Journal of Molecular Structure (Theochem) 639 (2003) 167176

www.elsevier.com/locate/theochem

A simple program to determine the reaction rate and

thermodynamic properties of reacting system
Patrcia R.P. Barretoa,*, Alessandra F.A. Vilelab, Ricardo Garganob
a

Laboratorio Associado de PlasmaLAP, Instituto Nacional de Pesquisas EspaciaisINPE/MCT, CP515,

Sao Jose dos Campos, SP, CEP 12247-970, Brazil
b
Instituto de Fsica, Universidade Braslia, CP04455, Braslia, DF, CEP 70919-970, Brazil
Received 14 April 2003; revised 14 April 2003; accepted 13 August 2003

Abstract
We developed a simple program to determine the reaction rate by using conventional transition state theory with the Wigner
transmission coefficient and also the thermodynamic properties of the species. The hydrogen abstraction in the reaction
NH3 H ! NH2 H2 is used as a model to demonstrate the program usage. The rate constants have been computed for the
gas-phase chemical reaction over the temperature range of 200 4000 K. Our data are in a good agreement with the published
data for this reaction.
q 2003 Elsevier B.V. All rights reserved.
PACS: 82.20.Pm; 82.20.Db; 82.20.Wt; 82.30.Hk; 82.30.Lp; 51.30. i; 82.60. 2 s
Keywords: Kinetics; Thermal rate constants; Conventional transition state theory; Direct dynamics; Bimolecular abstraction;
Thermodynamic properties

1. Introduction
There has been considerable interest in recent
years, in the growth of boron nitride thin films. Like
carbon, boron nitride has different allotropes, the most
common of which are the hexagonal (hBN) and cubic
(cBN) phases. The hBN, although electrically insulating, has properties that are very similar to graphite
while the cBN has properties comparable to diamond.
At present there is little understanding of the
chemical process which are involved in and which
* Corresponding author. Tel.: 55-12-3945-6694; fax: 55-123945-6710.
E-mail address: patricia@plasma.inpe.br (P.R.P. Barreto).
0166-1280/$ - see front matter q 2003 Elsevier B.V. All rights reserved.
doi:10.1016/j.theochem.2003.08.006

GAUSSIAN

98;

control the synthesis of either hexagonal or cubic

boron nitride from the vapor phase. Theoretical
research found in the literature includes thermodynamic equilibrium calculations for mixtures involving
B/F/N/H [1 5], B/Cl/N/H [4,5], and B/N/H [4], as
well as limited kinetics studies of the reactions
between BCl3 and NH3 [6,7].
P.R.P. Barreto et al. proposed a kinetic mechanism
to describe the growth of boron nitride films, for the
Ar/B/F/N/H system, using both CVD and arcjet
reactor [8 12]. The gas-phase mechanism includes
35 species and 1012 reactions and also extends a
previous mechanism that contained 26 species and
67 elementary reactions. Rate constants for 117
elementary reactions were obtained from published

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P.R.P. Barreto et al. / Journal of Molecular Structure (Theochem) 639 (2003) 167176

experimental/theoretical data and those for the other

895 reactions should be estimated using transition
state theory (TST). As the number of reactions as
large we developed a simple code to determine the
reaction rate using conventional TST with the Wigner
transmission coefficient, since we normally work at
high temperature, 1000 3000 K, in which the tunneling effects decreases.
To show the capability of our code we applied it to
the well-known reaction NH3 H ! NH2 H2,
since it has been studies by several groups who
provided many theoretical [13 18] and experimental
results [19 22] in the temperature range of 500
2000 K. Comparing the results obtained using our
code with published data, our data are in a good
agreement and now we can apply our code to the
reaction in a Ar/B/F/N/H system.
Following, we outline how the paper is organized.
In Section 2 we present the main characteristics of our
program. Our results and discussion are presented in
Section 3.

2. The program
Our program has basically two subroutines, one to
calculate the thermodynamic properties of the species
and the other one to determine the rate constants. The
input files are very easy to write down and the output
files are very simple to analyze, and they can be
exported, directly, to a graphical software. The
following sections will discuss the calculation of the
reaction rate using TST [23 26] and the determination of the thermodynamic properties [23,25].
2.1. Transition state theory
The TST was developed in the 1930s and has since
formed a framework for much of the discussion of rate
processes. It is a model to determine the rate constants
based in an interaction potential between reactant and
products with a statistical representation of the
dynamics. In addition to the Born Oppenheimer
approximation it uses more three assumptions: there
is a surface in phase space that divides into a reactant
region and a product region; the reactant equilibrium
is assumed to maintain a Boltzmann energy distribution and the transition state or activated complex is

assumed to have Boltzmann energy distribution

corresponding to the temperature of the reacting
system.
Considering a bimolecular reaction, such as:
A BC ! AB C

where A, B or C are atoms or group of atoms, the

thermal rate constants is given by:
!
kB T QX
VaG
kTST
2
exp 2
h QA QBC
RT
where QX ; QA and QBC are the partition functions of
the transition state, X (saddle point), and the reactant,
A and BC, respectively, kB Boltzmann constant, h
Planck constant, T temperature and R universal gas
constant, VaG is the barrier:
VaG V 1ZPE

where V is the classical potential energy of the saddle

point measured from the overall zero of energy and
1ZPE is the harmonic zero-point energyZPE.
The partition functions, QA ; QBC and QX ; are given
by:
Qj Qtrans Qrot Qvib Qelect ;

j A; BC; X
where Qtrans ; Qrot ; Qvib and Qelect mean the component
of the translation, rotation, vibration and electronic
partition functions.
The translation partition function is:


2pmkB T 3=2
5
Qtrans
h2
where m gives the mass of the atom or group of atom.
The rotation partition function depends on the
molecule structure, and for a linear molecule the
rotation partition function, Qrot22D ; is:
!
8p 2 I k B T
6
Qrot22D
s e h2
whereas for a nonlinear molecule the rotation partition
function, Qrot23D ; is
"
!3=2 #
p1=2 8p2 Im kB T
Qrot23D
7
se
h2

P.R.P. Barreto et al. / Journal of Molecular Structure (Theochem) 639 (2003) 167176

where I and Im IA IB IC denote the moment of inertia

and the product of inertia, respectively, se is the
symmetry number of the molecule.
The vibrational partition function and zero-point
energy, in the harmonic approximation, are given by:


Y
2hvi 2di
Qvib
1 2 exp
8
kB T
i
1ZPE

1 X
h di v i
2 i

where vi ; is the frequency, i 1; ; F and F is the

degree of freedom (F 3N 2 5 for linear molecule,
3N 2 6 for nonlinear molecule and F 2 1 for the
transition state) and di is the mode degeneracy.
The electronic partition function is given by:


X
2e i
Qelect
gi exp
10
kB T
i
where gi is the degeneracy, and e i is the energy of
electronic state g measured from the overall zero of
energy.
We have also included the transmission coefficient,
kT; in Eq. (2):
W
kTST
T kTkTST T

11

where the transmission coefficient is used to account

for the tunneling effect along the reaction coordinate.
We have decided to estimate the transmission
coefficient by using the Wigner correction [13,23,
26] instead of some semi-classical tunneling approximation [26]. The Wigner correction for tunneling
assumes a parabolic potential for the nuclear motion
near the transition state and therefore cannot be
considered as an accurate correction. The Wigner
transmission coefficient is given by:
2

1  "v 
kT 1
12


24  kB T 
where the imaginary frequency at the saddle point is
denoted by v :
For more precise rate constants calculation the
variational TST should be used and also semiclassical methods for the tunneling effect [26], yet in
this case more information about the potential energy
surface is required, but it is not employed in the
present work. A useful way to verify the importance

169

of using the variational transition state instead of

conventional transition state is the curvature of the
reaction path. A constraint on reaction-path curvature
is provided by the skew angle [26]:

1=2
mA mC
b Arc Cos
13
mA mB mB mC
where mA ; mB and mC are the masses of the A, B and
C moieties, respectively, for the schematic reaction
shown by Eq. (1). Large reaction-path curvature is
often encountered in the tunneling region in system
with small skew angles, so the tunneling effects
should be smaller.
For a generic bimolecular reaction:
A B Okkfr C D

14

where the rate constant in the forward direction, kf ;

determined by TST, may be conveniently writing in
the Arrhenius form as:


2Ea
n
kf AT exp
15
RT
where A is the pre-exponential factor, n is the
temperature power factor and Ea is the activation
energy.
The rate constants in the reverse direction, kr ; can
be determined using the forward constant rate and the
equilibrium constant, Kc ; as:
kr

kf
Kc

Remembering:


p Sn s
Kc Kp
RT

16

17

and:
DG 2RT ln Kp

18

so, we can rewrite the reverse reaction rate as:







RT Sns
DS
DH
kr kf
exp
exp 2
19
p
R
RT
where Sns is the stoichiometric factor that is defined
to be positive for products and negative for reactants
and p is the pressure.

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P.R.P. Barreto et al. / Journal of Molecular Structure (Theochem) 639 (2003) 167176

2.2. Thermodynamic properties

the previous properties as:

To determine the reverse rate constants, Eq. (16), it

is necessary to know the thermodynamic properties
such as entropy and enthalpy for the reactants and
products.
The thermodynamic properties, internal energy,
entropy, and heat capacity, can be written in terms of
the partition functions as:


ln Q
E kB T
20
lnT v


ln Q
S kB ln Q kB
21
ln T v
!


ln Q
2 ln Q
cv kB
k
:
22
ln T v B ln T2 v
The partition functions are given by Eqs. (4) (10).
Others thermodynamic properties such as enthalpy,
Gibbs free energy, can be obtained combining

H ; E pV

23

G H 2 ST:

24

Our code prints out the entropy and sensible enthalpy,

Hsen H 2 Df H 0 ; for all species, reactants, products
and saddle point, as a functions of temperature.

3. Results and discussion

To apply TST, we must know the geometries,
frequencies, and the potential energy for reactants and
saddle point. These properties are obtained from
accurate electronic structure calculation performed
using the GAUSSIAN 98 program [27]. First, we
determined the reactants and saddle point geometry
and frequencies using the second order Mller
Plesset perturbation theory and the triple-zeta plus
polarization 6-31G(d). Furthermore, we calculated

Table 1
Geometrical parameters (bond distance in Angstroms and bond angle in degree) of all stationary points of test reaction NH3 H ! NH2 H2
Parameter

This worka

NH3
RNH
AHNH

1.0168 (1.0124g)
106.4004 (106.67g)

NH2
RNH
AHNH

1.0283 (1.024g)
103.3089 (103.4g)

H2
RHH
TS
RNH
RNH1
RH1H2
AHNH
AHNH1
ANH1H2
DHNH1H2
a
b
c
d
e
f
g

Reference
Bb

Cc

1.007
107.4

1.012
106.1

1.01
106.1

1.023
102.7

1.02
102.7

0.734

0.73

0.7375 (0.7414g)
1.019
1.290
0.920
106.40
100.20
162.59
57.48

MP2/6-31G(d).
HF/SSANO [13].
MP2/6-31G(d) [14].
MP2/6-31p [15].
J. C. Corchado et al. [16].
MP2/6-31G(d,p) [17].
JANAF Table [28].

1.015
1.247
0.944
100.2
162.6
53.8

1.023
1.305
0.869
103.5
99.1
158.5
52.7

Dd

1.023
1.305
0.869
103.5
99.1
158.5

Ee

Ff

1.013
1.286
0.861

177.7

1.02
1.30
0.87
103.5
99.1
158.5
52.7

P.R.P. Barreto et al. / Journal of Molecular Structure (Theochem) 639 (2003) 167176

the energies for all species, reactants and saddle point,

at the MP2/6-311 G(3df,3pd), MP4(SDTQ)/631G p p and B3LYP/6-311 G(3df,3pd) level.
The geometries computed at MP2/6-31G(d) for
reactant, product and saddle point are shown in
Table 1. These geometries are also compared with
reference data. The interatomic distance and bond
angle absolute errors for the reactants and products
and 0.38, respectively,
are smaller than 0.0044 A
when comparing with the experimental results and
and 1.08, respectively, for the others
0.0098 A
calculated results. While the interatomic distance
and bond angle absolute errors for the transition
and 4.788, respectively, exception
state are 0.058 A
for the angle ANH1 H2 where this error is 15.118,
between our data and the Corchado and EspinosaGarcia one [16]. Fig. 1 shows the optimized
geometry of the saddle point, and also the notation
used in Table 1.
The harmonic vibrational frequencies calculated
from ab initio methods are overestimated, in this case,
in about 8%, then we have used a scaling factor of
92%. The scaled frequencies are also compared with
published data, as shown in Table 2. The absolute
error among our calculated and experimental frequencies is less than 118 cm21, except for the HH
stretching where this error is 235 cm21. Comparing
the absolute error among our calculated frequencies
with published calculated frequencies for the reactants
and products we observe for the NH stretching an
error of 480 cm21, when for the other frequencies this
error is less than 189 cm21. The absolute error in
frequency for the transition state is less than
435 cm21, except for the imaginary frequency
where the minimum error is 181 cm21 for the
Henon data [13] and the maximum error is
1119 cm21 for the Corchado data [16].

Fig. 1. Atomic numbering of the reaction system for reaction

NH3 H ! NH2 H2.

171

Table 2
Harmonic vibrational frequencies (cm21) and zero-point energy
(kcal mol21) of reaction NH3 H ! NH2 H2
This worka

Reference
Bb

Cc

1146
1803(2)
3709
3841(2)

1067
1642(2)
3386
3535(2)

1067
1642(2)
3386
3535(2)

NH2
1501 (1497g)
3147 (3219g)
3259 (3301g)

1516
3307
3417

1516
3307
3417

H2
4170

4301

4301

NH3
1068 (950g)
1614(2) (1627g)
3224 (3337g)
3368(2) (3444g)

TS
622
652
1033
1310
1490
1538
3243
3366
2536i
a
b
c
d
e
f
g

695
726
1209
1408
1633
1684
3666
3761
2717i

683
694
1089
1249
1530
1973
3314
3425
1920i

Dd

723
732
1258
1485
1541
1731
3647
3750
2833i

Ee

563
598
1038
1327
1640
1902
3383
3446
1417i

Ff

683
694
1089
1249
1530
1973
3314
3425
1920i

MP2/6-31G(d).
HF/SSANO [13].
MP2/6-31G(d) [14].
MP2/6-31 p [15].
J.C. Corchado et al. [16].
MP2/6-31G(d,p) [17].
JANAF Table [28].

3.1. Thermodynamic properties calculations

The first subroutine in our code calculates the
thermodynamic properties, particularly the entropy
and enthalpy, Eq. (21) and (23). Fig. 2 compares the
calculated properties with the reference data from the
JANAF tables [28] for the reactants, NH3 and H,
products, NH2 and H2 and, also, gives the thermodynamic properties for the transition state
(TS NH4).
Compared with reference data [28], the maximum
absolute errors in our calculation and the reference
data are 4.71 kcal K21 mol21 for the NH3 entropy at
4000 K and 2.41 kcal mol21 for the NH3 enthalpy at
298.15 K. Fig. 3 shows the maximum, minimum and

172

P.R.P. Barreto et al. / Journal of Molecular Structure (Theochem) 639 (2003) 167176

Fig. 2. Comparisons of thermodynamic properties, enthalpy and entropy, obtained by our code (symbols) with experimental data from JANAF
Table [28] (lines).

average error in the entropy and enthalpy for each

species analyzed here.
3.2. Rate constants calculations
The total energies for reactants, products and
saddle point as well as the reaction enthalpy
and potential barrier calculated by different methods
and basis set are shown in Table 3, in which we

applied the ZPE correction in the reaction enthalpy

and potential barrier. We found a large range of
values for the potential barrier, 14.39
25.37 kcal mol21, for the methods and basis set
used, as well as, for the reaction enthalpy, where
this range is 0.12 8.68 kcal mol21. The same
behavior, for the potential barrier, is found in the
literature, range of 7.6 22.6 kcal mol21 [13 15,17].
We would like to emphasize the calculation made in

P.R.P. Barreto et al. / Journal of Molecular Structure (Theochem) 639 (2003) 167176

Fig. 3. Absolute error for calculates thermodynamic properties,

enthalpy and entropy, obtained by our code with experimental data
from JANAF Table [28].

MP4(SDTQ)/6-31G p p , where the absolute error

in the potential barrier was 0.1 kcal mol21 when
compared with the Garrett et al. [15] results for the
same methods and basis set.

173

The skew angle in this case is 46.78, as it is a midvalue angle, we should expect same tunneling effects.
For reactions with intermediate/high-value of the
skew angle the Wigner transmission coefficient is not
the best correction. On the other hand, we are
interested in a high temperature range, 1000
3000 K, where this problem is greatly reduced.
Fig. 4 compares the reaction rate obtained in this
work, considering conventional TST and also applying the transmission coefficient of Wigner (TST/W)
with data from the Refs. [13 22]. Several reaction
rates were calculated, each one considering the
different energy calculated by the four methods and
basis set. One can see from Fig. 4 that the rate
constants obtained for MP4/6-31G p p level both
agree with experimental and theoretical results, in the
temperature range, 500 2000 K.
Fig. 5 compares the reaction rate obtained in this
work considering the energy determined by MP4/631G p p level, with the data from the POLYRATE 8.7
program [29], considering TST, TST/W, canonical
variational transition state theory (CVT) and also
CVT with zero curvature tunneling (CVT/ZCT). It is
possible to see that the POLYRATE curves from TST
and CVT are coincident. In the region of low
temperature, T , 500 K; the reaction rate obtained
by CVT/ZCT considerably differs from our calculation and also the TST and CVT calculation, since
the skew angle has a moderate-value, 46.78, it is
excepted a tunneling effects that is not well determined by the Wigner transmission coefficient. The
ratio between the POLYRATE rate constant (TST or
TST/W) and ours (TST or TST/W) are 22 times at

Table 3
Total energy Ea ; potential barrier and reaction enthalpy (kcal mol21) including ZPE correction, where A MP2/6-31g(d), B MP2/6311 g(d,p), C MP4/6-31g p p , D B3LYP/6-311 g(3df,3pd)

NH3
H
NH2
H2
TS
Reaction enthalpy
Potential barrier

256.354211
20.4982329
255.6908562
21.1441408
256.8096988
7.82
25.37

256.4567673
20.4998179
255.7728291
21.1649448
256.9196000
8.68
21.76

256.4013892
20.4982329
255.7298852
21.1645717
256.8693051
0.12
17.58

256.4284264
20.4998098
255.7544436
21.1683161
256.9030052
0.32
14.39

B3LYP/6-311 G [13] V 7.6 kcal mol21; CAS(3,3)/SANO [13] V 22.6 kcal mol21; PMP4/6-311 G(d,p) [14]
15.7 kcal mol21; MP2/6-31p [15] V 21.59 kcal mol21; MP4/6-31p p [15] V 17.68 kcal mol21; MP2/6-31G(d,p) [17]
10.8 kcal mol21.

V
V

174

P.R.P. Barreto et al. / Journal of Molecular Structure (Theochem) 639 (2003) 167176

Fig. 4. Comparisons of Arrhenius plot of k against the reciprocal temperature K in the range of 400 4000 K for reactions NH3
H ! NH2 H2 obtained in this paper with reference data where C, D, H, J and K are theoretical data from Espinosa-Garcia [14], Corchado
[16], Marshall [18], Garrett [15] and Espinosa-Garcia [17], respectively, and E, F, G and I are experimental results from Marshall [21], Hack
[22], Michael [20] and Ko [19], respectively.

Fig. 5. Comparisons of Arrhenius plot of k against the reciprocal temperature K in the range of 2004000 K for the reactions NH3
H ! NH2 H2 obtained in this paper with data from the POLYRATE program, considering TST, TST/W, TST/MEPSAG, CVT, CVT/ZCT.

P.R.P. Barreto et al. / Journal of Molecular Structure (Theochem) 639 (2003) 167176

500 K and drops for seven times at 800 K and drops

more while the temperature increases. It does not
differ considerable if we consider the TST or the TST/
W rate constants.

4. Conclusion
Our purpose was to develop a simple code to
determine the reaction rate for the B/F/H/N system
easily. We opted to write our own code instead of
using the available ones such as POLYRATE
program, for example, since in that way we can
simplify the inputs files and write output files that
can be used directly by some graphical software.
Our code allows us to determine several reaction
rates at once since we have one input file for all
the reactants, one input file for the transition state,
and one input file describing which and how many
reactions we want to analyze.
The analysis of reaction NH3 H ! NH2 H2
allowed us to check the capability of our code.
Our code reproduce the reaction rate from the
reference data and from the POLYRATE program in
a high temperature range, T . 500 K: Now we
can extend this methodology for other reactions
and systems.

Acknowledgements
The authors are grateful to the Centro Nacional
de Computacao Cientfica de Alto Desempenho de
Campinas-SP (CENAPAD-SP) for the provision of
computational facilities. A.F.A. Vilela acknowledges the Conselho Nacional de Desenvolvimento
Cientfico e Tecnolo gico (CNPq) for the
fellowship which provided her the opportunity to
perform this work.

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