CHAPTER VI I I

Synthesis, structure and spectral investigation of single stranded hydrogen bonded helical coordination polymer

with mixed ligand Cu (II) pyrimidone complex

8.1 Introduction

Hydrogen bonding [240] and metal coordination [241] are extensively

used in the fornnation of different crystal structures. Hydrogen bonding is an

efficient way of making monovalent linkages through hydrogen atoms. On the

other hand, metal coordination is multivalent and therefore it is a powerful tool

to make highly ordered networks. Moreover when metal-coordinated ligands

form hydrogen bonds with each other, highly ordered networks are often

constructed [242, 243]. Coordination polymers form an important class of

compounds with a potential for exhibiting unusual and desirable properties [244,

245]. The design of such compounds takes into account the coordination

characteristics (viz., geometrical and ligand atom preferences) of the metal ion

as well as the structural features (viz., charge, multifunctionality, and chelate

and bridge-forming ability) of the ligand.

Pyrimidines generally found in the deoxyribonucleic acid have attracted

immense interest among the biochemists [246-248].The role of metal ions in

probing the structure and biochemistry of nucleic acids have paved the way to

gain a wealth of information and understanding of nucleic acids in particular

[249-251]. Cytosine, one of the fundamental nucleic acids and its interaction

with Cu (II) center was studied using powder XRD and spectroscopic tools

165

[252]. Pyrimicline-2(1H)-one rearranges its hydrogen between nitrogen and

ketonic oxygen, as a result of which it exists both in keto (pyrimidone) and enol

(2-hydroxypyrimidine) forms. Cu (II) being a well recognized bio-element,

studies on the complexation and structural investigation of copper (II) with

nucleobases such as pyrimidine is considered to be very useful [253-255].

In the present study, a simple mixed ligand mononuclear Cu (II) complex

with pyrimidone possessing a simple nucleotide helical supramolecular

structure is reported. It also involves a thorough structural analysis and

spectroscopic investigation of the complex formed.

8.2. Experimental

8.2.1 Preparation of the complex

Cu(CI04)26H20 and 2-Hydroxypyrimidine hydrochloride were procured

from Aldrich & Co and were used as such Caution! Perchlorate salts can be

potential explosives during drying and grinding and hence proper care should

be exercised while handling such compounds. So far no problem has been

experienced during the preparation of these samples.

Synthesis: 2-Hydroxy pyrimidine hydrochloride (0.001 mmol, 25ml) was

dissolved in an ethanolic solution and mixed with copper (II) perchlorate

hexahydrate dissolved in ethanol (0.001 mmol, 25ml) and stirred for 30 minutes

with gentle heating. After the complete evaporation of the solvent the resultant

pasty material was dissolved in an excess of ethanol and allowed to crystallize

at room temperature. Glassy needle like crystals were obtained on slow

166

evaporation at room temperature after a period of tliree weeks. (1): ESI-IVIS,

[1]-H20 (m/z+Na*), Calc for [C4H4Cl2CuN20+Na1 253.8876. Found 254.

The chloride ion in the protonated ligand (N-H* CI") has formed a bond

with copper ion in copper perchlorate in addition to 2-pyrimidone and water

molecule forming a complex and perchloric acid. IR spectrum also justifies the

absence of perchlorate. The possible chemical reaction is given below.

2(C4N2H40.HCI)+2Cu(CI04)2.6H20—^2[Cu(C4N2H4O(CI)2(H2O)]+10H2O+2HCIO4

8.2.2 Physical measurements

X-ray diffraction data were collected using the Bruker AXS smart single

crystal diffractometer [72], using graphite monochromated MoKa

o

(A= 0.71073 A) radiation. The structure was solved by direct methods using SIR

2004 and refined with SHELX97 system of programmes [73]. Diagrams were

drawn using an ORTEP H [74] programs and mercury software. The refinement

was run in the normal way and all the non-hydrogen atoms were refined with

anisotropic displacement parameters. All the hydrogen atoms were found in the

difference Fourier map, positioned and refined well with greater accuracy. Mass

analysis was performed using electron spray ionization (ESI) technique on a

waters Q Tof-micro mass spectrometer. IR spectrum was recorded using KBr

pellets ( 1 % w/w) on a Perkin-Elmer Spectrum GX FTIR spectrophotometer.

Electronic spectrum was recorded on a Schimadzu UV 3101 PC

spectrophotometer. Thermogravimetric analysis (TGA) and differential thermal

analysis (DTA) were carried out simultaneously employing Perkin-Elmer

167

Differential thermal analyzer (Pyris Diamond TG/DTA). Single crystal Raman

spectrum was recorded using a BRUKER RFS 100/s FT-Raman

spectrophotometer and employing 1064 nm laser excitation and 2 cm"

resolution.

8.3 Results and discussion

8.3.1 Crystal structure analysis

Relevant crystallographic data and structural refinement details are given

in Table 8.1. The ORTEP diagram with atom numbering scheme for the

complex is shown in Fig. 8.1 and their corresponding bond length and angles

are given in Table 8.2. The complex crystallized in Pn space group, with two

molecules in the unit cell. The central metal ion Cu (II) is forming a square

planar geometry, coordinates with two chlorines (CM, CI2), nitrogens (N1)

of pyrimidine and oxygen of water molecule (02) sitting at the corner of

distorted square planar geometry. The water molecule coordinating strongly

with Cul with a distance Cu1-01 = 1.979A; whereas the chlorine and nitrogen

atoms possesses slightly longer distance from Cu [Cu l -N l = 2.033 A;

Cu1-CI1 = 2.239 A; CU1-CI2 = 2.246 A] with trans angle ZN1-Cu1-CI1 =

169.09°; Z02-Cu1-CI2 = 178.09° and cis angle: ZN1-Cu1-02 = 87.73°;

Z02-Cu1-CI1 = 88.02°; ZCI1-Cu1-CI2 = 93.36°; ZN1-Cu1-CI2 = 91.14°. Among

the four coordinating atoms with copper, the shortest bond distance observed in

water oxygen suggests that water was bound strongly with Cu (II) central metal

ion. The degree of distortion in the square planar complex can be easily

measured using the distortion parameter (x) suggested by Addison et al. [256].

168

According to them a perfect square pyramidal and trigonal bipyramidal

geometry should have a x value [(p-a/) 60° where p and a are the trans angles

i.e. ZCI1-Cu1-N1= 169.09° and CI2-Cu1-02 = 178.09°)] of zero and unity

respectively. The T value of 0.17, for the present complex suggests a significant

distortion in the geometry, which lies in an intermediate geometry between the

[Cu(dien)(2Melm)] (0104)* and [Cu(dien)(2MeBzlm)f the details of which have

been reported earlier [257]. The H-O-H angle in the present case is 112.57°,

which deviates from the H-O-H angle of free water molecule. This shows a

possible distortion in the water molecule arising due to its direct coordination

with the metal and the strong intermolecular hydrogen bonding prevailed in the

structure.

8.3.2 Weak exchange interaction and molecular association

Intermolecular H-bonding interaction and K-% interaction plays significant

roles in bringing the molecules together in solid state and forms a single

stranded helical assembly in the supramolecular assembly network. The

exocyclic ketonic oxygen (01) of the pyrazole ring of the pyrimidine is

interlinked through their H-bond contact with water molecule (02) of the next

neighboring molecule forming a chain. This extends as a one dimensional

helical chain that appears as P and M sense of helix as shown in Fig. 8.2. Thus

the supramolecular self assembled P and M sense of helix running through

O-H-O hydrogen bonding interaction formed between Cu1-02(w)"- 01(C=0)

with H21-01 = 1.853 A, 01 ••• 02= 2.644 A and angle Z02-H21-01 = 172.87°.

In addition to the O-H-O hydrogen bonding interaction, the molecules are

169

further involved in an additional weak n -n stacking interaction mediated

between the aromatic rings of the pyrimidine moiety within the chain. The plane

of the Cu (II) geometry (CI1CI2N102) and the plane of the phenyl ring

(N1C1N2C2C3C4) are twisted to each other with an angle 65.18°. The distance

between the crystallographically calculated centroid of the aromatic rings within

the chain suggests that they possess weak n- n stacking interaction and

possesses Cg1-••Cg1'= 3.857 A. Cg and Cg' represents the center of pyrimidine

rings of the adjacent molecules in the chain (Fig. 8.2). The other significant

short contacts are (1) between the chlorine atoms and the H atoms of the C2,

C4 and N1 of the ring (2) between the chlorine atom and H atom of water

molecule and (3) between 0(2) of water molecule and H atom of C3 ring. These

contribute to C-H"CI, N-H-Ci and 0-H-CI hydrogen bonds of bond lengths

2.752 A, 2.525 A and 2.722 A. One more hydrogen bond is established due to

the short contacts, is C-H-0 of bond length 2.638 A. The combined strong

hydrogen bonding interaction O-H-O, the strong C-H--CI, N-H-CI , 0-H-CI

hydrogen bonds and the weak n- u stacking interaction, brings the adjacent

Cu(ll) metal center into close proximity through its helical assembly within the

polymeric chain. The packing of the complex is shown in Fig. 8.3. A comparison

of the bond length of Cu-0, Cu-N and 0 - 0 hydrogen bonding of the present

complex with related complexes [131,174,258-260] are given in Table 8.3. It

justifies the strong bonding of water molecule with the metal and the strong

hydrogen bonding of the complex under study.

170

8.3.3 Thermogravimetric analysis

To understand the thermal stability of the coordinated water molecules in

the Cu (II) system, thermo gravimetric analysis at temperatures ranging from

30°C to 160°C were carried out. The 1®* derivative TGA curve (Fig. 8.4),

indicates a distinct weight loss at a temperature of 120°C. The endothermic

curve showing 7.12% (calc = 7.28) weight loss at 105°C -140°C corresponds to

one water molecule.

8.3.4 Factor group analysis

The crystal mono-aqua-dichloro copper (II) pyrimidone complex

crystallizes in the monoclinic system with the space group Pn (Cs). The primitive

cell contains two formulae units with Ci site group symmetry. The unit cell

contains 34 atoms giving rise to a total of 102 vibrational modes. These modes

were classified according to the irreducible representations of the point group

Ci. The site correlation method of factor group analysis [39] was applied to

classify the vibrational modes of the title crystal. The representation, f total, of all

the vibrations can be decomposed according to the irreducible representation of

the point group Cs as [51A+51A], among which are included the three

acoustic modes corresponding to the block translations of the crystal f vib,

acoustic = 2A +A. The remaining 99 vibrations are optic modes. Group

theoretical consideration shows that these 99 optical modes can be divided into

36 external modes (including rotational and translationai lattice modes) and 66

internal modes. Among the 66 internal modes, the irreducible representation of

171

pyrimidone molecule [C4N2H4O] is 27 A'+27A" and the remaining 12 [6 A '+6 A"]

shared by the water molecule and CuCb molecular group. The correlation

scheme of the internal vibrations of the molecular group 2- pyrimidone

[C4N2H4O] is given in Table 8.4. The internal vibrations of both water and CuCIa

molecular group each with six vibrations are given in Table 8.5. Total external

vibrations specifically translations and rotations for pyrimidone, water molecule

and CuClg molecular groups are given by 18 A' +18 A". Summary of the factor

group analysis is given in Table 8.6.

8.3.5 Spectral investigation

The FTIR spectrum obtained in the range 4000-400 cm'^ and the

FT Raman spectra in the range 10 - 3500 cm"\ are shown in Figs. 8.5 - 8.8

respectively. The detailed vibrational assignments are given in Table 8.7. The

IR spectrum shows medium bands at 3600, 3500, 3454 and 3402 cm'^ and

Raman spectrum shows weak bands at 3467, 3453 and 3417 cm' \ This

confirms the presence of a water molecule in the complex. The IR bands which

are medium intense may be due to the locking of water molecule strongly with

the metal in the lattice. Group of vibrational bands in the region between 3100-

2900 cm'^ in both IR and Raman are assigned to CH stretching vibrations.

However the medium strong band at 3088 cm' in IR and 3075 cm" in Raman

were assigned to NH stretching vibrations may be due to the shorter hydrogen

bonding distance of N-H--CI over C-H-CI and also based on earlier studies

[115,129].The weak band at 2300 cm' in IR has been assigned to OH

stretching mode and the combinational bands appear in these region (not

172

mentioned in the assignments) usually corresponds to the presence of

hydrogen bonds. The Raman bands in this high frequency region were found to

have lesser intensity. The weak band at 1733 cm" and strong band 1656 cm'^

in IR and medium bands at 1731 cm'^ and 1655 cm" in Raman can be ascribed

to C=0 stretching [261], in support of the short bond distance of CO (double

bond) found in our single crystal X-ray analysis. Further, the double bond of

carbonyl oxygen undergoes only small changes upon formation of the complex,

so that any strong bonding of 2-pyrimidone to the metal through C=0 oxygen

can be ruled out [262]. The band at 1606 cm" in IR and 1616 cm'^ in Raman

has been assigned to H-O-H bending [194]. CH and NH bending vibrations and

ring stretching vibrations were assigned to the region 1500 to 1000 cm" [263,

264]. The regions between 1000 and 450 cm" were assigned to asymmetric

bending vibrations of CH and NH and ring bending vibrations [238]. The band at

724 and 591 cm" in Raman has been assigned to rocking and wagging of water

molecule [265]. In the low wavenumber region, lattice water exhibits vibrational

modes due to restricted rotations and oscillations of the water molecule. The

other lower bands exclusively correspond to lattice vibrations. The very strong

band at 279 cm" has been assigned to Cu-N and Cu-CI stretching [266, 267] of

metal ligand covalent coordination.

8.3.6 UV studies

The solid state UV spectrum is shown in Fig. 8.9. The absorption band in

the 600 nm range predicts the distorted square planar nature of the complex,

confirming the results of single crystal X-ray analysis.

173

Usually Square planar complexes have absorption in the 500 - 600 nm

region in the UV-visible spectroscopy. Copper complexes have distorted

geometry due to John - Teller effect.

8.4 Conclusions

An important mixed ligand mono-aqua-dichloro copper (II) pyrimidone

complex is synthesized. X-ray diffraction of the single crystal brings out the

formation of a single stranded coordination polymer with left and right-handed

(P and M sense) helical superstructure. The extensive hydrogen bonding in the

crystal resulted in the formation of this structure. TGA confirms the presence of

a water molecule. Most of the internal modes of 2-pyrimidone and water

molecule of the crystal are identified and assigned using IR and Raman

analysis out of the estimated values found from factor group analysis. Fourteen

out of thirty six lattice modes are identified. The copper pyrimidone ligand

coordination through coordinate bond has also been confirmed from spectral

analyses. UV-Visible spectral studies are in support of the single crystal

analysis confirming the square planar structure.

Supporting information available

Crystallographic data for the structural analysis have been deposited

with the Cambridge Crystallographic Data Centre, CCDC No 634351. Copies of

this information may be obtained free of charge from The Director, CCDC 12

Union Road, Cambridge CB2 1EZ, UK (Fax: [D44-1223-336033; E-mail:

deposit@ccdc.cam.ac.uk or www: http: //www.ccdc. cam.ac.uk).

174

Table 8.1 Crystallographic data and structure refinement.

Identification code kalyal

Empirical formula C4H6N202Ci2CU

Formula weight 253.5286

Temperature 293(2) K

Wavelength 0.71073 A

Crystal system Monoclinic

Space group Pn

Unit cell dimensions a = 9.657(2) A a= 90.00.

b = 3.857(2) A p= 107.54(2)

c= 10.781(2) A Y= 90.00.

Volume 382.9(2) A 3

Z 2

Density (calculated) 3.081 Mg/m3

Absorption coefficient 3.234mm-''

F(OOO) 364

Crystal size 0.11x0.14x0.22 mm3

Theta range for data collection 2.49 to 29.14

Index ranges -13<=h<=12,-5<=k<=5, • .14<=|<=14

Reflections collected 4115

Independent reflections 1837 [R(int) = 0.0240]

Completeness to theta = 29.14 92.7%

Absorption correction none

Refinement method Full-matrix least-squares onF2

Data / restraints / parameters 1837/2/109

Goodness-of-fit on F^ 1.033

Final R indices [l>2sigma (1)] R1 = 0.0261, wR2 = 0.0658

R indices (all data) R1 = 0.0264, wR2 = 0.0660

Refine abs structure flack .055(11)

Largest diff. peak and hole 0.640 and -0.477 e.A-3

175

Table 8.2 Bond lengths [A ] and angles ["].

Cu1 02 1.979(3)

Cu1 N1 2.033(3)

Cu1 CM 2.2394(9)

Cu1 CI2 2.2462(9)

01 C1 1.232(4)

N1 C4 1.324(4)

N1 C1 1.379(4)

N2 02 1.338(4)

N2 01 1.379(4)

02 03 1.364(5)

03 04 1.390(4)

O2 0u1 N1 87.72(11)

02 Oul Oil 88.03(8)

N1 Oul Oil 169.08(8)

02 Oul 012 178.09(9)

N1 Ou1 012 91.14(8)

on Ou1 012 93.36(3)

04 N1 01 119.7(3)

04 N1 Oul 121.9(2)

01 N1 Oul 118.3(2)

02N2 01 123.8(3)

01 01 N1 123.7(3)

01 01 N2 119.8(3)

N1 01 N2 116.5(3)

N2 02 03 119.4(3)

02 03 04 117.0(3)

N1 04 03 123.5(3)

Symmetry transformations used to generate equivalent atoms:

176

Table 8.3

A comparison of the geometries of Cu—O interactions in some related

complexes

Compound Cu-0 O(1)---0(2) Cu-N Reference 0 0 0

A A A CU(C4N2H40(CI)2 (H2O) 1.979 2.644 2.033 This work

[Cu(2-pyrimidinone)4] 2+ 2.78, 2.95 2.90

[Cu2(PTMMC)2(MeCOO)2(H20)2]4EtOH 1.971, 2.74, 2.102 2.95

2.00, [131] 1.99

- - [258]

[Cu(N-salicylidene-N '-methylenediamine)(cytosine)] *

2.77 2.902, 2.761

2.01 [259]

Cu(glycylglycinato)(cytosine) 2.82 1.98 [260]

Cu (C4H5N30)4 (CI04)2.2H20 2.772, 2.741

2.027, 2.032

[174]

177

Table 8.4

Internal vibrations of 2-pyrimidone

Free ion

symmetry Cs

Site

symmetry Ci

Factor group

symmetry Cs

27 A'

27 A"

27 A'

27 A"

54

Table 8.5

Internal vibrations of Water and CuCb molecular group

Free ion Site Factor group

symmetry symmetry symmetry Cs

C2v Ci

2A i

As

^ ^ * cr ^ ^ _ _ ^ 3 A

2B i • - ^

2B2 ^ ^ 3A"

178

Table 8.6

Factor group analysis of mono-aqua-dichloro Copper (II) pyrimidone complex

Factor (C4N2 H4O) (H2O) CUCI2 General Group Cisites CiSites Cisites Ci sites

Species

Optical Acoustic modes modes

I E I E I E C H N O C I C u

A(R,IR) 27 3T,3R 3 3T,3 R 3 3T,3 R 12 18 6 6 6 3 49

A"(R,IR) 27 3T,3R 3 3T,3 R 3 3T,3 R 12 18 6 6 6 3 50

54 6T,6R 6 6T,6 R 6 6T,6 R 24 36 12 12 12 6 99

I refers to internal modes.

E refers to external modes.

179

Table 8.7

Assignment of various vibrational modes of mono-aqua-dichloro Copper

(II) pyrimidone complex

Mono-aqua-dichloro Copper (II) pyrimidone complex

Wave number (cm' ) Assignment

IR Raman

3600 m 3476 w v(OH) 3500 ms — v(OH)

3454 ms 3453 vw v(OH)

3402 m 3417 vw v(OH)

3397 vw v(NH) 3365 vw v(NH)

3303 w v(NH) 3241 w v(NH)

3212 w v(NH)

3189 w v(CH)

3133 w 3127 w v(CH) 3111 w v(CH)

3088 ms 3075 w v(NH)

3045 s 3058 vw v(CH) 3000 m 3000 vw v(CH)

2977 vw v(CH) 2924 m 2941 vw v(CH)

2905 vw v(CH)

2866 m 2866 vw v(CH)

2839 w v(CH)

2817 vw v(CH)

1792 w 5(OH)

1767 w 1750VW 5(0H)

1733 w — 5(0H)

1700 w 1671 w 6(0H)

1656 vs 1656 w v(C=0)

1606 ms 1602 m 6 H-O-H

1589 s 1563 m v(C-N),5(NH), V ring

1462 vw 1528 w v(C-N),5(NH), V ring

1424 vw 1444 w v(C-N),5(NH), V ring

1327 m 1336 ms v(C-N),8(CH), V ring

— 1266 w V ring, 8{NH)

180

1212 m 1212 m 5(CH)

1154W 1153W 6(CH) — 1099 s V ring

1077W 1079 m 5(CH) 1038 vw — 8(CH)

— 1010 w V ring, 5(CH)

— 971 w Y(NH)

— 934 w V ring, 6 ring

860 vw 872 s V ring, 5 ring

780 m 793 w Y(CH) — 724 w P (H2O)

600 w 650 s 8 ring — 591 w ©(HzO)

500 w 527 m Y(CO)

487 w 8 ring

458 w 8 ring

317w v(Cu-CI)

279 vs V(cu-pyrimidone) + v ( C U - C I )

189 w Lattice

171 m Lattice

155 m Lattice

148 w Lattice

126 w Lattice

106 m Lattice

vs-very strong ; s-strong ; ms-medium strong ; m-medium ; w-weak v:stretching

p: in- plane bending ; y : out- of- plane bending ; 8 : deformation ; co-wagging.

181

Fig. 8.1 ORTEP showing the atomic numbering scheme of cu(ll) pyrimidone complex.

IVI

Fig. 8.2 Packing diagram with n-n stacking between the aromatic rings and

the 0-H-O, H- bonding distance assembled in both P and M

sense of helical coordination polymeric adjacent chain.

182

Fig. 8.3 Packing of the complex in the unit cell.

Fig. 8.4 TGA Curve for compound 1 (inset DTA curve indicating two

endothermic curves)

183

40-3r

3000 2000 1500

Wavenumber (cftT')

1000 400

Fig. 8.5 FTIR spectrum of mono-aqua-dichloro Copper (II) pyrimidone complex.

500 -

100 — I — 150

1— 250 200 250 300

Wavenumber(cm"')

400

Fig. 8.6 Single crystal Raman spectrum of mono-aqua-dichloro Copper (II)

pyrimidone complex in the range 10-400 cm"

184

1 6 0 0

(0

*^ 'E 3

ji 1 2 0 0 ra (/> 1 0 0 0 -

c

c n E (0

3 0 0 -

6 0 0 -

Wl/ylUv^ v»Vv

4 0 0 1 —

6 0 0 8 0 0 1 0 0 0 1 2 0 0 1 4 0 0

W a v e n u m b e r ( c m " ' )

1 6 0 0 1 8 0 0

Fig. 8.7 Single crystal Raman spectrum of mono-aqua-dichloro Copper (II) pyrimidone complex in the range 400-1800 cm"

2800 2900 3000 3100 3200 3300 3400 3500

Wavenumber(cm"^)

Fig. 8.8 Single crystal Raman spectrum of mono-aqua-dichloro Copper (II) -1 pyrimidone complex in the range 2800-3500 cm .

185

T 1 1 ' 1 1 1 1 1 1 1 < 1 1 1 1 1 1 1 r-0 200 400 600 800 1000 1200 1400 1600 1800 2000 2200

Wavelength (nm)

Fig. 8.9 Optical transmission spectrum of mono-aqua-dichloro Copper (II)

pyrimidone complex.

186