1
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Tulsiyan KD, Panda SK, Rana MK, Biswal HS. Critical assessment of interactions between ct-DNA and choline-based magnetic ionic liquids: evidences of compaction. Chem Sci 2024; 15:5507-5515. [PMID: 38638223 PMCID: PMC11023040 DOI: 10.1039/d4sc00004h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 03/14/2024] [Indexed: 04/20/2024] Open
Abstract
Ionic liquids (ILs) have become an alternative green solvent for storage and for stability of DNA. However, an in-depth understanding of binding and molecular interactions between ILs and DNA is needed. In this respect, magnetic ILs (MILs) are promising due to their tunable physicochemical properties. Various spectroscopic techniques and molecular simulations have been employed to unravel the critical factors of the strength and binding mechanism of MILs with DNA. UV-vis spectra unravel the multimodal binding of MILs with DNA, and the intrusion of IL molecules into the minor groove of DNA has been observed from dye displacement studies. Fluorescence correlation spectroscopic studies and scanning electron microscopy confirm the compaction of the DNA. ITC and molecular docking studies estimate the binding affinity of DNA with MILs, of ∼7 kcal mol-1. The 1 μs long-MD simulations give insight into the structural changes in the DNA in the MIL environment. Due to strong interaction with choline ions in the close vicinity, DNA helixes bend or squeeze in length and dilate in diameter (elliptical → spherical), leading to compaction. The post-MD parameters suggest a stronger interaction with [Ch]2[Mn] IL than with [Ch][Fe] IL; hence, the former induces DNA compaction to a more significant extent. Furthermore, decompaction is observed with the addition of sodium salts and is characterized using spectroscopic methods.
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Affiliation(s)
- Kiran Devi Tulsiyan
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) PO - Bhimpur-Padanpur, Via-Jatni, District - Khurda, PIN - 752050 Bhubaneswar India
- Homi Bhabha National Institute, Training School Complex Anushakti Nagar Mumbai 400094 India
| | - Saroj Kumar Panda
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Berhampur Odisha-760010 India
| | - Malay Kumar Rana
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Berhampur Odisha-760010 India
| | - Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) PO - Bhimpur-Padanpur, Via-Jatni, District - Khurda, PIN - 752050 Bhubaneswar India
- Homi Bhabha National Institute, Training School Complex Anushakti Nagar Mumbai 400094 India
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2
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Nath S, Tulsiyan KD, Mohapatra B, Puthukkudi A, Alone PV, Biswal HS, Biswal BP. Covalent Organic Frameworks as Nano-Reservoir for Room Temperature RNA Storage. Chemistry 2024:e202304079. [PMID: 38441909 DOI: 10.1002/chem.202304079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Indexed: 03/23/2024]
Abstract
The emerging role of Ribonucleic acids (RNAs) as therapeutics is alluring. However, RNAs are extremely labile under ambient conditions and typically need to be stored in cryogenic conditions (-20 °C to -80 °C). Hence, storage, stabilization, and transportation of RNA under ambient conditions have been an arduous task and remain an unsolved problem. In this work, a guanidinium-based ionic covalent organic framework (COF), TTGCl with nanotubular morphology, was synthesized and used as nano-reservoirs for room-temperature storage of RNA. To understand the role of the nanotubular morphology and chemical nature of TTGCl in stabilizing the RNA structure and for comparison purposes, a neutral COF, TMT-TT, is synthesized and studied. Further, density functional theory (DFT) studies confirmed non-covalent interaction between the COFs and the RNA nucleobases, facilitating reversible storage of RNA. RNA loaded in COFs was found to be resistant to enzymatic degradation when treated with RNase. Gel electrophoresis and sequencing confirmed the structural integrity of the recovered RNAs and their further processibility.
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Affiliation(s)
- Satyapriya Nath
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) Bhubaneswar, Jatni, Khurda, Odisha, 752050, INDIA
- Homi Bhabha National Institute (HBNI), Training School Complex, Anushakti Nagar, Mumbai, 400094, INDIA
| | - Kiran D Tulsiyan
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) Bhubaneswar, Jatni, Khurda, Odisha, 752050, INDIA
- Homi Bhabha National Institute (HBNI), Training School Complex, Anushakti Nagar, Mumbai, 400094, INDIA
| | - Binayak Mohapatra
- Homi Bhabha National Institute (HBNI), Training School Complex, Anushakti Nagar, Mumbai, 400094, INDIA
- School of Biological Sciences, National Institute of Science Education and Research (NISER) Bhubaneswar, Jatni, Khurda, Odisha, 752050, INDIA
| | - Adithyan Puthukkudi
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) Bhubaneswar, Jatni, Khurda, Odisha, 752050, INDIA
- Homi Bhabha National Institute (HBNI), Training School Complex, Anushakti Nagar, Mumbai, 400094, INDIA
| | - Pankaj V Alone
- Homi Bhabha National Institute (HBNI), Training School Complex, Anushakti Nagar, Mumbai, 400094, INDIA
- School of Biological Sciences, National Institute of Science Education and Research (NISER) Bhubaneswar, Jatni, Khurda, Odisha, 752050, INDIA
- Centre for Interdisciplinary Sciences, National Institute of Science Education and Research (NISER) Bhubaneswar, Jatni, Khurda, Odisha, 752050, INDIA
| | - Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) Bhubaneswar, Jatni, Khurda, Odisha, 752050, INDIA
- Homi Bhabha National Institute (HBNI), Training School Complex, Anushakti Nagar, Mumbai, 400094, INDIA
- Centre for Interdisciplinary Sciences, National Institute of Science Education and Research (NISER) Bhubaneswar, Jatni, Khurda, Odisha, 752050, INDIA
| | - Bishnu P Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) Bhubaneswar, Jatni, Khurda, Odisha, 752050, INDIA
- Homi Bhabha National Institute (HBNI), Training School Complex, Anushakti Nagar, Mumbai, 400094, INDIA
- Centre for Interdisciplinary Sciences, National Institute of Science Education and Research (NISER) Bhubaneswar, Jatni, Khurda, Odisha, 752050, INDIA
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3
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Pollet R, Andronaco M, Biswal HS. Onset of Nitriles Hydration with an Environmentally Benign Catalyst: in-Water versus on-Water Conditions. Chemphyschem 2024:e202400108. [PMID: 38426263 DOI: 10.1002/cphc.202400108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/29/2024] [Accepted: 02/29/2024] [Indexed: 03/02/2024]
Abstract
The reaction yield of nitriles hydration using a catalyst depends on the aqueous medium. Using ab initio molecular dynamics, we probed whether "in-water" (in bulk medium) or "on-water" (at the interface with vacuum) conditions can change the onset of the reaction. Investigating a hydrogen-bond mediated mechanism, the lifetimes of the intermolecular interaction between benzonitrile and choline in the two protocols were compared, and the diffusion of the hydroxide anion around the cyano group was discussed.
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Affiliation(s)
- Rodolphe Pollet
- Université Paris-Saclay, CEA, CNRS, NIMBE, 91191, Gif-sur-Yvette, France
| | - Mathilde Andronaco
- Université Paris-Saclay, CEA, CNRS, NIMBE, 91191, Gif-sur-Yvette, France
| | - Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), 752050, Bhubaneswar, India
- Homi Bhabha National Institute, 400094, Mumbai, India
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4
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Jena S, Tulsiyan KD, Sahoo RR, Rout S, Sahu AK, Biswal HS. Critical assessment of selenourea as an efficient small molecule fluorescence quenching probe to monitor protein dynamics. Chem Sci 2023; 14:14200-14210. [PMID: 38098725 PMCID: PMC10718066 DOI: 10.1039/d3sc04287a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 09/26/2023] [Indexed: 12/17/2023] Open
Abstract
Organoselenium compounds have recently been the experimentalists' delight due to their broad applications in organic synthesis, medicinal chemistry, and materials science. Selenium atom replacement of the carbonyl oxygen of the urea moiety dramatically reduces the HOMO-LUMO gap and oxidation potential, which completely changes the physicochemical properties of selenocarbonyl compounds. To our surprise, the photophysics and utility of a simple molecule such as selenourea (SeU) have not been explored in detail, which persuaded us to investigate its role in excited state processes. The steady-state emission, temperature-dependent time-correlated single photon counting, and femtosecond fluorescence upconversion experimental results confirmed that SeU significantly enhances the fluorescence quenching through a photoinduced electron transfer (PET) mechanism with an ∼10 ps ultrafast intrinsic PET lifetime component which is mostly absent in thiourea (TU). A wide range of fluorophores, based on their different redox abilities and fluorescence lifetimes covering a broad spectral window (λex: 390-590 nm and λem: 490-690 nm), were chosen to validate the proof of the concept. It was extended to tetramethylrhodamine (TMR)-5-maleimide labeled lysozyme protein, where we observed significant fluorescence quenching in the presence of SeU. The present work emphasizes that the high quenching efficiency with an ultrafast PET process, reduced orbital energy gap, and higher negative free energy change of the electron transfer reaction are the representative characteristics of selenourea or selenoamides to enable them as potential surrogates of thioamides or oxoamides quenching probes to monitor protein conformational changes and dynamics.
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Affiliation(s)
- Subhrakant Jena
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) PO-Bhimpur-Padanpur, Via-Jatni, District-Khurda, PIN-752050 Bhubaneswar India
- Homi Bhabha National Institute, Training School Complex Anushakti Nagar Mumbai 400094 India
| | - Kiran Devi Tulsiyan
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) PO-Bhimpur-Padanpur, Via-Jatni, District-Khurda, PIN-752050 Bhubaneswar India
- Homi Bhabha National Institute, Training School Complex Anushakti Nagar Mumbai 400094 India
| | - Rudhi Ranjan Sahoo
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) PO-Bhimpur-Padanpur, Via-Jatni, District-Khurda, PIN-752050 Bhubaneswar India
- Homi Bhabha National Institute, Training School Complex Anushakti Nagar Mumbai 400094 India
| | - Saiprakash Rout
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) PO-Bhimpur-Padanpur, Via-Jatni, District-Khurda, PIN-752050 Bhubaneswar India
- Homi Bhabha National Institute, Training School Complex Anushakti Nagar Mumbai 400094 India
| | - Akshay Kumar Sahu
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) PO-Bhimpur-Padanpur, Via-Jatni, District-Khurda, PIN-752050 Bhubaneswar India
- Homi Bhabha National Institute, Training School Complex Anushakti Nagar Mumbai 400094 India
| | - Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) PO-Bhimpur-Padanpur, Via-Jatni, District-Khurda, PIN-752050 Bhubaneswar India
- Homi Bhabha National Institute, Training School Complex Anushakti Nagar Mumbai 400094 India
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5
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Burguera S, Sahu AK, Frontera A, Biswal HS, Bauza A. Spodium Bonds Involving Methylmercury and Ethylmercury in Proteins: Insights from X-ray Analysis and Computations. Inorg Chem 2023; 62:18524-18532. [PMID: 37902775 PMCID: PMC10647129 DOI: 10.1021/acs.inorgchem.3c02716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 10/19/2023] [Accepted: 10/20/2023] [Indexed: 10/31/2023]
Abstract
In this study, the stability, directionality, and physical nature of Spodium bonds (SpBs, an attractive noncovalent force involving elements from group 12 and Lewis bases) between methylmercury (MeHg) and ethylmercury (EtHg) and amino acids (AAs) have been analyzed from both a structural (X-ray analysis) and theoretical (RI-MP2/def2-TZVP level of theory) point of view. More in detail, an inspection of the Protein Data Bank (PDB) reported evidence of noncovalent contacts between MeHg and EtHg molecules and electron-rich atoms (e.g., O atoms belonging to the protein backbone and S atoms from MET residues or the π-systems of aromatic AAs such as TYR or TRP). These results were rationalized through a computational study using MeHg coordinated to a thiolate group as a theoretical model and several neutral and charged electron-rich molecules (e.g., benzene, formamide, or chloride). The physical nature of the interaction was analyzed from electrostatics and orbital perspectives by performing molecular electrostatic potential (MEP) and natural bonding orbital (NBO) analyses. Lastly, the noncovalent interactions plot (NCIplot) technique was used to provide a qualitative view of the strength of the Hg SpBs and compare them to other ancillary interactions present in these systems as well as to shed light on the extension of the interaction in real space. We believe that the results derived from our study will be useful to those scientists devoted to protein engineering and bioinorganic chemistry as well as to expanding the current knowledge of SpBs among the chemical biology community.
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Affiliation(s)
- Sergi Burguera
- Department
of Chemistry, Universitat de les Illes Balears, Ctra. de Valldemossa km 7.5, 07122 Palma, Baleares, Spain
| | - Akshay Kumar Sahu
- School
of Chemical Sciences, National Institute
of Science Education and Research (NISER), Bhubaneswar 752050, India
- Training
School Complex, Homi Bhabha National Institute, Mumbai 400094, India
| | - Antonio Frontera
- Department
of Chemistry, Universitat de les Illes Balears, Ctra. de Valldemossa km 7.5, 07122 Palma, Baleares, Spain
| | - Himansu S. Biswal
- School
of Chemical Sciences, National Institute
of Science Education and Research (NISER), Bhubaneswar 752050, India
- Training
School Complex, Homi Bhabha National Institute, Mumbai 400094, India
| | - Antonio Bauza
- Department
of Chemistry, Universitat de les Illes Balears, Ctra. de Valldemossa km 7.5, 07122 Palma, Baleares, Spain
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6
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Devi Tulsiyan K, Rani Prusty M, Biswal HS. Effect of Choline Amino Acid-Based Ionic Liquids on Stability and Structure of Hemoglobin. Chemphyschem 2023; 24:e202300201. [PMID: 37272734 DOI: 10.1002/cphc.202300201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/05/2023] [Accepted: 06/05/2023] [Indexed: 06/06/2023]
Abstract
Ionic liquids (ILs) can stabilize or destabilize proteins, which motivates us to examine their effect on hemoglobin. The native state of hemoglobin (Hb) is disrupted at different physical conditions such as pressure, temperature, and solvents. Herein, we have monitored the stability of Hb in a nontoxic and biocompatible IL, i. e., choline amino acid-based Ils (ChAAILs), using various spectroscopic techniques like UV-Vis and fluorescence spectroscopy, circular dichroism (CD), and isothermal titration calorimetry (ITC) measurements. It was observed that Hb stays neither in its native state nor in its fully denatured state; rather, it achieves an intermediate state in the presence of ChAAILs. The research on the intermediate state of Hb is still unexplored. Research has been pursued to find a suitable ligand or IL that can stabilize the intermediate state of Hb. In that context, ChAAILs are among the best choices. Molecular docking studies unravel the binding of ChAAILs with Hb. The obtained binding energies of the docked complex are -7.2 kcal/mol and -8.7 kcal/mol for binding of Hb with [Chl][Gly] and [Chl][Met], respectively, which was in line with the ITC results. The quantum chemical calculations show that H-bond plays a significant role for the interaction between Hb and ChAAILs.
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Affiliation(s)
- Kiran Devi Tulsiyan
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Jatni, Khurda, Bhubaneswar, 752050, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India
| | - Mallika Rani Prusty
- School of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Berhampur, Berhampur, Odisha, 760010, India
| | - Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Jatni, Khurda, Bhubaneswar, 752050, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India
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7
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Piña MDLN, Sahu AK, Frontera A, Biswal HS, Bauzá A. Tetrel bonds involving a CF 3 group participate in protein-drug recognition: a combined crystallographic and computational study. Phys Chem Chem Phys 2023; 25:12409-12419. [PMID: 37093130 DOI: 10.1039/d3cp00839h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
In this study, the ability of CF3 groups to bind to the electron-rich side chains and backbone groups of proteins has been investigated by combining a Protein Data Bank (PDB) survey and ab initio quantum mechanics calculations. More precisely, an inspection of the PDB involving organic ligands containing a CF3 group and electron-rich atoms (A = N, O and S) in the vicinity revealed 419 X-ray structures exhibiting CF3⋯A tetrel bonds (TtBs). In a posterior stage, those hits that exhibited the most relevant features in terms of directionality and intermolecular distance were selected for theoretical calculations at the RI-MP2/def2-TZVPD level of theory. Also, Hammett's regression plots of several TtB complexes involving meta- and para-substituted benzene derivatives were computed to shed light on the substituent effects. Moreover, the TtBs were characterized through several state-of-the-art computational techniques, such as the Quantum Theory of Atoms in Molecules (QTAIM) and Noncovalent Interactions plot (NCIplot) methodologies. We believe that the results gathered from our study will be useful for rational drug design and biological communities as well as for further expanding the role of this interaction to biomedical applications.
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Affiliation(s)
- María de Las Nieves Piña
- Department of Chemistry, Universitat de les Illes Balears, Crts de Valldemossa km 7.6, 07122 Palma de Mallorca, Baleares, Spain.
| | - Akshay Kumar Sahu
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Via-Jatni, Khurda, 752050, Bhubaneswar, India.
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears, Crts de Valldemossa km 7.6, 07122 Palma de Mallorca, Baleares, Spain.
| | - Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Via-Jatni, Khurda, 752050, Bhubaneswar, India.
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Antonio Bauzá
- Department of Chemistry, Universitat de les Illes Balears, Crts de Valldemossa km 7.6, 07122 Palma de Mallorca, Baleares, Spain.
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Dutta J, Routray C, Pandey S, Biswal HS. Intermolecular noncovalent interactions with carbon in solution. Chem Sci 2022; 13:14327-14335. [PMID: 36545132 PMCID: PMC9749111 DOI: 10.1039/d2sc05431k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/20/2022] [Indexed: 11/22/2022] Open
Abstract
One of the most familiar carbon-centered noncovalent interactions (NCIs) involving an antibonding π*-orbital situated at the Bürgi-Dunitz angle from the electron donor, mostly lone pairs of electrons, is known as n → π* interactions, and if it involves a σ* orbital in a linear fashion, then it is known as the carbon bond. These NCIs can be intra- or inter-molecular and are usually weak in strength but have a paramount effect on the structure and function of small-molecular crystals and proteins. Surprisingly, the experimental evidence of such interactions in the solution phase is scarce. It is even difficult to determine the interaction energy in the solution. Using NMR spectroscopy aided with molecular dynamics (MD) simulation and high-level quantum mechanical calculations, herein we provide the experimental evidence of intermolecular carbon-centered NCIs in solution. The challenge was to find appropriate heterodimers that could sustain room temperature thermal energy and collisions from the solvent molecules. However, after several trial model compounds, the pyridine-N-oxide:dimethyltetracyanocyclopropane (PNO-DMTCCP) complex was found to be a good candidate for the investigation. NBO analyses show that the PNO:DMTCCP complex is stabilized mainly by intermolecular n → π* interaction when a weaker carbon bond gives extra stability to the complex. From the NMR study, it is observed that the NCIs between DMTCCP and PNO are enthalpy driven with an enthalpy change of -28.12 kJ mol-1 and dimerization energy of ∼-38 kJ mol-1 is comparable to the binding energies of a conventional hydrogen-bonded dimer. This study opens up a new strategy to investigate weak intermolecular interactions such as n → π* interaction and carbon bonds in the solution phase.
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Affiliation(s)
- Juhi Dutta
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) PO - Bhimpur-Padanpur, Via-Jatni, District - Khurda PIN - 752050 Bhubaneswar India +91-674-2494-185, +91-674-2494-186
- Homi Bhabha National Institute, Training School Complex Anushakti Nagar Mumbai 400094 India
| | - Chinmay Routray
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) PO - Bhimpur-Padanpur, Via-Jatni, District - Khurda PIN - 752050 Bhubaneswar India +91-674-2494-185, +91-674-2494-186
- Homi Bhabha National Institute, Training School Complex Anushakti Nagar Mumbai 400094 India
| | - Shalini Pandey
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) PO - Bhimpur-Padanpur, Via-Jatni, District - Khurda PIN - 752050 Bhubaneswar India +91-674-2494-185, +91-674-2494-186
- Homi Bhabha National Institute, Training School Complex Anushakti Nagar Mumbai 400094 India
| | - Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) PO - Bhimpur-Padanpur, Via-Jatni, District - Khurda PIN - 752050 Bhubaneswar India +91-674-2494-185, +91-674-2494-186
- Homi Bhabha National Institute, Training School Complex Anushakti Nagar Mumbai 400094 India
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9
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Jena S, Routray C, Dutta J, Biswal HS. Hydrogen Bonding Directed Reversal of
13
C NMR Chemical Shielding. Angew Chem Int Ed Engl 2022; 61:e202207521. [DOI: 10.1002/anie.202207521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Indexed: 12/30/2022]
Affiliation(s)
- Subhrakant Jena
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) PO-Bhimpur-Padanpur Via-Jatni, District-Khurda PIN - 752050 Bhubaneswar India
- Homi Bhabha National Institute, Training School Complex Anushakti Nagar Mumbai 400094 India
| | - Chinmay Routray
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) PO-Bhimpur-Padanpur Via-Jatni, District-Khurda PIN - 752050 Bhubaneswar India
- Homi Bhabha National Institute, Training School Complex Anushakti Nagar Mumbai 400094 India
| | - Juhi Dutta
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) PO-Bhimpur-Padanpur Via-Jatni, District-Khurda PIN - 752050 Bhubaneswar India
- Homi Bhabha National Institute, Training School Complex Anushakti Nagar Mumbai 400094 India
| | - Himansu S. Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) PO-Bhimpur-Padanpur Via-Jatni, District-Khurda PIN - 752050 Bhubaneswar India
- Homi Bhabha National Institute, Training School Complex Anushakti Nagar Mumbai 400094 India
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10
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Pain T, Mondal S, Jena S, Dutta Gupta D, Biswal HS, Kar S. Synthesis, Characterization, and the N Atom Transfer Reactivity of a Nitridochromium(V) Complex Stabilized by a Corrolato Ligand. ACS Omega 2022; 7:28138-28147. [PMID: 35990448 PMCID: PMC9386825 DOI: 10.1021/acsomega.2c02267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
Metal complexes bearing nitrido ligands (M≡N) are at the forefront of current scientific research due to their resemblances with the metal complexes involved in the nitrogen fixation reactions. An oxo(corrolato)chromium(V) complex was used as a precursor complex for the facile synthesis of a new nitrido(corrolato)chromium(V) complex. The nitrido(corrolato)chromium(V) complex was characterized by various spectroscopic techniques. Density functional theory (DFT) calculations were performed on the nitrido(corrolato)chromium(V) complex to assign the vibrational and electronic transitions of this complex. The chromium-nitrogen (nitrido) bond distance obtained in the DFT-optimized structure is 1.530 Å and matches well with the earlier reported authentic Cr≡N bond distances obtained from the single-crystal X-ray diffraction data. This nitrido(corrolato)chromium(V) compound exhibited a sharp Soret band at 438 nm and a Q band at 608 nm. DFT calculations deliver that the origin of the bands at 438 and 608 nm is due to the intraligand charge transfer transitions. The nitrido(corrolato)chromium(V) complex showed one reversible oxidation and one reversible reduction couple at +0.53 and -0.06 V, respectively, vs the Ag/AgCl reference electrode. The simulation of the electron paramagnetic resonance data of the nitrido(corrolato)chromium(V) compound provided the following parameters: g iso = 1.987, A 53Cr = 26 G, and A 14N = 2.71 G. From all these analyses, we can conclude that the electronic configuration in the native state of nitrido(corrolato)chromium(V) can be best described as [(cor3-)CrV(N3-)]-. Reactions of nitrido(corrolato)chromium(V) with the chloro(porphyrinato)chromium(III) complex resulted in a complete intermetal N atom transfer reaction between chromium corrole and chromium porphyrin complexes. A second-order rate constant of 4.29 ± 0.10 M-1 s-1 was obtained for this reaction. It was also proposed that this reaction proceeds via a bimetallic μ-nitrido intermediate.
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Affiliation(s)
- Tanmoy Pain
- School
of Chemical Sciences, National Institute
of Science Education and Research (NISER), Bhubaneswar 752050, India
- Homi
Bhabha National Institute, Training School
Complex, Anushakti Nagar, Mumbai 400094, India
| | - Sruti Mondal
- School
of Chemical Sciences, National Institute
of Science Education and Research (NISER), Bhubaneswar 752050, India
- Homi
Bhabha National Institute, Training School
Complex, Anushakti Nagar, Mumbai 400094, India
| | - Subhrakant Jena
- School
of Chemical Sciences, National Institute
of Science Education and Research (NISER), Bhubaneswar 752050, India
- Homi
Bhabha National Institute, Training School
Complex, Anushakti Nagar, Mumbai 400094, India
| | - Dwaipayan Dutta Gupta
- School
of Chemical Sciences, National Institute
of Science Education and Research (NISER), Bhubaneswar 752050, India
- Homi
Bhabha National Institute, Training School
Complex, Anushakti Nagar, Mumbai 400094, India
| | - Himansu S. Biswal
- School
of Chemical Sciences, National Institute
of Science Education and Research (NISER), Bhubaneswar 752050, India
- Homi
Bhabha National Institute, Training School
Complex, Anushakti Nagar, Mumbai 400094, India
| | - Sanjib Kar
- School
of Chemical Sciences, National Institute
of Science Education and Research (NISER), Bhubaneswar 752050, India
- Homi
Bhabha National Institute, Training School
Complex, Anushakti Nagar, Mumbai 400094, India
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11
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Jena S, Tulsiyan KD, Kumari A, Das R, Biswal HS. Thiolumazines as Heavy-Atom-Free Photosensitizers for Applications in Daylight Photodynamic Therapy: Insights from Ultrafast Excited-State Dynamics. J Phys Chem B 2022; 126:6083-6094. [PMID: 35938784 DOI: 10.1021/acs.jpcb.2c03489] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Finding appropriate photosensitizers (PSs) for daylight photodynamic therapy (dPDT) applications is extremely challenging, even though heavy-atom-free photosensitizers (HAFPSs) such as thiocarbonyl-modified nucleobases have shown a ray of hope. Few attempts have been made to find alternative natural products for dPDT applications. Pteridine heterocycles consisting of a pyrazine ring and a pyrimidine ring, such as lumazine, which exhibit many structural similarities to the alloxazine ring of the flavin molecule, could be an option for HAFPSs. The photophysical and quantum mechanical studies of the thio-modified lumazines revealed that sequential thiomodifications in lumazine result in a bathochromic shift. Additionally, higher tissue penetration depths were observed for thiolumazines. The fluorescence quenching in the case of thiomodified lumazines was explained using triplet state formation, whereas the contribution from the photoinduced electron transfer process cannot be ignored. It was also noticed that a strong one-photon absorption influenced the two-photon absorption (TPA) process, leading to a self-focusing effect in the visible spectral region. The higher tissue penetration and larger TPA cross section are the hallmark characteristics of the thiolumazines to be considered as potential HAFPSs for dPDT applications.
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Affiliation(s)
- Subhrakant Jena
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Kiran Devi Tulsiyan
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Anupa Kumari
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India.,School of Physical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India
| | - Ritwick Das
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India.,School of Physical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India
| | - Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
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12
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Jena S, Dutta J, Tulsiyan KD, Sahu AK, Choudhury SS, Biswal HS. Noncovalent interactions in proteins and nucleic acids: beyond hydrogen bonding and π-stacking. Chem Soc Rev 2022; 51:4261-4286. [PMID: 35560317 DOI: 10.1039/d2cs00133k] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Understanding the noncovalent interactions (NCIs) among the residues of proteins and nucleic acids, and between drugs and proteins/nucleic acids, etc., has extraordinary relevance in biomolecular structure and function. It helps in interpreting the dynamics of complex biological systems and enzymatic activity, which is esential for new drug design and efficient drug delivery. NCIs like hydrogen bonding (H-bonding) and π-stacking have been researchers' delight for a long time. Prominent among the recently discovered NCIs are halogen, chalcogen, pnictogen, tetrel, carbo-hydrogen, and spodium bonding, and n → π* interaction. These NCIs have caught the imaginations of various research groups in recent years while explaining several chemical and biological processes. At this stage, a holistic view of these new ideas and findings lying scattered can undoubtedly trigger our minds to explore more. The present review attempts to address NCIs beyond H-bonding and π-stacking, which are mainly n → σ*, n → π* and σ → σ* type interactions. Five of the seven NCIs mentioned earlier are linked to five non-inert end groups of the modern periodic table. Halogen (group-17) bonding is one of the oldest and most explored NCIs, which finds its relevance in biomolecules due to the phase correction and inhibitory properties of halogens. Chalcogen (group 16) bonding serves as a redox-active functional group of different active sites of enzymes and acts as a nucleophile in proteases and phosphates. Pnictogen (group 15), tetrel (group 14), triel (group 13) and spodium (group 12) bonding does exist in biomolecules. The n → π* interactions are linked to backbone carbonyl groups and protein side chains. Thus, they are crucial in determining the conformational stability of the secondary structures in proteins. In addition, a more recently discovered to and fro σ → σ* type interaction, namely carbo-hydrogen bonding, is also present in protein-ligand systems. This review summarizes these grand epiphanies routinely used to elucidate the structure and dynamics of biomolecules, their enzymatic activities, and their application in drug discovery. It also briefs about the future perspectives and challenges posed to the spectroscopists and theoreticians.
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Affiliation(s)
- Subhrakant Jena
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| | - Juhi Dutta
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| | - Kiran Devi Tulsiyan
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| | - Akshay Kumar Sahu
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| | - Shubhranshu Shekhar Choudhury
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| | - Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
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13
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Sahu K, Dutta J, Nayak S, Nayak P, Biswal HS, Kar S. Investigation of the Nature of Intermolecular Interactions in Tetra(thiocyanato)corrolato-Ag(III) Complexes: Agostic or Hydrogen Bonded? Inorg Chem 2022; 61:6539-6546. [PMID: 35442024 DOI: 10.1021/acs.inorgchem.2c00353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Tetra(thiocyanato)corrolato-Ag(III) complexes presented here constitute a new class of metallo-corrole complexes. The spectroscopic properties of these complexes are quite unusual and interesting. For example, the absorption spectra of these β-substituted corrolato-Ag(III) complexes are very different from those of the β-unsubstituted corrolato-Ag(III) derivatives. Single-crystal XRD analysis of a representative tetra(thiocyanato)corrolato-Ag(III) derivative reveals C-H···Ag interactions. The C-H···Ag interactions are rarely demonstrated in the crystal lattice of a discrete coordination/organometallic compound. Optimization of the hydrogen positions of the crystal structure discloses the geometrical parameters of the said interaction as a Ag···H distance of 2.597 Å and ∠C-H···Ag of 109.62°. The natural bond orbital analysis provides information about the donor-acceptor orbitals involved in the interactions and their interaction energies. It was observed that the σC-H orbital overlaps with the vacant d-orbital of Ag with an interaction energy of 17.93 kJ/mol. The filled d-orbital of Ag overlaps with the σ*C-H orbital with an interaction energy of 4.79 kJ/mol. The highlights of this work are that the H···Ag distance is outside of the distance range for the typical agostic interaction but fitted with the weak H-bond distance. However, the ∠C-H···Ag angle is within the range of the agostic interaction. Both crystallographic data and electronic structure calculations reveal that these kinds of intermolecular interactions in square-planar d8 Ag(III) complexes are intermediate in nature. Thus, they cannot be categorically called either hydrogen bonding or agostic interaction.
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Affiliation(s)
- Kasturi Sahu
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Bhubaneswar 752050, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400 094, India
| | - Juhi Dutta
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Bhubaneswar 752050, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400 094, India
| | - Srimoy Nayak
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Bhubaneswar 752050, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400 094, India
| | - Panisha Nayak
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Bhubaneswar 752050, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400 094, India
| | - Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Bhubaneswar 752050, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400 094, India
| | - Sanjib Kar
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Bhubaneswar 752050, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400 094, India
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14
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Abstract
Hydrogen bonding (H-bonding) without lone pair(s) of electrons and π-electrons is a concept developed 2-3 years ago. H-bonds involving less electronegative tetrahedral carbon are beyond the classical concept of H-bonds. Herein, we present the first report on H-bonds with tetravalent carbons in proteins. A special bonding arrangement is needed to increase the negative charge density around the sp3-hybridized carbon atom. Therefore, less electronegative elements such as As and Mg, when bonded to sp3-C, enable the C-atoms as H-bond acceptors. Careful protein structure analysis aided by several quantum chemical calculations suggests that these H-bonds are weak to moderate in strength. We developed an empirical equation to estimate the C-H···C H-bond energy in proteins from the distances between the C- and H-atoms. In proteins, the binding energies range from -5.4 to -14.0 kJ/mol. The C-H···C H-bonds assist the substrate binding in proteins. We also explored the potential role of these carbon-centered H-bonds in C-H bond activation through σ-bond metathesis. To our surprise, contribution from these H-bonds is almost of similar magnitude as that from C-H···π H-bonds for C-H bond activation.
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Affiliation(s)
- Juhi Dutta
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Bhimpur-Padanpur, Via-Jatni, Khurda, Bhubaneswar 752050, India.,Training School Complex, Homi Bhabha National Institute, Anushakti Nagar, Mumbai 400094, India
| | - Akshay Kumar Sahu
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Bhimpur-Padanpur, Via-Jatni, Khurda, Bhubaneswar 752050, India.,Training School Complex, Homi Bhabha National Institute, Anushakti Nagar, Mumbai 400094, India
| | - Abhijeet S Bhadauria
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Bhimpur-Padanpur, Via-Jatni, Khurda, Bhubaneswar 752050, India.,Training School Complex, Homi Bhabha National Institute, Anushakti Nagar, Mumbai 400094, India
| | - Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Bhimpur-Padanpur, Via-Jatni, Khurda, Bhubaneswar 752050, India.,Training School Complex, Homi Bhabha National Institute, Anushakti Nagar, Mumbai 400094, India
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15
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Abstract
Hydrogen bonding (H-bonding) with heavier chalcogens such as polonium and tellurium is almost unexplored owing to their lower electronegativities, providing us an opportunity to delve into the uncharted territory of...
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16
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Tulsiyan K, Jena S, González-Viegas M, Kar RK, Biswal HS. Structural Dynamics of RNA in the Presence of Choline Amino Acid Based Ionic Liquid: A Spectroscopic and Computational Outlook. ACS Cent Sci 2021; 7:1688-1697. [PMID: 34729412 PMCID: PMC8554839 DOI: 10.1021/acscentsci.1c00768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Indexed: 05/03/2023]
Abstract
Ribonucleic acid (RNA) is exceedingly sensitive to degradation compared to DNA. The current protocol for storage of purified RNA requires freezing conditions below -20 °C. Recent advancements in biological chemistry have identified amino acid-based ionic liquids as suitable preservation media for RNA, even in the presence of degrading enzymes. However, the mechanistic insight into the interaction between ILs and RNA is unclear. To the best of our knowledge, no attempts are made so far to provide a molecular view. This work aims to establish a detailed understanding of how ILs enable structural stability to RNA sourced from Torula yeast. Herein, we manifest the hypothesis of multimodal binding of IL and its minimal perturbation to the macromolecular structure, with several spectroscopic techniques such as time-resolved fluorescence and fluorescence correlation spectroscopy (FCS) aided with molecular dynamics at microsecond time scales. Relevant structural and thermodynamic details from biophysical experiments confirm that even long-term RNA preservation with ILs is a possible alternative devoid of any structural deformation. These results establish a unifying mechanism of how ILs are maintaining conformational integrity and thermal stability. The atomistic insights are transferable for their potential applications in drug delivery and biomaterials by considering the advantages of having maximum structural retention and minimum toxicity.
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Affiliation(s)
- Kiran
Devi Tulsiyan
- School
of Chemical Sciences, National Institute
of Science Education and Research (NISER), Bhimpur-Padanpur, Via-Jatni, District, Khurda, 752050, Bhubaneswar, India
- Homi
Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Subhrakant Jena
- School
of Chemical Sciences, National Institute
of Science Education and Research (NISER), Bhimpur-Padanpur, Via-Jatni, District, Khurda, 752050, Bhubaneswar, India
- Homi
Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - María González-Viegas
- Institut
für Biologie, Humboldt Universität zu Berlin, Invalidenstraße 42, 10115 Berlin, Germany
| | - Rajiv K. Kar
- Faculty
II-Mathematics and Natural Sciences, Technische
Universität Berlin, Sekr. PC 14, Strasse des 17, Juni 135, D-10623 Berlin, Germany
| | - Himansu S. Biswal
- School
of Chemical Sciences, National Institute
of Science Education and Research (NISER), Bhimpur-Padanpur, Via-Jatni, District, Khurda, 752050, Bhubaneswar, India
- Homi
Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
- . Phone: +91-674-2494 185/186
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17
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Biswal HS, Sahu AK, Galmés B, Frontera A, Chopra D. Se⋅⋅⋅O/S and S⋅⋅⋅O Chalcogen Bonds in Small Molecules and Proteins: A Combined CSD and PDB Study. Chembiochem 2021; 23:e202100498. [PMID: 34693623 PMCID: PMC9298333 DOI: 10.1002/cbic.202100498] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/23/2021] [Indexed: 12/13/2022]
Abstract
The importance of selenium-centered noncovalent chalcogen bonds represented as Se⋅⋅⋅A (A=O/S) has been explored for short directional contacts in small molecules and proteins. In addition, S⋅⋅⋅O centered contacts have been analyzed. Computational analyses involving the quantitative assessment of the associated energetics, the molecular electrostatic potentials (MEP), and electron density derived topological parameters, namely, quantum theory of atom in molecules (QTAIM) analyses, and NBO (natural bond orbital) based calculations, have been performed to unequivocally establish the strength, stability, and attractive role of chalcogen bonds in the solid-state. This investigation has been performed in molecules from both the Cambridge Structural Database (CSD) and Protein Data Bank (PDB). Thus futuristic materials may be designed keeping in mind the significance of these interactions, including their relevance in biology.
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Affiliation(s)
- Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Via-Jatni, District-Khurda, Bhubaneswar, India.,Training School Complex, Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Akshay Kumar Sahu
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Via-Jatni, District-Khurda, Bhubaneswar, India.,Training School Complex, Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Bartomeu Galmés
- Departament de Química, Universitat de les Illes Balears, Crta de Valldemossa km 7.5, 07122, Palma de Mallorca, Spain
| | - Antonio Frontera
- Departament de Química, Universitat de les Illes Balears, Crta de Valldemossa km 7.5, 07122, Palma de Mallorca, Spain
| | - Deepak Chopra
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462066, Madhya Pradesh, India
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18
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Sakai N, Warren R, Zhang F, Nayak S, Liu J, Kesava SV, Lin YH, Biswal HS, Lin X, Grovenor C, Malinauskas T, Basu A, Anthopoulos TD, Getautis V, Kahn A, Riede M, Nayak PK, Snaith HJ. Adduct-based p-doping of organic semiconductors. Nat Mater 2021; 20:1248-1254. [PMID: 33888905 DOI: 10.1038/s41563-021-00980-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 03/09/2021] [Indexed: 06/12/2023]
Abstract
Electronic doping of organic semiconductors is essential for their usage in highly efficient optoelectronic devices. Although molecular and metal complex-based dopants have already enabled significant progress of devices based on organic semiconductors, there remains a need for clean, efficient and low-cost dopants if a widespread transition towards larger-area organic electronic devices is to occur. Here we report dimethyl sulfoxide adducts as p-dopants that fulfil these conditions for a range of organic semiconductors. These adduct-based dopants are compatible with both solution and vapour-phase processing. We explore the doping mechanism and use the knowledge we gain to 'decouple' the dopants from the choice of counterion. We demonstrate that asymmetric p-doping is possible using solution processing routes, and demonstrate its use in metal halide perovskite solar cells, organic thin-film transistors and organic light-emitting diodes, which showcases the versatility of this doping approach.
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Affiliation(s)
- Nobuya Sakai
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK
| | - Ross Warren
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK
| | - Fengyu Zhang
- Department of Electrical and Computer Engineering, Princeton University, Princeton, NJ, USA
| | - Simantini Nayak
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, Oxford, UK
- Materials Chemistry Department, CSIR-Institute of Mineral and Materials Technology, Bhubaneswar, India
| | - Junliang Liu
- Department of Materials, University of Oxford, Oxford, UK
| | - Sameer V Kesava
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK
| | - Yen-Hung Lin
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK
| | - Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research, Bhubaneswar, India
| | - Xin Lin
- Department of Electrical and Computer Engineering, Princeton University, Princeton, NJ, USA
| | - Chris Grovenor
- Department of Materials, University of Oxford, Oxford, UK
| | - Tadas Malinauskas
- Department of Organic Chemistry, Kaunas University of Technology, Kaunas, Lithuania
| | - Aniruddha Basu
- KAUST Solar Center (KSC), King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Thomas D Anthopoulos
- KAUST Solar Center (KSC), King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Vytautas Getautis
- Department of Organic Chemistry, Kaunas University of Technology, Kaunas, Lithuania
| | - Antoine Kahn
- Department of Electrical and Computer Engineering, Princeton University, Princeton, NJ, USA
| | - Moritz Riede
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK
| | - Pabitra K Nayak
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK.
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Hyderabad, India.
| | - Henry J Snaith
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK.
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19
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Abstract
Understanding the structural and functional implications of metal ions is of pivotal significance to chemical biology. Herein, we report first time the evidence of spodium bonds (SpB's, an attractive noncovalent force involving elements from group 12 and electron-rich species) in tetrahedral Zn-binding sites. Through a combined crystallographic (PDB analysis) and computational (ab initio calculations) study, we demonstrate that Zn SpB's are abundant and might be involved in protein structure and enzyme inhibition.
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Affiliation(s)
- Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Bhimpur-Padanpur, Via-Jatni, Khurda, 752050 Bhubaneswar, India.,Training School Complex, Homi Bhabha National Institute, Anushakti Nagar, 400094 Mumbai, India
| | - Akshay Kumar Sahu
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Bhimpur-Padanpur, Via-Jatni, Khurda, 752050 Bhubaneswar, India.,Training School Complex, Homi Bhabha National Institute, Anushakti Nagar, 400094 Mumbai, India
| | - Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma (Baleares), Spain
| | - Antonio Bauzá
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma (Baleares), Spain
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20
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Dhakad A, Jena S, Sahoo DK, Biswal HS. Quantification of the electric field inside protein active sites and fullerenes. Phys Chem Chem Phys 2021; 23:14755-14763. [PMID: 34195713 DOI: 10.1039/d1cp01769a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
While electrostatic interactions are exceedingly accountable for biological functions, no simple method exists to directly estimate or measure the electrostatic field in protein active sites. The electrostatic field inside the protein is generally inferred from the shift in the vibrational stretching frequencies of nitrile and thionitrile probes at the active sites through several painstaking and time-consuming experiments like vibrational Stark effect spectroscopy (VSS). Here we present a simple, fast, and reliable methodology, which can efficiently predict the vibrational Stark tuning rates (VSRs) of a large variety of probes within 10% error of the reported experimental data. Our methodology is based on geometry optimization and frequency calculations in the presence of an external electric field to predict the accurate VSR of newly designed nitrile/thionitrile probes. A priori information of VSRs is useful for difficult experiments such as catalytic/enzymatic study and in structural biology. We also applied our methodology successfully to estimate the electric field inside fullerenes and nano-onions, which is encouraging for researchers to adopt it for further applications in materials science and supramolecular chemistry.
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Affiliation(s)
- Ambuj Dhakad
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India. and Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Subhrakant Jena
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India. and Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Dipak Kumar Sahoo
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India. and Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India. and Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
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21
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Choudhury S, Jena S, Sahoo DK, Shekh S, Kar RK, Dhakad A, Gowd KH, Biswal HS. Gram-Scale Synthesis of 1,8-Naphthyridines in Water: The Friedlander Reaction Revisited. ACS Omega 2021; 6:19304-19313. [PMID: 34337267 PMCID: PMC8320145 DOI: 10.1021/acsomega.1c02798] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 06/29/2021] [Indexed: 06/13/2023]
Abstract
The products of the Friedlander reaction, i.e., 1,8-naphthyridines, have far-reaching impacts in materials science, chemical biology, and medicine. The reported synthetic methodologies elegantly orchestrate the diverse synthetic routes of naphthyridines but require harsh reaction conditions, organic solvents, and expensive metal catalysts. Here, we introduce gram-scale synthesis of 1,8-naphthyridines in water using an inexpensive and biocompatible ionic liquid (IL) as a catalyst. This is the first-ever report on the synthesis of naphthyridines in water. This is a one-step reaction, and the product separation is relatively easy. The choline hydroxide (ChOH) is used as a metal-free, nontoxic, and water-soluble catalyst. In comparison to other catalysts reported in the literature, ChOH has the advantage of forming an additional hydrogen bond with the reactants, which is the vital step for the reaction to happen in water. Density functional theory (DFT) and noncovalent interaction (NCI) plot index analysis provide the plausible reaction mechanism for the catalytic cycle and confirm that hydrogen bonds with the IL catalyst are pivotal to facilitate the reaction. Molecular docking and molecular dynamics (MD) simulations are also performed to demonstrate the potentialities of the newly synthesized products as drugs. Through MD simulations, it was established that the tetrahydropyrido derivative of naphthyridine (10j) binds to the active sites of the ts3 human serotonin transporter (hSERT) (PDB ID: 6AWO) without perturbing the secondary structure, suggesting that 10j can be a potential preclinical drug candidate for hSERT inhibition and depression treatment.
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Affiliation(s)
- Shubhranshu
Shekhar Choudhury
- School
of Chemical Sciences, National Institute
of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Via-Jatni,
Khurda, 752050 Bhubaneswar, India
- Homi
Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Subhrakant Jena
- School
of Chemical Sciences, National Institute
of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Via-Jatni,
Khurda, 752050 Bhubaneswar, India
- Homi
Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Dipak Kumar Sahoo
- School
of Chemical Sciences, National Institute
of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Via-Jatni,
Khurda, 752050 Bhubaneswar, India
- Homi
Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Shamasoddin Shekh
- Department
of Chemistry, Central University of Karnataka, Kalaburagi 585367, Karnataka, India
| | - Rajiv K. Kar
- Fritz
Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Ambuj Dhakad
- School
of Chemical Sciences, National Institute
of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Via-Jatni,
Khurda, 752050 Bhubaneswar, India
- Homi
Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Konkallu Hanumae Gowd
- Department
of Chemistry, Central University of Karnataka, Kalaburagi 585367, Karnataka, India
| | - Himansu S. Biswal
- School
of Chemical Sciences, National Institute
of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Via-Jatni,
Khurda, 752050 Bhubaneswar, India
- Homi
Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
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22
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Dolle A, Vijayasarathy M, Shekh S, Hunashal Y, Reddy KKA, Prakash S, Rana A, Biswal HS, Raghothama S, Gowd KH. The Redox-Active Conopeptide Derived from the Venom Duct Transcriptome of Conus lividus Assists in the Oxidative Folding of Conotoxin. Biochemistry 2021; 60:1299-1311. [PMID: 33829763 DOI: 10.1021/acs.biochem.1c00090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The tetrapeptides Li504 and Li520, differing in the modification of the 4-trans-hydroxylation of proline, are novel conopeptides derived from the venom duct transcriptome of the marine cone snail Conus lividus. These predicted mature peptides are homologous to the active site motif of oxidoreductases that catalyze the oxidation, reduction, and rearrangement of disulfide bonds in peptides and proteins. The estimated reduction potential of the disulfide of Li504 and Li520 is within the range of disulfide reduction potentials of oxidoreductases, indicating that they may catalyze the oxidative folding of conotoxins. Conformational features of Li504 and Li520 include the trans configuration of the Cys1-Pro2/Hyp2 peptide bond with a type 1 turn that is similar to the active site motif of glutaredoxin that regulates the oxidation of cysteine thiols to disulfides. Li504- and Li520-assisted oxidative folding of α-conotoxin ImI confirms that Li520 improves the yield of the natively folded peptide by concomitantly decreasing the yield of the non-native disulfide isomer and thus acts as a miniature disulfide isomerase. The geometry of the Cys1-Hyp2 peptide bond of Li520 shifts between the trans and cis configurations in the disulfide form and thiol/thiolate form, which regulates the deprotonation of the N-terminal cysteine residue. Hydrogen bonding of the hydroxyl group of 4-trans-hydroxyproline with the interpeptide chain unit in the mixed disulfide form may play a vital role in shifting the geometry of the Cys1-Hyp2 peptide bond from cis to trans configuration. The Li520 conopeptide together with similar peptides derived from other species may constitute a new family of "redox-active" conopeptides that are integral components of the oxidative folding machinery of conotoxins.
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Affiliation(s)
- Ashwini Dolle
- Department of Chemistry, School of Chemical Sciences, Central University of Karnataka, Kalaburagi 585367, Karnataka, India
| | | | - Shamasoddin Shekh
- Department of Chemistry, School of Chemical Sciences, Central University of Karnataka, Kalaburagi 585367, Karnataka, India
| | - Yamanappa Hunashal
- NMR Research Centre, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - K Kasi Amarnath Reddy
- Department of Chemistry, School of Chemical Sciences, Central University of Karnataka, Kalaburagi 585367, Karnataka, India
| | - Sunita Prakash
- Proteomic Facility, Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Abhijit Rana
- School of Chemical Sciences, National Institute of Science Education and Research, Bhubaneswar 752050, Odisha, India
| | - Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research, Bhubaneswar 752050, Odisha, India
| | | | - Konkallu Hanumae Gowd
- Department of Chemistry, School of Chemical Sciences, Central University of Karnataka, Kalaburagi 585367, Karnataka, India
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Naik S, Kalaiarasan S, Nath RC, Sarangi SN, Sahu AK, Samal D, Biswal HS, Samal SL. Nominal Effect of Mg Intercalation on the Superconducting Properties of 2H-NbSe 2. Inorg Chem 2021; 60:4588-4598. [PMID: 33689330 DOI: 10.1021/acs.inorgchem.0c03545] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
2H-NbSe2 is a phonon-mediated, Fermi-surface topology-dependent multiband superconductor with an incommensurate charge-density wave (CDW) that coexists at a local level with superconductivity. Usually, the intercalation in 2H-NbSe2 enriches the CDW, enhances the c-axis lattice parameter, and distorts the Fermi surface, which result in a decrease in the superconducting transition temperature (Tc). The rate of decrease of Tc depends on the electronic structure, size, valence, magnetic nature, and electronegativity of the intercalating species. Herein, we report an unusual effect of Mg intercalation on the superconductivity of 2H-MgxNbSe2 (x = 0.0, 0.02, 0.06, 0.08, 0.10, and 0.12) synthesized by a high-temperature solid-state reaction method. Unlike other s- and p-block elements/species as intercalants (Rb, Sn, Ga, and Al) that have a sharp detrimental effect on the Tc of 2H-NbSe2 within 1-5% of intercalation, Mg is found to be an exception. Upon Mg intercalation up to x = 0.06, no remarkable changes in Tc as compared to the parent 2H-NbSe2 (Tc ∼ 6.7 K) are observed, and further intercalation results in a small decrease in Tc (for x = 0.12, Tc = 6.2 K). From heat-capacity measurements, it is inferred that superconducting Mg-intercalated 2H-NbSe2 exhibits strong electron-phonon coupling. Electronic structure calculations on two s-block element intercalated compounds of formula M0.125NbSe2 (M = Mg, Rb) show that Rb s-, p-, and d-states completely overlap with the Nb d states, while the Mg s states lie in a low-energy region as compared to Nb d states, indicating a weak interaction between the intercalant and the Nb sublattice in Mg0.125NbSe2 as compared to Rb0.125NbSe2. These results suggest that the electronic states of the Nb network in 2H-NbSe2 are least altered with Mg intercalation, which could be one of the reasons for the minimal effect on the Tc with intercalation.
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Affiliation(s)
- Subham Naik
- Department of Chemistry, National Institute of Technology Rourkela, Rourkela 769008, India
| | - Somesh Kalaiarasan
- School of Physics, Indian Institute of Science Education and Research, Thiruvananthapuram 695551, India
| | - Ramesh C Nath
- School of Physics, Indian Institute of Science Education and Research, Thiruvananthapuram 695551, India
| | | | - Akshay K Sahu
- School of Chemical Sciences, National Institute of Science Education and Research, Bhubaneswar 752050, India
| | - Debakanta Samal
- Institute of Physics, Bhubaneswar 751005, India.,Homi Bhabha National Institute, Anushakti Nagar, Mumbai 400085, India
| | - Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research, Bhubaneswar 752050, India
| | - Saroj L Samal
- Department of Chemistry, National Institute of Technology Rourkela, Rourkela 769008, India
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24
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Jena S, Tulsiyan KD, Kar RK, Kisan HK, Biswal HS. Doubling Förster Resonance Energy Transfer Efficiency in Proteins with Extrinsic Thioamide Probes: Implications for Thiomodified Nucleobases. Chemistry 2021; 27:4373-4383. [PMID: 33210381 DOI: 10.1002/chem.202004627] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Indexed: 12/29/2022]
Abstract
Designing a potential protein-ligand pair is pivotal, not only to track the protein structure dynamics, but also to assist in an atomistic understanding of drug delivery. Herein, the potential of a small model thioamide probe being used to study albumin proteins is reported. By monitoring the Förster resonance energy transfer (FRET) dynamics with the help of fluorescence spectroscopic techniques, a twofold enhancement in the FRET efficiency of 2-thiopyridone (2TPY), relative to that of its amide analogue, is observed. Molecular dynamics simulations depict the relative position of the free energy minimum to be quite stable in the case of 2TPY through noncovalent interactions with sulfur, which help to enhance the FRET efficiency. Finally, its application is shown by pairing thiouracils with protein. It is found that the site-selective sulfur atom substitution approach and noncovalent interactions with sulfur can substantially enhance the FRET efficiency, which could be a potential avenue to explore in the design of FRET probes to study the structure and dynamics of biomolecules.
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Affiliation(s)
- Subhrakant Jena
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Jatni, Khurda, Bhubaneswar, 752050, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India
| | - Kiran Devi Tulsiyan
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Jatni, Khurda, Bhubaneswar, 752050, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India
| | - Rajiv K Kar
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel
| | - Hemanta K Kisan
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel.,Department of Chemistry, Utkal University, 751004, Bhubaneswar, India
| | - Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Jatni, Khurda, Bhubaneswar, 752050, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India
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25
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Kumar Sahoo D, Devi Tulsiyan K, Jena S, Biswal HS. Implication of Threonine-Based Ionic Liquids on the Structural Stability, Binding and Activity of Cytochrome c. Chemphyschem 2020; 21:2525-2535. [PMID: 33022820 DOI: 10.1002/cphc.202000761] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/04/2020] [Indexed: 12/28/2022]
Abstract
Ionic liquids (ILs) are useful in pharmaceutical industries and biotechnology as alternative solvents or sources for protein extraction and purification, preservation of biomolecules and for regulating the catalytic activity of enzymes. However, the binding mechanism, the non-covalent forces responsible for protein-IL interactions and dynamics of proteins in IL need to be investigated in depth for the effective use of ILs as alternatives. Herein, we disclose the molecular level understanding of the structural intactness and reactivity of a model protein cytochrome c (Cyt c) in biocompatible threonine-based ILs with the help of experimental techniques such as isothermal titration calorimetry (ITC), fluorescence spectroscopy, transmission electron microscopy (TEM) as well as molecular docking. Hydrophobic and electrostatic forces are responsible for the structural and conformational integrity of Cyt c in IL. The ITC experiments revealed the Cyt c-IL binding free energies are in the range of 10-14 kJ/mol and the molecular docking studies demonstrated that ILs interact at the surfaces of Cyt c. The results look promising as the ILs used here are non-toxic and biocompatible, and thus may find potential applications in structural biology and biotechnology.
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Affiliation(s)
- Dipak Kumar Sahoo
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN-752050, Bhubaneswar, India.,Homi Bhaba National Institute Training School Complex, Anushakti Nagar, Mumbai, 400094, India
| | - Kiran Devi Tulsiyan
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN-752050, Bhubaneswar, India.,Homi Bhaba National Institute Training School Complex, Anushakti Nagar, Mumbai, 400094, India
| | - Subhrakant Jena
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN-752050, Bhubaneswar, India.,Homi Bhaba National Institute Training School Complex, Anushakti Nagar, Mumbai, 400094, India
| | - Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN-752050, Bhubaneswar, India.,Homi Bhaba National Institute Training School Complex, Anushakti Nagar, Mumbai, 400094, India
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26
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Sahoo DK, Chand A, Jena S, Biswal HS. Hydrogen-bond-driven thiouracil dissolution in aqueous ionic liquid: A combined microscopic, spectroscopic and molecular dynamics study. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.114275] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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27
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Rana A, Galmés B, Frontera A, Biswal HS, Chopra D. Unravelling the electronic nature of C-FO-C non-covalent interaction in proteins and small molecules in the solid state. Phys Chem Chem Phys 2020; 22:25704-25711. [PMID: 33146185 DOI: 10.1039/d0cp05280a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The participation of organic fluorine as a halogen bond donor is rare and is sensitive to the electronic environment in the vicinity of the fluorine atom. The enhancement in the electropositive character (the σ-hole formalism) in fluorine is established by the presence of electron withdrawing groups and this has been examined in the solid-state structures in small molecules and proteins. Short, directional FO contacts have been observed and physical insights obtained, from quantum mechanical calculations, via the molecular electrostatic potential, an analysis of their topological features from atoms-in-molecules, and donor-acceptor characteristics from natural bond orbital analyses. It was observed that such contacts, cooperatively act in the presence of other interactions, and the formed aggregates are stabilizing in nature. In addition, the FO has a bonding character and is attractive in nature. The halogen bonding character of fluorine is relevant in supramolecular chemistry.
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Affiliation(s)
- Abhijit Rana
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Via-Jatni, District-Khurda, 752050, Bhubaneswar, India.
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28
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Jena S, Tulsiyan KD, Rana A, Choudhury SS, Biswal HS. Non-conventional Hydrogen Bonding and Aromaticity: A Systematic Study on Model Nucleobases and Their Solvated Clusters. Chemphyschem 2020; 21:1826-1835. [PMID: 32506748 DOI: 10.1002/cphc.202000386] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/02/2020] [Indexed: 12/25/2022]
Abstract
The conceptual development of aromaticity is essential to rationalize and understand the structure and behavior of aromatic heterocycles. This work addresses for the first time, the interconnection between aromaticity and sulfur/selenium centered hydrogen bonds (S/SeCHBs) involved in representative heterocycle models of canonical nucleobases (2-Pyridone; 2PY) and its sulfur (2-Thiopyridone; 2TPY) and selenium (2-Selenopyridone; 2SePY) analogs. The nucleus-independent chemical shift (NICS) and gauge induced magnetic current density (GIMIC) values suggested significant reduction of aromaticity upon replacement of exocyclic carbonyl oxygen with sulfur and selenium. However, we observed two-fold (57 %) and three-fold (80 %) enhancement in the aromaticity for 2TPY dimer, and 2SePY dimer, respectively which are connected through S/SeCHBs. Aromaticity enhancement was also noticed in 1 : 1 H-bonded complexes (heterodimers), micro hydrated clusters and for bulk hydration. It is expected that exocyclic S and Se incorporation into heterocycles without compromising aromatic loss would definitely reinforce to design new supramolecular building blocks via S/SeCH-bonded complexes.
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Affiliation(s)
- Subhrakant Jena
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Via-Jatni, District-Khurda, PIN-752050, Bhubaneswar, INDIA.,Homi Bhaba National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, INDIA
| | - Kiran Devi Tulsiyan
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Via-Jatni, District-Khurda, PIN-752050, Bhubaneswar, INDIA.,Homi Bhaba National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, INDIA
| | - Abhijit Rana
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Via-Jatni, District-Khurda, PIN-752050, Bhubaneswar, INDIA.,Homi Bhaba National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, INDIA
| | - Shubhranshu S Choudhury
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Via-Jatni, District-Khurda, PIN-752050, Bhubaneswar, INDIA.,Homi Bhaba National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, INDIA
| | - Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Via-Jatni, District-Khurda, PIN-752050, Bhubaneswar, INDIA.,Homi Bhaba National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, INDIA
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29
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Chand A, Sahoo DK, Rana A, Jena S, Biswal HS. The Prodigious Hydrogen Bonds with Sulfur and Selenium in Molecular Assemblies, Structural Biology, and Functional Materials. Acc Chem Res 2020; 53:1580-1592. [PMID: 32677432 DOI: 10.1021/acs.accounts.0c00289] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Hydrogen bonds (H-bonds) play important roles in imparting functionality to the basic molecules of life by stabilizing their structures and directing their interactions. Numerous studies have been devoted to understanding H-bonds involving highly electronegative atoms like nitrogen, oxygen, and halogens and consequences of those H-bonds in chemical reactions, catalysis, and structure and function of biomolecules; but the involvement of less electronegative atoms like sulfur and selenium in H-bond formation establishes the concept of noncanonical H-bonds. Initially belittled for the "weak" nature of their interactions, these perceptions have gradually evolved over time through dedicated efforts by several research groups. This has been facilitated by advancements in experimental methods for their detection through gas-phase laser spectroscopy and solution NMR spectroscopy, as well as through theoretical predictions from high level quantum chemical calculations.In this Account, we present insights into the versatility of the sulfur and selenium centered H-bonds (S/SeCHBs) by highlighting their multifarious applications in various fields from chemical reactions to optoelectronic properties to structural biology. Our group has highlighted the significance and strength of such H-bonds in natural and modified biomolecules. Here, we have reviewed several molecular assemblies, biomolecules, and functional materials, where the role of these H-bonds is pivotal in influencing biological functions. It is worth mentioning here that the precise experimental data obtained from gas-phase laser spectroscopy have contributed considerably to changing the existing perceptions toward S/SeCHBs. Thus, molecular beam experiments, though difficult to perform on smaller model thio- or seleno-substituted Molecules, etc. (amides, nucleobases, drug molecules), are inevitable to gather elementary knowledge and convincing concepts on S/SeCHBs that can be extended from a small four-atom sulfanyl dimer to a large 14 kDa iron-sulfur protein, ferredoxin. These H-bonds can also tailor a fascinating array of molecular frameworks and design supramolecular assemblies by inter- and intralinking of individual "molecular Lego-like" units.The discussion is indeed intriguing when it turns to the usage of S/SeCHBs in facile synthetic strategies like tuning regioselectivity in reactions, as well as invoking phenomena like dual phosphorescence and chemiluminescence. This is in addition to our investigations of the dispersive nature of the hydrogen bond between metal hydrides and sulfur or selenium as acceptor, which we anticipate would lead to progress in the areas of proton and hydride transfer, as well as force-field design. This Account demonstrates how ease of fabrication, enhanced efficiency, and alteration of physicochemical properties of several functional materials is facilitated owing to the presence of S/SeCHBs. Our efforts have been instrumental in the evaluation of various S/SeCHBs in flue gas capture, as well as design of organic energy harvesting materials, where dipole moment and polarizability have important roles to play. We hope this Account invokes newer perspectives with regard to how H-bonds with sulfur and selenium can be adequately adopted for crystal engineering, for more photo- and biophysical studies with different spectroscopic methods, and for developing next-generation field-effect transistors, batteries, superconductors, and organic thin-film transistors, among many other multifunctional materials for the future.
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Affiliation(s)
- Apramita Chand
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO Bhimpur-Padanpur, Via-Jatni, District Khurda, 752050 Bhubaneswar, India
- Homi Bhabha National Institute, Training School
Complex, Anushakti Nagar, Mumbai 400094, India
| | - Dipak Kumar Sahoo
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO Bhimpur-Padanpur, Via-Jatni, District Khurda, 752050 Bhubaneswar, India
- Homi Bhabha National Institute, Training School
Complex, Anushakti Nagar, Mumbai 400094, India
| | - Abhijit Rana
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO Bhimpur-Padanpur, Via-Jatni, District Khurda, 752050 Bhubaneswar, India
- Homi Bhabha National Institute, Training School
Complex, Anushakti Nagar, Mumbai 400094, India
| | - Subhrakant Jena
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO Bhimpur-Padanpur, Via-Jatni, District Khurda, 752050 Bhubaneswar, India
- Homi Bhabha National Institute, Training School
Complex, Anushakti Nagar, Mumbai 400094, India
| | - Himansu S. Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO Bhimpur-Padanpur, Via-Jatni, District Khurda, 752050 Bhubaneswar, India
- Homi Bhabha National Institute, Training School
Complex, Anushakti Nagar, Mumbai 400094, India
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30
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Dolle A, Reddy KKA, Gunaga SS, Krishnamurthy K, Senapati DK, Rana A, Sindogi K, Biswal HS, Raghothama S, Gowd KH. Characterization of (Boc-Cys/Sec-NHMe) 2 and (Boc-Cys/Sec-OMe) 2 : Evidence of local conformational difference between disulfide and diselenide. J Pept Sci 2020; 26:e3245. [PMID: 32103604 DOI: 10.1002/psc.3245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 02/11/2020] [Accepted: 02/11/2020] [Indexed: 11/11/2022]
Abstract
Conformations of disulfide and diselenide were compared in (Boc-Cys/Sec-NHMe)2 and (Boc-Cys/Sec-OMe)2 using X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, density functional theory (DFT), and circular dichroism (CD) spectroscopy. Conformations of disulfide/diselenide in polypeptides are defined based on the sign of side chain torsion angle χ3 (-CH2 -S/Se-S/Se-CH2 -); negative indicates left-handed and positive indicates right-handed orientation. In the crystals of (Boc-Cys-OMe)2 and (Boc-Sec-OMe)2 , the disulfide exhibits a left-handed and the diselenide a right-handed orientation. Characterization of cystine and selenocystine derivatives in solution using 1 H-NMR, natural abundant 77 Se NMR, 2D-ROESY, and chemical shift analysis coupled to DMSO titration has indicated the symmetrical nature and antiparallel orientation of Cys/Sec residues about the disulfide/diselenide bridges. Structural calculations of cystine and selenocystine derivatives using DFT further support the antiparallel orientation of Cys/Sec residues about disulfide/diselenide. The far-ultraviolet (UV) region CD spectra of cystine and selenocystine derivatives have exhibited the negative Cotton effect (CE) for disulfide and positive for diselenide confirming the difference in the conformational preference of disulfide and diselenide. In the previously reported polymorphic structure of (Boc-Sec-OMe)2 , the diselenide has right-handed orientation. In the X-ray structures of disulfide and diselenide analogues of Escherichia coli protein encoded by curli specific gene C (CgsC) retrieved from Protein Databank (PDB), disulfide has left-handed and the diselenide right-handed orientation. The current report provides the evidence for the local conformational difference between a disulfide and a diselenide group under unconstrained conditions, which may be useful for the rational replacement of disulfide by diselenide in polypeptide chains.
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Affiliation(s)
- Ashwini Dolle
- Department of Chemistry, School of Chemical Sciences, Central University of Karnataka, Kalaburagi, Karnataka, India
| | - K Kasi Amarnath Reddy
- Department of Chemistry, School of Chemical Sciences, Central University of Karnataka, Kalaburagi, Karnataka, India
| | - Shubha Shridhar Gunaga
- Solid State and Structural Chemistry Unit (SSCU), Indian Institute of Science, Bangalore, Karnataka, India
| | - Kiran Krishnamurthy
- NMR Research Centre, Indian Institute of Science, Bangalore, Karnataka, India
| | | | - Abhijit Rana
- School of Chemical Sciences, NISER, Bhubaneswar, Odisha, India
| | - Kishorkumar Sindogi
- Solid State and Structural Chemistry Unit (SSCU), Indian Institute of Science, Bangalore, Karnataka, India
| | | | | | - Konkallu Hanumae Gowd
- Department of Chemistry, School of Chemical Sciences, Central University of Karnataka, Kalaburagi, Karnataka, India
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Mondal S, Sahu K, Patra B, Jena S, Biswal HS, Kar S. A new synthesis of porphyrins via a putative trans-manganese(iv)-dihydroxide intermediate. Dalton Trans 2020; 49:1424-1432. [PMID: 31915769 DOI: 10.1039/c9dt03573g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new method for the synthesis of meso-substituted porphyrins was developed. In this two-step methodology, the first step involves the condensation of pyrroles/dipyrromethanes with aldehydes in a water-methanol mixture under acidic conditions. The second step involves manganese induced cyclization followed by oxidation via PhIO/O2. This methodology has been useful for the synthesis of a wide range of trans-A2B2 porphyrins and also symmetric porphyrins in moderate to good yields. A detailed investigation of the manganese induced cyclization reaction has allowed us to characterize a Mn-porphyrinogen complex. A series of analytical and spectroscopic techniques and DFT calculations have led us to the conclusion that the putative intermediate species are trans-manganese(iv)-dihydroxide complexes. EPR and magnetic susceptibility measurements helped us to assign the oxidation state of the manganese complexes in their native state. The assumption of trans-manganese(iv)-dihydroxide as the true intermediate for this porphyrin synthesis has been authenticated via in situ UV-Vis experiments. This new methodology is certainly different from other previously reported methodologies in many aspects and most importantly these reactions can be easily performed on a gram scale for the synthesis of porphyrins.
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Affiliation(s)
- Sruti Mondal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Bhubaneswar, 752050, India.
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Dutta J, Sahoo DK, Jena S, Tulsiyan KD, Biswal HS. Non-covalent interactions with inverted carbon: a carbo-hydrogen bond or a new type of hydrogen bond? Phys Chem Chem Phys 2020; 22:8988-8997. [DOI: 10.1039/d0cp00330a] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Crystal structure analysis and quantum chemical calculations enabled us to discover a new non-covalent interaction, coined as carbo-hydrogen bond (CH-bond).
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Affiliation(s)
- Juhi Dutta
- National Institute of Science Education and Research (NISER) PO-Bhimpur-Padanpur
- Bhubaneswar
- India
- Homi Bhaba National Institute
- Training School Complex Anushakti Nagar
| | - Dipak Kumar Sahoo
- National Institute of Science Education and Research (NISER) PO-Bhimpur-Padanpur
- Bhubaneswar
- India
- Homi Bhaba National Institute
- Training School Complex Anushakti Nagar
| | - Subhrakant Jena
- National Institute of Science Education and Research (NISER) PO-Bhimpur-Padanpur
- Bhubaneswar
- India
- Homi Bhaba National Institute
- Training School Complex Anushakti Nagar
| | - Kiran Devi Tulsiyan
- National Institute of Science Education and Research (NISER) PO-Bhimpur-Padanpur
- Bhubaneswar
- India
- Homi Bhaba National Institute
- Training School Complex Anushakti Nagar
| | - Himansu S. Biswal
- National Institute of Science Education and Research (NISER) PO-Bhimpur-Padanpur
- Bhubaneswar
- India
- Homi Bhaba National Institute
- Training School Complex Anushakti Nagar
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Sahoo DK, Jena S, Tulsiyan KD, Dutta J, Chakrabarty S, Biswal HS. Amino-Acid-Based Ionic Liquids for the Improvement in Stability and Activity of Cytochrome c: A Combined Experimental and Molecular Dynamics Study. J Phys Chem B 2019; 123:10100-10109. [DOI: 10.1021/acs.jpcb.9b09278] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Dipak Kumar Sahoo
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Subhrakant Jena
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Kiran Devi Tulsiyan
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Juhi Dutta
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Suman Chakrabarty
- Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Salt Lake, Kolkata 700106, India
| | - Himansu S. Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
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Abstract
The significance of dispersion contribution in the formation of strong hydrogen bonds (H-bonds) can no more be ignored. It was illustrated that less electronegative and electropositive H-bond acceptors such as S, Se, and Te are also capable of forming strong N-H···Y H-bonds, mostly due to the high polarizabilities of H-bond acceptor atoms. Herein, for the first time, we report the evidence of formation of nonconventional M-H···Y H-bonds between metal hydrides (M-H, M = Mn, Fe, Co) and chalcogen H-bond acceptors (Y = O, S, or Se). The nature and the strength of unusual M-H···Y H-bonds were revealed by several quantum chemical calculations and H-bond descriptors. The structural parameters, electron density topology, donor-acceptor natural bond orbital (NBO) interaction energies, and spectroscopic observables such as M-H stretching frequencies and 1H chemical shifts are well-correlated to manifest the existence and strength of M-H···Y H-bonding. The M-H···Y H-bonds are dispersive in nature, and the computed H-bond energies are found to be in the range from ∼5 to 30 kJ/mol, which can be compared to those of the conventional H-bonds such as O-H···O, N-H···O, and N-H···O═C H-bonds, etc.
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Affiliation(s)
- Dipak Kumar Sahoo
- School of Chemical Sciences , National Institute of Science Education and Research , 752050 Bhubaneswar , India.,Homi Bhabha National Institute , Training School Complex , Anushakti Nagar, Mumbai 400094 , India
| | - Subhrakant Jena
- School of Chemical Sciences , National Institute of Science Education and Research , 752050 Bhubaneswar , India.,Homi Bhabha National Institute , Training School Complex , Anushakti Nagar, Mumbai 400094 , India
| | - Juhi Dutta
- School of Chemical Sciences , National Institute of Science Education and Research , 752050 Bhubaneswar , India.,Homi Bhabha National Institute , Training School Complex , Anushakti Nagar, Mumbai 400094 , India
| | - Abhijit Rana
- School of Chemical Sciences , National Institute of Science Education and Research , 752050 Bhubaneswar , India.,Homi Bhabha National Institute , Training School Complex , Anushakti Nagar, Mumbai 400094 , India
| | - Himansu S Biswal
- School of Chemical Sciences , National Institute of Science Education and Research , 752050 Bhubaneswar , India.,Homi Bhabha National Institute , Training School Complex , Anushakti Nagar, Mumbai 400094 , India
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Mishra S, Sahoo DK, Hsu PJ, Matsuda Y, Kuo JL, Biswal HS, Patwari GN. A liquid crucible model for aggregation of phenylacetylene in the gas phase. Phys Chem Chem Phys 2019; 21:13623-13632. [DOI: 10.1039/c8cp07738j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Structural transformation from a π-stacked dimer to an aromatic C–H⋯π trimer and a tetramer.
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Affiliation(s)
- Saurabh Mishra
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai 400 076
- India
| | - Dipak Kumar Sahoo
- Homi Bhabha National Institute
- School of Chemical Sciences
- National Institute of Science Education and Research Bhubaneswar
- Khurda 752050
- India
| | - Po-Jen Hsu
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Taiwan
| | - Yoshiyuki Matsuda
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Taiwan
| | - Himansu S. Biswal
- Homi Bhabha National Institute
- School of Chemical Sciences
- National Institute of Science Education and Research Bhubaneswar
- Khurda 752050
- India
| | - G. Naresh Patwari
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai 400 076
- India
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Sahoo DK, Jena S, Dutta J, Chakrabarty S, Biswal HS. Critical Assessment of the Interaction between DNA and Choline Amino Acid Ionic Liquids: Evidences of Multimodal Binding and Stability Enhancement. ACS Cent Sci 2018; 4:1642-1651. [PMID: 30648148 PMCID: PMC6311687 DOI: 10.1021/acscentsci.8b00601] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Indexed: 05/07/2023]
Abstract
Long-term storage and stability of DNA is of paramount importance in biomedical applications. Ever since the emergence of ionic liquids (ILs) as alternate green solvents to aqueous and organic solvents, their exploration for the extraction and application of DNA need conscientious understanding of the binding characteristics and molecular interactions between IL and DNA. Choline amino acid ILs (CAAILs) in this regard seem to be promising due to their non-cytotoxic, completely biobased and environment-friendly nature. To unravel the key factors for the strength and binding mechanism of CAAILs with DNA, various spectroscopic techniques, molecular docking, and molecular dynamics simulations were employed in this work. UV-Vis spectra indicate multimodal binding of CAAILs with DNA, whereas dye displacement studies through fluorescence emission confirm the intrusion of IL molecules into the minor groove of DNA. Circular dichorism spectra show that DNA retains its native B-conformation in CAAILs. Both isothermal titration calorimetry and molecular docking studies provide an estimate of the binding affinity of DNA with CAAILs ≈ 4 kcal/mol. The heterogeneity in binding modes of CAAIL-DNA system with evolution of time was established by molecular dynamics simulations. Choline cation while approaching DNA first binds at surface through electrostatic interactions, whereas a stronger binding at minor groove occurs via van der Waals and hydrophobic interactions irrespective of anions considered in this study. We hope this result can encourage and guide the researchers in designing new bio-ILs for biomolecular studies in future.
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Affiliation(s)
- Dipak Kumar Sahoo
- School of Chemical
Sciences, National Institute of Science
Education and Research, PO-Bhimpur-Padanpur, Via-Jatni, District-Khurda,
PIN-752050, Bhubaneswar, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Subhrakant Jena
- School of Chemical
Sciences, National Institute of Science
Education and Research, PO-Bhimpur-Padanpur, Via-Jatni, District-Khurda,
PIN-752050, Bhubaneswar, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Juhi Dutta
- School of Chemical
Sciences, National Institute of Science
Education and Research, PO-Bhimpur-Padanpur, Via-Jatni, District-Khurda,
PIN-752050, Bhubaneswar, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Suman Chakrabarty
- Department of Chemical,
Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Salt Lake, Kolkata 700106, India
- E-mail: . (S.C.)
| | - Himansu S. Biswal
- School of Chemical
Sciences, National Institute of Science
Education and Research, PO-Bhimpur-Padanpur, Via-Jatni, District-Khurda,
PIN-752050, Bhubaneswar, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
- E-mail: . Phone: +91-674-2494
185/186. (H.S.B.)
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Mundlapati VR, Sahoo DK, Bhaumik S, Jena S, Chandrakar A, Biswal HS. Noncovalent Carbon-Bonding Interactions in Proteins. Angew Chem Int Ed Engl 2018; 57:16496-16500. [DOI: 10.1002/anie.201811171] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Indexed: 12/14/2022]
Affiliation(s)
- V. Rao Mundlapati
- School of Chemical Sciences; National Institute of Science Education and Research (NISER); PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
| | - Dipak Kumar Sahoo
- School of Chemical Sciences; National Institute of Science Education and Research (NISER); PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
| | - Suman Bhaumik
- School of Chemical Sciences; National Institute of Science Education and Research (NISER); PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
| | - Subhrakant Jena
- School of Chemical Sciences; National Institute of Science Education and Research (NISER); PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
| | - Amol Chandrakar
- School of Chemical Sciences; National Institute of Science Education and Research (NISER); PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
| | - Himansu S. Biswal
- School of Chemical Sciences; National Institute of Science Education and Research (NISER); PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
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Affiliation(s)
- V. Rao Mundlapati
- School of Chemical Sciences; National Institute of Science Education and Research (NISER); PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
| | - Dipak Kumar Sahoo
- School of Chemical Sciences; National Institute of Science Education and Research (NISER); PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
| | - Suman Bhaumik
- School of Chemical Sciences; National Institute of Science Education and Research (NISER); PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
| | - Subhrakant Jena
- School of Chemical Sciences; National Institute of Science Education and Research (NISER); PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
| | - Amol Chandrakar
- School of Chemical Sciences; National Institute of Science Education and Research (NISER); PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
| | - Himansu S. Biswal
- School of Chemical Sciences; National Institute of Science Education and Research (NISER); PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
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Jena P, Acharya AN, Mundlapati VR, Dash AC, Biswal HS. Kinetics and mechanistic study of the reduction of
$$\hbox {Mn}^{\mathrm{III}}$$
Mn
III
by oxalate in Salophen scaffold: relevance to oxalate oxidase. J CHEM SCI 2018. [DOI: 10.1007/s12039-018-1514-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Singh A, Sahoo DK, Sethi SK, Jena S, Biswal HS. Nature and Strength of the Inner-Core H⋅⋅⋅H Interactions in Porphyrinoids. Chemphyschem 2017; 18:3625-3633. [DOI: 10.1002/cphc.201700742] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Ankit Singh
- School of Chemical Sciences; National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur; Via-Jatni, District- Khurda, PIN 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
| | - Dipak Kumar Sahoo
- School of Chemical Sciences; National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur; Via-Jatni, District- Khurda, PIN 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
| | - Srikant Kumar Sethi
- School of Chemical Sciences; National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur; Via-Jatni, District- Khurda, PIN 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
| | - Subhrakant Jena
- School of Chemical Sciences; National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur; Via-Jatni, District- Khurda, PIN 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
| | - Himansu S. Biswal
- School of Chemical Sciences; National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur; Via-Jatni, District- Khurda, PIN 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
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Abstract
Thioamides are used as potential surrogates of amides to study the structure and dynamics of proteins and nucleic acids. However, incorporation of thioamides in biomolecules leads to changes in their structures and conformations mostly attributed to the strength of the amide-N-H···S═C hydrogen bond. In most cases, it is considered weak owing to the small electronegativity of sulfur, and in some cases, it is as strong as conventional H-bonds. Herein, adopting PDB structure analysis, NMR spectroscopy, and quantum chemistry calculations, we have shown that thioamides in a geometrical and structural constraint-free environment are capable of forming strong H-bonds like their amide counterparts. These studies also enabled us to determine the amide-N-H···S═C H-bond enthalpy (ΔH) very precisely. The estimated ΔH for the amide-N-H···S═C H-bond is ∼-30 kJ/mol, which suggests that the amide-N-H···S═C H-bond is a strong H-bond and merits its inclusion in computational force fields for biomolecular structure simulations to explore the role of amide-N-H···S═C H-bonds in nucleobase pairing and protein folding.
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Affiliation(s)
- V Rao Mundlapati
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) , PO-Bhimpur-Padanpur, Via-Jatni, District-Khurda, PIN-752050 Bhubaneswar, India
- Homi Bhabha National Institute , Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Sanjeev Gautam
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) , PO-Bhimpur-Padanpur, Via-Jatni, District-Khurda, PIN-752050 Bhubaneswar, India
- Homi Bhabha National Institute , Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Dipak Kumar Sahoo
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) , PO-Bhimpur-Padanpur, Via-Jatni, District-Khurda, PIN-752050 Bhubaneswar, India
- Homi Bhabha National Institute , Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Arindam Ghosh
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) , PO-Bhimpur-Padanpur, Via-Jatni, District-Khurda, PIN-752050 Bhubaneswar, India
- Homi Bhabha National Institute , Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) , PO-Bhimpur-Padanpur, Via-Jatni, District-Khurda, PIN-752050 Bhubaneswar, India
- Homi Bhabha National Institute , Training School Complex, Anushakti Nagar, Mumbai 400094, India
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Baishya A, Kumar L, Barman MK, Biswal HS, Nembenna S. N-Heterocyclic Carbene–Carbodiimide (“NHC–CDI”) Adduct or Zwitterionic-Type Neutral Amidinate-Supported Magnesium(II) and Zinc(II) Complexes. Inorg Chem 2017; 56:9535-9546. [DOI: 10.1021/acs.inorgchem.7b00879] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ashim Baishya
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Homi Bhabha National Institute (HBNI), Bhubaneswar 752 050, India
| | - Lokesh Kumar
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Homi Bhabha National Institute (HBNI), Bhubaneswar 752 050, India
| | - Milan Kr. Barman
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Homi Bhabha National Institute (HBNI), Bhubaneswar 752 050, India
| | - Himansu S. Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Homi Bhabha National Institute (HBNI), Bhubaneswar 752 050, India
| | - Sharanappa Nembenna
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Homi Bhabha National Institute (HBNI), Bhubaneswar 752 050, India
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Mundlapati VR, Sahoo DK, Ghosh S, Purame UK, Pandey S, Acharya R, Pal N, Tiwari P, Biswal HS. Spectroscopic Evidences for Strong Hydrogen Bonds with Selenomethionine in Proteins. J Phys Chem Lett 2017; 8:794-800. [PMID: 28145117 DOI: 10.1021/acs.jpclett.6b02931] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Careful protein structure analysis unravels many unknown and unappreciated noncovalent interactions that control protein structure; one such unrecognized interaction in protein is selenium centered hydrogen bonds (SeCHBs). We report, for the first time, SeCHBs involving the amide proton and selenium of selenomethionine (Mse), i.e., amide-N-H···Se H-bonds discerned in proteins. Using mass selective and conformer specific high resolution vibrational spectroscopy, gold standard quantum chemical calculations at CCSD(T), and in-depth protein structure analysis, we establish that amide-N-H···Se and amide-N-H···Te H-bonds are as strong as conventional amide-NH···O and amide-NH···O═C H-bonds despite smaller electronegativity of selenium and tellurium than oxygen. It is in fact, electronegativity, atomic charge, and polarizability of the H-bond acceptor atoms are at play in deciding the strength of H-bonds. The amide-N-H···Se and amide-N-H···Te H-bonds presented here are not only new additions to the ever expanding world of noncovalent interactions, but also are of central importance to design new force-fields for better biomolecular structure simulations.
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Affiliation(s)
- V Rao Mundlapati
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) , PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India
- Homi Bhabha National Institute , Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Dipak Kumar Sahoo
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) , PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India
- Homi Bhabha National Institute , Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Sanat Ghosh
- Tata Institute of Fundamental Research , Homi Bhabha Road, Mumbai 400005, India
| | - Umesh Kumar Purame
- Homi Bhabha National Institute , Training School Complex, Anushakti Nagar, Mumbai 400094, India
- School of Biological Sciences, National Institute of Science Education and Research (NISER) , PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India
| | - Shubhant Pandey
- Homi Bhabha National Institute , Training School Complex, Anushakti Nagar, Mumbai 400094, India
- School of Biological Sciences, National Institute of Science Education and Research (NISER) , PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India
| | - Rudresh Acharya
- Homi Bhabha National Institute , Training School Complex, Anushakti Nagar, Mumbai 400094, India
- School of Biological Sciences, National Institute of Science Education and Research (NISER) , PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India
| | - Nitish Pal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) , PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India
- Homi Bhabha National Institute , Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Prince Tiwari
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) , PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India
- Homi Bhabha National Institute , Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) , PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India
- Homi Bhabha National Institute , Training School Complex, Anushakti Nagar, Mumbai 400094, India
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Gagrai AA, Mundlapati VR, Sahoo DK, Satapathy H, Biswal HS. The Role of Molecular Polarizability in Designing Organic Piezoelectric Materials. ChemistrySelect 2016. [DOI: 10.1002/slct.201601043] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Arun Anand Gagrai
- School of Chemical Sciences; National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN -; 752050 Bhubaneswar India
| | - V. Rao Mundlapati
- School of Chemical Sciences; National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN -; 752050 Bhubaneswar India
| | - Dipak Kumar Sahoo
- School of Chemical Sciences; National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN -; 752050 Bhubaneswar India
| | - H. Satapathy
- Department of Basic Sciences; International Institute of Information Technology, Gothapatna, PO: Malipada, PIN -; 751 003 Bhubaneswar India
| | - Himansu S. Biswal
- School of Chemical Sciences; National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN -; 752050 Bhubaneswar India
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Sahoo DK, Mundlapati VR, Gagrai AA, Biswal HS. Efficient SO2Capture through Multiple Chalcogen Bonds, Sulfur-Centered Hydrogen Bonds and S•••π Interactions: A Computational Study. ChemistrySelect 2016. [DOI: 10.1002/slct.201600061] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Dipak Kumar Sahoo
- School of Chemical Sciences; National Institute of Science Education and Research (NISER); PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN- 752050 Bhubaneswar India
| | - V. Rao Mundlapati
- School of Chemical Sciences; National Institute of Science Education and Research (NISER); PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN- 752050 Bhubaneswar India
| | - Arun Anand Gagrai
- School of Chemical Sciences; National Institute of Science Education and Research (NISER); PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN- 752050 Bhubaneswar India
| | - Himansu S. Biswal
- School of Chemical Sciences; National Institute of Science Education and Research (NISER); PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN- 752050 Bhubaneswar India
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Mundlapati VR, Jena P, Acharya AN, Kar AK, Dash AC, Biswal HS. Water exchange reaction of a manganese catalase mimic: oxygen-17 NMR relaxometry study on (aqua)manganese(iii) in a salen scaffold and its reactions in a mildly basic medium. RSC Adv 2016. [DOI: 10.1039/c6ra23154c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Water exchange of trans-[MnIII(salen)(OH2)2]+ studied by line broadening 17OH2 NMR discloses its mechanism as associative interchange (Ia).
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Affiliation(s)
- V. Rao Mundlapati
- School of Chemical Sciences
- National Institute of Science Education and Research (NISER)
- Institute of Physics Campus
- Bhubaneswar 751 005
- India
| | - Priyambada Jena
- Department of Chemistry
- College of Engineering and Technology
- Bhubaneswar 751003
- India
| | - Achyut N. Acharya
- Department of Chemistry
- College of Engineering and Technology
- Bhubaneswar 751003
- India
| | - Akshaya K. Kar
- Department of Chemistry
- Utkal University
- Bhubaneswar 751004
- India
| | - Anadi C. Dash
- Department of Chemistry
- Utkal University
- Bhubaneswar 751004
- India
| | - Himansu S. Biswal
- School of Chemical Sciences
- National Institute of Science Education and Research (NISER)
- Institute of Physics Campus
- Bhubaneswar 751 005
- India
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Mundlapati VR, Ghosh S, Bhattacherjee A, Tiwari P, Biswal HS. Critical Assessment of the Strength of Hydrogen Bonds between the Sulfur Atom of Methionine/Cysteine and Backbone Amides in Proteins. J Phys Chem Lett 2015; 6:1385-1389. [PMID: 26263139 DOI: 10.1021/acs.jpclett.5b00491] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Gas-phase vibrational spectroscopy, coupled cluster (CCSD(T)), and dispersion corrected density functional (B97-D3) methods are employed to characterize surprisingly strong sulfur center H-bonded (SCHB) complexes between cis and trans amide NH and S atom of methionine and cysteine side chain. The amide N-H···S H-bonds are compared with the representative classical σ- and π-type H-bonded complexes such as N-H···O, N-H···O═C and N-H···π H-bonds. With the spectroscopic, theoretical, and structural evidence, amide N-H···S H-bonds are found to be as strong as the classical σ-type H-bonds, despite the smaller electronegativity of sulfur in comparison to oxygen. The strength of backbone-amide N-H···S H-bonds in cysteine and methionine containing peptides and proteins are also investigated and found to be of similar magnitudes as those observed in the intermolecular model complexes studied in this work. All such SCHBs also confirm that the electronegativities of the acceptors are not the sole criteria to predict the H-bond strength.
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Affiliation(s)
- V Rao Mundlapati
- †School of Chemical Sciences, National Institute of Science Education and Research, Institute of Physics Campus, Sachivalaya Marg, PO: Sainik School, Bhubaneswar 751 005, India
| | - Sanat Ghosh
- ‡Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400 005, India
| | - Aditi Bhattacherjee
- ‡Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400 005, India
- §Chemical Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Prince Tiwari
- †School of Chemical Sciences, National Institute of Science Education and Research, Institute of Physics Campus, Sachivalaya Marg, PO: Sainik School, Bhubaneswar 751 005, India
| | - Himansu S Biswal
- †School of Chemical Sciences, National Institute of Science Education and Research, Institute of Physics Campus, Sachivalaya Marg, PO: Sainik School, Bhubaneswar 751 005, India
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Biswal HS, Bhattacharyya S, Bhattacherjee A, Wategaonkar S. Nature and strength of sulfur-centred hydrogen bonds: laser spectroscopic investigations in the gas phase and quantum-chemical calculations. INT REV PHYS CHEM 2015. [DOI: 10.1080/0144235x.2015.1022946] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Alauddin M, Biswal HS, Gloaguen E, Mons M. Intra-residue interactions in proteins: interplay between serine or cysteine side chains and backbone conformations, revealed by laser spectroscopy of isolated model peptides. Phys Chem Chem Phys 2014; 17:2169-78. [PMID: 25482851 DOI: 10.1039/c4cp04449e] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Intra-residue interactions play an important role in proteins by influencing local folding of the backbone. Taking advantage of the capability of gas phase experiments to provide relevant information on the intrinsic H-bonding pattern of isolated peptide chains, the intra-residue interactions of serine and cysteine residues, i.e., OH/SH···OC(i) C6 and NH(i···)O/S C5 interactions in Ser/Cys residues, are probed by laser spectroscopy of isolated peptides. The strength of these local side chain-main chain interactions, elegantly documented from their IR spectral features for well-defined conformations of the main chain, demonstrates that a subtle competition exists between the two types of intra-residue bond: the C6 H-bond is the major interaction with Ser, in contrast to Cys where C5 interaction takes over. The restricted number of conformers observed in the gas phase experiment with Ser compared to Cys (where both extended and folded forms are observed) also suggests a significant mediation role of these intra-residue interactions on the competition between the several main chain folding patterns.
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Affiliation(s)
- Mohammad Alauddin
- CEA, IRAMIS, Laboratoire Interactions, Dynamique et Lasers, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France.
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