A computational study of cysteine and glutathione binding to small gold cluster Au₈

Science & Technology Development Journal, 23(1):430-438 Open Access Full Text Article Research Article 1Computational Chemistry Research Group, Ton Duc Thang University, Ho Chi Minh City, Viet Nam 2Department of Chemistry, CanTho University, Viet Nam Correspondence Nguyen Thanh Si, Computational Chemistry Research Group, Ton Duc Thang University, Ho Chi Minh City, Viet Nam History  Received: 2019-10-07  Accepted: 2019-12-10  Published: 2020-02-17 DOI : 10.32508/stdj.v23i1.1715 Copyright © VNU-HCM Press. This is an open- access article distributed under the terms of the Creative Commons Attribution 4.0 International license. A computational study of cysteine and glutathione binding to small gold cluster Au8 Nguyen Thanh Si1, Pham Vu Nhat2 Use your smartphone to scan this QR code and download this article ABSTRACT Introduction: Understanding the binding mechanism between gold nanoparticles and biomolecules is a fundamental step for numerous applications in biosensors and targeted drug delivery. This study aims to clarify the adsorption behaviors of CYS and GSH on the gold surface using a small gold Au8 cluster as a model reactant. Methods: Here, we examine in details the molecular interaction between Au8 cluster with cysteine (CYS) and glutathione (GSH) by means of density functional theory (DFT). The PBE functional is employed in combination with the cc-pVTZ basis set for non-metal atoms and the cc-pVTZ-PP basis set for gold. Harmonic vibrational frequen- cies are also computed to confirm optimized geometries as local minima or transition states on the potential energy surfaces. Results: The calculated results show that these molecules prefer to an- chor on the gold cluster via the sulfur atom with the adsorption energies of 20.3 and 30.8 kcal/mol for CYS and GSH, respectively, in gas phase. In water, such values are considerably reduced, namely 19.0 kcal/mol for CYS and 26.4 kcal/mol for GSH. If a visible light with a frequency of n = 6x1014 Hz (500 nm) is applied, the time for the recovery of CYS and GSH from the most stable complexes will be about 1.24 and 6.03x107 seconds at 298 K in gas phase. Conclusion: The Au8 cluster could be a promising material for designing sensor in CYS and GSH selective detection. Key words: Au8 cluster, cysteine, density functional theory, glutathione INTRODUCTION In the past decades, gold clusters have been the sub- ject of various studies owing to their potential applica- tions in biosensors1,2, catalysis3, biomedical dignos- tics4,5, organic synthesis6,7, environment4, drug de- livery systems8, analysis9, electrochemistry10,11. Re- cently, relevant studies have been carried out to eluci- date the nature of interactions between biomolecules including amino acids, peptides, DNA constituents and small gold clusters, using both experimental and theoretical techniques. According toXie et al.12, the interaction between gold cluster Aun (n = 3, 4) with cysteine and glycine is sta- bilized mainly due to Au-NH2 bond via the transfer of charge from the amine group to the Au atom. In another investigation on cysteine and larger gold Aun cluster (n = 8, 10 and 12) 13, the resulting complexes were found to be stabilized due to the strong AuS bonding. Interactions of proline amino acid with Au3 cluster was also examined by DFT calculations14. Ac- cordingly, two factors, i.e. the anchoring N-Au, O-Au bonds and the non-conventional O-H: : :Auhydrogen bond, dominate the interactions. Other striking find- ing is that gold clusters prefer to anchor on the termi- nal amide group13–15. In a study ofM3 clusters (M=Ag, Au andCu) binding to histidine in both neutral and anionic states, Javan et al.16 found that the metal clusters tend to oxidize histidine by getting electron from the lone pair or- bitals of N, O, S atoms, and form highly stable anchor bonds. Scanning tunneling microscopy was also em- ployed to probe the cysteine deposited on the Au(111) surface17. Novel network-like cluster structures of the layers with six and three cystine molecules on the Au surface have been found. A molecular dynamics sim- ulation study of the adsorption mechanism of twenty amino acids and four surfactants on Au(111) in aque- ous solution predicted an absorption energy around 3-26 kcal/mol18. The adsorption strength were found to correlate well with the degree of coordination of polarizable atoms (O, N, C) and determined by the molecular size/shape. Cysteine and glutathione are among the most impor- tant thiol-containing compounds due to their special role inmany biochemical reactions19. Cysteine (CYS) has many important cellular functions and its pres- ence in biological fluids such as human plasma and urine is essential for clinical diagnostics of several dis- eases. The molecule on a solid surface is an impor- tant issue for either protein study or differentiating amino acids19. Previous study of cysteine adsorption Cite this article : Thanh Si N, Vu Nhat P. A computational study of cysteine and glutathione binding to small gold cluster Au8. Sci. Tech. Dev. J.; 23(1):430-438. 430 Science & Technology Development Journal, 23(1):430-438 on Au(100) showed the tendency of flat adsorption geometries due to the thiolate-amino bonds20. Glutathione (GSH) or tripeptide g-L-glutamyl-L- cysteinyl-glycine iswell-known for its function in pro- tecting the blood red cells from oxidative damage and maintaining the standard reduced state of the cells. In addition, the molecule is an integral part in the detoxification of the cells, responsible for elim- ination of harmful organic peroxides and free rad- icals. Accordingly, it absorbs toxins including pes- ticides, solvents, and heavy metals, then converting them into forms that are able to be excreted in urine or bile19. Moreover, its anionic form exhibits the par- ticularly high tendencies to interact with gold clus- ters21. Recently, Thomas and co-workers22 intro- duced a novel approach for selective detection of cys- teine and glutathione in many biological systems us- ing gold nanorods. Despite numerous efforts devoted to the absorption of such thiol-containing compounds on AuN systems, the interaction mechanism is still not fully under- stood. Additionally, most of previous studies were performed in vacuum, while the effects of solvents have not been taken accounts. Understanding the interaction mechanism of gold nanoparticles with biomolecules is a fundamental step in designing and development of tiny biosensors. This theoretical study aims to elucidate the adsorption behaviors of two thiol-containing cysteine and glu- tathione on the gold surface using small goldAu8 clus- ter as a model reactant. Current results could provide us with fundamental insights into the functionaliza- tion of gold nanoclusters with biomolecules and en- visage their applicability in bio-chemical sensing and detection. COMPUTIONALMETHODS All calculations were performed with the aids of the Gaussian 09 program23. The geometries were fully optimized, making use of the functional PBE in con- junction with the basis sets cc-pVTZ-PP24 for gold and cc-pVTZ for non-metals. Initial structures of theAu8CYS andAu8GSH com- plexes for geometry optimizations were created by attaching biomolecules via electron-rich centers, i.e. the S, N and O atoms, to the lowest-energy form of Au8. Harmonic vibrational frequencies were also computed to verify that optimized geometries are true local minima and to estimate the zero-point vibra- tional energy (ZPE) corrections. Zero-point and ther- mal enthalpies corrections were then employed to predict free energies via the Equation (1). 4Go (298 K) = 4E + 4ZPE + 4TCG (1) whereDE is the relative electronic energy at 0 K;DZPE is the relative vibrational energy at 0 K; DTCG is rela- tive changes in Gibbs free energy going from 0 to 298 K. The complextion energy Ec of the interaction be- tweenAu8 cluster and CYS/GSHwas computed as the value of energy difference: Ec = EAu8:CYS=GSH (EAu8 +ECYS=GSH) (2) where EX is the lowest electronic energy of the X species. Hence, a negative value of Ec indicates a fa- vorable adsorption. The greater the computed value of the complexation energy, the stronger is the affin- ity of cysteine binding to the gold cluster. The effect of solvent (water) was simulated using the default model IEF-PCM (Integral Equation Formalism-Polarizable ContinuumModel)25 provided by Gaussian. For deeper insights into the effect of interacting species on each other, the electronic properties such as the HOMO-LUMO energy gap (Eg) and the den- sity of states (DOS) were examined. The Eg is a suit- able aspect for defining the kinetic reactivity of mate- rials26, and its conversion upon the adsorption pro- cess reflects the sensitivity of an adsorbent to an ad- sorbate. The GaussSum program27 has been used for DOS calculations. RESULTS - DISCUSSION Structural optimization As expected, Au8 cluster prefers to interact with CYS or GSH species through electron-rich atoms, i.e. S, N and O atoms. These atoms with lone pair are more willing to form bonding with the 5d and 6s orbitals of the Au atom. At the PBE/cc-pVTZ/cc-PVTZ-PP level of theory, we located four conformations for Au8CYS complexes, denoted as C1-C4 (Figure 1), while for Au8GSH complexes, eight isomersG1-G8 (Figure 2) have been obtained. Noticeably, the ge- ometries of both CYS, GSH and Au8 cluster are al- most unmodified during the complexation. In addi- tion, these structures have positive harmonic frequen- cies, indicating that they are local minima on the po- tential energy surfaces. The calculated complexation energies and bond lengths of the resulting complexes are listed in Table 1. The most stable conformation of Au8CYS complex, i.e. C1 form in Fig. 1, is formed by anchoring the thiol group on the low-coordinated gold atom of the Au8 ring. This can be understood by the hard-soft acid-base (HSAB) theory28, as the softer sulfur ele- ment ismorewilling to form strong bondswith soft el- ements like gold than the harder nitrogen and oxygen elements. In the C1 complex, the Au-S bond length 431 Science & Technology Development Journal, 23(1):430-438 Figure 1: Optimal structures located for the Au8CYScomplex in gas-phase (C1-C4). The relative values (kcal/mol) to the lowest-energy C1 conformation are given in brackets Table 1: Complexation energy (Ec, kcal/mol), Au-Y bond length (rAuY ; o A) of the Au8.CYS complexes (C1-C4) at the same PBE/cc-pVTZ/cc-pVTZ-PP level of theory Conformation Ec Bond C1 -20.27 Au- 2.395 C2 -18.50 Au- 2.520 Au-O 2.383 C3 -17.87 Au- 2.225 Au-H 2.156 C4 -14.06 Au-O 2.266 is 2.395 Å, which is slightly longer than the sum of covalent radii of Au (1.35 Å) and S (1.02 Å) atoms. Previous study also predicted that Au atom exhibits a higher affinity with S atom29. The second most stable species C2, which is con- structed by binding Au8 to the thiol and carbonyl groups of CYS is only about ~2 kcal/mol higher in en- ergy than the C1 conformation. The Au-S and Au-O distances in C1 are 2.520 and 2.383 Å, respectively, which are quite larger than the sum of covalent radii of Au-S (2.370 Å) and Au-O (2.080 Å) bonds. The remaining conformations including C3 and C4 con- formation are the most unstable conformations. In these conformations, they are formed by anchoring Au atom on CYS through N and O atoms, having stronger basicity than S atom. The second element is that their associated lengths are larger than the total of theirs covalent radii are 2.100 and 2.080 Å, respec- tively. For the interaction between Au8 cluster and GSH molecules, eight conformations, i.e. G1-G8 in Fig- ure 2, have been located. Among these, the most sta- ble structureG1 is formed by anchoring the Au8 moi- ety on the S and O atoms of the thiol and carbonyl group. The Au atom has strong affinity with S atom, but the formation of inter-molecular hydrogen bonds (H-bonds) in GSH is also a vital factor that signifi- cantly contributes to stabilizing the Au8.GSH com- plex21. In fact, in the G1 conformer, the calculated result obtain three H-bonds, namely N-H


O=C, S- H


O=C andCOOH


NH2 bonds. TheH-bonds in G1 are much shorter than those of other products. The next isomerG2 is only about ~3 kcal/mol less sta- ble than the ground-state form G1. In G2, the Au atom links with cystenyl (Au-S) and glutamyl (Au- O), increasing the internal H-bonds in GSH. The re- maining conformations (G3-G8) are quite unstable, being around 10-19 kcal/mol above the most stable formG1. InG3-G8 complexes, the gold cluster bind- 432 Science & Technology Development Journal, 23(1):430-438 Figure 2: Optimal structures located for the Au8GSH complex in gas-phase (G1-G8). The relative val- ues(kcal/mol) to the lowest-energy G1 conformation are given in brackets. 433 Science & Technology Development Journal, 23(1):430-438 Table 2: Complexation energy (Ec, kcal/mol), Au-Y bond length (rAuY , Å) of the Au8.GSH complexes (G1 -G8) at the same PBE/cc-pVTZ/cc-pVTZ-PP level of theory Conformation Ec Bond rAuY G1 -30.75 Au- 2.399 Au-O 2.368 G2 -27.99 Au- 2.394 Au-O 2.318 G3 -20.68 Au-O 2.291 Au-O 2.408 G4 -17.32 Au-O 2.312 Au-O 2.368 G5 -14.37 Au-O 2.491 Au-O 2.296 G6 -13.94 Au-O 2.328 Au-O 2.496 G7 -12.93 Au-O 2.545 Au-O 2.330 G8 -12.01 Au-O 2.264 Au-H 2.620 ing toGSHmolecule through theO atoms of carbonyl groups. Chemical re activity The quantum chemical descriptors of Au8 cluster, CYS andGSHmolecules including chemical potential m , total hardness h and electrophile index w are also examined to evaluate the chemical reactivity of sys- tems considered. The calculated results at the PBE/cc- pVTZ/cc-pVTZ-PP level of theory are presented in Table 3. As expected, the Au8 has a more negative chemical potential than CYS and GSH molecules. In addition, the cluster exhibits a much larger electrophile index than the biomolecules. This strongly supports for the view that the metals are more willing to act as an electron-acceptor, while both CYS and GSH tend to be an electron-donor. Such a charge transfer from the biomolecules to the gold atoms results in a signifi- cant change in the HOMO-LUMO energy gap (4Eg), which is reported as follows: 4Eg = Eg2 Eg1  Eg1 x 100% (3) where Eg1 and Eg2 are the value of the Eg for the bare Au8 cluster and the Au8X (X = CYS, GSH) com- plexes, respectively. This parameter can also be used to evaluate the sensitivity of the clusters to the pres- ence of biomolecules. As shown in the plot of DOS (Figure 3), the band gap of Au8 inC1 (1.64 eV) andG1 (1.69 eV) considerably increase by 17% and 21%, respectively, as compared to that in the free Au8 (1.40 eV). In general, the HOMO energy of Au8 cluster is almost unchanged, while its LUMO energy substantially modified. In fact, due to an electron transfer from biomolecules to cluster, the LUMO of Au8 increased from -4.35 eV in free cluser to -3.92 eV and -3.84 eV in C1 andG1 complexes, re- spectively. Solvent effect and recovery time Let us recall that all calculations above are performed in gas phase. In practice, sensors are often used to de- tect substances in solution, i.e. water environment. Therefore, further calculations have been carried out to examine the effects of water solvent on the inter- actions, using the IEF-PCM model (Integral Equa- tion Formalism-Polarizable Continuum Model). The computed results are summarized in Table 4. In water, complexation energies, the changes of en- thalpy and free energy become less negative, but also exhibit a similar trend as in gas phase. This is due to the fact that hydration energies of products are 434 Science & Technology Development Journal, 23(1):430-438 Table 3: Quantum chemical descriptors of Au8 cluster, CYS and GSH at the PBE/cc-pVTZ/cc-pVTZ-PP level of theory Structures EHOMO, eV ELUMO, eV m , eV h , eV w , eV Eg, eV 4Eg, % Au8 -5.75 -4.35 -5.05 0.70 18.22 1.40 - CYS -5.99 -1.11 -3.55 2.44 2.58 4.88 - GSH -5.79 -1.64 -3.72 2.08 3.33 4.15 - C1 -5.56 -3.92 -4.74 0.82 13.70 1.64 17.14 G1 -5.53 -3.84 -4.69 0.85 12.94 1.69 20.71 Figure 3: The DOS plot of C1 (top) và G1 (bottom) complexes. 435 Science & Technology Development Journal, 23(1):430-438 smaller than the sum of hydration energies of reac- tants. However, the interactions in water are still products favored with negative changes of free ener- gies. When exposed to the UV-Vis light, the biomolecules can undergo a desorption process. Very strong inter- actions are not favorable for chemical sensors because the desorption could be difficult and the sensor may suffer from long recovery times. According the transi- tion state theory30, the recovery time (t , seconds) ex- ponentially depends on the binding energy Ec as fol- lows: t = (n0)1:exp(Ec=kBT ) (4) where T is the temperature, kB is the Boltzmann’s con- stant, n0 is the attempt frequency and kBT = 0.059 kcal/mol at 298 K. For the binding energy of -20.27 kcal/mol in vacuum, the recovery of cysteine molecules from the Au8 sur- face at 298 K is in the range of 0.025 to 1.7 seconds (Table 5). In water, the recovery of the molecule from the Au8 surface turns out to be rather faster (3102 to 2101s). This indicates that theAu8 cluster could be a promising candidate for detection of cysteine, even at room temperature. Due to stronger interac- tions with Au8, the GSH molecules undergo much longer recovery times, namely from 1.2 x 106to 8.4 x 107s in gas phase and 8.2 x 102 to 5.7 x 104 s in wa- ter. Therefore, the Au8 cluster can be used to design tiny reusable sensors for selective detection of CYS and GSH molecules. CONCLUSION In this work, the structures, energetic properties and effects of water solution on the interaction of cys- teine and glutathione molecules with the Au8 clus- ter was thoroughly examined by means of DFT cal- culations. The CYS and GSH moieties prefers to in- teract with the gold cluster through their thiol group. The nature of interactions is mainly determined by the charge transfer from the non-bonding pair of the sulfur atom to the empty orbitals of the gold clus- ter. Another noticable finding is that reactions of the gold cluster with these species are facile in nature, i.e. either molecular or dissociative chemisorptions are involved, rather than breaking molecular bonds and making again stronger bonds between the resulting fragments and the metals. The tendency to retain the initial forms of adsorbed molecules makes these clus- ters of great potential for applications in biochemical sensing and detection. If a visible light with a fre- quency of n= 6 x 1014Hz (500 nm) is applied, the time for the recovery of CYS andGSH from themost stable complexes will be about 1.24 and 6.03 x 107 seconds at 298 K in gas phase. This indicates that Au8 cluster can be a promising candidate to develop tiny sensors in CYS and GSH selective detections. COMPETING INTERESTS The authors declare that there is no conflict of interest regarding the publication of this article. 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