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Prakash M, Rudharachari Maiyelvaganan K, Giri Lakshman N, Gopalakrishnan C, Hochlaf M. Microhydration of small protonated polyaromatic hydrocarbons: a first principles study. Phys Chem Chem Phys 2024; 26:17489-17503. [PMID: 38804893 DOI: 10.1039/d3cp06000d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Using first principles methodology, we investigate the microsolvation of protonated benzene (BzH+), protonated coronene (CorH+) and protonated dodecabenzocoronene (DbcH+). Gas phase complexes of these small protonated polyaromatic hydrocarbons (H+PAHs) with mono-, di-, and tri-hydrated water molecules are considered. Their most stable forms are presented, where we discuss their structural, energetic aromaticity and IR and UV spectral features. In particular, we focus on the analysis of the bonding and various non-bonded interactions between these protonated aromatics and water clusters. The strength of non-bonded interactions is quantified and correlated with their electron density profiles. Furthermore, insights into the interfacial interactions and stability of these complexes were obtained through non-covalent index and symmetry-adapted perturbation theory (SAPT0) analyses. We also discuss the effects of the extension of the π aromatic cloud on the water solvation of these protonated aromatics. In particular, we extended our predictions for the S0 → S1 and S0 → T1 wavelength transitions of micro hydrated H+PAHs to deduce those of these species solvated in aqueous solution. The present findings should be useful for understanding, at the microscopic level, the effects of water interacting with H+PAHs, which are relevant for organic chemistry, astrochemistry, atmospheric chemistry, combustion and materials science.
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Affiliation(s)
- Muthuramalingam Prakash
- Computational Chemistry Research Laboratory (CCRL), Department of Chemistry, SRM Institute of Science and Technology, Kattankulathur-603 203, Chengalpattu, Tamil Nadu, India.
| | - K Rudharachari Maiyelvaganan
- Computational Chemistry Research Laboratory (CCRL), Department of Chemistry, SRM Institute of Science and Technology, Kattankulathur-603 203, Chengalpattu, Tamil Nadu, India.
| | - N Giri Lakshman
- Computational Chemistry Research Laboratory (CCRL), Department of Chemistry, SRM Institute of Science and Technology, Kattankulathur-603 203, Chengalpattu, Tamil Nadu, India.
| | - C Gopalakrishnan
- Computational Chemistry Research Laboratory (CCRL), Department of Chemistry, SRM Institute of Science and Technology, Kattankulathur-603 203, Chengalpattu, Tamil Nadu, India.
| | - Majdi Hochlaf
- Université Gustave Eiffel, COSYS/IMSE, 5 Bd Descartes, 77454, Champs Sur Marne, France.
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Prakash M, Rudharachari Maiyelvaganan K, Lakshman NG, Mogren Al-Mogren M, Hochlaf M. Formation of Eigen or Zundel Features at Protonated Water Cluster-Aromatic Interfaces. Chemphyschem 2023; 24:e202300267. [PMID: 37283005 DOI: 10.1002/cphc.202300267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 05/27/2023] [Accepted: 06/02/2023] [Indexed: 06/08/2023]
Abstract
Interfacial interactions of protonated water clusters adsorbed at aromatic surfaces play an important role in biology, and in atmospheric, chemical and materials sciences. Here, we investigate the interaction of protonated water clusters ((H+ H2 O)n (where n=1-3)) with benzene (Bz), coronene (Cor) and dodecabenzocoronene (Dbc)). To study the structure, stability and spectral features of these complexes, computations are done using DFT-PBE0(+D3) and SAPT0 methods. These interactions are probed by AIM electron density topography and non-covalent interactions index (NCI) analyses. We suggest that the excess proton plays a crucial role in the stability of these model interfaces through strong inductive effects and the formation of Eigen or Zundel features. Also, computations reveal that the extension of the π-aromatic system and the increase of the number of water molecules in the H-bounded water network led to a strengthening of the interactions between the corresponding aromatic compound and protonated water molecules, except when a Zundel ion is formed. The present findings may serve to understand in-depth the role of proton localized at aqueous medium interacting with large aromatic surfaces such as graphene interacting with acidic liquid water. Besides, we give the IR and UV-Vis spectra of these complexes, which may help for their identification in laboratory.
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Affiliation(s)
- Muthuramalingam Prakash
- Department of Chemistry, Faculty of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, 603203, Chengalpattu District, Tamil Nadu, India
| | - K Rudharachari Maiyelvaganan
- Department of Chemistry, Faculty of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, 603203, Chengalpattu District, Tamil Nadu, India
| | - N Giri Lakshman
- Department of Chemistry, Faculty of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, 603203, Chengalpattu District, Tamil Nadu, India
| | - Muneerah Mogren Al-Mogren
- Department of Chemistry, College of Sciences, King Saud University, PO Box 2455, Riyadh, 11451, Saudi Arabia
| | - Majdi Hochlaf
- Université Gustave Eiffel, COSYS/IMSE, 5 Bd Descartes, 77454, Champs Sur Marne, France
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Palanisamy V, Sanphui P, Palanisamy K, Prakash M, Bansal AK. Design of Ascorbic Acid Eutectic Mixtures With Sugars to Inhibit Oxidative Degradation. Front Chem 2022; 10:754269. [PMID: 35615307 PMCID: PMC9125031 DOI: 10.3389/fchem.2022.754269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 03/25/2022] [Indexed: 11/24/2022] Open
Abstract
L-Ascorbic acid (ASC), commonly known as vitamin C, acts as an anti-oxidant in the biological system. It is extensively used as an excipient in pharmaceutical industry, food supplements in fruit juices, and food materials due to its free radicals scavenging activity. Main drawback of ASC is its poor aqueous stability owing to the presence of lactone moiety that is easily oxidized to dehydroascorbic acid and further degraded. To improve aqueous stability and inhibit oxidative degradation, ASC was co-crystallized to constitute binary eutectic compositions with mono and di-saccharides such as glucose, sucrose, lactose, and mannitol. The eutectics were confirmed by their (single) lower melting endotherm compared to ASC and sugars, although Powder X-ray diffraction (PXRD) and Fourier transform Infrared spectroscopy (FT-IR) data confirmed the characteristics of their physical mixture. Scanning electron microscope (SEM) images of the binary eutectics confirmed their irregular morphology. The ASC eutectics exhibited improved shelf-life by 2–5-fold in weakly acidic (pH 5) and neutral (pH 7) aqueous buffer medium, whereas the eutectic with glucose enhanced shelf-life only by 1.1–1.2-fold in acidic medium (pH 3.3 and 4). Notably, stabilizing effect of the sugar eutectics decreased with increasing acidity of the medium. In addition, higher binding energy of the disaccharide eutectics partially supports the aqueous stability order of ASC in the neutral pH medium due to more number of non-bonded interactions than that of monosaccharides.
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Affiliation(s)
- Vasanthi Palanisamy
- Department of Chemistry, Faculty of Engineering and Technology, SRM Institute of Science and Technology, Chennai, India
| | - Palash Sanphui
- Department of Chemistry, Faculty of Engineering and Technology, SRM Institute of Science and Technology, Chennai, India
- *Correspondence: Palash Sanphui, ; Arvind Kumar Bansal,
| | - Kandhan Palanisamy
- Department of Chemistry, Faculty of Engineering and Technology, SRM Institute of Science and Technology, Chennai, India
| | - Muthuramalingam Prakash
- Department of Chemistry, Faculty of Engineering and Technology, SRM Institute of Science and Technology, Chennai, India
| | - Arvind Kumar Bansal
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER), Mohali, India
- *Correspondence: Palash Sanphui, ; Arvind Kumar Bansal,
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Imamura K, Higashi M, Kobayashi Y, Kageyama H, Sato H. Chemical Shift of Solvated Hydride Ion: Comparative Study with Solvated Fluoride Ion. J Phys Chem B 2022; 126:3090-3098. [DOI: 10.1021/acs.jpcb.2c00326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kosuke Imamura
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Masahiro Higashi
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
- Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Kyoto 615-8520, Japan
| | - Yoji Kobayashi
- King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Hiroshi Kageyama
- Department of Energy & Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Hirofumi Sato
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
- Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Kyoto 615-8520, Japan
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
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A Benchmark Protocol for DFT Approaches and Data-Driven Models for Halide-Water Clusters. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27051654. [PMID: 35268757 PMCID: PMC8924895 DOI: 10.3390/molecules27051654] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 02/18/2022] [Accepted: 02/26/2022] [Indexed: 11/17/2022]
Abstract
Dissolved ions in aqueous media are ubiquitous in many physicochemical processes, with a direct impact on research fields, such as chemistry, climate, biology, and industry. Ions play a crucial role in the structure of the surrounding network of water molecules as they can either weaken or strengthen it. Gaining a thorough understanding of the underlying forces from small clusters to bulk solutions is still challenging, which motivates further investigations. Through a systematic analysis of the interaction energies obtained from high-level electronic structure methodologies, we assessed various dispersion-corrected density functional approaches, as well as ab initio-based data-driven potential models for halide ion-water clusters. We introduced an active learning scheme to automate the generation of optimally weighted datasets, required for the development of efficient bottom-up anion-water models. Using an evolutionary programming procedure, we determined optimized and reference configurations for such polarizable and first-principles-based representation of the potentials, and we analyzed their structural characteristics and energetics in comparison with estimates from DF-MP2 and DFT+D quantum chemistry computations. Moreover, we presented new benchmark datasets, considering both equilibrium and non-equilibrium configurations of higher-order species with an increasing number of water molecules up to 54 for each F, Cl, Br, and I anions, and we proposed a validation protocol to cross-check methods and approaches. In this way, we aim to improve the predictive ability of future molecular computer simulations for determining the ongoing conflicting distribution of different ions in aqueous environments, as well as the transition from nanoscale clusters to macroscopic condensed phases.
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Simultaneous Interaction of Graphene Nanoflakes with Cations and Anions: A Cooperativity Study. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Maiyelvaganan KR, Ravva MK, Prakash M, Subramanian V. Benchmark studies on protonated benzene (BZH+) and water (Wn, n = 1–6) clusters: a comparison of hybrid DFT with MP2/CBS and CCSD(T)/CBS methods. Theor Chem Acc 2020. [DOI: 10.1007/s00214-020-02660-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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Senthilkumaran M, Saravanan C, Ashwin BCMA, Shanmugavelan P, Muthu Mareeswaran P, Prakash M. Inclusion induced water solubility and binding investigation of acenaphthene-1,2-dione with p-sulfonatocalix[4]arene. J INCL PHENOM MACRO 2020. [DOI: 10.1007/s10847-020-01017-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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McNeill AS, Zhan CG, Appel AM, Stanbury DM, Dixon DA. The H•/H– Redox Couple and Absolute Hydration Energy of H–. J Phys Chem A 2020; 124:6084-6095. [DOI: 10.1021/acs.jpca.0c03833] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Ashley S. McNeill
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Chang-Guo Zhan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Aaron M. Appel
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - David M. Stanbury
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - David A. Dixon
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
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Maiyelvaganan KR, Ravva MK, Prakash M. Twisted Eigen Can Induce Proton Transfer at a Hydrophobic-Hydrophilic Interface. J Phys Chem A 2020; 124:3364-3373. [PMID: 32255630 DOI: 10.1021/acs.jpca.9b10149] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The investigation of proton localization at a hydrophobic-hydrophilic interface is an important problem in chemical and materials sciences. In this study, protonated benzene (i.e., benzenium ion) and water clusters [BZH+Wn (where n = 1-6)] are selected as prototype models to understand the interfacial interactions and proton transfer mechanism between a carbonaceous surface and water molecules. The excess protons can localize in the vicinity of the hydrophobic-hydrophilic interface, and these clusters are stabilized by various kinds of noncovalent interactions. Calculations are carried out using ab initio (MP2) and density functional theory B3LYP methods to shed more light on geometries, energetics, and spectral signatures of the protonated species [H+(H2O)n] at the interfaces. These calculations revealed few low-lying isomers, which have not been reported earlier. Scrutiny of the results reveals that proton localization in the hydrophilic environment is more stable than the hydrophobic benzene π-cloud. Furthermore, the occurrence of an O-H+···π hydrogen bond significantly influences the O-H+···O interactions in the water clusters and also intensively affects the vibrational modes of the Eigen cation. Thus, the aromatic π-clouds can stabilize the Eigen cation and at the same time, a twisted form of Eigen (one O-H+···π → two O-H+···π) can enhance the proton transfer through the water chain via a Grotthuss-type mechanism. The vibrational spectra of these clusters reveal that there is a large red-shifted frequency for the O-H+···O, O-H+···π, and O-H···π modes of interaction. The energetic values and vibrational frequencies obtained from the B3LYP method are in close agreement with the MP2 level and experimental values, respectively.
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Affiliation(s)
| | | | - Muthuramalingam Prakash
- Department of Chemistry, SRM Institute of Science and Technology, Kattankulathur 603203, Tamil Nadu, India
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Palanisamy K, Prakash M, Rajapandian V. Combined DFT and MD simulation studies of protein stability on imidazolium–water (ImH+Wn) clusters with aromatic amino acids. NEW J CHEM 2020. [DOI: 10.1039/d0nj03085f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The hydrated clusters of protonated imidazole (ImH+) can induce protein denaturation through various kinds of monovalent interactions such as cation···π (stacking), N–H⋯π (T-shaped) and water-mediated O–H⋯O H-bonds.
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Affiliation(s)
- Kandhan Palanisamy
- Department of Chemistry, Faculty of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar
- Kattankulathur-603203
- India
| | - Muthuramalingam Prakash
- Department of Chemistry, Faculty of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar
- Kattankulathur-603203
- India
| | - Varatharaj Rajapandian
- Department of Chemistry, Sri Ramakrishna Mission Vidyalaya College of Arts and Science
- Coimbatore-641020
- India
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Palanisamy V, Sanphui P, Prakash M, Chernyshev V. Multicomponent solid forms of the uric acid reabsorption inhibitor lesinurad and cocrystal polymorphs with urea: DFT simulation and solubility study. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2019; 75:1102-1117. [PMID: 31380793 DOI: 10.1107/s2053229619008829] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Accepted: 06/20/2019] [Indexed: 11/11/2022]
Abstract
Lesinurad (systematic name: 2-{[5-bromo-4-(4-cyclopropylnaphthalen-1-yl)-4H-1,2,4-triazol-3-yl]sulfanyl}acetic acid, C17H14BrN3O2S) is a selective uric acid reabsorption inhibitor related to gout, which exhibits poor aqueous solubility. High-throughput solid-form screening was performed to screen for new solid forms with improved pharmaceutically relevant properties. During polymorph screening, we obtained two solvates with methanol (CH3OH) and ethanol (C2H5OH). Binary systems with caffeine (systematic name: 3,7-dihydro-1,3,7-trimethyl-1H-purine-2,6-dione, C8H10N4O2) and nicotinamide (C6H6N2O), polymorphs with urea (CH4N2O) and eutectics with similar drugs, like allopurinol and febuxostat, were prepared using the crystal engineering approach. All these novel solid forms were confirmed by XRD, DSC and FT-IR. The crystal structures were solved by single-crystal and powder X-ray diffraction. The crystal structures indicate that the lesinurad molecule is highly flexible and the triazole moiety, along with the rotatable thioacetic acid (side chain) and cyclopropane ring, is almost perpendicular to the planar naphthalene moiety. The carboxylic acid-triazole heterosynthon in the drug is interrupted by the presence of methanol and ethanol molecules in their crystal structures and forms intermolecular macrocyclic rings. The caffeine cocrystal maintains the consistency of the acid-triazole heterosynthons as in the drug and, in addition, they are bound by several auxiliary interactions. In the binary system of nicotinamide and urea, the acid-triazole heterosynthon is replaced by an acid-amide synthon. Among the urea cocrystal polymorphs, Form I (P-1, 1:1) consists of an acid-amide (urea) heterodimer, whereas in Form II (P21/c, 2:2), both acid-amide heterosynthons and urea-urea dimers co-exist. Density functional theory (DFT) calculations further support the experimentally observed synthon hierarchies in the cocrystals. Aqueous solubility experiments of lesinurad and its binary solids in pH 5 acetate buffer medium indicate the apparent solubility order lesinurad-urea Form I (43-fold) > lesinurad-caffeine (20-fold) > lesinurad-allopurinol (12-fold) ≃ lesinurad-nicotinamide (11-fold) > lesinurad, and this order is correlated with the crystal structures.
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Affiliation(s)
- Vasanthi Palanisamy
- Department of Chemistry, SRM Institute of Science and Technology, Kattankulathur 603 203, India
| | - Palash Sanphui
- Department of Chemistry, SRM Institute of Science and Technology, Kattankulathur 603 203, India
| | - Muthuramalingam Prakash
- Department of Chemistry, SRM Institute of Science and Technology, Kattankulathur 603 203, India
| | - Vladimir Chernyshev
- Department of Chemistry, M. V. Lomonosov Moscow State University, 1-3 Leninskie Gory, Moscow 119991, Russian Federation
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Balamurugan K, Prakash M, Subramanian V. Theoretical Insights into the Role of Water Molecules in the Guanidinium-Based Protein Denaturation Process in Specific to Aromatic Amino Acids. J Phys Chem B 2019; 123:2191-2202. [PMID: 30672268 DOI: 10.1021/acs.jpcb.8b08968] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Noncovalent interactions between the guanidinium cation (Gdm+) and aromatic amino acids (AAs) in the water molecules have been studied using quantum chemical calculation and molecular dynamics (MD) simulations. Our studies show that there are two different modes of interactions between Gdm+ and AAs with and without water molecules. It is observed that nonhydrated Gdm+ interacts with AAs through N-H···π interactions, whereas hydrated clusters of Gdm+ are stabilized by stacking interactions with the help of the water-mediated hydrogen bond. Thus, different hydration patterns have significant effects on the predominant cation···π interactions in AAs-Gdm+ complexes. Findings from MD simulation elicit that the interaction pattern of Gdm+ with AAs varies as Phe < Tyr < Trp. Both the QM and MD calculations show a similar trend in the interaction of AAs with Gdm+. Moreover, the interaction of AAs with Gdm+ depends on the spatial orientation of AAs in the protein and the concomitant local structure, that is, the AAs present in the unstructured region of protein such as coils and bends exhibit higher binding for Gdm+ when compared to the AAs present in the structured region of the protein such as the α-helix and the β-sheet. Our study clearly reveals that H-bonded water molecules and the hydration pattern of Gdm+ as well as the positional presence of these AAs in the protein structure context play determining roles in the denaturation of protein by the Gdm+ cation.
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Affiliation(s)
- Kanagasabai Balamurugan
- Chemical Laboratory , CSIR-Central Leather Research Institute , Adyar, Chennai 600 020 , India
| | - Muthuramalingam Prakash
- Chemical Laboratory , CSIR-Central Leather Research Institute , Adyar, Chennai 600 020 , India
| | - Venkatesan Subramanian
- Chemical Laboratory , CSIR-Central Leather Research Institute , Adyar, Chennai 600 020 , India.,Academy of Scientific and Innovative Research (AcSIR) , CSIR-CLRI Campus , Chennai 600 020 , India
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Dahmani R, Ben Yaghlane S, Boughdiri S, Mogren Al-Mogren M, Prakash M, Hochlaf M. Insights on the interaction of Zn 2+ cation with triazoles: Structures, bonding, electronic excitation and applications. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 193:375-384. [PMID: 29272808 DOI: 10.1016/j.saa.2017.12.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Revised: 11/24/2017] [Accepted: 12/04/2017] [Indexed: 06/07/2023]
Abstract
At present, we investigate the structures, the stability, the bonding and the spectroscopy of the Zn2+-triazole complexes (Zn2+-Tz), which are subunits of triazolate based porous materials and Zn-enzymes. This theoretical work is performed using ab initio methods and density functional theory (DFT) where dispersion correction is included. Through these benchmarks, we establish the ability and reliability of M05-2X+D3 and PBE0+D3 functionals for the correct description of Zn2+-Tz bond since these DFTs lead to close agreement with post Hartree-Fock methods. Therefore, M05-2X+D3 and PBE0+D3 functionals are recommended for the characterization of larger organometallic complexes formed by Zn and N-rich linkers. For Zn2+-Tz, we found two stable σ-type complexes: (i) a planar structure where Zn2+ links to unprotonated nitrogen and (ii) an out-of-plane cluster where carbon interacts with Zn2+. The most stable isomers consist on a coordinated covalent bond between the lone pair of unprotonated nitrogen and the vacant 4s orbital of Zn2+. The roles of covalent interactions within these complexes are discussed after vibrational, NBO, NPA charges and orbital analyses. The bonding is dominated by charge transfer from Zn2+ to Tz and intramolecular charge transfer, which plays a vital role for the catalytic activity of these complexes. These findings are important to understand, at the microscopic level, the structure and the bonding within triazolate based macromolecular porous materials and Zn-enzymes.
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Affiliation(s)
- R Dahmani
- Université Paris-Est, Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, 5 bd Descartes, 77454 Marne-la-Vallée, France; Laboratoire de Spectroscopie Atomique, Moléculaire et Applications - LSAMA, Université de Tunis El Manar, Tunis, Tunisia; Unité de Recherche Physico-Chimie des Matériaux à l'Etat Condensé, Département de Chimie, Faculté des Sciences de Tunis, Université Tunis El Manar, Tunis 2092, Tunisia
| | - S Ben Yaghlane
- Laboratoire de Spectroscopie Atomique, Moléculaire et Applications - LSAMA, Université de Tunis El Manar, Tunis, Tunisia
| | - S Boughdiri
- Unité de Recherche Physico-Chimie des Matériaux à l'Etat Condensé, Département de Chimie, Faculté des Sciences de Tunis, Université Tunis El Manar, Tunis 2092, Tunisia
| | - M Mogren Al-Mogren
- Chemistry Department, Faculty of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - M Prakash
- SRM Research Institute and Department of Chemistry, SRM University, Kattankulathur 603203, Tamilnadu, India
| | - M Hochlaf
- Université Paris-Est, Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, 5 bd Descartes, 77454 Marne-la-Vallée, France.
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Ashwin BCMA, Herculin Arun Baby A, Prakash M, Hochlaf M, Muthu Mareeswaran P. A combined experimental and theoretical study on p-
sulfonatocalix[4]arene encapsulated 7-methoxycoumarin. J PHYS ORG CHEM 2017. [DOI: 10.1002/poc.3788] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | | | - Muthuramalingam Prakash
- SRM Research Institute and Department of Chemistry; SRM University; Kattankulathur Tamil Nadu India
| | - Majdi Hochlaf
- Laboratoire Modélisation et Simulation Multi-Echelle, UMR 8208 CNRS; University Paris-Est; Marne la Vallée Cedex 2 France
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Prakash M, Subramanian V. Ab initio and density functional theory (DFT) studies on triflic acid with water and protonated water clusters. J Mol Model 2016; 22:293. [PMID: 27888404 DOI: 10.1007/s00894-016-3158-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Accepted: 11/08/2016] [Indexed: 02/04/2023]
Abstract
The structure, stability and infrared spectral signatures of triflic acid (TA) with water clusters (Wn) and protonated water clusters (TAH+Wn, n = 1 - 6) were computed using DFT and MP2 methods. Our calculations show that a minimum of three water molecules are necessary to stabilize the dissociated zwitterionic form of TA. It can be seen from the results that there is no significant movement of protons in smaller (n = 1 and 2) and linear (n = 1 - 6) types of water clusters. Further, the geometries of TAWn clusters first form a neutral pair (NP) to contact ion pair (CIP), then form a solvent separated ion pair (SSIP) in a water hexamer. These findings reveal that proton transfer may take place through NP to CIP and then CIP to SSIP. The calculated binding energies (BEs) of ion pair clusters is always higher than that of NP clusters (i.e., more stable than the NP). Existing excess proton linear chain clusters transfer a proton to adjacent water molecules via a Grotthuss mechanism, whereas the same isomers in the branched motifs do not conduct protons. Examination of geometrical parameters and infrared frequencies reveals hydronium ion (H3O+ also called Eigen cation) formation in both TAWn and protonated TAWn clusters. The stability of Eigen water clusters is three times higher than that of other non-Eigen water clusters. Our study shows clearly that formation of ion pairs in TAWn and TAH+Wn clusters greatly favors proton transfer to neighboring water molecules and also enhances the stability of these complexes.
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Affiliation(s)
- M Prakash
- Department of Chemistry and Research Institute, SRM University, Kattankulathur, 603203, Tamil Nadu, India
- Chemical Laboratory, CSIR-Central Leather Research Institute, Adyar, Chennai, 600 020, India
| | - V Subramanian
- Chemical Laboratory, CSIR-Central Leather Research Institute, Adyar, Chennai, 600 020, India.
- Academy of Scientific and Innovative Research (AcSIR), CSIR-CLRI Campus, Chennai, 600 020, India.
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Structural investigation of (2E)-2-(ethoxycarbonyl)-3-[(4-methoxyphenyl)amino]prop-2-enoic acid: X-ray crystal structure, spectroscopy and DFT. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2016.04.090] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Boulmene R, Boussouf K, Prakash M, Komiha N, Al-Mogren MM, Hochlaf M. Ab Initio and DFT Studies on CO2Interacting with Znq+-Imidazole (q=0, 1, 2) Complexes: Prediction of Charge Transfer through σ- or π-Type Models. Chemphyschem 2016; 17:994-1005. [DOI: 10.1002/cphc.201501185] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Reda Boulmene
- Université Paris-Est; Laboratoire Modélisation et Simulation Multi-Échelle, MSME UMR 8208 CNRS; 5 bd Descartes 77454 Marne-la-Vallée France
| | - Karim Boussouf
- Université Paris-Est; Laboratoire Modélisation et Simulation Multi-Échelle, MSME UMR 8208 CNRS; 5 bd Descartes 77454 Marne-la-Vallée France
| | - Muthuramalingam Prakash
- Université Paris-Est; Laboratoire Modélisation et Simulation Multi-Échelle, MSME UMR 8208 CNRS; 5 bd Descartes 77454 Marne-la-Vallée France
| | - Najia Komiha
- LS3 ME-Team of theoretical chemistry and modeling; Faculty of Sciences; University Mohammed V; Rabat Morocco
| | - Muneerah M. Al-Mogren
- Chemistry Department; Faculty of Science; King Saud University; P.O. Box 2455 Riyadh 11451 Kingdom of Saudi Arabia
| | - Majdi Hochlaf
- Université Paris-Est; Laboratoire Modélisation et Simulation Multi-Échelle, MSME UMR 8208 CNRS; 5 bd Descartes 77454 Marne-la-Vallée France
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Boulmène R, Prakash M, Hochlaf M. Microscopic investigations of site and functional selectivity of triazole for CO2 capture and catalytic applications. Phys Chem Chem Phys 2016; 18:29709-29720. [DOI: 10.1039/c6cp04650a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ab initio and DFT studies on CO2 interacting with different tautomers and isomers of triazole (TZ) are carried out to understand the adsorption mechanism, site selectivity and their mutual preferential attracting sites.
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Affiliation(s)
- Reda Boulmène
- Université Paris-Est
- Laboratoire Modélisation et Simulation Multi Echelle
- MSME UMR 8208 CNRS
- 5 Bd Descartes
- 77454 Marne- La-Vallée
| | - Muthuramalingam Prakash
- Université Paris-Est
- Laboratoire Modélisation et Simulation Multi Echelle
- MSME UMR 8208 CNRS
- 5 Bd Descartes
- 77454 Marne- La-Vallée
| | - Majdi Hochlaf
- Université Paris-Est
- Laboratoire Modélisation et Simulation Multi Echelle
- MSME UMR 8208 CNRS
- 5 Bd Descartes
- 77454 Marne- La-Vallée
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Boussouf K, Khairat T, Prakash M, Komiha N, Chambaud G, Hochlaf M. Structure, Spectroscopy, and Bonding within the Zn(q+)-Imidazole(n) (q = 0, 1, 2; n = 1-4) Clusters and Implications for Zeolitic Imidazolate Frameworks and Zn-Enzymes. J Phys Chem A 2015; 119:11928-40. [PMID: 26565743 DOI: 10.1021/acs.jpca.5b09500] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Using density functional theory (DFT) with dispersion correction and ab initio post Hartree-Fock methods, we treat the bonding, the structure, the stability, and the spectroscopy of the complexes between Zn(q+) and imidazole (Im), Zn(q+)Imn (where q = 0, 1 and 2; n = 1-4). These entities are subunits of zeolitic imidazolate frameworks (ZIFs) and Zn-enzymes, which possess relevant roles in industrial and biological domains, respectively. We also investigate the Imn (n = 2-4) clusters for comparison. For each species, we determine several new structures that were not found previously. Our calculations show a competition between atomic metal solvation, by either σ-type interactions or π-stacking type interaction, and proton transfer through hydrogen bonding (H-bonding) in charged species. This results in several geometrical environments around the metal. These are connected with structural properties and the functional role of Zn cation within ZIFs and Zn-enzymes. Moreover, we show that the Zn(2+)Imn subunits do not absorb in the visible domain, which may be related to the photostability of ZIFs. Our findings are important for the development of new applications of ZIFs and metalloenzymes.
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Affiliation(s)
- K Boussouf
- LS3ME-Equipe de Chimie Théorique et Modélisation, Faculté des Sciences Rabat, Université Mohamed V , Rabat, Morocco.,Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, Université Paris-Est , 5 bd Descartes, 77454 Marne-la-Vallée, France
| | - T Khairat
- LS3ME-Equipe de Chimie Théorique et Modélisation, Faculté des Sciences Rabat, Université Mohamed V , Rabat, Morocco
| | - M Prakash
- Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, Université Paris-Est , 5 bd Descartes, 77454 Marne-la-Vallée, France
| | - N Komiha
- LS3ME-Equipe de Chimie Théorique et Modélisation, Faculté des Sciences Rabat, Université Mohamed V , Rabat, Morocco
| | - G Chambaud
- Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, Université Paris-Est , 5 bd Descartes, 77454 Marne-la-Vallée, France
| | - M Hochlaf
- Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, Université Paris-Est , 5 bd Descartes, 77454 Marne-la-Vallée, France
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Prakash M, Mathivon K, Benoit DM, Chambaud G, Hochlaf M. Carbon dioxide interaction with isolated imidazole or attached on gold clusters and surface: competition between σ H-bond and π stacking interaction. Phys Chem Chem Phys 2015; 16:12503-9. [PMID: 24833261 DOI: 10.1039/c4cp01292e] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Using first principle methodologies, we investigate the subtle competition between σ H-bond and π stacking interaction between CO2 and imidazole either isolated, adsorbed on a gold cluster or adsorbed on a gold surface. These computations are performed using MP2 as well as dispersion corrected density functional theory (DFT) techniques. Our results show that the CO2 interaction goes from π-type stacking into σ-type when CO2 interacts with isolated imidazole and Au clusters or surface. The balance between both types of interactions is found when an imidazole is attached to a Au20 gold cluster. Thus, the present study has great significance in understanding and controlling the structures of weakly-bound molecular systems and materials, where hydrogen bonding and van der Waals interactions are competing. The applications are in the fields of the control of CO2 capture and scattering, catalysis and bio- and nanotechnologies.
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Affiliation(s)
- Muthuramalingam Prakash
- Université Paris-Est, Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, 5 bd Descartes, 77454 Marne-la-Vallée, France.
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Boussouf K, Boulmene R, Prakash M, Komiha N, Taleb M, Mogren Al-Mogren M, Hochlaf M. Characterization of Znq+–imidazole (q = 0, 1, 2) organometallic complexes: DFT methods vs. standard and explicitly correlated post-Hartree–Fock methods. Phys Chem Chem Phys 2015; 17:14417-26. [DOI: 10.1039/c4cp06108j] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Benchmarking DFts for the characterization of the Znq+–imidazole (q= 0, 1, 2) complexes.
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Affiliation(s)
- K. Boussouf
- Université Paris-Est
- Laboratoire Modélisation et Simulation Multi Echelle
- MSME UMR 8208 CNRS
- 77454 Marne-la-Vallée
- France
| | - R. Boulmene
- Université Paris-Est
- Laboratoire Modélisation et Simulation Multi Echelle
- MSME UMR 8208 CNRS
- 77454 Marne-la-Vallée
- France
| | - M. Prakash
- Université Paris-Est
- Laboratoire Modélisation et Simulation Multi Echelle
- MSME UMR 8208 CNRS
- 77454 Marne-la-Vallée
- France
| | - N. Komiha
- LS3ME-Equipe de Chimie Théorique et Modélisation
- Université Mohamed
- Faculté des Sciences
- Rabat
- Maroc
| | - M. Taleb
- Laboratoire LIMME
- Université Sidi Med Ben Abdellah
- Fac des Sciences Dhar El Mehrez
- Fès
- Maroc
| | - M. Mogren Al-Mogren
- Chemistry Department
- Faculty of Science
- King Saud University
- Riyadh 11451
- Kingdom of Saudi Arabia
| | - M. Hochlaf
- Université Paris-Est
- Laboratoire Modélisation et Simulation Multi Echelle
- MSME UMR 8208 CNRS
- 77454 Marne-la-Vallée
- France
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Prakash M, Chambaud G, Al-Mogren MM, Hochlaf M. Role of size and shape selectivity in interaction between gold nanoclusters and imidazole: a theoretical study. J Mol Model 2014; 20:2534. [PMID: 25488624 DOI: 10.1007/s00894-014-2534-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 11/17/2014] [Indexed: 11/26/2022]
Abstract
We present a theoretical study on the structure, stability, spectra and electronic properties of imidazole (Im) adsorbed on gold nanoclusters (Aun, n = 2, 4, 6, 8, 10, and 20). These computations were performed using various density functional theories with and without inclusion of Grimme's (D3) dispersion correction. For small clusters, we also carried out wavefunction-based ab initio (MP2 and SCS-MP2) computations for comparison. Vibrational, atoms in molecules (AIM) and natural bond orbital (NBO) analyses clearly reveal the occurrence of charge transfer (CT) through covalent (N1-Au) and noncovalent interactions that play important roles in the stability of the Im@Aun complexes with anchor assisted H-bonds (Cα-H · Au). Therefore, gold clusters can act as H-bond acceptors with biomolecules for development of new materials and applications. Our study establishes also the ability and reliability of PBE0 and M05-2X functionals compared to B3LYP and PBE for an accurate description of covalent and noncovalent interactions between Im and gold clusters since they lead to close agreement with MP2. Finally, we show that the Au8 cluster may be viewed as large enough to mimic the 3D gold surface.
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Affiliation(s)
- Muthuramalingam Prakash
- Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR, Université Paris-Est, 8208 CNRS, 5 bd Descartes, 77454, Marne-la-Vallée, France
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A qualitative study of the effect of a counterion and polar environment on the structure and spectroscopic signatures of a hydrated hydroxyl anion. Theor Chem Acc 2013. [DOI: 10.1007/s00214-013-1361-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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