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ACS Omega
ACS Omega
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acsodf
ACS Omega
2470-1343
American Chemical Society

10.1021/acsomega.4c05684
Article
Detection of Phenylalanine by Iridium Nanoclusters Using Time-Dependent Density Functional Theory Calculations
Agrawal Neelam †
Bahota Ashok Singh †
Khan Areeba †
Chaudhary Rajni †
Singh Keshav Kumar †
https://orcid.org/0000-0002-8120-0498
Tandon Poonam *†‡
† Department of Physics, University of Lucknow, Lucknow, 226007 Uttar Pradesh, India
‡ Vice Chancellor in Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, 273009 Uttar Pradesh, India
* Email: tandon_poonam@lkouniv.ac.in.
28 08 2024
10 09 2024
9 36 3818638194
18 06 2024
22 08 2024
01 08 2024
© 2024 The Authors. Published by American Chemical Society
2024
The Authors
https://creativecommons.org/licenses/by-nc-nd/4.0/ Permits non-commercial access and re-use, provided that author attribution and integrity are maintained; but does not permit creation of adaptations or other derivative works (https://creativecommons.org/licenses/by-nc-nd/4.0/).

Metal nanoclusters have several applications in biological processes, medicine, cancer therapy, catalysis, etc. Iridium (Ir) nanoclusters exhibit excellent detection behavior compared to their bulk material. This work includes a deep insight into the interaction of Ir nanoclusters of four atoms (Ir4) with amino acids and the analysis of Ir–amino acid (Ir–AAc) complexes. UV–visible spectroscopy of the Ir4 nanocluster, amino acids, and their complexes was discussed as a way to detect amino acids with the help of the Ir4 nanocluster. In UV–visible analysis, the UV–visible peak of phenylalanine (Phe) appeared at 204 nm with an excitation energy of 6.02 eV with a 0.0516 oscillator strength. Meanwhile, only in the Ir4 nanocluster–phenylalanine (Ir–Phe) complex, the UV–visible peak was observed at 661 nm with an excitation energy of 1.87 eV and oscillator strength of 0.0051. This peak was observed due to the transition from HOMO–1 to LUMO+3. In the other complexes, no UV–visible peaks are observed. Thus, the results predict that the Ir4 nanocluster can be used in the detection of Phe via UV–visible spectra.

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Special Issue

Published as part of ACS Omegaspecial issue “Celebrating the 25th Anniversary of the Chemical Research Society of India”.
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pmcIntroduction

Nanomaterials can be distinguished on the basis of their physical and chemical properties, which mainly depend on their size, shape, surface area, and composition. Their unique and enhanced properties have led to numerous applications in various fields, such as nanobiotechnology, cancer therapy development, phase engineering, energy storage, detection, and sensors.1−6 Metal nanoclusters are a category of nanomaterials consisting of a small number of metallic atoms, typically ranging from a few to several hundred. The size of the nanocluster is in the range of 2 to 100 nm. Unlike their bulk materials, nanoclusters have different electronic, optical, magnetic, and mechanical properties. The small size of nanoclusters makes them efficient catalysts for reactions including hydrogenation, oxidation, and carbon dioxide reduction.7−16 The pressure can be used to control and manipulate the optical properties of the metal nanoclusters. Pressure-dependent optical absorption spectra of silver and gold nanoclusters offer valuable insights into their optical properties and behavior under different environmental conditions.17 Boron nanoclusters have been demonstrated as effective adsorbents for heavy metals in aqueous environments. These materials have the potential to be used in a variety of applications, including wastewater treatment and remediation.18

For several years, the structure, geometry, and possible application of clusters made up of various metals have been investigated, and iridium nanoclusters are one of these. Iridium is a nontoxic substance known for its high melting point, corrosion resistance, low reactivity, and biocompatibility. Iridium has drawn the attention of researchers due to its wide range of applications, including jewelry, medical devices, automotive catalysis, electrocatalysis, catalytic reactions, molecular imaging, and energy storage devices.19−21 There are many research groups working on nanoclusters, and some are discussed here. Yonezawa et al.22 studied the Ir nanocluster and reported that with increasing cluster size and mono oxide (MO) coverage, the adsorption energy of MO with the Ir cluster increases, suggesting that larger Ir clusters and higher MO coverage are more conducive to MO adsorption. Their works are in brief about the dependency of the Ir cluster’s stability on MO absorption, which is crucial information for developing and improving Ir-based catalysts and sensors. Tomihara et al.23 reported on anions clusters of iridium oxide IrnOm– (n = 5–8 and m = 0–14). Their work gives a detailed description of the evolution and binding modes of oxygen atoms and the motif of the iridium framework as a function of m through ion mobility mass spectrometry and theoretical calculations. The IrnOm– (n ≥ 8 and m = 0–14) clusters have high structural diversity due to smaller surface energy. The small iridium oxide cluster has significant importance in establishing the structure–catalysis correlation, which is essential for designing and optimizing its catalytic performance. Kong et al.24 have prepared a new type of dual-emitting gold nanoclusters (d-Au NCs) for the detection of phenylalanine and Fe3+. Dual-emitting gold nanoclusters have an average decay time of 5.8 μs for 430 nm and 10 μs for 600 nm emission. The dual-emitting gold nanocluster particle size is uniform; and the diameter is 1.75 ± 0.3 nm, and it represents two different species simultaneously. Therefore, the prepared gold nanocluster detects two different species (phenylalanine and Fe3+). D-Au NCs show a higher detection efficiency compared to single-emission metal clusters. Shang et al.25 work on water-soluble fluorescent Ag nanoclusters as fluorescent sensors for Cu2+. Due to paramagnetic properties via electron transfer, Cu2+ is a highly efficient fluorescence quencher. For the detection of Cu2+, Ag nanoclusters are capable of detecting at low concentrations. The preparation of the fluorescent Ag nanocluster consisted of photoreduction and mixing of silver salt and PMAA (poly methacrylic acid). The absorption spectrum of the PMAA-Ag nanocluster shows a possible quenching mechanism of energy transfer between Ag and Cu2+. Therefore, the Ag nanocluster is used as a sensor for Cu2+.

In this work, we used an iridium nanocluster to detect amino acids with the help of UV–visible spectroscopy. Phenylalanine is an essential amino acid. The critical role of phenylalanine amino acid supplements is in treating the central nervous system. It is also used for depression, Parkinson’s disease, chronic pain, osteoarthritis, rheumatoid arthritis, alcohol withdrawal symptoms, and vitiligo skin disease. Additionally, plants utilize phenylalanine to synthesize proteins and shield their skin from the damaging effects of ultraviolet light.26−32

Computational Details

In our work, we have chosen the stable iridium nanocluster with the least number of atoms, i.e., 4 (Ir4), whose geometrical structure (i.e., pyramidal structure) was already reported by El-Bayyari et al.33 All quantum chemical calculations were performed by Gaussian 1634,35 software. To select the best method for the calculation of the Ir4 nanocluster, we chose some methods that have already been used for the optimization of nanoclusters. We have optimized the Ir4 nanocluster with the B3LYP, CAM-B3LYP, MN15, M062X, MP2, and CCSD methods with the LanL2DZ basis set. Further, the HOMO–LUMO gaps36−38 obtained from these methods are compared in Figure 1 and Table S1, as the HOMO–LUMO energy gap is an important characteristic for the stability of molecules. It was observed that the HOMO–LUMO gaps corresponding to the MP2 and CCSD methods were similar (Eg = 7.82 eV). Thus, these two methods show the most appropriate candidature for this research work. As the CCSD method is computationally expensive, we opted for the MP2 method for the quantum calculations. Hence, the initial structure of the Ir4 nanocluster, amino acids, and their complexes (Ir4 adsorbed amino acids) were optimized using the MP2/LanL2DZ level of theory.

Figure 1 HOMO–LUMO comparison of the Ir4 nanocluster with different types of methods.

The analytical frequency calculations of all structures were performed using the MP2/Lan2DZ level of theory to examine the nature of the stationary points. All of the investigated structures show positive analytical frequency, which implies that all of the optimized structures are true minima. Density functional theory (DFT) is commonly used for straightforward calculation of properties related to electron distribution such as charge transfer and electron density distribution in excited states. Time-dependent density functional theory (TD-DFT) is an extension of DFT, providing valuable information about molecules’ ground-state electronic structure. TD-DFT is a widely used computational method for simulating UV–visible spectra of a molecular structure.39−42 Tamm–Dancoff approximation has been considered to analyze the electronic absorption spectra of the Ir4 nanocluster, amino acids, and Ir–AAc complexes via TD-DFT with the CAM-B3LYP/LanL2DZ level of theory. For the calculation of TD-DFT on the scale of accuracy, the order of methods CAM-B3LYP > PBE0 > B3LYP > PBE shows that CAM-B3LYP has been found to provide reasonably accurate predictions of excitation energies and UV–visible spectra for a wide range of molecular systems.43,44

Results and Discussion

The UV–visible spectra offer insights into the absorption or transmission of light in the UV–visible part of the electromagnetic spectrum. This type of spectrum helps us to understand the optical characteristics of nanoparticles, transition metals, and highly conjugated organic compounds. The UV–visible spectrum encompasses the wavelength range of 200 to 800 nm. The ultraviolet region covers 200 to 400 nm, while the visible region spans from 400 to 800 nm.45

The electronic configuration of the Ir atom is [Xe] 4f14 5d7 6s2. Therefore, it is clear that in the Ir atom there are three unpaired electrons in its outermost subshell, which allows it to form complex compounds. Thus, the Ir atom shows electrophilic behaviors. When an Ir4 nanocluster is optimized as shown in Figure 2[A], the bond length between the Ir–Ir atom is 2.592 Å, and the angle between Ir–Ir–Ir is 60° with a 3D pyramidal structure. The HOMO–LUMO energy gap is 7.820 eV, as provided in the Supporting Information, Table S2. The iridium atom interacts with three neighboring Ir atoms, forming a bond with the contribution of its valence electron. The electrons spread out over the entire cluster, forming metallic bonds that reduce the overall energy with increased stability. The tetrahedral arrangement allows each Ir atom to bond with three neighboring Ir atoms, resulting in a stable configuration. So, the Ir4 nanocluster is more stable. The Ir4 nanocluster does not emit/absorb high energy photons. When the TD-DFT calculation is performed for Ir4 nanoclusters, it is observed that there is no UV–visible peak in the UV–visible range. The UV–visible plot of the Ir4 nanocluster is shown in Figure 2[B] while for the single atom spectrum it is obtained at 300 nm (given Supplementary Figure S1).

Figure 2 [A] Optimized structure of the Ir4 nanocluster and [B] UV–visible spectra of the Ir4 nanocluster.

Amino acids show absorbance in different wavelength positions, depending on the presence of specific chromospheres in their molecular structure. These chromospheres are present in a side chain, which includes branches of hydrocarbon, functional group, and aromatic ring (benzene ring). The UV region (200–320 nm) show the electronic absorption of amino acids.46−48 The UV–visible peaks of all 20 basic amino acids (Ala, Arg, Asn, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, The, Trp, Tyr, and Val) are observed in the 200–250 nm range. We have compared these (theoretically observed) UV–visible peaks of all of the amino acids with previously reported experimental data of pure amino acids. We have observed that theoretical UV–visible peaks of most amino acids (Histidine, Serine, Alanine, Arginine, Cysteine, etc.) have found the approximate same peak position as already reported in the experimental data. Therefore, we can say that the MP2/CAM-B3LYP level of theory provides nearly the same result as reported in the experimental research papers. Theoretical observed UV–visible peak position, excitation energy, oscillator strength, major contribution, and experimentally reported peak position are in Table 1.

Table 1 Theoretical UV–Visible Peak Positions (nm), Excitation Energies (eV), Oscillation Strengths, Major Contributions, and Experimental Reported UV–Visible Peak Positions (nm) of AAs and Ir4-AAc Complexes Calculated at the CAM-B3LYP/LanL2DZ Level of Theory

Amino acids/Complex	Theoretical observed wavelength (nm)	Excitation Energy (eV)	Oscillator Strength	Major contribution	Experimental reported wavelength (nm)	
Alanine (Ala)	236	5.19	0.0037	H-1→LUMO (59%)	24049	
Arginine (Arg)	214	5.74	0.0033	H-1→LUMO (69%)	21050	
Asparagine (Asn)	207	5.93	0.0109	HOMO→LUMO (67%)	20351	
Aspartic (Asp)	238	5.16	0.0045	HOMO→LUMO (49%)	22752	
Cysteine (Cys)	212	5.79	0.0022	HOMO→LUMO (78%)	21453	
Glutamic (Glu)	228	5.38	0.008	HOMO→LUMO (80%)	23854	
Glutamine (Gln)	216	5.66	0.0037	HOMO→LUMO (77%)	22752	
Glycine (Gly)	239	5.16	0.0006	H-1→LUMO (65%)	23055	
Histidine (His)	234	5.27	0.0026	HOMO→LUMO (92%)	23556	
Isoleucine (Ile)	242	5.11	0.003	H-1→LUMO (62%)	Not Found	
Leucine (Leu)	241	5.11	0.0025	H-1→LUMO (54%)	23557	
Lysine (Lys)	241	5.11	0.0031	H-2→LUMO (61%)	23058	
Methionine (Met)	240	5.15	0.0093	H-1→LUMO (40%)	23659	
Phenylalanine (Phe)	204	6.02	0.0516	HOMO→L+1 (45%)	20960	
Proline (Pro)	229	5.37	0.0021	H-1→LUMO (72%)	22661	
Serine (Ser)	209	5.88	0.0066	HOMO→LUMO (60%)	20862	
Threonine (The)	211	5.83	0.0972	HOMO→LUMO (59%)	22063	
Tryptophan (Trp)	245	4.97	0.027	H-4→L+1 (28%)	25064	
Tyrosine (Tyr)	209	5.89	0.1315	HOMO→L+2 (70%)	20065	
Valine (Val)	216	5.69	0.0092	HOMO→LUMO (59%)	22066	
Ir–Phenylalanine	661	1.87	0.0051	H-1→L+3 (14%)	 	

After optimizing the structure of the Ir4 nanocluster and amino acids, we checked the Mulliken charges on them. We observed that at each corner atoms of the Ir4 nanocluster have the same charge (zero charge). Therefore, Ir4 nanoclusters have neutral behavior and show a strong interaction between the Ir–Ir atom. The Mulliken charge ranges present in the −NH2, −OH, and −C=O groups of amino acids are −0.42 to −0.61 eV, −0.47 to −0.50 eV, and −0.22 to −0.26 eV, respectively, in most of the amino acids. Both −NH2 and −COOH groups in amino acids are negatively charged, while in other amino acids both groups show different properties. It is clear that amino acids show both behavior nucleophilic and electrophilic nature with different sides. Therefore, we have considered interaction of the Ir4 nanocluster with −NH2, −OH, and −C=O groups of amino acids. We have shown examples of the initial input structure of all possible sides of the Ir4 nanocluster–amino acid complexes (Ir–AAs complexes), which are shown in Figure 3. The initial distance between the nitrogen atom of the −NH2 group and the iridium atom of the Ir4 nanocluster is 3.68 Å (sum of the van der Waals radius of nitrogen and iridium). The initial distance between the oxygen atom of the −COOH group of the amino acid and the iridium atom of the Ir4 nanocluster is 3.65 Å (sum of the van der Waals radius of oxygen and iridium).

Figure 3 Initial input structure of all possible intact sides. [A] Ir4 nanocluster with the −NH2 group, [B] Ir4 nanocluster with the −OH group, and [C] Ir4 nanocluster with the −C=O group.

After the interaction of Ir4 nanocluster with amino acids, the distances between the Ir atom and −OH, −C=O, and −NH2 groups of amino acids are decreased and are approximately in the 2.07–2.61 Å, 2.02–2.40 Å, and 2.07–2.40 Å ranges, respectively. Therefore, we can say they are attracted to each other and form complexes. In the interaction of the Ir4 nanocluster with amino acid, the Ir–Ir bond length of the Ir4 nanocluster also changes. These changes are detailed in Supplementary Table S3. The optimized structure of the complexes with the bond distance of the interaction side is shown in Figure 4 (Ir4 nanocluster with the −OH group of the carboxylic group), Figure S2 (Ir4 nanocluster with the −NH2 group), and Figure S3 (Ir4 nanocluster with the oxygen atom of the carboxylic group).

Figure 4 Optimized structures of Ir4 nanocluster–amino acid (possible side with the −OH group of the amino acid) complexes.

The excited state of the complexes involved in absorption can be calculated through TD-DFT. We used these excited states to simulate the UV–visible spectrum of the Ir4 nanocluster, pure amino acids, and Ir4-amino acids complexes. The UV–visible spectra of the pure amino acids and amino acid absorbed Ir4 nanocluster are shown in Figure 5. In the amino acids, only Phe has aromatic R-groups and the lowest excitation energy 6.02 eV compared to other amino acids as shown in Table 1. Due to the presence of a benzene ring in these amino acids, they have an n → π* transition present. Being hydrophobic and having an aromatic ring structure, phenylalanine is an important amino acid that is categorized as an aromatic amino acid due to its strong interaction. In the Phe and Trp amino acids, they interact with the Ir4 nanocluster with two side benzene rings and −COOH group as shown in Figure 4 and Figures S1 and S2. The bond lengths between the Ir atom and −OH in the Ir–Phe and Ir–Trp complexes are 2.18 and 2.24 Å, respectively, and are shown in Figure 4. Therefore, the interaction between the Ir4 nanocluster and Phe amino acid is stronger than that of the Ir–Trp complex. Due to this effect, internal bonding is affected. Thus, the Ir4 adapts to a different type of structure after breaking from its initial structure.

Figure 5 [A–E] UV–visible spectra graphs of pure amino acids and amino acid–Ir4 nanocluster complexes.

After adsorption of the amino acids on the Ir4 nanocluster, only the Ir–Phe complex has shown the UV–visible peak in the UV–visible region (400–800 nm), while other complexes have observed no peak in the UV–visible region as shown in Figure 5. The pure phenylalanine (Phe) shows a UV–visible peak at 204 nm with 6.02 eV excitation energy. The optimized structures are shown in Figure 6for the cases of the Ir4 nanocluster interacting with the sides of an −NH2 group and −COOH group of Phe.

Figure 6 Optimized structures of the Ir–Phe complex with the sides of [A] −OH, [B] −NH2, and [C] −C=O.

The Ir–Phe complex has 1.49 and 1.47 eV excitation energies with 0.0011 and 0.0001 oscillation strengths with the sides of an −NH2 group and −C=O group, respectively. The peaks of the Ir–Phe complex are not shown in the UV–visible region due to the interaction with the side of the −NH2 group and −C=O group. Meanwhile Ir4 interacts with the −OH side of Phe, and the Ir–Phe complex has an excitation energy 1.87 eV with a 0.0051 oscillation strength. When we compared the adsorption energies of the Ir4 nanoclusters with −C=O, −OH, and −NH2 groups, it was observed that the Ir4 nanocluster showed the maximum absorption energy with the −OH group (given the information in Supplementary Table S4). Therefore, after interaction of the Ir4 nanocluster with Phe, the UV–visible peak of the Ir–Phe complex has a 661 nm red shift with 4.89 eV adsorption energy shown in Figure 5[D]. As shown in Figure 7, pure Ir4 nanoclusters have no peak in the UV–visible region. Phe has a peak at 204 nm with a 0.0516 oscillator strength in the UV–visible region. After the interaction, the Ir–Phe complex shows a peak at 661 nm with an 0.0051 oscillator strength. This peak is shown as a consequence of the transition from the Ir4 nanocluster with different HOMO–LUMO orbitals. This transition occurs due to the transition of H-1→L+3 (14%).

Figure 7 Comparison UV–visible plots of the Ir4 nanocluster, Phe amino acid, and Ir–Phe complex.

Conclusion

In this work, we selected the smallest stable Ir4 nanocluster. We have studied the optimized structure of the Ir4 nanocluster, pure amino acids, and complexes of Ir–amino acids with the help of the MP2/LanL2DZ level of theory. After the optimization, TD-DFT was used to understand the UV–visible adsorption properties. In the UV–visible spectra of the Ir4 nanocluster and its complexes with amino acids, calculations were performed with the help of CAM-B3LYP/LanL2DZ. We found that the Ir4 nanocluster has no peak in the UV–visible spectra. Meanwhile, the peaks are observed between the range 200–250 nm in the amino acids. With analysis of the UV–visible spectra of the formed complexes, we observed that only the Ir–Phe complex has a peak at 661 nm with a 0.4721 oscillator strength, which is suitable for the experimental observation. Therefore, the Ir4 nanocluster can be used as a Phe amino acid detector. As a result of our research, we are able to identify the Phe amino acid in mixtures of two or more amino acids.

Supporting Information Available

The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acsomega.4c05684.HOMO–LUMO comparison of Ir4 nanocluster with different types of methods; geometrical information on the optimized iridium nanocluster (Ir4); after the interaction of the Ir4 nanocluster with amino acids, the Ir–Ir bond length of the Ir4 nanocluster; comparison of interactions of the Ir–Phe complex (Ir4 nanocluster–phenylalanine amino acid) with different sides; images of the optimized structure of the Ir4 nanocluster amino acid complexes with the side of −NH2 group; and images of the optimized structure of the Ir4 nanocluster amino acid complexes with the side of −C=O (PDF)

Supplementary Material

ao4c05684_si_001.pdf

Author Contributions

Neelam Agrawal: conceptualization, data curation, formal analysis, investigation, methodology, validation, writing original draft and plotting of figures. Ashok Singh Bahota: conceptualization, writing review and editing. Areeba Khan: introduction and methodology. Rajni Chaudhary: introduction and methodology. Keshav Kumar Singh: writing–review and editing. Poonam Tandon: resources, software, supervision, validation, and visualization.

The authors declare no competing financial interest.

Acknowledgments

We would like to express our gratitude to Department of Physics, Lucknow University, for providing high performance computational facilities. This work did not receive any specific funding from external sources.

Abbreviations

Ir Iridium

Ir4 Iridium nanocluster of four atoms

Ir–Aac Iridium–amino acids

Ala Alanine

Arg Arginine

Asn Asparagine

Asp Aspartic

Cys Cysteine

Gln Glutamine

Glu Glutamic

Gly Glycine

His Histidine

Iso Isoleucine

Leu Leucine

Lys Lysine

Met Methionine

Phe Phenylalanine

Pro Proline

Ser Serine

The Threonine

Trp Tryptophan

Tyr Tyrosine

Val Valine

UV–visible Ultraviolet–visible

HOMO Highest occupied molecular orbital

LUMO Lowest unoccupied molecular orbital
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