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Lu T, Zhang J, Xu Y, Wang Z, Feng G, Zeng Z. Hydrogen bond interactions between thioethers and amides: A joint rotational spectroscopic and theoretical study of the formamide⋯dimethyl sulfide adduct. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 288:122199. [PMID: 36473293 DOI: 10.1016/j.saa.2022.122199] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/17/2022] [Accepted: 11/27/2022] [Indexed: 06/17/2023]
Abstract
The rotational spectrum of the binary adduct of formamide (HCONH2) with dimethyl sulfide (DMS) has been investigated employing cavity-based Fourier transform microwave spectroscopy combined with theoretical computations. Experimentally, only one isomer of the adduct was unambiguously observed and assigned according to the theoretically predicted spectroscopic parameters, and its rotational spectrum displays the hyperfine splittings associated with the 14N nuclear quadrupole coupling effect. The observed isomer exhibits Cs symmetry, such that the ∠CSC angle of the DMS subunit is bisected by the ab-plane of the HCONH2 moiety. The two moieties in the detected isomer are connected via one primary NH···S and two secondary CH···O hydrogen bonds. Quantum theory of atoms in molecules (QTAIM), non-covalent interaction (NCI), natural bond orbital (NBO) and symmetry-adapted perturbation theory (SAPT) approaches were utilized for characterizing the intermolecular interactions occurring in the titled adduct. Additionally, the adduct of HCONH2 with dimethyl ether (DME) was also theoretically investigated to compare the difference in structure and energy characteristics between the NH···S and NH···O hydrogen bonds.
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Affiliation(s)
- Tao Lu
- School of Biology and Engineering, Guizhou Medical University, Guiyang 550025, China; School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, Chongqing 401331, China.
| | - Jiaqi Zhang
- School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, Chongqing 401331, China
| | - Yugao Xu
- School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, Chongqing 401331, China
| | - Zhen Wang
- School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, Chongqing 401331, China
| | - Gang Feng
- School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, Chongqing 401331, China
| | - Zhu Zeng
- School of Biology and Engineering, Guizhou Medical University, Guiyang 550025, China.
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2
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Lampkin BJ, VanVeller B. Hydrogen Bond and Geometry Effects of Thioamide Backbone Modifications. J Org Chem 2021; 86:18287-18291. [PMID: 34851645 DOI: 10.1021/acs.joc.1c02373] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Thioamide substitution of backbone peptide bonds can probe interactions along the main chain of proteins. Despite theoretical predictions of the enhanced hydrogen bonding propensities of thioamides, previous studies often do not consider the geometric constraints imposed by folded peptide secondary structure. This work addresses drawbacks in previous studies that ignored the geometry dependence and local dielectric properties of thioamide hydrogen bonding and identifies cases where thioamides may be either stronger or weaker hydrogen-bonding partners than amides.
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Affiliation(s)
- Bryan J Lampkin
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Brett VanVeller
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
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3
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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: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [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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4
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Wang Q, Shao Y, Shi X. Mechanism of charge redistribution at the metal–semiconductor and semiconductor–semiconductor interfaces of metal–bilayer MoS2 junctions. J Chem Phys 2020; 152:244701. [DOI: 10.1063/5.0010849] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Affiliation(s)
- Qian Wang
- Harbin Institute of Technology, Harbin 150080, China
- Department of Physics, Guangdong Provincial Key Laboratory for Computational Science and Material Design, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yangfan Shao
- Department of Physics, Guangdong Provincial Key Laboratory for Computational Science and Material Design, Southern University of Science and Technology, Shenzhen 518055, China
- Joint Key Laboratory of the Ministry of Education, Institute of Applied Physics and Materials Engineering, University of Macau, Macau, China
| | - Xingqiang Shi
- Department of Physics, Guangdong Provincial Key Laboratory for Computational Science and Material Design, Southern University of Science and Technology, Shenzhen 518055, China
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Ghosh S, Chopra P, Wategaonkar S. C-HS interaction exhibits all the characteristics of conventional hydrogen bonds. Phys Chem Chem Phys 2020; 22:17482-17493. [PMID: 32531006 DOI: 10.1039/d0cp01508c] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
This is a tale of a pair of a hydrogen bond donor and acceptor, namely the CH donor and sulphur acceptor, neither of which is a conventional hydrogen bond participant. Sulfur (S), being less electronegative (2.58) compared to its first row analogue oxygen (3.44), has not been considered as a potential HB acceptor for a long time. The C-HY (Y = HB acceptor) interaction has its own history of exhibiting omnidirectional shifts in the CH stretching frequency upon complex formation. Therefore, a systematic investigation of the C-HS interaction was the primary goal of the work presented here. Together with gas-phase vibrational spectroscopy and ab initio quantum chemical calculations, the nature and strength of the C-HS hydrogen bond (HB) have been investigated in the complexes of 1,2,4,5-tetracyanobenzene (TCNB) with various sulfur containing solvents. Despite the unconventional nature of both HB donor and HB acceptor (C-H and S, respectively), it was found that the C-HS hydrogen bond exhibits all the characteristics of the conventional hydrogen bond. The binding strength of the C-HS H-bond in these complexes was found to be comparable to that of the conventional hydrogen bonds. The unusual stabilities of these HBs have been mainly attributed to the attractive dispersion interaction.
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Affiliation(s)
- Sanat Ghosh
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India.
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6
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Uras-Aytemiz N, Balcı FM, Devlin JP. Can sulfur-containing molecules solvate/ionize HCl? Solid state solvation of HCl on/in methanethiol clusters/nanoparticles. J Chem Phys 2019; 151:194309. [DOI: 10.1063/1.5126029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Nevin Uras-Aytemiz
- Department of Chemistry, Karabük University, 78050 Karabük, Turkey and Department of Basic Science, Bandırma Onyedi Eylül University, 10200 Bandrma, Balikesir, Turkey
| | - F. Mine Balcı
- Department of Chemistry, Süleyman Demirel University, 32260 Isparta, Turkey
| | - J. Paul Devlin
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, USA
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7
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Chand A, Biswal HS. Hydrogen Bonds with Chalcogens: Looking Beyond the Second Row of the Periodic Table. J Indian Inst Sci 2019. [DOI: 10.1007/s41745-019-00140-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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8
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Kjaersgaard A, Lane JR, Kjaergaard HG. Room Temperature Gibbs Energies of Hydrogen-Bonded Alcohol Dimethylselenide Complexes. J Phys Chem A 2019; 123:8427-8434. [DOI: 10.1021/acs.jpca.9b06855] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alexander Kjaersgaard
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Joseph R. Lane
- School of Science, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Henrik G. Kjaergaard
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
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9
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Tang S, Du L. Effects of methylation in acceptors on the hydrogen bond complexes between 2,2,2-trifluoroethanol and cyclic ethers. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 217:237-246. [PMID: 30947132 DOI: 10.1016/j.saa.2019.03.088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 03/24/2019] [Accepted: 03/25/2019] [Indexed: 05/15/2023]
Abstract
In order to explore the effect of methylation on the stability and spectral shift of hydrogen bond complexes, the complexes of 2,2,2-trifluoroethanol (TFE) with propylene oxide (PO) and isobutylene oxide (IBO) were investigated by Fourier transform infrared (FTIR) spectroscopy and ab initio computations. The comparable OH-stretching red shifts were observed upon complexation, and an enhancement of the OH-stretching band is shown with the partial pressure of monomers increasing. The OH-stretching frequency of TFE is red shifted by 180 and 201 cm-1 with PO and IBO, respectively. By using quantum chemical calculations, we predicted the geometric parameters, binding energies, and spectral shifts of TFEPO/IBO hydrogen bond complexes. The calculated and observed spectral shifts follow the same trends. Compared with the TFEethylene oxide (EO) complex, the strength of the hydrogen bond in complex increases with the addition of methyl group, which likely results from the increase in basicity of the hydrogen bond acceptor. By combining the experimental integrated absorbance and the calculated IR intensity of the OH-stretching vibrational transition, the equilibrium constant for the complex formation was determined. In addition, atoms-in-molecules (AIM) and natural bond orbital (NBO) analyses were carried out to explain the red shift and the nature of the interaction in these complexes.
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Affiliation(s)
- Shanshan Tang
- Environment Research Institute, Shandong University, Binhai Road 72, Qingdao 266237, China
| | - Lin Du
- Environment Research Institute, Shandong University, Binhai Road 72, Qingdao 266237, China.
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10
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Sarkar S, Ramanathan N, Sruthi PK, Sundararajan K. Conformations of diethyl ether and its interaction with pyrrole at low temperatures. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 213:361-369. [PMID: 30721851 DOI: 10.1016/j.saa.2019.01.076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/25/2019] [Accepted: 01/26/2019] [Indexed: 06/09/2023]
Abstract
Conformations of diethyl ether (DEE) were studied at low temperatures in N2 and Ar matrixes. Computations performed at B3LYP/aug-cc-pVDZ level of theory yielded three minima corresponding to tt, tg± and g±g± conformers of DEE. Of the three, the tt and tg± conformers of DEE were experimentally identified in N2 and Ar matrixes. Furthermore, hydrogen bonded complexes of pyrrole (py) with DEE have been investigated using Density Functional Theory (DFT) and matrix isolation infrared spectroscopy. Computations performed at B3LYP level of theory using aug-cc-pVDZ basis set on pyrrole with tt and tg± conformers of DEE gave py-DEE-tt and py-DEE-tg± complexes, both characterized by NH⋯O interaction. Experimental evidence for the formation of py-DEE-tt and py-DEE-tg± complexes was affirmed from the shifts in the NH stretching, NH bending regions of pyrrole and COC and CH stretching regions of DEE. NBO analysis was carried out to understand the charge-transfer delocalization interactions in the conformers of DEE and its hydrogen bonded complexes.
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Affiliation(s)
- Shubhra Sarkar
- Materials Chemistry and Metal Fuel Cycle Group, Indira Gandhi Centre for Atomic Research, Homi Bhabha National Institute, Kalpakkam 603 102, India
| | - N Ramanathan
- Materials Chemistry and Metal Fuel Cycle Group, Indira Gandhi Centre for Atomic Research, Homi Bhabha National Institute, Kalpakkam 603 102, India
| | - P K Sruthi
- Materials Chemistry and Metal Fuel Cycle Group, Indira Gandhi Centre for Atomic Research, Homi Bhabha National Institute, Kalpakkam 603 102, India
| | - K Sundararajan
- Materials Chemistry and Metal Fuel Cycle Group, Indira Gandhi Centre for Atomic Research, Homi Bhabha National Institute, Kalpakkam 603 102, India.
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11
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Lobo IA, Robertson PA, Villani L, Wilson DJD, Robertson EG. Thiols as Hydrogen Bond Acceptors and Donors: Spectroscopy of 2-Phenylethanethiol Complexes. J Phys Chem A 2018; 122:7171-7180. [PMID: 30113835 DOI: 10.1021/acs.jpca.8b06649] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Evidence and understanding of sulfur-centered hydrogen bonding, especially where the donor is a thiol, lags far behind that for conventional OH interactions. To help address this deficiency, conformer specific IR spectra of 2-phenylethanethiol (PET) and associated 1:1 solvent complexes have been measured in SH, OH, and CH stretch regions using resonant-two-photon-ionization (R2PI) and IR-UV ion dip spectroscopic techniques. The aromatic and aliphatic CH stretch regions show signature differences between anti and gauche conformers. Supported by ab initio calculations, a PET-water cluster with an OH···S arrangement and a PET-diethyl ether cluster expressing an SH···O interaction were identified. The SH stretch band of the SH···O complex is red-shifted and undergoes significant intensity enhancement compared to the bare molecule, which is characteristic of hydrogen bonding. These findings offer insight into the nature of the thiol functional group as a potential hydrogen bond donor and acceptor.
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Affiliation(s)
- Isabella A Lobo
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science , La Trobe University , Melbourne , 3086 , Victoria Australia
| | - Patrick A Robertson
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science , La Trobe University , Melbourne , 3086 , Victoria Australia
| | - Luigi Villani
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science , La Trobe University , Melbourne , 3086 , Victoria Australia
| | - David J D Wilson
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science , La Trobe University , Melbourne , 3086 , Victoria Australia
| | - Evan G Robertson
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science , La Trobe University , Melbourne , 3086 , Victoria Australia
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12
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Behera B, Das PK. Blue- and Red-Shifting Hydrogen Bonding: A Gas Phase FTIR and Ab Initio Study of RR'CO···DCCl 3 and RR'S···DCCl 3 Complexes. J Phys Chem A 2018; 122:4481-4489. [PMID: 29683668 DOI: 10.1021/acs.jpca.7b11962] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Blue-shifting H-bonded (C-D···O) complexes between CDCl3 and CH3HCO, (CH3)2CO, and C2H5(CH3)CO, and red-shifting H-bonded (C-D···S) complexes between CDCl3 with (CH3)2S and (C2H5)2S have been identified by Fourier transform infrared spectroscopy in the gas phase at room temperature. With increasing partial pressure of the components, a new band appears in the C-D stretching region of the vibrational spectra. The intensity of this band decreases with an increase in temperature at constant pressure, which provides the basis for identification of the H-bonded bands in the spectrum. The C-D stretching frequency of CDCl3 is blue-shifted by +7.1, +4, and +3.2 cm-1 upon complexation with CH3HCO, (CH3)2CO, and C2H5(CH3)CO, respectively, and red-shifted by -14 and -19.2 cm-1 upon complexation with (CH3)2S and (C2H5)2S, respectively. By using quantum chemical calculations at the MP2/6-311++G** level, we predict the geometry, electronic structural parameters, binding energy, and spectral shift of H-bonded complexes between CDCl3 and two series of compounds named RCOR' (H2CO, CH3HCO, (CH3)2CO, and C2H5(CH3)CO) and RSR' (H2S, CH3HS, (CH3)2S, and (C2H5)2S) series. The calculated and observed spectral shifts follow the same trends. With an increase in basicity of the H-bond acceptor, the C-D bond length increases, force constant decreases, and the frequency shifts to the red from the blue. The potential energy scans of the above complexes are done, which show that electrostatic attraction between electropositive D and electron-rich O/S causes bond elongation and red shift, and the electronic and nuclear repulsions lead to bond contraction and blue shifts. The dominance of the two opposing forces at the equilibrium geometry of the complex determines the nature of the shift, which changes both in magnitude and in direction with the basicity of the hydrogen-bond acceptor.
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Affiliation(s)
- B Behera
- Department of Inorganic and Physical Chemistry , Indian Institute of Science , Bangalore 560012 , India
| | - Puspendu K Das
- Department of Inorganic and Physical Chemistry , Indian Institute of Science , Bangalore 560012 , India
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13
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Orabi EA, English AM. Modeling Protein S-Aromatic Motifs Reveals Their Structural and Redox Flexibility. J Phys Chem B 2018. [PMID: 29533644 DOI: 10.1021/acs.jpcb.8b00089] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
S-aromatic motifs are important noncovalent forces for protein stability and function but remain poorly understood. Hence, we performed quantum calculations at the MP2(full)/6-311++G(d,p) level on complexes between Cys (H2S, MeSH) and Met (Me2S) models with models of Phe (benzene, toluene), Trp (indole, 3-methylindole), Tyr (phenol, 4-methylphenol), and His (imidazole, 4-methylimidazole). The most stable gas-phase conformers exhibit binding energies of -2 to -6 kcal/mol, and the S atom lies perpendicular to the ring plane. This reveals preferential interaction with the ring π-system, except in the imidazoles where S binds edge-on to an N atom. Complexation tunes the gas-phase vertical ionization potentials of the ligands over as much as 1 eV, and strong σ- or π-type H-bonding supports charge transfer to the H-bond donor, rendering it more oxidizable. When the S atom acts as an H-bond acceptor (N/O-Har···S), calibration of the CHARMM36 force field (by optimizing pair-specific Lennard-Jones parameters) is required. Implementing the optimized parameters in molecular dynamics simulations in bulk water, we find stable S-aromatic complexes with binding free energies of -0.6 to -1.1 kcal/mol at ligand separations up to 8 Å. The aqueous S-aromatics exhibit flexible binding conformations, but edge-on conformers are less stable in water. Reflecting this, only 0.3 to 10% of the S-indole, S-phenol, and S-imidazole structures are stabilized by N/O-Har···S or S-H···Oar/Nar σ-type H-bonding. The wide range of energies and geometries found for S-aromatic interactions and their tunable redox properties expose the versatility and variability of the S-aromatic motif in proteins and allow us to predict a number of their reported properties.
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Affiliation(s)
- Esam A Orabi
- Centre for Research in Molecular Modeling (CERMM) and PROTEO , Department of Chemistry and Biochemistry , Concordia University , 7141 Sherbrooke Street West , Montréal , Québec H4B 1R6 , Canada
| | - Ann M English
- Centre for Research in Molecular Modeling (CERMM) and PROTEO , Department of Chemistry and Biochemistry , Concordia University , 7141 Sherbrooke Street West , Montréal , Québec H4B 1R6 , Canada
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Zheng D, Yuan XA, Ma H, Li X, Wang X, Liu Z, Ma J. Unexpected solvent effects on the UV/Vis absorption spectra of o-cresol in toluene and benzene: in contrast with non-aromatic solvents. ROYAL SOCIETY OPEN SCIENCE 2018; 5:171928. [PMID: 29657794 PMCID: PMC5882718 DOI: 10.1098/rsos.171928] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 02/09/2018] [Indexed: 06/07/2023]
Abstract
Cresol is a prototype molecule in understanding intermolecular interactions in material and biological systems, because it offers different binding sites with various solvents and protonation states under different pH values. It is found that the UV/Vis absorption spectra of o-cresol in aromatic solvents (benzene, toluene) are characterized by a sharp peak, unlike the broad double-peaks in 11 non-aromatic solvents. Both molecular dynamics simulations and electronic structure calculations revealed the formation of intermolecular π-complexation between o-cresol and aromatic solvents. The thermal movements of solvent and solute molecules render the conformations of o-cresol changing between trans and cis isomers. The π-interaction makes the cis configuration a dominant isomer, hence leading to the single keen-edged UV/Vis absorption peak at approximately 283 nm. The free conformation changes between trans and cis in aqueous solution rationalize the broader absorption peaks in the range of 260-280 nm. The pH dependence of the UV/Vis absorption spectra in aqueous solutions is also rationalized by different protonation states of o-cresol. The explicit solvent model with long-ranged interactions is vital to describe the effects of π-complexation and electrostatic interaction on the UV/Vis absorption spectra of o-cresol in toluene and alkaline aqueous (pH > 10.3) solutions, respectively.
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Affiliation(s)
| | | | | | | | | | | | - Jing Ma
- Author for correspondence: Jing Ma e-mail:
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15
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Lane JR, Hansen AS, Mackeprang K, Kjaergaard HG. Kinetic Energy Density as a Predictor of Hydrogen-Bonded OH-Stretching Frequencies. J Phys Chem A 2017; 121:3452-3460. [DOI: 10.1021/acs.jpca.7b02523] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joseph R. Lane
- School
of Science, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Anne S. Hansen
- Department
of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Kasper Mackeprang
- Department
of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Henrik G. Kjaergaard
- Department
of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
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16
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Møller KH, Tram CM, Kjaergaard HG. Side-by-Side Comparison of Hydroperoxide and Corresponding Alcohol as Hydrogen-Bond Donors. J Phys Chem A 2017; 121:2951-2959. [DOI: 10.1021/acs.jpca.7b01323] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kristian H. Møller
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Camilla Mia Tram
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Henrik G. Kjaergaard
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
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Du L, Tang S, Hansen AS, Frandsen BN, Maroun Z, Kjaergaard HG. Subtle differences in the hydrogen bonding of alcohol to divalent oxygen and sulfur. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2016.11.045] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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18
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Bhattacharyya S, Roy VP, Wategaonkar S. Acid-Base Formalism Extended to Excited State for O-H···S Hydrogen Bonding Interaction. J Phys Chem A 2016; 120:6902-16. [PMID: 27529293 DOI: 10.1021/acs.jpca.6b04396] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hydrogen bond can be regarded as an interaction between a base and a proton covalently bound to another base. In this context the strength of hydrogen bond scales with the proton affinity of the acceptor base and the pKa of the donor, i.e., it follows the acid-base formalism. This has been amply demonstrated in conventional hydrogen bonds. Is this also true for the unconventional hydrogen bonds involving lesser electronegative elements such as sulfur atom? In our previous work, we had established that the strength of O-H···S hydrogen bonding (HB) interaction scales with the proton affinity (PA) of the acceptor. In this work, we have investigated the other counterpart, i.e., the H-bonding interaction between the photoacids with different pKa values with a common base such as the H2O and H2S. The 1:1 complexes of five para substituted phenols p-aminophenol, p-cresol, p-fluorophenol, p-chlorophenol, and p-cyanophenol with H2O and H2S were investigated experimentally and computationally. The investigations were also extended to the excited states. The experimental observations of the spectral shifts in the O-H stretching frequency and the S1-S0 band origins were correlated with the pKa of the donors. Ab initio calculations at the MP2 and various dispersion corrected density functional levels of theory were performed to compute the dissociation energy (D0) of the complexes. The quantum theory of atoms in molecules (QTAIM), noncovalent interaction (NCI) method, natural bonding orbital (NBO) analysis, and natural decomposition analysis (NEDA) were carried out for further characterization of HB interaction. The O-H stretching frequency red shifts and the dissociation energies were found to be lower for the O-H···S hydrogen bonded systems compared to those for the O-H···O H-bound systems. Despite being dominated by the dispersion interaction the O-H···S interaction in the H2S complexes also conformed to the acid-base formalism, i.e., the D0 and the O-H red shift scaled with the pKa of the donor, similar to that observed in the O-H···O interaction. However, the two classes of H-bonds follow different correlations. In addition we also discuss the nuances associated with the similarity and differences in the hydrogen bonding properties of the two classes in the ground electronic state as well as in the excited state.
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Affiliation(s)
- Surjendu Bhattacharyya
- Department of Chemical Sciences, Tata Institute of Fundamental Research , Homi Bhabha Road, Colaba, Mumbai 400 005, India
| | - Ved Prakash Roy
- Department of Chemical Sciences, Tata Institute of Fundamental Research , Homi Bhabha Road, Colaba, Mumbai 400 005, India
| | - Sanjay Wategaonkar
- Department of Chemical Sciences, Tata Institute of Fundamental Research , Homi Bhabha Road, Colaba, Mumbai 400 005, India
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Orabi EA, English AM. Sulfur-Aromatic Interactions: Modeling Cysteine and Methionine Binding to Tyrosinate and Histidinium Ions to Assess Their Influence on Protein Electron Transfer. Isr J Chem 2016. [DOI: 10.1002/ijch.201600047] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Esam A. Orabi
- Department of Chemistry and Biochemistry; Concordia University; 7141 Sherbrooke Street West Montréal Québec H4B 1R6 Canada
- Center for Research in Molecular Modeling (CERMM)Quebec; Network for Research on Protein Function, Engineering, and Applications (PROTEO)
- On leave from Department of Chemistry, Faculty of Science; Assiut University; Assiut 71516 Egypt
| | - Ann M. English
- Department of Chemistry and Biochemistry; Concordia University; 7141 Sherbrooke Street West Montréal Québec H4B 1R6 Canada
- Center for Research in Molecular Modeling (CERMM)Quebec; Network for Research on Protein Function, Engineering, and Applications (PROTEO)
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20
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Affiliation(s)
- Dana J. DiScenza
- Department of Chemistry, University of Rhode Island, Kingston, RI, USA
| | - Mindy Levine
- Department of Chemistry, University of Rhode Island, Kingston, RI, USA
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21
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Zhang L, Liu S, Cheng M, Du Y, Zhu Q. Vibrational Spectra and Theoretical Calculations of cis- and trans-3-Fluoro-N-methylaniline in the Neutral (S(0)) and Cationic (D(0)) Ground States. J Phys Chem A 2016; 120:81-94. [PMID: 26669268 DOI: 10.1021/acs.jpca.5b11991] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The mass-analyzed threshold ionization spectra of jet-cooled cis- and trans-3-fluoro-N-methylaniline (3FNMA) were recorded by ionizing via the vibrationless 0(0) and various vibrational levels of the S1 state. The adiabatic ionization energies of cis- and trans-3FNMA are determined to be 61,742 ± 5 and 61,602 ± 5 cm(-1), respectively. In the 0-1800 cm(-1) region, most of the observed vibrations in the D0 state result from the in-plane ring deformation and substituent-sensitive modes. For the high-frequency vibration region, the infrared-ultraviolet double-resonance and autoionization-detected infrared spectroscopies were applied to investigate the N-H and C-H stretching vibrations of bare 3FNMA in the S0 and D0 states. The C-H stretching vibrational information, which we failed to obtain for the bare 3FNMA cation, is complemented by recording the infrared-photodissociation spectra of its Ar cluster cation. It is revealed that a red-shifted frequency and an enhanced intensity are observed for the N-H stretch, while blue-shifted frequencies and greatly decreased intensities are found for both aromatic and the methyl C-H stretches. The blue shift of the C-H stretches is first explained by the balance of two factors, namely, the hyperconjugative interaction and the rehybridization effect. Analysis of the vibrational frequencies reveals a correlation between the relative stability of two rotamers in different electronic states and the relative rigidity of aromatic ring, indicating a mechanism of the long-range interactions "through bond" between the substituents. The density functional theory calculations can well reproduce the vibrational spectra in both S0 and D0 states. With the experimental and theoretical data, the substitution and conformation effects on the properties of 3FNMA in the S0 and D0 states, including the molecular structures, the reactive sites of electrophilic attack, and the vibrational behaviors, were discussed in detail.
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Affiliation(s)
- Lijuan Zhang
- Beijing National Laboratory of Molecular Sciences, State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, P. R. China.,Department of Chemical Engineering, Binzhou University , Binzhou 256600, Shandong, P. R. China
| | - Sheng Liu
- Beijing National Laboratory of Molecular Sciences, State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, P. R. China
| | - Min Cheng
- Beijing National Laboratory of Molecular Sciences, State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, P. R. China
| | - Yikui Du
- Beijing National Laboratory of Molecular Sciences, State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, P. R. China
| | - Qihe Zhu
- Beijing National Laboratory of Molecular Sciences, State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, P. R. China
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22
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Ghosh S, Bhattacharyya S, Wategaonkar S. Dissociation Energies of Sulfur-Centered Hydrogen-Bonded Complexes. J Phys Chem A 2015; 119:10863-70. [DOI: 10.1021/acs.jpca.5b08185] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sanat Ghosh
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400 005, India
| | - Surjendu Bhattacharyya
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400 005, India
| | - Sanjay Wategaonkar
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400 005, India
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23
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Pitsevich GA, Malevich AE, Kozlovskaya EN, Doroshenko IY, Pogorelov VE, Sablinskas V, Balevicius V. Theoretical study of the C-H/O-H stretching vibrations in malonaldehyde. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 145:384-393. [PMID: 25795613 DOI: 10.1016/j.saa.2015.02.067] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 12/20/2014] [Accepted: 02/16/2015] [Indexed: 06/04/2023]
Abstract
IR and Raman spectra of the malonaldehyde molecule and its deuterated analogues were calculated in the B3LYP/cc-pVQZ approximation. Anharmonicity effects were taken into account both in the context of a standard model of the second order perturbation theory and by constructing the potential energy surfaces (PES) with a limited number of dimensions using the Cartesian coordinates of the hydroxyl hydrogen atom and the stretching coordinates of С-Н, C-D, O-H, and O-D bonds. It was shown that in each of the two equivalent forms of the molecule, besides the global minimum, an additional local minimum at the PES is formed with the energy more than 3,000 cm(-1) higher than the energy in the global minimum. Calculations carried out by constructing the 2D and 3D PESs indicate a high anharmonicity level and multiple manifestations of the stretching О-Н vibrations, despite the fact that the model used does not take into account the splitting of the ground-state and excited vibrational energy levels. In particular, the vibration with the frequency 3,258 cm(-1) may be associated with proton transfer to the region of a local minimum of energy. Comparing the results obtained with the experimental data presented in the literature allowed us to propose a new variant of bands assignments in IR and Raman spectra of the molecule in the spectral region 2,500-3,500 cm(-1).
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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] [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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25
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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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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26
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Hydrogen Bonds Involving Sulfur: New Insights from ab Initio Calculations and Gas Phase Laser Spectroscopy. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2015. [DOI: 10.1007/978-3-319-14163-3_2] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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27
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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] [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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28
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Andersen CL, Jensen CS, Mackeprang K, Du L, Jørgensen S, Kjaergaard HG. Similar Strength of the NH···O and NH···S Hydrogen Bonds in Binary Complexes. J Phys Chem A 2014; 118:11074-82. [DOI: 10.1021/jp5086679] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Cecilie L. Andersen
- Department of Chemistry, University of Copenhagen, Universitetsparken
5, DK-2100 Copenhagen
Ø, Denmark
| | - Christine S. Jensen
- Department of Chemistry, University of Copenhagen, Universitetsparken
5, DK-2100 Copenhagen
Ø, Denmark
| | - Kasper Mackeprang
- Department of Chemistry, University of Copenhagen, Universitetsparken
5, DK-2100 Copenhagen
Ø, Denmark
| | - Lin Du
- Department of Chemistry, University of Copenhagen, Universitetsparken
5, DK-2100 Copenhagen
Ø, Denmark
| | - Solvejg Jørgensen
- Department of Chemistry, University of Copenhagen, Universitetsparken
5, DK-2100 Copenhagen
Ø, Denmark
| | - Henrik G. Kjaergaard
- Department of Chemistry, University of Copenhagen, Universitetsparken
5, DK-2100 Copenhagen
Ø, Denmark
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29
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Liu H, Man R, Wang Z, Liao J, Li X, Ma S, Yi P. Study on the cooperativity of hydrogen bonds between H2Y and HX (X = F, Cl, Br; Y = O, S, Se). JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2014. [DOI: 10.1142/s0219633614500370] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The structure characteristics, interaction energies, cooperative energies of the complexes between chalcogen hydrides ( H 2 Y ) and halogen hydrides (HX) have been studied theoretically at the MP2 level with aug-cc-pVTZ basis set in this paper. The conclusions show that there are strong interactions between H 2 Y and HX. The stability of the complex is decided by the electronegativity of the negatively charged atom. The cooperativity is observed in the two or three hydrogen bonds of each trimer structures in title system. The values of the cooperative energies and the cooperative contributions all illustrate that the cooperativity is of great importance in these complexes. The "atoms in molecules" (AIM) analyses show that the complexes in title system are mainly electrostatic interactions (closed-shell interactions) in character. For H ⋯ O bonds in H 2 O ⋯ HF ⋯ H 2 O , H 2 O ⋯ HBr ⋯ H 2 O and HF ⋯ H 2 O ⋯ HF , the 1 < |Vc|/Gc < 2 and -Gc < Hc < 0 indicate the interactions in these compounds are between closed-shell interaction and opened-shell interaction.
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Affiliation(s)
- Hexiu Liu
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, P. R. China
- School of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Ruilin Man
- School of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Zhaoxu Wang
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, P. R. China
| | - Jianping Liao
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, P. R. China
| | - Xiaofang Li
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, P. R. China
| | - Songjiang Ma
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, P. R. China
| | - Pinggui Yi
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, P. R. China
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30
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Kumar A, Samal SK, Dash R, Ojha U. Polyacryloyl hydrazide based injectable & stimuli responsive hydrogels with tunable properties. J Mater Chem B 2014; 2:7429-7439. [DOI: 10.1039/c4tb01257g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthesis and characterization of a series of injectable and stimuli responsive hydrogels based on polyacryloyl hydrazide have been accomplished using dimethyl 2,2′-thiodiacetate, acrylic acid, diethyl malonate and polyethylene glycol diacrylate as cross-linkers through a chemical or dual cross-linking pathway.
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Affiliation(s)
- Anuj Kumar
- Department of Chemistry
- Rajiv Gandhi Institute of Petroleum Technology Raebareli
- , India
| | | | | | - Umaprasana Ojha
- Department of Chemistry
- Rajiv Gandhi Institute of Petroleum Technology Raebareli
- , India
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31
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Biswal HS, Bhattacharyya S, Wategaonkar S. Molecular-Level Understanding of Ground- and Excited-State OH⋅⋅⋅O Hydrogen Bonding Involving the Tyrosine Side Chain: A Combined High-Resolution Laser Spectroscopy and Quantum Chemistry Study. Chemphyschem 2013; 14:4165-76. [DOI: 10.1002/cphc.201300670] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Indexed: 11/09/2022]
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Bhattacharyya S, Bhattacherjee A, Shirhatti PR, Wategaonkar S. O-H···S hydrogen bonds conform to the acid-base formalism. J Phys Chem A 2013; 117:8238-50. [PMID: 23947570 DOI: 10.1021/jp405414h] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrogen bonding interaction between the ROH hydrogen bond donor and sulfur atom as an acceptor has not been as well characterized as the O-H···O interaction. The strength of O-H···O interactions for a given donor has been well documented to scale linearly with the proton affinity (PA) of the H-bond acceptor. In this regard, O-H···O interactions conform to the acid-base formalism. The importance of such correlation is to be able to estimate molecular property of the complex from the known thermodynamic data of its constituents. In this work, we investigate the properties of O-H···S interaction in the complexes of the H-bond donor and sulfur containing acceptors of varying proton affinity. The hydrogen bonded complexes of p-Fluorophenol (FP) with four different sulfur containing acceptors and their oxygen analogues, namely H2O/H2S, MeOH/MeSH, Me2O/Me2S and tetrahydrofuran (THF)/tetrahydrothiophene (THT) were characterized in regard to its S1-S0 excitation spectra and the IR spectra. Two-color resonantly enhanced multiphoton ionization (2c-R2PI), resonant ion-dip infrared (RIDIR) spectroscopy, and IR-UV hole burning spectroscopic techniques were used to probe the hydrogen bonds in the aforementioned complexes. The spectroscopic data along with the ab initio calculations were used to deduce the strength of the O-H···S hydrogen bonding interactions in these system relative to that in the O-H···O interactions. It was found that, despite being dominated by the dispersion interaction, the O-H···S interactions conform to the acid-base formalism as in the case of more conventional O-H···O interactions. The dissociation energies and the red shifts in the O-H stretching frequencies correlated very well with the proton affinity of the acceptors. However, the O-H···S interaction did not follow the same correlation as that in the O-H···O H-bond. The energy decomposition analysis showed that the dissociation energies and the red shifts in the O-H stretching frequencies follow a unified correlation if these two parameters were correlated with the sum of the charge transfer and the exchange component of the total binding energy.
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Affiliation(s)
- Surjendu Bhattacharyya
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai, India
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33
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Michielsen B, Verlackt C, van der Veken B, Herrebout W. C–H⋯X (X=S, P) hydrogen bonding: The complexes of halothane with dimethyl sulfide and trimethylphosphine. J Mol Struct 2012. [DOI: 10.1016/j.molstruc.2012.02.063] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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34
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Ban Q, Li R, Li Q, Li W, Cheng J. Symmetry-adapted perturbation theory interaction energy decomposition for H2CY-XF (Y=O, S, Se; X=H, Li, Cl) complex. COMPUT THEOR CHEM 2012. [DOI: 10.1016/j.comptc.2012.04.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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35
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36
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Naktode K, Kottalanka RK, Panda TK. N-(2,6-Dimethylphenyl)diphenylphosphinamine chalcogenides (S, Se) and a zirconium complex possessing phosphanylamide in the coordination sphere. NEW J CHEM 2012. [DOI: 10.1039/c2nj40646b] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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37
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Biswal HS, Wategaonkar S. OH···X (X = O, S) hydrogen bonding in thetrahydrofuran and tetrahydrothiophene. J Chem Phys 2011; 135:134306. [DOI: 10.1063/1.3645107] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
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38
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Chen J, Vannucci AK, Mebi CA, Okumura N, Borowski SC, Lockett LT, Swenson M, Lichtenberger DL, Evans DH, Glass RS. Catalysis of Electrochemical Reduction of Weak Acids to Produce H2: Role of O‒H…S Hydrogen Bonding. PHOSPHORUS SULFUR 2011. [DOI: 10.1080/10426507.2010.523035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Jinzhu Chen
- a Department of Chemistry and Biochemistry , The University of Arizona , Tucson, Arizona, USA
| | - Aaron K. Vannucci
- a Department of Chemistry and Biochemistry , The University of Arizona , Tucson, Arizona, USA
| | - Charles A. Mebi
- a Department of Chemistry and Biochemistry , The University of Arizona , Tucson, Arizona, USA
| | - Noriko Okumura
- a Department of Chemistry and Biochemistry , The University of Arizona , Tucson, Arizona, USA
| | - Susan C. Borowski
- a Department of Chemistry and Biochemistry , The University of Arizona , Tucson, Arizona, USA
| | - L. Tori Lockett
- a Department of Chemistry and Biochemistry , The University of Arizona , Tucson, Arizona, USA
| | - Matthew Swenson
- a Department of Chemistry and Biochemistry , The University of Arizona , Tucson, Arizona, USA
| | - Dennis L. Lichtenberger
- a Department of Chemistry and Biochemistry , The University of Arizona , Tucson, Arizona, USA
| | - Dennis H. Evans
- a Department of Chemistry and Biochemistry , The University of Arizona , Tucson, Arizona, USA
| | - Richard S. Glass
- a Department of Chemistry and Biochemistry , The University of Arizona , Tucson, Arizona, USA
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Kumar S, Biswas P, Kaul I, Das A. Competition between Hydrogen Bonding and Dispersion Interactions in the Indole···Pyridine Dimer and (Indole)2···Pyridine Trimer Studied in a Supersonic Jet. J Phys Chem A 2011; 115:7461-72. [DOI: 10.1021/jp202658r] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Sumit Kumar
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), 900, NCL Innovation Park, Dr. Homi Bhabha Road, Pune-411008, Maharashtra, India
| | - Partha Biswas
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), 900, NCL Innovation Park, Dr. Homi Bhabha Road, Pune-411008, Maharashtra, India
| | - Indu Kaul
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), 900, NCL Innovation Park, Dr. Homi Bhabha Road, Pune-411008, Maharashtra, India
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), 900, NCL Innovation Park, Dr. Homi Bhabha Road, Pune-411008, Maharashtra, India
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40
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Kaur D, Sharma R, Aulakh D. The hydrogen bond donor and acceptor ability of thioformic acid. Struct Chem 2011. [DOI: 10.1007/s11224-011-9794-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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41
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Biswal HS, Gloaguen E, Mons M, Bhattacharyya S, Shirhatti PR, Wategaonkar S. Structure of the Indole−Benzene Dimer Revisited. J Phys Chem A 2011; 115:9485-92. [DOI: 10.1021/jp1119684] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Himansu S. Biswal
- Laboratoire Francis Perrin, CEA/DSM/IRAMIS/SPAM—CNRS URA
2453, CEA/Saclay, 91191 Gif-sur-Yvette, France
| | - Eric Gloaguen
- Laboratoire Francis Perrin, CEA/DSM/IRAMIS/SPAM—CNRS URA
2453, CEA/Saclay, 91191 Gif-sur-Yvette, France
| | - Michel Mons
- Laboratoire Francis Perrin, CEA/DSM/IRAMIS/SPAM—CNRS URA
2453, CEA/Saclay, 91191 Gif-sur-Yvette, France
| | - Surjendu Bhattacharyya
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai
400 005, India
| | - Pranav R. Shirhatti
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai
400 005, India
| | - Sanjay Wategaonkar
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai
400 005, India
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42
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Hazra MK, Mukherjee M, Goswami D, Chakraborty T. Structure and hydrogen bond vibrations of the jet-cooled 1:1 complex between 7-azaindole and formamide: A laser-induced fluorescence spectroscopy study. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.01.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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43
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Liu Y, Yang Y, Jiang K, Shi D, Sun J. Excited-state N–H⋯S hydrogen bond between indole and dimethyl sulfide: time-dependent density functional theory study. Phys Chem Chem Phys 2011; 13:15299-304. [DOI: 10.1039/c1cp20729f] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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44
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Miller BJ, Yekutiel M, Sodergren AH, Howard DL, Dunn ME, Vaida V, Kjaergaard HG. Overtone Spectra of 2-Mercaptoethanol and 1,2-Ethanedithiol. J Phys Chem A 2010; 114:12692-700. [DOI: 10.1021/jp9112798] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | | | | | | | | | - Henrik G. Kjaergaard
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, Copenhagen Ø, Denmark
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45
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Biswal HS, Shirhatti PR, Wategaonkar S. O−H···O versus O−H···S Hydrogen Bonding. 2. Alcohols and Thiols as Hydrogen Bond Acceptors. J Phys Chem A 2010; 114:6944-55. [DOI: 10.1021/jp102346n] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Himansu S. Biswal
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai, India 400 005
| | - Pranav R. Shirhatti
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai, India 400 005
| | - Sanjay Wategaonkar
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai, India 400 005
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