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Combinatorial Vibration-Mode Assignment for FTIR Spectrum of Crystalline Melamine: a Strategic Approach towards Theoretical IR Vibrational Calculations of Triazine-Based Compounds Xiaohong Yuan, Kun Luo, Keqin Zhang, Julong He, Yuanchun Zhao, and Dongli Yu J. Phys. Chem. A, Just Accepted Manuscript • DOI: 10.1021/acs.jpca.6b06015 • Publication Date (Web): 06 Sep 2016 Downloaded from http://pubs.acs.org on September 11, 2016

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The Journal of Physical Chemistry

Combinatorial Vibration-Mode Assignment for FTIR Spectrum of Crystalline Melamine: a Strategic Approach towards Theoretical IR Vibrational Calculations of Triazine-Based Compounds Xiaohong Yuan, Kun Luo, Keqin Zhang, Julong He, Yuanchun Zhao,* and Dongli Yu* State Key Laboratory of Metastable Materials Science and Technology, Yanshan University, Qinhuangdao 066004, P.R. China

ACS Paragon Plus Environment

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ABSTRACT: Although polymeric graphitic carbon nitride (g-C3N4) has been widely studied as metal-free photocatalyst, the description of its structure still remains a great challenge. Fourier transform infrared (FTIR) spectroscopy can provide complementary structural information. In this paper, we reconsider the representative crystalline melamine and develop a strategic approach to theoretically calculate the IR vibrations of this triazine-based nitrogen-rich system. IR calculations were based on three different models: a single molecule, a 4-molecule unit cell and a 32-molecule cluster, respectively. By this comparative study the contribution of the intermolecular weak interactions were elucidated in detail. An accurate and visualized description on the experimental FTIR spectrum has been further presented by a combinatorial vibration-mode assignment based on the calculated potential energy distribution of the 32molecule cluster. The theoretical approach reported in this study opens the way to the facile and accurate assignment for IR vibrational modes of other complex triazine-based compounds, such as g-C3N4.

INTRODUCTION In recent years, tri-s-triazine-based polymeric graphitic carbon nitride (g-C3N4) has attracted great attention due to its potential application as multipurpose metal-free photocatalyst.1–3 An orthorhombic structure of g-C3N4 has been proposed based on the linearly polycondensed tri-striazine units (melon), in which the melon chains are paralelly arranged and tightly linked by hydrogen bonds.4 However, the crystallinity of g-C3N4 is remarkably affected by specific synthesis process,5–9 and the description of its structure remains a great challenge.10 Other characterization technique is highly desired to provide complementary structural information. Fourier transform infrared (FTIR) spectroscopy has been widely used to characterize g-C3N4 because distinct FTIR spectrum of g-C3N4 can be easily measured whereas its Raman signals are


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usually obscure, especially for the visible laser excitation. An accurate IR-mode assignment is not only helpful to recognize the basic skeleton structure, but also very important to determine the hydrogen bonding environments; however, it is still difficult due to the complexity of g-C3N4 structure.7 In order to develop a strategy to perform theoretical calculations on IR vibrational modes of this nitrogen-rich C-N-H system, here we reconsider the crystal structure and IR vibrations of melamine (2, 4, 6-triamino-s-triazine, C3N6H6), the simplest and representative nitrogen-rich triazine-based molecule. Melamine is an important organic compound and widely used to synthesize melamineformaldehyde resins,11 fire retardants,12 supramolecular derivatives,13 as well as to prepare gC3N4 by thermal condensation.14,15 A single melamine molecule is of D3h symmetry with a planar 1, 3, 5 s-triazine ring (C3N3) and three amino groups bonded with each C atom. Bulk melamine is a typical molecular crystal and its monoclinic unit cell contains four molecules with space group of P21/a or P21/c. The crystal structure of melamine at room temperature has been studied since 1941 by X-ray diffraction (XRD),16 neutron diffraction,17 FTIR and Raman spectroscopies.18,19 The molecular geometry and crystal structure of melamine have been further studied by semiempirical and ab initio Hattee-Fock methods and density functional theory (DFT) calculations,19– 21

revealing that the molecule exhibits a non-planar structure of Cs geometry where the triazine

ring is approximately coplanar while the amino groups have a pyramidal structure. In the crystal structure, each melamine molecule is linked with its neighbours through eight N—H…N hydrogen bonds. Although FTIR spectrum of crystalline melamine has been reported since 1959,18 the definitive and complete vibrational assignment, to the best of our knowledge, has not been made yet. It’s well known that the vibrational modes of crystalline melamine are related to not only the


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molecular geometry, but also the intermolecular hydrogen bonding, both these effects must be comprehensively considered. Very recently Mircescu et al.19 built a 10-molecule cluster of melamine based on B3LYP/6-31G(d) optimization and calculated the corresponding IR spectrum by using Gaussian 03W program, which takes the contribution of intermolecular hydrogen bonding into account. In comparison to the IR spectrum calculated based on a single melamine molecule, the IR spectrum of the cluster structure matches the experimental results much better. However, it should be noted that the proposed 10-molecule cluster doesn’t involve all the hydrogen bonds formed within the representative unit cell (4 melamine molecules), and thus the calculated IR spectrum still exhibits obvious discrepancies from the experimental one. In this study, we first checked the crystal structure of melamine by structural optimization process based on the DMOL3 code of Material Studio. Then a 32-molecule cluster was designed based on the optimized crystal structure, in which all the hydrogen bonds formed within the unit cell were included. The IR spectrum of the cluster was calculated by using Gaussian 09 program package, providing a nearly one-to-one combinatorial vibration-mode assignment to the experimental FTIR spectrum. A single molecule and a 4-molecule unit cell of melamine have also been calculated for comparison to elucidate both the effects of molecular geometry and hydrogen bonding on the IR spectrum. This process would provide important clues to analyze IR vibrations of other triazine-based pyrolysates, in particular g-C3N4. EXPERIMENTAL SECTION Experimental. Structural identification of melamine was performed with an X-ray powder diffractometer (D8 Discover) with Cu Kα radiation (λ = 1.54 Å). FTIR spectrum of melamine was recorded on a FTIR spectrometer (Bruker, Equinox 55) in transmission mode. The


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measurements were carried out on the KBr pellets (1 mg melamine, 100 mg KBr and handly pressed with a capacity of 6 MPa) at ambient conditions between 400 and 4000 cm-1. Calculation methods. In our previous work, a crystal structure of melamine based on P21/c space group has been built (Figure 1a).22 We started from this structure and carried out further geometry optimization. Molecules in the monoclinic unit cell were rearranged based on the high birefringence feature of melamine, making the co-planar triazine ring of the molecule approximately normal to the acute bisectrix.16 The modified crystal structure was further allelectron optimized with 2×2×1 k-point by using DMOL3,23,24 a first-principles linear combination of atomic orbitals method with triple numerical plus polarization (TNP)25 basis set and the Perdew (PBE)26 exchange-correlation functional, within the gradient-correlation approximation (GGA). The tolerances for geometry optimization: the difference in total energy within 10−5 Ha, the maximum force within 0.002 Ha/Å, and the maximum displacement within 0.005 Å. The theoretical XRD pattern of the obtained structure was generated by the Reflex package of Materials Studio.27 Molecular geometry optimization and IR vibrational wavenumber calculation were performed by using Gaussian 09 software package.28 No imaginary frequencies were obtained for optimized geometries, and thus all the optimized structures represent true minima on the potential energy surface. To take the effect of intermolecular hydrogen-bonding into account, a cluster containing 32 melamine molecules (Figure 1c) was extracted from the crystal structure optimized by DMOL3 code. As shown in Figure 1c, four black molecules representing the monoclinic unit cell were set free to vibrate and the nearest neighbouring 28 molecules (in red and green), with which all the hydrogen bonds and weak van der Walls interactions related to the four black molecules are involved, were kept frozen during both the geometry optimization and IR calculation by Gaussian 09 software package. A single melamine


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molecule and a 4-molecule unit cell were also extracted from the optimized crystal structure for geometry optimization and vibrational wavenumber calculations, to reveal both the influences of molecular geometry and intermolecular hydrogen bonding on the calculated IR spectrum. The DFT calculations had been carried out with the B3LYP29 exchange correlation function and the 6-311G(d,p) basis set, considering both the accuracy and computational expense. The structure models, calculation methods and corresponding total energies for the optimized structures have been summarized in Table S1 (see Supporting Information). To plot the calculated IR spectrum, pure Lorentzian function was used with a full width at half height (FWHH) of 20 cm-1.30 The computed wavenumbers had been scaled by 0.967931 to reduce the calculation error caused by ignoring the anharmonic effect and the calculation method itself for the calculations performed with 6-311G(d,p) basis set. The calculated FTIR spectra are compared with the experimental spectrum with respect to the number, relative position and the lineshape of the absorption peaks. Finally, the visualized description on the combinatorial vibrational modes of the calculated IR spectrum was made by the Gaussview program based on the calculated potential energy distribution (PED),32 which is generated from the calculated vibrational frequencies by decomposing each of the normal vibration modes, and to analyze the contribution of each characteristic vibrations. The option “Freq=InternalModes” was applied to perform these analyses based on the combination of the redundant internal coordinates. RESULT AND DISCUSSION Two equivalent crystal structures of melamine were reported based on the experimental X-ray diffraction, with space groups of P21/a and P21/c, respectively. The former (P21/a) was proposed much earlier, and thus applied for most of the structural calculations;33,34 while the latter (P21/c, lattice parameter: a = 7.27 Å, b = 7.48 Å, c = 10.57 Å, β = 112.33°) matches the


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Figure 1. Crystal structures and a 32-molecule cluster of melamine used for IR vibrational calculation. (a) Crystal structure of melamine reported by Yu et al. in ref. 22 (lattice parameter: a = 7.27 Å, b = 7.48 Å, c = 10.57 Å, β = 112.33°). (b) GGA-PBE optimized crystal structure of melamine by using DMOL3 code (lattice parameter: a = 7.23 Å, b = 7.42 Å, c = 10.66 Å, β = 112.36°). The C, N and H atoms are distinguished with dark gray, blue and light gray colors, respectively. (c) A 32-molecule cluster of melamine for vibrational wavenumbers calculation, in which the 4 bold black molecules are in the representative monoclinic unit cell, the 12 red molecules are hydrogen bonded with the black ones and the 16 green molecules are the left nearest-neighbouring molecules to the black ones. experimental XRD pattern slightly better.22 Previously we built a simplified monoclinic unit cell of melamine based on the P21/c space group (as shown in Figure 1a), in which the four molecules are nearly parallelly arranged and normal to axis c of the unit cell. Although this


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Intensity (a.u.)


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Experimental

Calculated PDF#39-1950 10

20

30

40

50

2 Theta (deg) Figure 2. Experimental and theoretically generated XRD patterns of melamine and the featured diffraction lines in the standard PDF card 39-1950. Table 1. Atomic coordinates in the optimized monoclinic unit cell of melaminea atom x/a y/b z/c C1 0.07470 0.65308 0.67522 C2 0.31507 0.51364 0.62024 C3 0.23970 0.80762 0.56402 N4 -0.06773 0.64897 0.72725 N5 0.42399 0.36701 0.62019 N6 0.27476 0.96632 0.51217 N7 0.34927 0.66361 0.55950 N8 0.09853 0.81054 0.61800 N9 0.18319 0.50212 0.68227 H10 -0.12263 0.76925 0.74714 H11 -0.08342 0.53450 0.77626 H12 0.38743 0.24827 0.65167 H13 0.50488 0.36215 0.55838 H14 0.34542 0.95460 0.44623 H15 0.15424 1.05318 0.47765 a Space group: P21/c; lattice parameter: a = 7.26 Å, b = 7.42 Å, c = 10.66 Å, α=γ=90°, and β= 112.36°


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structure was used to properly demonstrate the phase transition from the ambient pressure to high temperature and high pressure conditions,22 the corresponding XRD pattern produced by Reflex exhibits a great discrepancy from the experimental data. In this study, we follow this P21/c structure and further rearrange the melamine molecules in the unit cell according to the high birefringence feature of melamine,16 making the planar triazine ring approximately normal to the acute bisectrix, and then carrying out the structure optimization process by using the DMOL3 code of Materials Studio. Panel b of Figure 1 shows the optimized crystal structure, the lattice parameter exhibits a slight variation because it was set free during the structural optimization, while the arrangement of the four molecules in the unit cell is well consistent with that reported by the previous works.11,16,17,20,35 The atomic coordinates in the optimized monoclinic unit cell are listed in Table 1. The generated XRD pattern matches the experimental XRD pattern as well as the standard PDF card 39-1950 very well, as shown in Figure 2. This indicates the structure optimization process based on DMOL3 code is effective to calculate the crystal structure of melamine. Then the following IR vibrational calculations are based on the optimized crystal structure, as shown in Figure 1b. A single melamine molecule, a naked unit cell containing four molecules and a 32-molecule cluster were extracted from the optimized crystal structure of melamine to perform geometry optimization and IR vibrational calculation by using Gaussian 09 software. In comparison to the unit cell commonly presented in the previous works,11,16,17,20,35 here the selected unit cell shifts 0.5 primitive vector along axes b; and thus the centred two molecules in the current unit cell form hydrogen bonds with each other, which makes the corresponding vibrational calculations partially involving the intermolecular hydrogen bonding. The extracted 32-molecule cluster, nevertheless, contains all the intermolecular hydrogen bonds related to the four molecules in the


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unit cell, as shown in Figure 1c. A comparative study based on these three models has been conducted to reveal the effects of molecular geometry and intermolecular hydrogen bonding on IR vibrations in detail. The vibration frequency and intensity of the calculated FTIR spectra and the experimental data have been summarized in Table S2 (see Supporting Information). As far as the single melamine molecule is concerned, the molecular geometry exhibits a significant difference after geometry optimization by Gaussian 09 from that in the DMOL3 optimized crystal structure (see Supporting Information, Figure S1). Therefore, the corresponding calculated IR spectrum is close to the gas-phase FTIR data,36 rather than that of the solid-state crystalline phase, as shown in Figure 3b. First, 2 intense peaks appear at 1424 cm-1 and 1577 cm-1 in range of 1100-1700 cm-1, corresponding to NCN and NH2 bending coupled with ring deformation and CN stretching (1424 cm-1), CN stretching and NH2 bending (1577 cm1

), respectively. Second, the low-wavenumber vibrational bands in range of 400-1100 cm-1 are

associated with out-of-plane NH2 bending (525 cm-1), ring out of plane deformation (808 cm-1) and ring deformation with NH2 swinging (973 cm-1), respectively. The characteristic band of outof-plane ring bending at 814 cm-1 in the experimental IR spectrum (Figure 3a) is particularly strong, however, the corresponding calculated vibrational mode at 808 cm-1 is much less pronounced. Moreover, the calculated NH2 swinging vibrations at 973 cm-1 are also much weaker than that of the experimental data. Last but not least, only two weak peaks at 3494 cm-1 (symmetrical NH2 stretching) and 3621 cm-1 (asymmetrical NH2 stretching) appear in the highwavenumber range of 3100-3650 cm-1, which is associated with the stretching vibrations of N-H bonds. To sum up, the calculated IR spectrum based on a single melamine molecule is remarkably simplified and exhibits much less featured vibration peaks with respect to the


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experimental data, revealing both the molecular geometry and the intermolecular hydrogen bonding in melamine crystal have a significant influence on the related IR vibrations.

(b)

3129 3331 3420 3494 3468 3621

462 463 495 582 525 665 736 619 808 820 818 814 973 1007 1026 1031 1158 1195 1190 1469 1424 1435 1438 1424 1462 1547 1548 1549 1651 1582 1647 1577 1650

(a)

(c)

(d)

3170 3233 3221 3318 3370 3393 3494 34263518 3555 3595

Transmittance (a.u.)

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 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


500 1000 1500 2000 2500 3000 3500 4000

Wavenumber (cm-1) Figure 3. (a) Experimental FTIR spectrum of melamine. Calculated IR spectra with the B3LYP exchange correlation function and the 6-311G(d,p) basis set based on three different models: (b) a single melamine molecule, (c) 4-molecule unit cell with two hydrogen bonds (the red dashed line) formed between the centred two molecules and (d) 32-molecule cluster.

Then, a unit cell containing four melamine molecules was employed to performed geometry optimization and IR vibration calculations. As shown in Figure 3c, the calculated IR spectrum matches the experimental results much better. In the prominent absorption range of 1100-1700 cm-1, the vibrational peak at 1577 cm-1 (C-N stretching and NH2 bending) in the single-molecule IR spectrum splits into two peaks centred at 1547 cm-1 and 1582 cm-1, respectively. The newly appeared peak at 1647 cm-1, although very weak, is consistent with the experimental FTIR spectrum (Figure 3a), corresponding to the scissoring mode of NH2. Meanwhile, a vibration peak


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at 1158cm-1 is found and related to the ring deformation and NH2 swinging. In particular, new vibrational peaks observed at 3233 and 3318 cm-1 are well consistent with the experimental spectrum; their high vibrational intensity and lower wavenumbers probably due to the strong effect of hydrogen bonding between the centred two molecules. However, after the geometry optimization process, both the molecular structure and their relative position have been rearranged, no longer maintain the periodic manner in the crystal structure (see Supporting Information, Figure S1). This makes the relevant vibrations possess more specific features than that in the experimental spectrum: the out-of-plane NH2 bending vibrations shows a series of splitting peaks in range of 450-800 cm-1; and the stretching vibrations of N-H bonds also exhibit severe splits in range of 3100-3650 cm-1. In both cases the resulted vibration modes are even more complicated than that in the experimental data. Figure 3d shows the calculated IR spectrum based on the 32-molecule cluster, in which 30 intermolecular hydrogen bonds are considered: 28 of them are formed between the molecules in the representative unit cell (black molecules, in Figure 1c) and their outside-unit-cell neighbours (red molecules, in Figure 1c) and the last 2 formed between the two centred molecules in the unit cell. Due to the confinement of the outside frozen 28 molecules, the inside representative unit cell (bold black molecules in Figure 1c) is almost identical to that in the crystal structure after geometry optimization (see Supporting Information, Figure S1). As a result, by thoroughly considering the intermolecular weak interactions in this 32-molecule cluster model, a satisfied calculated IR spectrum can be reproduced in comparison to the experimental results. The vibrational peak at 1424 cm-1 (semicircle stretching of the triazine ring) in the single-molecule IR spectrum splits into two peaks at 1435 cm-1 and 1462 cm-1, respectively. The small peak at 1647 cm-1 (NH2 scissoring) in the 4-molecule unit cell IR spectrum exhibits further splitting, more


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vibrational modes appear around 1651 cm-1 and their intensities also show further enhancement. The peak at 820 cm-1 also exhibits a notably intense feature, corresponding to the characteristic band at 814 cm-1 (out-of-plane ring bending) in the experimental FTIR spectrum. The two peaks at 1031 cm-1 and 1190 cm-1 (NH2 swinging) also become more pronounced comparing with the corresponding ones in Figure 3c, which is more consistent with that of the experimental spectrum (Figure 3a). The vibrational bonds in range of 3100-3650 cm-1 (stretching vibrations of N-H) also match the experimental data much better. The observed vibration peaks exhibit the featured lineshape corresponding to the vibrational bonds around 3129 cm-1, 3331 cm-1, 3420 cm-1 and 3468 cm-1 in the experimental FTIR spectrum. It should be noted that the frequency differences are observed between the calculated IR spectrum of the 32-molecule cluster and the experimental one, probably because the temperature effect has not been taken into account during the structural optimization. However, a nearly one-to-one consistency is definitely obtained with respect to the number, relative position as well as the lineshape of the vibrational peaks. Thus, a qualitative explanation of the experimental spectrum can be further noted by the aid of the model simulation. According to the normal coordinate analysis, the measured vibrational peaks are used to be roughly assigned as following:37 3100-3650 cm-1, N–H characteristic stretching modes; 11001700 cm-1, C–N rings characteristic modes and 814 cm-1, N–H or C–N bending modes. However, the overlapping vibrational frequencies of different functional groups make the traditional assignment merely propose the possible, isolated vibrational modes and their coupling. Based on the detailed calculation of PED, here we propose a combinatorial vibration-mode assignment for the FTIR spectrum of crystalline melamine. The detailed descriptions on every peak observed in the experimental measurements are listed in Table 2, and some characteristic vibrational modes


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are schematically presented in Figure 4. The peaks around 3170 cm-1 are attributed to the symmetrical stretching vibration (υs) of N-H bonds (M3, M4), the peaks around 1651 cm-1 are associated with the in-plane shear vibration (δ) of all the N-H bonds (M), and the peak at 1549 cm-1 is a kind of complex combinatorial vibrations, which is associated with the in-plane bending vibration of all the N-H bonds (Mβ) and two of the out-of-ring C-N bonds (T1,3), the stretching vibration (υ) of out-of-ring C-N bonds (T2) and the in-ring C-N bonds (P). Moreover, the vibrational peak in 820 cm-1 is assigned to out-of-plane bending (γ) of the whole molecular (M+T+P). Note that the two Mβ mentioned above are both the in-plane bending vibration of the N-H bonds but in different modes. That is to say, these symbols are only the description of the

Figure 4. The calculated eigenvectors of the characteristic vibrational modes at 3170, 1651, 1549 and 820 cm-1 corresponding to the experimental FTIR spectrum of melamine. The C, N and H atoms are distinguished by gray, blue and white colors, respectively.


14

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Table 2. Comparison between the experimental absorption peaks and calculated frequencies of melamine (32-molecule cluster) at the B3LYP/6-311G(d,p) level and the corresponding combinatorial vibration-mode assignmentsa calculated frequencies (cm-1)

combinatorial vibrationmode assignmentb

frequencies (cm-1)

assignment37

3494, 3555

3 4 5 6 𝑀𝑀𝜐𝜐𝜐𝜐𝜐𝜐 +𝑀𝑀𝜐𝜐𝜐𝜐𝜐𝜐 ; 𝑀𝑀𝜐𝜐𝜐𝜐𝜐𝜐 +𝑀𝑀𝜐𝜐𝜐𝜐𝜐𝜐

3468, 3420

NH2 stretching, typical of melamine

1 2 𝑀𝑀𝜐𝜐𝜐𝜐𝜐𝜐 +𝑀𝑀𝜐𝜐𝜐𝜐𝜐𝜐

3331

asymmetrical NH2 stretching

𝑀𝑀𝜐𝜐𝜐𝜐

3129

symmetrical NH2 stretching

𝑀𝑀𝛽𝛽(𝛿𝛿)

1650

NH2 deformation

1548

1,3,5-s-triazine ring “quadrant stretching”

1469,1438

1,3,5-s-triazine ring “semicircle stretching”

𝑀𝑀𝛽𝛽(𝜌𝜌)

1195

C-N stretching, primary amines, tertiary C

𝑀𝑀𝛽𝛽(𝜌𝜌)

1026

---

𝑀𝑀𝛾𝛾 + 𝑇𝑇𝛾𝛾 + 𝑃𝑃𝛾𝛾

814

1,3,5-s-triazine ring, out-ofplane ring bending by “sextants”

𝑀𝑀𝛽𝛽 + 𝑇𝑇𝛽𝛽 + 𝑃𝑃𝛽𝛽

---

---

3370,3393 3170,3221 1651 1549 1462 1435 1190 1031 850-500

Combinatorial Vibration-Mode Assignment for the ... - ACS Publications

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