1
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Yadav NP, Yadav T, Pattanaik S, Shakerzadeh E, Chakroborty S, Xiaofeng C, Vishwkarma AK, Pathak A, Malviya J, Pandey FP. Understanding the Interaction Mechanism between the Epinephrine Neurotransmitter and Small Gold Nanoclusters (Au n; n = 6, 8, and 10): A Computational Insight. ACS OMEGA 2024; 9:3373-3383. [PMID: 38284044 PMCID: PMC10809666 DOI: 10.1021/acsomega.3c06382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/30/2024]
Abstract
In this study, the interaction between the neurotransmitter epinephrine and small gold nanoclusters (AunNCs) with n = 6, 8, and 10 is described by density functional theory calculations. The interaction of Au6, Au8, and Au10 nanoclusters with epinephrine is governed by Au-X (X = N and O) anchoring bonding and Au···H-X conventional hydrogen bonding. The interaction mechanism of epinephrine with gold nanoclusters is investigated in terms of electronic energy and geometrical properties. The adsorption energy values for the most favorable configurations of Au6NC@epinephrine, Au8NC@epinephrine, and Au10NC@epinephrine were calculated to be -17.45, -17.86, and -16.07 kcal/mol, respectively, in the gas phase. The results indicate a significant interaction of epinephrine with AunNCs and point to the application of the biomolecular complex AunNC@epinephrine in the fields of biosensing, drug delivery, bioimaging, and other applications. In addition, some important electronic properties, namely, the energy gap between HOMO and LUMO, the Fermi level, and the work function, were computed. The effect of aqueous media on adsorption energy and electronic parameters for the most favorable configurations was also studied to explore the influence of physical biological conditions.
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Affiliation(s)
- Nagendra Prasad Yadav
- School
of Electrical and Electronics Information Engineering, Hubei Polytechnic University, NO.16 North Guilin Road, Huangshi, Hubei 435003, China
| | - Tarun Yadav
- Department
of Basic Sciences, IITM, IES University, Bhopal, MP 462044, India
| | - Sangram Pattanaik
- Sri
Satya Sai University of Technology & Medical Sciences, Sehore, MP 466002, India
| | - Ehsan Shakerzadeh
- Chemistry
Department, Faculty of Science, Shahid Chamran
University of Ahvaz, Ahwaz 6135783151, Iran
| | | | - Cai Xiaofeng
- School
of Electrical and Electronics Information Engineering, Hubei Polytechnic University, NO.16 North Guilin Road, Huangshi, Hubei 435003, China
| | - Anil Kumar Vishwkarma
- Department
of Physics, Institute of Science, Banaras
Hindu University, Varanasi 221005, India
| | - Amit Pathak
- Department
of Physics, Institute of Science, Banaras
Hindu University, Varanasi 221005, India
| | - Jitendra Malviya
- Department
of Life Sciences and Biological Sciences, IES University, Bhopal, MP 462044, India
| | - Fanindra Pati Pandey
- Scitechesy
Research and Technology Private Limited, Central Discovery Center, Banaras Hindu University, Varanasi 221005, India
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2
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Liang X, Li X, Gao N, Wu X, Zhao Z, Shi R, Su Y, Zhao J. Theoretical prediction for growth behavior and electronic properties of monoanionic Ru2Gen− (n = 3–20) clusters. Inorganica Chim Acta 2022. [DOI: 10.1016/j.ica.2022.121141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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3
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Nguyen HT, Cuong NT, Lan NT, Tung NT, Nguyen MT, Tam NM. First-row transition metal doped germanium clusters Ge 16M: some remarkable superhalogens. RSC Adv 2022; 12:13487-13499. [PMID: 35527729 PMCID: PMC9068264 DOI: 10.1039/d1ra08527a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 04/26/2022] [Indexed: 11/21/2022] Open
Abstract
A theoretical study of geometric and electronic structures, stability and magnetic properties of both neutral and anionic Ge16M0/− clusters with M being a first-row 3d transition metal atom, is performed using quantum chemical approaches. Both the isoelectronic Ge16Sc− anion and neutral Ge16Ti that have a perfect Frank–Kasper tetrahedral Td shape and an electron shell filled with 68 valence electrons, emerge as magic clusters with an enhanced thermodynamic stability. The latter can be rationalized by the simple Jellium model. Geometric distortions from the Frank–Kasper tetrahedron of Ge16M having more or less than 68 valence electrons can be understood by a Jahn–Teller effect. Remarkably, DFT calculations reveal that both neutral Ge16Sc and Ge16Cu can be considered as superhalogens as their electron affinities (≥3.6 eV) exceed the value of the halogen atoms and even that of icosahedral Al13. A detailed view of the magnetic behavior of Ge16M0/− clusters shows that the magnetic moments of the atomic metals remain large even when they are quenched upon doping. When M goes from Sc to Zn, the total spin magnetic moment of Ge16M0/− increases steadily and reaches the maximum value of 3 μB with M = Mn before decreasing towards the end of the first-row 3d block metals. Furthermore, the IR spectra of some tetrahedral Ge16M are also predicted. A theoretical study of geometric and electronic structures, stability and magnetic properties of both neutral and anionic Ge16M0/− clusters with M being a first-row 3d transition metal atom, is performed using quantum chemical approaches.![]()
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Affiliation(s)
- Huu Tho Nguyen
- Faculty of Natural Sciences Education, Sai Gon University 273 An Duong Vuong Street Ho Chi Minh City Vietnam
| | - Ngo Tuan Cuong
- Center for Computational Science, Faculty of Chemistry, Hanoi National University of Education Hanoi Vietnam
| | - Ngo Thi Lan
- Institute of Materials Science and Graduate University of Science and Technology, Vietnam Academy of Science and Technology 18 Hoang Quoc Viet Hanoi Vietnam.,Institute of Science and Technology, TNU-University of Sciences Tan Thinh Ward Thai Nguyen City Vietnam
| | - Nguyen Thanh Tung
- Institute of Materials Science and Graduate University of Science and Technology, Vietnam Academy of Science and Technology 18 Hoang Quoc Viet Hanoi Vietnam
| | - Minh Tho Nguyen
- Institute for Computational Science and Technology (ICST) Quang Trung Software City Ho Chi Minh City Vietnam
| | - Nguyen Minh Tam
- Laboratory of Theoretical and Computational Biophysics, Advanced Institute of Materials Science, Ton Duc Thang University Ho Chi Minh City Vietnam .,Faculty of Pharmacy, Ton Duc Thang University Ho Chi Minh City Vietnam
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4
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Tran VT, Tran QT. Electronic structures of
NbGe
n
−/0/+
(
n
= 1–3) clusters from multiconfigurational
CASPT2
and density matrix renormalization group
‐CASPT2
calculations. J Comput Chem 2020; 41:2641-2652. [DOI: 10.1002/jcc.26420] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 07/01/2020] [Accepted: 08/28/2020] [Indexed: 11/09/2022]
Affiliation(s)
- Van Tan Tran
- Theoretical and Physical Chemistry Division Dong Thap University Cao Lanh Dong Thap Vietnam
| | - Quoc Tri Tran
- Theoretical and Physical Chemistry Division Dong Thap University Cao Lanh Dong Thap Vietnam
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5
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Affiliation(s)
- Jijun Zhao
- Key Laboratory of Materials Modification by Laser, Ion and Electron Beams (Dalian University of Technology), Ministry of Education, Dalian 116024, China
| | - Qiuying Du
- Key Laboratory of Materials Modification by Laser, Ion and Electron Beams (Dalian University of Technology), Ministry of Education, Dalian 116024, China
| | - Si Zhou
- Key Laboratory of Materials Modification by Laser, Ion and Electron Beams (Dalian University of Technology), Ministry of Education, Dalian 116024, China
| | - Vijay Kumar
- Center for Informatics, School of Natural Sciences, Shiv Nadar University, NH-91, Tehsil Dadri, Gautam Buddha Nagar 201314, U. P., India
- Dr. Vijay Kumar Foundation, 1969 Sector 4, Gurgaon 122001, Haryana, India
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6
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7
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Structural characterization of Co-doped Pd (n=1–12) clusters: First-principles calculations. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2018.11.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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8
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First-Principles Study of the Structures and Electronic Properties for NinGe (n = 19–29) Clusters. J CLUST SCI 2018. [DOI: 10.1007/s10876-018-1462-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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9
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Song W, Li HQ, He CZ, Zhang W. Structures and electronic properties of germanium-doped Ni
n
clusters, n = 13–23. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2017. [DOI: 10.1134/s0036024417110322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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10
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Qi YJ, Lu HN, Liang JX, Zhao YM, Wang XE, Jin NZ. Comparison of the molecular interactions of 7'-carboxyalkyl apigenin derivatives with S. cerevisiae α-glucosidase. Comput Biol Chem 2017; 67:182-193. [PMID: 28131019 DOI: 10.1016/j.compbiolchem.2017.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 12/09/2016] [Accepted: 01/16/2017] [Indexed: 11/26/2022]
Abstract
As one of the most investigated flavonoids, apigenin, is considered to be a strong α-glucosidase inhibitor. However, the clinical utility of apigenin is limited due to its low solubility. It was reported that the solubility and biological activity can be improved by introducing sole carboxyalkyl group into apigenin, especially the 7'-substitution. With the increase of length of the alkyl chain in carboxyalkyl group, B ring of the apigenin derivative is embedded much more deeply into the binding cavity while the carboxyalkyl stretches to the neighboring cavity. All of the terminal carboxyl groups form hydrogen bonding interactions easily with the surrounding polar amino acids, such as His239, Ser244, Arg312 and Asp349. Thus, the electron density values of the carbonyl in the carboxyl group become higher than the solution status due to the strong molecular interactions. In fact, electron densities of most of the chemical bonds are decreased after molecular docking procedure. On compared with the solution phase, however, dipole moments of most of these molecules are increased, and their vectors are reoriented distinctly in the active sites. It is noticed that all of the Highest Occupied Molecular Orbital (HOMO) and Lowest Unoccupied Molecular Orbital (LUMO) are distributed throughout the whole parent apigenin ring in solution phase, whereas the disappeared situation happened on the B rings of some molecules (II-IV) in the active site, leading to higher energy gaps.
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Affiliation(s)
- Y J Qi
- Department of Chemical Engineering, Northwest University for Nationalities, Lanzhou 730124, PR China.
| | - H N Lu
- Department of Life Sciences and Biological Engineering, Northwest University for Nationalities, Lanzhou 730124, PR China
| | - J X Liang
- Department of Chemical Engineering, Northwest University for Nationalities, Lanzhou 730124, PR China
| | - Y M Zhao
- Department of Chemical Engineering, Northwest University for Nationalities, Lanzhou 730124, PR China
| | - X E Wang
- Department of Chemical Engineering, Northwest University for Nationalities, Lanzhou 730124, PR China
| | - N Z Jin
- Gansu Province Computing Center, Lanzhou 730000, PR China
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11
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Qi Y, Zhao Y, Wang X, Lu H, Jin N. Comparative analysis of interactions between the hydropyridine dicarboxylate derivatives and different proteins by molecular docking and charge density analysis. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2016. [DOI: 10.1142/s0219633616500504] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Molecular docking and charge density analysis were carried out to understand the geometry, charge density distribution and electrostatic properties of one of newly synthesized 4-substituted-2,6-dimethyl-1,4-dihydropyridine-3,5-dicarboxylates (PDE), which is regarded as the best [Formula: see text]-Glucosidase inhibitor among the hydropyridine dicarboxylate derivatives. The different bonding models of the PDE molecule in the active sites of proteins Human serum albumin (HSA) and Saccharomyces cerevisiae [Formula: see text]-glucosidase (SAG) are firstly compared, which is important to understand the different intermolecular interactions between drug-transport protein and drug-target protein. The deformation density maps suggest that the electron densities of the PDE molecule are redistributed when it presents in the active sites. When the molecule presents in the active site of the SAG, it is evident to find that the negative region does not appear at the vicinity of the oxygen atoms on one of the carboxylic acid dimethyl ester group. Frontier molecular orbital density distributions for the PDE molecule are similar in all forms. The highest occupied molecular orbital (HOMO) and lowest occupied molecular orbital (LUMO) energy gaps in the active sites are higher than that of the molecule in pure solution phase. It is generally noticed that all of the orientations of the dipole moment vectors are reoriented in both active sites. These fine details at electronic level allow to better understand the exact drug-transport protein and drug-target protein interactions.
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Affiliation(s)
- Yanjiao Qi
- Department of Chemical Engineering, Northwest University for Nationalities, Lanzhou 730124, P. R. China
| | - Yaming Zhao
- Department of Chemical Engineering, Northwest University for Nationalities, Lanzhou 730124, P. R. China
| | - Xiaoe Wang
- Department of Chemical Engineering, Northwest University for Nationalities, Lanzhou 730124, P. R. China
| | - Huining Lu
- Department of Life Sciences and Biological Engineering, Northwest University for Nationalities, Lanzhou 730124, P. R. China
| | - Nengzhi Jin
- Gansu Province Computing Center, Lanzhou 730000, P. R. China
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12
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Dhaka K, Bandyopadhyay D. Magnetism, structures and stabilities of cluster assembled TM@Si nanotubes (TM = Cr, Mn and Fe): a density functional study. Dalton Trans 2016; 45:12432-43. [DOI: 10.1039/c6dt01252c] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Four different types (Type 1 to Type 4) of empty and transition metal (Cr, Mn and Fe) doped silicon nanotubes have been studied. The calculated band structures and DOS assigned them as metallic, semiconductor, semi-metallic and half-metallic depending upon the combination of the type of nanotube and the transition metal doping.
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Affiliation(s)
- Kapil Dhaka
- Department of Physics
- Birla Institute of Technology and Science
- Pilani
- India
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13
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Dhaka K, Bandyopadhyay D. Study of the electronic structure, stability and magnetic quenching of CrGen (n = 1–17) clusters: a density functional investigation. RSC Adv 2015. [DOI: 10.1039/c5ra13849c] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The current DFT based study of CrGen (n = 1–20) series shows that the enhanced stability of the ground state clusters CrGe10 and CrGe14 can be explained by means of 18-electron rule. However, it cannot be applied for highly symmetric CrGe12 cluster.
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Affiliation(s)
- Kapil Dhaka
- Department of Physics
- Birla Institute of Technology and Science
- Pilani
- India
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14
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Deng XJ, Kong XY, Xu XL, Xu HG, Zheng WJ. Structural and magnetic properties of CoGe(n)- (n=2-11) clusters: photoelectron spectroscopy and density functional calculations. Chemphyschem 2014; 15:3987-93. [PMID: 25294751 DOI: 10.1002/cphc.201402615] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Indexed: 11/08/2022]
Abstract
A series of cobalt-doped germanium clusters, CoGe(n)(-/0) (n=2-11), are investigated by using anion photoelectron spectroscopy combined with density functional theory calculations. For both anionic and neutral CoGe(n) (n=2-11) clusters, the critical size of the transition from exo- to endohedral structures is n=9. Natural population analysis shows that there is electron transfer from the Ge(n) framework to the Co atom at n=7-11 for both anionic and neutral CoGe(n) clusters. The magnetic moments of the anionic and neutral CoGe(n) clusters decrease to the lowest values at n=10 and 11. The transfer of electrons from the Gen framework to the Co atom and the minimization of the magnetic moments are related to the evolution of CoGe(n) structures from exo- to endohedral.
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Affiliation(s)
- Xiao-Jiao Deng
- State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190 (P.R. China)
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15
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Trivedi R, Dhaka K, Bandyopadhyay D. Study of electronic properties, stabilities and magnetic quenching of molybdenum-doped germanium clusters: a density functional investigation. RSC Adv 2014. [DOI: 10.1039/c4ra11825a] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The evolution of electronic structures, properties and stabilities of neutral and cationic molybdenum encapsulated germanium clusters (Mo@Gen, n = 1 to 20) has been investigated.
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Affiliation(s)
- Ravi Trivedi
- Department of Physics
- Birla Institute of Technology and Science
- Pilani, India
| | - Kapil Dhaka
- Department of Physics
- Birla Institute of Technology and Science
- Pilani, India
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