Platinum complexation with glutamate amino acid: Computational study

Abstract

In this research work, complex formation of platinum (Pt) metal particle with the glutamate (Glu) amino acid was investigated by performing density functional theory (DFT) calculations. Such application could be very much important regarding the importance of developing metal based biosensors for biological media. To achieve the purpose of this work, two spin numbers of 0 and 1 were considered for Pt for locating separately towards neutral and anionic forms of Glu for Pt / Glu complexes formations. The obtained results of optimization and QTAIM analyses indicated various configurations for different spin numbers of Pt metal particle towards each of neutral and anionic forms of Glu. Existence of covalent bond was observed for most cases in addition to existence of weak van der Waals interactions for the complexes.

Keywords

Glutamate amino acid platinum density functional theory (DFT)QTAIM

1 Introduction

Glutamate (Glu) amino acid acts as a major excitatory neurotransmitter presented in various structures of the human and animal brains involving in various physiological effects such as learning, memory and brain development, and synaptic flexibility [1]. Glu is not able to cross the blood brain barrier made from glucose or glutamine in mitochondria of nerve cells [2, 3]. Increased concentration of Glu in the synapse space and extracellular fluid through the process of excitatory toxicity leads to nerve cell damage causing neurons to die from Glu [4]. Glu transporters are responsible for regulating synaptic transmission and the amount of Glu in the synaptic space [5]. Recent physiological studies have shown that the Glu transporters could keep the concentration of Glu at the synapse low enough to prevent stimulus sensitivity or toxicity and any disorder in Glu transporter activity might lead to occurrence of a neurological diseases [6, 7]. Therefore, such concentration of existence of Glu should be screened avoiding any attack to human health system. In this regard, nanostructures have been seen useful to interact with biological molecules for various detection purposes through complex formations [8 –10]. In this case, metal nanoparticles have shown variety of application from catalytic industry to biological systems, even in pharmacotherapy of cancer tumors [11]. Platinum (Pt) has also shown significant advantages for applications in biological systems, in which cisplatin has been one of the important drugs for medication in chemotherapy [12 –14]. Indeed, investigating materials features have been always seen as importat topic for researchers of various fileds [15]. Moreover, combinations of substances could yield new substnces for different purposes [16 –18]. In this regard, inorganic based biological compounds could work important functions for specified purposes [19 –21]. Nanoparticle-related materials have been also used for sensor applications in living systems as nanobiosensors to detect biological molecules [22 –24]. It is worth to note that such nano-based systems have important functions not only directed with biological systems but with important functions for environments [25, 26]. For the case of biological systems, because of electronic configurations of biological molecules with atoms including lone pairs of electrons, metal nanoparticles could work very well for complexation processes due to their plenty of vacant orbitals [27]. Therefore, it could be an advantage of employing such metal nanoparticles for detection of Glu acting in the form of nanobiosensor for detection at the lowest concentration of analytes [28 –30]. It is also important to mention that such metal-related complexes could make possible better detection of materials due to characteristic electronic configurations and transitions [31 –33]. To make sense such idea, computer-based works could help to examine the investigated systems at the lowest molecular and atomic scales revealing insightful information for the targeted problems [34 –36]. First principles computations could help to reveal insightful information for the investigated systems avoiding complexity of experimental media in addition to employing predictive methodologies for describing experiments [37, 38].

Hereby, Pt complexation with Glu amino acid was investigated in this work employing computer-based methodologies. To this aim, each of various configurations of Pt and Glu were investigated based on achieving minimized electronic energy complex formations through the use of DFT which also allows for determination of Gibbs free energy and entropy values in addition to enthalpy values. It is important to mention that the coordination systems and geometries are very much important for assigning functions for complex of materials systems [39 –41]. Indeed, exploring effects of such systems are also important regarding the changes of electric environments and generated signals [42 –44]. Therefore, the importance of this work could be oriented to investigate geometries of complex formations of the external substances at the smallest size such as a Pt particle for Glu detection especially in nervous system. On the other hand, computer-evaluated features could help to analyze the complex formation systems in details to show the advantage and disadvantage of considering such process for Glu detection.

2 Computational methods

In this work, density functional theory (DFT) calculations were performed at the level of B3LYP/6-31 + G^* using the Gaussian software, in which the LANL2DZ base set was used for Pt atom [45 –47]. The geometries of singular Glu were optimized in two forms of neutral and anionic states (Glu° and Glu^–) to reach the minimized energy structures. Next, possible configurations for Pt complexation with Glu were examined through performing further optimizations of Pt/Glu complex systems. All optimized geometries were summarized as supporting information in a supplementary file. Further calculations were performed regarding the evaluation of quantum theory atom in molecule (QTAIM) features for better analyzing the complex systems. Additionally, thermodynamic features were evaluated for the investigated systems in the reaction pathway as indicated by eq. (1), in which energy of complex formation (ΔE) was obtained by eq. (2) based on energy differences of singular components and complex. $Pt + Glu \to [Pt / Glu]$ (1) $Δ E = E_{[Pt / Glu]} - E_{Pt} - E_{Glu}$ (2)

3 Result and discussion

The optimized structures of neutral and anionic forms of Glu were shown in Fig. 1. In addition to performing optimization processes to reach the minimized energy structures, other possibilities of achieving the most stable structures were examined by scanning energies for rotatable bonds. As indicated in Fig. 2, the dihedral angles φ1 = (N2-C2-C1-O1), φ2 = (C4-C3-C2-N2), φ3 = (C5-C4-C3-C2) and φ4 (O5-C5-C4-C3) with 5° change were scanned to obtain the most stable system, in which the results confirmed the already optimized structures as the minimized energy systems.

Fig. 1

Optimized structures of neutral (a), and anion (b) forms of Glu molecule. Please see the supplementary file for obtaining the optimized geometries.

Fig. 2

Displaying scanned dihedral angles of Glu molecule.

To investigate Pt complexation with Glu, each of neutral and anionic forms of Glu were studied resulting five models based on positioning of Pt towards the molecular surface assigned by Fig. 2. In the first model, complexation of Pt with the amine section of Glu was investigated to form [Pt / Glu (N)] complex. In the second model, complexation of Pt with carbonyl attached to Cα of Glu was investigated to yield [Pt/Glu (C₁O)] complex. In the third model, complexation of Pt simultaneously with carbonyl and hydroxyl groups of Cα of Glu was investigated to yield [Pt / Glu(C₁OOH)] complex. In the fourth model, complexation of Pt with carbonyl of Cγ of Glu was investigated to yield [Pt / Glu(C₅O)] complex. And in the fifth model, complexation of Pt simultaneously with carbonyl and hydroxyl attached to Cγ of Glu was investigated to yield [Pt / Glu(C₅OOH)] complex. In all cases, two spin state wits summations of S = 0 and S = 1 were considered for the Pt metal particle to interact with each of Glu° and Glu^– components as discussed by the following text.

4 Formations of [Pt (S = 0) / Glu° (NH₂)] and [Pt (S = 0) / Glu (NH₂)] Complexes

In this step, the most stable Glu conformers in neutral and anionic forms were optimized separately in the presence of Pt (S = 0) towards the amine group. As shown in panels a and b of Fig. 3, the Pt metal particle (S = 0) was relaxed in distances of 2 Å and 1.99 Å with the nitrogen atom for neutral and anionic forms of Glu, respectively. In this complex formation, energies (ΔE) of –42.2 kcal.mol^–1 and –57.5 kcal.mol^–1 were obtained for Pt (S = 0) / Glu° (NH₂)] and [Pt (S = 0) / Glu (NH₂)] complexes, respectively.

Fig. 3

Optimized structures of complexes of Pt (S = 0) with Glu: (a) and (b) from the amine group, (c) and (d) from the head carbonyl bonded to carbon-α, (e) and (f) from the carboxylic acid attached to carbon-α, (g) and (h) from the carbonyl head attached to carbon-γ, (i) and (j) from the carboxylic head attached to carbon-γ. The distances were shown in angstrom. Please see the supplementary file for obtaining the optimized geometries.

5 Formations of [Pt (S = 0) / Glu° (C₁O)] and [Pt (S = 0) / Glu (C₁O)] Complexes

In this step, the most stable conformers of Glu in neutral and anionic forms were optimized separately in the presence of Pt (S = 0) metal particle. Due to the created resonance of the carboxyl group in the anionic form, both positions of O₁′ and O₁ were possible for interacting with the Pt metal particle as shown in Fig. 4. The results showed that the Pt metal particle interacted with the O₁′ atom of anionic and neutral forms of Glu but only with the O₁ atom of the anionic Glu, in which the distances were obtained 2.23 Å from the O₁′ atom in the neutral form and 1.98 Å from each of the atoms O₁′ and O₁ of the anionic form as shown by c and panels of Fig. 3. Accordingly, three values of ΔE including –27.8 kcal.mol^–1, –42.3 kcal.mol^–1, and –43.8 kcal.mol^–1 were obtained for the mentioned three models, respectively.

Fig. 4

Resonance generated in the carboxylic group attached to carbon α and creating the position of interaction with the O₁ atom with platinum metal particle (S = 0).

6 Formations of [Pt (S = 0) / Glu° (C₁OOH)] and [Pt (S = 0) / Glu (C₁OO)] complexes

The most stable Glu conformers in neutral and anionic forms were optimized separately in the presence of Pt (S = 0) metal particle paced at the middle point towards O₁′ and O₁ atoms. The results show that the Pt nanoparticles (S = 0) interact with the atom of the carboxylic fraction C₁OOH. As shown in panels e and f of Fig. 3, the Pt metal center was relaxed with the distances of 2.94 Å from the O₁ atom and 2.03 Å from the O₁′ atom of neutral form. It was also relaxed with the distances of 1.98 Å from the O₁ atom and 3.29 Å from the O₁′ atom in the anionic form. Accordingly, values of ΔE including –27.8 kcal.mol^–1 and –41.4 kcal.mol^–1 were obtained for the mentions configurations, respectively.

7 Formations of [Pt (S = 0) / Glu° (C₅O)] and [Pt (S = 0) / Glu (C₅O)] complexes

Complexations of Pt (S = 0) metal particle with each of neutral and anionic forms of Glu were optimized regarding the relaxation of Pt towards O5′ atomic site. The calculated results showed interaction distances of 2.02 Å and 2.01 Å with each of neutral and anionic forms as exhibited in panels g and h of Fig. 3. The values of ΔE for formation of these complexes were found to be –27.7 kcal.mol^–1 and –21.3 kcal.mol^–1 for neutral and anionic complexes, respectively.

8 Formations of [Pt (S = 0) / Glu° (C₅OOH)] and [Pt (S = 0) / Glu (C₅OOH)] complexes

In the final model, Pt (S = 0) metal particle was relaxed towards O₅′ and O₅ atoms of C₅OOH group in each of neutral and anionic forms of Glu for formation of corresponding complexes. Accordingly, distances of 2.02 Å for Pt from the O₅′ atom and 2.96 Å from the O₅ atom were found in the neutral form and distances of 2.96 Å for Pt from the O₅ atom and 2.01 Å from the O₅′ atom were found in the anionic form of complexes as exhibited in panels i and j of Fig. 3. The values of ΔE were found to be –24.3 kcal.mol^–1 and –32.6 kcal.mol^–1 for each of neutral and anionic complexes, respectively.

9 Complexation of Pt (S = 1) metal particle with neutral and anionic forms of Glu

As described within the previous section, parallel calculations were performed to examine complexes formations of Pt (S = 1) metal particle with each of already defined atomic position of Glu in neutral and anionic forms. Avoiding duplication of texts about complex formations of this part, all results were exhibited in Table 1 and Fig. 5 to be reached visually for the corresponding complexes. Generally, more or less significant variations were found comparing the results of Pt (S = 1) with those of Pt (S = 0) models formations.

Table 1
Energies of complex formations (ΔE kcal.mol^–1) for Pt (S = 0) and Pt (S = 1) metal particles with neutral and anionic forms of Glu

Atomic Site of Glu Glu° Glu^–

Pt (S = 0) Pt (S = 1) Pt (S = 0) Pt (S = 1)

[N₂] –42.19 –9.90 –57.47 –21.58

[C₁O₁′] –27.84 –4.23 –42.28 –20.48

[C₁O₁] – – –43.77 –19.18

[C₁OOH]/[C₁OO^–] –27.84 –4.23 –41.45 –28.43

[C₅OOH] –24.28 –4.59 –32.56 –8.35

[C₅O] –27.69 –4.23 –21.28 –8.37

Atomic Site of Glu		Glu°		Glu^–
[N₂]	–42.19	–9.90	–57.47	–21.58
[C₁O₁′]	–27.84	–4.23	–42.28	–20.48
[C₁O₁]	–	–	–43.77	–19.18
[C₁OOH]/[C₁OO^–]	–27.84	–4.23	–41.45	–28.43
[C₅OOH]	–24.28	–4.59	–32.56	–8.35
[C₅O]	–27.69	–4.23	–21.28	–8.37

Fig. 5

Optimized structures of complexes of Pt (S = 1) with Glu: (a) and (b) from the amine group, (c) and (d) from the head carbonyl bonded to carbon-α, (e) and (f) from the carboxylic acid attached to carbon-α, (g) and (h) from the carbonyl head attached to carbon-γ, (i) and (j) from the carboxylic head attached to carbon-γ. The distances were shown in angstrom. Please see the supplementary file for obtaining the optimized geometries.

Table 2

QTAIM results for Pt metal particle complexes formations with the neutral form of Glu

	Complex	∇²ρ	ρ
1	Pt(S = 0)-N	–0.127731	0.125679
	Pt(S = 1)-N	–0.053877	0.060778
2	Pt(S = 0)-O₁′	–0.142046	0.102859
	Pt(S = 1)-O₁′	–0.014929	0.027453
3	Pt(S = 0)-O₅′	–0.017470	0.038517
	Pt(S = 1)-O₅′	–0.040017	0.039470
4	Pt(S = 0)-O₅′	–	–
	Pt(S = 0)-O₅	0.017484	0.038524
	Pt(S = 1)-O₅′	–0.042729	–0.045154
	Pt(S = 1)-O₅	–0.014780	0.025900
5	Pt(S = 0)-O₁′	–	–
	Pt(S = 0)-O₁	–0.017671	0.041888
	Pt(S = 1)-O₁′	–0.041015	0.042369
	Pt(S = 1)-O₁	–0.014911	0.027395

Table 3

QTAIM results for Pt metal particle complexes formations with the anionic form of Glu

	Complex	∇²ρ	ρ
1	Pt(S = 0)-N	–0.119465	0.131100
	Pt(S = 1)-N	–0.010011	–0.009631
2	Pt(S = 0)-O₁	–	–
	Pt(S = 1)-O₁	–	–
3	Pt(S = 0)-O₁′	–	–
	Pt(S = 1)-O₁′	0.443373	0.338997
4	Pt(S = 0)-O₅′	–	–
	Pt(S = 1)-O₅′	–0.019598	0.019187
5	Pt(S = 0)-O₅′	–0.031655	–0.025879
	Pt(S = 0)-O₅
	Pt(S = 1)-O₅′	–0.019736	0.019346
	Pt(S = 1)-O₅
6	Pt(S = 0)-O₁′	–	–
	Pt(S = 0)-O₁	–	–
	Pt(S = 1)-O₁′	–0.035679	0.030825
	Pt(S = 1)-O₁

The results of Table 1 showed that the Pt (S = 0) was more suitable than Pt (S = 1) for complex formation with the Glu amino acid with more favorability of anionic form rather than neutral form. The Pt (S = 0) metal particle showed greater tendency to react with the amine sections of both of neutral and anionic forms of Glu with the values of –42.2 kcal.mol^–1 –57.5 kcal.mol^–1 for ΔE, respectively. The Pt (S = 1) metal particle was in more favorable complex formation with the amine group of neutral Glu but it was more favorable for compex formation with (C₁OO^–) of anionic Glu. The results indicated the importance of geometrical configurations for the complex formations of Pt with Glu as described for different spin states of Pt and neutral and anionic forms of Glu.

10 QTAIM analysis

The quantum theory of atom in molecule (QTAIM) was used to investigate the nature of interacting bonds of the Pt metal particle with each of neutral and anionic forms of Glu as important descriptive features of interacting systems [48, 49]. To this aim, AIM2000 software was used for analyzing QTAIM results [50 –52]. Table 1 included the values of electron density (ρ) and Laplacian (▿²ρ) features to investigate interactions between the components of complexes. Negative value of ∇²ρ were found for most cases of complex formations showing the existence of a covalent bond in the corresponding system. On the other hand, the complexes could show lower covalent property and higher van der Waals property in lower values of ρ. For the Pt (S = 1) with O₁′ complex formation, the positive value of ∇²ρ and the amount of ρ both could predict the weak van der Waals interactions for the complex system. For other complexes formations, the negative value of ∇²ρ, indicated the existence of covalent bond for the interacting system.

11 Conclusion

The major goal of this work was to perform DFT computations to investigate Pt complex formations with neutral and anionic forms of Glu. Different spin numbers summations of 0 and 1 were considered for Pt. Various configurations of possible complex formations were optimized to reach the minimized energy structures of Pt / Glu. The obtained results indicated more favorability of complex formations for Pt metal particle and anionic form of Glu in comparison with the neutral form of Glu. Additionally, the performed QTAIM analyses to find the nature of the bonds of complexes indicated that the negative value of ∇²ρ indicated possibility of covalent bond formation in most cases of complexes. Moreover, van der Waals interactions were also seen for some cases based on values of both of ∇²ρ and ρ features. As a consequence, the results indicated that Pt metal particle could very well participate in complex formation with Glu amino acid for different purposes of diagnosis and capturing regarding the importance of biological applications.

Footnotes

The supplementary material is available in the electronic version of this article: .

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Platinum complexation with glutamate amino acid: Computational study

Abstract

Keywords

1 Introduction

2 Computational methods

7 Formations of [Pt (S = 0) / Glu° (C5O)] and [Pt (S = 0) / Glu (C5O)] complexes

8 Formations of [Pt (S = 0) / Glu° (C5OOH)] and [Pt (S = 0) / Glu (C5OOH)] complexes

9 Complexation of Pt (S = 1) metal particle with neutral and anionic forms of Glu

11 Conclusion

Footnotes

References

7 Formations of [Pt (S = 0) / Glu° (C₅O)] and [Pt (S = 0) / Glu (C₅O)] complexes

8 Formations of [Pt (S = 0) / Glu° (C₅OOH)] and [Pt (S = 0) / Glu (C₅OOH)] complexes