Vibrational spectra (experimental and theoretical), molecular structure, natural bond orbital, HOMO–LUMO energy, Mulliken charge and thermodynamic analysis of N′-hydroxy-pyrimidine-2-carboximidamide by DFT approach

Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 144 (2015) 215–225

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Vibrational spectra (experimental and theoretical), molecular structure, natural bond orbital, HOMO–LUMO energy, Mulliken charge and thermodynamic analysis of N0 -hydroxy-pyrimidine-2-carboximidamide by DFT approach N. Jeeva Jasmine a, P. Thomas Muthiah a, C. Arunagiri b, A. Subashini c,⇑ a

School of Chemistry, Bharathidasan University, Tiruchirappalli 620 024, (TN), India PG & Research Department of Physics, Government Arts College, Ariyalur 621 713, (TN), India c PG & Research Department of Chemistry, Seethalakshmi Ramaswami College, Tiruchirappalli 620 002, (TN), India b

h i g h l i g h t s

g r a p h i c a l a b s t r a c t

 A detailed vibrational assignments of

The compound HPCI adopts an E configuration across the C5@N3 double bond, as the OH group and benzene ring are on opposite sides of the double bond while the hydrogen atom of the hydroxy group is directed away from the NH2 group.

experimental and theoretical wave numbers of HPCI were reported.  Optimized geometrical parameters of HPCI on B3LYP/6-311+G(d,p) level along with experimental were performed.  Calculated electronic absorption spectral data were reported.  NBO, HOMO and LUMO analysis were also performed by DFT.  Kinetic and thermodynamic stabilities of the molecules were determined.

a r t i c l e

i n f o

Article history: Received 8 November 2014 Received in revised form 1 February 2015 Accepted 19 February 2015 Available online 27 February 2015 Keywords: FT-IR FT-Raman NBO HPCI Computational study

a b s t r a c t The FT-IR, FT-Raman, 1H, 13C NMR and UV–Visible spectral measurements of N0 -hydroxy-pyrimidine-2carboximidamide (HPCI) and complete analysis of the observed spectra have been proposed. DFT calculation has been performed and the structural parameters of the compound was determined from the optimized geometry with 6-311+G(d,p) basis set and giving energies, harmonic vibrational frequencies and force constants. The results of the optimized molecular structure are presented and compared with the experimental. The geometric parameters, harmonic vibrational frequencies and chemical shifts were compared with the experimental data of the molecule. The title compound, C5H6N4O, is approximately planar, with an angle of 11.04 (15)°. The crystal structure is also stabilized by intermolecular N–H  O, N–H  N, O–H  N, C–H  O hydrogen bond and offset p–p stacking interactions. The influences of hydroxy and carboximidamide groups on the skeletal modes and proton chemical shifts have been investigated. Moreover, we have not only simulated highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) but also determined the transition state and

⇑ Corresponding author. Tel.: +91 431 2231521. E-mail address: [email protected] (A. Subashini). http://dx.doi.org/10.1016/j.saa.2015.02.100 1386-1425/Ó 2015 Elsevier B.V. All rights reserved.

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band gap. The kinetic, thermodynamic stability and chemical hardness of the molecule have been determined. Complete NBO analysis was also carried out to find out the intermolecular electronic interactions and their stabilization energy. The thermodynamic properties like entropies and their correlations with temperatures were also obtained from the harmonic frequencies of the optimized structure. Ó 2015 Elsevier B.V. All rights reserved.

Introduction

Physical measurements

In general, oximate ligands exhibit a greater ability to form homo and hetero metallic polynuclear complexes, in which the oximate bridging ligands efficiently transmit magnetic exchange [1–3]. Substituted N0 -hydroxybenzamidines is a key intermediate obtained during the synthesis of pharmaceutically important 1,2,4-oxadiazole derivatives [4]. It is well known for their biological activities such as anti-HIV and anti-microbial [5]. Pyrimidine and some of its derivatives exhibit several potentially useful biological activities. In the study of agrochemicals and new pharmaceuticals, pyrimidine is warranted to improve the biological activities and properties and many pyridyl-containing compounds contain a wide range of pharmacological and biological activities [6–8], for example an antimycobacterial activity [8–11], in addition to low toxicity towards mammals. Modern spectroscopic studies of pyrimidine and its derivatives have been encouraged by their biological and pharmaceutical significance [12]. The vibrational spectroscopic studies on pyrimidine ring fused to six-membered inward bound considerable attention for many years [13]. Consideration of all these factors led to undertake a detailed spectroscopic studies and vibrational assignments of N0 -hydroxy-pyrimidine-2-carboximidamide (HPCI). Thus, all the above mentioned pharmacological properties render the analysis of hydroxy-pyrimidine structure relevant in order to enhance the understanding of its bioactivity. A theoretical study of this bioactive molecule is of interest in order to gain a deeper insight on their action and thus helping in the design with biological effects. The knowledge of their physicochemical properties and sites of reaction will provide a deeper insight of their probable action. Despite their widespread use, very little information is available about the chemical behavior of HPCI molecule. To our knowledge, the literature survey reveals that, there are no theoretical calculations or detailed vibrational analysis that have been performed on HPCI molecule so far. The crystal structure of HPCI has been very recently reported from our laboratory [14]. A systematic study of the molecular structure and vibrational spectra will help in understanding the property of the title molecule in detail. So, in the present work the geometrical parameters, vibrational wavenumbers, UV, NMR and NBO analysis were calculated using B3LYP method with 6-311+G(d,p) as basis set. The NBO analysis was performed to provide valuable information about various intermolecular interactions. The calculated HOMO and LUMO energies show that charge transfer occurs in the molecule. Finally electronegativity (v), hardness (g), softness (S), Mullikan population analysis and thermodynamic properties were calculated.

The FT-IR spectrum was recorded in the 4000–400 cm1 region with a JASCO 460 PLUS FT-IR spectrometer using KBr pellet. The spectrum was recorded at room temperature, with a scanning speed of 10 cm1 per minute and at the spectral resolution of 2.0 cm1. The FT-Raman spectrum of this compound was also recorded in the region 4000–50 cm1 with BRUKER RFS 27 Raman module equipped with Nd:YAG laser source operating at 1064 nm line width 100 mW power. The spectrum was recorded with scanning speed of 50 cm1 min1 of spectral width 4 cm1. The reported wavenumbers are believed to accurate within ±1 cm1. 1H and 13C-NMR spectra were recorded at 500 MHz, in DMSO-d6, on a Bruker 500 MHz Avance III spectrometer. The chemical shifts are reported in parts per million (ppm) downfield from internal tetramethylsilane (TMS) (chemical shift in d values). Electronic absorption spectrum was measured on a Unicam UV– Vis spectrophotometer in ethanol solvent.

Experimental A hot methanol solution (20 ml) of N0 -hydroxy-pyrimidine-2carboximidamide (69 mg, Aldrich) was warmed over a magnetic stirrer hot plate for a few minutes. The resulting solution was allowed to cool slowly at room temperature. After a few days, colorless block shaped crystals were obtained from the mother liquor.

Computational methods DFT computations were performed by using Gaussian 09W [15] program in combination with the Becke’s three parameter hybrid exchange functional with Lee–Yang–Parr correlation functional (B3LYP) [16–20] for computing the molecular structure, vibrational frequencies and energies of the optimized structure of HPCI. Full geometry optimizations were carried out without symmetry constraints. The basis set 6-311+G(d,p) augmented by ‘d’ polarization functions on heavy atoms and ‘p’ polarization functions on hydrogen atoms as well as diffuse functions for both hydrogen and heavy atoms were used [21,22]. The normal mode analysis was performed and the potential energy distribution was calculated along the internal coordinates using localized symmetry [23,24]. For this purpose, a complete set of 56 internal coordinates were defined using Pulay’s recommendations [25]. The vibrational assignments of the normal modes were made on the basis of the PED calculated results by using the VEDA 4 program [26]. Finally the calculated normal mode vibrational wavenumbers also provided the thermodynamic properties through the principles of statistical mechanics. The optimized geometries have been used to calculate all parameters reported in this study along with harmonic vibrational frequencies of the title molecule. Results and discussion Structural properties The HPCI molecule is of great importance in determining its structural and vibrational properties. The bond lengths, bond angles and torsion angles obtained from the X-ray crystallographic data are compared with computational results by B3LYP/6311+G(d,p) method as shown in Table 1. The molecular structure with atom numbering scheme adopted in this study is shown in Fig. 1. The title molecule has C–C, C@C, N–O, O–H, N–H, C–H, C– N and C@N bonds. As seen from Table 1, C–C bond lengths differ from the expected value, which is due to the substitutions on the

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N. Jeeva Jasmine et al. / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 144 (2015) 215–225 Table 1 Optimized geometrical parameters of HPCI on B3LYP/6-311+G(d,p) level along with experimental.

a

Bond length

B3LYP (Å)

a

C1–C2 C2–C3 C3–N2 N2–C4 C4–N1 N1–C1 C4–C5 C5–N4 N4–H4 N4–H5 C5–N3 N3–O1 O1–H6 C1–H1 C2–H2 C3–H3

1.388 1.394 1.330 1.337 1.341 1.335 1.491 1.365 1.007 1.008 1.291 1.418 0.962 1.086 1.082 1.087

1.378 1.376 1.343 1.347 1.336 1.343 1.494 1.362 0.920 0.890 1.295 1.424 0.940 0.950 0.950 0.950

Expt. (Å)

Bond angle

B3LYP (°)

a

N3–O1–H6 C1–N1–C4 C3–N2–C4 O1–N3–C5 C5–N4–H4 C5–N4–H5 H4–N4–H5 N1–C1–H1 N1–C1–C2 H1–C1–C2 C1–C2–H2 C1–C2–C3 H2–C2–C3 N2–C3–C2 N2–C3–H3 C2–C3–H3 N1–C4–N2 N1–C4–C5 N2–C4–C5 N3–C5–N4 N3–C5–C4 N4–C5–C4

102.5 116.9 116.4 108.9 117.4 116.7 119.5 116.5 122.1 121.4 121.8 116.2 121.8 122.6 116.3 118.1 125.8 115.3 118.9 125.4 117.9 116.6

106.1 116.0 116.2 108.7 118.2 112.9 117.0 118.6 122.8 121.6 121.6 116.7 121.6 122.4 118.8 118.8 125.9 115.6 118.5 125.5 117.4 117.1

Expt. (°)

Dihedral angle

B3LYP (°)

a

H6–O1–N3–C5 C4–N1–C1–H1 C4–N1–C1–C2 C1–N1–C4–N2 C1–N1–C4–C5 C4–N2–C3–C2 C4–N2–C3–H3 C3–N2–C4–N1 C3–N2–C4–C5 O1–N3–C5–N4 O1–N3–C5–C4 H4–N4–C5–N3 H4–N4–C5–C4 H5–N4–C5–N3 H5–N4–C5–C4 N1–C1–C2–H2 N1–C1–C2–C3 H1–C1–C2–H2 H1–C1–C2–C3 C1–C2–C3–N2 C1–C2–C3–H3 H2–C2–C3–N2 H2–C2–C3–H3 N1–C4–C5–N3 N1–C4–C5–N4 N2–C4–C5–N3 N2–C4–C5–N4

178.96 179.97 0.04 0.10 179.73 0.16 179.98 0.202 179.62 1.99 179.03 14.29 166.72 166.34 14.67 179.98 0.067 0.02 179.94 0.4 179.87 179.87 0.03 173.06 7.86 6.77 172.28

– – 0.2 1.3 179.8 0.8 – 1.8 179.3 1.7 179.51 – – – – – 1.1 – – 0.5 – – – 168.3 9.7 12.7 169.3

Expt. (°)

Ref. [14].

sides of the double bond while the hydrogen atom of the hydroxy group is directed away from the NH2 group [14]. The bond lengths and angles are within normal ranges. From Table 1, the C–H bond lengths are (C1–H1 = 1.086 Å, C2–H2 = 1.082 Å and C3–H3 = 1.087 Å) larger (for B3LYP method) than experimental values (0.950 Å). The C–C–C, N–C–N and N–O– H bond angles that are calculated by B3LYP method are little shorter than experimental values [14]. Vibrational assignments

Fig. 1. The molecular structure with atom numbering scheme of HPCI.

pyrimidine ring. The bond lengths of C1–C2 = 1.388 Å and C2– C3 = 1.394 Å which are larger than the experimental values of C1–C2 = 1.378 Å and C2–C3 = 1.376 Å. The C4–C5 bond distance calculated 1.491 Å by B3LYP is just 0.003 Å lower than the reported experimental value of 1.494 Å [14]. In single crystal X-ray crystallographic analysis, the amino and hydroxyl group bond lengths are N4–H4 = 0.920 Å, N4–H5 = 0.890 Å and O1–H6 = 0.940 Å whereas the computed bond lengths are N4–H4 = 1.007 Å, N4– H5 = 1.008 Å and O1–H6 = 0.962 Å. The bond angles N1–C4–N2 (cal. 125.8°; expt. 125.9°) and N3–C5–N4 (cal. 125.4°; expt. 125.5°) exactly matches with each other but larger than typical hexagonal angle of 120°. This is because of the effect of substitution of oxime and amino groups attached to the C5 which is attached to C4 of the pyrimidine ring. From X-RD analysis we found that, the essentially planar pyrimidine ring [N1/N2/C1–C4, maximum deviation of 0.009(2) Å at atom C4] forms a dihedral angle of 11.04 (15)° with the hydroxyacetimidamide (N4/C5/N3/ O1). The compound adopts an E configuration across the C5@N3 double bond, as the OH group and benzene ring are on opposite

The vibrational spectral assignments have been performed by recorded FT-IR and FT-Raman spectra based on the theoretical predicted wavenumber by density functional B3LYP/6-311+G(d,p) method as shown in Table 2. The title molecule consists of 16 atoms, which undergo 42 normal modes of vibrations. The molecule under investigation possess Cs point group symmetry. For Cs point group symmetry the title molecule is distributed as

Cvib ¼ 29A0 þ 13A00 Here A0 represents the symmetric planar and A00 represents asymmetric non-planar vibrations. All vibrations are active both in IR and Raman spectra. The detailed vibrational assignment of the experimental wavenumbers is based on normal mode analysis and a comparison with theoretically scaled wavenumbers. In Figs. 2 and 3, the calculated frequencies are usually higher than the corresponding experimental quantities, due to the combination of electron correlation effects and basis set deficiencies. After applying the scaling factors, the theoretical calculations reproduce the experimental data well in agreement. O–H vibrations The O–H stretching vibrations are extremely sensitive to hydrogen bonding. The non-hydrogen bonded (or) free hydrogen group absorbs strongly in the region 3550–3700 cm1 [27]. Hydroxyl group bonded with carboximidamide group displays a very broad

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Table 2 Detailed vibrational assignments of experimental and theoretical wavenumbers of HPCI. S. No.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42

Sy

A0 A0 A0 A0 A0 A0 A0 A0 A0 A0 A0 A0 A0 A0 A0 A0 A0 A0 A0 A0 A0 A0 A0 A0 A0 A0 A00 A00 A00 A0 A00 A00 A00 A0 A0 A00 A00 A00 A00 A00 A00 A00

a

Experimental (in cm1)

Theoretical B3LYP/6-311+G(d, p)

Vibrational assignments (% PED) IR

FT-IR

FT-Raman

Unscaled

Scaled

I

3421(s) 3329(ms) 3284(ms) 3103(w) – – 1652(s) – 1585(vs) – 1505(w) 1473(s) 1375(s) 1272(w) 1189(w) 1110(w) – 1078(w) 1005(w) 941(vs) – 841(w) 814(w) 774(w) – 702(w) 658(w) 641(w) – – 521(w) 500(w) – 452(w) – – – – – – – –

– – – – 3080(w) 3057(w) – 1643(s) – 1569(vs) – 1475(vs) 1375(w) 1272(w) 1186(w) 1109(w) 1092(w) 1074(w) 1004(vs) – 938(w) 846(w) – – 715(w) – – – 634(w) 529(w) – – 494(w) – 412(w) 392(w) 364(w) 281(w) 227(w) 129(w) 115(vs) 85(s)

3714 3589 3416 3203 3155 3105 1802 1795 1758 1698 1684 1610 1519 1406 1294 1246 1225 1120 1105 1084 1012 1005 999 950 845 838 815 712 680 648 545 488 475 411 392 382 356 337 269 180 121 59

3432 3345 3293 3111 3091 3068 1786 1756 1639 1574 1516 1482 1363 1283 1191 1115 1108 1068 1014 954 945 841 822 785 726 689 647 639 628 538 520 512 483 461 399 412 377 322 257 172 115 56

150.11 80.96 40.46 7.94 19.02 18.05 104.57 140.98 49.66 139.48 137.41 6.24 32.91 66.24 16.96 3.60 31.81 20.48 51.41 15.16 1.03 0.17 0.00 175.91 7.15 22.25 10.56 38.26 17.70 8.76 13.23 13.04 24.37 17.62 14.15 15.77 270.97 2.64 1.98 6.23 6.52 0.75

F

const.

9.016 8.977 7.928 6.626 6.403 6.376 11.856 8.134 5.624 2.143 4.953 2.538 2.364 1.468 1.572 8.394 2.565 1.073 1.237 1.765 5.829 0.850 0.807 6.248 1.688 1.729 0.595 1.625 1.330 1.979 0.217 0.337 0.552 0.325 0.236 0.173 0.088 0.239 0.317 0.107 0.051 0.011

tO–H(100) tN–H(58) tN–H(42) tC–H(95) tC–H(92) tC–H(92) tC@N(61), dC–H(11) tC–N(31), dO–H(28) tC–N(11), dC–H(14) tC–N(14), dO–H(18), dC–N(13) tC–N(19), dC–C(12) tC–N(16), dC–N(12) tC–C(21), dN–H(16), dC–H(11) tC–C(27), dC–N(14), tRtrigd(17) tC–C(61), dO–H(12) dO–H(69) dN–H(17), tN–O(78) dN–H(13), tC@N(66) dC–H(12), tC–N(22) dC–H(26), cN–O(41), tRtrigd(10) tN–O(78) dC–H(27), dN–H(46), tC@N(06) dC@N(17), dC–H(34) dC–C(11), dC–H(29), cC–H(11) dC–N(12), tC–N(14) dN–O(69), cC–H(16) cO–H(14), tRtrigd(31), cC@N(46) cN–H(25), Rasymd(11), cC@N(26) cN–H(49), Rsymd(10), cC–N(17) cC–H(32), dC–C(11), Rsymd(10) cC–H(22), tRtrigd(10), cC@N(11) cC–H(26), dC–H(49), Rsymd(10) Rtrigd(26), cC@N(16), cC–H(06) cC@N(37), cC–C(23), tRsymd(20) Rsymd(22), cN–O(12), dN–H(08) Rasymd(26), cO–H(11), cC@N(06) tRtrigd(49), tC–N(12), dC–N(10) cC–N(20), dN–H(18), cC–C(45) cC–C(17), dN–O(19), cC–H(12) cN–O(22), dN–H(18), tRsymd(47) tRsymd(14), tC–H(12), tC–N(10) tRasymd(14), tC–H(10), tC–N(08)

Sy: symmetry species. a s: strong; vs: very strong; m: medium; w: weak; vw: very weak. t: stretching; d: in-plane bending; c: out-of plane bending; IIR: IR intensity; Fconst.: forces constant.

band. The free hydroxyl group absorbs strongly in the region 3700– 3584 cm1, whereas the existence of intermolecular hydrogen bond formation can lower the O–H stretching frequency in the range 3500–3200 cm1 with increase in intensity and breadth [28,29]. In our present study, the strong band at 3421 cm1 in FT-IR spectrum is assigned to O1–H6 stretching vibration while the computed scaled wavenumber for this mode is at 3432 cm1 as shown in Table 2. Deviation of about 10 cm1 may be due to the presence of intermolecular hydrogen bonding. The O–H inplane bending vibration in the hydroxy imidamide generally lies in the region 1150–1250 cm1 and is not much affected due to hydrogen bonding unlike the stretching and out-of-plane bending frequencies [30]. In the present study, the O–H in-plane bending weak vibrations observed at 1110/1109 cm1 in FT-IR/FT-Raman spectrum is assigned to O1–H6 in-plane bending vibration which shows good correlation with computed wavenumber at 1115 cm1. The out-of-plane bending vibration lies in the region 710–517 cm1 in both intermolecular and intramolecular association [27]. The computed scaled wavenumber at 647 cm1 is assigned to O1–H6 out-of-plane bending vibration which shows good agreement with recorded FT-Raman spectrum at 658 cm1 for HPCI.

C–H vibrations Pyrimidine structure shows the presence of C–H stretching vibration in the region 3100–3000 cm1 which is the characteristic region for the ready identification of C–H stretching vibration [31]. In present case, the bands are not affected appreciably by the nature of substituents and three C–H stretching vibrations correspondings to C1–H1, C2–H2 and C3–H3 units were observed. In the FT-Raman spectrum of HPCI, the weak bands at 3080 cm1 and 3057 cm1 are assigned to C–H stretching vibrations, while in the FT-IR spectrum shows only one weak band at 3103 cm1. The theoretically computed wavenumber by B3LYP/6-311+G(d,p) method fall at 3203, 3155 and 3105 cm1(unscaled) and 3111, 3091 and 3068 cm1 (scaled) as shown in Table 2. The in-plane C–H bending vibrations appear in the range 1300– 1000 cm1 in the substituted benzenes and the out-of-plane bending vibrations occurs in the frequency range 1000–750 cm1 and 870–565 cm1 [32,33]. These vibrations are very useful for characterization purpose [34]. In the FT-IR/FT-Raman and FT-IR spectra, the weak to very strong bands at 1005/1004, 841/846 cm1 and 941 cm1 are assigned to C–H in-plane bending modes in HPCI of C1–H1, C2–H2 and C3–H3 units. The computed hetero aromatic

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219

Fig. 2. Experimental FT-IR spectrum of HPCI.

Fig. 3. Experimental FT-Raman spectrum of HPCI.

C–H out-of-plane bending vibrations fall at 538, 520 and 512 cm1 and is in agreement with the recorded weak FT-Raman and weak FT-IR bands at 521, 500 and 529 cm1 respectively are assigned to C–H in-out-plane bending vibrations. The computed as well as recorded spectral data are found to match well with already reported values [35,28].

stretching in HPCI dwell in slightly higher scaled wavenumber by the calculated value. In HPCI, the N–H in-plane deformation modes are identified at 1092(w) and 1078(w)/1074(w) cm1 in FT-IR and FT-IR/FT-Raman spectra while a red shift is observed in the deformation mode of amino group. The other fundamental modes are also assigned in accordance with literature [36] and are presented in Table 2.

NH2 vibrations C–N vibrations The NH2 stretching vibrations generally appear around 3500– 3000 cm1 [37]. The bands of medium intensity observed at 3329 and 3284 cm1 in the infrared spectrum are assigned to the N–H stretching modes of HPCI. In contrast, the band due to N–H stretching vibration in HPCI exists at higher wavenumber with deviations in the range 5–10 cm1 due to high force constant. The NH2 group

The characteristic regions of 1700–1500 cm1 [28] can be used to identify the C–N bonds. The title compound shows a strong stretching band at 1652 cm1 which is assigned to C–N stretching vibration mode of C5@N3 for HPCI in FT-IR spectrum. The characteristics group frequencies of the N–O are independent of the rest

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of the molecule. The N–O stretching vibration in aromatic compounds has strong absorption at 960 cm1 [37]. Hence, the stretching mode of N–O group for HPCI is identified at 938(w) cm1 in FT-Raman spectrum is due to N3–O1 stretching vibration for HPCI. The C–N stretching vibrations corresponds to C1–N1, C3–N2, C4–N1, C4–N2 and C5–N4 units respectively. The vibrations that occured at 1643(s), 1569(vs), 1475(vs) and 1585(vs), 1505(w), 1473(s) cm1 respectively in FT-Raman and FT-IR spectral bands are due to C–N stretching vibrations. C–C vibrations

1.80

Absorbance

The ring stretching vibrations are very much important in the spectrum of benzene and their derivatives. The bands between 1650 and 1400 cm1 in benzene derivatives are usually assigned to C–C stretching modes [38]. Varsanyi observed five bands, 1625–1590, 1590–1575, 1540–1470, 1465–1430 and 1380– 1280 cm1 in this region [39]. In this compound, the C4–C5, C1– C2 and C2–C3 stretching vibrations are found at 1375(s), 1275(w) and 1189(w) cm1 in FT-IR spectra respectively. The counter part of FT-Raman spectrum show bands appeared at 1375(w), 1275(w) and 1186(w) cm1 respectively. It shows the good agreement between theoretical and experimental C–C stretching vibrations. The absorption bands arising from C–C inplane bending vibration is observed at 774(w) cm1 in IR spectrum. The band is assigned to C–C out-of-plane bending vibration is observed in both experimental and calculated B3LYP/6311+G(d,p) value is 227(w) cm1 in Raman.

1.35

0.90

0.45

0.00 200

Electronic absorption spectra In order to understand electronic transitions in terms of energies and oscillator strengths, the TD-DFT calculations excited electronic states were performed in the gaseous phase and in the solvent phase (PCM model) [40–44]. Both the frontier molecular orbitals (FMO), highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) are the main orbitals taking part in chemical reaction. The electron delocalization between HOMO and LUMO is the principal factor in determining the easiness of a chemical reaction and the stereoselective path, irrespective of intra- and intermolecular process. Therefore, they are the most important orbitals which help in determining the way molecule interacts with other species. TD-DFT [36,38] was employed for obtaining these FMOs. The electronic transition corresponds from HOMO (characterizes of electron giving) to the LUMO (characterizes of electron accepting) orbital [45]. The theoretical and experimental UV spectra are shown in Fig. 4. Calculations involving the vertical excitation energies, oscillator strength (f) and wave length have been carried out and listed in Table 3. The energy gap between the HOMO and LUMO molecular orbitals characterizes the chemical reactivity and kinetic stability along with spectroscopic properties [41]. The transitions observed in the UV spectra are all p–p⁄. From Table 3, it was clearly visible that in LUMO the charge was mainly accumulated on the C@C and C@N parts of the rings. However, in case of isolated gaseous phase in HOMO and HOMO-2 charge density along with ring is visible on the carboximidamide group, on the O–H group atom

250

300

350

400

Wavelength (nm) Fig. 4. Comparison of experimental (bottom) and theoretical (top) UV–Vis spectrum of HPCI.

and on the amino group. In HOMO  2 it shifted from carboximidamide to pyrimidine. But as far as solvent is concerned in case of HOMO and HOMO  2 the charge is shifted from the ring to amino group chain with some portions on the carboximidamide group, whereas in HOMO the whole charge is concentrated on the ring. Electronic transitions are usually classified according to the orbitals engaged or according to the specific parts of the molecule involved. Common types of electronic transitions in organic compounds are p–p⁄ and p⁄ (acceptor)–p (donor). The UV– Visible bands in HPCI are observed at 211.14, 206.13 and 201.44 nm are due to the p–p⁄. The less intense band centered at 201.44 nm is due to the partly forbidden transition from HOMO  1 to LUMO + 1. The more intense band observed at 211.14 nm belong to the dipole-allowed p–p⁄ transition. As per the Frank–Condon principle, the maximum absorption peak (kmax) in an UV spectra corresponds to vertical excitation. The TD-DFT/ B3LYP/6-311+G(d,p) calculations predict one intense electronic transition at 5.8721 eV (211.14 nm) with an oscillator strength f = 0.5756, which is attributed to the fact that the electron-donating atom is substituted in the ring and two other electronic transitions are mentioned in Table 3.

Table 3 Calculated electronic absorption spectral data of HPCI by B3LYP/6-311+G(d, p) method. Excitation

CI expansion coefficient

Wave length (nm)

Oscillator strength (f)

Energy (eV)

Transition type/assignment

HOMO ? LUMO + 1 HOMO  2 ? LUMO + 2 HOMO  2 ? LUMO + 1

0.63750 0.49263 0.58307

211.14 206.13 201.44

0.5756 0.0132 0.0030

5.8721 6.0148 6.1550

p–p⁄ p–p⁄ p–p⁄

N. Jeeva Jasmine et al. / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 144 (2015) 215–225

Global reactivity descriptors The HOMO–LUMO energy transitions are shifted from the theoretical value, because these bands are observed in gas phase without considering the solvent effect. HOMO and LUMO are the very important parameters for quantum chemistry. The energy calculations were done with the commonly used exchange–correlation functional B3LYP followed by a comprehensive analysis of the calculated highest-occupied and lowest-unoccupied orbital energies. The directly calculated HOMO and LUMO energies, the energy gap (DE), ionization potential (IP), electron affinity (EA), absolute

Table 4 Calculated energy values of HPCI in its ground state. Molecular energy (in eV)

Gas phase

EnergyTotal (Hatree) HOMO LUMO HOMO – LUMO gap (DE) Ionization potential (IP) Electron affinity (EA) Electronegativity (v) Chemical potential (l) Chemical hardness (g) Electrophilicity index (x) Chemical softness (S)

488.460648075 6.12379 1.77694 4.34685 6.12379 1.77694 3.95037 3.95037 2.17346 3.58999 0.46010

HOMO(E): −6.12379eV

LUMO(E):−1.77694eV

electronegativity (v), chemical potential (l), absolute hardness (g), electrophilicity index (x) and softness (S) of the HPCI molecule have been computed at the B3LYP6-311+G(d,p) level are listed in Table 4. The chemical potential [46] provides a global reactivity index and is related to charge transfer from a system of higher chemical potential to lower chemical potential. The reactivity index is the measure of stabilization in energy when the system acquires an additional electronic charge. According to Parr et al. [47], the electrophilicity index (x) is a global max reactivity index similar to chemical hardness and chemical potential. The electrophilicity index (x) is a positive, definite quantity and direction of the charge transfer is fully determined by the chemical potential (l) of the molecule. The chemical hardness [48–51] is the second derivative of the electronic energy with respect to the number of electrons for a constant external potential. From the computed value of HOMO and LUMO energy values for the HPCI molecule, the electronegativity and chemical hardness can be calculated as follows: v = (IP + EA)/2 (electronegativity), l = (IP + EA)/2 (chemical potential), g = 1/2(ELUMO  EHOMO)  (IP  EA)/2 (hardness), x = l2/2g (electrophilicity index), S = 1/g (softness), IP = EHOMO and EA = ELUMO respectively as shown in Table 4. In the present study, the band gap energy of the one electron excitation from HOMO to LUMO is calculated to about 4.34685 eV, which is responsible for the bioactive property of the compound HPCI. The HOMO (36) is located over the carboximidamide part and LUMO (37) is located over the pyrimidine ring. The atomic orbital components of the frontier molecular orbital are shown in Fig. 5. The global minimum energy obtained by the DFT structure optimization based on B3LYP/6-311+G(d,p) for the title compound is 488.46064804 Hartrees. 1

Eg = −4.34685eV

HOMO(E): −6.12334eV

HOMO -2(E): − 7.87076eV

LUMO +1(E): −1.67777eV

LUMO +2(E): −0.12598eV

221

H and

13

C NMR chemical shift

13 C NMR chemical shift is one of the important tools in determining the presence or the absence of a particular atom in a molecule. In a molecule, shielding of atoms is greatly affected by the neighboring bonded atoms. Similar bonded atoms give different shielding values in different environments. In the present investigation, the chemical shift values for carbon atoms were studied by adopting the procedure recommended by Cheeseman et al. [52]. The structural parameter for NMR calculation was taken from the optimized geometries at B3LYP/6-311+G(d,p) level of theory. The experimental and calculated values (GIAO) for 13C and 1HNMR are shown in Table 5, correlates well with each other. The result shows that the range 13C NMR chemical shift of the typical organic molecule usually is >100 ppm [53–58], the accuracy ensures reliable interpretation of spectroscopic parameters. The values obtained for all the carbon atoms show similar range except few. It is reasonable to discuss those carbon atoms, which possess distinguished chemical shift values from the others. The carbon atom C5 has the shift value 157.20 ppm in the structure HPCI.

Table 5 Experimental and theoretical chemical shifts values (with respect to TMS) of HPCI. Atoms

HOMO -2(E): − 7.87077 eV

LUMO +1(E): − 1.67777eV

Chemical shifts, d (ppm) Experimental

Theoretical (B3LYP/6-311+G(d,p))

11.16 9.82–9.83 9.82–9.83 6.90–7.50

9.9169 8.8732 8.9546 7.9473, 7.837, 7.134

158.25 157.20 148.90–121.13

167.01 155.6 163.945, 161.778, 124.656

1

H NMR O1–H6 N4–H5 N4–H4 Aromatic proton 13

Fig. 5. The atomic orbital components of the frontier molecular orbital of HPCI.

C NMR C4 C5 Aromatic carbon

N. Jeeva Jasmine et al. / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 144 (2015) 215–225

This can be attributed to the bond formed with electronegative atom, which causes the transfer of electron cloud around electronegative atoms from carbon thus deshielding the carbon. This value may be due to more electronegative oxime and amino groups, where the electron cloud from carbon is completely delocalized towards imidamide group thereby down shielding the carbon atom. In 1H NMR spectrum, the pyrimidine ring proton (aromatic protons) signals appear as a mutiplet at 6.90–7.40 ppm region. The – OH group exhibits a signal at 11.16 ppm and –NH proton at 9.83 ppm respectively. The peculiar thing is to be noted that the functional groups has been greatly affected in NMR studies, and high shift values are found in the structure requiring low field for resonance.

0.2

0.0

O1

N1

N2

N3

N4

C1

H1

C2

Atoms

Charge(e)

222

-0.2

-0.4

-0.6

Fig. 7. Histogram of Mulliken atomic charges of HPCI.

Mulliken charges

Natural bond orbital analysis

Atomic charge has been used to describe the processes of electronegativity equalization and charge transfer in reactions [49,59], and to model the electrostatic potential outside molecular surfaces [60,61]. The Mulliken charges at various atoms of HPCI calculated at the B3LYP/6-311+G(d,p) level were collected in Table 6. The substitution of imidine group in the pyrimidine ring lead to the redistribution of electron density. The shift of partial charge from carboximidamide to pyrimidine demonstrates the conjugation effect. Mulliken charge distribution and Histogram of Mulliken atomic charges of HPCI are shown in Figs. 6 and 7. The magnitudes of the five carbon atomic charges of the pyrimidine ring for the title compound are found to be 0.140864(C1) e¯, 0.187383(C2) e¯, 0.148264(C3) e¯, 0.176787(C4) e¯ and 0.267798(C5) e¯ respectively at B3LYP/6-311+G(d,p) level calculation. It is worthy to mention that C1, C3 and C5 atoms of pyrimidine ring exhibit positive charge. The presence of negative charge on N3, N4 atoms and net positive charge on H4, H5 and H6 atoms may suggest the formation of intermolecular interaction in solid forms. Similarly, the magnitudes of charges calculated on atoms N1, N2 and O1 have negative charges to other atoms for title molecule. Table 6 Mulliken atomic charges for HPCI. Atoms

Charges (e¯)

Atoms

Charges (e¯)

O1 N1 N2 N3 N4 C1 H1 C2

0.150850 0.188927 0.186863 0.561974 0.601195 0.140864 0.175937 0.187383

H2 C3 H3 C4 C5 H4 H5 H6

0.181809 0.148264 0.175122 0.176787 0.267798 0.324007 0.329063 0.311118

The natural bond orbital (NBO) calculation [62] of the title compound was performed using NBO 5.0 program implemented in the Gaussian 09 package at the DFT/B3LYP/6-311+G(d,p) level. Natural bond orbital analysis is an essential tool for studying intra and intermolecular bonding interaction of HPCI. It also provides a convenient basis for investigating charge transfer or conjugative interaction in molecular systems. Some electron donor orbital, acceptor orbital and the interacting stabilization energy resulting from the second–order micro disturbance theory is reported [63,64]. The filled NBOs of the natural Lewis structure are well adopted to describe covalency effects in molecule. The anti-bonds represent empty valence-shell capacity and spanning portions of the atomic valence space that are formally unsaturated by covalent bond formation. Since the non-covalent delocalization effects are associated with r–r⁄ (interactions between filled (donor) and unfilled (acceptor) orbitals, it is natural to describe them as being of donor–acceptor, charge transfer, or generalized ‘‘Lewis base– Lewis acid’’ type. Weak occupancies of the valence antibonds signal irreducible departures from an idealized localized Lewis picture, i.e., true ‘‘delocalization effects’’. The interactions formed by the orbital overlap between r(O–N), r⁄(C–C), p(C–N), p⁄(C–N), p(C–C), p⁄(C–C), r(C–H), r⁄(C–H) bond orbital which results intermolecular charge transfer (ICT) causing stabilization of the system. These charge transfer (r ? r⁄, p ? p⁄, LP ? r⁄, LP ? p⁄) can induce large nonlinearity of the molecule. The strong intermolecular hyperconjugative interaction of the p electron of N1–C4 and N2–C3 distribute to p⁄N1–C4, C1–C2, C1–C2 and N1–C4, C1–C2 of the ring as evident from Table 7. On the other hand, the r (O1–N3) in the ring conjugate to the anti–bonding orbital of r⁄(C4–C5) which leads to strong energy difference between donor and acceptor orbitals of 1.21 a.u. The very strong p(N1–C4) bond is obtained to the anti–bonding orbital of p⁄ (C1–C2) distributed energy of 168.29 kJ/mol. The LP(1)N4 bond is conjugated to the anti–bonding orbital of p⁄ (N3–C5) contributing energy of 48.84 kJ/mol.

Thermodynamic properties

Fig. 6. Mulliken charge distribution of HPCI.

The vibrational analysis of HPCI at B3LYP/6-311+G(d,p) level and several thermodynamic parameters, rotational constants and energy have been presented in Table 8. The zero point vibrational energies (ZPVE) and the entropy are calculated to the extent of accuracy and the variations in ZPVEs seem to be insignificant. The thermodynamic data provide helpful information for the further study on the HPCI, when these may be used as a reactant to take part in a new reaction. The total energies and the change in the total entropy of HPCI at room temperature is only marginal.

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N. Jeeva Jasmine et al. / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 144 (2015) 215–225 Table 7 Second Order perturbation theory analysis of Fock matrix in NBO basis of HPCI. Donor (i)

ED (i) (e)

r(O1–N3) p(N1–C4)

1.98579 1.98655 1.93231 1.63080 1.63080 1.70280 1.63080 1.63080 1.70280 1.97990 1.70280 1.91988 1.91455 1.91033 1.95508 1.78243

p(N2–C3) p(C1–C2) r(C2–H2) LP LP LP LP LP a b c

(2) (1) (1) (1) (1)

Energy (i) (a.u.)

O1 N1 N2 N3 N4

Acceptor (j) ⁄

r (C4–C5) p⁄(N2–C3) p⁄(N3–C5) p⁄(C1–C2) p⁄(C1–C2) p⁄(N1–C4) p⁄(C1–C2) p⁄(N1–C4) p⁄(N2–C3) r⁄(N1–C1) r⁄(N2–C3) p⁄(N3–C5) r⁄(N2–C4) r⁄(N1–C4) r⁄(N4–C5) p⁄(N3–C5)

0.7075 0.7754 0.7742 0.7031 0.6686 0.7872 0.6686 0.7872 0.7754 0.7722 0.7698 0.7742 0.7658 0.7692 0.7709 0.7742

ED (i) (e)

Energy (i) (a.u.)

E(2)a (kJ/mol)

E(j)  E(i)b (a.u)

F(i, j)c (a.u)

0.04844 0.33069 0.30229 0.02397 0.28060 0.30229 0.28060 0.39861 0.33069 0.01471 0.01374 0.30229 0.03428 0.03749 0.03061 0.30229

0.7753 0.7872 0.7742 0.6686 0.7437 0.7872 0.7437 0.7437 0.6315 0.7820 0.6315 0.6329 0.6431 0.6390 0.6370 0.6329

4.77 10.61 10.49 28.75 168.29 60.95 11.87 14.44 29.80 4.07 3.91 12.99 11.85 12.71 10.04 48.84

1.21 0.31 0.35 0.32 0.02 0.04 0.32 0.27 0.27 1.07 1.08 0.34 0.88 0.86 0.89 0.29

0.068 0.052 0.054 0.087 0.077 0.072 0.055 0.056 0.081 0.059 0.058 0.063 0.092 0.094 0.085 0.109

E(2) means energy of hyperconjugative interactions (stabilization energy). Energy difference between donor and acceptor i and j NBO orbitals. F(i, j) is the Fock matrix element between i and j NBO orbitals.

Table 8 Thermodynamic properties for HPCI obtained by B3LYP/6-311+G(d,p) method.

300

Parameters

75.01934

Entropy (cal mol1 K)

Total Translation Rotational Vibrational

80.423 0.889 0.889 78.646

32.673 2.981 2.981 26.711

250

200

0

Total Translation Rotational Vibrational Enthalpy (cal mol1 K) Total Translation Rotational Vibrational

3.66709 0.86773 0.70279

Values -1 -1

Values

Zero-point vibrational energy (kcal mol1) Rotational constants (GHZ) A B C Thermal energy (kcal mol1)

Heat capacity(C p,m )(cal mol k )

Parameters

91.078 40.679 29.354 21.045

150

100

50 Table 9 Thermodynamic properties of HPCI at different temperatures.

100 200 298.15 300 400 500 600 700 800 900 1000

277.38 335.34 386.66 387.6 436.54 482.26 524.65 563.84 600.1 633.73 665.05

1

K

)

C0p, m

(cal mol

63.89 108.58 150.79 151.55 189.46 220.27 244.52 263.69 279.14 291.84 302.45

1

K

1

)

0 H0m(cal

mol

1

K

200

)

4.6 13.22 25.98 26.26 43.36 63.91 87.2 112.64 139.81 168.38 198.11

600

800

1000

Fig. 8. Correlation graph of heat capacity and temperature of HPCI.

700 650 600 550 500 450

0

On the basis of vibrational analysis, the statically thermodynamic functions, heat capacity (C0p,m), entropy (S0m) and enthalpy (H0m) for HPCI molecule were computed from the theoretical harmonic frequencies and tabulated in Table 9. From this table, we conclude that the computed thermodynamic parameters increases with increase in temperature ranging from 100 to 1000 K due to the fact that, the molecular vibrational intensities increases with increase in temperature [65]. The correlation equations between heat capacity, entropy, enthalpy changes and temperatures were fitted by quadratic formulae. The corresponding fitting factors (R2) for these thermodynamic properties are 0.99947, 0.99996 and 0.9994, respectively. The corresponding fitting equations are as follows and the correlation graphics of those are show in Figs. 8–10.

400

Temperature(K)

1

-1 -1

(cal mol

1

Entropy(S m)(cal mol k )

T (K)

S0m

400 350 300 250 0

200

400

600

800

1000

Temperature(K) Fig. 9. Correlation graph of entropy and temperature of HPCI.

224

N. Jeeva Jasmine et al. / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 144 (2015) 215–225

150

100

0

-1 -1

Enthalpy (H m) (calmol k )

200

50

0

0

200

400

600

800

1000

Temperature(K) Fig. 10. Correlation graph of enthalpy and temperature of HPCI.

C 0p;m ¼ 13:57777 þ 0:53254T  2:46497  104 T 2 ðR2 ¼ 0:99947Þ S0m ¼ 219:9749 þ 0:60478T  1:60753  104 T 2 ðR2 ¼ 0:99996Þ H0m ¼ 7:0354 þ 0:07758T þ 1:29743  104 T 2 ðR2 ¼ 0:9994Þ All the thermodynamic data supply helpful information for the further study on the HPCI. They can be used to compute the other thermodynamic energies according to relationships of thermodynamic functions and may help estimate directions of chemical reactions according to the second law of thermodynamics in thermochemical field. (Notice: all thermodynamic calculations were done in gas phase and they could not be used in solution.) Conclusion A complete vibrational analysis of N0 -hydroxy-pyrimidine-2carboximidamide was performed based on calculation at the B3LYP/6-311+G(d,p) level. The theoretical results were compared with the experimental vibrations. Scaling factors results are in good agreement with the experimental values. The computed geometrical parameters are in good agreement with the observed X-ray diffraction data of this compound. The influences of amino and hydroxyl groups to the vibrational frequencies were also discussed. Other electronic structure properties such as NBO and HOMO–LUMO analysis put the lights on molecular conjugation, intermolecular stabilization, electron donor and acceptor aptitudes. The lowering of HOMO–LUMO band gap supports bioactive property of the molecule. The kinetic, thermodynamic stability and chemical hardness of the molecule have been determined. Acknowledgements N.J.J. thanks the UGC–SAP for the award of RFSMS. Prof. P.T.M. thanks the UGC for a one-time BSR grant. References [1] [2] [3] [4]

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