Mechanism of α-Amino Acids decomposition in the gas phase. Experimental and theoretical study of the elimination kinetics of N-Benzyl Glycine Ethyl Ester

Article abstract of DOI:10.1021/jp9108943

The gas-phase elimination kinetics of N-benzylglycine ethyl ester was examined in a static system, seasoned with allyl bromide, and in the presence of the free chain radical suppressor toluene. The working temperature and pressure range were 386.4-426.7 °C and 16.7-40.0 torr, respectively. The reaction showed to be homogeneous, unimolecular, and obeys a first-order rate law. The elimination products are benzylglycine and ethylene. However, the intermediate benzylglycine is unstable under the reaction conditions decomposing into benzyl methylamine and CO₂ gas. The variation of the rate coefficients with temperature is expressed by the following Arrhenius equation: log k₁ (s^-1) = (11.83 ± 0.52) - (190.3 ± 6.9) kJ mol ^-1 (2.303RT)^-1. The theoretical calculation of the kinetic parameters and mechanism of elimination of this ester were performed at B3LYP/6-31G*, B3LYP/6-31+G**, MPW1PW91/6-31G*, and MPW1PW91/6-31+G** levels of theory. The calculation results suggest a molecular mechanism of a concerted nonsynchronous six-membered cyclic transition state process. The analysis of bond order and natural bond orbital charges implies that the bond polarization of C(=O)O-C, in the sense of C(=O)O^δ-...C^δ+, is rate determining. The experimental and theoretical parameters have been found to be in reasonable agreement.

Full text of DOI:10.1021/jp9108943

J. Phys. Chem. A 2010, 114, 2483–2488
2483
Mechanism of r-Amino Acids Decomposition in the Gas Phase. Experimental and
Theoretical Study of the Elimination Kinetics of N-Benzyl Glycine Ethyl Ester
Maria Tosta,† Jhenny C. Oliveros,‡ Jose R. Mora,† Tania Co´rdova,‡ and Gabriel Chuchani*,†
Centro de Qu´ımica, Instituto Venezolano de InVestigaciones Cient´ıficas (I.V.I.C.), Apartado 21827, Caracas,
Venezuela and Escuela de Qu´ımica, Facultad de Ciencias, UniVersidad Central de Venezuela,
Apartado 1020- A, Caracas, Venezuela
ReceiVed: NoVember 16, 2009; ReVised Manuscript ReceiVed: January 20, 2010
The gas-phase elimination kinetics of N-benzylglycine ethyl ester was examined in a static system, seasoned
with allyl bromide, and in the presence of the free chain radical suppressor toluene. The working temperature
and pressure range were 386.4-426.7 °C and 16.7-40.0 torr, respectively. The reaction showed to be
homogeneous, unimolecular, and obeys a first-order rate law. The elimination products are benzylglycine
and ethylene. However, the intermediate benzylglycine is unstable under the reaction conditions decomposing
into benzyl methylamine and CO2 gas. The variation of the rate coefficients with temperature is expressed by
the following Arrhenius equation: log k1 (s-1) ) (11.83 ( 0.52) - (190.3 ( 6.9) kJ mol-1 (2.303RT)-1. The
theoretical calculation of the kinetic parameters and mechanism of elimination of this ester were performed
at B3LYP/6-31G*, B3LYP/6-31+G**, MPW1PW91/6-31G*, and MPW1PW91/6-31+G** levels of theory.
The calculation results suggest a molecular mechanism of a concerted nonsynchronous six-membered cyclic
transition state process. The analysis of bond order and natural bond orbital charges implies that the bond
polarization of C(dO)O-C, in the sense of C(dO)Oδ- · · · Cδ+, is rate determining. The experimental and
theoretical parameters have been found to be in reasonable agreement.
1. Introduction
However, the gas-phase pyrolysis of 2-(N-Arylamino)pro-
panoic11 was reported to give ArNH2, CH3CHO, and CO as final
Amino acids of low molecular weight are solids that on
heating sinter or decompose into amorphous materials. More-
over, their insolubility in organic solvents and tendency to form
zwitterionic species in aqueous solution makes it difficult to
study the amino acids decomposition in gas phase as neutral
molecules. Despite these limitations, the kinetics of the gas phase
elimination of N,N-dimethylglycine,1 picolinic acid,2 and N-
phenylglycine,3 and their ethyl ester have been reported. These
amino acids as substrate or as intermediate of corresponding
ethyl ester decomposed very fast to give CO2 gas and the
corresponding amino compound [reaction 1].1-3
products. The mechanism was thought to involve a five-
membered cyclic transition state depicted in reaction 3.
Reaction 3 appears to follow a process similar to reaction 2.
The factors affecting the decomposition mechanism of neutral
amino acids in the gas phase are thus uncertain. The mechanisms
of reactions 1 and 2 create a conflict when comparing
PhNHCH2COOH3 to PhNHCH(CH3)COOH,11 with the only
difference when the H at the R-C is replaced by the CH3. To
have more information about the decomposition process of this
type of amino acids, the present work was addressed to study
the gas-phase elimination kinetics of PhCH2NHCH2COOH, that
is, N-benzylglycine and its ethyl ester, to find whether mech-
anism 1 or mechanism 3 takes place. Moreover, we additionally
carried out a theoretical study of the reaction at several
computational levels and compare the estimated parameters with
the experimental results.
The mechanism of reaction 1 differs from the gas-phase
elimination of several types of 2-substituted carboxylic acids
which are found to decarbonylate4-10 as described in reaction
2.
2. Experimental Sections
L ) leaving group: Cl, Br, OH, OR, OPh, OAc.
Ethyl N-Benzylglycidate. This substrate (Aldrich) of 97.0%
purity (GC-MS: Saturn 2000 Varian, with a DB-5MS capillary
column 30 m × 0.53 mm. I.D., 0.53 µm film thickness) was
used. The quantitative chromatographic analysis of ethylene
* To whom correspondence should be addressed.
† Venezolano de Investigaciones Cient´ıficas.
‡ Universidad Central de Venezuela.
10.1021/jp9108943  2010 American Chemical Society
Published on Web 02/03/2010

2484 J. Phys. Chem. A, Vol. 114, No. 7, 2010
Tosta et al.
TABLE 1: Temperature and Pressure Data for Pyrolysis
product was determined by using a Porapak Q column. The
identification of the product N-benzylmethylamine was made
with a Varian Saturn 2000 GC-MS instrument with a DB-5MS
capillary column.
Reaction
temperature
P0
Pf
compound
(°C)
(torr)
(torr)
Pf/P0
ave
2.9
N-Benzyl Glycine. We wanted to examine the elimination
kinetics of N-benzylglycine as a neutral amino acid. For this
purpose, N-benzylglycine was prepared from N-benzylglycine
hydrochloride (Aldrich) by treatment with 10% NaOH solution.
Unfortunately, the prepared amino acid N-benzylglycine, which
is a solid, could not be examined in the gas phase due to its
insolubility in most inert organic solvents. Solid substrates can
not be examined in our static system. N-benzylglycine is very
soluble in water, forming a zwitterion specie, which limits its
examination as neutral molecules in the gas phase. Our
procedure requires that we dissolve the substrate in an inert
solvent and then inject the material into the reactor.
ethyl ester
396.1
34.3
94.3
2.8
N-benzylglycine
407.1
416.5
426.7
26.0
22.0
25.2
72.0
67.0
74.3
2.8
3.1
3.0
TABLE 2: Stoichiometry of the Elimination Reaction
temperature
compound
ethyl ester
(°C)
parameter
time (min)
value
407.6
2.5 5.5 9.5 11.5 16
N-benzylglycine
reaction (%)
(pressure. torr)
23.8 42.2 57.3 68.5 76.8
ethylene (%) (GC) 21.4 42.2 59.9 71.3 79.6
Kinetics. The kinetic determinations were performed in a
static reaction system as described before.12-14At each temper-
ature, 6-9 runs have been carried out in our experiments. The
rate coefficients for the ethyl ester decomposition were calcu-
lated from the pressure increase manometrically and/or by
formation of ethylene product. The temperature was maintained
within (0.2 °C through control with a Shinko DC-PS resistance
thermometer controller and was measured with a calibrated iron
constant thermocouple. No temperature gradient was observed
along the reaction vessel. The substrate was dissolved in dioxane
and injected directly into the reaction vessel with a syringe
through a silicone rubber septum. The amount of substrate used
for each reaction was ∼0.05 to 0.1 mL.
The first order rate coefficient k(T) was calculated using the
TST18,19 and assuming that the transmission coefficient is equal
to 1, as expressed in the following relation:
k(T) ) (KT/h) exp(-∆G#/RT)
where ∆G# is the Gibbs free energy change between the reactant
and the transition state and K and h are the Boltzmann and Plank
constants respectively.
∆G# was calculated using the following relations:
∆G# ) ∆H# - T∆S#
3. Computational Method and Model
The thermal elimination reaction of ethyl N-benzylglycidate
was studied using electronic structure methods to gain insight
into the kinetics and its mechanisms. The methods used included
Møller-Plesset perturbation MP2/6-31G and DFT B3LYP/6-
31G, B3LYP/6-31G*, and B3LYP/6-31++G** as implemented
in Gaussian 98W.15 The results indicate that the ethyl ester of
N-benzylglycine decomposes to give N-benzylglycine and
ethylene in a slow step. The subsequent decarboxylation reaction
of unstable intermediate benzylglycine was also studied to
determine unequivocally the rate determining step of the
reaction. Structures for reactants and products were optimized
at each theory level. The transition states were searched and
optimized using synchronous transit (QST2, QST3) methodolo-
gies. The Berny analytical gradient optimization routines were
used. The requested convergence on the density matrix was 10-9
atomic units, the threshold value for maximum displacement
was 0.0018 Å, and that for the maximum force was 0.00045
hartree/bohr. The nature of the stationary points was established
by calculating and diagonalizing the Hessian matrix (force
constant matrix). TS structures were characterized by means of
normal-mode analysis. The transition vector (TV) associated
with the unique imaginary frequency, that is, the eigenvector
associated with the unique negative eigenvalue of the force
constant matrix has been characterized.
and
∆H# ) V # + ∆(ZPVE) + ∆E(T)
V# is the potential energy barrier, and ∆(ZPVE) and ∆E(T) are
the differences of ZPVE and temperature corrections between
the TS and the reactant, respectively.
Frequency calculations were carried out at the same level of
theory used for optimization for consistency. Thermodynamic
quantities such as zero point vibrational energy (ZPVE),
temperature corrections (E(T)), energy, and enthalpy energies
were obtained from vibrational analysis performed at T )
400 C.
4. Results and Discussion
4.1. Experimental Results. N-Benzylglycine was prepared
from N-Benzylglycine hydrochloride (Aldrich). Unfortunately,
the solid neutral amino acid could not be examined in the gas
phase due to its insolubility in most inert organic solvents.
The molecular decomposition of ethyl ester of N-benzyl-
glycine in the gas phase proceeds according to reaction 4:
Thermodynamic quantities such as the zero point vibrational
energy (ZPVE), the temperature corrections to E(T), and the
absolute entropies S(T), were obtained by frequency calculations.
The rate coefficient can then be estimated assuming that the
transmission coefficient is equal to 1. Temperature corrections
and absolute entropies were obtained assuming ideal gas
behavior from the harmonic frequencies and moments of inertia
by standard methods.16 Scaling factors for frequencies and zero
point energies are taken from the literature.17
The stoichiometry of reaction 4 requires that for long reaction
time a 3-fold increase in the final pressure, Pf, is required, that
is, Pf ) 3P0, where P0 is the initial pressure. The average

R-Amino Acids Decomposition Mechanism
J. Phys. Chem. A, Vol. 114, No. 7, 2010 2485
TABLE 3: Homogeneity of the Reaction
temperature
a
b
c
compound
ethyl ester
(°C)
S/V (cm-1
)
104 k1 (s-1
)
104 k1 (s-1
)
407.1
1
16.39 ( 0.50 15.61 ( 0.39
15.28 ( 0.45 16.99 ( 0.40
N-benzylglycine
6
a S ) surface area (cm2); V ) volume (cm3). b Clean Pyrex
vessel. c Vessel seasoned with allyl bromide.
TABLE 4: Effect of the Inhibitor Toluene on Ratesa
Figure 1. Plot of log(3P0 - Pt) against time at 396.4 °C.
temperature
Ps
Pi
compound
ethyl ester
N-benzylglycine
(°C)
(torr) (torr) Pi/Ps 104 k1 (s-1
)
407.1
38.0
16.39 ( 0.50
33.0
32.5
34.0 105
48
76
1.5 15.60 ( 0.57
2.3 16.08 ( 0.57
3.1 16.74 ( 0.40
a Ps ) pressure of the substrate; Pi ) pressure of the inhibitor.
Vessel seasoned with allyl bromide.
experimental, Pf/P0 values at four different temperatures and
after 10 half-lives is 2.9 (Table 1).
Additional checking of stoichiometry (4) was possible by
comparing, up to 75% decomposition, the pressure measure-
ments with the results of quantitative chromatographic analyses
of the product ethylene (Table 2).
Figure 2. Arrhenius plot for the elimination kinetic of ethyl ester of
To examine the effect of the surface on the rate of elimination,
several runs in the presence of toluene inhibitor were carried
out in a Pyrex vessel with a surface-to-volume ratio of six times
greater than the normal vessel, which is equal to one. Studies
were carried out in both clean Pyrex vessels and after seasoning
the reactors via in situ pyrolysis of allyl bromide. No discernible
effects on the reaction were observed (Table 3), which suggests
that there is no significant heterogeneous component to the
reaction.
N-benzylglycine in the gas phase.
in Table 6, Figure 1 (90% confidence coefficient obtained from
the least-squares procedure).
According to the results shown in Table 6, the most probable
mechanism for the elimination of ethyl ester of N-benzylglycine
is described in reaction 5. In this respect, a theoretical study has
been carried out to verify or modify the proposed mechanism 5.
The effect of the addition of different proportions of toluene
inhibitor is described in Table 4. However, the experiments of the
amino ester were always carried out in seasoned vessels and in
the presence of at least an equal amount of toluene in order to
impede any possible free radical chain reaction. No induction period
was observed and the rates were reproducible with a relative
standard deviation not greater than 5% at a given temperature.
The first-order rate coefficients of this amino ester, expressed
from k1 ) -(2.303/t) log [(3P0 - Pt)/2P0 were invariable to
initial pressures (Table 5). A plot of log(3P0 - Pt) against time
t gave a good straight line up to 75% reaction (Figure 1). The
k-value from Figure 1 is estimated as follows: k1 ) -2.303 ×
slope (slope ) -0.00044 at 396.4 °C) of the straight line at a
given temperature. The temperature dependence of the rate
coefficients and the corresponding Arrhenius equation is given
4.2. Theoretical Results. 4.2.1. Kinetic and Thermody-
namic Parameters. The elimination of ethylene from the
N-benzylglycine ethyl ester was studied using various
TABLE 5: Variation of Rate Coefficients with Initial Pressurea, b
substrate
temperature (°C)
parameters
value
ethyl ester
N-benzylglycine
407.2
P0 (torr)
16.7
16.74 ( 0.40
27.7
16.39 ( 0.50
32.5
16.05 ( 0.46
40.0
16.00 ( 0.41
104 k1 (s-1
)
a Vessel seasoned with allyl bromide. b In the presence of the inhibitor toluene.
TABLE 6: Temperature Dependence of the Rate Coefficientsa
substrate
parameters
value
ethyl ester
N-benzylglycine
temp. (°C)
104 k1 (s-1
386.4
5.49 ( 0.01
396.4
10.50 ( 0.38
407.1
16.39 ( 0.37
416.5
26.70 ( 0.09
426.7
41.74 ( 0.42
)
a Rate equation log k1 (s-1) ) (11.83 ( 0.52) - (190.3 ( 6.9) kJ mol-1 (2.303RT)-1; r ) 0.9995.

2486 J. Phys. Chem. A, Vol. 114, No. 7, 2010
Tosta et al.
amino acid
TABLE 7: Kinetic and Thermodynamic Parameters for the
Pyrolysis at 400 °C (673.15 K) of N-Benzylglycine Ethylester
TABLE 8: Geometric Parameters
interatomic distances (Å)
∆H‡
∆G‡
∆S‡
Ea
‡
ester
TS
(kJ/mol) (kJ/mol) (J/K mol) (kJ/mol) log A
C20-O21
C20-O22
O22-C23
C23-C26
C26-H29
H29-O21
1.214
1.350
1.454
1.521
1.093
2.902
1.277
1.269
2.028
1.405
1.312
1.321
1.348
1.215
3.831
1.337
2.446
1.215
experimental
182.7
193.4
179.7
201.8
207.2
189.1
178.5
206.4
195.2
174.4
160.3
-36.38
6.39
1.78
-6.88
-11.49
-1.51
-8.40
188.3
199.0
185.3
207.4
193.0
167.7
160.2
11.68
13.92
15.21
13.22
12.98
13.50
13.14
B3LYP/6-31G*
B3LYP/6-31+G**
MPW1PW91/6-31G*
MPW1PW91/6-31+G** 187.4
PBE/6-31G*
173.3
154.6
PBE/6-31+G**
TABLE 9: Dihedral Angles in TS Structure
electronic structure methods. The derived kinetic and ther-
modynamic parameters are shown in Table 7. Ea is Arrhenius
activation energy, and A is the pre-exponential factor in
Arrhenius equation k ) A exp(-Ea/RT). The experimental
Ea allows the estimation of ∆H‡. We compare the experi-
mental values with the parameters from theoretical calcula-
tions in Table 7.
dihedral angles (°)
atoms
ester
TS
amino acid
O21-C20-O22-C23
C20-O22-C23-C26
O22-C23-C26-H29
C23-C26-H29-O21
C26-H29-O21-C20
H29-O21-C20-O22
-2.011
-86.883
64.664
12.332
-1.856
-4.289
8.966
10.243
-88.895
35,967
175.881
95.854
-1.042
-6.591
-50.684
42.665
0.304
#
Theoretical parameters Ea and ∆H# were found in better
-12.605
agreement with experimental values at DFT method B3LYP/
6-31+G**; also MPW1PW91/6-31+G** are in reasonable
agreement. Entropy deviations are due to the use of the
harmonic approximation and the presence of low-frequency
modes, which are highly anharmonic. However, we found
that the error in entropy calculations is smaller when using
MPW1PW91/6-31+G**. DFT functionals B3LYP and
MPW1PW91 performance was better and larger basis set
including polarization functions and diffuses improved the
results as expected.
The second step, that is, the decarboxylation was also
examined and it was found to be faster than the first step of the
reaction. The estimated value for decarboxylation is Ea ) 56.30
kJ/mol at the B3LYP/6-31G** level of theory. Consequently,
the rate determining step is the ethylene elimination.
SCHEME 1
distance is smaller (0.22 Å). To better understand the relative
progress in the formation and breaking of the bonds involved
in the reaction, an analysis of NBO bond orders is presented in
the next section. The TS topology is a six-member ring close
to planar with small deviations as seen in dihedral angles (Table
9).
4.2.2. Transition State and Mechanism. The calculated
transition state for ethylene elimination is a six-membered
cyclic structure as shown in Figure 3. Geometric parameters
for reactant and transition state at B3LYP/6-31+G** level
are shown in Tables 8 and 9. Atom numbers are illustrated
in Scheme 1 for clarity.
4.2.3. Natural Bond Orbital (NBO). NBO calculations were
carried to obtain charges and carry out NBO bond order a
calculations.20-22 Wiberg bond indexes23 were computed using
the natural bond orbital NBO program24 as implemented in
Gaussian 98W, to further investigate the nature of the TS along
the reaction pathway.
Atom distance O22-C23 has increased considerably in the
TS compared to reactant, indicating bond breaking. Also the
C26-H29 distance is augmented on the TS, while C23-C26
bond is shortening due to the hybridization changing from sp3
to sp2 as the double CdC bond forms. Furthermore H29-O21
distance is decreasing as the new O-H bond forms.
Bond breaking and making process involved in the reaction
mechanism can be monitored by means of the synchronicity
(Sy) concept proposed by Moyano et al.25 defined by the
expression:
n
The changes in atom distances suggest that the reaction is
dominated by the breaking of O22-C23 bond, which is
elongated by 0.57 Å, while the change in C26-H29 bond
Sy ) 1 - [
|δB - δB |/δB ]/2n - 2
i av av
∑
i)1
where n is the number of bonds directly involved in the reaction
and the relative variation of the bond index is obtained from:
δBi ) [BTi S - BRi ]/[BiP - BRi ]
where the superscripts R, TS, and P, represent reactant, transition
state, and product, respectively.
The evolution in bond change is calculated as:
%Ev ) δBi × 100
Figure 3. The TS atoms in ethylene elimination are in the same
plane.
The average value is calculated from:

R-Amino Acids Decomposition Mechanism
J. Phys. Chem. A, Vol. 114, No. 7, 2010 2487
n
TABLE 10: Wiberg Index Evolution Changes and
Synchronicity for Ethylene Elimination from
N-Benzylglycine Ethyl Ester
δBave ) 1/n
δB
i
∑
i)1
atoms
%Ev
synchronicity
0.88
C20-O21
C20-O22
O22-C23
C23-C26
C26-H29
O21-H29
60.407
46.141
67.244
31.269
50.416
62.901
In this analysis, the Bi values indicate bond order and δBi
is the change in bond order as the reaction progress from
reactant (BiR), to the transition state TS (BiTS) and to products
(BiP). The percent evolution %Ev is used to show the relative
advance of the different reaction coordinates considered. The
synchonicity parameter Sy varies between 0 and 1, with a
value of Sy ) 0 for asynchronic processes and Sy ) 1 for a
concerted synchronic.
This study was carried out for the rate-determining step.
Bonds indexes were calculated for those bonds that change as
the reaction proceeds, that is: C20-O21, C20-O22, O22-C23,
C23-C26, C26-H29, and O21-H29 (Scheme 1, Figure 2).
The remaining bonds stay practically unchanged.
the hydrogen abstraction by the carbonyl oxygen. The TS
topology is planar and the process is polar in nature, that is,
occurring in a concerted but moderately asynchronic fashion.
Acknowledgment. TC is grateful to the Consejo de Desar-
rollo Cient´ıfico y Human´ıstico (C.D.C.H.) for Grant No. PG-
03-00-6499-2006.
NBO charges also show a strong O22-C23 bond polarization
in the sense Oδ-sCδ+. NBO charges and charge density plots
of the TS can be found as Supporting Information.
Supporting Information Available: This information is
available free of charge via the Internet at http://pubs.acs.org.
The relative advance in the reaction coordinate (%Ev,
Table 10) suggests that the most important factor in the
thermal elimination of ethylene is the breaking of bond
O22-C23 67%. This fact has also been described in several
theoretical works on other related elimination reactions, where
the breaking of C-O bond is more advanced than the
migration of the hydrogen, demonstrating an asynchronous
process.26,27 This is also observed in the atom distances in
Table 8 as describe above. The migration of hydrogen H29
to oxygen O21 has advanced to a lesser extent than the
breaking of O22-C23, as well as the change in bond order
in C20-O21 associated with it. In other words, the elongation
of the O-C bond of the alcohol part of the ester is dominating
in the reaction, and it is accompanied in less extent, by the
abstraction of hydrogen at the ethyl group by the carbonyl
oxygen. These facts indicates that the breaking of C-O bond
occur before the hydrogen transfer indicating a late TS in
this reaction coordinate. The described changes in bond order
demonstrate asymmetric TS. The synchronicity value of 0.88
reveals a process that is concerted but not completely
synchronic.
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5. Conclusions
The thermal decomposition of N-benzyl glycine ethyl ester
has been studied both experimental and theoretically. The
reaction proceeds in two steps, the elimination of ethylene
followed by the rapid decarboxylation of the intermediate
amino acid N-benzyl glycine to give benzylmethylamine. The
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in the presence of the free chain radical suppressor and
follows the rate expression log k1 (s-1) ) (11.83 ( 0.52) -
(190.3 ( 6.9) kJ mol-1 (2.303 RT)-1. The study of the
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experimental values. The results of the theoretical calculation
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cyclic six-member TS to produce the amino acid N-
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methylamine. The reaction is governed by the breaking of
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