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Yamasaki K, Tsuzuki S, Tateno H. Stabilization of the Protein Structure by the Many-Body Cooperative Effect in the NH/π Hydrogen-bonding Tryptophan Triad. J Phys Chem B 2024; 128:7401-7406. [PMID: 39018377 DOI: 10.1021/acs.jpcb.4c02391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/19/2024]
Abstract
The indole ring of tryptophan can form NH/π hydrogen bonds, acting both as a hydrogen donor at the NH group in the pyrrole subring and as a hydrogen acceptor at the benzene subring. In the structural core of the trimeric stable protein Pholiota squarrosa lectin (PhoSL), three indoles are symmetrically arranged and form NH/π hydrogen bonds among each other. Here, we conducted quantum chemical calculations on this indole triad by using various methods and basis sets. The analyses revealed cooperativity in triad formation, with the many-body effect contributing approximately -2 kcal mol-1, which significantly stabilizes this protein. Symmetry-adapted perturbation theory ascribed this effect to the induced polarization. The electrostatic potential and atomic charges indeed revealed a charge redistribution through the NH/π hydrogen bond, which was favorable for triad formation.
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Affiliation(s)
- Kazuhiko Yamasaki
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba 305-8566, Japan
| | - Seiji Tsuzuki
- Department of Applied Physics, The University of Tokyo, 7-3-1 Hongo, Tokyo 113-8656, Japan
| | - Hiroaki Tateno
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba 305-8566, Japan
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2
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Li X, Yue W, Li W, Zhao J, Zhang Y, Gao Y, Gao N, Feng D, Wu B, Wang B. Rational design of 3D net-like carbon based Mn 3O 4 anode materials with enhanced lithium storage performance. NEW J CHEM 2022. [DOI: 10.1039/d2nj01618d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A three-dimensional net-like Mn3O4/carbon paper composite was realized, which delivers a remarkably enhanced rate performance and excellent cycling stability for lithium-ion storage.
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Affiliation(s)
- Xue Li
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Science, Beijing, 100190, P. R. China
| | - Wence Yue
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Science, Beijing, 100190, P. R. China
| | - Wenbiao Li
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Science, Beijing, 100190, P. R. China
| | - Jie Zhao
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Science, Beijing, 100190, P. R. China
| | - Yujiao Zhang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Science, Beijing, 100190, P. R. China
| | - Yibo Gao
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Science, Beijing, 100190, P. R. China
| | - Ning Gao
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Science, Beijing, 100190, P. R. China
| | - Dan Feng
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Science, Beijing, 100190, P. R. China
| | - Bin Wu
- Young Investigator Group Nanoscale Solid-Liquid Interfaces, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Albert-Einstein-Straße 15, 12489 Berlin, Germany
- Institute of Physics, Humboldt University Berlin, Newton-Straße 15, 12489 Berlin, Germany
| | - Bao Wang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Science, Beijing, 100190, P. R. China
- College of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing, 100000, P. R. China
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3
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Abstract
At the heart of drug design is the discovery of molecules that bind with high affinity to their drug targets. Biotin forms the strongest known noncovalent ligand-protein interactions with avidin and streptavidin, achieving femtomolar and picomolar affinities, respectively. This is made even more exceptional because biotin achieves this with a meagre molecular weight of 240 Da. Surprisingly, the approaches by which biotin achieves this are not in the standard repertoire of current medicinal chemistry practice. Biotin's biggest lesson is the importance of nonclassical H-bonds in protein-ligand complexes. Most of biotin's affinity stems from its flexible valeric acid side chain that forms CH-π, CH-O, and classical H-bonds with the lipophilic region of the binding pocket. Biotin also utilizes an oxyanion hole, a sulfur-centered H-bond, and water solvation in the bound state to achieve its potency. The facets and advantages of biotin's approach to binding should be more widely adopted in drug design.
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Affiliation(s)
- Darryl B McConnell
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
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4
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Jordaan MA, Ebenezer O, Mthiyane K, Damoyi N, Shapi M. Amide imidic prototropic tautomerization of efavirenz, NBO analysis, hyperpolarizability, polarizability and HOMO–LUMO calculations using density functional theory. COMPUT THEOR CHEM 2021. [DOI: 10.1016/j.comptc.2021.113273] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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5
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Sarkar S, Ramanathan N, Sruthi P, Sundararajan K. Computational and experimental evidence of N–H…π and cooperative πN…π∗ interactions in pyrrole…benzene and pyrrole…ethylene heterodimers at low temperatures. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.127983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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7
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Mukhopadhyay DP, Biswas S, Chattopadhyay A, Chakraborty T. Conformational Preference Determined by C-H···π Interaction of an O-H···O Hydrogen-Bonded Binary Complex of p-Fluorophenol with 2,5-Dihydrofuran: A Laser-Induced Fluorescence Spectroscopy Study. J Phys Chem A 2018; 122:3787-3797. [PMID: 29578709 DOI: 10.1021/acs.jpca.8b01384] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Conformational preferences of a binary hydrogen-bonded complex between p-fluorophenol (pFP) and 2,5-dihydrofuran (DHF) have been studied by means of laser induced fluorescence (LIF) spectroscopy in a supersonic jet expansion. Calculation predicts two major conformers for this complex, one having a nearly linear geometry in which the two molecular moieties are bound only by an O-H···O H-bond, but in the other an additional C-H···π type interaction between an ortho C-H group of pFP and ethylene group of DHF contributes to the binding stabilization and results in a folded geometry for the complex with respect to a global view, although the H-bond angle of the latter is relatively larger. This prediction is realized experimentally by identifying transitions corresponding to the two discrete conformers in a vibrationally resolved LIF excitation spectrum of the complex, and the red shifts of S1-S0 origin band of pFP moiety of the two conformers are 542 and 659 cm-1, respectively. The assignments are corroborated by means of dispersed fluorescence (DF) spectroscopy. In comparison, the LIF spectral bands for the pFP-tetrahydrofuran complex can be corresponded to only one conformer, whose S1-S0 origin transition shows a red shift (563 cm-1) somewhat similar to the linear conformer of pFP-DHF complex. Such similarities in spectral shifting behavior is consistent with the predictions of electronic structure calculations. The DF spectra also reveal that the energy threshold and pathways of vibrational dynamics in S1 of the two conformers show different behavior. Excitation to 6a1 level of pFP moiety of the folded conformer displays signatures of restricted intramolecular vibrational energy redistribution (IVR), whereas the linear form displays the emission feature for dissipative IVR.
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Affiliation(s)
- Deb Pratim Mukhopadhyay
- Department of Physical Chemistry , Indian Association for the Cultivation of Science 2A Raja S C Mullick Road , Jadavpur , Kolkata 700032 , India
| | - Souvick Biswas
- Department of Physical Chemistry , Indian Association for the Cultivation of Science 2A Raja S C Mullick Road , Jadavpur , Kolkata 700032 , India
| | - Aparajeo Chattopadhyay
- Department of Physical Chemistry , Indian Association for the Cultivation of Science 2A Raja S C Mullick Road , Jadavpur , Kolkata 700032 , India
| | - Tapas Chakraborty
- Department of Physical Chemistry , Indian Association for the Cultivation of Science 2A Raja S C Mullick Road , Jadavpur , Kolkata 700032 , India
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8
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Reva I, Lapinski L, Lopes Jesus AJ, Nowak MJ. Photoinduced transformations of indole and 3-formylindole monomers isolated in low-temperature matrices. J Chem Phys 2017; 147:194304. [DOI: 10.1063/1.5003326] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Igor Reva
- CQC, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Leszek Lapinski
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - A. J. Lopes Jesus
- CQC, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
- CQC, Faculty of Pharmacy, University of Coimbra, 3004-295 Coimbra, Portugal
| | - Maciej J. Nowak
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
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9
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Mundlapati VR, Gautam S, Sahoo DK, Ghosh A, Biswal HS. Thioamide, a Hydrogen Bond Acceptor in Proteins and Nucleic Acids. J Phys Chem Lett 2017; 8:4573-4579. [PMID: 28876948 DOI: 10.1021/acs.jpclett.7b01810] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
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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10
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Kumar S, Singh SK, Vaishnav JK, Hill JG, Das A. Interplay among Electrostatic, Dispersion, and Steric Interactions: Spectroscopy and Quantum Chemical Calculations of π-Hydrogen Bonded Complexes. Chemphyschem 2017; 18:828-838. [PMID: 28124829 DOI: 10.1002/cphc.201601405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 01/24/2017] [Indexed: 11/07/2022]
Abstract
π-Hydrogen bonding interactions are ubiquitous in both materials and biology. Despite their relatively weak nature, great progress has been made in their investigation by experimental and theoretical methods, but this becomes significantly more complicated when secondary intermolecular interactions are present. In this study, the effect of successive methyl substitution on the supramolecular structure and interaction energy of indole⋅⋅⋅methylated benzene (ind⋅⋅⋅n-mb, n=1-6) complexes is probed through a combination of supersonic jet experiments and benchmark-quality quantum chemical calculations. It is demonstrated that additional secondary interactions introduce a subtle interplay among electrostatic and dispersion forces, as well as steric repulsion, which fine-tunes the overall structural motif. Resonant two-photon ionization and IR-UV double-resonance spectroscopy techniques are used to probe jet-cooled ind⋅⋅⋅n-mb (n=2, 3, 6) complexes, with redshifting of the N-H IR stretching frequency showing that increasing the degree of methyl substitution increases the strength of the primary N-H⋅⋅⋅π interaction. Ab initio harmonic frequency and binding energy calculations confirm this trend for all six complexes. Electronic spectra of the three dimers are broad and structureless, with quantum chemical calculations revealing that this is likely to be due to multiple tilted conformations of each dimer possessing similar stabilization energies.
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Affiliation(s)
- Sumit Kumar
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune, 411008, Maharashtra, India.,Present address: Department of Dynamics at Surfaces, Max Planck Institute of Biophysical Chemistry, Am Faßberg 11, 37077, Gottingen, Germany
| | - Santosh K Singh
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune, 411008, Maharashtra, India
| | - Jamuna K Vaishnav
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune, 411008, Maharashtra, India.,Present address: Indian Institute of Technology (IIT) Indore, Khandwa Rd, Simrol, Madhya, Pradesh, 452020, India
| | - J Grant Hill
- Department of Chemistry, University of Sheffield, Sheffield, S3 7HF, UK
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune, 411008, Maharashtra, India
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11
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Singh SK, Vaishnav JK, Das A. Experimental observation of structures with subtle balance between strong hydrogen bond and weak n → π* interaction: Gas phase laser spectroscopy of 7-azaindole⋯fluorosubstituted pyridines. J Chem Phys 2016; 145:104302. [DOI: 10.1063/1.4962358] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Santosh K. Singh
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, Maharashtra, India
| | - Jamuna K. Vaishnav
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, Maharashtra, India
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, Maharashtra, India
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12
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Frey JA, Holzer C, Klopper W, Leutwyler S. Experimental and Theoretical Determination of Dissociation Energies of Dispersion-Dominated Aromatic Molecular Complexes. Chem Rev 2016; 116:5614-41. [DOI: 10.1021/acs.chemrev.5b00652] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jann A. Frey
- Departement
für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Christof Holzer
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, D-76131 Karlsruhe, Germany
| | - Wim Klopper
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, D-76131 Karlsruhe, Germany
| | - Samuel Leutwyler
- Departement
für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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13
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Armaković S, Armaković SJ, Pelemiš S, Mirjanić D. Influence of sumanene modifications with boron and nitrogen atoms to its hydrogen adsorption properties. Phys Chem Chem Phys 2016; 18:2859-70. [DOI: 10.1039/c5cp04497a] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We investigate the influence of sumanene modifications on its adsorption properties towards the hydrogen molecule.
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Affiliation(s)
- Stevan Armaković
- University of Novi Sad, Faculty of Sciences
- Department of Physics
- Novi Sad
- Serbia
| | - Sanja J. Armaković
- University of Novi Sad
- Faculty of Sciences
- Department of Chemistry
- Biochemistry and Environmental Protection
- Novi Sad
| | - Svetlana Pelemiš
- University of East Sarajevo
- Faculty of Technology
- 75400 Zvornik
- Bosnia and Herzegovina
| | - Dragoljub Mirjanić
- University of Banja Luka
- Medical Faculty
- 78000 Banja Luka
- Bosnia and Herzegovina
- Academy of Sciences and Arts of the Republic of Srpska
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14
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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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15
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Scott AM, Burns EA, Lafferty BJ, Hill FC. Theoretical predictions of thermodynamic parameters of adsorption of nitrogen containing environmental contaminants on kaolinite. J Mol Model 2015; 21:21. [DOI: 10.1007/s00894-015-2577-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Accepted: 01/07/2015] [Indexed: 10/24/2022]
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16
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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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17
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Banerjee P, Chakraborty T. Correlation of νOH Spectral Shifts of Phenol–Benzene O–H···π Hydrogen-Bonded Complexes with Donor’s Acidity: A Combined Matrix Isolation, Infrared Spectroscopy, and Quantum Chemistry Study. J Phys Chem A 2014; 118:7074-84. [DOI: 10.1021/jp5033993] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Pujarini Banerjee
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Calcutta 700032, India
| | - Tapas Chakraborty
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Calcutta 700032, India
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18
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Aguado E, León I, Millán J, Cocinero EJ, Jaeqx S, Rijs AM, Lesarri A, Fernández JA. Unraveling the Benzocaine–Receptor Interaction at Molecular Level Using Mass-Resolved Spectroscopy. J Phys Chem B 2013; 117:13472-80. [DOI: 10.1021/jp4068944] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Edurne Aguado
- Departamento de Química
Física, Facultad de Ciencia
y Tecnología, Universidad del País Vasco (UPV/EHU), B°
Sarriena s/n, 48940 Leioa, Spain
| | - Iker León
- Departamento de Química
Física, Facultad de Ciencia
y Tecnología, Universidad del País Vasco (UPV/EHU), B°
Sarriena s/n, 48940 Leioa, Spain
| | - Judith Millán
- Departamento
de Química, Facultad de
Ciencias, Estudios Agroalimentarios
e Informática, Universidad de La Rioja, Madre de Dios,
51, 26006 Logroño, Spain
| | - Emilio J. Cocinero
- Departamento de Química
Física, Facultad de Ciencia
y Tecnología, Universidad del País Vasco (UPV/EHU), B°
Sarriena s/n, 48940 Leioa, Spain
| | - Sander Jaeqx
- Radboud
University Nijmegen, Institute for Molecules and Materials, FELIX Facility, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Anouk M. Rijs
- Radboud
University Nijmegen, Institute for Molecules and Materials, FELIX Facility, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Alberto Lesarri
- Departamento de Química Física y Química
Inorgánica, Facultad de
Ciencias, Universidad de Valladolid, E-47011 Valladolid, Spain
| | - José A. Fernández
- Departamento de Química
Física, Facultad de Ciencia
y Tecnología, Universidad del País Vasco (UPV/EHU), B°
Sarriena s/n, 48940 Leioa, Spain
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19
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Kumar S, Das A. Observation of exclusively π-stacked heterodimer of indole and hexafluorobenzene in the gas phase. J Chem Phys 2013; 139:104311. [DOI: 10.1063/1.4820532] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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20
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Kellie JL, Wetmore SD. Selecting DFT methods for use in optimizations of enzyme active sites: applications to ONIOM treatments of DNA glycosylases. CAN J CHEM 2013. [DOI: 10.1139/cjc-2012-0506] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
When using a hybrid methodology to treat an enzymatic reaction, many factors contribute to selecting the method for the high-level region, which can be complicated by the presence of dispersion-driven interactions such as π–π stacking. In addition, the proper treatment of the reaction center often requires a large number of heavy atoms to be included in the high-level region, precluding the use of ab initio methods such as MP2 as well as large basis sets, in the optimization step. In the present work, popular DFT methods were tested to identify an appropriate functional for treating the high-level region in ONIOM optimizations of reactions catalyzed by nonmetalloenzymes. Eight different DFT methods (B3LYP, B97-2, MPW1K, MPWB1K, BB1K, B1B95, M06-2X, and ωB97X-D) in combination with four double-ζ quality Pople basis sets were tested for their ability to optimize noncovalent interactions (hydrogen bonding and π–π) and characterize reactions (proton transfer, SN2 hydrolysis, and unimolecular cleavage). Although the primary focus of this study is accurate structure determination, energetics were also examined at both the optimization level of theory, and with triple-ζ quality basis set and select (M06-2X or ωB97X-D) methods. If dispersion-driven interactions exist within the active site, then MPWB1K/6-31G(d,p) or M06-2X/6-31+G(d,p) are recommended for the optimization step with subsequent triple-ζ quality single-point energies. However, since dispersion-corrected functionals (M06-2X and ωB97X-D) generally require diffuse functions to yield appropriate geometries, the possible size of the high-level region is greatly limited with these methods. In contrast, if the model is large enough to recover steric constraints on π–π interactions, then B3LYP with a small basis set performs comparatively well for the optimization step and is significantly less computationally expensive. Interestingly, the functionals that afford the best geometries often do not yield the best energetics, which emphasizes the importance of structural benchmark studies.
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Affiliation(s)
- Jennifer L. Kellie
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB T1K 3M4, Canada
| | - Stacey D. Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB T1K 3M4, Canada
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21
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Kumar S, Das A. Effect of acceptor heteroatoms on π-hydrogen bonding interactions: a study of indole···thiophene heterodimer in a supersonic jet. J Chem Phys 2013; 137:094309. [PMID: 22957571 DOI: 10.1063/1.4748818] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Resonant two photon ionization (R2PI), IR-UV, and UV-UV double resonance spectroscopic techniques combined with quantum chemistry calculations have been used to determine the structure of indole···thiophene dimer observed in a supersonic jet. With the help of combined experimental and theoretical IR spectra it has been found that the observed dimer has a N-H···π hydrogen bonded slanted T-shaped structure. The present study demonstrates the effect of heteroatoms present in the acceptors on the strength of the π-hydrogen bonding interactions. It was concluded by Sherrill and co-workers from their theoretical study of benzene···pyridine dimer that aromatic rings containing heteroatoms are poorest π-hydrogen bond acceptors [E. G. Hohenstein and C. D. Sherrill, J. Phys. Chem. A 113, 878 (2009)]. But the current spectroscopic investigation exhibits that five membered aromatic heterocycles are favorable π-hydrogen bond acceptors. In this study, it has also been shown that thiophene is a better π-hydrogen bond acceptor than furan. The present work has immense biological significance as indole is the chromophore of tryptophan residue in the proteins and thiophene derivatives have potential therapeutic applications. Thus, understanding the binding motif between indole and thiophene in the heterodimer studied in this work may help in designing efficient drugs.
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Affiliation(s)
- Sumit Kumar
- Department of Chemistry, Indian Institute of Science Education and Research, 900 NCL Innovation Park, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
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22
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Saggu M, Levinson NM, Boxer SG. Experimental quantification of electrostatics in X-H···π hydrogen bonds. J Am Chem Soc 2012; 134:18986-97. [PMID: 23098379 PMCID: PMC3511793 DOI: 10.1021/ja305575t] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Hydrogen bonds are ubiquitous in chemistry and biology. The physical forces that govern hydrogen-bonding interactions have been heavily debated, with much of the discussion focused on the relative contributions of electrostatic vs quantum mechanical effects. In principle, the vibrational Stark effect, the response of a vibrational mode to electric field, can provide an experimental method for parsing such interactions into their electrostatic and nonelectrostatic components. In a previous study we showed that, in the case of relatively weak O-H···π hydrogen bonds, the O-H bond displays a linear response to an electric field, and we exploited this response to demonstrate that the interactions are dominated by electrostatics (Saggu, M.; Levinson, N. M.; Boxer, S. G. J. Am. Chem. Soc.2011, 133, 17414-17419). Here we extend this work to other X-H···π interactions. We find that the response of the X-H vibrational probe to electric field appears to become increasingly nonlinear in the order O-H < N-H < S-H. The observed effects are consistent with differences in atomic polarizabilities of the X-H groups. Nonetheless, we find that the X-H stretching vibrations of the model compounds indole and thiophenol report quantitatively on the electric fields they experience when complexed with aromatic hydrogen-bond acceptors. These measurements can be used to estimate the electrostatic binding energies of the interactions, which are found to agree closely with the results of energy calculations. Taken together, these results highlight that with careful calibration vibrational probes can provide direct measurements of the electrostatic components of hydrogen bonds.
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Affiliation(s)
- Miguel Saggu
- Department of Chemistry, Stanford University, Stanford, CA 94305-5012, USA
| | | | - Steven G. Boxer
- Department of Chemistry, Stanford University, Stanford, CA 94305-5012, USA
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Kumar S, Mukherjee A, Das A. Structure of Indole···Imidazole Heterodimer in a Supersonic Jet: A Gas Phase Study on the Interaction between the Aromatic Side Chains of Tryptophan and Histidine Residues in Proteins. J Phys Chem A 2012; 116:11573-80. [DOI: 10.1021/jp309167a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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
| | - Ankita Mukherjee
- 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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24
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Kumar S, Das A. Mimicking trimeric interactions in the aromatic side chains of the proteins: A gas phase study of indole…(pyrrole)2 heterotrimer. J Chem Phys 2012; 136:174302. [DOI: 10.1063/1.4706517] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
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25
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Kumar S, Pande V, Das A. π-Hydrogen Bonding Wins over Conventional Hydrogen Bonding Interaction: A Jet-Cooled Study of Indole···Furan Heterodimer. J Phys Chem A 2012; 116:1368-74. [DOI: 10.1021/jp211366z] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sumit Kumar
- Department of Chemistry, Indian Institute of Science Education & Research (IISER), 900 NCL Innovation Park, Dr. Homi Bhabha Road, Pune-411008, Maharashtra, India
| | - Vedant Pande
- Department of Chemistry, Indian Institute of Science Education & Research (IISER), 900 NCL Innovation Park, Dr. Homi Bhabha Road, Pune-411008, Maharashtra, India
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education & Research (IISER), 900 NCL Innovation Park, Dr. Homi Bhabha Road, Pune-411008, Maharashtra, India
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