Computational study of molecular structures and antioxidant mechanism of ovothiols - Le Tien Dung

Journal of Science and Technology 54 (2C) (2016) 328-333 COMPUTATIONAL STUDY OF MOLECULAR STRUCTURES AND ANTIOXIDANT MECHANISM OF OVOTHIOLS Le Tien Dung1, Pham Thi Thanh Xuan1, Dinh Tuan2, Pham Le Minh Thong3, Pham Cam Nam1, * 1University of Danang - University of Science and Technology, Faculty of Chemistry, 54 Nguyen Luong Bang, Da Nang and VN-UK, Institute for Research & Executive Education 2Hue University’s College of Sciences, Department of Chemistry, 77 Nguyen Hue, Hue 3Duy Tan University, Institute of Research and Development, 03 Quang Trung, Da Nang *Email: pcnam@dut.udn.vn; camnamp@yahoo.com Received: 15 June 2016; Accepted for publication: 23 October 2016 ABSTRACT In this paper, the molecular structure and antioxidant activity of ovothiols (OSH) have been studied by using four DFT functionals, namely B3LYP, B3PW91, X3LYP, M06 with the basis set of 6-311++G(2df,2p). Two major antioxidant mechanisms, namely, hydrogen atom transfer (HAT) and stepwise electron transfer-proton transfer (SET-PT) have been investigated and applied on three optimized conformations of ovothiols. Bond dissociation enthalpy (BDE), vertical ionization energy (IE), proton dissociation enthalpy (PDE), chemical potential (µ), chemical hardness (η) and global electrophilicity (ω), have been calculated and discussed in the gas phase. Keywords: ovothiols, antioxidant, HAT, SET-PT, BDE, IE, PDE, density functional theory. 1. INTRODUCTION Sulfur containing functional groups have been found to play an important in both primary and secondary metabolites [1]. The maintenance of cellular redox homeostasis, the maintenance of protein thiol-disulfide ratios and the protection of cells from reactive oxygen species occur under the presence of thiols in living systems. Ovothiols (1-methyl-4-mercaptohistidines) are present in millimolar concentrations in sea urchin eggs [2]. Such high concentrations of these heterothiols might be needed to protect the fertilized sea-urchin egg from free radical induced damage. Recently, there has been a renewed interest in ovothiols arising from the identification and characterization of a 5-histidylcysteine sulfoxide synthase (OvoA), the enzyme that catalyzes the first step of their biosynthesis [3]. Experimentally, OSH has been proposed to be one of the more powerful natural antioxidants and to be comparable to that of ascorbic acid and water-soluble vitamin E analogue [3]. Although, the scavenging reactions of radicals dissociated from ovothiols were investigated by pulse and gamma radiolysis techniques, how do ovothiols act as a H-atom and/or electron donors need to be illumined. Obviously, the antioxidant activity Computational study of molecular structures and antioxidant mechanism of ovothiols 329 of ovothiols was experimentally determined and can be predicted based on their optimized structures and the proved mechanisms. To the best of our knowledge, detailed computational study for antioxidant activity of OSH based on hydrogen atom transfer (HAT) and stepwise electron transfer-proton transfer (SET-PT) have not been reported elsewhere, encouraging us to fully examine the antioxidant reactivity of OSHs using DFT methods. 2. THEORETICAL MODELS AND COMPUTATIONAL METHODS Antioxidants are functionally divided into two major groups, preventive and chain-breaking, according to whether they reduce the rate of chain-initiation or capture the alternating alkyl (R•) and peroxyl (ROO•) radicals responsible for the oxidative propagation in organic matter. The mechanism of hydrocarbon autoxidation and antioxidant protection is illustrated in Figure 1 [4]. initiator RX preventive antioxidants ROO ROO non radical products RH X ROOH ROOH + OS OSH chain-breaking antioxidants kinh O2 initiation propagation termination kp kt kp rate constant of propagation kinh rate constant of inhibition kt rate constant of termination RH: hydrocarbon (lipid) OSH: Ovothiol Figure 1. Simplified mechanism of hydrocarbon autoxidation and antioxidant protection. According to the reaction pathways of antioxidant protection in Figure 2, two acceptable mechanisms are described hereafter: i) Hydrogen atom transfer (HAT) mechanism: In this mechanism, the antioxidant capacity of ovothiols (OSH) can be explained via the hydrogen transfer process (R1) to the reactive oxygen/nitrogen species. The bond dissociation enthalpy of S-H bond is a key parameter. OSH + ROO• = OS• + ROOH (R1) ii) Single electron transfer followed by -proton transfer (SET-PT) OSH → OSH•+ + e- (R2) OSH•+ → OS• + H+ (R3) In Reaction R2, ionization energy (IE) of ovothiols (OSH) is a key thermo-parameter. The experimental and theoretical data have proved that the first step in this mechanism is significant to control the rate of reaction. Reaction R3 is characterized by proton dissociation enthalpy (PDE). All thermoparameters (BDE, IE and PDE) are calculated via the reaction enthalpy in the gas phase at 298.15 K and 1 atm of each reaction from R1 to R3. BDE(S−H) = H(OS•) + Hf(H•) + Hf(OSH) (1) IE(OSH) = Hf(OSH•+) + Hf(e-) – Hf(OSH) (2) PDE = Hf(OS•) + Hf(H+) – Hf(OSH•+) (3) Pham Cam Nam, Tien Dung Le, Xuan Thi Thanh Pham, Tuan Dinh, Pham Le Minh Thong 330 where Hf is the total enthalpy of the studied species at the temperature of 298.15 K and usually estimated from the expression below: Hf = E0 + ZPE + Htrans + Hrot + Hvib + RT. (4) The Htrans, Hrot, and Hvib are the translational, rotational, and vibrational contributions to the enthalpy, respectively. E0 is the total energy at 0 K and ZPE is the zero-point vibrational energy. Finite differences method proposed by Parr et al. allows approximating chemical potential as μ = − ½(IE + EA), chemical hardness as η = ½(IE + EA) and global electrophilicity as [5]. All computational calculations were performed by using Gaussian 09 program [6]. The structures of three OSHs, the corresponding radicals and anions were fully optimized by using the B3LYP/6-311G(d,p) level of theory. Single point calculations were carried out using several DFT methods at the basis set of 6-311++G(2df,2p). Restricted open shell (RO) procedures were applied for radical species at the same methods. 3. RESULTS AND DISCUSSION 3.1. Optimized structure of ovothiol Ovothiols with chemical formula of C7H8O2N2SNH3-x(CH3)x (x = 0, 1, 2) are abbreviated as OSHA, OSHB and OSHC respectively. It should be mentioned that there are more than one conformation for each ovothiol. Due to this reason, the calculated thermoparameters depend on the optimized conformations that we obtained. Therefore the examination for finding the most stable conformation for each OSH is necessary. OSHA OSHB OSHC Figure 2. Optimized structures of ovothiols at the B3LYP/6-311G(d,p) level of theory. The structure conformations described in Figure 2 correspond to the most stable one of OSHA or OSHB or OSHC. The hydrogen bond between oxygen of carbonyl and amino groups has been observed for all three OSHs. This leads to conclude that three optimized conformations given in Figure 2 are considered as the most stables ones. By comparing the bond lengths in three conformations, we recognized that the replacement of one or two methyl groups (CH3) for H of NH3 group, the deviations of bond lengths in the five membered ring are not significant. 3.2. Antioxidants of ovothiols 3.2.1. HAT mechanism By examining the structures of three OSHs, one can recognize that although there are several X-H bonds in OSHs, but only two bonds namely, S-H and C2-H at the imidazole ring need to be evaluated their BDEs. The comparison of bond strength between S-H and C2-H Computational study of molecular structures and antioxidant mechanism of ovothiols 331 bonds for three OSHs using the B3LYP/6-311++G(2df,2p) level of theory shows that S-H bond strength is the more weaker than C2-H in twice. For example, in case of OSHA, BDE(S-H) and BDE(C2-H) are 72.8 kcal/mol and 117.69 kcal/mol, respectively. To ensure the reliability of the calculated results, four DFT functionals namely, B3LYP, B3PW91, X3LYP and M06 were applied for determining the BDE(S-H) of three OSHs. The results are given in Table 1. Table 1. Calculated BDE(S-H) of ovothiols using four DFT functionals in kcal/mol. Compounds B3LYP B3PW91 X3LYP M06 OSHA 72.18 (0.00) 73.40 (1.22) 70.72 (-1.46) 71.95 (-0.27) OSHB 73.55 (0.00) 74.78 (1.23) 72.10 (-1.45) 73.62 (0.07) OSHC 69.87 (0.00) 70.98 (1.11) 68.46 (-1.41) 69.78 (-0.09) Data in parenthesis: ΔBDE= BDE(S-H)DFT-BDE(S-H)B3LYP The computed BDEs of (S-H) bond are consistent in four DFT functionals, the deviations among them are very slightly as can be seen in Table 3 (data in parenthesis). Among three ovothiols, the calculated BDE(S-H) can be arranged in the sequence: BDE(S-H) of OSH ovothiol C < BDE(S-H) of ovothiol A < BDE(S-H) of ovothiol B. It should be noted that the BDE(S-H)’s of the ovothiols are smaller than the BDE(O-H) of phenol (88.60 kcal/mol). As mentioned above, hydrogen atom transfer takes place at the weakest bond whose BDE value is the smallest. 3.2.2. SET-PT mechanism SET-PT reactions are usually slow and require long times to reach completion, so antioxidant capacity calculations are based on percent decrease in product rather than kinetics. In general, the first reaction (R1) plays more important role than the second one (R2). The calculated data for IE and PDE using DFT/6-311++G(2df,2p) are presented in Tables 2 and 3. The result at the PM6 is also given for the sake of the comparison. Table 2. Calculated IE in kcal/mol at different DFT/6-311++G(2df,2p) and PM6 methods. Ovothiols B3LYP B3PW91 X3LYP M06 PM6 OSHA 167.26 (0.00) 166.85 (-0.41) 166.43 (-0.16) 167.10 (0.64) 180.75 (13.48) OSHB 171.92 (0.00) 172.18 (0.26) 171.05 (-0.86) 171.98 (0.06) 177.57 (5.65) OSHC 172.17 (0.00) 172.14 (-0.03) 171.91 (-0.26) 174.01 (1.84) 179.67 (7.50) Obviously, the results obtained by using B3PW91, X3LYP and M06 at the same basis set are quite similar with the deviations are smaller than 1 kcal/mol (See data in bracket of Table 2). The largest deviation of 1.84 kcal/mol was observed for OSHC when using M06 method. IE value computed at PM6 method in in the last column is larger than IEs generating from DFT methods with amount of 6 to 13.5 kcal/mol. The lower IE value the higher antioxidant activity. Data in Table 3 shows the calculated results at four DFT methods are converged and the PDE at S-H bond of three ovothiols can be placed in order: OSHC <≈ OSHB < OSHA. Pham Cam Nam, Tien Dung Le, Xuan Thi Thanh Pham, Tuan Dinh, Pham Le Minh Thong 332 Table 3. Calculated PDE(S-H) bond using DFT/6-311++G(2df,2p), kcal/mol. Ovothiols B3LYP B3PW91 X3LYP M06 OSHA 205.93 207.15 204.48 205.66 OSHB 235.56 236.79 234.11 235.63 OSHC 204.71 205.82 203.30 204.62 3.2.3. Antioxidant mechanism and chemical reactivity of ovothiol radicals As mentioned above, the question raised here that do ovothiols act as an H-atom and/or electron donors. To answer this question, two factors need to be analyzed (ΔBDE = BDE(S- H)ovothiol – BDE(O-H)phenol and ΔIE = IEovothiol - IEphenol) in order to decide which mechanism is favor [7]. The BDE gap of OSHA, OSHB and OSHC referred to BDE(O-H) of phenol of 88.30 ± 0.70 kcal/mol are -16.12, -14.75 and -18.43 kcal/mol. In comparison with IE of phenol at the PM6 (193.4 kcal/mol), the difference between IE of three OSHs and phenol are within the range of -12 to -16 kcal/mol. Relative reactivity in HAT is determined by the BDE of the H-donating group in the potential antioxidant, dominating for compounds with the absolute values of ΔBDE are around 15 kcal/mol and the absolute values of ΔIE are not larger 36 kcal/mol [7]. Moreover, to predict the antioxidant capacity of three OSHs, we also examined the reactivity of the radicals formed from ovothiols by hydrogen removal at S-H bond via the global and local theoretical reactivity descriptors such as chemical potential (µ), chemical hardness (η) and global electrophilicity (ω). The estimated values of these global descriptors are shown in Table 4. Table 4. Global reactivity descriptors in kcal/mol. Ovothiol radicals µ η ω OS•A -140.11 64.82 151.43 OS•B -121.46 60.60 122.46 OS•C -132.44 64.45 136.08 In principle, the compound with the lowest value of hardness (η) and global electrophilicity (ω) is predicted to have the highest reactivity. Comparing the data from Table 4, the OS•B and OS•C radicals possess η and ω lower than that of OS•B, as a result they display less reactivity. This leads to the same conclusion stated above. 4. CONCLUSIONS In this work, the antioxidant activity of OSHA , OSHB and OSHC has been computationally. Several thermo-parameters including BDE, IE, PDE and quantum chemical indexes η, ω and µ were calculated using DFT/6-311++G(2df,2p) basis sets show that the antioxidant capacities of OSHA and OSHC are bettter than that of OSHB. In terms of theoretical reactivity descriptors, the radicals generated from OSHA and OSHC are more stable than from OSHB. The analysis of BDE and IE have led to a conclusion that for ovothiols, HAT is a major antioxidant mechanism and the BDE(S-H) for OSHA, OSHB, OSHC are 72.18, 73.55 and 69.87 kcal/mol. Computational study of molecular structures and antioxidant mechanism of ovothiols 333 Acknowledgements.This research is funded by Vietnam National Foundation for Science and Technology Development (NAFOSTED) under grant number 104.06-2015.09. PCN also thanks VN-UK, Institute for Research & Executive Education for partially financial support. REFERENCES 1. Fontecave M., Ollagnier C. S., Mulliez E. - Biological radical sulfur insertion reactions, Chemical Reviews 103 (2003) 2149-2166. 2. Shapiro B. M., Hopkins P. B. - Ovothiols: biological and chemical perspectives, Advances in enzymology and related areas of molecular biology 64 (1991) 291-316. 3. Marjanovic B., Simic M. G., Jovanovic S. V. - Heterocyclic thiols as antioxidants: why ovothiol C is a better antioxidant than ergothioneine, Free Radical Biology and Medicine 18 (1995) 679-685. 4. Amorati R., Foti M. C., Valgimigli L. - Antioxidant activity of essential oils, Journal of Agricultural and Food Chemistry 61 (2013) 10835-10847. 5. Parr R. G., Szentpály L. V, Liu S. - Electrophilicity Index, Journal of the American Chemical Society 121 (1999) 1922-1924. 6. Frisch M., Trucks G., Schlegel H. B., Scuseria G., Robb M., Cheeseman J., et al. - Gaussian 09. Gaussian, Inc. Wallingford, CT, 2009. 7. Wright J. S., Johnson E. R., DiLabio G. A. - Predicting the activity of phenolic antioxidants: theoretical method, analysis of substituent effects, and application to major families of antioxidants, Journal of the American Chemical Society 123 (2001) 1173- 1183. TÓM TẮT NGHIÊN CỨU BẰNG PHƯƠNG PHÁP TÍNH TOÁN CẤU TRÚC VÀ CƠ CHẾ CHỐNG OXY HÓA CỦA CÁC HỢP CHẤT OVOTHIOL Lê Tiến Dũng1, Phạm Thị Thanh Xuân1, Đinh Tuấn2, Phạm Lê Minh Thông3, Phạm Cẩm Nam1, * 1Khoa Hóa, Trường Đại học Bách khoa, Đại học Đà Nẵng, 54 Nguyễn Lương Bằng, Đà Nẵng và Viện Nghiên cứu và Đào tạo Việt Anh, 41 Lê Duẩn, Đà Nẵng 2Khoa Hóa, trường Đại học Khoa học Huế, 77 Nguyễn Huệ, Huế 3Viện Nghiên cứu và Phát triển – Đại học Duy Tân, 03 Quang Trung, Đà Nẵng *Email: pcnam@dut.udn.vn; camnamp@yahoo.com Trong bài báo này, cấu trúc phân tử và hoạt tính chống oxy hóa của các ovothiol (OSH) đã được nghiên cứu bằng cách sử dụng bốn hàm mật độ DFT là B3LYP, B3PW91, X3LYP, M06 tại bộ hàm cơ sở 6-311++G(2df,2p). Hai cơ chế chống oxy hóa chính bao gồm cơ chế chuyển hydro (HAT) và cơ chế chuyển tuần tự điện tử - chuyển proton (SET-PT) đã được nghiên cứu và áp dụng trên ba cấu trúc tối ưu của ovothiol. Năng lượng phân li liên kết (BDE), năng lượng ion hóa (IE), năng lượng phân li proton (PDE), thế hóa học (µ), độ cứng hóa học (η) và ái lực điện tử toàn phần (ω), đã được tính toán và thảo luận đối với các phân tử ovothiol trong pha khí. Từ khóa: ovothiols, chống oxy hóa, HAT, SET-PT, BDE, IE, PDE, density functional theory.