Solvent effects on binding energy, stability order and hydrogen bonding of guanine–cytosine base pair

Journal of Molecular Liquids 209 (2015) 526–530

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Journal of Molecular Liquids journal homepage: www.elsevier.com/locate/molliq

Solvent effects on binding energy, stability order and hydrogen bonding of guanine–cytosine base pair Mehdi Yoosefian a, Adeleh Mola b,c,⁎ a b c

Department of Chemistry, Graduate University of Advanced Technology, Kerman, Iran Department of Medical Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran Department of Chemistry, Payame-Noor University, Mashhad, Iran

a r t i c l e

i n f o

Article history: Received 15 January 2015 Received in revised form 2 May 2015 Accepted 8 June 2015 Available online xxxx Keywords: Guanine Cytosine Solvent effect DFT study QTAIM

a b s t r a c t In this study, the effect of various solvents on the stability order, binding energy and hydrogen bond (HB) strength of cytosine–guanine (C–G) complex are investigated by using the density functional theory. The results show that the stability of cytosine–guanine complex in polar solvent is higher than non-polar solutions while it is lower than solution in vacuum. The binding energy of cytosine–guanine complex in polar solvent is lower than non-polar solutions. Its HB strength in polar solvent with respect to water as natural solvent is close to each other. The natural bond orbital and frontier molecular orbital analysis have been carried out from the optimized structure. The Quantum Theory of “Atoms in Molecules” (QTAIM) of Bader is also applied here to get more details about the nature of intermolecular interactions. Finally, the chemical properties have been presented to investigate the chemical stability of cytosine–guanine complex. © 2015 Elsevier B.V. All rights reserved.

1. Introduction The polymer of DNA is composed of nucleotides which are constructed from three elements including: deoxyribose, base and phosphate group. DNA has four kinds of nucleotides named in abbreviated form as follows: A (adenine), G (guanine), C (cytosine), and T (thymine). A nucleoside is one of the four DNA bases covalently attached to the C1′ position of a sugar; the sugar in deoxynucleosides is 2′-deoxyribose. Nucleosides differ from nucleotides in that they lack phosphate groups. The DNA backbone is constructed by the covalent bond between sugar and phosphate which are called the “phosphodiester” bonds. Two DNA strands make a helical spiral structure and the two polynucleotide chains locate in opposite directions. The bases of each strand are inside of the helix. As DNA is double helix, there is another bond in DNA which maintains each polynucleotide chain near each other that would form the double strand DNA molecule. The DNA bases are classified to purine (adenine and guanine) and pyrimidine (cytosine and thymine). The hydrogen link is made between a purine base from one strand and a pyrimidine base from another strand which means it forms between A and T in one hand and C and G in the other hand. Two hydrogen bonds form between T and A on each opposite strand, and C forms three hydrogen bonds with G on the opposite strand [1]. Hydrogen bonding has an important role in DNA replication, repairing and ⁎ Corresponding author at: Department of Medical Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran. E-mail address: [email protected] (A. Mola).

http://dx.doi.org/10.1016/j.molliq.2015.06.029 0167-7322/© 2015 Elsevier B.V. All rights reserved.

mutation [2]. The impaired hydrogen bonds resulted to damage in DNA and genetic problems [3]. Solvents are widely used in biological research. So, it is possible they cause changes in DNA hydrogen bonds and motive in producing harm genes. Therefore, if any of them cause changes in deoxy/ribo nucleic acids, it will not be a suitable candidate in cell assays. Some of the solvents and their applications which are used in the biological research are as follows. Ethanol and chloroform are used in manual DNA extraction method. Their safety should be proved; otherwise they cannot be led to good results of gene evaluation due to the destruction of DNA bonds. As DMSO (dimethyl sulfoxide) is used in cell freezing, therefore it should not cause any manipulation in DNA structure and bonds. Methanol and acetone are also used for cell fixation [4] and ether is used for permeabilizing of cells prior to some tests and as a constructor material of some synthetic medicinal compounds. Water, also is involved in the majority compound of the cells (70% of cell volume is water). The aim of the current study is to assess the effect of different solvents on hydrogen bonds between G and C pair by means of DFT theory to find the stability and binding energy of them in various solvents and compare their results with gas phase (solvent free). 2. Computational details All quantum chemical calculations were performed with the Gaussian 03 [5] sets of codes. Full geometry optimization was computed at B3LYP [6] method with 6-311++G** (253 basis functions, 387 primitive Gaussians) basis set. Several different solvents (Water, methanol,

M. Yoosefian, A. Mola / Journal of Molecular Liquids 209 (2015) 526–530

ethanol, ether, chloroform, DMSO and acetone) to study the effect of solvent on hydrogen bonds were investigated and their effects were compared with together and also with gas phase. The computational calculations were modeled using the polarizable continuum model (PCM) [7] by the united atom cavity approach in which the cavity is created via a series of overlapping spheres. In this exploration, the estimated values of the intermolecular HB energies were calculated approximately by the Espinosa and Molins method [8]. The binding energy (Ebinding) due to C–G complex formation was calculated as defined: Ebinding ¼ EG–C −ðEG þ EC Þ:

ð1Þ

In this formula, EG–C is the total energy of cytosine–guanine formation, EG and EC are total energies of guanine and cytosine, respectively. Stability order of C–G complex in various solvents was also considered. The quantum theory of Bader of atom in molecule (QTAIM) basing on topological analysis of the electronic charge density was performed to find deeper understanding of the analyzed interactions. Hence, bond critical points (BCPs) [9] of the hydrogen bonds between C and G interaction were found and analyzed in terms of electron densities and their Laplacians. The QTAIM calculations was done by AIM2000 suit of program [10] using the B3LYP/6-311++G** wave functions as input. Natural bond orbital (NBO) analyses [11] to study the orbital interaction were performed using the same level. The molecular orbital (MO) calculations such as difference between the highest occupied MO (HOMO) and lowest unoccupied MO (LUMO) were also performed with the same level of DFT theory. 3. Results and discussion 3.1. Solvent effects Many materials are used in wide range in many aspects of laboratory trials. For example methanol, ethanol, ether, acetone and chloroform usually are used for manual DNA extraction [12] to achieve a pristine DNA sample which is the goal of DNA extraction techniques. DMSO is also used for cell cryopreservation [13]. Therefore, it is very important to know whether they can affect on DNA bonds and its structure or not. Therefore, in the present study, we chose them to evaluate their effect on DNA hydrogen bonds, DNA binding energies, DNA stability and DNA double helix. It should be noted that 70% of cell volume is occupied with water and it can change HB characters such as energy, structure and electron density [14–18]. As a result, it is expected that water has a special effect on the HB of DNA bases. So, in the present study, we

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also chose water as a natural compound of the cells to compare its effect with other solvents. Structure of a full optimized cytosine–guanine and the numbering of atoms is presented in Fig. 1. As shown in Fig. 1 two kinds of hydrogen bonds exist between C–G interaction, N–H…O and N–H…N that N and O atoms are as proton donor and H atom is as proton acceptor. The configuration of C, G and C–G were fully optimized in water, methanol, ethanol, ether, chloroform, acetone and DMSO solvents using B3LYP/6311++G** level of DFT theory to find optimized geometry and investigated intermolecular HB energy in the various solvents. The PCM method was used to calculate the effect of solvent on HB strength. According to the average of the calculated HB energies given in Table 1, it is clear that HB strength in gas phase is stronger than in solution phase. Among the solvents, HB strength decreases as follows: Water ≈ methanol ≈ ethanol ≈ DMSO ≈ acetone N ether ≈ chloroform As seen, this order was shown that polar solvents cause stronger HB and non-polar solvents cause weaker HB strength. So, cytosine–guanine interaction in ether and chloroform solvents is weaker than other solvents. Stability of cytosine, guanine and C–G increased in polar solvents while formation energy of C–G complex decreased in these solvents (see Fig. 2). The binding energies of C–G complex have been given in Table 1. As shown, binding energy (B.E.) decreases when the dielectric constant (Ԑ) of the solvents increases. So, according to the binding energies, formation of C–G complex in ether and chloroform, as non-polar solvents, are more favorable than other polar solvents. The dielectric constant curve in terms of binding energy is presented in Fig. 3. Stability order (S.O.) of C–G complex also changes with the dielectric constant. The smaller dielectric constant, the lower stability order will be. On the other hand, when the dielectric constant decreases, the stability also decreases. The C–G stability order values in different solvents and the change curves of dielectric constant in terms of the stability order have been shown in Table 1 and Fig. 3, respectively. Also, there is an excellent linear correlation between stability order and binding energy with correlation coefficient (R2) equal to 0.999 with an equation as: B.E. = − 0.665 S.O.–56.01. This correlation with negative slope shows that although C–G complex has the most binding energies in ether and chloroform (as non-polar solvents), its stability in non-polar solvent is lower than others. 3.2. AIM analyses In order to describe atomic interaction, the AIM calculation was carried out. The atomic interaction is classified in two general classes. The nature of interaction is exposed by the electron density (ρ) at bond

Fig. 1. The optimized structure of C–G complex and the numbering of atoms.

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M. Yoosefian, A. Mola / Journal of Molecular Liquids 209 (2015) 526–530

Table 1 Hydrogen bonds energies (EHB in kJ/mol), binding energy (B.E.) and stability order (S.O.) of the cytosine–guanine complex and dielectric constants (Ԑ) of the solvents. Media

EHB(O8…H26)

EHB(O28…H6)

27 EHB(N …H10)

B.E.

S.O.

Ԑ

Gas phase Water DMSO Methanol Ethanol Acetone Chloroform Ether

−53.40 −32.04 −32.27 −32.33 −32.45 −32.68 −35.08 −35.43

−38.84 −34.84 −34.49 −34.46 −34.56 −34.23 −32.71 −32.51

−43.34 −34.95 −34.85 −34.89 −34.94 −34.85 −34.83 −34.83

−109.66 −56.04 −56.59 −57.83 −58.75 −59.55 −73.01 −74.68

80.75 0.00 1.22 2.52 3.84 5.00 24.61 27.09

… 80 46.8 32.7 24.5 20.7 4.81 4.33

critical point (BCP), and it's Laplacian, ∇2ρ. When ρ is large and ∇2ρ b 0, it indicates existing concentration of electronic charge in the internuclear region and defines covalent bond (polar bond). When ρ is small, and ∇2ρ N 0, the internuclear region is diminution of electronic charge and identifies closed-shell interactions such as ionic interactions, van der Waals interactions or HBs [19,20]. The topological parameters of C–G interaction in the selected solvents are presented in Table 2. It is known that electron density of N…H bond (ρN…H) and O…H bond (ρO…H) in gas phase is larger than in the solvents and the calculated Laplacian at

Table 2 Topological parameters of C–G in different solvents at B3LYP/6-311++G** level. Media

ρO8…H26

∇2ρO8…H26

ρO28…H6

∇2ρO28…H6

ρN27…H10

∇2ρN27…H10

Gas phase Water DMSO Methanol Ethanol Acetone Chloroform Ether

0.0434 0.0293 0.0294 0.0294 0.0295 0.0297 0.0313 0.0315

0.1190 0.1015 0.1020 0.1021 0.1023 0.1028 0.1069 0.1074

0.0336 0.0311 0.0309 0.0309 0.0309 0.0307 0.0297 0.0296

0.1143 0.1061 0.1055 0.1055 0.1057 0.1051 0.1025 0.1021

0.0380 0.0330 0.0329 0.0329 0.0329 0.0329 0.0328 0.0328

0.1001 0.0860 0.0859 0.0860 0.0861 0.0860 0.0866 0.0867

the critical points for N…H (∇2ρN…H) and for O…H (∇2ρO…H) is positive. These features are characteristic for closed-shell interactions indicating electrostatic character of the N…H and O…H bondings. The geometrical parameters of the EHB and HBs of C–G in gas phase and the solvents have been given in Tables 1 and 3, respectively. There is a good relationship between the geometrical parameters of HB and its strength. Generally, the shorter the hydrogen bond distance, the stronger the EHB will be. Finally, Fig. 4 presents the contour map of C, G and C–G in water solution obtained from the B3LYP/6-311++G** wave function.

Fig. 2. Dependency chart between stability order and binding energy of cytosine, guanine and C–G complex.

40.00 S.O. = -10.05ln(ε) + 39.309 R² = 0.9258

20.00

dielectric constant (ε) 0.00

Energy

0

20

40

60

80

B.E. S.O.

-20.00

-40.00

-60.00

-80.00

100

B.E. = 6.9519ln(ε) -83.186 R² = 0.9288 Fig. 3. The relationship between S.O. and B.E. versus solvent dielectric constant.

M. Yoosefian, A. Mola / Journal of Molecular Liquids 209 (2015) 526–530 Table 3 Geometrical parameters of HBs in C–G complex in different solvents (length in Ǻ). Media

N24–H26

N7–H10

N4–H6

O8…H26

O28…H6

N27…H10

Gas phase Water DMSO Methanol Ethanol Acetone Chloroform Ether

1.035 1.024 1.024 1.024 1.025 1.025 1.027 1.027

1.032 1.037 1.036 1.036 1.036 1.036 1.035 1.035

1.020 1.024 1.024 1.024 1.024 1.024 1.023 1.023

1.772 1.877 1.875 1.874 1.873 1.871 1.848 1.845

1.919 1.854 1.857 1.857 1.856 1.859 1.872 1.874

1.920 1.920 1.921 1.921 1.920 1.921 1.921 1.921

3.3. NBO analyses In terms of NBO theory [21], the X–Y…Z interaction can be attributed to the localized Lp(Z) → σ⁎(X–Y) interaction due to electronic delocalization from the filled lone pair (Z) of “electron donor” Z into the unfilled antibond σ⁎(X–Y) of “electron acceptor” X–Y bonds [22–28]. Stabilization energy, E(2), reflects the attractive interaction in the X–Y…Z bonding and thus can be used to characterize the strength of the X–Y…Z bond. The theoretical results of NBO analysis show that two lone pair electrons of oxygen (or nitrogen) atoms take part as donor and σ⁎(N–H) antibonds as acceptor. Some of the most important donor–acceptor interactions in the selected solvents at B3LYP/ 6-311++G** level of DFT theory are listed in Table 4. In C–G complex, oxygen and nitrogen atoms of C (or G) interact with the N–H bond of G (or C), furthermore, charge transfer takes place from the lone pair of oxygen (or nitrogen) to σ⁎(N–H) antibond. In comparison with water, antibonding orbital occupancy in polar solvents is the same as water, specifying the polar solvents don't have a special effect on HB of C–G complex.

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Table 5 Orbital energies (HOMO and LUMO), energy gap (Eg in eV) and hardness (η) of C–G complex in the selected solvents. Media

HOMO

LUMO

Eg

η

Gas phase Water DMSO Methanol Ethanol Acetone Chloroform Ether

−5.501 −5.972 −5.966 −5.958 −5.950 −5.943 −5.825 −5.811

−1.696 −1.454 −1.455 −1.458 −1.461 −1.462 −1.505 −1.512

3.805 4.519 4.511 4.500 4.489 4.481 4.320 4.299

1.902 2.259 2.255 2.250 2.244 2.240 2.160 2.150

the chemical stability of molecule is to study the chemical hardness and softness of that one [31,32]. From energy gap between HOMO and LUMO, one can find whether the molecule is hard or soft. Large energy gap is an indication of hard molecule and small energy gap is the sign of soft molecule. The soft molecules are more polarizable than the hard ones because they need small energy for excitation. The hardness value of a molecule can be determined as η = (ELUMO − EHOMO) / 2 [33]. Table 5 summarizes the HOMO, LUMO, band gaps and the hardness value of cytosine–guanine complex in the different solvents. Based on Table 5, Eg in gas phase is smaller than other solvents and it shows that charge transfer is higher than in gas phase. Also, η value in gas phase is lower than other cases, indicating stability of cytosine–guanine complex in gas phase is lower than in solution. It is obvious there is not big difference between gap energy of water and the polar solvents. Accordingly, these solvents are not more polarizable than water and the stability of C–G complex among them is the same. As a result, polar solvents are safe and can be used in biological research. There is an excellent linear relationship between hardness value versus stability order and binding energy with the same correlation coefficient as 0.999 which their formulas are indicated as follows, respectively:

3.4. Molecular orbital analyses The energy gap between HOMO and LUMO (Eg) has an important role in getting polarizability of a molecule [29]. Small energy gap indicates that molecule is more polarizable [30]. One way to investigate

η ¼ ð−0:004Þ S:O: þ 2:260

ð2Þ

η ¼ ð0:0058Þ B:E: þ 2:585:

ð3Þ

Fig. 4. The contour map of cytosine, guanine and C–G complex in water solvent obtained from the B3LYP/6-311++G** wave function.

Table 4 NBO analysis of C–G complex, Occupation numbers of Donor (O.N.D) and Acceptor (O.N.A) orbitals and their energies (in kcal/mol) of some important orbitals. Media

Gas phase Water DMSO Methanol Ethanol Acetone Chloroform Ether

LP(2)O28 → σ *N4–H6

LP(1)O28 → σ *N4–H6

LP(1)N27 → σ *N7–H10

LP(2)O8 → σ *N24–H26

LP(1)O8 → σ *N24–H26

O.N.D

O.N.A

E(2)

O.N.D

O.N.A

E(2)

O.N.D

O.N.A

E(2)

O.N.D

O.N.A

E(2)

O.N.D

O.N.A

E(2)

1.8577 1.8657 1.8657 1.8656 1.8654 1.8654 1.8636 1.8633

0.0314 0.0390 0.0387 0.0386 0.0387 0.0384 0.0367 0.0365

8.40 11.39 11.25 11.23 11.27 11.13 10.47 10.38

1.9707 1.9693 1.9694 1.9694 1.9694 1.9694 1.9697 1.9698

0.0314 0.0390 0.0387 0.0386 0.0387 0.0384 0.0367 0.0365

3.88 4.74 4.70 4.69 4.70 4.67 4.49 4.47

1.8714 1.8719 1.8720 1.8720 1.8719 1.8720 1.8719 1.8719

0.0589 0.0637 0.0635 0.0635 0.0635 0.0633 0.0622 0.0620

18.83 19.98 19.91 19.92 19.93 19.86 19.60 19.57

1.8568 1.8701 1.8699 1.8697 1.8694 1.8692 1.8660 1.8656

0.0529 0.0391 0.0393 0.0394 0.0396 0.0398 0.0425 0.0429

14.54 9.63 9.68 9.72 9.78 9.84 10.77 10.90

1.9624 1.9688 1.9687 1.9686 1.9686 1.9684 1.9672 1.9670

0.0529 0.0391 0.0393 0.0394 0.0396 0.0398 0.0425 0.0429

7.59 5.09 5.15 5.15 5.17 5.23 5.71 5.78

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These correlations also confirm very well that by increasing the hardness, the binding energy diminishes and the stability increases. 4. Conclusion In this paper, we investigated the effect of various solvents on hydrogen bond of cytosine–guanine complex at B3LYP/6-311++G** level of DFT theory. The NBO and AIM analyses were employed to get more details about the nature of hydrogen bond strength. Theoretical results showed that hydrogen bond of C–G complex in gas phase is stronger than liquid phase and in the polar solvents is approximately the same as water and higher than non-polar solvents. Also, binding energy in ether higher than other solvents illustrating formation of C–G complex in this solvent is more favorable. According to this, the more binding energy, the more trend of DNA to double-stranded will be. The calculations performed on stability showed that among the solvents, the C–G complex stability in the polar solvents is approximately equal and higher than non-polar solvents. Therefore, these solvents are safe and harmless materials without producing any side effects on DNA bonds. References [1] D.L. Nelson, A.L. Lehninger, M.M. Cox, Lehninger principles of biochemistry, Macmillan, 2008. [2] E.T. Kool, Hydrogen bonding, base stacking, and steric effects in DNA replication, Annu. Rev. Biophys. Biomol. Struct. 30 (2001) 1–22. [3] K. Magnander, K. Elmroth, Biological consequences of formation and repair of complex DNA damage, Cancer Lett. 327 (2012) 90–96. [4] B.E. Reubinoff, M.F. Pera, C.-Y. Fong, A. Trounson, A. Bongso, Embryonic stem cell lines from human blastocysts: somatic differentiation in vitro, Nat. Biotechnol. 18 (2000) 399–404. [5] M. Frisch, G. Trucks, H. Schlegel, G. Scuseria, M. Robb, J. Cheeseman, et al., Gaussian 03, revision D. 01, Gaussian Inc., Wallingford, CT, 2004. [6] A.D. Becke, Density‐functional thermochemistry. III. The role of exact exchange, J. Chem. Phys. 98 (1993) 5648–5652. [7] J. Tomasi, R. Cammi, B. Mennucci, C. Cappelli, S. Corni, Molecular properties in solution described with a continuum solvation model, Phys. Chem. Chem. Phys. 4 (2002) 5697–5712. [8] E. Espinosa, E. Molins, C. Lecomte, Hydrogen bond strengths revealed by topological analyses of experimentally observed electron densities, Chem. Phys. Lett. 285 (1998) 170–173. [9] R. Bader, P. MacDougall, C. Lau, Bonded and nonbonded charge concentrations and their relation to molecular geometry and reactivity, J. Am. Chem. Soc. 106 (1984) 1594–1605. [10] K. Biegler, J. Schonbohm, R. Derdan, D. Bayles, R. Bader, AIM2000, Version 2.000, 2000. [11] E. Glendening, A. Reed, J. Carpenter, F. Weinhold, NBO, Version 3.1, Gaussian Inc., Pittsburg, PA, CT, 2003. [12] A.S. Moreira, F.G. Horgan, T. Kakoul-Duarte, T.E. Murray, Bumblebee (Hymenoptera: Apidae) sample storage for a posteriori molecular studies: Interactions between sample storage and DNA-extraction techniques, Eur. J. Entomol. 110 (2013). [13] J.M. Baust, R. Van Buskirk, J.G. Baust, Cell viability improves following inhibition of cryopreservation-induced apoptosis, In Vitro Cell. Dev. Biol. Anim. 36 (2000) 262–270.

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