Vibrational Spectroscopy: A tool for characterization of nucleic acid constituents: Cytosine and...

Vibrational Spectroscopy: A tool for characterization of nucleic acid constituents: Cytosine and Uracil 33

Asian Journal of Physics Vol. 24, No 1 (2015) 33-59

Vibrational Spectroscopy: A tool for characterization of nucleic acid constituents: Cytosine and Uracil

M A Palafox1, S K Rathor2, Rachna Rastogi2, Daisy Bhat3, V Bena Jothy4 and V K Rastogi2,3

1Nofima AS - the Norwegian Institute of Food, Fisheries and Aquaculture Research,Osloveien 1, 1430 Ås, Norway

2Indian Spectroscopy Society, KC-68/1, Old Kavinagar, Ghaziabad-201 002, India3R D Foundation Group of Institutions, NH-58, Kadrabad (Modinagar), Ghaziabad-201 204, India

4Department of Physics and Research Centre, Women’s Christian College, Nagercoil-629 001, IndiaDedicated to Prof G D Baruah

Vibrational spectroscopy is one of the most powerful methods for the characterisation of nucleic acid constituents and their spectroscopic studies may help to throw light on their role in biological systems. The main advantage of vibrational spectroscopy in the characterisation of molecules is its applicability in all physical forms, i .e. solids, liquids and gaseous states. The motivation for predicting theoretically the vibrational spectra is to make vibrational spectroscopy a more practical tool. In the present work, the vibrational spectroscopy with the help of DFT calculations was used for the characterization of the nucleic acid constitutents: cytosine (Cy) and uracil (U). Here, the molecular structure of Cy and U are analyzed from the data available in the bibliography as determined theoretically by quantum chemical methods and experimentally by x-ray diffraction, whereas their IR and Raman spectra were analyzed with the support of ab initio (HF, MP2) and DFT (B3LYP, PBE, B-P, CCSD, etc) calculations using several basis sets. In addition, the 30 ring normal modes of uracil and cytosine molecules were characterized and numbered for their use as notations in the spectra of their derivatives. © Anita Publications. All rights reserved.Keywords: Cytosine,Uracil, Vibrational wavenumbers, DFT, IR and Raman spectra

1 Introduction

Cellisthefirststepinthecreationoflife.Thefundamentalstructuralunitsofacellarethenucleicacids, the proteins and the phosphates. All the evidences indicate that the nucleic acids are the molecules that exert primary control over the basic life processes in all organisms. The nucleic acids consists of two types of nitrogen bases: pyrimidines and purines. Though pyrimidine does not exist in nature but pyrimidines are considered to be important because they are the integral part of the genetic material, viz DNA and RNA as nucleotides and nucleosides. The important pyrimidine bases found in the nucleic acid comprise cytosine, uracil and thymine. Infrared spectroscopy in conjunction with Raman spectroscopy has undergone a renaissance in recent years and moved away from the straight forward technique encountered early in a chemistry course [1]. Today biomolecules are the most fascinating molecules. The largest and most fascinating molecules, found in living organisms today are the nucleic acid molecules. Cytosine (in short Cy, Fig 1a), also named as 4-amino-2(1H)-pyrimidinone or 4-amino-2-hydroxypyrimidine, is a pyrimidine base and a constituent of nucleotides and as such one member of the base pair guanine-cytosine. Uracil (in short U, Fig 1b) also named as 2,4-dihydroxypyrimidine, 2,4(1H,3H)-pyrimidinedione, 2,4-pyrimidinediol, 2,4-dioxopyrimidine, 2,4-pyrimidinedione, is also a pyrimidine base and a constituent of nucleotides and as such one member of the base pair AU. They belong to a group of the most important pyrimidines that play a fundamental role in the structure and function of enzymes and drugs. The importance of Cy and U and their derivatives has been indicated actually by the considerable number of publications appeared in the bibliography. The motivation for predicting theoretically the vibrational spectra is to make vibrational spectroscopy a more practical tool [2]. From a practical point of view, the main disadvantage of vibrational spectroscopy is the lack of a direct spectra-structure relation.Thismakes it imposible or difficult to determinate the

Corresponding author :e-mail: [email protected]; (M Alcolea Palafox); [email protected] (V K Rastogi)

34 M Alcolea Palafox, Rachna Rastogi, S K Rathor, Daisy Bhat, V Bena Jothy and V K Rastogi

structure of a molecule from its vibrational spectrum, however, the vibrational spectroscopy has a number of advantages over other spectroscopies, such as NMR. Most of these relate to the inherently greater sensitivity of vibrational spectroscopy, which makes it possible to detect very small amounts. Further advantages are the wider scope of vibrational spectroscopy, e.g. its applicability to solids, liquids and gases, as well as to adsorbed layers, etc. Instrument cost of IR spectroscopy also generally lower than for other spectroscopies. It is thus clear that main advantages of vibrational spectroscopy could be increased if a method could be found to predict vibrational spectra reliably. Such a method could be used to calculate the expected spectra of proposed structures.Comparisonwith the observed spectrawould confirm the identity of a product,even that of a completely new molecule. DFT methods are the most adequate for this purpose, in special B3LYP.

(a) (b)

Fig 1. Structures of (a) Cytosine and (b) uracil with the label of their atoms.

In general, the computation of the vibrational spectrum of a polyatomic molecule of even modest size is lengthy. The more accurate quatum chemical methods are still too expensive and cumbersome to apply as a routine research. Thus, one may be forced to work at small level, and consequently, one must expect with a large over estimation of the calculated vibrational frequencies. This overestimation can be remarkably reduced with the use of transferable empirical parameters for the calculated frequencies [2]. The scale factor is therefore designed to correct the calculated harmonic frequencies to be compared with the anharmonic frequencies found by experiment. The present manuscript shows the use of this scaling in the vibrational frequencies of Cy and U molecules, which can permit an accurate assignment of them. The parameters collected here are the most accurate calculated today for these compounds.

2 Tautomerism in nucleic acid bases

Nucleic acid bases are constituents of DNA and RNA and play important role in the genetic code transformation. Although for this process they occur as one predominant isomer, other minor tautomeric forms also exist. In the famous 1953 publication [3,55], Watson and Crick stated the importance of tautomeric forms of pyrimidine and purine nucleic acid bases with respect to the three-dimensional stacking in DNA. Further studies [4,56] have shown that the tautomeric equilibrium strongly depends on the chemical environment and might differ from crystalline state, aqueous or other solution and gas phase. Tautomerism in nucleic acid bases is believed to have a role in mutagenesis of DNA [5,57]. The process is intimately connected with the energetics of the chemical bonds. Generally, the keto form of Cyexists as themain form in the double helix.The formationof specificGCWatson-CrickH-bonds is


responsible for the maintenance of the genetic code. If Cy is replaced by another type of base, it may lead to the introduction of a wrong genetic code. In fact, it has been known for a long time that Cy may also exist in other noncanonical tautomeric forms. Some of the tautomeric forms may cause the base mispairing, which has been proven to be one of the origins of gene mutation [5-7]. The various tautomeric forms of Cy differ from each other by the position of the proton, which may be bound to either ring nitrogen atoms or oxygen atoms. There are at least 14 tautomers of Cy that have beenidentifiedbyab initio calculations [8,9], most of which have not been experimentally observed. These tautomers are grouped into four main types, namely the amino-keto, amino-enol, imino-keto and imino-enol forms. When the amino group transfers a hydrogen to the neighbouring ring nitrogen the imino tautomer is formed. However, experimental studies are not in complete agreement, some authors indicate the existence of two tautomers [10-12] while others have observed three [4,13]. It is not entirely clear whether these differences arise from the methods used to prepare the samples or if the effects of the local environment (vacuum,matrix, solid, solution, etc.) significantly change the tautomerdistributions.Of all thepossiblecombinations, the six Cy tautomers of Scheme 1 are the most stable, important and studied tautomers.

C1

Scheme 1. Cytosine tautomers with standard numbering and adopted nomenclature: Nonaromatic 2-oxo form (C1), aromatic 2-hydroxy trans form (C2a), aromatic 2-hydroxy cis form (C2b), non-aromatic 4-imino cis form (C3a), non-aromatic 4-imino trans form (C3b), and non-aromatic amino-oxo form (C4).

The uracil molecule has also several tautomeric forms. The most stable ones are collected in Scheme 2. In contrast to the enol form C2b found in Cy, the keto form U1 of uracil is the most stable one, in the isolated state and as well in solution.


Scheme 2. Uracil tautomers with standard numbering and adopted nomenclature.

3 Theoretical Methods

The molecular structure of Cy and U are analyzed from the data available in the bibliography determined theoretically by quantum chemical methods and experimentally by x-ray diffraction. The values are collected in the Tables 1-3. Among the quantum chemical methods, Density Functional (DFT) [14] Methods result concretely with those obtained by B3LYP, were selected as more appropriate. DFT methods because they provide a very good overall description of medium-size molecules. Moreover, for the wavenumber calculations [2,15] they appear more accurate than HF and MP2 [16] methods, and at lower computational cost. Among the DFT methods, the Becke’s three-parameter exchange functional (B3) [17] in combination with the correlation functional of Lee, Yang and Parr (LYP) [18], i.e. B3LYP, appears as the best and more used. The results obtained with several basis set differing in size and contraction are shown in the different Tables of the manuscript. The 6-311++G(3df,pd) basis sets represents the most accurate for geometrical parameters, but it is prohibited in computational memory required for wavenumber calculations. The 6-31G** and 6-311+G(2d,p) basis are optimum for this purpose. All the results were determined with the GAUSSIAN 09 [19] program package. In Fig 1 is plotted the molecules of Cy and U with the labeling of their atoms. The optimized bond lengths and angles obtained with HF and MP2 ab initio methods, and different DFT methods are shown in Tables 1-2. Table 1 corresponds to the values of the cytosine ring and Table 2 is related to the bond angles and torsional angles of the NH2 group in Cy. The results with different basis sets, and as well the available experimental values are included. The optimized ring structure of the molecule is planar, in agreement with that determined by X-ray.


Table 1. Equilibrium geometries of cytosine, bond lengths in Å and bond angles in degrees. The calculated values are with different ab initio and DFT methods and basis set.

ParametersHF MP2 B3LYP HCTH407 PBE B-P BH-LYP CCSDa

Exp.b6-31+G(2d,p)

6-311++G(2df,2pd)c cc-pVTZd 6-311++G

(3df,pd)6-311++G(2df,2pd)c

6-311++G(2df,2pd)c

6-311++G(2df,2pd)c

6-311++G(2df,2pd)c 6-31G**

Bond lengths

N1-C2C2-N3N3=C4C4-C5C5=C6N1-C6C2=OC4-N9Bond anglesN-C2-NC2-N=C4N3=C4-C5C4-C5=C6N1-C6=C5C2-N1-C6N3-C2=O

1.39741.36041.29491.44301.33871.34491.19381.3480

116.75120.35123.84

123.02124.89

1.4131.3731.313

1.2181.362

1.40831.36841.30791.42591.35031.34611.21471.3556

115.98120.21124.25116.04119.76123.75125.18

1.42261.36641.31421.43571.35281.34951.21391.3562

116.05120.66123.75116.16120.10123.28125.61

1.4261.3621.316

1.2161.353

1.4361.3721.326

1.2251.362

1.4311.3731.324

1.2261.370

1.4041.3561.300

1.2011.342

1.4131.3851.3131.4571.3541.3631.2201.368

116.3119.6124.6115.9119.8123.7124.8

1.3991.3561.3341.4261.3371.3641.2371.334

aFrom ref. [3].bFrom x-ray and neutron diffraction data summarised in a statistical survey of the Cambridge Structural Database [3,4]. cRef. [5].dRef. [6].

Table 2. Equilibrium geometries of the amino group of cytosine, bond angles and torsional angles in degrees.

Parameters HF MP2 B3LYP CCSDa

6-31G* 6-31+G(2d,p) 6-31G** DZP b DZ(2d) b cc-pVTZc 6-311++G

(3df,pd) 6-31G**

N3-C4-N9C4-N9-H12C4-N9-H13H12-N9-H13N3=C4-N9-H12C5-C4-N9-H13C2-N3=C4-N9Inversion Barrier(kcal/mol)b

115.6119.5117.411.7−20.8

−0.15

117.66117.01120.16118.0810.08

178.26

114.4118.4116.213.9−26.1

−0.32

114.2117.4115.615.0−24.9

−0.64

114.2117.6115.515.3−24.7

−0.34

117.10

11.7−18.9176.6

117.13117.69121.25118.896.96−10.91178.71

117.1114.7118.4116.213.7−25.4176.9

aFrom ref. [20]. bRef. [21].cRef. [23].

Table 3 lists the optimised bond lengths and bond angles in uracil molecule (U), for simplicity only at two levels of computation. The crystal structure of uracil belongs to the space group of C2h-P21/a and includes four molecules in a unit-cell [54]. The molecues are arranged in a H-bonded layer, in which one oxygen atom forms two H-bonds with nitrogen atoms in the neighbouring molecules. An schematic representation of the dimer form of this unit-cell is shown in Fig 2.


Fig 2. Schematic representation of the dimer found in the crystal structure of uracil as determined in ref. [54].

Table 3. Geometrical parameters optimized, bond lengths in Å and bond angles in degrees optimized in uracil molecule at two levels of computation.

Parameters B3LYP/6-311++G(3df,pd) MP2/6-31G(d,p)Bond lengthsN1-C2C2-N3N3-C4C4-C5C5=C6N1-C6N1-HC2=OC4=OC-XBond anglesN-C2-NC-N3-CN-C4-CC-C5=CC2-N1-H7N3-C2=OC4-N3-H9N3-C4=OC4-C5-XN1-C6=C5C5=C6-X

1.38991.37901.40841.45461.34381.37001.00811.21011.2127

-

113.04127.99113.61119.81115.15124.27116.27120.20118.27122.02122.17

1.38961.38451.40801.45681.35131.37581.00781.22361.2270

-

112.41128.86113.16119.94114.91124.41115.88120.56118.47121.76122.52

5 Vibrational wavenumbers

5.1 Characterisation of the ring modes

The ring modes characterized at the B3LYP/6-311+G** level in Cy and U molecules, with their calculated wavenumbers, appear plotted in Figs 2 and 3, respectively. The atomic displacements for each computed wavenumber are presented as XYZ coordinates, in the standard orientation, which are plotted to identify each vibration.The normalmodes of uracil structure, numbered from 1 to 30, are brieflyanalyzed.


Fig 3. Characterization of the normal modes in cytosine molecule at B3LYP/6-311+G** DFT level with three water molecules (*strongly coupled with water vibrational modes)

It is interesting to observe that a few skeletal ring modes retain a certain resemblance to the pseudo normal modes of a hypothetical C6 ring and the skeletal modes of benzene, although the uracil ring has no symmetry within the molecular plane. A correlation between these modes has been reported [25].

5.2 Wavenumber calculation

Cytosine molecule: as one of the constituents of nucleic acids, it has been studied intensively by IR spectroscopy in the free monomeric state (in the gas phase [26] or in low temperature inert matrices [27-29] ) and in the crystalline phase at room [28,30-31] or at low temperatures [32]. The vibrational spectra show that different aggregate states contain different tautomeric forms [33]: the gas phase contains both the enol and the ketone forms, whereas in the crystalline state and polar solvents only the ketone form has been observed [29,34]. The shifts of the absorption bands observed in the experimental spectra is due to the different tautomeric forms of Cy that appear under particular experimental conditions. Theoretically vibrational spectrum of Cy has been predicted at different levels of approximation [28,29,35]. The simulated IR and Raman spectra at B3LYP/6-31G** level with scaled wavenumbers are shown in Figs 4 to 6, corresponding to the stretching region, the bending region and the far-infrared region (< 500 cm–1), respectively.


Fig 4. Characterization of the normal modes in uracil molecule at B3LYP/6-311+G** DFT level.

Fig 5. Simulated IR and Raman spectrum of citosine molecule at B3LYP/6-31G** level in the 3650-3000 cm–1 range.


Fig 6. Simulated IR and Raman spectrum of citosine at B3LYP/6-31G** level in the 1750-500 cm–1 range.

Fig. 7. Simulated IR and Raman spectrum of citosine at B3LYP/6-31G** level in the 500-150 cm–1 range.


Fig 8. Schematic representation of the crystal structure of cytosine as determined in ref. [36]. The molecules are tilted ∼27.5º from parallel to the plane of the page. Hydrogen bonds are formed by all three available protons and are indicated by dashed lines.

In crystals (Fig 7) with differently bound multiple NH- groups the bands due to the N-H stretching and out-of-plane bending N-H modes are usually broad and extensively overlapped [36]. However, at low temperature, the broadening originated from the interaction of both modes with thermally excited low frequency intermolecular deformational modes (librations) can be suppressed [36].On the other hand,in isotopically doped crystals, the vibrational coupling between neighboring H-bonds in the differently organized H-bonded chains is removed. Thus, in the low temperature spectra of isotopically doped crystals the spectral resolution is in general remarkably improved. Based on this fact, the FTIR spectra of both the pure and isotopically substituted ND polycrystalline Cy have been reported in the range 400-4000 cm–1 as a function of temperature (10-300 K) [36]. The vibrational bands computed with the HF and B3LYP theoretical methods and two different basis set are examined in Table 4.Thefirstcolumnreferstothenumbersassignedtothecalculatedvibrations,which are given in increasing order of wavenumbers. These normal modes of Cy structure, numbered in Fig 2,arebrieflyanalyzedinparagraphsbelow.Thesecondandthethirdcolumnlistthecalculatedwavenumbersat the HF/6-31G** and HF/6-31+G(2d,p) levels, respectively, with their absolute infrared intensities (fourth column)andtheirrelativevalues(fifthcolumn).TherelativeIRintensitieswereobtainedbynormalizingthe computed values to the intensity of the strongest line, no. 28. The calculated HF Raman intensities (sixth-seventh columns), the Raman depolarization ratios (eighth column) were also included. Columns 9th to 14th correspond to B3LYP calculations. Columns 11-13th only show the values with the 6-311+G(2d,p) basis set, due to the small difference with 6-31G**.


Tabl

e 4.

Com

paris

on o

f th

e ex

perim

enta

l wav

enum

bers

(ν,

cm

–1)

and

calc

ulat

ed h

arm

onic

val

ues

(ω, c

m–1

) at

the

HF

and

B3L

YP

leve

ls, t

oget

her

with

thei

r ab

solu

te (I

, km

/mol

) and

rela

tive

(A, %

) inf

rare

d in

tens

ities

, abs

olut

e (R

, Å4 /a

mu)

and

rela

tive

(S, %

) Ram

an s

catte

ring

activ

ities

, Ram

an d

epol

ariz

atio

n ra

tios

(D),

Forc

e co

nsta

nts

(f, m

Dyn

e/Å

), an

d ch

arac

teriz

atio

n ob

tain

ed in

the

norm

al ri

ng m

odes

of c

ytos

ine

mol

ecul

e.

No.

HF

B3L

YP

Infr

ared

wIR

Int.

Ram

Int.

Dw

IR In

t.f

Cha

ract

eriz

atio

naN

ebA

rb,c

Ard

6-31

+ G

**6-

31+

G(2

d,p)

IA

RS

6-31

+ G

**6-

311+

G

(2d,

p)I

A

196

152

10

0.3

00.

7513

413

42

00.

06(1

00%

) puc

kerin

g N

1

215

322

113

10

00.

6420

220

2.3

51

0.17

(100

%) p

ucke

ring

N3

321

829

126

729

2.2

20.

6915

625

7.4

231

310.

05(9

5%) γ

(NH

2) w

aggi

ng22

0 (4

7)23

6 (3

0)

439

139

23

00.

30

0.69

358

359.

23

00.

26(4

3%) δ(C=O

)+(42%

)δas

(NH

2) +

(15%

) δ,Γ

(rin

g)34

2 (2

)34

3 (5

)

543

343

031

31.

82

0.75

398

398.

921

30.

25(4

5%) γ

(N1-

C=C

) + (3

0%) γ

(rin

g)+

(25%

) τ(N

H2)

397

(6)

400

(4)

657

956

516

20.

30

0.66

527

520.

316

20.

2(8

0%) τ

(NH

2)51

1 (5

6)50

7 (2

2)50

7 (1

4)

757

958

08

12.

83

0.45

533

533.

52

00.

68(6

0%) δ(C=O

)+(25%

)δ,Γ

(rin

g) +

(15%

) δas

(NH

2)52

5 (3

2)52

0 (5

7)51

9 (3

2)

858

559

02

00.

40

0.27

545

547.

23

00.

8(8

0%) δ

(rin

g) m

ainl

y in

N1,

N3

+ (2

0%) τ

(NH

2)53

1 (1

7)53

5 (1

6)53

5 (5

)

962

562

54

04.

74

0.4

577

580.

73

01.

83(9

5%) δ(ring)mainlyinO8

571

(3)

568

(8)

574

(7)

1066

164

778

80.

20

0.68

624

618.

859

80.

27(7

0%) γ

(N1-

H) +

(25%

) γ(C

4-N

9)61

4 (2

7)61

3 (1

7)61

3 (1

5)

1179

379

538

40.

81

0.68

724

722.

838

50.

45(6

2%) γ

(C5-

H) +

(27%

) γ(r

ing)

+ (1

1%) τ

(NH

2)71

1 (3

)71

0 (3

)70

9 (3

)

1283

082

62

018

.817

0.03

763

765.

56

12.

02(7

5%) δ

,γ(r

ing)

+ (2

5%) δ

s(NH

2)71

7 (8

)71

7 (8

)

1385

685

828

30.

91

0.59

769

770.

47

11.

45(4

3%) γ

(C4-

C5)

+ (3

0%) γ

(C5-

H)+

(27%

) γ, δ

(rin

g)74

9 (5

)74

7 (4

)74

9 (5

)

1487

288

967

70.

40

0.72

773

789.

239

54.

17(6

5%) γ

(C-N

3=C

) mai

nly

in C

2 +

(35%

) γ(r

ing)

767

(3)

767

82)

767

(3)

1510

1210

143

02.

93

0.31

924

923.

54

11.

58(6

5%) ν

(rin

g) +

(35%

) δas

(NH

2)

1610

6910

681

02.

83

0.4

962

963.

81

00.

72(7

5%) γ

(C6-

H) +

(25%

) γ(C

5-H

)

1711

0911

020

03.

13

0.74

988

989.

61

02.

67(8

0%) ν

(rin

g) +

(20%

) δas

(NH

2)94

8 (0

)95

5 (1

)98

0 (3

)

1812

0512

1021

26.

46

0.22

1088

1094

.949

71.

46(5

0%) δ

as(N

H2)

+ (3

5%) δ(C=O

)+(15%

)δ(r

ing)

1085

(10)

1083

(12)

1082

(15)

1912

1712

2130

31.

51

0.73

1128

1126

.62

01.

14(5

0%) δ

(C5-

H)+

(30%

) δ(N

1-H

) +(2

0%) ν

(C=C

-N)

1103

(3)

1091

(6)

1090

(8)

2013

0913

0686

912

.311

0.28

1220

1213

.347

61.

27(5

0%) δ

(HC

6-N

H)+

(35%

) δ(C

5-H

)+(1

5%) ν

(N-C

6)11

98 (3

4)11

96 (2

9)11

93 (3

3)

2113

8813

7615

212

.311

0.1

1264

1251

.527

42.

89(4

8%) ν

(C2-

N3)

+22%

ν(C

-N9)

+17%

δ(N

H2)

+13%

δ(r

ing)

1237

(11)

1244

(5)

1223

(10)

44 M Alcolea Palafox, Rachna Rastogi, S K Rathor, Daisy Bhat, V Bena Jothy and V K Rastogi22

1472

1465

104

1117

.416

0.11

1359

1355

.561

82.

12(3

7%) δ

(C6-

H) +

(34%

) ν(C

4-N

9) +

(22%

) ν(r

ing)

1324

(17)

1320

(16)

1318

(28)

2315

7515

7216

818

4.3

40.

1114

4314

4186

123.

03(4

2%) δ

(N1-

H)+

(30%

) ν(C

-N3-

C) +

(22%

) ν(N

1-C

6)13

82 (9

)13

82 (1

7)13

76 (2

3)

2416

2616

2015

317

8.8

80.

2915

0814

99.9

167

233.

65(4

0%) ν

(C-N

9)+(

25%

) δ(C

6-H

)+(2

0%) δ

(rin

g)+(

15%

) δ(N

H2)

1441

(47)

1439

(51)

1438

(97)

2517

2317

1728

731

23.4

210.

3115

7015

62.2

153

216.

81(5

5%) ν

(C4-

C5)

+ (3

2%) ν

(rin

g) +

(13%

) δ(N

H2)

1540

(18)

1539

(21)

1559

(17)

2617

8617

8895

1010

.810

0.18

1637

1632

.612

917

2.06

(90%

) βs(N

H2)

1569

(18)

1570

(14)

1595

(25)

2718

4118

3374

180

15.6

140.

0916

9216

81.4

470

648.

22(5

0%) ν

(C=C

) + (3

0%) ν

(N3=

C4)

+ (1

2%) ν

(rin

g)16

25

(100

)16

22 (9

1)16

20

(100

)

2819

4319

2892

410

016

.215

0.26

1774

1758

739

100

16(8

0%) ν(C=O

)+(20%

)ν(r

ing)

1725

(58)

1718

(1

00)

1714

(56)

2933

8333

693

067

.461

0.53

3211

3191

.72

06.

55(7

5%) ν

(C6-

H) +

(25%

) ν(C

5-H

)

3034

0633

962

010

0.7

920.

232

3632

16.8

20

6.69

(75%

) ν(C

5-H

) + (2

5%) ν

(C6-

H)

3138

5138

3395

1010

9.6

100

0.11

3610

3590

.680

117.

94(9

8%) ν

s(NH

2)34

74 (3

3)34

71 (1

2)34

68 (7

)

3238

8538

8611

112

83.6

760.

2136

2936

16.1

7310

8.31

(98%

) ν(N

1-H

)35

75 (3

6)35

64 (1

8)

3339

9739

7064

743

390.

7237

5237

19.3

476

8.99

(100

%) ν

as(N

H2)

3618

(50)

3600

(18)

a Abb

revi

atio

ns: ν

, stre

tchi

ng; δ

, in-

plan

e be

ndin

g; γ

, out

-of-

plan

e be

ndin

g.

b Ref

. [34

]. c Ex

perim

enta

l wav

enum

bers

sel

ecte

d as

fund

amen

tal f

or th

e co

mpa

rison

with

the

theo

retic

al v

alue

s. d R

ef, [

27].


The characterization established by B3LYP for each calculated wavenumber is very close to that calculated with HF, which was omitted in the Table 4. The % of contribution of the different modes to a computed wavenumber is shown in parentheses. Contributions lower than 10% were not considered. Slight differences in the % of contribution of the different modes appear by HF. The 15-17th columns collect the experimental wavenumbers reported in Neon [29] and Argon [27,29] matrix. Due to our calculated wavenumbers refer to an isolated molecule, they can be compared satisfactory with the experimental Ar matrix data. The most detailed study of the Ar matrix data corresponds to Nowak et al [29]. Thus, their experimental values were selected for comments. In matrix isolation infrared studies, both C1 and C2 tautomers have been detected, with likely a small amount of C3 [28].

Fig 9. IR spectrum of uracil (a) in KBr pellet., (b) in nujol mull.

Because the accuracy in the wavenumber calculation with the B3LYP method is much higher than with HF [2], in the discussion below of the results we had used mainly the B3LYP/6-311+G(2d,p). Although wavenumber calculations on Cy have been reported with other DFT methods [23, 27] the values shown in the columns of Table 4 represent the most accurate today.

(b)

(a)


Fig. 10. Simulated IR spectrum of uracil at two DFT levels in the 3550-3350 cm–1 range.

Fig. 11. Simulated IR spectrum of uracil at two DFT levels in the 2000-50 cm–1 range.

Fig. 12. Simulated Raman spectrum of uracil at two DFT levels in the 3550-3050 cm–1 range.


Tabl

e 5.

Com

paris

on o

f th

e ex

perim

enta

l wav

enum

bers

(ν,

cm

–1)

and

calc

ulat

ed h

arm

onic

val

ues

(ω, c

m–1

) w

ith th

e 6-

31G

** b

asis

set

, tog

ethe

r w

ith th

eir

rela

tive

(A, %

) inf

rare

d in

tens

ities

, rel

ativ

e R

aman

sca

tterin

g ac

tiviti

es (S

, %),

forc

e co

nsta

nts

(f, m

Dyn

e/Å

), an

d ch

arac

teriz

atio

n ob

tain

ed in

the

norm

al ri

ng

mod

es o

f ura

cil m

olec

ule

with

som

e of

the

met

hods

use

d.

No.

Cha

ract

eriz

atio

naM

P2c

B3P

86B

3PW

91B

3LY

PB

3LY

PeIn

frar

edb

Ram

an

ww

ww

wδ

AF

wS

Arm

atrix

fga

sgga

shso

lidso

lid+H

2Oso

lu-

tione

1pu

cker

ing

N3

139

151

151

150

147

00.

1215

40

2pu

cker

ing

N1

161

171

171

170

165

00.

117

10

185

w18

5 w

3δ)

OC

NC

O(

383

385

385

385

387

41.

0738

41

391

m37

7 m

374

vw

40

1

4γ)

21H

-C=C

(37

939

739

639

639

54

0.26

405

141

1 m

411

m39

5 w

426

426

5δ)

γνir

(51

851

951

851

952

34

1.26

519

251

6.5

m52

7 m

512

w52

6.6

526.

6

6δ+

)γνi

r( δ

)O=C

(54

154

354

254

154

31

1.09

539

453

6.4

m

53

453

453

6

7δ s

a+

)γνi

r( δ

)O=C

(56

056

055

955

854

71

0.2

556

255

9 w

588

w

552.

555

4.3

553

8γ)

H-1

N(

566

571

570

563

560

81.

2458

00

551.

2 m

556

m54

5 w

574.

657

4.6

573

9γ)

H-3

N(

698

693

692

687

677

140.

3169

91

662.

1 s

633

m65

9.5

w

10γ+

)O=4

C( γ

)H-5

C(

782

732

731

729

728

20.

6372

70

718

w

717.

4 vw

11γ)

O=2

C(

722

760

759

752

765

102.

7376

30

76

9 s

756.

5 w

12ν)

γνir

(73

878

177

977

276

90

2.92

769

2375

9.2

sh?

786.

978

6.9

782

13γ+

)H-5

C( γ

)O=4

C(

799

814

814

813

819

100.

9782

10

804

s81

0 s

802

w

14ν+

)C-C

( δ)H

-N(

990

975

970

965

962

11.

4396

23

958.

3 w

946

vw95

2 w

15γ)

H-6

C(

930

971

973

970

972

00.

7297

02

963

w97

4 w

972

sh98

2.3,

98

998

2.3,

993

966

16δ)

CC

N(

999

994

993

990

994

13.

4398

81

982

w99

9 w

?99

0 sh

1005

.110

06.8

1001

17ν+

)γνi

r( δ

)H-5

C(

1113

1098

1097

1091

1086

11.

4210

856

1073

w10

89 s?

1082

m10

97.3

1099

1095

18ν(

+)N

-Cδ)

H1N

,H6C

(12

3612

1012

0911

9811

9114

2.03

1195

011

84 v

s

1172

s

19δ+

)H-5

C( δ

)H-N

(12

7312

4012

3712

3112

271

1.22

1224

1512

17.4

w12

28 m

12

34.4

1232

.712

32

20δ+

)H-3

N( δ

)H-C

(14

1313

8813

8713

8213

823

2.28

1378

1313

59.3

vw

1360

m13

56 sh

1393

.613

93.6

48 M Alcolea Palafox, Rachna Rastogi, S K Rathor, Daisy Bhat, V Bena Jothy and V K Rastogi21

ν+ )N

-C( δ

)H-3

N(

1436

1417

1415

1407

1406

202.

9514

012

1388

.7 v

s13

80 s

1387

s14

16.9

1416

.913

87

22δ+

)H-6

C( δ

)H-N

(14

4914

2814

2614

2214

233

2.08

1411

113

99.6

vs

1396

ms

1400

s14

58.4

1457

.5

23δ+

)H-1

N( ν

)C-1

N(

1536

1520

1518

1506

1498

183.

4114

9710

1472

ms

1480

s14

61 s

1503

1503

24ν)

C=C

(17

1217

0417

0116

9016

7012

8.51

1672

2416

44 m

1632

vs

1641

s16

43.2

1644

.616

31

25ν)

O=4

C(

1826

1830

1826

1808

1757

100

14.6

817

6055

1741

vs

1688

vs

26ν)

O=2

C(

1868

1868

1864

1845

1791

9215

.17

1791

2417

57.5

vs

1734

vs

1756

vs

1712

.317

12.2

1708

27ν)

H-6

C(

3263

3234

3231

3221

3200

16.

5932

1290

30

76 w

30

79.7

3079

.730

79

28ν)

H-5

C(

3304

3281

3278

3264

3242

06.

7832

5110

030

84i

3101

w31

24 m

3095

.730

94.4

3094

29ν)

H-3

N(

3612

3643

3642

3620

3592

118.

1935

8868

3434

.5 s

3427

w34

36 s

30ν)

H-1

N(

3656

3682

3681

3658

3636

178.

436

3289

3484

.3 s

3450

w34

84 s

a Abb

revi

atio

ns: ν

, stre

tchi

ng; δ

, in-

plan

e be

ndin

g; γ

, out

-of-

plan

e be

ndin

g.

b Not

atio

n: s

h, s

houl

der;

vs, v

ery

stro

ng; s

, stro

ng; m

, med

ium

; w, w

eak;

vw,

ver

y w

eak.

c W

ith th

e 6-

31G

* ba

sis

set.

d With

the

6-31

1+G

(2d,

p) b

asis

set

.e W

ith th

e au

g-cc

-pV

DZ

basi

s se

t.f R

efs.

[39-

41].

g Ref

s. [4

0,41

].h R

ef. [

42].

i Ram

an, r

ef. [

40].


Uracil molecule: The wavenumbers and intensities of U, calculated at different levels, is examined inTable5.Thefirstcolumnreferstothenumbersassignedtothecalculatedvibrationsplottedinthecentrumof the rings in Fig. 3, and are given in increasing order of wavenumbers [15,38]. For simplicity, in the second column the assignments include only the contributions of predominant modes. The columns with relative intensities were obtained by dividing the computed values by the intensity of the strongest line. The 12-14th columns collect the experimental wavenumbers reported in Argon matrix [39-41] and in gas phase [40,42]. Although wavenumber calculations on uracil have been reported with HF [43], MP2 [44], B3LYP [45], and other DFT methods [46], the values shown in the columns 3rd-12th of Table 3 represents the most accurate today [15,38]. The experimental IR spectrum of uracil in KBr pellets and in Nujol mull is shown in Fig. 8, while simulated IR and Raman spectra at two DFT levels with scaled wavenumbers are shown in Figs. 9 to 12. The infrared spectrum corresponding to the strechingand bending regionare shown in Fig. 9 and 10, respectively, while the simulated Raman spectra are plotted in Figs. 11 and 12, stretching and bending regions, respectively. In general, good accordance is found of our simulated spectra with the experimental ones.

Fig.13. SimulatedRaman spectrum of uracil molecule at two DFT levels in the 2000-50 cm–1 range.

Unfortunately few studies undertake the gas-phase vibrational spectrum of U: the early work in the 70’s by Nowak et al [47], studying the NH and C-H stretching region, and the most complete work today was reported by Colarussoet al [42]. We select this one [42] for comments, since the assignments given there correspond most closely to our own. The comparison of the theoretical values was also performed on the gas phase data [40,41], and in few cases from spectra in argon matrices [39,45,48].

6 Scaling

To improve the computed wavenumbers, two procedures of scaling were used [2,15,38]. In Table 6 appears the results obtained in Cy. (a)Thefirstprocedureusesasingleoverallscalefactorforthecalculatedwavenumbers,νexp./ωcalc. It is the easiest and thus it is the procedure generally used in the bibliography to scale the wavenumbers. To correct the overestimation of the calculated wavenumbers, several authors have reported scale factors for different levels. The most complete set of values have been determined by Scott and Radom [49], with the particularity of use two scale factors, one for the high and medium-wavenumber vibrations, and the another for the low-wavenumbers. Thus with these scale factors were obtained in Cy the scaled wavenumbers of the columns (a) of Table 6.

50 M Alcolea Palafox, Rachna Rastogi, S K Rathor, Daisy Bhat, V Bena Jothy and V K RastogiTa

ble

6. S

cale

d w

aven

umbe

rs w

ith d

iffer

ent

proc

edur

es a

nd v

alue

s of

the

abs

olut

e er

ror

(ωca

l. – νe

xp. )

in c

m–1

, obt

aine

d in

the

cal

cula

ted

and

scal

ed

wav

enum

bers

of c

ytos

ine.

No.

Scal

ed w

aven

umbe

rsA

bsol

ute

erro

r

HF

B3L

YP

Cal

cula

ted

wav

enum

ber

Scal

ed w

ith a

n ov

eral

l fac

tor

Scal

ed w

ith a

n eq

uatio

n

(a)

(b)

(c )

(a)

(b)

(c )

HFd

HFe

B3L

YPd

B3L

YPe

HFd

B3L

YPd

HFd

HFe

B3L

YPd

B3L

YPe

187

8212

313

414

413

8

213

913

318

615

616

520

2

319

819

124

920

220

924

5-1

855

-34

12-3

8-3

4-4

513

-27

9

435

534

634

135

835

935

148

4915

1512

153

-216

8

539

438

437

539

939

739

333

30-2

2-6

-1-1

6-2

5-3

-7

652

651

549

752

852

051

072

5820

1619

218

-10

133

752

651

551

153

452

651

959

6013

136

14-5

-96

-1

853

252

052

054

653

753

250

5510

11-3

11-1

5-1

52

-3

956

855

655

257

856

856

457

579

110

10-1

2-1

60

-4

1060

158

857

162

561

360

848

3411

12-1

212

-25

-42

0-5

1171

370

770

569

670

870

883

8514

193

-14

-3-4

-2-2

1274

674

073

473

474

674

611

310

946

5129

1723

1729

29

1377

076

376

373

975

175

310

911

122

2823

-816

164

6

1478

477

879

174

375

576

610

512

26

2217

-24

1124

-12

-1

1591

090

390

488

890

090

0

1696

195

495

392

593

693

3

1799

799

098

395

096

195

815

414

733

3342

-535

286

3

1810

8410

7610

8110

4610

5610

6312

212

75

141

-37

-7-2

-27

-20

1910

9410

8710

9110

8410

9510

9312

613

037

373

-7-4

04

2

2011

7711

6911

6811

7311

8311

8211

311

024

25-1

9-2

3-2

7-2

8-1

3-1

4

2112

4812

4012

3112

1512

2512

2114

413

220

174

-29

-4-1

3-1

9-2

3

2213

2413

1613

1213

0713

1613

1315

214

539

374

-13

-4-8

-4-7

2314

1614

0814

0913

8713

9613

9819

319

061

6334

526

2714

16


2414

6214

5414

5214

5014

5814

5718

718

169

6723

1115

1319

18

2515

4915

4115

4015

0915

1715

1618

417

831

2910

-30

21

-22

-23

2616

0615

9716

0415

7415

8115

8421

621

867

6836

427

3411

14

2716

5516

4616

4516

2716

3416

3121

921

170

6533

524

2312

9

2817

4717

3817

3117

0617

1217

0822

521

056

4929

-12

2013

-6-1

0

2930

4230

2930

3630

8730

8630

90

3030

6330

4930

6031

1131

1031

16

3134

6334

4834

5634

7134

6734

7338

036

213

912

9-8

0-2

3-1

5-4

2

3234

9334

7935

0434

8934

8634

99

3335

9435

7935

8036

0736

0336

0339

737

015

213

5-6

7-2

1-2

03

3

Rm

sf16

7.2

161.

353

.549

20.8

17.2

19.4

19.2

13.5

12

(a) W

ith th

e 6-

31+G

** b

asis

set

. Wav

enum

bers

sca

led

with

the

scal

e fa

ctor

of 0

.908

9 fo

r HF

(1.0

013

for B

3LY

P) fo

r cal

cula

ted

wav

enum

bers

low

er th

an 8

00

cm-1

, and

the

scal

e fa

ctor

of 0

.899

2 fo

r HF

(0.9

614

for B

3LY

P) fo

r hig

her w

aven

umbe

rs [4

9].

(b) W

ith th

e 6-

31+G

** b

asis

set

and

with

the

corr

espo

ndin

g sc

ale

equa

tions

of T

able

6.

(c) W

ith th

e 6-

31+G

(2d,

p) b

asis

set

and

with

the

corr

espo

ndin

g sc

ale

equa

tions

of T

able

6.

(d) W

ith th

e 6-

31+G

** b

asis

set

. (e

) With

the

6-31

+G(2

d,p)

bas

is s

et.

(f)R

ms,definedas(∑∆(ω

cal.

- νex

p.)2 /

n)1/

2 , whe

re th

e su

m is

ove

r all

the

mod

es, n

, and

νex

p. is

from

the

colu

mn

16th

of T

able

3


(b) A remarkable improvement in the accuracy of the scaled wavenumbers is obtained if a linear relationship is established between the calculated and experimental wavenumbers. This procedure called scaling equation,usesascalingequationtocorrectthecomputedwavenumbersofamoleculeataspecificleveloftheory.This procedure, developed by one of the authors, represents a compromise between accuracy and simplicity, and thus only the results obtained with this procedure are the enough accurate for the stadard today. Table 7 collets the scaling equations obtained in the ring modes of Cy molecule and at different levels of computation. The results obtained are shown in the columns (b) and (c) of Table 6. The scaling equations have good transferability for their Cy derivatives, which permits an accurate assignment of the experimental values.

Table 7. Linear scaling equations νscaled= a + b · ωcalculated obtained in cytosine and uracil molecules.

Methods a b correlationcoeffient,r

Cytosine moleculeHF/6-31+G**HF/6-31+G(2d,p)B3LYP/6-31+G**B3LYP/6-31+G(2d,p)B3LYP/6-311+G(2d,p)

Uracil moleculeHF/6-31G**HF/6-31++G**MP2/6-31G*BP86/6-31G**BLYP/6-31G**B3P86/6-31G**B3LYP/6-31G*B3LYP/6-31G**B3LYP/6-311+G(2d,p)B3LYP/6-311++G(3df,pd)B3LYP/dgdzvpB3PW91/6-31G*B3PW91/6-31G**

–4.1–14.316.36.24.8

5.710.534.546.046.434.130.834.630.831.939.230.134.9

0.89650.90530.95600.96310.9671

0.89280.89380.93720.96780.97180.93890.94680.94470.95380.95120.94720.94210.9393

0.99970.99970.99990.99990.9999

0.99970.99980.99960.99980.99980.99990.99990.99990.99990.99990.99990.99990.9999

Table 8 shows the results obtained in U molecule with the corresponding scaling equations of Table 7. These scaling equations were obtained in the ring modes of uracil molecule [38]. For experimental wavenumbers, the values reported by gas phase were selected as more appropriate In the lack of these data, the values obtained by Ar-matrix, Raman spectroscopy, and Infrared spectroscopy (IR) were used. These scaling equations also show a good transferability for their uracil derivatives.

6.1 Errors obtained with the scaling

For a better comparison of the accuracy of the different scaling procedures and the two theoretical methods used, in Table 6 is shown the absolute error obtained in the wavenumbers of Cy molecule. It also helps in the assignment and analysis of the experimental fundamental modes. To calculate the errors were selected the experimental values of the 16th column of Table 4. In the last row is determined the root-mean square (rms) error of each case. The errors obtained in the predicted wavenumbers were very small with the scaling equation, the mean deviation was 10 cm–1 (1%). The value of these rms errors are very close to other compounds studied by us [50-52].


Remarkably differences also appear in Table 6 between the calculated wavenumbers by HF and B3LYP. Due to the results by B3LYP are more in accordance to the experimental data, therefore, they were taken as reference. The large rms error in the calculated wavenumbers is remarkably reduced with the scaling, especially by HF. The large error obtained after scaling by HF, mainly in the vibrations nos. 17, 23 and 26 leads to arms error by HF higher than by B3LYP.

Table 8. Absolute error (ωcal.- νexp) in cm–1 obtained in the calculated wavenumbers, scaled values and the error obtained with them in the molecule of uracil.

No. exp.freq.

error scaled error

HFa MP2b B3P86a B3LYPa B3LYPc B3PW91a B3LYPc,d

123456789

10111213141516171819

20 21222324252627282930

185391395512

536.4559545

659.5

717.4756.5759.2

802952972990

10731172

1217.4

13561387140014611641174117563076312434363484

–635344957504370

8610547

10310113886

102134160

174167157186206254256318305427418

–24–8

–16651

2138

65–35–44–338

–429

406486

574949757185

112187180176172

–14–62771

2633

153

–11223–14

253853

323028596389

112158157207198

–15–6175

–11827

12–5

–101113–20

182644

26202245496789

145140184174

–20–40

117

–121517

118

–13171004

131940

26192337291635

124118156152

–14–61660

2532

142

–3121813

243750

312826576085

108155154206197

171.1188.2400.0407.6529.7548.8552.6565.0676.6

725.2760.5764.3812.0948.4957.9978.9

1066.71166.81201.2

1349.01371.91388.11459.61623.71706.71739.13083.03123.13456.93498.9

–39

131813–62018

845

10–4

–14–11–6–5

–16

–7–15–12–1

–17–34–17

7–12115

rms 184 82 77 66 54 75 70 13.7aWith the 6–31G** basis set. bWith the 6-31G* basis set. cWith the 6-311+G(2d,p) basis set. dWith the scaling eqns. hRms,definedas (∑ (ωcal. - νexp.)2 / n)1/2, where the sum is over all the modes, n, and νexp. is from the second column.

DuetothedeficienciesbyHFinthecalculationofseveralmodesinthismoleculeofCy,theuseofascalingequationdoesnotrepresentasignificantimprovementinthewavenumbersovertheuseofan


overall scale factor procedure. However, by B3LYP is obtained a remarkable reduction of the error and thus the risk to a mislay. The best for this purpose is the 6-311+G(2d,p) basis set, together with the use of the scaling equation procedure, last column of Table 6. Larger basis set represents an excessive increase of the computational cost for a very slight improvement. The largest error in the last column corresponds to vibration no. 12, a ring bending. Large errors also appear in the vibrations nos. 21 and 25, corresponding to C-N and C-C stretchings, respectively. Table 8 shows the values of the absolute errors obtained in the calculated wavenumbers of uracil. ThefirstcolumnreferstothenumberofthemodesofFig. 4. The experimental values selected in the second column were those reported in gas phase by Colarussoet al [42], and several in Ar matrix. Remarkable differences are observed between the calculated and experimental wavenumbers, columns 3-8th. The bottom of the Table shows the root-mean square (rms) error obtained for the calculated wavenumbers with several of the methods used. The largest errors are marked in bold type. With DFT methods the wavenumbers are significantlyclosetotheexperimental,althoughtheresultsdonotadequatelyreproducealltheexperimentalpattern of wavenumbers. The use of scale procedures solves this problem. Table 8 collects all the errors otained in the calculated and scaled wavenumbers by the two procedures of scaling. Thus, it can be concluded that the scaling equation procedure leads to very low errors, and even lower thanusing theuniformscalingprocedure.WithB3LYPthewavenumbersaresignificantlyclose tothe experimental and much better than by HF.

Table 9. Errors obtained in the calculated and scaled wavenumbers of the uracil modes by the different procedures and methods.

Method

calculated wavenumbers scaled wavenumberswith an overall factor

scaled wavenumbers with the scaling equations

rmslargest error

rmslargest error

rmslargest error

positive negative positive negative positive negative HF/6-31G** HF/6-31++G** MP2/6-31G* BP86/6-31G**BLYP/6-31G** B3P86/6-31G** B3LYP/6-31G** B3LYP/6-311+G(2d,p)B3PW91/6-31G**

18417782353477665475

427 (29)418 (29)187 (27)86 (29)73 (29)

207 (29)184 (29)156 (29)206 (29)

6 (2)11 (2)

44 (12)44 (11)

49 (11,15)14 (2)15 (2)20 (2)14 (2)

23

3733342421

25

53(25,26)

53 (9)56 (29)54 (29)46 (29)44 (29)

50 (29)

37 (12)

95 (15)50 (11)54 (15)44 (15)40 (12)

41 (15)

22.616.725.418.119.615.013.813.714.9

46 (26)27 (19)50 (10)34 (9)34 (9)

32 (26)24 (9)

21 (29)30 (26)

57 (28)50 (28)66 (15)32 (21)36 (21)26 (15)23 (21)34 (25)26 (22)

7 Assignments for the vibrational modes

Cytosine molecule N1-H modes: The N1-H stretching (mode no. 32) appears clearly characterized as pure mode and with strong intensity, and it was scaled at 3499 cm–1 using the B3LYP/6-311+G(2d,p) level. The N1-H in-plane bending is more complicated. It appears mixed with other modes and in some cases with low IR intensity. Seven calculated vibrations have noticeable contribution of this mode. The highest contribution corresponds to the computed band at 1441 cm–1. The N1-H out-of-plane bend is predicted at 618.8 cm–1 as almost pure mode (70% of contribution), with medium IR intensity and null Raman activity, in agreement with the medium-strong intensity band observed in Ar matrix [29] at 613 cm–1. C-H modes: The stretching modes appear as pure modes and with almost null IR intensity in accordance with its no detection in the experimental spectra. The ν(C5-H) mode is coupled (75% of


contribution) with ν(C6-H) and vice verse. C-H in-plane bending modes appear mixed mainly with ν(N-C) modes. The band at 1320 cm-1 in Argon matrix [26] was assigned to δ(C6-H) in accordance to a scaled wavenumber between 1307-1324 cm–1. δ(C5-H) mode appears with very low IR intensity and thus it was assigned to the experimental band at 1091 cm–1 also with low IR intensity, and in good accordance with a scaled value between 1084-1095 cm–1. A high contribution of this mode was also determined in the computed band at 1213.3 cm–1. The C6-H out-of-plane bending mode appears as almost a pure mode (75% of contribution) at 963.8 cm–1, with null IR intensity, and thus it was not detected in the experimental Ar matrix spectra. Mode γ(C5-H) appears spread out in the computed bands at 963.8 (coupled with C6-H), 7704 and mainly at 722.8 cm-1 (62% of contribution). C=O modes: IntheUmoleculethestretchingregionisstronglyinfluencedbyFermiinteractionsand many bands appears in this region [38].InCythecalculatedC2=OstretchisthestrongestIRbandinaccordance with that observed in the Ar matrix spectra [29]. However, Radchenko et al [27] in the Ar matrix spectra pointed as the most intense the IR band at 1620 cm–1 corresponding to the ν(C=C) stretching, while the ν(C=O)bandat1714cm–1 has only strong IR intensity. The Ne matrix spectrum [29] shows similar result in contradiction with our calculations. The scaled wavenumber at ca. 1720 cm–1 is in accordance with the experimental ones at 1718 cm–1. TheC=Oin-planebendingappearsmixedwithδas(NH2) and δ(ring) modes. The main contribution was determined at 533.5 cm–1 and scaled at ca. 520 cm–1 in agreement with the experimental band detected at 520 cm–1. However, a remarkable disagreement appears in the intensity. Thus it was calculated with very weak IR intensity in contrast to the strong band observed experimentally. C=C and ring modes: The stretching C=C vibration appears with very strong IR intensity and strongly coupled with the ν(N3=C4) and ν(ring) modes, in accordance with that observed experimentally. The ring stretching appears spread out in several computed bands at 1758.0, 1681.4, 1562.2 and 1355.5 cm–1, but mainly at 989.6 and 923 cm–1. Ring deformations appear also spread out in several computed bands at 1499.9, 1251.5, 1094.9, 533.5 and 359.2 cm–1, but mainly at 765.5, 580.7 and 547.2 cm–1. These bands were accurately related to the Ar matrix ones. NH2 substituent: The antisymmetric νas and symmetric νs(NH2) stretching vibrations were computed at 3719.3 and 3590.6 cm–1, respectively, and as pure modes. They appear with medium IR intensity, but with a slightly higher value for the symmetric mode than for the antisymmetric ones. However, experimentally the symmetric mode has slightly lower IR intensity than the antisymmetric ones. In the Raman spectra mode νs was computed with the highest intensity of the spectra, while mode νas appears with strong intensity. The in-plane bending βs mode was also computed as a pure mode at 1632.6 cm–1 (scaled at 1584cm–1) and with strong intensity in accordance with the strong experimental band observed at 1570 cm–1. The antysymmetric mode appears strongly coupled with δ(C=O)andδ(ring) modes at 1094.9 cm–1. The torsional motion τ appears as almost pure mode (80% of contribution) at 520.3 cm–1 and with weak IR intensity, although experimentally was observed with strong intensity at 507 cm–1. However, the wagging γ mode was computed with strong intensity (31%) in perfect agreement with the experimental IR band at 236 cm–1 with an intensity of 30%.

Uracil Molecule:

N-H modes: The N-H stretching appear as pure modes and with strong intensity, and thus they were clearly characterized and assigned. The N-H in-plane bending are more complicated due to they appear mixed with other modes. Seven calculated vibrations have noticeable contribution of these modes. In some cases they also appear with very low IR intensity. The description of mode 22 is complex as can be seen in Fig. 4. Mainly, it was characterized as δ(C6-H)+ δ(N-H), with some contribution of ν(C-N), in agreement


with the assignment by Harsányiet al [40] and Colarussoet al [42]. Although mode 21 has some small contribution of δ(C6-H) and δ(C5-H) modes, it has been characterized as ν(C-N)+ δ(N3-H) in agreement with Harsányiet al [40], but in contrast to Colarussoet al [42] and Léset al [48]. Mode 20 is characterized as δ(N3-H) with a high contribution of δ(C6-H, C5-H), differing of the assignment reported by Harsányiet al [40] and Császáret al [53] as β(C-H).Significantcontributionofν(N3-C4) is not observed in the mode 19 as indicated by refs. [40,42,54], and it was characterized as δ(C5-H)+ δ(N-H). Due to its weak IR intensity, it has not been detected in gas phase [42], although Harsányiet al [40] reported a band with medium intensity at 1228 cm–1. Mode 18 was calculated with strong IR intensity and scaled at 1166.8 cm–1, column 9th of Table 7, which was related to the strong IR band [42] at 1172 cm–1, differing from the band detected and assigned to this mode at 1089 cm–1 [40]. The N-H out-of-plane bends are predicted as almost pure modes and with strong and medium intensity, N3-H and N1-H respectively, in agreement with the strong and medium bands observed in Ar matrix [39f] at 662.1 and 551.2 cm–1 and to that obtained by other calculations [46,53]. In gas phase the N1-H mode is clearly related to the band at [40] 556 cm–1 or at [42] 545 cm–1, in disagreement with Aamoucheet al [44], who related this band to the two calculated wavenumbers, corresponding to δ(C2=O)and γ(N1-H) modes. The very weak gas phase band [40] at 672 cm–1 or [42] at 692 cm–1 should be changed the assignment and related to the γ(N3-H) mode. C-H modes: The stretching modes appear as pure modes and with weak or almost null IR intensity in accordance with the experimental results. Mode ν(C5-H) was scaled at 3123.1 cm–1, Table 7, and related to the Raman band at 3084 cm–1 and to the IR band in gas phase [42] at 3124 cm–1. Similarly, mode ν(C6-H) is scaled at 3083 cm–1, in accordance with the experimental IR bands observed at 3076 cm–1 and 3080 cm–1 in Ar matrix [40] and KBr pellet [55], respectively. C-H in-plane bending modes appears mixed mainly with δ(N-H) modes. The band at 1228 cm–1 in gas phase [40] was related to the band at 1217.4 cm–1 in Argon matrix, instead [44] of to the band at 1184 cm–1, and it was assigned to δ(C5-H) instead of to ν(C-N). The C6-H out-of-plane bending mode appears as a pure mode with null IR intensity. However, this mode was detected in the gas phase at 974 cm–1, but assigned [40] simultaneously to the ∆(ring) and γ(C6-H) modes, instead of only to γ(C6-H). The assignment appears corrected in Table 4, due to the mode ∆(ring) should be related to the gas phase band at 999 cm–1. Several authors [42,44] also mislay the assignment of several C-H bands. C=O modes: the stretching region is strongly influencedbyFermi interactions, and thusmanybands appears in this region, althoughonly two fundamental bands are expected.The calculatedC2=OandC4=Ostretchesare the strongest IRbands, and theyarepredictedwith similar intensity.The scaledwavenumber of both modes is very close, at 1739.1 and 1706.7 cm–1,modesC2=OandC4=O,respectively,and in accordance with the gas phase results. TheC=Oout-of-planebendingappearsingeneralmixedwithγ(C-H) modes. The description of mode 13 asγ(C5-H)+ γ(C4=O)isinagreementwithColarussoet al [42] and other authors [45a,48,53]. The band reported in gas phase [42] at 717.4 cm–1, and in Argon matrix at 707.4 and 719 cm–1 by Ivanov et al [41] and Szczepaniaket al [45a],respectively,wererelatedtomode10,definedasγ(C4=O)+γ(C5-H). The C=Oin-planebendingsappearmixedinmodes6and7.Thebandcorrespondingtomode6wasobservedonly in Ar matrix at 536.4 cm–1. It has been computed at 527 cm–1 by Peticolas and Rush [43] from ab initio (HF+CI)/6-31G* calculus, and at 529 cm–1 by Estrinet al [46] from LDA (Local Density Aproximation)-DFT/6-31G**. C=C and ring modes: The stretching C=C vibrations appears as an almost pure mode and with medium IR intensity. The null IR intensity predicted for mode 12 is in accordance with the lack of bands in the gas phase IR spectra, although the shoulder in Ar matrix at 759.2 cm–1 has been assigned [41] to this mode in agreement with other authors [39f,48]. The strong Raman activity calculated for this mode is in


accordance with the very strong lines detected [44] at 786 and 789 cm–1. The wavenumber predicted for mode 17 corresponds to the IR band [42] at 1082 cm–1, in contrast to the assignment reported in ref. [40]. The characterization of this mode as ν(ring) involves a high contribution of the N1-C6 stretch in accordance to a recent assignment [45a] of the IR band at 1073 cm–1 in Ar matrix. The ring deformation, mode 7, is predicted with weak intensity and was related to the band in Ar matrix [41,48] at 559 cm–1 (588 cm–1 in gas phase [40] ). The out-of-plane bending of the ring, mode 4, has a strong contribution of the C=C-H moiety.

Resume ane Conclusions

(i) The 30 ring normal modes of uracil and cytosine molecules were characterized and numbered for their use as notations in the spectra of their derivatives. (ii) The vibrational spectra of cytosine and uracil nucleo basis were accurately simulated by DFT methods, compared with the experimental IR and Raman spectra, and assigned all their bands. (iii) Two scaling procedures are presented and used in the calculated spectra of cytosine, and uracil. The use of the accurate linear scaling equation procedure remarkably reduces the error in the calculated wavenumbers, and it is the best for this purpsose. Thus, the assignment of most of the fundamentals provided in this work is believed to be unambiguous. (iv) The linear scaling equations obtained for uracil and cytosine molecules at different levels of computation are shown in the present manuscript. They are recommended to be used in the calculated wavenumbers of uracil and cytosine derivatives.

Acknowledgements

The authors are thankful to Prof Shabbir Ahmad, and Dr Mohammad Jane Alam, Department of Physics,AligarhMuslimUniversity,Aligarhfortheirsuggestionsandfinallygoingthroughthemanuscript.Two of the authors (DB and VKR) are thankful to Sri Rakesh Mohan Garg, Chairman R D Foundation Group of Institutions, NH 58, Kadrabad, Modinagar for providing computer facility in the Institute.

References 1. Schmitt M, Popp J, Kiefer W, in Applications of Raman spectroscopy in life sciences and mineralogy, Anita

Publications, Ghaziabad, Delhi, India, 2002. 2. Alcolea Palafox A, Recent Res. Devel. in Physical Chem. Transworld Research Network: Trivandruw, India, 2(1998)

213. 3. Watson J D, Crick FHC, Nature, 171(1953)737. 4. Brown R D, Godfrey P D, McNaughton D, Pierlot A P, J Am Chem Soc, 111(1989)2308. 5. Topal M D, Fresco J R, Nature, 263(1976)285. 6. Holbrook S R, Cheong C, Kim S H, Nature, 353(1991)579. 7. Shi K, Wahl M, Sundaralingam M, Nucleic Acids Res, 27(1999)2196. 8. Estrin D A, Paglieri L, Corongiu G, J Phys Chem, 98(1994)5653. 9. ShishkinOV,GorbL,HobzaP,LeszczynskiJ,Int J Quantum Chem, 80(2000)1116. 10. Szczesniak M, Szczepaniak K, Kwiatkowski J S, Kubulat K, Person W B, J Am Chem Soc, 110(1988)8319. 11. Nowak M J, Lapinski L, Fulara J, Spectrochim Acta, 45A(1989)229. 12. Gould I R, Vincent MA, Hillier IH, Lapinski L, Nowak M, Spectrochim Acta, 48A(1992)811. 13. Dong F, Miller R E, Science, 298(2002)1227. 14. (a) Seminario J M, Politzer P (Eds.), Modern Density Functional Theory: a tool for Chemistry, vol. 2, Elsevier,

Amsterdam, 1995.


(b) March N H, Electron Density Theory of atoms and molecules. Acad. Press, London, 1991. (c) Parr R G, Yang W, Density Functional Theory of atoms and molecules,OxfordUniv.Press.,1989. 15. Palafox M Alcolea, Rastogi V K, Spectrochim. Acta, 58A(2002)411. 16. (a) Hehre W J, Radom L, Schleyer PvR, Pople J A, Ab initio Molecular Orbital Theory, Wiley & Sons, New york,

USA, 1986. (b) Lawley K P, Ab initio methods in Quantum Chemistry, Part. 1, John Wiley & Sons, Ltd., Chichester, UK,

1987. 17. Becke A D, J Chem Phys, 97(1992)9173; 98(1993)5648. 18. Lee C, Yang W, Parr R G, Phys Rev, B37(1988)785. 19. Gaussian 09, Revision D.01, Frisch M. J.; Trucks G W, Schlegel H B, Scuseria G E, Robb M A, Cheeseman J R,

Scalmani G, Barone V, Mennucci B, Petersson G A, Nakatsuji H, Caricato M, Li X, Hratchian H P, Izmaylov A F, Bloino J, Zheng G, Sonnenberg J L, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T,HondaY,KitaoO,NakaiH,VrevenT,MontgomeryJA (Jr),Peralta JE,OgliaroF,BearparkM,HeydJ J,Brothers E, Kudin K N, Staroverov V N, Kobayashi R, Normand J, Raghavachari K, Rendell A, Burant J C, Iyengar S S, Tomasi J, Cossi M, Rega N, Millam N J, Klene M, Knox J E, Cross J B, Bakken V, Adamo C, Jaramillo J, GompertsR,StratmannRE,YazyevO,AustinAJ,CammiR,PomelliC,OchterskiJW,MartinRL,MorokumaK, Zakrzewski V G, Voth G A, Salvador P, Dannenberg J J, Dapprich S, Daniels A D, Farkas Ö, Foresman J B, OrtizJV,CioslowskiJ,FoxDJ,Gaussian,Inc.,WallingfordCT,2009.

20. AlparoneA,MillefioriA,MillefioriS,Chem Phys, 312(2005)261. 21. ClowneyL,JainSC,SrinivasanAR,WestbrookJ,OlsonWK,BermanHM,J Am Chem Soc, 118(1996)509. 22. Piacenza M, Grimme S, J Comput Chem, 25(2004)83. 23. Fogarasi G, J Phys Chem A, 106(2002)1381. 24. Šponer J, Hobza P, Int J Quantum Chem, 57(1996)959. 25. Susi H, Ard J S, Spectrochim Acta, 27A(1971)1549. 26. Ferro D, Bencivenni L, Teghil R, Mastromarino R, Thermochim Acta, 42(1980)75. 27. Radchenko E D, Sheina G G, Smorygo N A, Blagoi Y P, J Mol Struct, 116(1984)387. 28. Szczesniak M, Szczepaniak K, Kwiatkowski J S, Kubulat K, Person W B, J Am Chem Soc, 110(1988)8319. 29. Nowak M J, Lapinski L, Fulara J, Spectrochim Acta, 45A(1989)229. 30. Susi H, Ard J S, Purcell J M, Spectrochim Acta, 29A(1973)725. 31. Florian J, Baumruk V, Leszczynski J, J Phys Chem, 100(1996)5578. 32. Aamouche A, Ghomi M, Grajar L, Baron M H, Romain F, Baumruk V, Stepanek J, Coulombeau C, Jobic H,

Berthier G, J Phys Chem A, 101(1997)10063. 33. Ten G N, Baranov V I, Opt & Spectrosc, 97(2004)195. 34. Radchenko E D, Plokhitnichenko A M, Ivanov A Yu, et al, Biofizika, 31(1986)373. 35. Gould I R, Vincent M A, Hillier I H, Lapinski L, Nowak M, Spectrochim Acta, 48A(1992)811. 36. Rozenberg M, Shoham G, Reva I, Fausto R, Spectrochim Acta, 60A(2004)463. 37. Pulay P, Saebo S, Malagoli M, Baker J, J Comput Chem, 26(2005)599. 38. Alcolea Palafox M, Iza N, Gil M, J Molec Struct,(Theochem), 585(2002)69. 39. (a) Szczepaniak K, Szczesniak M, Nowak M, Scott I, Person W B, Int J Quantum Chem; Quant Chem Symp, 18

(1984)547. (b) Szczesniak M, Nowak M J, Rostkowska H, Szczepaniak K, Person W B, Shugar D, J Am Chem Soc, 105

(1983)5969. (c) Chin S, Scott V, Szczepaniak K, Person W B, J Am Chem Soc, 106(1984)3415. (d) Maltese M, Passerini S, Nunziante-Cesaro S, Dobos S, Harsányi L, J Mol Struct, 116(1984)49.

(e) Radchenko E D, Plokhotnichenko A M, Sheina G G, Blagoi Y P, Biofizika, 28(1983)923. (f) Barnes A J, Stuckey M A, Gall L L, Spectrochim Acta, 40A(1984)419. 40. Harsányi L, Császár P, Császár A, Boggs J E, Int J Quantum Chem, 29(1986)799.


41. Ivanov A Y, Plokhotnichenko A M, Radchenko E D, Sheina G G, Blagoi Y P, J Mol Struct, 372 (1995)91. 42. Colarusso P, Zhang K, Guo B, Bernath P F, Chem Phys Letts, 269(1997)39. 43. Peticolas W L, Rush III Th, J Comp Chem, 16(1995)1261. 44. Aamouche A, Ghomi M, Coulombeau C, Jobic H, Grajcar L, Baron M H, Baumruk V, Turpin P Y, Henriet C,

Berthier G, J Phys Chem, 100(1996)5224. 45. (a) Szczepaniak K, Person W B, Leszczynski J, Kwiatkowski J S, Polish J Chem, 72(1998)402. (b) Chandra A K, Nguyen M T, Zeegers-Huyskens Th, J Phys Chem A, 102(1998)6010. 46. Estrin D A, Paglieri L, Corongiu G, J Phys Chem, 98(1994)5653. 47. Nowak M J, Szczepaniak K, Barski A, Shugar D, Z Naturforsch, 33C(1978)876. 48. Lés A, Adamowicz L, Nowak M J, Lapinski L, Spectrochim Acta, 48A(1992)1385. 49. Scott A P, Radom L, J Phys Chem, 100(1996)16502. 50. Palafox M Alcolea, J Phys Chem, 103 A(1999)11366. 51. Rastogi V K, Singh C, Jain V, Palafox M Alcolea, J Raman Spectrosc, 31(2000)1005. 52. (a) Rastogi V K, Jain V, Yadav R A, Singh C, Palafox M Alcolea, J Raman Spectrosc, 31(2000)595 (b) Palafox M A, Rastogi V K, Kumar H, Kostova I, Vats J K, Spectrosc Letts, 44(2011)300. (c) Palafox M Alcolea, Int J Quantum Chem, 77(2000)661. (d) Anupma, Vats J K, Palafox M Alcolea, Bhat Daisy, Rastogi V K, Asian Chem Lett,18(2014)115. 53. Császár P, Harsányi L, Boggs J E, Int J Quantum Chem, 33(1988)1. 54. Aamouche A, Berthier G, Coulombeau C, Flament J P, Ghomi M, Henriet C, Jobic H, Turpin P Y, Chem Phys,

204(1996)353. 55. Nishimura Y, Tsuboi M, Kato S, Morokuma K, J Am Chem Soc, 103(1981)1354.

[Received: 25.02.2015; accepted: 6.03.2015]

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