1
|
Kumar YB, Kumar N, John L, Mahanta HJ, Vaikundamani S, Nagamani S, Sastry GM, Sastry GN. Analyzing the cation-aromatic interactions in proteins: Cation-aromatic database V2.0. Proteins 2024; 92:179-191. [PMID: 37789571 DOI: 10.1002/prot.26600] [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: 06/22/2023] [Revised: 08/17/2023] [Accepted: 09/07/2023] [Indexed: 10/05/2023]
Abstract
The cation-aromatic database (CAD) is a comprehensive repository of cation-aromatic motifs found in experimentally determined protein structures, first reported in 2007 [Proteins, 2007, 67, 1179]. The present article is an update of CAD that contains information of approximately 27.26 million cation-aromatic motifs. CAD uses three distance parameters (r, d1, and d2) to determine the position of the cation relative to the centroid of the aromatic residue and classifies the motifs as cation-π or cation-σ interactions. As of June 2023, about 193 936 protein structures were retrieved from Protein Data Bank, and this resulted in the identification of an impressive number of 27 255 817 cation-aromatic motifs. Among these motifs, spherical motifs constituted 94.09%, while cylindrical motifs made up the remaining 5.91%. When considering the interaction of metal ions with aromatic residues, 965 564 motifs are identified. Remarkably, 82.08% of these motifs involved the binding of metal ions to the amino acid HIS. Moreover, the analysis of binding preferences between cations and aromatic residues revealed that the HIS-HIS, PHE-ARG, and TRP-ARG pairs exhibited a preferential geometry. The motif pair HIS-HIS was the most prevalent, accounting for 19.87% of the total, closely followed by TYR-LYS at 10.17%. Conversely, the motif pair TRP-HIS had the lowest occurrence, representing only 4.20% of the total. The data generated help in revealing the characteristics and biological functions of cation-aromatic interactions in biological molecules. The updated version of CAD (Cation-Aromatic Database V2.0) can be accessed at https://acds.neist.res.in/cadv2.
Collapse
Affiliation(s)
- Y Bhargav Kumar
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Nandan Kumar
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India
| | - Lijo John
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India
| | - Hridoy Jyoti Mahanta
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - S Vaikundamani
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India
| | - Selvaraman Nagamani
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | | | - G Narahari Sastry
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| |
Collapse
|
2
|
Bhargav Kumar Y, Kumar N, Narahari Sastry G. First-principles calculations on the micro-solvation of 3d-transition metal ions: solvation versus splitting water. Theor Chem Acc 2023. [DOI: 10.1007/s00214-023-02974-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
|
3
|
Electronic structures and ligand effect on redox potential of iron and cobalt complexes: a computational insight. Struct Chem 2023. [DOI: 10.1007/s11224-022-02119-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
|
4
|
Meyer KAE, Nickson KA, Garand E. The impact of the electric field of metal ions on the vibrations and internal hydrogen bond strength in alkali metal ion di- and triglycine complexes. J Chem Phys 2022; 157:174301. [DOI: 10.1063/5.0117311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Using infrared predissociation spectroscopy of cryogenic ions, we revisit the vibrational spectra of alkali metal ion (Li+, Na+, K+) di- and triglycine complexes. We assign their most stable conformation, which involves metal ion coordination to all C=O groups and an internal NH⋯NH2 hydrogen bond in the peptide backbone. An analysis of the spectral shifts of the OH and C=O stretching vibrations across the different metal ions and peptide chain lengths shows that these are largely caused by the electric field of the metal ion, which varies in strength as a function of the square of the distance. The metal ion–peptide interaction also remotely modulates the strength of internal hydrogen bonding in the peptide backbone via the weakening of the amide C=O bond, resulting in a decrease in internal hydrogen bond strength from Li+ > Na+ > K+.
Collapse
Affiliation(s)
- Katharina A. E. Meyer
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, Wisconsin 53706, USA
| | - Kathleen A. Nickson
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, Wisconsin 53706, USA
| | - Etienne Garand
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, Wisconsin 53706, USA
| |
Collapse
|
5
|
Kumar N, Kumar YB, Sarma H, Sastry GN. Fate of Sc-Ion Interaction With Water: A Computational Study to Address Splitting Water Versus Solvating Sc Ion. Front Chem 2021; 9:738852. [PMID: 34733820 PMCID: PMC8558820 DOI: 10.3389/fchem.2021.738852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 09/13/2021] [Indexed: 11/29/2022] Open
Abstract
An exhaustive study of Sc-ion interaction with water molecules in all its possible oxidation and spin states has been carried out to delineate the relative propensity of Sc ions toward solvation and water splitting. Potential energy surface analysis of the Sc-ion reaction with water molecules, topological analysis of bonds, and the effect of sequential solvation up to 6 water molecules have been examined. Calculated values showed good agreement with the available experimental results. Close-shell systems such as singlet mono- and tricationic Sc ions prefer to split the water molecules. In contrast, the open-shell systems such as triplet mono- and doublet dicationic Sc ions prefer to get solvated than split the water molecule. Topological analysis of electron density predicted the Sc+/2+–water bond as a noncovalent bond while Sc3+–OH2, Sc2+–OH, and Sc+–H bonds as partially covalent in nature. Energy decomposition analysis revealed that Sc ion–water interactions are driven by electrostatic energy followed by polarization energy. The current study reveals that transition metal catalysis can be one of the most effective tools to employ in water splitting, by properly tuning the electrons, spin, and ligands around the catalytic center.
Collapse
Affiliation(s)
- Nandan Kumar
- Centre for Molecular Modelling, CSIR-Indian Institute of Chemical Technology, Hyderabad, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Y Bhargav Kumar
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.,Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, India
| | - Himakshi Sarma
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, India
| | - G Narahari Sastry
- Centre for Molecular Modelling, CSIR-Indian Institute of Chemical Technology, Hyderabad, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.,Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, India
| |
Collapse
|
6
|
|
7
|
Cox CS, Cossich Galicia V, Lessio M. Computational Investigation of Adsorptive Removal of Pb. Aust J Chem 2021. [DOI: 10.1071/ch21139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Adsorption using metal–organic frameworks (MOFs) such as UiO-66 has shown great promise in remediating water sources contaminated with toxic heavy metals such as Pb2+, but detailed information about the adsorption process remains limited. In this article, we gained mechanistic insights into Pb2+ adsorption using both functionalised and defective UiO-66 by performing density functional theory calculations using cluster models. Our benchmarked approach led to a computational model of solvated Pb2+ (a hemidirected Pb(H2O)62+ complex) fully consistent with experimental reports. The analysis of Pb2+ adsorption using functionalised UiO-66 determined that factors such as electrostatic attraction, chelation, and limited constraints on the Pb2+ coordination geometry lead to enhanced binding affinity. For these reasons, UiO-66-COO– was identified as the most promising functionalised MOF, consistent with experimental literature. We additionally explored a novel aspect of Pb2+ adsorption by UiO-66: the role of missing linker defects that often characterise this MOF. We found that the defects expected to form in an aqueous environment can act as excellent adsorption sites for Pb2+ and the preferred adsorption geometry is again determined by electrostatic attraction, chelation, and constraints on the Pb2+ coordination geometry. Overall, we conclude that functional groups and defect sites can both contribute to Pb2+ adsorption and our study provides crucial design principles for improving the UiO-66 MOF performance in toxic Pb2+ removal from water.
Collapse
|
8
|
Kumar N, Saha S, Sastry GN. Towards developing a criterion to characterize non-covalent bonds: a quantum mechanical study. Phys Chem Chem Phys 2021; 23:8478-8488. [DOI: 10.1039/d0cp05689h] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Chemical bonds are central to chemistry, biology, and allied fields, but still, the criterion to characterize an interaction as a non-covalent bond has not been studied rigorously.
Collapse
Affiliation(s)
- Nandan Kumar
- Centre for Molecular Modeling
- CSIR-Indian Institute of Chemical Technology
- Hyderabad 500007
- India
- Academy of Scientific and Innovative Research (AcSIR)
| | - Soumen Saha
- Centre for Molecular Modeling
- CSIR-Indian Institute of Chemical Technology
- Hyderabad 500007
- India
- Nagoya University
| | - G. Narahari Sastry
- Centre for Molecular Modeling
- CSIR-Indian Institute of Chemical Technology
- Hyderabad 500007
- India
- Academy of Scientific and Innovative Research (AcSIR)
| |
Collapse
|
9
|
Dixit VA, Warwicker J, Visser SP. How Do Metal Ions Modulate the Rate‐Determining Electron‐Transfer Step in Cytochrome P450 Reactions? Chemistry 2020; 26:15270-15281. [DOI: 10.1002/chem.202003024] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Vaibhav A. Dixit
- Department of Pharmacy Birla Institute of Technology and Sciences Pilani (BITS-Pilani) Vidya Vihar Campus 41 Pilani 333031 Rajasthan India
| | - Jim Warwicker
- Manchester Institute of Biotechnology The University of Manchester 131 Princess Street Manchester M17DN United Kingdom
- Department of Chemistry The University of Manchester Oxford Road Manchester M139PL United Kingdom
| | - Sam P. Visser
- Manchester Institute of Biotechnology The University of Manchester 131 Princess Street Manchester M17DN United Kingdom
- Department of Chemical Engineering and Analytical Science The University of Manchester Oxford Road Manchester M13 9PL United Kingdom
| |
Collapse
|
10
|
Blagojevic V, Lavrov VV, Koyanagi GK, Bohme DK. Ligation kinetics as a probe for gas-phase ligand field effects: Ligation of atomic transition metal cations with ammonia at room temperature. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2019; 25:44-49. [PMID: 30773917 DOI: 10.1177/1469066718800844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The kinetics of ammonia ligation to atomic first and second row transition metal cations were measured in an attempt to assess the role of ligand field effects in gas-phase ion-molecule reaction kinetics. Measurements were performed at 295 ± 2 K in helium bath gas at 0.35 Torr using an inductively coupled plasma/selected-ion flow tube tandem mass spectrometer. The atomic cations were produced at ca. 5500 K in an inductively coupled plasma source and were allowed to decay radiatively and to thermalize by collisions with argon and helium atoms prior to reaction. A strong correlation was observed across the periodic table between the measured rate coefficients for ammonia ligation and measured/calculated bond dissociation energies. A similar strong correlation is seen with the ligand field stabilization energy. So ligand field stabilization energies should provide a useful predictor of relative rates of ligation of atomic metal ions.
Collapse
Affiliation(s)
- Voislav Blagojevic
- Department of Chemistry, Centre for Research in Mass Spectrometry and Centre for Research in Earth and Space Science, York University, Toronto, Canada
| | - Vitali V Lavrov
- Department of Chemistry, Centre for Research in Mass Spectrometry and Centre for Research in Earth and Space Science, York University, Toronto, Canada
| | - Gregory K Koyanagi
- Department of Chemistry, Centre for Research in Mass Spectrometry and Centre for Research in Earth and Space Science, York University, Toronto, Canada
| | - Diethard K Bohme
- Department of Chemistry, Centre for Research in Mass Spectrometry and Centre for Research in Earth and Space Science, York University, Toronto, Canada
| |
Collapse
|
11
|
|
12
|
Chakraborty P, Baksi A, Mudedla SK, Nag A, Paramasivam G, Subramanian V, Pradeep T. Understanding proton capture and cation-induced dimerization of [Ag29(BDT)12]3−clusters by ion mobility mass spectrometry. Phys Chem Chem Phys 2018; 20:7593-7603. [DOI: 10.1039/c7cp08181b] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We present a unique reaction of [Ag29(BDT)12]3−cluster with protons and dimerization of the cluster induced by alkali metal ions.
Collapse
Affiliation(s)
- Papri Chakraborty
- DST Unit of Nanoscience (DST UNS) and Thematic Unit of Excellence, Department of Chemistry, Indian Institute of Technology Madras
- Chennai 600036
- India
| | - Ananya Baksi
- DST Unit of Nanoscience (DST UNS) and Thematic Unit of Excellence, Department of Chemistry, Indian Institute of Technology Madras
- Chennai 600036
- India
| | | | - Abhijit Nag
- DST Unit of Nanoscience (DST UNS) and Thematic Unit of Excellence, Department of Chemistry, Indian Institute of Technology Madras
- Chennai 600036
- India
| | - Ganesan Paramasivam
- DST Unit of Nanoscience (DST UNS) and Thematic Unit of Excellence, Department of Chemistry, Indian Institute of Technology Madras
- Chennai 600036
- India
| | | | - Thalappil Pradeep
- DST Unit of Nanoscience (DST UNS) and Thematic Unit of Excellence, Department of Chemistry, Indian Institute of Technology Madras
- Chennai 600036
- India
| |
Collapse
|
13
|
Hou JH, Wu D, Liu JY, Li SY, Yu D, Li Y. The effect of hydration on the electronic structure and stability of the superalkali cation Li3+. Phys Chem Chem Phys 2018; 20:15174-15182. [DOI: 10.1039/c8cp00862k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Insights into the interaction between the superalkali cation Li3+ and water molecules and the stability of the resulting hydrates.
Collapse
Affiliation(s)
- Jia-Huan Hou
- Laboratory of Theoretical and Computational Chemistry
- Institute of Theoretical Chemistry
- Jilin University
- Changchun 130023
- P. R. China
| | - Di Wu
- Laboratory of Theoretical and Computational Chemistry
- Institute of Theoretical Chemistry
- Jilin University
- Changchun 130023
- P. R. China
| | - Jia-Yuan Liu
- Laboratory of Theoretical and Computational Chemistry
- Institute of Theoretical Chemistry
- Jilin University
- Changchun 130023
- P. R. China
| | - Si-Yi Li
- Laboratory of Theoretical and Computational Chemistry
- Institute of Theoretical Chemistry
- Jilin University
- Changchun 130023
- P. R. China
| | - Dan Yu
- Laboratory of Theoretical and Computational Chemistry
- Institute of Theoretical Chemistry
- Jilin University
- Changchun 130023
- P. R. China
| | - Ying Li
- Laboratory of Theoretical and Computational Chemistry
- Institute of Theoretical Chemistry
- Jilin University
- Changchun 130023
- P. R. China
| |
Collapse
|
14
|
Bhattacharyya PK. Exploring Cation−π Interaction in the Complexes with B≡B Triple Bond: A DFT Study. J Phys Chem A 2017; 121:3287-3298. [DOI: 10.1021/acs.jpca.7b01326] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
15
|
Sarma D, Saha B, Chandra Deka B, Bhattacharyya PK. Unique cation–cyclohexane interactions in tri- and hexa-fluorocyclohexane multidecker complexes in the gas phase: a DFT study. RSC Adv 2016. [DOI: 10.1039/c6ra24508k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The formation of stable sandwich and multidecker complexes through electrostatic interaction in tri- and hexa-fluorocyclohexane has been analyzed in the light of density functional theory.
Collapse
Affiliation(s)
| | - Bapan Saha
- Department of Chemistry
- Arya Vidyapeeth College
- Guwahati
- India
| | | | | |
Collapse
|