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Pantelic L, Skaro Bogojevic S, Andrejević TP, Pantović BV, Marković VR, Ašanin DP, Milanović Ž, Ilic-Tomic T, Nikodinovic-Runic J, Glišić BĐ, Lazic J. Copper(II) and Zinc(II) Complexes with Bacterial Prodigiosin Are Targeting Site III of Bovine Serum Albumin and Acting as DNA Minor Groove Binders. Int J Mol Sci 2024; 25:8395. [PMID: 39125963 PMCID: PMC11313072 DOI: 10.3390/ijms25158395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Revised: 07/23/2024] [Accepted: 07/24/2024] [Indexed: 08/12/2024] Open
Abstract
The negative environmental and social impacts of food waste accumulation can be mitigated by utilizing bio-refineries' approach where food waste is revalorized into high-value products, such as prodigiosin (PG), using microbial bioprocesses. The diverse biological activities of PG position it as a promising compound, but its high production cost and promiscuous bioactivity hinder its wide application. Metal ions can modulate the electronic properties of organic molecules, leading to novel mechanisms of action and increased target potency, while metal complex formation can improve the stability, solubility and bioavailability of the parent compound. The objectives of this study were optimizing PG production through bacterial fermentation using food waste, allowing good quantities of the pure natural product for further synthesizing and evaluating copper(II) and zinc(II) complexes with it. Their antimicrobial and anticancer activities were assessed, and their binding affinity toward biologically important molecules, bovine serum albumin (BSA) and DNA was investigated by fluorescence emission spectroscopy and molecular docking. The yield of 83.1 mg/L of pure PG was obtained when processed meat waste at 18 g/L was utilized as the sole fermentation substrate. The obtained complexes CuPG and ZnPG showed high binding affinity towards target site III of BSA, and molecular docking simulations highlighted the affinity of the compounds for DNA minor grooves.
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Affiliation(s)
- Lena Pantelic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11000 Belgrade, Serbia; (L.P.); (S.S.B.); (T.I.-T.); (J.N.-R.)
| | - Sanja Skaro Bogojevic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11000 Belgrade, Serbia; (L.P.); (S.S.B.); (T.I.-T.); (J.N.-R.)
| | - Tina P. Andrejević
- Department of Chemistry, Faculty of Science, University of Kragujevac, Radoja Domanovića 12, 34000 Kragujevac, Serbia; (T.P.A.); (B.V.P.); (V.R.M.)
| | - Bojana V. Pantović
- Department of Chemistry, Faculty of Science, University of Kragujevac, Radoja Domanovića 12, 34000 Kragujevac, Serbia; (T.P.A.); (B.V.P.); (V.R.M.)
| | - Violeta R. Marković
- Department of Chemistry, Faculty of Science, University of Kragujevac, Radoja Domanovića 12, 34000 Kragujevac, Serbia; (T.P.A.); (B.V.P.); (V.R.M.)
| | - Darko P. Ašanin
- Department of Science, Institute for Information Technologies Kragujevac, University of Kragujevac, Jovana Cvijića bb, 34000 Kragujevac, Serbia; (D.P.A.); (Ž.M.)
| | - Žiko Milanović
- Department of Science, Institute for Information Technologies Kragujevac, University of Kragujevac, Jovana Cvijića bb, 34000 Kragujevac, Serbia; (D.P.A.); (Ž.M.)
| | - Tatjana Ilic-Tomic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11000 Belgrade, Serbia; (L.P.); (S.S.B.); (T.I.-T.); (J.N.-R.)
| | - Jasmina Nikodinovic-Runic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11000 Belgrade, Serbia; (L.P.); (S.S.B.); (T.I.-T.); (J.N.-R.)
| | - Biljana Đ. Glišić
- Department of Chemistry, Faculty of Science, University of Kragujevac, Radoja Domanovića 12, 34000 Kragujevac, Serbia; (T.P.A.); (B.V.P.); (V.R.M.)
| | - Jelena Lazic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11000 Belgrade, Serbia; (L.P.); (S.S.B.); (T.I.-T.); (J.N.-R.)
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Kumar Panja S, Kumar S. Weak Intra and Intermolecular Interactions via Aliphatic Hydrogen Bonding in Piperidinium Based Ionic Liquids: Experimental, Topological and Molecular Dynamics Studies. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Wakchaure PD, Ganguly B. Unraveling the Role of π-Stacking Interactions in Ligand Binding to the Thiamine Pyrophosphate Riboswitch with High-level Quantum Chemical Calculations and Docking Study. J Phys Chem B 2022; 126:1076-1084. [PMID: 35089046 DOI: 10.1021/acs.jpcb.1c08587] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The thiamine pyrophosphate (TPP) riboswitch has emerged as the new target for designing new ligands for antibiotic purpose. Binding of the natural ligand TPP to the TPP riboswitch causes downregulation of the genes responsible for its biosynthesis. We have reported the role of π-stacking energy contributions to ligand binding with a TPP riboswitch. In conjunction with the docking study, the higher-level quantum chemical calculations performed with the wB97XD and Def2TZVPP basis set in the aqueous phase revealed that the optimum ring size is crucial to attain the effective binding efficiency of ligands with a TPP riboswitch. The π-stacking energy contributions observed for the ligands studied are largely similar; however, the cases studied with higher π-stacking energies with larger rings have a weaker ability to displace the radiolabeled thiamine from the riboswitch. The EDA and NCI analyses suggest the role of larger dispersive interactions in stabilizing the π-stacking rings. The contribution from hydrogen-bonding interactions of the hydrogen-bond donor groups on the A ring augments the binding affinity of the ligand. This study sheds light on various factors that contribute to the design of new ligands for efficient binding with a TPP riboswitch and inhibition of gene expression.
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Affiliation(s)
- Padmaja D Wakchaure
- Computation and Simulation Unit (Analytical Discipline and Centralized Instrument Facility), CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, Gujarat, India.,Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh 201 002, India
| | - Bishwajit Ganguly
- Computation and Simulation Unit (Analytical Discipline and Centralized Instrument Facility), CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, Gujarat, India.,Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh 201 002, India
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Bhattacharyya S, Ghosh S, Wategaonkar S. O-H stretching frequency red shifts do not correlate with the dissociation energies in the dimethylether and dimethylsulfide complexes of phenol derivatives. Phys Chem Chem Phys 2021; 23:5718-5739. [PMID: 33662068 DOI: 10.1039/d0cp01589j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this perspective, we present a comprehensive report on the spectroscopic and computational investigations of the hydrogen bonded (H-bonded) complexes of Me2O and Me2S with seven para-substituted H-bond donor phenols. The salient finding was that although the dissociation energies, D0, of the Me2O complexes were consistently higher than those of the analogous Me2S complexes, the red-shifts in phenolic O-H frequencies, Δν(O-H), showed the exactly opposite trend. This is in contravention of the general perception that the red shift in the X-H stretching frequency in the X-HY hydrogen bonded complexes is a reliable indicator of H-bond strength (D0), a concept popularly known as the Badger-Bauer rule. This is also in contrast to the trend reported for the H-bonded complexes of H2S/H2O with several para substituted phenols of different pKa values wherein the oxygen centered hydrogen bonded (OCHB) complexes consistently showed higher Δν(O-H) and D0 compared to those of the analogous sulfur centered hydrogen bonded (SCHB) complexes. Our effort was to understand these intriguing observations based on the spectroscopic investigations of 1 : 1 complexes in combination with a variety of high level quantum chemical calculations. Ab initio calculations at the MP2 level and the DFT calculations using various dispersion corrected density functionals (including DFT-D3) were performed on counterpoise corrected surfaces to compute the dissociation energy, D0, of the H-bonded complexes. The importance of anharmonic frequency computations is underscored as they were able to correctly reproduce the observed trend in the relative OH frequency shifts unlike the harmonic frequency computations. We have attempted to find a unified correlation that would globally fit the observed red shifts in the O-H frequency with the H-bonding strength for the four bases, namely, H2S, H2O, Me2O, and Me2S, in this set of H-bond donors. It was found that the proton affinity normalized Δν(O-H) values scale very well with the H-bond strength.
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Affiliation(s)
- Surjendu Bhattacharyya
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India.
| | - Sanat Ghosh
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India.
| | - Sanjay Wategaonkar
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India.
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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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6
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Su P, Tang Z, Wu W. Generalized Kohn‐Sham energy decomposition analysis and its applications. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1460] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Peifeng Su
- The State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering Xiamen University Xiamen China
| | - Zhen Tang
- The State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering Xiamen University Xiamen China
| | - Wei Wu
- The State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering Xiamen University Xiamen China
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Roy TK, Mani D, Schwaab G, Havenith M. A close competition between O–H⋯O and O–H⋯π hydrogen bonding: IR spectroscopy of anisole–methanol complex in helium nanodroplets. Phys Chem Chem Phys 2020; 22:22408-22416. [DOI: 10.1039/d0cp02589e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Anisole forms O–H⋯O as well O–H⋯π bound complexes with methanol.
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Affiliation(s)
- Tarun Kumar Roy
- Lehrstuhl für Physikalische Chemie II
- Ruhr-Universität Bochum
- Bochum
- Germany
| | - Devendra Mani
- Lehrstuhl für Physikalische Chemie II
- Ruhr-Universität Bochum
- Bochum
- Germany
| | - Gerhard Schwaab
- Lehrstuhl für Physikalische Chemie II
- Ruhr-Universität Bochum
- Bochum
- Germany
| | - Martina Havenith
- Lehrstuhl für Physikalische Chemie II
- Ruhr-Universität Bochum
- Bochum
- Germany
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Singh SK, Panwaria P, Mishra KK, Das A. Steric as well as n→π* Interaction Controls the Conformational Preferences of Phenyl Acetate: Gas‐phase Spectroscopy and Quantum Chemical Calculations. Chem Asian J 2019; 14:4705-4711. [DOI: 10.1002/asia.201901158] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 09/03/2019] [Indexed: 01/26/2023]
Affiliation(s)
- Santosh K. Singh
- Department of ChemistryIndian Institute of Science Education and Research (IISER) Pune Dr. Homi Bhabha Road Pashan, Pune- 411008 India
- Current Address: Department of ChemistryUniversity of Hawaii, Manoa Honolulu Hawaii 96822 USA
| | - Prakash Panwaria
- Department of ChemistryIndian Institute of Science Education and Research (IISER) Pune Dr. Homi Bhabha Road Pashan, Pune- 411008 India
| | - Kamal K. Mishra
- Department of ChemistryIndian Institute of Science Education and Research (IISER) Pune Dr. Homi Bhabha Road Pashan, Pune- 411008 India
| | - Aloke Das
- Department of ChemistryIndian Institute of Science Education and Research (IISER) Pune Dr. Homi Bhabha Road Pashan, Pune- 411008 India
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Abstract
Dimers of furan, 2,3-dihydrofuran, 2,5-dihydrofuran and tetrahydrofuran were investigated with the use of theoretical methods to determine the interactions that keep the molecules together. The QTAIM and NCI methods confirmed that for furan dimers the C-H⋯O hydrogen bond and stacking interactions can form the dimers with similar energy. For 2,3-dihydrofuran, 2,5-dihydrofuran and tetrahydrofuran, the decisive mechanism of dimer formation is the stacking interaction between the furan rings.
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Sheng X, Jiang X, Zhao H, Wan D, Liu Y, Ngwenya CA, Du L. FTIR study of hydrogen bonding interaction between fluorinated alcohol and unsaturated esters. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 198:239-247. [PMID: 29549865 DOI: 10.1016/j.saa.2018.03.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 02/25/2018] [Accepted: 03/08/2018] [Indexed: 06/08/2023]
Abstract
The 1:1 complexes of two unsaturated esters with 2,2,2-trifluoroethanol (TFE) were investigated experimentally and computationally. The experimental observations of the spectral shifts of the OH-stretching vibrational transitions were obtained at 113cm-1 for TFE-methyl acrylate (MA) and 92cm-1 for TFE-vinyl acetate (VA). There are three docking sites in the two unsaturated esters for the incoming TFE. The predicted red shifts of the OH-stretching vibrational transitions were found to be larger for the OH⋯OC hydrogen bonded conformer than those for the OH⋯π and OH⋯O ones. The binding energies further prove that the OH⋯OC hydrogen bonded conformers are the most stable ones. On the basis of the DFT calculations as well as previous works, the carbonyl group is the best docking site for TFE. Furthermore, the thermodynamic equilibrium constants of TFE-MA and TFE-VA were obtained at 0.28 and 0.15 by combining the experimental spectra data and the DFT calculations. Consequently, the Gibbs free energies of formation were determined to be 3.2 and 4.8kJmol-1 for TFE-MA and TFE-VA, respectively. The quantum theory of atoms in molecules (AIM) and generalized Kohn-Sham energy decomposition analysis (GKS-EDA) were carried out for further characterization of the hydrogen bonding interactions. GKS-EDA shows an "electrostatic" dominated hydrogen bonding character for the OH⋯OC hydrogen bonds.
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Affiliation(s)
- Xia Sheng
- College of Chemistry, Chemical and Environmental Engineering, Henan University of Technology, Lianhua Street 100, 450001 Zhengzhou, China
| | - Xiaotong Jiang
- Environment Research Institute, Shandong University, Shanda South Road 27, 250100 Jinan, China
| | - Hailiang Zhao
- College of Chemistry, Chemical and Environmental Engineering, Henan University of Technology, Lianhua Street 100, 450001 Zhengzhou, China; Environment Research Institute, Shandong University, Shanda South Road 27, 250100 Jinan, China
| | - Dongjin Wan
- College of Chemistry, Chemical and Environmental Engineering, Henan University of Technology, Lianhua Street 100, 450001 Zhengzhou, China
| | - Yongde Liu
- College of Chemistry, Chemical and Environmental Engineering, Henan University of Technology, Lianhua Street 100, 450001 Zhengzhou, China
| | - Cleopatra Ashley Ngwenya
- College of Chemistry, Chemical and Environmental Engineering, Henan University of Technology, Lianhua Street 100, 450001 Zhengzhou, China
| | - Lin Du
- Environment Research Institute, Shandong University, Shanda South Road 27, 250100 Jinan, China.
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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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Wategaonkar S, Bhattacherjee A. N–H···S Interaction Continues To Be an Enigma: Experimental and Computational Investigations of Hydrogen-Bonded Complexes of Benzimidazole with Thioethers. J Phys Chem A 2018; 122:4313-4321. [DOI: 10.1021/acs.jpca.8b01943] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sanjay Wategaonkar
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India
| | - Aditi Bhattacherjee
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India
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Yu T, Wang J, Jiang W, Zhang Z, Zhu Y, Tang Y, Wang Z. The Dissociation Mechanism of Poly-α-methylstyrene (PAMS) Dimers Induced by Spin Polarization. ChemistrySelect 2018. [DOI: 10.1002/slct.201702671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Tianrong Yu
- Institute of Atomic and Molecular Physics; Jilin University; Changchun 130012 China
- Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy; Jilin University; Changchun 130012 China
| | - Jia Wang
- Institute of Atomic and Molecular Physics; Jilin University; Changchun 130012 China
- Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy; Jilin University; Changchun 130012 China
| | - Wanrun Jiang
- Institute of Atomic and Molecular Physics; Jilin University; Changchun 130012 China
- Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy; Jilin University; Changchun 130012 China
| | - Zhanwen Zhang
- China Academy of Engineering Physics; Mianyang 621900 China
| | - Yu Zhu
- Institute of Atomic and Molecular Physics; Jilin University; Changchun 130012 China
- Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy; Jilin University; Changchun 130012 China
| | - Yongjian Tang
- China Academy of Engineering Physics; Mianyang 621900 China
| | - Zhigang Wang
- Institute of Atomic and Molecular Physics; Jilin University; Changchun 130012 China
- Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy; Jilin University; Changchun 130012 China
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Jiang X, Tsona NT, Tang S, Du L. Hydrogen bond docking preference in furans: OH⋯π vs. OH⋯O. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 191:155-164. [PMID: 29028507 DOI: 10.1016/j.saa.2017.10.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 09/23/2017] [Accepted: 10/01/2017] [Indexed: 05/15/2023]
Abstract
The docking sites of hydrogen bonds in complexes formed between 2,2,2-trifluoroethanol (TFE), furan (Fu), and 2-methyl furan (MF) have been investigated. Using density functional theory (DFT) calculations, gas phase and matrix isolation FTIR spectroscopies, the strengths of OH⋯O and OH⋯π hydrogen bonds in the complexes were compared to find the docking preference. Calculations suggest that the hydrogen bond donor, TFE, is more likely to dock onto the oxygen atom of the aromatic furans ring, and consequently, the OH⋯O type hydrogen bond is relatively stronger than the OH⋯π type. The FTIR spectrum in the OH-stretching fundamental range obtained at room temperatures has been compared with that obtained at extremely low temperatures in the matrix. The fundamental and the red shifts of OH-stretching vibrations were observed in both FTIR spectra, confirming the formation of hydrogen bonded complexes. By assessing the ability of furan and MF to participate in the formation of OH⋯O hydrogen bond, the effect of ring methylation has been highlighted. From the calculated geometric and thermodynamic parameters as well as the frequency shift of the OH-stretching vibrations in complexes, TFE-MF is found to be more stable than TFE-Fu, which suggests that the strength of the OH⋯O hydrogen bond in TFE-MF originates from the high activity of the furan molecule caused by the methylation of the aromatic ring. The present study furthers the knowledge of docking preference in heteroaromatic molecules and is helpful to understand the nature of intermolecular interactions between hydrogen bond donors and acceptors, including both electron-deficient atoms and π cloud.
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Affiliation(s)
- Xiaotong Jiang
- Environment Research Institute, Shandong University, Shanda South Road 27, 250100, Shandong, China
| | - Narcisse T Tsona
- Environment Research Institute, Shandong University, Shanda South Road 27, 250100, Shandong, China
| | - Shanshan Tang
- Environment Research Institute, Shandong University, Shanda South Road 27, 250100, Shandong, China
| | - Lin Du
- Environment Research Institute, Shandong University, Shanda South Road 27, 250100, Shandong, China.
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Poblotzki A, Gottschalk HC, Suhm MA. Tipping the Scales: Spectroscopic Tools for Intermolecular Energy Balances. J Phys Chem Lett 2017; 8:5656-5665. [PMID: 29094953 DOI: 10.1021/acs.jpclett.7b02337] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Intermolecular energy balances are supramolecular complexes with a nearly degenerate bistable docking structure and low barriers in between, which can be tuned by chemical substitution to prefer one or the other site. The docking preference can be probed by forming the complexes in a supersonic jet expansion and by measuring their spectroscopic signature. Linear spectroscopies are shown to be well suited for this purpose, in particular when they are assisted by more sensitive techniques and by approximate computed photon interaction cross sections. Molecular analogues of conventional beam balances, seesaw balances, and torsional balances are discussed, all based on noncovalent interactions. The discrimination of energy differences down to the sub-kJ/mol level is demonstrated. The correspondence to intramolecular torsional balances in NMR spectroscopy is outlined. Besides highlighting conformational preferences, the results of intermolecular balance experiments can serve as critical benchmarks for an accurate description of intermolecular forces and zero-point vibrational energies.
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Affiliation(s)
- Anja Poblotzki
- Institut für Physikalische Chemie, Universität Göttingen , Tammannstraße 6, 37077 Göttingen, Germany
| | - Hannes C Gottschalk
- Institut für Physikalische Chemie, Universität Göttingen , Tammannstraße 6, 37077 Göttingen, Germany
| | - Martin A Suhm
- Institut für Physikalische Chemie, Universität Göttingen , Tammannstraße 6, 37077 Göttingen, Germany
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17
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Bhattacherjee A, Wategaonkar S. Nature and Hierarchy of Noncovalent Interactions in Gas-Phase Binary Complexes of Indole and Benzimidazole with Ethers. J Phys Chem A 2017; 121:8815-8824. [DOI: 10.1021/acs.jpca.7b08627] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Aditi Bhattacherjee
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India
| | - Sanjay Wategaonkar
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India
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18
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Cheng S, Tang S, Tsona NT, Du L. The Influence of the Position of the Double Bond and Ring Size on the Stability of Hydrogen Bonded Complexes. Sci Rep 2017; 7:11310. [PMID: 28900230 PMCID: PMC5596019 DOI: 10.1038/s41598-017-11921-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 08/31/2017] [Indexed: 11/18/2022] Open
Abstract
To study the influence of the position of the double bond and ring size on the stability of hydrogen bonded complexes, the 1:1 complexes formed between 2,2,2-trifluoroethanol (TFE) and three heterocyclic compounds including 2,3-dihydrofuran (2,3-DHF), 2,5-dihydrofuran (2,5-DHF) and 3,4-dihydropyran (3,4-DHP) were investigated systematically. The formation of hydrogen bonded TFE−2,3-DHF, TFE−2,5-DHF and TFE−3,4-DHP complexes were identified by gas phase FTIR spectroscopy at room temperature, and the OH-stretching fundamental transition of TFE was red shifted upon complexation. The competition between the O atom and π-electrons bonding sites within the complexes was studied, and the O−H···π type hydrogen bond was found to be less stable than the O−H···O in all three cases. The observed red shifts of the OH-stretching fundamental transitions in the complexes were attributed to the formation of O−H···O hydrogen bond. Equilibrium constants of the complexation reactions were determined from measured and calculated OH-stretching fundamental intensities. Both theoretical calculations and experimental results reveal that the hydrogen bond strengths in the complexes follow the sequence: TFE−2,5-DHF > TFE−2,3-DHF ≈ TFE−3,4-DHP, thus the position of the double bond exerts significantly larger influence than ring size on the stability of the selected hydrogen bonded complexes.
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Affiliation(s)
- Shumin Cheng
- Environment Research Institute, Shandong University, Shanda South Road 27, 250100, Shandong, China
| | - Shanshan Tang
- Environment Research Institute, Shandong University, Shanda South Road 27, 250100, Shandong, China
| | - Narcisse T Tsona
- Environment Research Institute, Shandong University, Shanda South Road 27, 250100, Shandong, China
| | - Lin Du
- Environment Research Institute, Shandong University, Shanda South Road 27, 250100, Shandong, China.
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Bhattacherjee A, Wategaonkar S. Conformational Heterogeneity and the Role of the C(2)-H Donor in Mono- and Dihydrated Clusters of Benzoxazole. J Phys Chem A 2017; 121:5420-5427. [PMID: 28665613 DOI: 10.1021/acs.jpca.7b04058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The significance of the heteroatom in influencing the acidity and binding affinity of the C(2)-H donor in five-membered heterocyclic rings is explored. The water clusters of benzoxazole (BOX) are studied in a supersonic jet by IR-UV double resonance spectroscopy and compared with those of benzimidazole (BIM) and its N-methyl derivative (MBIM). Two conformers are identified for the monohydrated cluster, both of which are O-H···N bound and differ in their orientation with respect to the intermolecular hydrogen bond. IR spectroscopy of the doubly hydrated cluster shows the presence of an intensity enhanced C(2)-H (carbon atom between the heteroatoms in the five-membered ring) stretching mode in addition to two red-shifted bound OH stretches, indicating that the water molecules form a hydrogen-bonded bridge encompassing the N acceptor and the weakly activated C(2)-H bond in oxazole. Comparison of the topological parameters of electron density, natural bond orbital analyses, and computed binding energies of the analogous hydrated structures of BOX, BIM, and MBIM indicates that the C(2)-H bond in the former is a more potent H-bond donor.
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Affiliation(s)
- Aditi Bhattacherjee
- Department of Chemical Sciences, Tata Institute of Fundamental Research , Homi Bhabha Road, Mumbai 400 005, India
| | - Sanjay Wategaonkar
- Department of Chemical Sciences, Tata Institute of Fundamental Research , Homi Bhabha Road, Mumbai 400 005, India
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20
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Zhao H, Tang S, Du L. Hydrogen bond docking site competition in methyl esters. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 181:122-130. [PMID: 28351818 DOI: 10.1016/j.saa.2017.03.038] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 03/07/2017] [Accepted: 03/17/2017] [Indexed: 06/06/2023]
Abstract
The OH⋯O hydrogen bonds in the 2,2,2-trifluoroethanol (TFE)-methyl ester complexes in the gas phase have been investigated by FTIR spectroscopy and DFT calculations. Methyl formate (MF), methyl acetate (MA), and methyl trifluoroacetate (MTFA) were chosen as the hydrogen bond acceptors. A dominant inter-molecular hydrogen bond was formed between the OH group of TFE and different docking sites in the methyl esters (carbonyl oxygen or ester oxygen). The competition of the two docking sites decides the structure and spectral properties of the complexes. On the basis of the observed red shifts of the OH-stretching transition with respect to the TFE monomer, the order of the hydrogen bond strength can be sorted as TFE-MA (119cm-1)>TFE-MF (93cm-1)>TFE-MTFA (44cm-1). Combining the experimental infrared spectra with the DFT calculations, the Gibbs free energies of formation were determined to be 1.5, 4.5 and 8.6kJmol-1 for TFE-MA, TFE-MF and TFE-MTFA, respectively. The hydrogen bonding in the MTFA complex is much weaker than those of the TFE-MA and TFE-MF complexes due to the effect of the CF3 substitution on MTFA, while the replacement of an H atom with a CH3 group in methyl ester only slightly increases the hydrogen bond strength. Topological analysis and localized molecular orbital energy decomposition analysis was also applied to compare the interactions in the complexes.
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Affiliation(s)
- Hailiang Zhao
- Environment Research Institute, Shandong University, Shanda South Road 27, 250100, Shandong, China
| | - Shanshan Tang
- Environment Research Institute, Shandong University, Shanda South Road 27, 250100, Shandong, China
| | - Lin Du
- Environment Research Institute, Shandong University, Shanda South Road 27, 250100, Shandong, China.
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21
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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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22
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Min A, Ahn A, Moon CJ, Lee JH, Seong YG, Kim SK, Choi MY. Conformational structures of jet-cooled acetaminophen-water clusters: a gas phase spectroscopic and computational study. Phys Chem Chem Phys 2017; 19:4840-4848. [PMID: 28134364 DOI: 10.1039/c6cp06863d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Jet-cooled acetaminophen (AAP)-water clusters, AAP-(H2O)1, were investigated by mass-selected resonant two-photon ionization (R2PI), ultraviolet-ultraviolet hole-burning (UV-UV HB), infrared-dip (IR-dip), and infrared-ultraviolet hole-burning (IR-UV HB) spectroscopy. Each syn- and anti-AAP rotamer has three distinctive binding sites (-OH, >CO, and >NH) for a water molecule, thus 6 different AAP-(H2O)1 conformers are expected to exist in the molecular beam. The origin bands of the AAP(OH)-(H2O)1 and AAP(CO)-(H2O)1 conformers (including their syn- and anti-conformers) in the R2PI spectrum are shifted to red and blue compared to those of the AAP monomer, respectively. These frequency shifts upon complexation between a water molecule and a specific binding site of AAP are also predicted by theoretical calculations. The spectral assignments of the origin bands in the R2PI spectra and the IR vibrational bands in the IR-dip spectra of the four lowest-energy conformers of AAP-(H2O)1, [syn- and anti-AAP(OH)-(H2O)1 and syn- and anti-AAP(CO)-(H2O)1], are aided by ab initio and time-dependent density functional theory (TDDFT) calculations. Further investigation of the IR-dip spectra has revealed a hydrogen-bonded NH stretching mode, supporting the presence of the syn-AAP(NH)-(H2O)1 conformer. Moreover, by employing IR-UV HB spectroscopy, we have reconfirmed the existence of the syn-AAP(NH)-(H2O)1 conformer, which happened to be buried underneath the broad background contributed by the AAP(OH)-(H2O)1 conformers. These observations have led us to conclude that all of the possible conformers of AAP-(H2O)1 have been found in this study.
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Affiliation(s)
- Ahreum Min
- Department of Chemistry (BK21+) and Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Republic of Korea.
| | - Ahreum Ahn
- Department of Chemistry (BK21+) and Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Republic of Korea.
| | - Cheol Joo Moon
- Department of Chemistry (BK21+) and Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Republic of Korea.
| | - Ji Hoon Lee
- Department of Chemistry (BK21+) and Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Republic of Korea.
| | - Yeon Guk Seong
- Department of Chemistry (BK21+) and Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Republic of Korea.
| | - Seong Keun Kim
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea.
| | - Myong Yong Choi
- Department of Chemistry (BK21+) and Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Republic of Korea.
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23
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Jiang X, Liu S, Tsona NT, Tang S, Ding L, Zhao H, Du L. Matrix isolation FTIR study of hydrogen-bonded complexes of methanol with heterocyclic organic compounds. RSC Adv 2017. [DOI: 10.1039/c6ra26076d] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Hydrogen bonded complexes of heterocyclic compounds with methanol were studied using matrix isolation FTIR spectroscopy and theoretical calculations.
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Affiliation(s)
| | - Shijie Liu
- Environment Research Institute
- Shandong University
- China
| | | | - Shanshan Tang
- Environment Research Institute
- Shandong University
- China
| | - Lei Ding
- Environment Research Institute
- Shandong University
- China
| | - Hailiang Zhao
- Environment Research Institute
- Shandong University
- China
| | - Lin Du
- Environment Research Institute
- Shandong University
- China
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24
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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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25
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Yuan C, Wu H, Jia M, Su P, Luo Z, Yao J. A theoretical study of weak interactions in phenylenediamine homodimer clusters. Phys Chem Chem Phys 2016; 18:29249-29257. [DOI: 10.1039/c6cp04922b] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Utilizing dispersion-corrected density functional theory (DFT) calculations, we demonstrate the weak intermolecular interactions of phenylenediamine dimer (pdd) clusters, emphasizing the local lowest energy structures and decomposition of interaction energies by natural bond orbital (NBO) and atoms in molecule (AIM) analyses.
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Affiliation(s)
- Chengqian Yuan
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- CAS Key Laboratory of Photochemistry
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry
- Chinese Academy of Sciences
| | - Haiming Wu
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- CAS Key Laboratory of Photochemistry
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry
- Chinese Academy of Sciences
| | - Meiye Jia
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- CAS Key Laboratory of Photochemistry
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry
- Chinese Academy of Sciences
| | - Peifeng Su
- Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry
- and College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen
- China
| | - Zhixun Luo
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- CAS Key Laboratory of Photochemistry
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry
- Chinese Academy of Sciences
| | - Jiannian Yao
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- CAS Key Laboratory of Photochemistry
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry
- Chinese Academy of Sciences
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26
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Poblotzki A, Altnöder J, Suhm MA. Subtle solvation behaviour of a biofuel additive: the methanol complex with 2,5-dimethylfuran. Phys Chem Chem Phys 2016; 18:27265-27271. [DOI: 10.1039/c6cp05413g] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Solvent roaming on furans is structurally elucidated and energy-ordered by deuteration and relaxation experiments in jet expansions.
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Affiliation(s)
- Anja Poblotzki
- Institut für Physikalische Chemie
- Universität Göttingen
- 37077 Göttingen
- Germany
| | - Jonas Altnöder
- Institut für Physikalische Chemie
- Universität Göttingen
- 37077 Göttingen
- Germany
| | - Martin A. Suhm
- Institut für Physikalische Chemie
- Universität Göttingen
- 37077 Göttingen
- Germany
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27
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Prakash M, Mathivon K, Benoit DM, Chambaud G, Hochlaf M. Carbon dioxide interaction with isolated imidazole or attached on gold clusters and surface: competition between σ H-bond and π stacking interaction. Phys Chem Chem Phys 2015; 16:12503-9. [PMID: 24833261 DOI: 10.1039/c4cp01292e] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Using first principle methodologies, we investigate the subtle competition between σ H-bond and π stacking interaction between CO2 and imidazole either isolated, adsorbed on a gold cluster or adsorbed on a gold surface. These computations are performed using MP2 as well as dispersion corrected density functional theory (DFT) techniques. Our results show that the CO2 interaction goes from π-type stacking into σ-type when CO2 interacts with isolated imidazole and Au clusters or surface. The balance between both types of interactions is found when an imidazole is attached to a Au20 gold cluster. Thus, the present study has great significance in understanding and controlling the structures of weakly-bound molecular systems and materials, where hydrogen bonding and van der Waals interactions are competing. The applications are in the fields of the control of CO2 capture and scattering, catalysis and bio- and nanotechnologies.
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Affiliation(s)
- Muthuramalingam Prakash
- Université Paris-Est, Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, 5 bd Descartes, 77454 Marne-la-Vallée, France.
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28
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El-Sheshtawy HS, Salman HMA, El-Kemary M. Halogen vs hydrogen bonding in thiazoline-2-thione stabilization with σ- and π-electron acceptors adducts: theoretical and experimental study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 137:442-449. [PMID: 25238182 DOI: 10.1016/j.saa.2014.08.077] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Revised: 08/16/2014] [Accepted: 08/23/2014] [Indexed: 06/03/2023]
Abstract
Molecular charge-transfer complexes (CT) between thiazoline-2-thione (THZ) and different σ- (I2) and π-acceptors (Tetracyanoethylene (TCNE), 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ), and 2,3,5,6-tetrachloro-1,4-benzoquinone (CHL)) were investigated. UV-Vis absorption spectroscopy and theoretical calculations using both MP2/aug-cc-pVDZ-PP and B3LYP/6-311++G(d,p) level of theory were corroborated to study the nature of the stabilizing forces for THZ-I2, THZ-DDQ, THZ-TCNE, and THZ-CHL. Halogen bonding (XB) was the stabilizing attractive force in THZ-I2 and THZ-CHL whereas; hydrogen bonding (HB) was dominated in both THZ-TCNE, and THZ-DDQ complexes. Formation constant (K), extinction coefficient (ɛ), thermodynamic parameters such as enthalpy change (ΔH), entropy (ΔS), and Gibbs free energy (ΔG) were measured in different solvents.
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Affiliation(s)
- Hamdy S El-Sheshtawy
- Biotechnology and Fish Processing Department, Faculty of Aquatic and Fisheries Sciences, Kafrelsheikh University, 33516 Kafr ElSheikh, Egypt; Nanochemistry Laboratory, Chemistry Department, Faculty of Science, Kafrelsheikh University, 33516 Kafr ElSheikh, Egypt.
| | - Hassan M A Salman
- Chemistry Department, Faculty of Science, South Valley University, Qena 83523, Egypt
| | - Maged El-Kemary
- Nanochemistry Laboratory, Chemistry Department, Faculty of Science, Kafrelsheikh University, 33516 Kafr ElSheikh, Egypt
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29
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Heger M, Altnöder J, Poblotzki A, Suhm MA. To π or not to π – how does methanol dock onto anisole? Phys Chem Chem Phys 2015; 17:13045-52. [DOI: 10.1039/c5cp01545f] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Supersonic jet spectroscopy reveals that methanol opts against aromatic docking onto anisole despite a very close competition.
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Affiliation(s)
- Matthias Heger
- Institut für Physikalische Chemie
- Georg-August-Universität Göttingen
- D-37077 Göttingen
- Germany
| | - Jonas Altnöder
- Institut für Physikalische Chemie
- Georg-August-Universität Göttingen
- D-37077 Göttingen
- Germany
| | - Anja Poblotzki
- Institut für Physikalische Chemie
- Georg-August-Universität Göttingen
- D-37077 Göttingen
- Germany
| | - Martin A. Suhm
- Institut für Physikalische Chemie
- Georg-August-Universität Göttingen
- D-37077 Göttingen
- Germany
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30
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Boussouf K, Boulmene R, Prakash M, Komiha N, Taleb M, Mogren Al-Mogren M, Hochlaf M. Characterization of Znq+–imidazole (q = 0, 1, 2) organometallic complexes: DFT methods vs. standard and explicitly correlated post-Hartree–Fock methods. Phys Chem Chem Phys 2015; 17:14417-26. [DOI: 10.1039/c4cp06108j] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Benchmarking DFts for the characterization of the Znq+–imidazole (q= 0, 1, 2) complexes.
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Affiliation(s)
- K. Boussouf
- Université Paris-Est
- Laboratoire Modélisation et Simulation Multi Echelle
- MSME UMR 8208 CNRS
- 77454 Marne-la-Vallée
- France
| | - R. Boulmene
- Université Paris-Est
- Laboratoire Modélisation et Simulation Multi Echelle
- MSME UMR 8208 CNRS
- 77454 Marne-la-Vallée
- France
| | - M. Prakash
- Université Paris-Est
- Laboratoire Modélisation et Simulation Multi Echelle
- MSME UMR 8208 CNRS
- 77454 Marne-la-Vallée
- France
| | - N. Komiha
- LS3ME-Equipe de Chimie Théorique et Modélisation
- Université Mohamed
- Faculté des Sciences
- Rabat
- Maroc
| | - M. Taleb
- Laboratoire LIMME
- Université Sidi Med Ben Abdellah
- Fac des Sciences Dhar El Mehrez
- Fès
- Maroc
| | - M. Mogren Al-Mogren
- Chemistry Department
- Faculty of Science
- King Saud University
- Riyadh 11451
- Kingdom of Saudi Arabia
| | - M. Hochlaf
- Université Paris-Est
- Laboratoire Modélisation et Simulation Multi Echelle
- MSME UMR 8208 CNRS
- 77454 Marne-la-Vallée
- France
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31
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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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32
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Kumar S, Singh SK, Calabrese C, Maris A, Melandri S, Das A. Structure of saligenin: microwave, UV and IR spectroscopy studies in a supersonic jet combined with quantum chemistry calculations. Phys Chem Chem Phys 2014; 16:17163-71. [DOI: 10.1039/c4cp01693a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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33
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Su P, Jiang Z, Chen Z, Wu W. Energy decomposition scheme based on the generalized Kohn-Sham scheme. J Phys Chem A 2014; 118:2531-42. [PMID: 24611964 DOI: 10.1021/jp500405s] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this paper, a new energy decomposition analysis scheme based on the generalized Kohn-Sham (GKS) and the localized molecular orbital energy decomposition analysis (LMO-EDA) scheme, named GKS-EDA, is proposed. The GKS-EDA scheme has a wide range of DFT functional adaptability compared to LMO-EDA. In the GKS-EDA scheme, the exchange, repulsion, and polarization terms are determined by DFT orbitals; the correlation term is defined as the difference of the GKS correlation energy from monomers to supermolecule. Using the new definition, the GKS-EDA scheme avoids the error of LMO-EDA which comes from the separated treatment of EX and EC functionals. The scheme can perform analysis both in the gas and in the condensed phases with most of the popular DFT functionals, including LDA, GGA, meta-GGA, hybrid GGA/meta-GGA, double hybrid, range-separated (long-range correction), and dispersion correction. By the GKS-EDA scheme, the DFT functionals assessment for hydrogen bonding, vdW interaction, symmetric radical cation, charge-transfer, and metal-ligand interaction is performed.
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Affiliation(s)
- Peifeng Su
- The State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University , Xiamen, Fujian 361005, China
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34
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Grant Hill J, Das A. Interaction in the indole⋯imidazole heterodimer: structure, Franck–Condon analysis and energy decomposition. Phys Chem Chem Phys 2014; 16:11754-62. [DOI: 10.1039/c4cp01360c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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35
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Adhikari U, Scheiner S. First steps in growth of a polypeptide toward β-sheet structure. J Phys Chem B 2013; 117:11575-83. [PMID: 24028425 DOI: 10.1021/jp406326h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The full conformational energy surface is examined for a molecule in which a dipeptide is attached to the same spacer group as another peptide chain, so as to model the seminal steps of β-sheet formation. This surface is compared with the geometrical preferences of the isolated dipeptide to extract the perturbations induced by interactions with the second peptide strand. These interpeptide interactions remove any tendency of the dipeptide to form a C5 ring structure, one of its two normally stable geometries. A C7 structure, the preferred conformation of the isolated dipeptide, remains as the global minimum in the full molecule. However, the stability of this structure is highly dependent upon interpeptide H-bonds with the second chain. The latter forces include not only the usual NH···O interaction, but also a pair of CH···O H-bonds. The secondary minimum is also of C7 type and likewise depends in part upon CH···O H-bonds for its stability. The latter interactions also play a part in the tertiary minimum. A two-strand β-sheet structure is not yet in evidence for this small model system, requiring additional peptide units to be added to each chain.
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Affiliation(s)
- Upendra Adhikari
- Department of Chemistry and Biochemistry, Utah State University , Logan, Utah 84322-0300, United States
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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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37
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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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Sasaki H, Daicho S, Yamada Y, Nibu Y. Comparable strength of OH-O versus OH-π hydrogen bonds in hydrogen-bonded 2,3-benzofuran clusters with water and methanol. J Phys Chem A 2013; 117:3183-9. [PMID: 23517236 DOI: 10.1021/jp400676x] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two different types of hydrogen bond, which are classified into a familiar OH-O and a relatively weak OH-π one, have been compared in the 1:1 hydrogen-bonded 2,3-benzofuran clusters with water and methanol molecules. By applying fluorescence-detected infrared spectroscopy and dispersed fluorescence spectroscopy, two isomers having different types of hydrogen bonds are distinguished. From the calculated stabilization energy as well as the frequency shift of the OH stretching vibration in each cluster, these two isomers are almost equally stable, although that of OH-π type is usually thought to be relatively weak. It is suggested that the origin of the weak OH-O hydrogen bond is derived from the lower availability for a hydrogen bond acceptor on the oxygen atom of a heteroaromatic ring, which is attributed to the larger furan aromaticity.
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Affiliation(s)
- Hiroko Sasaki
- Department of Chemistry, Graduate School of Science, Fukuoka University, Fukuoka 814-0180, Japan
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39
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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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Jaeqx S, Du W, Meijer EJ, Oomens J, Rijs AM. Conformational Study of Z-Glu-OH and Z-Arg-OH: Dispersion Interactions versus Conventional Hydrogen Bonding. J Phys Chem A 2012; 117:1216-27. [DOI: 10.1021/jp3053339] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Weina Du
- van’t
Hoff Institute
for Molecular Sciences and Amsterdam Center for Multiscale Modeling, University of Amsterdam, Science Park 904, 1098 XH
Amsterdam, The Netherlands
| | - Evert Jan Meijer
- van’t
Hoff Institute
for Molecular Sciences and Amsterdam Center for Multiscale Modeling, University of Amsterdam, Science Park 904, 1098 XH
Amsterdam, The Netherlands
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Sánchez-García E, Jansen G. Competition between H···π and H···O Interactions in Furan Heterodimers. J Phys Chem A 2012; 116:5689-97. [DOI: 10.1021/jp301710y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Elsa Sánchez-García
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1,
45470 Mülheim an der Ruhr, Germany
| | - Georg Jansen
- Theoretische Organische Chemie,
Fakultät für Chemie, Universität Duisburg-Essen, 47057 Duisburg, Germany
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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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