Computational Combinatorial Chemistry.
A Theoretical Analysis on the
Thermodynamic Stability of Various
Constitutional Isomers of ...
University of Toronto
SCIENCE ABROAD (CHM396Y0)
Chemistry in Szeged
at the
Department of Chemical Informatics, Faculty of Education,
University of Szeged
COURSE REPORT
Student Name: …
UofT Student Number: …
2014.
Summary
1
Introduction
2
Methods
The three-dimensional initial geometries of all (ground state) constitutional isomers of …
were selected from all possible permutations of atoms by applying restrictions arising
from valence, leading us to consider molecules as networks of nodes. The hydrogen,
carbon and oxygen atoms are allowed to form bonds with 1, 4 and 2 valences,
respectively. To explore all possible closed shell isomers of the … species, nitrogen is
allowed to be tri- or pentacovalent. Besides molecular species, supermolecular complexes
are also generated (bimolecular, trimolecular, complexes etc.). Fulfilling all these criteria,
a number of … molecular configurations are generated utilizing graph theoretical
methods as implemented in the Molgen 5.0 program []. All of these are chemically
meaningful and are used as initial structures in search of local minima on the
multidimensional ab initio potential energy surface of … species.
In order to get accurate standard thermochemical properties (H°, S° and G°), the
G3MP2B3 composite method was applied []. According to the G3MP2B3 scheme,
geometries were optimized at the B3LYP/6-31G(d) level of theory. Analytical second
derivatives were calculated in each optimization step. The maximum optimization step
size (the initial trust radius) was limited to 0.01 Bohr or radians and the number of
optimization steps is restricted to 300. To obtain only real local minima of the
multidimensional potential energy surface, normal mode analysis was carried out and
only those structures will be discussed which have no imaginary harmonic frequencies. In
order to obtain the heat of formation, fH°(g), the atomization scheme was applied
(detailed description needed). Accurate atomic heats of formation were obtained from ref
3
[]. The relative Gibbs free energies of the species, relG°(g), compared to the lowest one
were also calculated. All quantum chemistry calculations were carried out using the
Gaussian09 program package.
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Results and discussion
Ordering of species and the applied energetic criteria
Species with the lowest Gibbs free energy and structural properties
Validation of the computational method
Entropy funnel and molecularity
Conclusions
Acknowledgement
The authors thank M. Labádi and L. Müller for the administration of the computer
clusters used for this work. The authors acknowledge the financial support within
TÁMOP-4.2.2.A-11/1/KONV-2012-0047 “New functional material and their biological
and environmental answers”, TÁMOP-4.2.2.C-11/1/KONV-2012-0010 “Supercomputer
— the national virtual laboratory”, HUSRB/1002/214/193 “Bile Acid Nanosystems as
Molecule Carriers in Pharmaceutical Applications” and TÁMOP 4.2.4. A/2-11-1-20120001, “National Excellence Program Elaborating and operating an inland student and
researcher personal support system”, subsidized by the European Union, Hungary and cofinanced by the European Social Fund.
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Table 1 Thermochemical properties of the … entities with the lowest Gibbs free energy. Relative Gibbs free energies (ΔrelG0) are
given in kJ/mol and standard entropies (S0) are in J/mol K. Gas phase heats of formation (ΔfH0) were obtained by G3MP2B3
calculation using atomization scheme and from literature. For molecular complexes, the heat of formation of the separated molecules
are also calculated and their sums are listed (ΣΔf,calc. H0) and compared with the corresponding sum of the literature values ΣΔf,lit. H0.
All thermochemical properties are calculated at standard condition (1 atm and 298.15 K).
ID
Structure and
name
ΔfH°(g)
Gas Phase
ΔrelG°(g)
S°(g)
Ref.
G3MP2B3
Complex
ΣΔf,calc. H°(g)
Lit.
Species
ΣΔf,lit.H°(g)
N1
N2
N3
N4
N5
N6
6
N7
N8
N9
N10
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Figure Caption
Figure 1 Relative Gibbs free energies (relG˚ in kJ/mol) of the … isomers as a function
of entropies (S˚ in J/mol K). Blank and filled circles indicate gas phase (g) and aqueous
phase (aq) results obtained at the G3MP2B3 level of theory.
Figure 2 Geometries of thermodynamically favored … complexes in gas phase obtained
at the B3LYP/6-31G(d) level of theory.
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References
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