Journal of Molecular Structure 1074 (2014) 107–117

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Journal of Molecular Structure

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Synthesis, structure, spectral, thermal analyses and DFT calculationof a hydrogen bonded crystal: 2-Aminopyrimidiniumdihydrogenphosphate monohydrate

http://dx.doi.org/10.1016/j.molstruc.2014.05.0540022-2860/� 2014 Published by Elsevier B.V.

⇑ Corresponding author. Tel.: +91 9787100212.E-mail address: crystallographer@rediffmail.com (S. Athimoolam).

S. Thangarasu a, S. Suresh Kumar b, S. Athimoolam b,⇑, B. Sridhar c, S. Asath Bahadur a, R. Shanmugam d,A. Thamaraichelvan d

a Department of Physics, Kalasalingam University, Krishnankoil 626 190, Indiab Department of Physics, University College of Engineering Nagercoil, Anna University, Tirunelveli Region, Nagercoil 629 004, Indiac Laboratory of X-ray Crystallography, Indian Institute of Chemical Technology, 500 007 Hyderabad, Indiad Department of Chemistry, Thiagarajar College, Madurai 625009, India

h i g h l i g h t s

� 2APDHP have been grown by the slow evaporation technique.� Theoretical study was attempted by the Density Functional Theory.� Spectroscopic properties were observed by FT-IR and Raman techniques.� NBO analysis of the title molecule were studied.� Thermal studies of the title compound was analyzed by TGA/DSC.

a r t i c l e i n f o

Article history:Received 14 March 2014Received in revised form 21 May 2014Accepted 23 May 2014Available online 4 June 2014

Keywords:Crystal growthHydrogen bondingFT-IR and Laser Raman spectraTGA/DTA/DSC studiesFactor group analysisDFT

a b s t r a c t

A proton transfer complex of 2-aminopyrimidine with phosphoric acid was synthesized and crystallized.Single crystal X-ray studies, the vibrational spectral analysis using Laser Raman and FT-IR spectroscopy inthe range of 4000–400 cm�1, UV–Vis-NIR studies and thermogravimetric analyses were carried out in thesolid crystalline form. The single crystal X-ray studies shows that the crystal packing is dominated byNAH� � �O and OAH� � �O hydrogen bonds leading to a hydrogen bonded ensemble. The two dimensionalcationic layers, connected through the centrosymmetric anionic dimer of R2

2ð8Þ motif, is extending alongab plane of the crystal leading to zig-zag infinite chain C1

2ð6Þ and C22ð6Þmotifs. To investigate the strength

of the hydrogen bonds, vibrational spectral studies were adopted and the shifting of bands due to theintermolecular interactions were analyzed. Density Functional Theory (DFT) using the B3LYP functionwith the 6-311++G(d,p) basis set was applied to the solid state molecular geometry obtained from singlecrystal X-ray studies. The optimized molecular geometry and computed vibrational spectra are comparedwith experimental results which shows appreciable agreement. NBO analysis has been carried out by DFTlevel. In this study explains charge delocalization of the present molecule which shows the possible bio-logical/pharmaceutical activity of the molecule. The number of normal modes were also attempted by thefactor group analysis method. It is evident that the influence of extensive intermolecular hydrogen bondsreduces the Td symmetry of the phosphate anion to the lower C2v symmetry. The existence of exothermicpeaks in DTA iterate the breaking of intermolecular hydrogen bonds and the phase change of the crystal.The presence of water molecule is also confirmed in the thermal analyses.

� 2014 Published by Elsevier B.V.

Introduction the DNA and RNA in many forms. The large number of amino

Derivatives of pyrimidine play an essential role in many biolog-ical and pharmacological processes. Pyrimidines occur widely in

substituted pyrimidines as antagonists of folic acid [1] wasobserved in the 1948. The enzyme of dihydrofolate reductase(DHFR) is amino substituted pyrimidine drug, which act as a inhib-itor of malarial plasmodia [2,3]. Many of the pyrimidine derivativesare found with the activities such as antibacterial, antineoplastic,antiviral, antifungal and anti-cancer agent [4–8].

Fig. 1. As-grown single crystals of 2APDHP.

108 S. Thangarasu et al. / Journal of Molecular Structure 1074 (2014) 107–117

The biological properties of pyrimidines arise due to their ten-dency of making extensive intermolecular contacts, which areplaying essential role in molecular recognition and crystal engi-neering [9,10]. Because of their strength as well directional naturecompared with other intermolecular non-covalent interactions,hydrogen bonds are normally used as a tool in designing the struc-ture of the organic crystals [11]. Crystal engineering or the designof organic crystals with the specific physical and chemical proper-ties continues to elicit intense interest. This new subject encom-passes a wide variety of research activity ranging from theunderstanding of crystal packing in organic and semi organic crys-tals to the design of open network structures. This structure exten-sion property through non-covalent interactions was recognized asa possible tool for promoting cocrystallization [12]. As it is knownthat co-crystals are crucial for the production of pharmaceuticalcompounds. The most widely used application is in drug develop-ment and more specifically, the formation, design and implemen-tation of active pharmaceutical ingredients (API’s) [13].

Based on the above facts, the synthesis of new semiorganiccrystal, which contains the inorganic frame work was attemptedhere. The tendency of making extensive hydrogen bonding net-work was exploited here to obtain the hydrogen bonded crystal,namely 2-aminopyrimidinum dihydrogenphosphate monohydrate(2APDHP) single crystal. In the present study, 2APDHP was per-formed by combining the single crystal X-RD, thermal studies,experimental and theoretical vibrational spectral analysis usingDFT to derive information about electronic effects and intermolec-ular charge transfer responsible for biological activity. Though themolecular structure already reported with single crystal X-raystudies [14], a detailed account on hydrogen bonding networkattempted here.

Experimental details

Material preparation

The commercially available 2-aminopyrimidine (2AP) (C4H5N3)(Alfa Acer, purity > 98%) is a weak Bronsted base and can acquire aproton in a strongly acidic aqueous medium at lower pH, leading tothe formation of salts. The formation of 2APDHP on chemical reac-tion with orthophosphoric acid is indicated as molecular structuresin Scheme 1. The 2APDHP crystal is obtained by slow evaporationmethod of dissolving 2AP in an orthophosphoric acid solution atroom temperature in the molecular ratio 1:1. The good quality sin-gle crystals with the maximum dimensions of 9 � 4 � 2 mm wereharvested after a distinctive growth within the period of twoweeks. The grown single crystals with the sharp edges in devel-oped faces, are shown in Fig. 1.

X-ray crystal structure determination

The unit cell parameters and the crystal structure weredetermined from single-crystal X-ray diffraction data obtained

N N+ H3PO4

NH2

H2O

Scheme 1. Reaction of 2AP w

with a Bruker SMART APEX CCD area detector diffractometer(graphite-monochromated, Mo Ka = 0.71073 Å). The observed cellvalues were compared with reported structure [14]. The data col-lection, cell refinement and data reduction were made using SAINTprogram [15]. The structure solution, structure refinement and therelated calculations were performed using SHELXTL/PC [16]. Thestructure was solved by direct methods, and full-matrix least-squares refinements were performed on F2 using all unique reflec-tions. All non-hydrogen atoms were refined with anisotropicatomic displacement parameters and hydrogen atoms were refinedisotropically. The H atoms participating in hydrogen bonds werelocated from difference Fourier map and all the other hydrogenatoms were positioned geometrically and refined using a ridingmodel, with CAH = 0.93 Å Uiso(H) = 1.5Ueq(parent). Drawings ofthe molecular structure and the packing diagram were obtainedusing Mercury [17] and PLATON [18] programs respectively.Further crystal data, experimental conditions, and structuralrefinement parameters are presented in Table 1.

Computational details

The entire theoretical calculations were performed at DensityFunctional Theory using Gaussian 03W [19] program package,invoking gradient geometry optimization [20]. The first task forthe computational work was to determine the optimized geometryof the compound. The spatial coordinate positions of 2APDHP, asobtained from an X-ray structural analysis, were used as the initialcoordinates for the theoretical calculations. At B3LYP level, initialgeometry was minimized without any constraint in the potentialenergy using the 6-311++G(d,p) basis set. The optimized structuralparameters were used to calculate vibrational frequencies. Thenvibrationally averaged nuclear positions of 2APDHP were used

N NH

NH2+

(H2PO4)-. . H2O

ith Orthophosphoric acid.

Table 1Crystallographic data for 2APDHP single crystal.

Compound name 2-Aminopyrimidinium dihydrogenphosphatemonohydrate

Chemical formula (C4H6N3)+ � (H2PO4)� � H2OFormula weight 211.12Temperature 293(2) KWavelength 0.71073 ÅCrystal system, space

groupTriclinic, P�1

Unit cell dimensions a = 6.216(6) Å a = 109.57(11)�b = 8.601(5) Å b = 106.41(9)�c = 9.468(7) Å c = 95.49(10)�

Volume 447.3(1) Å3

Z, calculated density 2, 1.568 Mg/m3

Absorption coefficient 0.306 mm�1

F(000) 220Crystal size 0.18 � 0.15 � 0.12 mmTheta range for data

collection2.42–24.98�

Limiting indices �7 6 h 6 7, �10 6 k 6 10, �11 6 l 6 11Reflections collected/

unique3933/1567 [R(int) = 0.0180]

Completeness totheta = 24.98

99.40%

Absorption correction NoneRefinement method Full-matrix least-squares on F2

Data/restraints/parameters

1567/0/146

Goodness-of-fit on F2 1.049Final R indices [I > 2r(I)] R1 = 0.0275, wR2 = 0.0759R indices (all data) R1 = 0.0289, wR2 = 0.0771Largest diff. peak and

hole0.212 and �0.345 e �3

CCDC No. 791243

S. Thangarasu et al. / Journal of Molecular Structure 1074 (2014) 107–117 109

for harmonic vibrational frequency calculations resulting in IR andRaman frequencies. We have used the Density Functional Theory[21] with the three-parameter hybrid function (B3) [22] for theexchange part and the Lee–Yang–Parr (LYP) correlation function[23], accepted as a cost-effective approach, for the computationof molecular structure and vibrational frequencies. Vibrational fre-quencies computed at DFT level have been adjudicated to be morereliable. Finally, the calculated normal mode vibrational frequen-cies provide thermodynamic properties also through the principleof statistical mechanics. Vibrational frequency assignments weremade with a high degree of accuracy, by combining the results ofthe GAUSSVIEW program [24] with symmetry considerations.

FT-IR and Laser Raman studies

The FTIR spectrum of the grown crystals was recorded in theKBr phase in the frequency region of 4000–400 cm�1 using a PerkinElmer Spectrometer at a resolution of 1.0 cm�1. The Laser Ramanspectrum of the grown crystal was recorded in the frequencyregion of 100–3300 cm�1 using a Renishaw InVia Laser RamanMicroscope. The 633 nm line of a HeANe laser source was usedas the source of excitation with the laser power of 18mW.

Fig. 2. The asymmetric unit of 2APDHP, showing the atomic-labeling scheme.Displacement ellipsoids are drawn at the 50% probability level. H-bonds are shownas dashed lines.

Thermal analysis

Thermogravimetric analysis (TGA), Differential Thermal Analy-sis (DTA) and Differential Scanning Calorimetric analysis (DSC)were carried out for the crystals using a SDT Q600 thermal ana-lyzer. The crystals were powdered and used for the analysis inthe temperature range of 28–600 �C with a heating rate of 25 �C/min in the air atmosphere.

Optical analysis

The UV–Vis-NIR transmission and absorption spectra of thecrystal were recorded in the range of 190–1090 nm using a Shima-dzu UV–Vis-NIR spectrometer (model UV-3101).

Results and discussion

Structural studies

The molecular structure of 2APDHP, which contains a 2-amino-pyrimidinium cation, a dihydrogenphosphate anion and a latticewater molecule in the asymmetric unit, is shown in Fig. 2. Thetransfer of a proton from the inorganic acid (orthophosphoric acid)leads to the protonation in the 2-aminopyrimidine and forms 2-aminopyrimidinium cation. This protonation on the N site of thecation is confirmed from the CAN bond distances and CANACbond angle (Table 2). The PAO bond distances in the phosphateanion are as expected, with average single- and double-bondedPAO bond distances of 1.55 and 1.49 Å, respectively [25]. The slightlengthening of the PAO double bonds is due to the formation ofstrong OAH� � �O hydrogen bonds. The tetrahedral geometry of thedihydrogenphosphate anion has also suffered due to the extensivehydrogen bonding interactions. All the four phosphate O atoms areinvolved in hydrogen bonding, with two as donors and two asacceptors. Selected interatomic distances and bond angles arelisted in Table 2. The hydrogen bonds present in the crystal struc-ture are listed in Table 3 and shown in Fig. 3.

The crystal structure of 2APDHP is stabilized by an intricatethree-dimensional hydrogen bonding network (Table 3). The pack-ing diagram of 2APDHP in Fig. 3 shows hydrophobic layers formedby the stacking of aromatic rings at z = 0. Hence, the alternatehydrophobic and hydrophilic layers are formed along the c axisof the unit cell. The cations are connected through anionic dimersand making chain and ring motifs [26]. Centrosymmetric R2

2ð8Þdimers are observed around the inversion centers of the unit cellthrough O24AH24� � �O21 hydrogen bond. These anionic dimerare connected to cation through two NAH� � �O hydrogen bondsmaking another ring R2

2ð8Þ motif, shown in Fig. 4. These pairs ofring motifs are further connected through an N11AH11B� � �O22

Table 2Optimized geometrical parameters of 2APDHP single crystal [bond length (Å) andangle (�)].

Parameters B3LYP/6-311++G(d,p) Experimental (2APDHP)

Bond length (Å)2-Aminopyrimidinium cation

N11AC11 1.325 1.316N11AH11A 1.047 0.861N11AH11B 1.008 0.857C11AN12 1.352 1.348C11AN16 1.367 1.350N12AC13 1.320 1.317C13AH13 1.087 0.930C13AC14 1.405 1.394C14AH14 1.080 0.930C14AC15 1.373 1.351C15AH15 1.086 0.930C15AN16 1.349 1.343N16AH16 1.074 0.863

Dihydrogenphosphate anionP2AO21 1.525 1.504P2AO22 1.502 1.504P2AO23 1.630 1.562P2AO24 1.628 1.558O23AH23 0.964 0.840O24AH24 0.964 0.762

WaterO1WAH1W 0.979 0.811O1WAH2W 0.960 0.786

Bond angle (�)2-Aminopyrimidinium cation

C11AN11AH11A 123.69 119.92C11AN11AH11B 116.20 118.17H11AAN11AH11B 120.01 121.11N11AC11AN12 119.53 119.72N11AC11AN16 119.54 118.99N12AC11AN16 120.93 121.27C11AN12AC13 117.68 116.85N12AC13AH13 115.66 117.83N12AC13AC14 124.13 124.34H13AC13AC14 120.21 117.83C13AC14AH14 122.06 121.69C13AC14AC15 116.40 116.61H14AC14AC15 121.54 121.69C14AC15AH15 125.44 120.13C14AC15AN16 119.71 119.75H15AC15AN16 114.85 120.12C11AN16AC15 121.14 121.18C11AN16AH16 121.21 118.75C15AN16AH16 117.62 120.05

Dihydrogenphosphate anionO21AP2AO22 117.61 114.85O21AP2AO23 105.60 106.53O21AP2AO24 109.28 111.50O22AP2AO23 111.39 110.50O22AP2AO24 107.93 105.94O23AP2AO24 104.23 107.33P2AO23AH23 111.52 114.25P2AO24AH24 112.21 114.06

WaterH1WAO1WAH2W 106.04 105.15

Table 3Hydrogen bond geometry (Å, �).

DAH� � �A d(DAH)(Å)

d(H� � �A)(Å)

d(D� � �A)(Å)

<(DHA)(�)

N(11)AH(11A)� � �O(21)#1 0.86(2) 2.05(2) 2.909(2) 174(2)N(11)AH(11B)� � �O(22)#2 0.86(2) 2.03(2) 2.877(2) 167(2)N(16)AH(16)� � �O(22)#1 0.86(2) 1.79(2) 2.656(2) 175(2)O(23)AH(23)� � �O(1W)#3 0.84(3) 1.77(3) 2.612(2) 175(2)O(24)AH(24)� � �O(21)#4 0.76(3) 1.88(3) 2.641(2) 177(3)O(1W)AH(1W)� � �O(21) 0.81(3) 1.98(3) 2.787(2) 175(2)O(1W)AH(2W)� � �O(22)#1 0.79(2) 2.02(3) 2.791(2) 165(2)

Symmetry transformations used to generate equivalent atoms: #1 �x + 1, �y,�z + 1; #2 �x, �y, �z + 1; #3 x � 1, y, z; #4 �x + 1, �y + 1, �z + 1.

Fig. 3. Packing diagram for 2APDHP viewed down the a axis. H-bonds are shown asdashed lines.

110 S. Thangarasu et al. / Journal of Molecular Structure 1074 (2014) 107–117

hydrogen bonds leading to two zig-zag infinite chain C12ð6Þ and

C22ð6Þmotifs extending along the a axis of the unit cell. This molec-

ular aggregation is leading to a layered structure for the cation–anion hydrogen bonded assembly (excluding the donor O atomsof the anion). These layers are separated by a distance of4.869(2) Å and making a dihedral angle of 48.9(2)� to the ab planeof the unit cell.

These cationic layers, formed by intermolecular hydrogenbonds between cation and anion, are connected through the latticewater molecules present in the crystal. Water molecules are mak-ing exclusive hydrogen bonding interactions with dihydrogen-phosphate anions. Doubled bonded O atoms of the anion act as

the acceptors for the hydrogen bonds of water molecule and inanother orientation water molecule is acting as acceptor for thehydrogen bond of anion (Fig. 4). The centrosymmetric anionicdimers [R2

2ð8Þmotifs] are connected through water molecule along

the b axis of the unit cell. This form an another ring R44ð12Þ motif

and a zig-zag chain C32ð8Þ motif through the hydrogen bonds of

water molecule (Fig. 5). Further, these intersected ring and chainmotifs are connected along the a axis of the unit cell throughO23AH23� � �O1W hydrogen bond. This together withO1WAH1W� � �O21 hydrogen bond form a chain C2

2ð6Þ running

along the a axis of the unit cell. These two chain C23ð8Þ and C2

2ð6Þmotifs, extending along b and a axes respectively, made theanion-water molecule hydrogen bonded assembly on the ab planeof the unit cell. Hence, the entire three dimensional hydrogenbonding network on the ab plane is situated nearly z = ½ and mak-ing this region as hydrophilic region.

Optimized molecular geometry by quantum chemical method

The geometrical parameters were optimized by DFT/B3LYP with6-311++G(d,p) basis set are listed in Table 4 in accordance with theatom numbering scheme (Fig. 6). The calculated bond lengths andangles for 2APDHP compares with experimental data are listed inTable 4. The optimized bond length of CAC in phenyl ring fall inthe range from 1.391 Å to 1.400 Å for B3LYP/6-311++G(d,p)method, which are reliable agreement with experimental valuesfor CAC bond length of phenyl ring [27].

The donor(N) and acceptor(O) are same for the both crystallineand gaseous phase. The H bond predominant and making the crys-tal in the solid crystalline state, hence H bond was attached close tothe donor N atom. But in the case of gaseous phase, due to themore electro negativity for O atom (0.796) than the N atom

Fig. 4. Molecular aggregation formed through cations and anionic dimers showing ring and chain motifs. Hydrogen bonds are shown as dashed lines.

Fig. 5. Molecular aggregation formed through anionic dimers and water molecules showing ring and chain motifs. Hydrogen bonds are shown as dashed lines.

Table 4Factor group analysis of 2-aminopyrimidinium dihydrogenphosphate monohydrate (C4H6N3)+ � (H2PO4)� � H2O; space group P�1 ¼ C1

i ; Zb = 2.

Modes and degrees of freedom Molecular symmetry Site symmetry species C1 Factor group species Ci

C1

2-Aminopyrimidinium(C4H6N3)+ Vibrational 66 33Ag + 33Au

C2v*

Dihydrogenphosphate (H2PO4)� Vibrational 30 6A1 6Ag + 6Au

2A2 A 2Ag + 2Au

4B1 4Ag + 4Au

3B2 3Ag + 3Au

Translational 6 A 3Ag + 3Au

Libration 6 3Ag + 3Au

C2v

Water (H2O) Vibrational 6 2A1 A 2Ag + 2Au

B2 Ag + Au

Translational 6 A 3Ag + 3Au

Libration 6 A 3Ag + 3Au

Ctotalcrystal ¼ CðC4 H6 N3Þþ þ CðH2 PO4Þ� þ CðH2 OÞ ¼ 63AIR;R

g þ 63AIRu ;

Cvibrational ¼ 51AIR;Rg þ 51AIR

u ; Ctranslational ¼ 6AIR;Rg þ 6AIR

u

Crotational ¼ 6AIR;Rg þ 6AIR

u ; Cacoustic ¼ 3AIRu

Copticalcrystal ¼ Ctotal

crystal � Cacoustic ¼ 63AIR;Rg þ 60AIR

u

* Due to the presence of extensive hydrogen bonding interactions, the symmetry of anion is reduced to C2v from Td. It is explained in Table 6.

S. Thangarasu et al. / Journal of Molecular Structure 1074 (2014) 107–117 111

(0.312). Hence H atom moved towards the acceptor O atom. Thisresult reiterate the fact of hydrogen bonding interaction. Theexperimental hydrogen bond NAH� � �O and OAHW� � �O has stron-ger then the theoretical calculation whereas the amine NAH� � �Ohas stronger in theoretical calculation due to the orientation ofphosphate anion. From the theoretical values, it is observed thatthe most of the optimized bond lengths and bond angles areslightly larger than experimental value, because theoretical

calculations carried out on molecule in gaseous phase whereasthe experimental results correspond to molecules in solidcrystalline states [28].

Factor group analysis

Factor group analysis is a method used for determining symme-try of vibrations. It is useful to determine how many bands are

Fig. 6. Optimized Structure with atomic numbering for 2APDHP.

112 S. Thangarasu et al. / Journal of Molecular Structure 1074 (2014) 107–117

expected of each type of molecule in the unit [29–31]. The num-bers of normal modes of the crystals 2APDHP were determinedby group theory analysis using the correlation method based uponthe symmetry of the molecules. The results obtained are presentedin the Table 4.

The crystal 2APDHP [(C4H6N3)+ � (H2PO4)� � H2O] belongs to thespace group P�1 and has a triclinic symmetry with two formulaunits per cell. The factor group analysis using the standard correla-tion method was carried out. Excluding the acoustic modes, 123normal modes are predicted. These genuine modes can be decom-posed into the irreducible representations of the factor group Ci asC ¼ 63AIR;R

g þ 60AIRu , where Ag species are Infrared and Raman active

and Au species are only Infrared active.The formation of charge transfer complex by the reaction of

2-aminopyrimidine with orthophosphoric acid is strongly evi-denced through the realization of important bands in the resultantspectrum. The system is identified with many functional groupslike NH2, NAH, CAH, C@N, CAN, PAOH, P@O and OAH. In additionskeletal vibrations like CAC, CAC@C, CACAN, O@PAO and OAPAOalso exhibit in this compound. A recorded FTIR spectrum and theLaser Raman spectrum of 2APDHP were compared with the stan-dard spectrum of the functional groups.

It is known that the vibrational spectroscopic signature of thehydrogen bond formation is the shift to the lower frequency andthe increase in intensity of the stretching vibrations of the bondsinvolving in hydrogen bond. Our aim is to predict the changes inthe vibrational characteristics (vibrational frequencies) of 2APDHPdue to the extensive hydrogen bonding interactions. The Wilsonnotation is used throughout this work for assigning the wavenum-bers of the functional groups in both the spectra [32].

Fig. 7. Comparative representation of FT-IR spectra for 2APDHP.

Vibrational assignments

The single crystal analysis of the 2APDHP obviously predict themolecular structure, crystal symmetry, atomic vibrations (via ther-mal displacement parameters) and different types of bonds. But,the vibrational spectroscopy can only give valuable informationregarding the bonding forces and strength of intermolecular bondsin addition to symmetry of the individual molecule. The effect ofhydrogen bond is vital in crystal environment. The strong, normaland weak hydrogen bonds will cause downshifting of stretchingmode of vibrations and up shifting of deformation modes with dif-ferent numerical values of the wave numbers depends upon theirstrength (strong/normal/weak). Normally, the stretching modes

vibrational shifts are greater than the deformation modes whichindicate that the linear distortion is much greater than the angulardistortion.

The present molecule of 2APDHP with 23 atoms and 63 normalmodes of vibration has C2v point group symmetry. The experimen-tal FTIR and theoretical IR spectra of the title compound are shownin Fig. 7. The experimental Laser Raman and theoretical Ramanspectra of title compound are shown in the Figs. 8 and 9respectively. The calculated harmonic vibrational frequencies byDFT/B3LYP have been compared with experimental results. Theassignments are shown in the Table 5.

Vibrations of the 2-aminopyrimidinium cation

2-Aminopyrimidine can exist in two tautomeric forms: one isimine form, produced by a proton transfer from the NH2 group toring nitrogen and the second is unchanged amino form. In the pres-ent structure, 2APDHP, 2-aminopyrimidine is in protonated struc-ture in the N site of the pyrimidine ring with unchanged NH2 group[33] as it is evidenced from structural elucidation. In general, theNAH stretching wave numbers associated with the amino groupand pyrimidine ring ANH group show its stretching absorptionsin the region 3500–3220 cm�1. The position and intensity ofabsorptions are disturbed due to the presence of hydrogen bond-ing. Since hydrogen bonding weakens the NAH bond, stretchingwave numbers are downshifted and bending wave numbers areupshifted [34,35].

The NAH asymmetric stretching (hydrogen bond dimer) isobserved in theoretical calculations at 3656 cm�1 (mode 4). TheNH2 asymmetric stretching vibrations are observed as doubletsat 3320 and 3127 cm�1 in the FT-IR spectrum of the present

Fig. 8. Laser Raman spectrum of 2APDHP.

Fig. 9. Theoretical Raman spectrum of 2APDHP.

S. Thangarasu et al. / Journal of Molecular Structure 1074 (2014) 107–117 113

compound. These wavenumbers are found to be red shifted withD = 30–100 cm�1 than that of microcrystalline pure 2-aminopyrimidine [36]. These specifics reiterate the presence ofunchanged amino group and its hydrogen bonding tendency. Thesevibrations are slightly deviated (��90 and �33) with the theoret-ical computed values (mode 6 and 7). This negative deviation occurdue to the overlapping of CAH stretching vibration which is pre-dominate in gaseous phase. The region around 3500–2400 cm�1

in FT-IR spectrum is observed as a broad band due to the NAH� � �Ohydrogen bonding network. The pyrimidine NH stretching wavenumbers is over shaded in this region. The NH2 wagging vibrationobserved at 1130 cm�1 in Raman spectra. The computed NH2 wag-ging vibration negatively deviated (��24) from the experimentalresults due to the mixing of CAH stretching vibration (mode 22).The same NH2 wagging vibration also occur in the region1047 cm�1 in FT-IR spectra, good agreement with the theoreticalcalculated value (mode 26). A weak band around 889 cm�1 in FT-IR spectrum and 890 cm�1 in Raman spectrum shows the presenceof NH2 twisting vibration. This assignment is correlated withthe theoretical calculation at (mode 32). The NH2 rocking modesare observed at 531 cm�1 and 530 cm�1 in the FT-IR Ramanrespectively, was good agreement with the computed values

(mode 42). A band at 463 cm�1 in FT-IR spectra assigned to theNH2 torsional vibration. This same vibration was good agreementwith the theoretical calculated value (mode 45). The NAH stretch-ing vibration from the amine group observed at strong FT-IR bandin the region 3038 cm�1. The theoretically computed value shows apositive deviation (�82), when compare with the experimentalvalue (mode 9). The out-of-plane NAH bending observed a strongpeak at 1118 cm�1 in FT-IR shows good agreement with theoreti-cally predicted value (mode 23).

The aromatic structure shows the presence of CAH stretchingvibrations in the region 3100–3000 cm�1. The weak FT-IR band at3086 cm�1 has its origin in the CAH stretching vibration. However,the calculated wave number shows a slight deviation (��67) byB3LYP method (mode 8).

Vibrations of the dihydrogenphosphate anion

Vibrational assignment of various phosphate ions have beenreported by Chapman et al. [37,38] and also identified the wavenumbers of the different vibrational species of the [PO4]3� ion [Td

symmetry], the [HPO4]2� ion [C3v symmetry] and the [H2PO4]�

ion [C2v symmetry]. The symmetry reduced from Td to C2v isresponsible for the degeneracy as one moves from [PO4]3� to[H2PO4]� ion [39]. In the present structure, 2APDHP, the anionexists as [H2PO4]� ion with C2v symmetry. The internal vibrationsof [PO4]3� ion are distributed as U = A1 + E + 2F2. These frequenciesoccur at 936 (msym), 420 (dsym), 1004 (masym) and 573(dasym) cm�1.The A1 and E are only Raman active whereas the two F2 speciesare active in both IR and Raman spectra [40]. The vibrations ofthe free [H2PO4]� ion are distributed as U = 6A1 + 2A2 + 4B1 + 3B2.Except A2 species, which is only Raman active, all other speciesare both infrared and Raman active. Among these 15 vibrations,nine are correlated from the [PO4]3� ion. The correlated vibrationsare given in Table 6. The remaining six modes (U = 2A1 + A2 +2B1 + B2) must involve the stretching and bending modes of thePAOAH bonds.

The stretching vibration of P@O generally give rise to strongband in the region 1300–1140 cm�1 in dihydrogenphosphate dueto the extensive hydrogen bonding between the two ions. In thepresent structure, 2APDHP, the phosphorus atom attached to elec-tronegative groups, because of that P@O bond gets stiffer and thevibrational mode is expected to shift to higher wave numbers.But, hydrogen bonding plays a vital role has decreasing the stretch-ing wave numbers.

In the solid state most of dihydrogenphosphate form a doubletstructure that is due to the result of hydrogen bonding betweentwo neighboring P@O group. In such a case two PO2 are expected,one in-phase (symmetric stretching vibration) and the other one,out-of-phase (asymmetric stretching vibration) [41]. The mediumband at 1190 cm�1 in FT-IR spectrum is assigned to P@O stretchingmode. The theoretical calculation slightly negatively deviated(��18) due to overlapping of OAH stretching vibration (mode 21).

The weak band at 518 cm�1 in Raman is assigned to PO2 rockingvibration, good agreement with the computed value (mode 43).The PO2 wagging vibration observed strong band at 517 cm�1 inIR, this result positively deviated (�35) in calculated value due tothe influence of NH2 rocking vibration from the 2-aminopyrimidi-nium ring (mode 44). In the present structure, OAPAO stretchingmodes appear medium band at 463 cm�1, good agreement withthe calculated value (mode 45). The P(OH)2 stretching modes areassigned at 975 cm�1 and 980 cm�1 in the FT-IR and Raman,respectively. The theoretical value slightly deviated (��23) fromthe experimental result due to the addition of CAH stretchingvibration (mode 30). The weak band of P(OH)2 deformation modesappeared at 416 cm�1 and 420 cm�1 in FT-IR and Raman spectra,respectively. The computed value deviated (��28 and �-24) from

Table 5Experimental and B3LYP level computed vibrational frequencies (cm�1) obtained for 2APDHP.

Mode number Experimental B3LYP/6-311++G(d,p) Assignment

FT-IR Raman

1 3893 m OAH (water)2 3837 m OAH3 3834 m OAH4 3656 m NAH (NH2)5 3541 m OAH6 3320s 3230 mas NH2

7 3127vs 3160 mas NH2 + m CAH8 3086w 3153 m CAH9 3038s 2956 m NAH (NH2)

10 2413s 2535 ms NAH + m NAH� � �O + mas CAN11 1728 mas C@N + mas CAN12 1700 d NH2 + m NAH13 1689vs 1669 m C@N + ms CAN14 1652m 1645 d OH15 1627s 1572 m C@N + m C@C16 1542w 1530s 1520 b NH2

17 1489w 1450w 1476 ms CAN + ms CAH18 1414w 1400w 1395 CAH bending19 1355s 1350s 1338 CAH bending20 1234s 1270w 1278 b CAH + b NAH21 1190m 1208 m P@O + m OAH22 1130s 1154 x NH2 + m CAH23 1118vs 1110 c NAH + c CAH24 1074vs 1070s 1095 ms PO2 (A1) + ms CAN25 1080 ms P@O + m OAH26 1047s 1053 x NH2 + m CAH27 1038 c CAH28 1020s 1017 m OAH (phosphate)29 1002 c PAOH30 975vs 980s 998 m PA(OH)2 (B2) + c CAH31 994 ms CAH32 889w 890s 897 t NH2 + CH def33 872w 870 s 888 b NH2

34 820sh 861 m PAOH35 795w 810 c PAOH (A1)36 807 CH o.p.def.37 709m 720w 792 c CAN38 702 t H2O39 638m 640s 648 Planar ring distortion40 584m 580 591 b CANH2

41 554m 540s 549 OH ring def.42 531s 530s 528 PO2 sym. bend + q NH2 + c CAH43 518w 510 q PO2 + q NH2

44 517s 482 x PO2 + q NH2

45 463w 479 m OAPAO + q NH2

46 416w 420s 444 P(OH)2 def + x NH2 + x OH (water)47 432 q OH48 412 PAOH o. p. def.49 380m and 390m 407 CACAN def.+ t P(OH)2

50 351 t P(OH)2

51 264 b OAH52 210w 228 c OAH53 127w 198 m OAH54 110w 186 m OAH (water) + m OAH (phosphate)55 181 m NH56 177 Lattice vibration57 146 Lattice vibration58 114 Lattice vibration59 99 Lattice vibration60 93 Lattice vibration61 49 Lattice vibration62 30 Lattice vibration63 21 Lattice vibration

w, weak; vs, very strong; m, medium; sh, shoulder; m, stretching; ms, sym.stretching; mas, asym.stretching; c, out-of-plane bending; b, in – plane bending; q, rocking; x,wagging; d, scissoring; def, deformation; t, twisting.

114 S. Thangarasu et al. / Journal of Molecular Structure 1074 (2014) 107–117

the observed value due to overlying of NH2 and OH waging vibra-tion (mode 46).

The Td symmetry of the phosphate anion is reduced to the lowersymmetry C2v owing to the extensive intermolecular hydrogenbond, it changes the position and intensity of several band. The

splitting of degenerate modes and the appearance of infrared-inac-tive modes indicate the effect of the crystalline field on molecularvibrations. The downshifting of several stretching wavenumberstogether with increases in many of the deformation wavenumbersconfirms the presence of hydrogen bond.

Table 6Distribution of vibration of [PO4]3� ion to [H2PO4]� ion.

Td symmetry

[PO4]3- ion

C2v symmetry

[H2PO4]- ion

A1 (936) A1(870)

E (420)

A1(420)

A2(390)

F2 (1004)

A1(1047)

B1(1118)

B2(980)

F2 (573)

A1(580)

B1(518)

B2(517)

S. Thangarasu et al. / Journal of Molecular Structure 1074 (2014) 107–117 115

Vibration of water molecule

Water has a C2v symmetry with normal modes 2A1 and B2 activein both infrared and Raman. The medium band at 1652 cm�1 in FT-IR spectrum is due to scissoring OH vibration. The same vibration isreliable agreement with the theoretical calculations (mode 14).The calculated value observed at 432 cm�1 is assigned to the rock-ing OH vibration (mode 47). The OH stretching vibration occur at110 cm�1 in Raman spectrum. In comparison with the theoreticalspectrum the band is downshifted about 76 cm�1 which is due tothe extensive O---H� � �O intermolecular interactions in crystallinestate (mode 54).

NBO analysis

NBO analysis was carried out by all possible interactionbetween the donor (i) and acceptor (j) level. These interactionsare capable to strengthen and weaken the bonds.

The stabilization energy E(2) associates with the delocalizationbetween the i ? j. For the larger E(2) value show that more stronginteraction between the donor (i) and acceptor (j) [42]. It can becalculated by the following formula,

Eð2Þ ¼ qiFði; jÞ2

ðej � eiÞ

Table 7Second order perturbation theory analysis of Fock matrix in NBO basis for 2APDHP.

Donor (i) ED (i) (e) Acceptor (j) ED (j) (e)

p(C15AN16) 1.98597 n1(C14) 1.04313p(C15AN16) 1.98597 p�(N11AC11) 0.5237n1(N 12) 1.91323 r�(C11AN16) 0.04662n1(C14) 1.04313 p�(N12AC13) 0.26888n1(C14) 1.04313 p�(C15AN16) 0.55439p�(N11AC11) 0.5237 p�(N12AC13) 0.26888p�(C15AN16) 0.55439 p�(N11AC11) 0.0529n1(O22) 1.97984 r�(P2AO21) 0.10881n1(O22) 1.8591 r�(P2AO23) 0.20595n1(O22) 1.85008 r�(P2AO24) 0.18826n1(O21) 1.98299 r�(P2AO24) 0.18826n1(O21) 1.8511 r�(P2AO22) 0.11571n1(O21) 1.84143 r�(P2AO23) 0.20595n1(O23) 1.94169 r�(P2AO24) 0.18826n1(O24) 1.96394 r�(P2AO23) 0.20595

a E(2) means energy of hyper conjugative interactions.b Energy difference between donor and acceptor i and j NBO orbitals.c F(i,j) is the Fock matrix element between i and j NBO orbitals.

where qi is the donor orbital occupancy, ej and ei are diagonal ele-ments orbital energies and F(i,j) is the off diagonal NBO Fock matrixelement. NBO analysis has been performed on the title molecule atthe DFT/B3LYP with 6-311++G(d,p) basis set in order to explaincharge transfers or conjugative interaction, the intra-moleculerehybridization and delocalization of electron density within themolecule. The second order perturbation theory analysis of Fockmatrix in the NBO basis of the molecule shows the strong intramolecular hyper conjugative interactions which are presented inTable 7.

The intramolecular interaction between p(C15AN16) bondingwith lone pair C14 is resulting with the stabilization energy10.72 kJ/mol which indicates larger delocalization. Another intra-molecular interaction is formed by the orbital overlap betweenbonding p(C15AN16) and p�(N11AC11) antibonding orbital withstabilization energy 30.89 kJ/mol. The interaction between lonepair C14 bonding with p�(C15AN16) antibonding orbital with thehigh stabilization energy 275.31 kJ/mol which indicates largerdelocalization. Similar interactions from the lone pair C14 bondingwith p�(N12AC13) with stabilization energy 88.73 kJ/mol. Theinteraction p�(C15AN16) ? p�(N11AC11) is giving the high stabil-ization energy 124.97 kJ/mol. Similarly, intra-molecular interac-tions is formed by the orbital overlap between antibondingp�(N1AC11) and antibonding p�(N12AC13) with stabilizationenergy 82.38 kJ/mol. The overall results show that large delocaliza-tion around the pyrimidine ring which induces present molecule(2APDHP) as bioactive.

Thermal analysis

The thermogravimetric analysis of the 2APDHP shows verygood thermal stability up to 171 �C. The DSC shows sharp endo-thermic peak at 171 �C, which is the melting point of the growncrystal. The decomposition of 2APDHP occurs in three steps inScheme 2. TGA/DTA and DSC of the 2APDHP are shown in Figs. 10and 11, respectively.

The first weight loss (9.71%), occurring between 75 �C and149 �C, is due to the removal of water molecule from the com-pound. The second weight loss (41.02%), occurring between149 �C and 281 �C, is due to the loss of metaphosphoric acid andwater molecule from the previous intermediate of C4H8N3O4P.The third weight loss (13.46%), occurring between 281 �C and500 �C is due to loss one molecule of ammonia from the last inter-mediate of C4H5N3. The final residue (above 500 �C) has the combi-nation of the carbon, hydrogen and nitrogen atoms. The above

E(2)a (kJ/mol) E (j) � E(i)b (a.u) F (i, j)c (a.u)

10.72 0.25 0.06230.89 0.35 0.10211.76 0.8 0.08788.73 0.13 0.117

275.31 0.07 0.13782.38 0.04 0.076

124.97 0.02 0.06610.68 0.65 0.07516.68 0.53 0.08622.15 0.55 0.09919.68 0.53 0.09213.31 0.63 0.08216.78 0.52 0.08410.11 0.69 0.07713.21 0.65 0.086

Scheme 2. Decomposition steps of 2APDHP. Note: The values given in parenthesisstand for the molecular weights of the respective species.

Fig. 10. TGA/DTA thermogram of 2APDHP.

Fig. 11. Differential scanning calorimetry curve of 2APDHP.

Fig. 12. Transmission spectrum of 2APDHP.

116 S. Thangarasu et al. / Journal of Molecular Structure 1074 (2014) 107–117

decomposition pattern is confirmed by the weight losses observedin the TGA curve [43].

The two weak endothermic peaks observed in the temperature113 �C and 126 �C is due to the loss of lattice water molecule. Itshows presence of lattice with different binding forces. A thirdendothermic peak observed in the temperature 171 �C is due to

decomposition of second water molecule in the parent compound.Also this temperature may be the melting point of the compound.The soft exothermic peaks at 344 �C and 431 �C due to the decom-position of the organic compound.

Optical analysis

The UV–Vis-NIR spectrum gives the information about absorp-tion and transmission of the crystal. The crystal shows a goodtransmittance in the visible region which facilitate it to be a goodmaterial for optoelectronic applications. The 2APDHP crystal wastransparent in the region from 350 nm and 1090 nm. The widerange of transparency suggests that the crystals are applicablefor third harmonic generation The lower cut off wavelength for2APDHP found at 340 nm corresponding band gap of grown crystalhas 3ev. The observed UV absorption spectrum in the range of190–350 nm due to the n ? p� transition. The theoretical valueof transparency for this compound (352 nm) is nearly equal tothe observed value (kmax). Transmission spectrum of 2APDHP ispresented in Fig. 12.

Conclusions

The molecular structure of the crystallized material has beenidentified by the single crystal X-ray diffraction. Exclusive focuson hydrogen bonding network is reported here as compared tothe previous report. The theoretical study was attempted topredict the optimized geometry and computed spectra by theDensity Functional Theory (DFT) using the B3LYP function withthe 6-311++G(d,p) basis set. Further, the molecular vibrationsare correlated with the different functional groups by factorgroup analyses, by correlation method. The stabilization energycalculated from NBO analysis shows the possible bioactivity ofthe title compound. The thermal behavior of the compound wereanalyzed by TGA/DTA and DSC. The existence of exothermic peaksin DTA iterate the breaking of intermolecular hydrogen bonds andthe phase change of the crystal. The presence of water molecule isalso confirmed in the thermal analyses. The optical property isalso attempted by UV–Vis-NIR studies. A good correlationbetween the observed and scaled wave numbers was obtainedfor the compound. From the factor group analysis intermolecularhydrogen bonds reduces the Td symmetry of the phosphate anionto the lower C2v symmetry. Inorganic network (H2PO4) withorganic molecule for hydrogen bonded crystal is attempted andachieved with 2APDHP.

S. Thangarasu et al. / Journal of Molecular Structure 1074 (2014) 107–117 117

Acknowledgments

ST and SAB sincerely thank the Vice Chancellor and manage-ment of the Kalasalingam University, Anand Nagar, Krishnankoil,for their support and encouragement. The authors SA and SSKgrateful to Department of Science and Technology, SERB for thefinancial support of this work in the form of Fasttrack ResearchProject scheme.

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