4.1. Intrinsic reaction coordinate analysis and classification of isomers
The crystal structure of 2APP is optimized at wB97XD/6-311 + + G(d,p) level of approximation and the optimized structure of 2APP (hereafter abbreviate as isomer 1) and presented in Fig. 1. The coplanar structures of picrate (Ring 1) and pyrimidine (Ring 2) molecules in isomer1 (total energy = -1240.3495 Hartree, herein total energy = electronic energy + zero point vibrational energy corrections) during the optimization are not much varied which confirms the cocrystal formation through higher binding energy. In isomer 1, the pyrimidine ring has NH2 group and N-H bond and they facilitate to bond with picrate ring through N-H···O hydrogen bonds. The crystal structure of isomer 1 is predicted to be a polar molecule where ring 2 donates some of its charges to the ring1 and forms an anionic–cationic system.
To understand the chemical reactivity of isomer 1, local reactivity descriptors were calculated at the wB97XD/6-311 + + G (d, p) level of theory. The local reactivity descriptors are important tools to predict the possible binding sites of a particular reaction complex[41, 42]. The picrate molecule (ring 1) of isomer 1 is a highly reactive compound with strong nucleophilic sites such as O25, O26 and O31. The Fukui descriptors s+ and s of isomer 1 and 2 represent the sites prone to nucleophile and electrophilic attack and are tabulated in Tables S1 and S2 (Supplementary Information). Among O25, 26 and O31, the O25 has strong nucleophile character (s− = 0.6523 a.u) as compared to the other reactive sites of the ring 1 i.e. O26 (s− = 0.1922 a.u) and O31 (s− = 0.1966 a.u). On the other hand, there are two atoms of hydrogen (H3 and H6) on the pyrimidine ring (ring 2) in the vicinity of the O25 are prone to the attack by O25. Hence, the atom O25 makes strong hydrogen bonds O25···H6 (1.6261 Å) and O25···H3 (1.9656 Å). A ring 2 in isomer 1 is a heterocyclic six-membered ring that holds strongly electronegative nitrogen atoms N5 and N13. This results in the less nucleophile character of the heterocyclic ring as the nitrogen atoms withdraw the majority of the electron density towards themselves [43]. Additionally, the amine group (N1H2) at C2 position also withdraws some of the electron density. This behavior makes the hydrogen of the N5H6 group strongly positive as nitrogen N5 strip electron form H6 and ring is also depleted from the electron density and hence cannot act as an electron donor. These considerations make the H6 a stronger electrophilic as compared to H3 of the ring 2 in the isomer 1.
Additionally, the O25 carries the largest negative partial charge in the isomer 1 (-0.273e) while H6 carries the largest positive charge among all the hydrogen in the isomer 1 (0.098e). This charge difference creates a strong electrostatic interaction between O25 and H6. Thus, oxygen O25 donates one of its lone pair electrons to the H6 inducing a heterolithic dissociation in the N5H6 bond of ring 2. The free hydrogen H6 then makes a covalent bond with O25 and forms the product (isomer 2, total energy = -1240.4037 Hartree) as shown in Fig. 2. The enthalpy of the formation from isomer 1 to isomer 2 is calculated at about 15.22298 kJ/mol with respect to the isomer 1. This represents an endogenic isomerization with activation energy (~ 3.6777 kJ/mol, transition state total energy = -1240.4059 Hartree) (Fig. 3). Since very small energy is required to change isomer 1 into isomer 2 and isomerization is very slightly endogenic, it is expected that both isomers exist in thermodynamic equilibrium at room temperature.
There is one more possibility of isomerization in this system. The nucleophilic site O25 can donate its lone pair electrons to the hydrogen H3. The local minima structure along this root is studied by breaking up of the bond N1H3 and forming O25H3 bond manually followed by optimization. However, when this structure is optimized, hydrogen H3 always tend to move back to N1. Since no local minima could be located for this root, we propose that the local minima structure along this root is not feasible. The primary reason for this would be the instability of the amino group (N1H2) at C2 for proton transfer to O26. Additionally, the distance between the O25 and H3 is large (1.9656 Å) compared to the distance between O25 and H6 (1.6261 Å). Hence, the electron transfer is more feasible between O25 and H6 than between O25 and H3.
The isomer 2 has similar structure as isomer 1. Besides the hydrogen transfer from N5 to O25, a slight out of plane shift of pyrimidine ring from the planer structure of isomer 1. The reason for this shift has been explained in the following paragraph. After the formation of isomer 2, the distance between the H3 and O25 has increased and becomes 2.3315 Å while distance between H6 (now attached to O25) and N5 becomes 1.5348 Å (Fig. 2). The change in distances is due to the out of plane shift of pyrimidine ring from the planer structure of isomer 1. The new structure that the previous hydrogen bond H3⋅⋅⋅O25 has now becomes weak due to increases in the distance of donor and accepter atoms and a new hydrogen bond H6⋅⋅⋅N5 has formed. The HOMO-LUMO energy gap for the isomer 1 and 2 is observed to be 0.2245 0.2808 au respectively. This shows that isomer 2 is less reactive compared to isomer 1. The reason for this less reactivity is that after the formation of isomer 2, the HOMO of the isomer 2 is completely shifted from pictrate ring to the pyrimidine ring. Now whatever electron density pyrimidine ring gain form the transfer of H6 to the pictrate ring, it is distribute that throughout the ring. This will ingresses the stability of the pyrimidine ring and of isomer 2 in general and decrees the overall reactivity of isomer 2.
To reveal more about the mechanism for the formation of isomer 2 from the 1, we picked equidistance points on the IRC (that includes TS) and performed single-point energy calculations on each point. This provides us the wave functions of that particular structure which helps to see the structural changes during the reaction as well as the change in the molecular orbitals and charge delocalization upon the change in the energy. The highest occupied molecular orbitals (HOMO) of these intermediate points are displayed in Fig. 4. Form point 3 it can be seen that the electron cloud of the highest occupied orbital is mostly contained over the picrate ring and over oxygen atoms attached to this ring which is because the picrate ring is a homogenous carbon ring having much of its electron density in the π electron cloud and some of its electron density is contained exposed lone pair electrons in the oxygen atoms. When one electron pair is transferred from the oxygen atom to the nearest hydrogen, it induces a proton transfer, while the hydrogen leaving the –NH group of pyrimidine ring gives back its electron involved in the NH bonding. This electron goes back to the pyrimidine ring and thus shifting the HOMO to the pyrimidine ring (point 0 to -2). After completing the reaction, the electron cloud in the pyrimidine ring will start repelling the nearest oxygen atoms results in the slight out of the plane tilt of picrate ring in the product complex (point − 2).
4.2. Electron density distribution
Analysis of electron density distribution is a straightforward approach to unravel the hydrogen bonding interactions between the electron donor and acceptor species of the electronic structure of the molecule or cocrystals. Quantum topological atoms in molecules (QTAIM) [44] offers an elegant approach that provides pictorial evidence to the hydrogen bonding interactions in terms of line critical points (LCP) and the type and strength of the interactions can be characterized by quantum topological parameters such as electron density (ρ(r)), Laplacian of electron density (∇2ρ(r)), bond ellipticity (ε) and hydrogen bond (HB) energies (EHB). The quantum topological descriptors of isomer 1 and 2 are collected in Table 1 and molecular graphs are presented in Fig. 5.
According to Bader's theory of QTAIM, the value of ρ(r) is quite small (∼10− 2 a.u. or less for H-bonded complexes and 10− 3 a.u. for van der Waals complexes) and ∇2ρ(r) is positive. The predicted topological parameters of the intermolecular interactions for isomer 1 and 2 are within the range of H-bonded complexes as given by Bader. The intermolecular interactions such as O26···H8, O25···H3, O31···H3, O31···O25, O25···O26 commonly exist in both the isomers, among them O31···O25, O25···O26 are non-classical hydrogen bonds. The prominent intermolecular interactions O25···H6 (isomer 1) and N5···H6 (isomer 2) discriminate the isomeric forms of 2APP. The calculated binding energy of complexes in isomer 1 and isomer 2 are 171.88 kJ/mol and 168.82 kJ/mol respectively. The difference in the binding energy of the complexes isomer 1 and 2 are calculated as 3.06 kJ/mol. The bond ellipticity (ε) measures the extent to which electron density (ρ(r)) is accumulated in a given plane containing the bond path [45]. The higher value of ε illustrates the structural instability and its value close to zero represents the bond is cylindrically symmetrical [46]. Hence, the lesser ε value and higher hydrogen bonding energy (EHB) for the interactions O25···H3 and O25···H6 are more prominent interactions of isomer 1 while in isomer 2, N5···H6 is the most prominent interaction.
Table 1
QTAIM parameters of non-bonded classical/non-classical HBs isomer 1 and isomer 2 of 2APP.
Classical/ Non-classical HBs
|
Bond
|
Bond distance
|
electron density
|
Laplacian of electron density
|
Bond ellipticity
|
EHB
|
Binding Energy
|
isomer 1
|
Classical
|
O26···H6
|
2.1760
|
0.0158
|
0.0651
|
1.17
|
15.49
|
171.88
|
Classical
|
O26···H8
|
2.3702
|
0.0104
|
0.0445
|
0.35
|
9.29
|
Classical
|
O25···H3
|
1.9656
|
0.0244
|
0.0967
|
0.06
|
25.06
|
Classical
|
O25···H6
|
1.6261
|
0.0531
|
0.1608
|
0.03
|
71.56
|
Classical
|
O31···H3
|
2.0859
|
0.0165
|
0.0690
|
0.13
|
15.29
|
non-classical
|
O31···O25
|
2.6940
|
0.0168
|
0.0627
|
0.23
|
17.43
|
non-classical
|
O25···O26
|
2.6958
|
0.0172
|
0.0638
|
0.48
|
17.76
|
isomer 2
|
Classical
|
O26···H8
|
2.3770
|
0.0114
|
0.0405
|
0.16
|
9.47
|
168.82
|
Classical
|
O25···H3
|
2.3315
|
0.0117
|
0.0434
|
0.33
|
10.19
|
Classical
|
N5···H6
|
1.5348
|
0.0818
|
0.0847
|
0.03
|
110.87
|
Classical
|
O31···H3
|
2.2363
|
0.0119
|
0.0456
|
0.04
|
9.66
|
non-classical
|
O31···O25
|
2.7417
|
0.0144
|
0.0563
|
0.39
|
15.04
|
non-classical
|
O25···O26
|
2.7963
|
0.0132
|
0.0533
|
0.83
|
13.59
|
4.4. Analysis of vibration spectra
To confirm the isomeric conformation in the solid phase, the Fourier-transform mid-IR and Raman spectra of both the isomers of 2APP were recorded and the observed results were compared with their respective theoretically simulated spectra (see, Figs. 6 and 7). The assignment of the peaks was confirmed with the aid of potential energy distribution (PED) results. A broad and very weak intensity band in the region 3850 to 3650 cm−1 in the FT-IR spectrum are recognized as N−H stretching vibrations of the amino group of picrate [47]. The scaled wavenumbers of 3772 and 3646 cm−1 for isomer 2 and 3529 and 3274 cm−1 for isomer 1 are ascribed to N−H stretching vibrations of the amino group. It reflects that the stretching modes of N−H bonds in the amino group are greatly affected upon the transfer of hydrogen atom from the pyrimidine ring to picrate ring (from isomer 1 to isomer 2 conversion). The conformational isomerism of 2APP could be identified by the careful investigation of N5−H6 (isomer 1) and O25−H6 (isomer 2) stretching bands. The presence of N5−H6 stretching band and absence of O25−H6 bond confirms isomer 1 of 2APP and the absence of N5−H6 stretching band and the presence of O25−H6 bond confirms isomer 2 of 2APP. A peak identified at 3437 cm−1 belongs to intermolecular O25···H6 stretching mode and the N5−H6 stretching peak centered at 2913 cm−1 in the FT-IR confirms the structure of isomer 1. The assignments of all the vibrational modes of isomers 1 and 2 are given in Tables S5 and S6 (Supplementary Material) respectively.
Our spectroscopic investigations along with theoretical calculations shed light on the structural insights of isomers 1 and 2. We have seen a broad small peak of NH stretching at 2835 cm−1 in isomer 1. It’s quite evident N5H6 of pyrimidine molecule is involved in the formation of intermolecular H-bonding with an Oxygen atom (O25) of picrate molecule. On the other hand, we have not seen such spectroscopic features (IR and Raman) in isomer 1. Similarly, we have observed the O25H6 stretching at 3106 cm−1 in isomer 2 which signifies OH of picrate molecule is involved in H-bonding with a nitrogen atom (N5) of pyrimidine molecule while such traces are completely missing in isomer 1. Additionally, C = O stretching in both the isomers 1 and 2 were found at 1545 and 1534 cm−1, respectively which suggests C = O involved in the formation of intermolecular H-bonding. Thus, our spectroscopic results confirmed the theoretical findings and support our predicted molecular structure.