To evaluate the accuracy of the calculation method and the basis set used in this study, first the geometrical structure of the molecules participating in the reaction is optimized and the bond lengths and angles obtained (with the PBE method and the DNP basis set) were compared with the experimental data. It is in excellent agreement with the corresponding experimental value for these molecules [19, 20]. The computational results clearly show that the computational surface used (PBE/DNP) in this research has sufficient accuracy and as a result, it can be used for the computational study of the adsorption of CO molecules and S-methyl thioesters on the substrate of copper oxide nano-surface (CuO-NS)and their reaction to be employed.
The geometrical structure of copper oxide nanocatalyst can be seen in Fig. 1. One of the important conditions of the catalyst used in the CO reduction reaction is its thermal stability. Table 1 shows the thermodynamic and structural parameters of the nanocatalyst with the structure of the materials participating in the carbon monoxide reduction reaction and its products.
As the results show, the total energy of copper oxide nanocatalyst is negative (Etotal= -202.64 kcal.mol− 1), which indicates its structural stability. The calculated enthalpy for the nanocatalyst shows that it is endothermic. This means that at relatively high temperatures its structure is very stable. As a result, it can be used as a stable surface in carbon monoxide reduction reaction.
To investigate the production and reactions of S-methyl thioesters by carbon monoxide, the following three reactions have been simulated based on the concentration of carbon monoxide, the first path (A) with an equal ratio of the reactant [5]:
CO + 2CH3SH→ CH3SCOH + H2S
After optimizing the geometrical structure of all the compounds, the approach steps of carbon monoxide and sulfur-containing compounds to produce S-methyl esters (Fig. 2) have been calculated by PBE method and the DNP basis set. The absorption process of carbon monoxide and sulfur compounds takes place in five completely separate stages, as shown in Fig. 2:
I- Movement of carbon monoxide and sulfur-containing compounds towards copper oxide nanocatalyst.
II- Their diffusion in chemically active sites.
III- Absorption of carbon monoxide and sulfur-containing compounds and intermediate formation.
IV- Conducting the reaction and product production in the chemically active site of the nanocatalyst.
V- Separating the product from the nano catalyst and placing it in the surrounding environment.
The catalytic process of copper oxide nanoparticles is physical. Therefore, by producing the product, the nanocatalyst can be revived and reused by applying some physical processes.
Now, the adsorption of molecules on the surface of the nanocatalyst is considered in three different paths, and all the interaction steps are evaluated computationally. Table 2 shows the thermodynamic parameters of the calculation. Among the three investigated interactions, carbon monoxide, the first interaction, has a lower total energy, which represents the most probable reaction. The positive heat of reaction formation in all stages shows the stability of the nano catalyst in the reaction.
While the difference in the heat of reaction formation (ΔHo(V−I)=-10.56 kcal.mol− 1) only for the first path is negative, which indicates the greater tendency of this reaction to produce S-methyl ester. By comparing the dipole moment of all three paths, the dipole moment of copper oxide nanocatalyst has decreased from 6.13 to 4D, which its lowest value is in the first path (µ = 4.36 D).
Table 2
Thermodynamic parameters of the interaction of carbon monoxide and hydrogen with nano-surfaces and their conversion into products.
Thermodynamic properties
|
|
Etotal
kcal.mol− 1
|
Dipole moment
D
|
RMS
|
Ho
kcal.mol− 1
|
Eelec
kcal.mol− 1
|
En
kcal.mol− 1
|
Eb
kcal.mol− 1
|
CO + CH3SH→ CH3SCOH
|
A-I
|
-120.73
|
4.39
|
5150
|
728.11
|
-404.11
|
382.03
|
634.62
|
A-II
|
-171.57
|
4.31
|
5244
|
727.24
|
-404.49
|
387.32
|
723.76
|
A-III
|
-151.55
|
4.55
|
5512
|
717.28
|
-418.84
|
393.68
|
743.81
|
A-IV
|
-126.87
|
4.17
|
5447
|
731.97
|
-409.87
|
392.18
|
768.48
|
A-V
|
-191.29
|
4.48
|
5270
|
707.55
|
-407.08
|
387.96
|
704.07
|
2CO + CH3SSH → HCOSCH3 + COS
|
B-I
|
-184.64
|
4.93
|
5459
|
744.90
|
-435.42
|
406.96
|
671.12
|
B-II
|
-195.87
|
4.06
|
5540
|
723.66
|
-438.08
|
418.42
|
719.88
|
B-III
|
-276.60
|
4.46
|
6473
|
891.87
|
-431.08
|
428.21
|
888.09
|
B-IV
|
-239.08
|
4.48
|
6054
|
856.30
|
-431.41
|
425.03
|
851.85
|
B-V
|
-174.46
|
4.63
|
5776
|
785.076
|
-429.17
|
411.72
|
741.30
|
CO + 2CH3SH→ CH3SCOH + H2S
|
C-I
|
-153.88
|
4.85
|
5461
|
756.54
|
-417.63
|
402.24
|
752.61
|
C-II
|
-166.44
|
4.66
|
5731
|
743.98
|
-426.63
|
409.98
|
740.05
|
C-III
|
-112.88
|
4.59
|
5817
|
769.09
|
-418.62
|
417.78
|
788.16
|
C-IV
|
-117.27
|
4.81
|
5502
|
793.15
|
-418.58
|
406.85
|
789.22
|
C-V
|
-142.59
|
4.91
|
5458
|
767.82
|
-415.37
|
401.11
|
763.89
|
One of the topics discussed in the absorption of compounds by the catalyst and carrying out the reaction is the issue of charge transfer between the electron-donor and the acceptor, the adsorbed groups create a complex with the copper oxide nano-catalyst using electrostatic force. The calculated adsorption energy, net charge transfer and copper atom charge of the given complex in the nanocatalyst of these adsorption structures are reported in Table 3.
According to the following relationship, the absorption energy calculated for all paths [21, 22]:
Ead = Ecop – (ECuO−NS + Ey + Ex)
|
(1)
|
In this equation, Ecop is the total energy calculated for the intermediate stage in each path, and ECuO−NS, Ey, and Ex are the total energy of the nano-catalyst, CO, and Volatile sulfur compound, are subtracted (Table 3).
According to Hirschfeld's analysis, charge transfer from CO and CH3SH to the surface is equal to 0.26 eV, which is mainly related to the hybridization of CO and CH3SH atoms with copper atoms. The absorption energy of the second reaction (B path) is lower than the other reactions, because of which it can be repulsive between the participating substances.
In the first path (A), the carbon monoxide reacts with methanethiol is in an equal ratio and its product is S-methyl ester. Compared to the other two reaction paths, it has more total and absorption energy, and less heat of reaction formation.
Table 3
Adsorption energy, net charge transfer (from surface to adsorbed species) and atomic charge of copper for adsorpti on of reactive molecules on copper oxide nanocatalyst.
The absorbing group
|
Ead (eV)
|
Charge transport (│e│)
|
Charge of Cu(│e│)
|
CO + CH3SH
|
18.16
|
0.26
|
0.25
|
2CO + CH3SSH
|
6.20
|
0.35
|
0.17
|
CO + 2CH3SH
|
15.17
|
0.47
|
0.22
|
The mechanism of CO and methanethiol on CuO-NS As shown in Figure 2, both materials are first placed in the vicinity of the nano catalyst, the length of the hydrogen and sulfur bond is increased, and hydrogen and sulfur are separated near the carbon atom in carbon monoxide. In methanethiol, the hydrogen bond with S (-S-H) is equal to 1.3406 Å, which increases to 1.5903 Å in the third stage (A-III) (adsorption of methanethiol and carbon monoxide and intermediate formation). Which create an intermediate state and activate this complex on the surface. This process is very endothermic, which explains its thermodynamic data (table 2). It indicates the electron exchange between the nanocatalyst and the adsorbed molecules. Its mechanism is as follows:
In the fourth stage (A-IV), methyl thioformate intermediate (S-methyl ester) is formed on the copper oxide nano catalyst, which is also heat-absorbing, and the transfer from the substrate to the created intermediate is about 0.23, and the dipole moment in this case is equal 4.55 D. Finally, the created product leaves the surface.
Investigating the geometrical structure of methyl thioformate (S-methyl ester)
Computational investigation of stereoelectronic effects on the dynamic behavior of halomethylthioformates. For this purpose, structural properties, bond length changes and electron transfers, electrostatic effects in the formation of cis, trans and transition state systems for thioformate according to Fig. 3 has been evaluated and reviewed by LC-WPBE, B3LYP, and MP2 calculation methods 6-311 + G** basis set.
Thermodynamic and structural stability occurs when the system is in the most stable basic state and chemical equilibrium with its surroundings. Chemical equilibrium may be dynamic, so that the bond lengths and angles in the molecule change so that the molecule reaches the equilibrium state with the lowest energy. Any system tends to maintain this type of equilibrium indefinitely unless changes are made to the system. In this case, the system goes out of equilibrium and naturally tends to reach a steady state again. The molecule can have different geometric structure and configuration. In terms of electronic structure, deformation in a molecular system can be attributed to different minimum potential energy levels separated by energy barriers. Transition states between these structures usually shift under external disturbances, in most types of different structures, these disturbances are formed around double bonds. In the continuation of the study are determined the molecular structure and different configurations of cis and trans methyl, that thioformate are investigated and more stable configurations. The study of the cause of this stability is based on bond energy, orbital interactions and molecular geometric parameters and hydrogen bond energy within the molecule in the enolic form of these compounds.
For this purpose, different formulations of this structure (thioformate) have been studied using density functional theory (DFT) and calculations of natural or intrinsic bonding orbitals (NBO). Bond length, degree of bonds, orbital interactions and atomic charge of compounds as well as natural bond orbital analysis of NBO have been investigated.
The LC-WPBE, B3LYP, and MP2 calculations based on 6-311 + G** were used on all atoms to optimize structural parameters. To calculate the electronic energies and thermodynamic functions of the compounds, it was done with the GAMESS US program package. From the interpretation of NBO-LC-wPBE/6-311 + G** to scrutinize the formulation analysis and determine the contribution of the factors affecting the relative stability of the compounds using NBO 5.G program.
In this study, the contribution and role of stereoelectronic and steric effects on the structural and energetic behavior of methyl thioformate with cis and trans configuration has been investigated using quantum mechanical calculation methods, NBO analyzes and ab-initio studies. It is assumed that stereoelectronic effects (electrostatic effects and stability energies resulting from quadratic perturbation) are effective on the dynamic behavior of methyl thioformates, and the process of changes in Gibbs free energy, entropy and enthalpy. They are investigated the factors affecting the stability of the molecule, and whether the results of these Gibbs free energy values are justified, the answer is given. These factors include: Dipole moment, anomeric effect and spatial effects. The dipole moment is effective on the stability of the structure. In the fermi gas phase, a molecule with a lower dipole moment is more stable. The dipole moment is calculated for different configurations of methyl thioformate by different calculation methods in Table 4. It shows the stability of the trans form in Fig. 3. With the rotation of the methyl group relative to the carboxyl group, the structural symmetry of the compound changes and increases the polarity of the compound. Therefore, the difference of dipole moments between axial-axial forms (trans); Equatorial-axial (TS) and equatorial-equatorial (cis) justify the relative stability of axial-axial forms in relation to equatorial-axial and that in relation to equatorial-equatorial.
Table 4
The calculated enthalpy (in a.u.), entropy (in cal.mol− 1.K− 1), Gibbs free energy (in a.u.) and their corresponding differences (ΔH, ΔS, ΔG) for the cis-, transition state- (TS) and trans-conformations of compounds methyl formate and other halogen compounds by LC-WPBE, B3LYP and MP2 with basis set 6-311 + G**.
LC-WPBE/6-311 + G**
|
|
Ho
a.u.
|
So
cal.mol− 1.K− 1
|
Go
a.u.
|
µ
D
|
Cv
cal.mol− 1.K− 1
|
Eth
kcal.mol− 1
|
Zero point
Kcal.mol− 1
|
Methyl -tioformate
|
Cis
|
-551.80244
|
72.317
|
-551.83680
|
4.461
|
17.82
|
35.86
|
32.30
|
TS
|
-551.78393
|
70.082
|
-551.81722
|
2.911
|
16.01
|
35.17
|
32.04
|
Trans
|
-551.79758
|
73.862
|
-551.83268
|
5.319
|
17.86
|
35.83
|
32.29
|
B3LYP/6-311 + G**
|
Methyl -tioformate
|
Cis
|
-552.04312
|
73.531
|
-552.07806
|
4.368
|
18.32
|
35.08
|
31.43
|
TS
|
-552.02379
|
70.636
|
-552.05735
|
2.877
|
16.55
|
34.36
|
31.15
|
Trans
|
-552.03962
|
69.884
|
-552.07282
|
5.165
|
18.40
|
35.03
|
31.39
|
MP2/6-311 + G**
|
Methyl -tioformate
|
Cis
|
-551.05851
|
72.361
|
-551.09289
|
4.720
|
17.95
|
35.61
|
32.03
|
TS
|
-551.04001
|
70.164
|
-551.07411
|
3.297
|
16.16
|
34.87
|
31.72
|
Trans
|
-551.05427
|
69.685
|
-551.08738
|
5.711
|
18.02
|
35.56
|
31.99
|
The entropy of rotation of the structure from cis to trans increased, which expresses the tendency of methyl thioformate structure from cis to trans form. While the amount and sign of Gibbs free energy difference is effective on the balance of cis and trans systems and expresses the physical and chemical properties of the systems. The obtained results show that the values of Gibbs free energy difference and enthalpy to reach the trans form are positive and it is an endothermic reaction that requires energy expenditure.
These structural changes can be partially justified by the anomeric effect. So that the form of the molecule that has more anomeric effect is more stable than the form that has less anomeric effect (Table 5). In carbohydrates expressed the anomeric effect as the priority of changing the electronegativity property of the structure by rotating from the axial position to the equatorial position, and it is the cause of many different steric and stereo electron interactions.
Table 5. Structural parameters optimized for methyl-tioformate at the computational level of B3LYP/6-311+G**.
Distance Å
|
|
Cis
|
TS
|
Trans
|
r1O = 2C
|
1.19871
|
1.18936
|
1.19449
|
r5H-2C
|
1.10358
|
1.10425
|
1.10753
|
r2C-3S
|
1.74985
|
1.81142
|
1.75801
|
r3S-4C
|
1.79337
|
1.80616
|
1.79997
|
r4C-6H
|
1.08824
|
1.08997
|
1.08931
|
r4C-8H
|
1.08870
|
1.08879
|
1.08899
|
r4C-7H
|
1.08824
|
1.08899
|
1.08916
|
Angle according to degree
|
|
Cis
|
TS
|
Trans
|
A1O = 2C-3S
|
125.03904
|
123.55738
|
122.95962
|
A1O = 2C-5H
|
123.10327
|
122.17646
|
123.48393
|
A5H-2C-3S
|
111.85768
|
114.26613
|
113.55616
|
A3S-4C-6H
|
110.41989
|
111.59836
|
111.45878
|
A3S-4C-8H
|
106.99944
|
106.50696
|
106.53719
|
A6H-4C-7H
|
109.39938
|
110.36491
|
110.44582
|
A7H-4C-8H
|
109.78681
|
108.94451
|
108.39280
|
D1O = 2C-3S-4C
|
-0.01925
|
88.421150
|
180.00000
|
Moreover, the anomeric effect is a part of the contribution of dipolar dipolar and molecular orbital interactions between different systems and solvents. By examining the structure of cis, intermediate and trans configurations of methyl thioformate in Table 5. In the equatorial position, the tendency of the structure is more than in the axial position. Because there are many unfavorable steric interactions in the axial conformer.
Despite this, electronegative substitution appears in the axial position, contrary to spatial predictions. This phenomenon is called anomeric effect. There are two arguments to explain the source of this work: one by using electrostatic models, which is the dipole dipole model, and the other by relying on the molecular orbital model, which is the hyperconjugation model. Changing the bond length causes changes in the amount of spatial interactions. The length of the 1O = 2C bond in the trans (r1O = 2C =1.19449 Å)form is shorter than the cis form, which indicates the tendency of this satari rotation to be a stable form, so that in the trans form, the methyl group is placed at a greater distance from the sulfur atom (r3S − 4C = 1.79997Å) and its rotation angle increases.
In general, by examining the structural configuration of methyl thioformate in Table 5, the less destabilizing steric effects a molecule has, the more stable it becomes. which natural bond orbital analysis (NBO) is used to evaluate it. In the NBO method is used from the first order matrix of the reduced density of multi-electron wave functions in the form of bonding and antibonding orbitals, stability of cis and trans structure. Figure 4 of the diagram shows the interaction of a bonding orbital and of the Lewis structure type with an anti-bonding orbital, and the resulting energy of the interaction (ΔEij) using the SCF theory is as follows:
where F is the Fock operator and Ei and Ej are the NBO orbital energies.
The antibonding orbital contribution of energy is usually much less than 1% of the covalent contribution (ΔEij). The results obtained from the population in the naturally settled orbitals help to distinguish the small or large population of orbital types, which effect is seen in the form of classified orbitals in the results. The information extracted from the NBO program can be seen in Tables 6 and 7, it includes hybrid atoms, electron population, deviation of orbitals forming the bond, orbital energy and stability energy resulting from donor-acceptor transitions.
Table 6. Second order perturbation energies (E (2)) in kcal.mol-1 by LC-ωPBE/6-311+G** computational method.
Methyl-tioformate
|
Cis
|
LP→σ* or π*
|
E (2)
kcal.mol-1
|
F(i, j)
|
Donor NBO (i)
|
Acceptor NBO (j)
|
LP(1) (O 1)
|
σ*(C 2-H 5)
|
0.94
|
0.031
|
LP(2) (O 1)
|
σ*(C 2-H 5)
|
28.66
|
0.142
|
LP(2) (S 3)
|
π*(O 1-C 2)
|
53.38
|
0.135
|
LP(2) (O 1)
|
σ*(C 2-S 3)
|
39.18
|
0.148
|
|
TS
|
LP→σ* or π*
|
E (2)
kcal.mol-1
|
F(i, j)
|
Donor NBO (i)
|
Acceptor NBO (j)
|
LP(1) (O 1)
|
σ*(C 2-H 5)
|
0.80
|
0.029
|
LP(2) (O 1)
|
σ*(C 2-H 5)
|
28.28
|
0.141
|
LP(2) (S 3)
|
π*(O 1-C 2)
|
8.99
|
0.089
|
LP(2) (O 1)
|
σ*(C 2-S 3)
|
39.91
|
0.146
|
|
Trans
|
LP→σ* or π*
|
E (2)
kcal.mol-1
|
F(i, j)
|
Donor NBO (i)
|
Acceptor NBO (j)
|
LP(1) (O 1)
|
σ*(C 2-H 5)
|
0.93
|
0.031
|
LP(2) (O 1)
|
σ*(C 2-H 5)
|
30.39
|
0.144
|
LP(2) (S 3)
|
π*(O 1-C 2)
|
48.67
|
0.130
|
LP(2) (O 1)
|
σ*(C 2-S 3)
|
38.52
|
0.149
|
In order to obtain the effects of hyperconjugative bonding on the structural properties of these configurations, the effect of LP1 (lone pair (LP) indicates the number of non-bonding electron pairs) electron removal on the structural properties of the Cis, TS and Trans forms is investigated.
In Table 6, the oxygen atom has two pairs of electrons of different nature, the second lone pair of oxygen atom LP2 (O1) always shows a higher perturbation energy than the first lone pair of oxygen atom LP1 (O1) in NBO analysis. LP2 has greater disorder with 99% participation in p orbitals, but LP1 has 40% s and 60% p. The E2 for LP(2) (O 1)→ σ*(C 2-H 5) is more in the trans form than in the cis form, while the E2 for LP(2) (O 1)→ σ*(C 2-S 3) for the cis form is increased compared to the trans form. The results of NBO analysis show that the anomeric effect resulting from electron transfers between cis and trans configurations increases in methyl thioformate and the trans form is more stable than the cis form.
In Table 7, the population of orbitals (occupancy) and reciprocal spatial exchange energy (ΔEij(kcal.mol-1)) are calculated for different forms of cis- and trans-methyl thioformate.
Electron distribution in LP2 on O and S atoms is lower than LP1 and its energy is higher, which indicates the increase of occupancy in the π*(O1-C2) to the two antibonding orbitals σ*(C2-H5) and σ*(C2-S3). In other words, the distribution of electrons is towards the oxygen atom in the compound. which the occupancy in the π*(O1-C2) increased with the rotation of the configuration towards trans- and shows the tendency of the structure to be placed in trans form.
Table 7
Population of orbitals and reciprocal spatial exchange energy (ΔEij(kcal.mol-1)) by LC-ωPBE/6-311 + G** computational method.
Methyl-tioformate
|
Cis
|
NBO
|
Occupancy
|
ΔEij
|
LP(1) O (1)
|
1.98358
|
-0.82714
|
LP(2) O (1)
|
1.84891
|
-0.39144
|
LP(1) S (3)
|
1.98480
|
-0.74634
|
LP(2) S (3)
|
1.79308
|
-0.35356
|
σ*(C2-H 5)
|
1.98636
|
-0.70536
|
π*(O1-C 2)
|
1.99811
|
-0.53617
|
σ*(C2-S 3)
|
1.98756
|
-0.80756
|
TS
|
NBO
|
Occupancy
|
ΔEij
|
LP(1) O (1)
|
1.98425
|
-0.84076
|
LP(2) O (1)
|
1.85169
|
-0.40802
|
LP(1) S (3)
|
1.97575
|
-0.40802
|
LP(2) S (3)
|
1.93897
|
-0.35858
|
σ*(C2-H 5)
|
1.98853
|
-0.71282
|
π*(O1-C 2)
|
1.99629
|
-0.55396
|
σ*(C2-S 3)
|
1.98340
|
-0.75787
|
Trans
|
NBO
|
Occupancy
|
ΔEij
|
LP(1) O (1)
|
1.98405
|
-0.82302
|
LP(2) O (1)
|
1.84532
|
-0.39005
|
LP(1) S (3)
|
1.98618
|
-0.74971
|
LP(2) S (3)
|
1.80914
|
-0.35506
|
σ*(C2-H 5)
|
1.98801
|
-0.70905
|
π*(O1-C 2)
|
1.99839
|
-0.53715
|
σ*(C2-S 3)
|
1.98600
|
-0.80161
|