electron
spray Ionization Mass Spectrometry Studies on Interactions between
Lithium and
Other Group 1 Cations with Biologically-Active Amines and
Neurotransmitters”, 54th American Society for
Mass
Spectrometry Conference on Mass Spectrometry, Seattle, Washington,
USA.
60.
Matta
C. F., Boyd R. J., Castillo N. (2005) “An electron density study and the
characterization of extended weak bonding in DNA: pi-Stacking
(base-base),
base-backbone, and backbone-backbone interactions”, Lecture
Series on Computer and Computational Sciences, 4 B,
(Advances in Computational Methods in Sciences and Engineering), Brill
Academic Publishers, pp.1247-1250.
61. Jiang, G.-P.;
Lu, X.;
Matta, C.F.; Naumkin, F.Y.; Petsalakis, I.; Polanyi, J.C.; Rajamma, H.;
Rogers,
D.; Theodorakopoulos, G. and Yang, J. (2003) “Thermal, photoinduced and
electron-induced reaction of adsorbates on Si, followed by STM”, 226nd American Chemical Society
(ACS)National Meeting and
Exposition, Philadelphia, Pennsylvania, USA.
62. Matta, C.F.
(2001) “The
properties of morphine, the oripavine PET, and enkephalins theoretically
synthesized from fragments”, 222nd American
Chemical Society (ACS)National
Meeting and Exposition, Philadelphia, Pennsylvania,
USA.
63.
Matta,
C. F. and Brukhardt, S. (2005) “Cellular telephones: A risk to public
health?”,
Canadian Public Health Association
(CPHA) Health DigestXXIX(1),
p.4.
64.
Matta, C. F. and Brukhardt, S. (2003)
“Health hazards of
cellular telephones: The myth and the reality”, Ontario
Public Health Association (OPHA) Position Paper2003-02,
pp.1-22.