Electronic structure analysis of glycine oligopeptides and glycine–tryptophan oligopeptides

Electronic structure analysis of glycine oligopeptides and glycine–tryptophan oligopeptides

Physica E 57 (2014) 63–68 Contents lists available at ScienceDirect Physica E journal homepage: www.elsevier.com/locate/physe Electronic structure ...

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Physica E 57 (2014) 63–68

Contents lists available at ScienceDirect

Physica E journal homepage: www.elsevier.com/locate/physe

Electronic structure analysis of glycine oligopeptides and glycine–tryptophan oligopeptides Xin Li a, Shuai Yu a, Mengshi Yang a, Can Xu c, Yu Wang b, Liang Chen b,n a

School of Engineering, Zhejiang Agriculture and Forestry University, Lin'an 311300, Zhejiang, China School of Science, Zhejiang Agriculture and Forestry University, Lin'an 311300, Zhejiang, China c Key Lab for Magnetism and Magnetic Materials of Ministry of Education, School of Physical Science and Technology, Lanzhou University, Lanzhou Gansu 73000, China b

H I G H L I G H T S

 Chemical reaction activity on oligopeptides has size effect in growth process.  The shortest chain of Gn and GWn oligopeptieds are determined which has the same reaction activity as that of longer size peptide.  It is easy in self-assembly for Glycine oligopeptides chain, but difficult for Glycine–Tryptophan.

art ic l e i nf o

a b s t r a c t

Article history: Received 24 July 2013 Received in revised form 15 October 2013 Accepted 20 October 2013 Available online 6 November 2013

Using the density functional theory (DFT), we have studied the energy gap, charge distribution, density of states and chemical activity of glycine (Gn) oligopeptides and glycine–tryptophan (GWn) oligopeptides. The results show that: (1) with the increasing of Gn residues, the chemical activity of Gn oligopeptides focuses on the terminal amino and carboxyl groups, which may be the main cause of self-assembly behaviors in Gn oligopeptide chains; (2) the chemical reaction activity has size effect. The size effect disappears when the residue number exceeds 7. The Gn oligopeptides with 7 residues is the shortest chain which has the same reaction activity as that of longer size peptide; (3) the activity of GWn oligopeptides presents size effect and odd-even effect. However, the size effect and odd-even effect both vanish when the chain of GWn oligopeptides is longer than 12 residues. (4) It is difficult in self-assembly for GWn oligopeptide chains, because its activity mainly focuses on the indole ring and the Gn residues at the end of oligopeptides. (5) The big side groups result in the very near energy level of LUMO and LUMOþ 1 of GWn oligopeptide chains. It shows that the electron-accepting ability of oligopeptide chainsis composed of two orbitals addition. The results in the paper may help us understand the changes of physical and chemical properties of peptide synthesis process. & 2013 Elsevier B.V. All rights reserved.

Keywords: Oligopeptides Density of states Frontier obital Size effect Electronic structure

1. Introduction Because of the advantages of high removal efficiency, less usage, good solubility and non-toxic, amine derivative formaldehyde elimination is regarded as the most promising method for removing formaldehyde [1–4]. Wang et al. [5,6] used aminated collagen to make formaldehyde scavenger. It has a good removal effect. Another effective method to deal with free formaldehyde in the sheets [7] is using urea, non-volatile amine and amino acids etc. The fundamental principle of this method is sealing epoxy with amine and formaldehyde. Recently, nanofiller with high efficiency of removing formaldehyde has been widely

n

Corresponding author. E-mail address: [email protected] (L. Chen).

1386-9477/$ - see front matter & 2013 Elsevier B.V. All rights reserved. http://dx.doi.org/10.1016/j.physe.2013.10.028

studied [8,9]. Due to high activity, the amino group on oligopeptides can react with formaldehyde to achieve the purpose of capturing formaldehyde. Moreover, the nano oligopeptides have excellent properties of self-assembly and degradability [10,11]. For the good ecological effects, nano oligopeptides now present great potential application in formaldehyde elimination. There has been a lot of research work about amino acid and protein in this field [12–15]. Perczel [16,17] studied how residue number affects the conformation propensity, and find that conformational propensity will change with the increasing of residues. In the field of nanotechnology, physical and chemical properties of nanoscale system show transitional change with unit number increasing [18–22]. And nanoscale system often has different properties from solid material and single molecule, such as size effect and anisotropic phenomena in the nanoparticles. Yu [23–25] has done a detailed analysis of the amino acid, dipeptide and tripeptide.

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However, it is not clear whether the number of peptide residues (especially the length) would affect physical and chemical properties in the oligopeptide chains growth process. And oligopeptides used to remove formaldehyde as nanometer fillers is rarely reported. In our previous work [26], we have simulated the oligopeptides growth process using density functional method. We find that the oligopeptide chain trends to grow into larger group in energy through the average binding energy analysis, and the infrared (IR) frequencies of typical functional groups shift with the number of residues increasing. In this study, we will calculate electronic structure and investigate how the residue number and existing of large side groups affect the activity of other groups and terminal amino. In addition, we also attempt to explore the effect of oligopeptides type and length on the activity of terminal amino and other groups. The results may be of great an importance in modification of oligopeptides and nano oligopeptides as filler to remove formaldehyde.

2. Computational methodology In this work, we selected RB3LYP/6-31G(d) basis set to optimize 7 Gn (n represents the number of residue) oligopeptide chains and 6 GWn oligopeptide chains and then calculated the density of states, HOMO–LUMO and atomic charge distribution. Cluster geometries were optimized using DFT which was based on Becke's hybrid three-parameter exchange function [27] combined with the LYP correlation functional [28] (B3LYP) method with the 6-31G (d) basis set. And we also computed 5 oligopeptide chains at WB97XD/6-311 þG(d, p) level [29] which is a dispersion-corrected density functional theory (DFT-D) [30] includes empirical dispersion and long range corrections, to analysis the influences on the accuracy of the calculation results produced by various DFT methods and different sets. The structure models of oligopeptide chains are showed in Fig. 1. Frequency calculation shows no imaginary frequency existed, the optimized structures are stable. All calculations were performed by using Gaussian 09 software package [31].

3. Results and discussion 3.1. Oligopeptide chain's density of states and atomic charge distribution The frontier orbitals of different residues from two kinds of different oligopeptides, the electronic (HOMO–LUMO) gaps, and Fermi level are given in Table 1. Eg and EF are given by Eg ¼ LUMO HOMO; EF ¼ HOMO þ 12 ðLUMO  HOMOÞ

where HOMO is the highest occupied molecular orbital and LUMO is the lowest unoccupied molecular orbital. We focus on the Eg of all structures, because they determine the chemical stability of oligopeptides. The value of the Eg reflects the ability for an electron to jump from the occupied orbital to the unoccupied orbital. To some degree, it represents the intensity of chemical reactions. The smaller the Eg is, the greater chemical activity oligopeptide chain will have. It can be seen from Table 1 that: Eg is monotonically decreasing with the increasing Gn residues; with the increasing of GWn residues, Eg trends to declining with fluctuations, which indicates that the chemical reactivity of two types of oligopeptide chains is enhanced and electronic structure is unstable with the increasing residues. Through further analysis, we find that Eg of Gn and GWn converge at 5.09 eV and 4.05 eV, respectively. When n is odd, Eg is well consistent with that of GW11. Meanwhile, Eg is in good agreement with that of GW12 when n is even. Furthermore, when the number of residue is more than 7, Gn oligopeptides hold the same chemical reactivity. Correspondingly, when the number of residue is more than 12, the fluctuations of GWn oligopeptides disappear, and they will present the same chemical reactivity. Therefore, G7 may be the shortest oligopeptide which has the same activity as large oligopeptides, and GW12 could be the most active structure in small GWn oligopeptides. In addition, Eg of GWn is always smaller than that of Gn when they have the same “n”. It shows that the chemical activity of GWn oligopeptides which have large side groups is higher than that of Gn oligopeptides. Fig. 2 shows two kinds of total density of state of Gn and GWn. With the increasing residues, peaks become wider and higher because of the increasing same electron orbital. It is found that little change happens in Eg, which converge to a fixed value when the oligopeptide chain is short. This phenomenon is obviously different from inorganic MgO nanotubes and SiO2 nanotubes [32–34]. Longer MgO nanotubes and SiO2 nanotubes still have size effect. The converged Eg of oligopeptide is one of reasons why proteins have stable functions. Atomic charge distributions were analyzed. The charge of nitrogen (N) atom in ending amino from Gn and GWn was kept stable at  0.7221, and two hydrogen (H) atoms at 0.3205 and 0.2930, respectively. In Gn: the charge of carbon (C) and oxygen (O) atom in the ending epoxy (4C ¼O) were stabilized at 0.5658 and  0.4583, and the charge of O and H atom of the Hydroxy (– OH) is about  0.5574 and 0.4227, respectively. In the main chain of the Gn, the charge of C and N atom of peptide bond is about 0.5957 and  0.6218. Because of the different kinds of the ending residue in GWn, the atomic charge distribution in the terminal carboxyl of GWn exist odd–even effect. When n is even, the charge of C and O atom of ending epoxy (4C ¼O) is close to 0.5738 and  0.4733, and the charge of O and H atom of the Hydroxy (–OH) is

Fig. 1. The optimized structures of Gn oligopeptide chains (a) and GWn chains (b) (

carbon atom,

oxygen atom,

nitrogen atom,

hydrogen atom).

X. Li et al. / Physica E 57 (2014) 63–68

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Table 1 HOMO  2, HOMO  1, HOMO, LUMO, LUMOþ 1, LUMO þ 2, Eg and EF of two types of opeptide chains. n

Gn

2 3 4 5 6 7 8 2 3 4 5 6 7

GWn

Density of State (arb.u.)

12

-20

HOMO  2 (eV)

HOMO  1 (eV)

 7.15  6.87  6.74  6.66  6.62  6.59  6.57  6.24  6.11  5.70  5.82  5.54  5.51

-16

-12

 7.01  6.79  6.68  6.61  6.57  6.55  6.53  5.83  5.95  5.66  5.63  5.53  5.50

-8

-4

HOMO (eV)

LUMO (eV)

LUMOþ 1 (eV)

LUMOþ 2 (eV)

Eg (eV)

EF (eV)

 6.25  6.10  6.02  5.97  5.94  5.92  5.90  5.31  5.45  5.16  5.13  5.04  5.01

 0.31  0.52  0.63  0.69  0.73  0.76  0.78  0.22  0.22  0.56  0.57  0.70  0.72

0.66 0.26 0.05  0.06  0.13  0.17  0.20 0.00  0.18  0.42  0.47  0.55  0.57

1.56 0.88 0.48 0.28 0.16 0.09 0.04 0.67 0.28 0.04  0.07  0.31  0.29

5.94 5.58 5.39 5.28 5.21 5.16 5.12 5.09 5.23 4.60 4.56 4.34 4.29

 3.28  3.31  3.33  3.33  3.34  3.34  3.34  2.77  2.84  2.86  2.85  2.87  2.87

0

10

6 4

-16

-12

-8

-4

-8

-4

0

12

10

10

8

8

4 2

-20

-12

10

6

2

-16

12

8

G8 G7 G6 G5 G4 G3 G2

8

-20

12

Density of State (arb.u.)

Oligopeptides

6

6

GW7 GW6 GW5 GW4 GW3 GW2

4

4 2

2

0

-20

-16

-12

Energy (eV)

-8

-4

0

Energy (eV)

Fig. 2. Total density of state of Gn oligopeptides and GWn oligopeptides.

near  0.5506 and 0.4157. Correspondingly, when n is odd, the charge of C, O, O, H atom of ending carboxyl group is 0.5798, 0.4574,  0.5543 and 0.4179, respectively. However, the charge on peptide bond of GWn is quite in accordance with Gn's, and is almost not changed with residual number. There is no size effect in atomic charge distribution. It shows that the oligopeptide chains have good stability.

TOTAL-G5 H N O C

5

Statistical analysis of partial density of state data is done. Partial state density figure of some typical oligopeptide chains are shown in Figs. 3 and 4. HOMO of Gn is mainly composed of N and H atoms, the percentage of contribution is 92%, and the remain comes from C, O atoms; LUMO is entirely composed of C, O, H atoms. And the proportion of atoms is not changing with oligopeptide length. HOMO of GWn is composed of C, N atoms by 97%, and O, H atoms with small part; and the contribution of atoms is near a constant as increasing residues. Remarkably, the energy difference between LUMO and LUMO þ1 of GWn is very small; the two levels have obvious odd–even effect, because the terminal residues alternate with residual number. When the residues n is even, the end of oligopeptide chains is W residue, LUMO is mainly composed of C, O atoms, 72% and 24% is the percentage; LUMOþ 1 is mainly composed of the same atoms by 85% and 10%, respectively. When n is odd, oligopeptide chains is end with G residue, LUMO of GW3 is completely contributed by C, O, H atoms; while GW5, GW7 mainly contributed by C atom, the contribution is about 94%; in the LUMOþ 1 orbital, GW3 oligopeptide chain is mainly composed of C atom, the percentage is about 93%, while GW5, GW7 oligopeptides completely contributed by C, O, H atoms.

Density of State (arb.u.)

4

3.2. Partial density of states and frontier orbitals

3 2 1 0 -1 -20

-15

-10

-5

0

Energy (eV) Fig. 3. partial density of state of G5 oligopeptide chain.

In short, our analysis shows that HOMO orbital of Gn is mainly determined by N, H atoms; LUMO orbital have an entire contribution from C, O, H atoms. HOMO of GWn has the same distribution as Gn's, but LUMO is different. The electron accepting ability is provided together by LUMO and LUMO þ1 of GWn, as the small energy difference of the two levels. Odd–even effect still exists. When the residues n is even, LUMO and LUMO þ1

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TOTAL-GW2 H N O C

5

5

Density of State (arb.u.)

Density of State (arb.u.)

4 3 2 1 0 -1 -20

TOTAL-GW3 H N O C

4 3 2 1 0

-15

-10

-5

-1 -20

0

-15

Energy (eV)

-10

-5

TATOL-GW4 H N O C

TATOL-GW5 H N O C

5

4

4 Density of State (arb.u.)

Density of State (arb.u.)

5

3 2 1 0 -1 -20

3 2 1 0

-15

-10

-5

-1 -20

0

-15

Energy (eV)

-10

-5

H N O C

5

TOTAL-GW7 H N O C

5 4 Density of State (arb.u.)

4 Density of State (arb.u.)

0

Energy (eV)

TOTAL-GW6

3 2 1

3 2 1 0

0 -1 -20

0

Energy (eV)

-15

-10

-5

0

Energy (eV)

-1-20

-15

-10

-5

0

Energy (eV)

Fig. 4. partial density of state of GWn oligopeptide chains. (a)GW2, (b)GW3, (c)GW4, (d)GW5, (e)GW6, (f) GW7.

orbitals have same distribution; when n is odd, however, LUMO and LUMO þ1 orbitals are located on different atoms, as shown in Fig. 4. Large side groups of GWn oligopeptides result in the odd– even effect.

3.3. Electron density distribution of oligopeptide chains Electron density distribution of frontier orbitals is shown in Fig. 5. In agreement with the results in preceding section, the

X. Li et al. / Physica E 57 (2014) 63–68

HOMO of Gn is mainly distributed in the amino and methylene groups at the end of oligopeptide chains; meanwhile, there is a small amount of distribution in N, O atoms of peptide bond near the amino. Distribution of the LUMO is mostly located on the carboxyl and methylene groups, which is in another end of Gn chains, and there is also a very small distribution in the epoxy (4 C¼ O) of peptide bond near terminal carbonyl. In contrast with Gn, HOMO of GWn is mainly located on the first indole ring and methylene, and a small distribution is in the first and second peptide bonds near amino. When n is even, the ending tryptophan residue is the location of LUMO and LUMOþ1, and a small amount is distributed in the epoxy ( 4C ¼O) on peptide bond near terminal carbonyl. However, distribution of LUMOþ 1 is different with LUMO when n is odd; LUMO focus on indole ring of tryptophan side group, as shown in Fig. 6, but LUMOþ 1 has the same distribution as Gn residues. Moreover, GW3 has an abnormal distribution, which is influenced by the large side group when chain is short. Its dipole moment is almost not the direction along the oligopeptide chain. From the distribution of frontier orbitals above, we draw a conclusion that, chemical activity of Gn mostly concentrates on amino, methylene and carboxyl groups at the two ends of chain, Oligopetide HOMO

LUMO

orbital

67

and the location of activity is unchanged with length of residues. The location is conducive to a chainlike growth in self-assembly process. Compared with the Gn, loss of electrons in GWn chains mainly occur at the indole ring near N-terminal, instead of the amino and methylene. The big side groups weaken the loss of electrons of amino. In addition, electron-accepting ability of oligopeptide chains which determined by LUMO and LUMO þ1, exists distinct odd–even effect in the growth process. When n is even, the whole terminal tryptophan residues easily accept electrons; when n is odd, indole ring in the LUMO and glycine residue in the LUMOþ 1 easily accept electrons. The presence of large side groups affects the location of HOMO, LUMO and LUMO þ1. It makes reactive groups turn from ending group to indole ring and glycine residues, and the ending amino is inactive. So, GWn is difficult to accomplish self-assembly due to the location of chemical activity on GWn. In general, amino acids, oligopeptides and collagen have good effect on removing aldehydes [7,35,36]. The essence is sealing carbonyl with the reaction of active amine and formaldehyde, thus enabling function of formaldehyde absorption. From such an analysis of electronic properties, Gn oligopeptide chains will have better absorption capacity than GWn oligopeptide chains for the activity of amino groups, as a nano filler to removal formaldehyde. The GWn end amino almost has no activity. The results have an important guiding significance to oligopeptides, chemically modified proteins. 3.4. Comparison of DFT methods for electronic structure

G2

G4

G5

G7 Fig. 5. HOMO and LUMO of Gn at B3LYP/6-31G(d) level.

The deviations between DFT and DFT-D are very small, though the DFT-D results agree better with the experimental data than those of DFT [37]. In our work, the result of WB97XD/6-311 þG(d, p) level has not obvious difference with that of RB3LYP/6-31G(d) method. Energies of LUMO are not changed, although energy gaps become a little wider for HOMO decreased with high level; the optimized structures using two different methods are basically the same; variation of bond length is about 0.01–0.05 nm; and there is almost unchanged in the distribution of HOMO and LUMO, as

Oligopeptide residues orbital

HOMO

LUMO

LUMO+1

GW2

even GW4

GW6

GW3

odd

GW5

GW7 Fig. 6. HOMO, LUMO and LUMO þ1 of GWn at B3LYP/6-31G(d) level.

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X. Li et al. / Physica E 57 (2014) 63–68

Oligopetide

HOMO

LUMO

Acknowledgments

orbital G5

GW4

Fig. 7. HOMO and LUMO of G5 and GW4 at WB97XD/6-311þ G(d, p) level.

shown in Fig. 7. The datum of two methods is in a reasonable range. With the costs of high-level quantum chemistry calculation method considered, we use the B3LYP/6-31G(d) to analysis a growth process of oligopeptide chains is reasonable. It lowered computer demands so that energy optimization of large residues is possible. 4. Conclusion In summary, we have investigated the electronic structures of Gn and GWn oligopeptide using density functional theory. In the simulation of the oligopeptides growth process, the Eg of Gn residues decreases monotonically, and quickly converges to a fixed value; but the energy gap of GWn shows a decline with the odd– even effect, and fast approaches to a fixed value either. The atomic charges are almost unchanged on the chains. These results can partially explain why oligopeptides and protein have good stability. With increasing Gn residues, the activity is focused on the ending amino and carboxyl groups of chains. It explains the selfassembly of Gn oligopeptide chains. The energy levels of LUMO and LUMOþ 1 of GWn containing large side groups are very near; the electron-accepting ability of GWn is composed of the two orbitals. The activity of GWn presents an apparent odd–even effect. When the number of residues turns from even to odd, chemical activity which initial focuses on the terminal tryptophan residue, diverts to locates on indole ring in tryptophan and ending glycine residues. According to the analysis of activities on amino groups, we find that Gn oligopeptides are good nanofiller with high efficiency of removing formaldehyde, however GWn oligopeptides is not a potential material for the inactivity on amino groups. The results help us understand the transitional changes of physical and chemical properties of peptide synthesis process. It can also provide important theoretical guidance for choosing nano oligopeptide chains with high activity and short segments as filler and formaldehyde absorbents.

The authors are indebted to the reviewers for valuable comments.

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