ORIGINAL RESEARCH

MP2 study on the hydrogen-bonding interaction between 5-fluorouracil and DNA bases: A,C,G,T

Zai Ming Qiu • Gai Ling Wang • Hua Li Wang •

Hui Ping Xi • DaNian Hou

Received: 14 November 2013 / Accepted: 12 March 2014

� Springer Science+Business Media New York 2014

Abstract The 5-fluorouracil is a pyrimidine analog

effective in the treatment of cancer. In this work, we

present the hydrogen-bonding base pairs involving 5-FU

bound to the four bases in DNA: adenine, cytosine, guan-

ine, and thymine. Full geometry optimizations have been

performed for the studied complexes by MP2 method. The

interaction energies were corrected for the basis-set

superposition error, using the full Boys-Bernardi counter-

poise correction scheme. Hydrogen-bonding patterns of

these base pairs were characterized using NBO analysis

and AIM analysis. According to the calculated binding

energies and structural parameters, the stability of the base

pairs decrease in the following order: 5-FU:A [ 5-

FU:G [ 5-FU:T [ 5-FU:C.

Keywords MP2 � DNA bases � Hydrogen bond �5-fluorouracil

Introduction

Hydrogen-bonding interaction plays a unique role in

chemical and biochemical systems, especially between

nucleic acid bases [1]. These interactions contribute to the

stability and conformational variability of nucleic acids. A

proper description of these non-bonded interactions helps

to understand the basic principles governing the formation

of the 3D nucleic acid architectures [2, 3]. Due to the

importance, there have been numerous studies, experi-

mental [4] and computational [5, 6], concerned with the

association of nucleotide base pairs.

The computational studies range from Watson–Crick

base pairs [7, 8] to unusual base pairs [9, 10]. J. Sponer

et al. [11] discussed the key electronic properties of stan-

dard and modified nucleobases and the energetics of stan-

dard base pairs, mismatched base pairs, thio-base pairs, and

others. Ol’ha O. Brovarets’ reported the tautomerization of

the DNA base pair via double proton transfer and some

intermolecular CH…O/N H-bonds in the biologically

important pairs of natural nucleobases [12–14]. The

hydrogen-bonded complexes of nucleobases are primarily

stabilized by the electrostatic interaction, while the dis-

persion attraction is also important [15]. The reliability of

the ab initio calculations depends on two factors: the

quality (size) of the basis set of atomic orbitals, and the

inclusion of electron correlation effects.

The 5-fluorouracil (5-FU) is an anti-metabolite of the

pyrimidine analog type, and is one of the most commonly

used chemotherapeutic drugs in the treatment of human

malignancies. Misincorporation of 5-FU into DNA is

associated with the formation of DNA strand breaks. 5-FU

incorporation into RNA is in relation to thymidylate syn-

thase inhibition of human colorectal cancers. [16] More-

over, the 5-fluorodeoxyridine can induce imbalance of

intracellular deoxyribonucleoside triphosphate pools and

subsequent double strand breaks in mature DNA, accom-

panied by cell death. [17] Miquel Coll reported the effects

of 5-fluorouracil/guanine wobble base pairs in Z-DNA:

molecular and crystal structure of d(CGCGFG) [18]. The

two 5-FU:G base pairs in the hexamer helix are in the

Z. M. Qiu (&) � H. L. Wang � H. P. Xi

Henan Quality Polytechnic, Pingdingshan 467000, China

e-mail: qiuzaiming@hotmail.com

G. L. Wang

Bengbu College, Bengbu 233000, China

D. Hou

Institute of Chemistry Henan Academy of Sciences,

Zhengzhou 450000, China

123

Struct Chem

DOI 10.1007/s11224-014-0427-1

wobble geometry with two hydrogen bonds between the

bases. In both structures, no evidence is seen of a three

hydrogen bonds base pair involving the common tautomer

form of the 5-FU base. Lawrence C. Sowers reported the

structure and dynamic properties of a fluorouracil-adenine

base pair in DNA, and the equilibrium between a wobble

and ionized base pair formed between fluorouracil and

guanine in DNA as studied by proton and fluorine NMR.

[19] It has been determined that the 7-mer duplex con-

taining a central FU:A base pair adopts a normal right-

handed configuration and the A residue in the FU:A pair is

oriented in the normal anticonfiguration giving a Watson–

Crick base pair. The FU:A base pair is dynamic less stable

than normal A:T base pairs in the oligonucleotide.

It has been shown that 5-FU is both mutagenic and

oncogenic and may act directly to inhibit DNA replication. In

the present work, we study the hydrogen bond characters and

the binding energies of the base pairs between the 5-FU and

DNA bases, which may be useful to the study the structure of

DNA and the pairing property of the pyrimidine 5-FU.

Computational details

The conformations which have at least two hydrogen

bonding interactions were chosen as the computed base

pairs. Taking into account that H-bonding between bases

cannot occur through the N9–H of purine and the N1–H of

pyrimidine (the sites that are connected to sugars in DNA),

the calculations were carried out with exclusion of base

pairs directly involving the H(N1) pyrimidine and H(N9)

purine.

After geometry optimization and frequency analysis, fif-

teen conformations were characterized as stable complex by

using GAUSSIAN 09 [20] at MP2/6-31G** level. Subse-

quently energy calculations were performed at the MP2/6-

311??G** level starting from the MP2/6-31G** geome-

tries. Generally, the systematic energy will decrease during

the course of new complex formation. The decreased energy

is binding energy, which is generally related to the stability

of corresponding complex. Interaction energies were

obtained as the difference between the energy of the complex

and the energies of the molecules in isolation, using the su-

permolecule method [21]. This procedure is known to be

subject to a major error: the basis-set superposition error

(BSSE) [22]. This error is a purely mathematical artifact due

to the fact that different basis sets are used for energy eval-

uations of the supersystem and the subsystems. To avoid it,

the counterpoise (CP) correction was used to correct for the

basis-set superposition error (BSSE).

According to the Møller–Plesset perturbation theory, the

MP2 stabilization energy of the base pair describing the

interaction between monomers is given by

DEMP2 ¼ DEHF þ DECOR ð1Þ

where

DEHF ¼ EHFAB�AB � EHF

A�AB � EHFB�AB ð2Þ

is the HF interaction energy between bases, and

DECOR ¼ DEMP2 � DEHF ð3Þ

is the correlation interaction energy within the framework

of the second-order Møller–Plesset perturbation theory.

At the same time, the MP2 stabilization energy is given

by

DEMP2 ¼ EMP2AB�AB � EMP2

A�AB � EMP2B�AB ð4Þ

In the above-mentioned expression, EX–ZY is energy of a

system X computed by the Y method with basis set Z.

The Natural Bond Orbital (NBO) [23] analysis was

performed at the MP2/6-31G** level. This is carried out by

examining all possible interactions between filled (donor)

Lewis-type NBOs and empty (acceptor) non-Lewis NBOs

and estimating their energetic importance by second-order

perturbation theory. For each donor NBO(i) and acceptor

NBO(j) the stabilization energy E(2) associated with delo-

calization (2e-stabilization) i/j is estimated as

Eð2Þ ¼ DEij ¼ qi½F2ði;jÞ= ðei � ejÞ� ð5Þ

where qi is the donor orbital occupancy, ei and ej are

diagonal elements (orbital energies) and F(i,j) is the off-

diagonal NBO Fock matrix element.

Atoms in molecules theory (AIM) is a very useful tool in

analyzing hydrogen bonds. Electron densities qc, Lapla-

cians r2qc, and local potential energy density V(r) at bond

critical points have been calculated at the MP2/6-31G**

level. The results are evaluated in terms of atom volumes V

and atomic charges q obtained using the electron density

integrated over atomic basins (up to 0.001 e/Bohr3 level).

With a large electronic density at the hydrogen bond crit-

ical point and a positive value of r2qc indicating a strong

hydrogen bond [24], and were considered as the criteria for

the formation of van der Waals (vdW) contact and H-bond.

These are points where the electron density gradient qc

vanishes, and additional characterization is done by the

corresponding Hessian matrix (a 3 9 3 matrix of second

derivations). Diagonalization of this matrix yields the

coordinate invariant eigenvalues: k1,k2,k3. Laplacian,

r2qc, of charge density at the bond critical point is defined

as:

r2qc ¼X3

i¼1

ki ð6Þ

The topological analysis was performed using the

AIM2000 program.

Struct Chem

123

The energies of the conventional intermolecular H-bonds

were evaluated by the empirical Iogansen’s formula:

EHB ¼ 0:33 �ffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiDm� 40p

ð7Þ

where Dm is the magnitude of the redshift (relative to the

free molecule) of the stretching mode of H-bonded groups

involved in the H-bonding. [25, 26] The energies of the

O…O vdW contact EO…O were evaluated by the empirical

5-FU:A1 5-FU:A2 5-FU:A3

5-FU:A4 5-FU:A5 5-FU:C1

5-FU:C2 5-FU:C3 5-FU:G1

5-FU:G2 5-FU:T1 5-FU:T2

5-FU:T3 5-FU:T4 5-FU:T5

Fig. 1 Optimized structures of the hydrogen-bonding complexes

Struct Chem

123

Espinosa-Molins-Lecomte (EML) formula, based on the

electron density distribution at the (3,-1) BCPs of the vdW

contact:

EO���O ¼ 0:5 � VðrÞ ð8Þ

where V(r) is the value of a local potential energy density at

the (3,-1) BCPs. [27]

Results and discussion

Calculations at MP2/6-31G** level led to 5-FU:A (A1–

A5), 5-FU:C(C1–C3), 5-FU:G (G1–G2), 5-FU:T(T1–T5)

structures for the damaged base pairs, in Fig. 1. These

complexes are stabilized with near-linear hydrogen bonds.

Table 1 lists the interaction energies, and Table 2 collects

the selected structural properties for the hydrogen-bonded

complexes studied in this work.

Interaction energy

The interaction energies with BSSE correction of each of

the damaged base pairs are reported in the Table 1, under

the convention that a negative DE corresponds to a favor-

able-binding energy. The results show that MP2/6-31G**

and MP2/6-311 ??G** give similar results. Table 1

shows that the binding energies of the base pairs range

form -5.5 to -16.4 kcal/mol, and the binding energies of

normal base pairs G:C and A:T are -23.8 and -13.4 kcal/

mol(6-31G**), respectively. Moreover, the stabilization of

H-bonded base pair is primarily due to the electrostatic

interactions. However, for weakly hydrogen-bonded base

pairs, the correlation interaction energy amounts to about

30 % of the stabilization energy.

The comparison of the formation energies of the systems

shows that G2 complex is the most negative among all the

studied complexes. MP2 calculation shows the formation

energy is -16.4 kcal/mol. The interaction energy of the

G:C-WC A:T-WC A:T-rWC

A:T-H A:T-rH A:U-WC

A:U-Rwc A:U-H A:U-rH

Fig. 1 continued

Struct Chem

123

structure G2 is *7 kcal/mol lower than for the pairing

energy of the canonical G:C base pair [28]. It can be

deduced that the binding ability of 5-FU is lower than C

when bound in structure G2. In the case of 5-FU: C com-

plex, Table 1 shows that the stabilization energy of the C2

and C3 are more negative, they are -13.3 and -12.9 kcal/

mol, respectively.

The BSSE-corrected pairing energies of pairs A1–A5

are -14.8, -13.8, -13.9, -6.2, and -14.7 kcal/mol

(6-31G**), respectively. The binding energies of A1, A2,

A3, and A5 are more negative than the pairing energy of

the normal A:T and A:U base pairs [29–31]. In the case of

5-FU:T, the interaction energy for T5 is found to be more

negative (-11.6 kcal/mol), and the next complex is T3

with the interaction energy of -11.4 kcal/mol.

In the recent years, ab initio and DFT quantum chemical

studies have appeared on the geometry, energy and other

aspects of the Watson–Crick A:T and G:C pairs. The cal-

culation at BP86/TZ2P level shows the binding energies of

pairs G:C and A:T are -25.2 and -12.3 kcal/mol [32]. The

MP2/6-31G* calculation shows the binding energies of

G:C and A:T are -25.8 and -11.7 kcal/mol [33]. That is to

say, these calculation results are similar. In this study, the

interaction energy difference between some of the studied

complexes and the A:T complex is small. Therefore, we

need to carry out the NBO and AIM analysis of the

hydrogen bonds in the complexes.

The H-bond analysis

The energy difference method can only be used to evaluate

the overall hydrogen-bonding energy of the base pair.

Identifying the strength of each individual H-bond using

this procedure is impossible. To obtain further insight into

the nature of the hydrogen bond in the base pairs, we studied

the electron density-based topological parameters within

the framework of Bader’s Atoms in Molecule theory. The

strength of a localized H-bond maybe found from the length

of H-bond, the second-order perturbation energy E(2), and

electron density qc. All of these parameters are easily cal-

culated from the MP2-optimized structures. Table 2 lists

the equilibrium distance between the proton and the proton

acceptor atom. This quality is generally correlated with DE,

with a stronger H-bond associated with a shorter length. For

every H-bond, the second-order perturbation energy E(2)

and electron density qc were listed in Table 2.

Table 1 Interaction energies of

5-FU:A, 5-FU:C, 5-FU:G, and

5-FU:T complexes (kcal/mol)

obtained by the MP2 method at

6-31G** and 6-311??G**

levels

DEHF is the HF interaction

energy, DECORR is the

correlation interaction energy,

DEMP2 is the MP2 stabilization

energy, DECP is the BSSE-

corrected binding energy

Pair MP2/6-31G** MP2/6-311??G**

DEHF DECORR DEMP2 DECP DEHF DECORR DEMP2 DECP

G:C-WC -25.5 -5.0 -30.5 -23.8 -22.6 -4.2 -26.8 -22.6

A:T-WC -13.6 -5.7 -19.3 -13.4 -12.0 -5.4 -17.4 -13.1

A:T-rWC -13.3 -5.7 -19.0 -13.1 -11.9 -5.4 -17.3 -13.0

A:T-H -14.2 -5.9 -20.1 -14.3 -12.8 -5.7 -18.5 -14.0

A:T-rH -14.0 -5.9 -19.9 -14.1 -12.6 -5.7 -18.3 -13.9

A:U-WC -13.9 -5.6 -19.5 -13.6 -12.3 -5.5 -17.8 -13.4

A:U-rWC -13.2 -5.6 -18.8 -13.0 -11.8 -5.3 -17.1 -12.9

A:U-H -14.2 -5.9 -20.1 -14.3 -12.9 -5.7 -18.6 -14.0

A:U-rH -14.1 -5.8 -19.9 -14.2 -12.7 -5.6 -18.3 -13.8

A1 -14.0 -6.5 -20.5 -14.8 -12.1 -6.0 -18.1 -14.5

A2 -13.2 -6.4 -19.6 -13.8 -11.7 -5.8 -17.5 -13.6

A3 -13.0 -6.6 -19.6 -13.9 -11.5 -6.1 -17.6 -13.7

A4 -6.3 -3.6 -9.9 -6.2 -5.7 -3.3 -9.0 -6.2

A5 -14.6 -5.8 -20.4 -14.7 -12.0 -6.0 -18.0 -14.4

C1 -6.2 -2.6 -8.8 -5.6 -5.6 -2.5 -8.1 -5.7

C2 -12.6 -6.3 -18.9 -13.3 -11.1 -6.0 -17.1 -13.0

C3 -12.0 -6.2 -18.2 -12.9 -11.1 -5.8 -16.9 -12.7

G1 -8.1 -5.3 -13.4 -9.5 -7.0 -4.9 -11.9 -9.4

G2 -17.0 -4.9 -21.9 -16.4 -14.3 -4.7 -19.0 -16.1

T1 -6.5 -2.8 -9.3 -5.5 -6.3 -2.6 -8.9 -5.6

T2 -6.5 -3.1 -9.6 -5.6 -6.2 -2.8 -9.0 -5.6

T3 -10.9 -5.2 -16.1 -11.4 -9.6 -4.9 -14.3 -11.3

T4 -11.3 -4.6 -15.9 -11.4 -9.8 -4.3 -14.1 -11.2

T5 -11.4 -4.9 -16.3 -11.6 -9.9 -4.5 -14.4 -11.4

Struct Chem

123

Table 2 The optimized geometry parameters, electron density qc (e/Bohr3), Laplacian of electron density r2qc (e/Bohr5), selected NBO charge,

and the hydrogen bond stabilization energy E(2) (kcal/mol) calculated for base pairs at MP2/6-31G** level

H-bond d(A) h NBO charge E(2) qc r2qc EHB /EO…O

G:C-WC

O7…H24 N22 1.786 178.4 -0.783, 0.492, -0.880 29.28 0.033 0.112 6.4

N8H9…N25 1.904 174.9 -0.764, 0.493, -0.787 25.48 0.031 0.090 5.4

N11H12…O27 1.928 175.7 -0.921, 0.468, -0.794 17.07 0.025 0.082 4.9

A:T-WC

N7H9…O24 1.961 173.9 -0.894, 0.470, -0.757 15.58 0.023 0.076 4.4

N10…H26N25 1.793 178.7 -0.728, 0.508, -0.794 36.80 0.040 0.112 6.8

C11H12…O28 2.732 133.9 0.390, 0.237, -0.750 0.85 0.005 0.021 0.6

A:T-rWC

N7H9…O28 1.995 174.0 -0.884, 0.463, -0.784 13.85 0.023 0.079 4.3

N10…H26N25 1.828 178.6 -0.727, 0.503, -0.788 33.51 0.039 0.116 6.9

C11H12…O24 2.760 133.8 0.393, 0.234, -0.717 0.79 0.005 0.028 0.7

A:T-H

N7H8…O24 2.025 168.8 -0.883, 0.461, -0.751 12.44 0.020 0.073 3.9

N4…H26N25 1.805 173.7 -0.612, 0.503, -0.786 34.57 0.040 0.123 7.1

C2H3…O28 2.709 123.1 0.327, 0.248, -0.760 0.77 0.006 0.025 0.8

A:T-rH

C2H3…O24 2.686 123.4 0.328, 0.250, -0.730 0.84 0.006 0.026 0.8

N4…H26N25 1.801 174.5 -0.613, 0.503, -0.786 34.87 0.040 0.124 7.2

N7H8…O28 2.044 169.0 -0.883, 0.460, -0.780 11.49 0.020 0.070 3.7

A:U-WC

N18H20…O7 1.971 173.9 -0.882, 0.466, -0.750 15.30 0.024 0.081 4.5

N21…H9N8 1.830 179.4 -0.730, 0.503, -0.794 33.63 0.039 0.116 6.8

C22H23…O11 2.783 133.3 0.394, 0.232, -0.744 0.70 0.005 0.021 0.6

A:U-rWC

C22H23…O7 2.744 133.9 0.393, 0.235, -0.711 0.84 0.005 0.022 0.7

N21…H9N8 1.827 178.5 -0.727, 0.503, -0.794 33.66 0.039 0.116 6.9

N18H20…O11 2.005 173.8 -0.884, 0.462, -0.780 13.34 0.022 0.077 4.2

A:U-H

N18H19…O7 2.023 168.8 -0.883, 0.461, -0.745 12.54 0.021 0.074 3.9

N15…H9N8 1.806 173.8 -0.613, 0.504, -0.792 34.55 0.040 0.123 7.1

C13H14…O11 2.712 122.9 0.327, 0.248, -0.756 0.75 0.006 0.025 0.7

A:U-rH

C13H14…O7 2.686 123.4 0.328, 0.250, -0.730 0.88 0.006 0.027 0.8

N15…H9N8 1.801 174.6 -0.613, 0.503, -0.786 35.19 0.041 0.125 7.2

N18H19…O11 2.045 169.0 -0.883, 0.460, -0.780 11.35 0.020 0.070 3.7

A1

N22H26…O6 2.038 169.6 -0.881, 0.460, -0.720 11.75 0.020 0.071 3.8

N17…H8N7 1.788 174.3 -0.617, 0.508, -0.791 37.05 0.041 0.126 7.4

C14H16…O10 2.678 123.4 0.329, 0.248, -0.753 0.84 0.006 0.026 0.8

A2

C21H24…O6 2.735 134.5 0.394, 0.234, -0.686 0.86 0.005 0.022 0.7

N23…H8N7 1.811 179.9 -0.733, 0.507, -0.794 35.96 0.041 0.120 7.1

N22H25…O10 1.998 172.8 -0.883, 0.463, -0.776 13.47 0.022 0.078 4.2

A3

N22H25…O6 2.000 173.3 -0.882, 0.462, -0.724 13.66 0.022 0.078 4.2

N23…H8N7 1.812 178.8 -0.732, 0.507, -0.793 35.90 0.041 0.119 7.1

C21H24…O10 2.740 134.1 0.393, 0.233, -0.741 0.83 0.005 0.021 0.7

Struct Chem

123

The calculated value of the electron density (qc),

Laplacian of electron density (r2qc) at the BCP for

CH…O, NH…O, and NH…N bonds in the base pairs are

summarized in the Table 2. The strong hydrogen bonds are

found to be associated with maximum electron density at

BCPs and higher stability, which is observed for the

complexes. As the stable complex, the G2 shows a con-

figuration with a HB between the N23H25 and O6 with

distance of 1.825 A, and a HB between the O22 and H8N7

with distance of 1.834 A. And the HBs in G2 (bond angles

N23H25…O6 and O22…H8N7 are 173.1� and 176.1�,

respectively) are essentially linear. The HB N23H25…O6

Table 2 continued

H-bond d(A) h NBO charge E(2) qc r2qc EHB /EO…O

A4

N22H25…F12 2.104 179.4 -0.880, 0.438, -0.387 6.71 0.015 0.062 3.1

N23…H3C2 2.235 168.4 -0.708, 0.295, 0.040 9.14 0.018 0.055 2.8

A5

C14H16…O6 2.665 123.8 0.331, 0.459, -0.699 0.90 0.006 0.026 0.7

N17…H8N7 1.787 173.9 -0.618, 0.508, -0.792 37.00 0.041 0.126 6.5

N22H26…O10 2.052 169.4 -0.883, 0.458, -0.772 11.08 0.019 0.069 3.2

C1

C20H22…F12 2.486 164.1 -0.460, 0.259, -0.374 1.63 0.006 0.032 1.0

C20H22…O6 2.745 131.3 -0.460, 0.259, -0.716 0.69 0.005 0.023 0.7

N21H24…O6 2.065 165.6 -0.887, 0.440, -0.716 6.87 0.017 0.069 3.3

C2

N21H23…O6 1.912 174.9 -0.882, 0.470, -0.737 17.38 0.027 0.095 5.2

N16…H8N7 1.906 170.7 -0.782, 0.512, -0.787 25.18 0.032 0.098 5.6

O13…O10 3.398 – -0.733, -0.708 – 0.003 0.017 0.5

C3

O13…O6 3.424 – -0.731, -0.649 – 0.003 0.016 0.4

N16…H8N7 1.902 170.6 -0.781, 0.511, -0.789 25.32 0.033 0.100 5.6

N21H23…O10 1.915 174.4 -0.884, 0.470, -0.788 16.61 0.027 0.093 5.1

G1

O22…O6 3.917 – -0.691, -0.657 – 0.001 0.005 0.2

N17…H8N7 1.931 163.8 -0.572, 0.510, -0.789 22.36 0.030 0.093 5.2

C14H16…O10 2.285 130.5 0.296, 0.258, -0.774 3.30 0.014 0.051 2.3

G2

N23H25…O6 1.825 173.1 -0.757, 0.480, -0.756 25.21 0.034 0.117 6.5

O22…H8N7 1.834 176.1 -0.764, 0.510, -0.784 26.67 0.032 0.109 6.0

T1

N13H15…F12 2.081 175.7 -0.774, 0.474, -0.385 7.52 0.015 0.063 3.2

O20…H3C2 2.126 167.5 -0.780, 0.293, 0.037 8.64 0.018 0.062 3.2

T2

N13H15…F12 2.067 179.9 -0.774, 0.473, -0.385 7.94 0.015 0.065 3.3

O18…H3C2 2.128 168.7 -0.751, 0.293, 0.037 8.88 0.018 0.062 3.3

T3

N13H15…O6 1.901 172.3 -0.779, 0.498, -0.724 19.22 0.027 0.095 5.1

O18…H8N7 1.844 173.6 -0.760, 0.505, -0.786 23.81 0.031 0.109 5.9

T4

O20…H8N7 1.854 172.7 -0.787, 0.505, -0.787 22.30 0.030 0.106 5.7

N13H15…O10 1.896 170.7 -0.780, 0.498,-0.776 18.98 0.027 0.097 5.2

T5

O18…H8N7 1.849 173.1 -0.758, 0.505, -0.787 23.27 0.031 0.107 5.8

N13H15…O10 1.888 172.5 -0.779, 0.498, -0.777 19.72 0.028 0.099 5.3

Struct Chem

123

has a E(2) energy of 25.21 kcal/mol, an electron density, qc,

of 0.034 e/Bohr3, and Laplacian of the electron density,

r2qc, of 0.117 e/Bohr5. And the HB N11…H31N29 has a

E(2) energy of 26.67 kcal/mol, an electron density, qc, of

0.032 e/Bohr3, and Laplacian of the electron density, r2qc,

of 0.109 e/Bohr5. It is clear that the short strong HBs

NH…O contribute to the stability of complex G2. The

increasing of qc and r2qc at H-bond critical points results

in the increasing H-bond strength.

The pairs 5-FU:C2 and 5-FU:C3 are essentially nonplanar

and have propeller-like structures. These base pairs are sta-

bilized by the two antiparallel canonical H-bonds and a vdW

contact: N21H23…O6 (5.2 kcal/mol), N16…H8N7(5.6 kcal/

mol),and O13…O10 (0.5 kcal/mol) for the 5-FU:C2 base

pair, and N16…H8N7(5.6 kcal/mol), N21H23…O10 (5.1 kcal/

mol), and O13…O6 (0.4 kcal/mol) for the 5-FU:C3 base pair

(Table 2). It is evident that the NH…N H-bond is the

strongest in the 5-FU:C base pair, whereas the O…O vdW

contact is the weakest interaction in both complexes.

It would be of interest to investigate the pyramidaliza-

tion of the amino groups in the base pairs. Earlier ab initio

calculations carried out at the Hartree–Fock level indicate a

rather weak amino group pyramidalization. [34, 35] Our

MP2 calculations result shows the amino groups deviate

from planarity. For adenine in base pair 5-FU:A5 we obtain

a dihedral angle of 12.2�, and for guanine in base pair

5-FU:G2 we obtain a dihedral angle of 27.8�. The hydro-

gen-bonded bases possess nonplanar geometries due to sp3

hybridization of nitrogen atoms and because of the soft

intermolecular vibrations in the molecular complexes.

Furthermore, the substantial conformational flexibility of

amino groups is important for biological functions of DNA.

Since the hydrogen bond properties are sometimes

evaluated by charge distributions; for the better under-

standing of the problem, we considered the atomic charges

for the included atoms. As presented in Fig. 1, the H-bonds

are the main factors of the base pairs. Strong HBs are

formed between the 5-FU and the DNA bases, and the HB

lengths are found to be within 2.8A. For the most strongly

H-bonded conformers G2, A3, T3, and C2, the corre-

sponding NH…O and NH…N contacts have preferable

H…O/N separations and near-linear H-bond arrangements.

In conclusion, the results of the NBO and AIM analysis are

in accordance with the binding energies. The study used in

the manuscript for comparison has only single point MP2

interaction energies.

Hydrogen-bonding energy as a function of geometry

parameter

Apart from characterization of DNA base pairs, an

important task is the evaluation of interaction energies of

DNA base pairs in ‘‘away from equilibrium’’ geometries

present in actual structural contexts, and to compare these

geometries and interaction energies with the fully-opti-

mized geometries of these base pairs. The hydrogen-

bonding configurations found in DNA exhibit great vari-

ability and usually do not correspond to most favorable

arrangements of isolated monomers in hydrogen-bonding

conformations. Consequently, the essential base–base

interactions are significantly affected by DNA polymor-

phism. Thus, it seems to be interesting to see how the

polymorphism affects the structural and energetic proper-

ties of the base pairs.

The buckle angle was set according to the definition as

described in Fig. 2a. We have investigated the dependence

of interaction energy on the angle between 5-FU and DNA

base. Figure 2b gives the torsional potential energy curve

for the four conformers from -90 to 908 at MP2/6-31G**

level. Four minima are shown on the potential energy

curves. The relative energy of G2 compared to T3, about

5 kcal/mol, is in good agreement with the results from the

Table 1. It is clear from the figure that the interaction

energy is dependent considerably on the buckle angle.

More importantly, the DE curve shows how sensitive the

interaction energy is to this rising angle, rapidly losing its

attractive character (negative DE), and becoming progres-

sively more repulsive as the angle is brought larger.

Figure 2c shows the interaction energies, calculated

with the MP2 procedure, of four hydrogen-bonded com-

plexes as a function of the separation. By definition, a

larger negative energy indicates a stronger hydrogen-

bonding interaction. Results presented in Fig. 2c show that,

for each complex, there is a sharp energy minimum at a

separation of *1.9 A. At larger separation, the interaction

energy for each complex decays slowly, at a rate propor-

tional to the distance, resembling the behavior of electro-

static interactions. There is marked difference in the

interaction energies: ranging from -16.4 kcal/mol for the

G2 to -11.4 kcal/mol for the T3. The minimum interaction

energies for A3 and C2 are -13.9 and -13.3 kcal/mol,

respectively.

The differences between the rare pairs and normal pair

Here, a detailed structural study on the base mispairing

specificities and underlying pairing energies of the rare

base would throw light on the pairing property of 5-FU.

The calculated N1…N9(N1) distances and binding energies

of the damaged base pairs were compared to the Watson–

crick A:T pair as shown in Fig. 3. The N1… N9(N1) dis-

tances presented are in consonance with available experi-

mental reports. For example, the N1…N9 distance of the

classical G:C base pair is 9.06 A [36], derived from its

X-ray crystal structure, and the calculated value is 9.00 A,

which corresponds to about 0.66 % deviation. The percent

Struct Chem

123

difference of binding energy is defined as (Ecomplex–EA:T)/

EA:T.

As shown in Fig. 3, the binding energy of A1 is more

negative than A:T, but the N1…N9 distance (6.670 A)

indicates the 5-FU cannot accommodated into a DNA

double helix in the optimized structure. While N1…N9

distances for the A2, A3 pairs are identical to that of the

normal A:T pair, and the binding energies are more neg-

ative than normal A:T. This means that 5-FU may forms a

base pair with adenine in conformation A2, or A3. In

addition, only the base mispairs with cis-oriented

glycosidic bonds relative each other incorporate into the

DNA double helix [37]. So the pair A3 is more favorable

than A2 in the DNA double helix. As to base pair G1, the

binding energy of G1 pair is less negative than the normal

G:C pair. It can be deduced that 5-FU may not easily pairs

with guanine in conformer G1. As to base pair G2, the

binding energy of G2 pair is less negative than the normal

G:C pair, but N1…N9 distance(9.527 A) is near to normal

pair. It can be deduced that 5-FU may pairs with guanine in

conformer G2. Moreover, there are five possibilities where

5-FU pairs with thymine. In the structure, T3 is energeti-

cally near to the normal A:T pair. And the N1–N1 distance

of T3 is similar to the normal A:T and G:C base pairs.

While, only the base mispairs with cis-oriented glycosidic

bonds relative each other incorporate into the DNA double

helix. So the pair T3 is less favorable in the DNA double

helix.

Akiko Yoshika and coworkers reported the 5-fouor-

odeoxyuridine-induced DNA double strand breaks in

mouse FM3A cells and the mechanism of cell death. They

presented evidence that FdUrd treatment of FM3A cells

in vitro is associated with a Dntp pool imbalance and

subsequent DNA double strand breaks and that a protein

factor responsible for the DNA double strand breaks is

induced by the treatment. [17] JM Carethers reported the

mismatch repair proficiency and in vitro response to

5-fluorouracil. Incorporation of 5-FU into DNA does not

interfere with hydrogen bonding (positions N3 and C4 of

the pyrimidine rings) [38]. Misincorporation of 5-FU into

DNA is associated with the formation of DNA strand

breaks. Though only of theoretical interest, the calculated

results show that 5-FU may form a base pair with adenine

or guanine. Moreover, the nonplanar structure of 5-FU base

pairs may cause the torsion structure of DNA, and leading

to a polymerase block at the damaged site.

Fig. 2 a Molecular diagram showing the definition of the buckle

angle h. b Interaction energy (in kcal/mol) as a function of the buckle

angle (in degree) for the base pairs A3,C2,G2 and T3. Variation of the

H-bond energy as h is varied between -90� and 90�. c The interaction

energy (in kcal/mol) as a function of the separation (in A) between the

donor and the acceptor for the base pairs A3,C2,G2 and T3

Fig. 3 The percent difference between the damaged base pairs and

normal A:T pair. In all cases the binding energy and the N1…N9

distance of the standard A:T pair were set as the reference point

Struct Chem

123

Conclusions

We have investigated the base pairs between 5-FU and

DNA bases using MP2 method. It is observed that the 5-FU

binds strongly with the DNA bases through hydrogen-bond

interactions. The calculated interaction energies for the

complexes vary from -5.5 to -16.4 kcal/mol. A signifi-

cant measurement of qc and r2qc for all the observed

H-bonds is positive within the following ranges:

0.005–0.041e/Bohr3 for the electron density and

0.021–0.120 e/Bohr5 for its Laplacian. Among the inter-

acting complexes, G2 and A1 are found to have the more

negative interaction energies. The bond lengths, collinear

angles, NBO analysis, and AIM analysis also support the

result which obtained upon binding energy values.

Finally, according the calculated binding energies and

structural parameters compared to normal base pair G:C

and A:T, the stability of the base pairs decrease in the

following order: 5-FU:A [ 5-FU:G [ 5-FU:T [ 5-FU:C.

It is clear that the non-complementary base-pairing G2, A3,

T3, and C2 are stabilizing enough to play significant role in

DNA structures. It is expected that inclusion of appropriate

consideration for many of these non-canonical base pairs

would improve the accuracy of DNA structure prediction.

Acknowledgments Supported by the Science and Technology

Development Project of Pingdingshan (2012064).

References

1. Watson JD, Crick FHC (1953) Nature 171:737–738. doi:10.1038/

171738a0

2. Parthasarathi R, Subramanian V (2006) Chem Phys Lett

418:530–534. doi:10.1016/j.cplett.2005.10.153

3. Dkhissi A, Blossey R (2007) Chem Phys Lett 439:35–39. doi:10.

1016/j.cplett.03.065

4. Thiviyanathan V, Somasunderam A, Volk DE, Hazra TK, Mitra

S, Gorenstein DG (2008) Biochem Biophys Res Commun

366:752–757. doi:10.1016/j.bbrc.2007.12.010

5. Padermshoke A, Katsumoto Y, Masaki R, Aida M (2008) Chem

Phys Lett 457:232–236. doi:10.1016/j.cplett.2008.04.029

6. Qiu ZM, Wang HJ, Xia YM (2010) Struct Chem 21:931–937.

doi:10.1007/s11224-010-9629-3

7. Villani G (2006) Chem Phys 324:438–446. doi:10.1016/j.chem

phys.2005.11.006

8. Grunenberg J (2004) J Am Chem Soc 126:16310–16311. doi:10.

1021/ja046282a

9. Bhattacharyya D, Koripella SC, Mitra A, Rajendran VB, Sinha B

(2007) J Biosci 32:809–825. doi:10.1007/s12038-007-0082-4

10. Qiu ZM, Xia YM, Wang HJ, Diao KS (2010) Struct Chem

21:99–105. doi:10.1007/s11224-009-9528-7

11. Sponer J, Leszczynski J, Hobza P (2001) Biopolymers

61(1):3–31. doi:10.1002/1097-0282

12. Brovarets’ OO, Hovorun DM (2014) J Biomol Struct Dyn

32(1):127–154. doi:10.1080/07391102.2012.755795

13. Brovarets’ OO, Yurenko YP, Hovorun DM (2013) J Biomol

Struct Dyn 32:993–1022. doi:10.1080/07391102.2013.799439

14. Brovarets’ OO, Hovorun DM (2013) J Biomol Struct Dyn

31(8):913–936. doi:10.1080/07391102.2012.715041

15. Sponer J, Leszczynski J, Hobza P (1996) J Biomol Struct Dyn

14(1):117–135

16. Noorduis P, Holwerda U, van der Wilt CL, Van Croeningen CJ,

Smid K, Meijer S, Pinedo HM, Peters GJ (2004) Ann Oncol

15(7):1025–1032. doi:10.1093/annonc/mdh264

17. Yoshiok A, Tanak S, Hiraok O, Koyam Y, Hirot Y, Ayusawa D,

Seno T, Garrett C, Wataya Y (1987) J Biol Chem 262:8235–8241

18. Coll M, Saal D, Frederick CA, Aymami J, Rich A, Wang AHJ

(1989) Nucl Acids Res 17(3):911–923. doi:10.1093/nar/17.3.911

19. Sowers LC, Eritja R, Kaplan B, Goodman MF, Fazakerly GV

(1988) J Biol Chem 263:14794–14801

20. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA,

Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson

GA, Nakatsuji H, Caricato M, Li X, Hratchian HP, Izmaylov AF,

Bloino J, Zheng G, Sonnenberg JL, Hada M, Ehara M, Toyota K,

Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao

O, Nakai H, Vreven T, Montgomery JA, Peralta JE, Ogliaro F,

Bearpark M, Heyd JJ, Brothers E, Kudin KN, Staroverov VN,

Kobayashi R, Normand J, Raghavachari K, Rendell A, Burant JC,

Iyengar SS, Tomasi J, Cossi M, Rega N, Millam JM, Klene M,

Knox JE, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts

R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C,

Ochterski JW, Martin RL, Morokuma K, Zakrzewski VG, Voth

GA, Salvador P, Dannenberg JJ, Dapprich S, Daniels AD, Farkas

O, Foresman JB, Ortiz JV, Cioslowski J, Fox DJ (2009) Gaussian

Inc., Wallingford CT

21. Hobza P, Zahradnik R (1988) Intermolecular complexes. Else-

vier, Amsterdam

22. van Duijneveldt FB, van Duijneveldt-van de Rijdt JGCM, van

van Lenthe JH (1994) Chem Rev 94:1873–1885. doi:10.1021/

cr00031a007

23. Alkorta I, Rozas I, Elguero J (1998) Struct Chem 9:243–247.

doi:10.1023/A:1022424228462

24. Bader RFW (1991) Chem Rev 91:893–928. doi:10.1021/

cr00005a013

25. Iogansen V (1999) Spectrochim Acta, Part A 55:1585–1612.

doi:10.1016/S1386-1425(98)00348-5

26. Brovarets’ OO, Hovorun DM (2013) Adasdfsadf. Phys Chem

Chem Phys 15:20091–20104. doi:10.1039/c3cp52644e

27. Espinosa E, Molins E, Lecomte C (1998) Chem Phys Lett

285:170–173. doi:10.1016/S0009-2614(98)00036-0

28. Reynisson J, Steenken S (2002) Phys Chem Chem Phys

4:5353–5358. doi:10.1039/b206342e

29. Sharma P, Mitra A, Sharma S, Singh H (2007) J Chem Sci

119:525–531. doi:10.1007/s12039-007-0066-9

30. Warmlander S, Sponer JE, Sponer J, Leijon M (2002) J Biol

Chem 277:28491–28497. doi:10.1074/jbc.M202989200

31. Kawahara SI, Uchimaru T, Sekine M (2000) J Mol Struct

530:109–117. doi:10.1016/S0166-1280(00)00329-8

32. Guerra CF, Bickelhaupt FM, Snijders JG, Baerends EJ (1999)

Chem Eur J 5:3581–3595

33. Sponer J, Leszczynski J, Hobza P (1996) J Phys Chem

100:1965–1974. doi:10.1021/jp952760f

34. Leszczynski J (1992) Int J Quantum Chem 44:43–55. doi:10.

1002/qua.560440708

35. Gorb L, Podolyan Y, Dziekonski P, Sokalski WA, Leszczynski J

(2004) J Am Chem Soc 126:10119–10129. doi:10.1021/

ja049155n

36. Rosenberg JM, Seeman NC, Day RO, Rich A (1976) J Mol Biol

104:145–167. doi:10.1016/0022-2836(76)90006-1

37. Brovarets’ OO, Hovorun DM (2013) J Comput Chem

34:2577–2590. doi:10.1002/jcc.23412

38. Carethers JM, Chauhan DP, Fink D, Nebel S, Bresalier RS,

Howell SB, Boland CR (1999) Gastroenterology 117:123–131

Struct Chem

123