1
|
Zhang D, Kishimoto N. Theoretical Analysis of Coordination Geometries in Transition Metal-Histidine Complexes Using Quantum Chemical Calculations. Molecules 2024; 29:3003. [PMID: 38998956 PMCID: PMC11243457 DOI: 10.3390/molecules29133003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 06/13/2024] [Accepted: 06/22/2024] [Indexed: 07/14/2024] Open
Abstract
A theoretical investigation utilizing density functional theory (DFT) calculations was conducted to explore the coordination complexes formed between histidine (His) ligands and various divalent transition metal ions (Mn2+, Fe2+, Co2+, Ni2+, Cu2+, and Zn2+). Conformational exploration of the His ligand was initially performed to assess its stability upon coordination. Both 1:1 and 1:2 of metal-to-ligand complexes were scrutinized to elucidate their structural features and the relative stability of the complexes. This study examined the ability of His to act as a bidentate or tridentate coordinating ligand, along with the differences in coordination geometry when solvent effects were incorporated. The reduced density gradient (RDG) analysis and local electron attachment energy (LEAE) analysis were employed to elucidate the interaction planes and the nucleophilic and electrophilic properties. The electronic properties were analyzed through electrostatic potential (ESP) maps and natural population analysis (NPA) of atomic charge distributions. This computational study provides valuable insights into the diverse coordination modes of His and its interactions with divalent transition metal ions, contributing to a better understanding of the role of this amino acid ligand in the formation of transition metal complexes. The findings can aid in the design and construction of self-assembled structures involving His-metal coordination.
Collapse
Affiliation(s)
- Dapeng Zhang
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Naoki Kishimoto
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| |
Collapse
|
2
|
Boulesteix D, Buch A, Samson J, Millan M, Jomaa J, Coscia D, Moulay V, McIntosh O, Freissinet C, Stern JC, Szopa C. Influence of pH and salts on DMF-DMA derivatization for future Space Applications. Anal Chim Acta 2023; 1266:341270. [PMID: 37244655 DOI: 10.1016/j.aca.2023.341270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/24/2023] [Accepted: 04/23/2023] [Indexed: 05/29/2023]
Abstract
For gas chromatography - mass spectrometry (GC-MS) analyses performed in situ, pH and salts (e.g., chlorides, sulfates) may enhance or inhibit the detection of targeted molecules of interest for astrobiology (e.g. amino acids, fatty acids, nucleobases). Obviously, salts influence the ionic strength of the solutions, the pH value, and the salting effect. But the presence of salts may also produce complexes or mask ions in the sample (masking effect on hydroxide ion, ammonia, etc.). For future space missions, wet chemistry will be conducted before GC-MS analyses to detect the full organic content of a sample. The defined organic targets for space GC-MS instrument requirements are generally strongly polar or refractory organic compounds, such as amino acids playing a role in the protein production and metabolism regulations for life on Earth, nucleobases essential for DNA and RNA formation and mutation, and fatty acids that composed most of the eukaryote and prokaryote membranes on Earth and resist to environmental stress long enough to still be observed on Mars or ocean worlds in geological well-preserved records. The wet-chemistry chemical treatment consists of reacting an organic reagent with the sample to extract and volatilize polar or refractory organic molecules (i.e. dimethylformamide dimethyl acetal (DMF-DMA) in this study). DMF-DMA derivatizes functional groups with labile H in organics, without modifying their chiral conformation. The influence of pH and salt concentration of extraterrestrial materials on the DMF-DMA derivatization remains understudied. In this research, we studied the influence of different salts and pHs on the derivatization of organic molecules of astrobiological interest with DMF-DMA, such as amino acids, carboxylic acids, and nucleobases. Results show that salts and pH influence the derivatization yield, and that their effect depend on the nature of the organics and the salts studied. Second, monovalent salts lead to a higher or similar organic recovery compared to divalent salts regardless of pH below 8. However, a pH above 8 inhibits the DMF-DMA derivatization influencing the carboxylic acid function to become an anionic group without labile H. Overall, considering the negative effect of the salts on the detection of organic molecules, future space missions may have to consider a desalting step prior to derivatization and GC-MS analyses.
Collapse
Affiliation(s)
- D Boulesteix
- Laboratoire Génie des Procédés et Matériaux, CentraleSupélec, University Paris-Saclay, 8-10 Rue Joliot-Curie, 91190, Gif-sur-Yvette, France.
| | - A Buch
- Laboratoire Génie des Procédés et Matériaux, CentraleSupélec, University Paris-Saclay, 8-10 Rue Joliot-Curie, 91190, Gif-sur-Yvette, France.
| | - J Samson
- Laboratoire Génie des Procédés et Matériaux, CentraleSupélec, University Paris-Saclay, 8-10 Rue Joliot-Curie, 91190, Gif-sur-Yvette, France
| | - M Millan
- LATMOS/IPSL, UVSQ University Paris-Saclay, Sorbonne University, CNRS, 11 Bd d'Alembert, 78280, Guyancourt, France
| | - J Jomaa
- Planetary Environments Laboratory (Code 699), NASA Goddard Space Flight Center, Greenbelt, MD, 20771, USA; School of Medicine, Wayne State University, 42 W. Warren Ave, Detroit, MI, 48202, USA
| | - D Coscia
- LATMOS/IPSL, UVSQ University Paris-Saclay, Sorbonne University, CNRS, 11 Bd d'Alembert, 78280, Guyancourt, France
| | - V Moulay
- LATMOS/IPSL, UVSQ University Paris-Saclay, Sorbonne University, CNRS, 11 Bd d'Alembert, 78280, Guyancourt, France
| | - O McIntosh
- LATMOS/IPSL, UVSQ University Paris-Saclay, Sorbonne University, CNRS, 11 Bd d'Alembert, 78280, Guyancourt, France
| | - C Freissinet
- LATMOS/IPSL, UVSQ University Paris-Saclay, Sorbonne University, CNRS, 11 Bd d'Alembert, 78280, Guyancourt, France
| | - J C Stern
- Space Science Exploration Division (Code 690), NASA, Goddard Space Flight Center, Greenbelt, MD, 20771, USA
| | - C Szopa
- LATMOS/IPSL, UVSQ University Paris-Saclay, Sorbonne University, CNRS, 11 Bd d'Alembert, 78280, Guyancourt, France
| |
Collapse
|
3
|
Mononuclear half-sandwich nd 7 metallo drug complexes based on bidentate N∩N dendritic scaffolds: DFT (B3LYP; BP86 and B3PW91) examination. J Mol Graph Model 2023; 120:108417. [PMID: 36706572 DOI: 10.1016/j.jmgm.2023.108417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 01/04/2023] [Accepted: 01/13/2023] [Indexed: 01/24/2023]
Abstract
Through an use of three functionals (B3PW91, B3LYP and BP86) associated to a generic basis set LanL2DZ for transition metals (as well as halogen atoms) and 6-311+G (d,p) for others atoms, an examination of the bonding properties of a series of mononuclear half-sandwich nd7 transition metal (anticancer) complexes based on N∩N dendritic scaffolds (L) has been done. Collectively, complexes studied have adopted the piano-stool environment. An examination of the performance of each functional has shown that for the most reliable geometrical analysis of Metal-Nitrogen and Metal-Halogen bonds, the B3LYP and B3PW91 functionalities are suitable respectively. Regardless of the halogen ligand adopted, the B3LYP metal-nitrogen bond lengths are the most widely overestimated. A correlation has been built between the retained charge on each divalent transition metal cation and its metal ion affinity (MIA). Topological examinations reveal the higher instability of metal-N bonds compared to metal-X ones (X = Cl and Br). By the mean of the energy decomposition analysis, a predominant electrostatic character of metal … halogen and [LCP]- … [MX]+ interaction has been demonstrated. The transition metal atom … (hydrophobic) surface (Cp*) interaction is most pronounced for the chloride rhodium complexes of rhodium (combined with (E)-N-(pyridin-2-ylmethylene) Propan-1-amine and 2,2'- dipyridylketone ligands and iridium combined with 2,2'- dipyridylketone ligand. The charge decomposition analysis displays the weakening of the [Formula: see text] bonds in the studied complexes.
Collapse
|
4
|
Anitha S, Selvapriya R, Shankar R, Nalini B, Sasirekha V, Mayandi J. Evidence of charge donation through synergistic effect of bioconjugated silver nanoparticles with flavanols accomplishing augmented antimicrobial and antioxidant activities. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
5
|
Advanced hydrogen adsorption on benzene: Cation-π interaction effects. Chem Phys 2022. [DOI: 10.1016/j.chemphys.2022.111649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
6
|
Lu L, Li RZ, Xu XY. Interaction of Cysteine with Li + and LiF in the Presence of (H 2O) n ( n = 0-6) Clusters. ACS OMEGA 2022; 7:18646-18659. [PMID: 35694486 PMCID: PMC9178773 DOI: 10.1021/acsomega.2c01315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
The interaction between cysteine with Li+ and LiF in the microcosmic water environment was investigated to elucidate how ions interact with amino acids and the cation-anion correlation effect involved. The structures of Cys·Li+(H2O) n and Cys·LiF(H2O) n (n = 0-6) were characterized using ab initio calculations. Our studies show that the water preferentially interacts with Li+/LiF. In Cys·Li+(H2O)0-6, Li+ interacts with amino nitrogen, carbonyl oxygen, and hydrophobic sulfur of Cys to form a tridentate mode, whereas in Cys·LiF(H2O) n , Li+ and F- work in cooperation and interact with carbonyl oxygen and hydroxyl hydrogen of Cys to form a bidentate type. The neutral and zwitterionic forms are essentially isoenergetic when the water number reaches three in the presence of Li+, whereas this occurs at four water molecules in the presence of LiF. Further research revealed that the interaction between Li+/LiF and Cys was mainly electrostatic, followed by dispersion, and the weakest interaction occurs at the transition from the neutral form to zwitterionic form. Natural population analysis charge analyses show that for Cys·Li+(H2O) n , the positive charge is mostly concentrated on Li+ except for the system containing three water molecules. For Cys·LiF(H2O) n , the positive charge is centered on the LiF unit in the range n = 0-6, and at n = 5, electron transfer from Cys to water occurs. Our study shows that the contribution of anions in zwitterionic state stabilization should be addressed more generally along with cations.
Collapse
|
7
|
Liu X, Wu M, Li C, Yu P, Feng S, Li Y, Zhang Q. Interaction Structure and Affinity of Zwitterionic Amino Acids with Important Metal Cations (Cd 2+, Cu 2+, Fe 3+, Hg 2+, Mn 2+, Ni 2+ and Zn 2+) in Aqueous Solution: A Theoretical Study. Molecules 2022; 27:molecules27082407. [PMID: 35458605 PMCID: PMC9028192 DOI: 10.3390/molecules27082407] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/31/2022] [Accepted: 04/06/2022] [Indexed: 01/25/2023] Open
Abstract
Heavy metals are non-biodegradable and carcinogenic pollutants with great bio-accumulation potential. Their ubiquitous occurrence in water and soils has caused serious environmental concerns. Effective strategies that can eliminate the heavy metal pollution are urgently needed. Here the adsorption potential of seven heavy metal cations (Cd2+, Cu2+, Fe3+, Hg2+, Mn2+, Ni2+ and Zn2+) with 20 amino acids was systematically investigated with Density Functional Theory method. The binding energies calculated at B3LYP-D3/def2TZVP level showed that the contribution order of amino acid side chains to the binding affinity was carboxyl > benzene ring > hydroxyl > sulfhydryl > amino group. The affinity order was inversely proportional to the radius and charge transfer of heavy metal cations, approximately following the order of: Ni2+ > Fe3+ > Cu2+ > Hg2+ > Zn2+ > Cd2+ > Mn2+. Compared to the gas-phase in other researches, the water environment has a significant influence on structures and binding energies of the heavy metal and amino acid binary complexes. Collectively, the present results will provide a basis for the design of a chelating agent (e.g., adding carboxyl or a benzene ring) to effectively remove heavy metals from the environment.
Collapse
Affiliation(s)
- Xinning Liu
- Environment Research Institute, Shandong University, Qingdao 266237, China; (X.L.); (Q.Z.)
| | - Menghan Wu
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China; (M.W.); (P.Y.)
| | - Chenchen Li
- School of Management, Ocean University of China, Qingdao 266101, China;
| | - Peng Yu
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China; (M.W.); (P.Y.)
| | - Shanshan Feng
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China;
| | - Yanwei Li
- Environment Research Institute, Shandong University, Qingdao 266237, China; (X.L.); (Q.Z.)
- Shenzhen Research Institute, Shandong University, Shenzhen 518057, China
- Correspondence: ; Tel.: +86-0532-58631990
| | - Qingzhu Zhang
- Environment Research Institute, Shandong University, Qingdao 266237, China; (X.L.); (Q.Z.)
| |
Collapse
|
8
|
Shi Y, Liao X, Chen R, Ge Q. pH-Responsive Polyoxometalates that Achieve Efficient Wastewater Reclamation and Source Recovery via Forward Osmosis. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:12664-12671. [PMID: 34494436 DOI: 10.1021/acs.est.1c04245] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Forward osmosis (FO) has been increasingly used for water treatment. However, the lack of suitable draw solutes impedes its further development. Herein, we design pH-responsive polyoxometalates, that is, (NH4)6Mo7O24 and Na6Mo7O24, as draw solutes for simultaneous water reclamation and resource recovery from wastewater via FO. Both polyoxometalates have a cage-like configuration and release multiple ionic species in water. These characteristics allow them to generate high osmotic pressures to drive the FO separation efficiently with negligible reverse solute diffusion. (NH4)6Mo7O24 and Na6Mo7O24 at a dilute concentration (0.4 M) produce water fluxes of 16.4 LMH and 14.2 LMH, respectively, against DI water, outperforming the frequently used commercial NaCl and NH4HCO3 draw solutes, and other synthetic materials. With an average water flux of 10.0 LMH, (NH4)6Mo7O24 reclaims water from the simulated glutathione-containing wastewater more efficiently than Na6Mo7O24 (9.1 LMH), NaCl (3.3 LMH), and NH4HCO3 (5.6 LMH). The final glutathione treated with (NH4)6Mo7O24 and Na6Mo7O24 remains intact but that treated with NaCl and NH4HCO3 is either denatured or contaminated owing to their severe leakage in FO. Remarkably, both polyoxometalates are readily recycled by pH regulation and reused for FO. Polyoxometalate is thus proven to be an appropriate candidate for FO separation in wastewater reclamation and resource recovery.
Collapse
Affiliation(s)
- Yiru Shi
- College of Environment and Safety Engineering, Fuzhou University, No. 2 Xueyuan Road, Fuzhou, Fujian 350116, China
| | - Xialu Liao
- College of Environment and Safety Engineering, Fuzhou University, No. 2 Xueyuan Road, Fuzhou, Fujian 350116, China
| | - Rongzhen Chen
- College of Environment and Safety Engineering, Fuzhou University, No. 2 Xueyuan Road, Fuzhou, Fujian 350116, China
| | - Qingchun Ge
- College of Environment and Safety Engineering, Fuzhou University, No. 2 Xueyuan Road, Fuzhou, Fujian 350116, China
| |
Collapse
|
9
|
Ji B, Yi G, Gui Y, Zhang J, Long W, You M, Xia Z, Fu Q. High-Efficiency and Versatile Approach To Fabricate Diverse Metal-Organic Framework Coatings on a Support Surface as Stationary Phases for Electrochromatographic Separation. ACS APPLIED MATERIALS & INTERFACES 2021; 13:41075-41083. [PMID: 34420301 DOI: 10.1021/acsami.1c10481] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
A large number of metal-organic frameworks (MOFs) have exhibited increasingly wide utilization in the field of chromatographic separation owing to their intrinsic fascinating properties. However, the previous studies on supported MOF coating-based chromatographic separation focused only on the synthesis and chromatographic performance of a certain kind of supported MOF coatings as stationary phases using the multiple-step, complicated, and time-consuming modification methods, which severely impeded the widespread application of MOFs in separation science. Herein, a high-efficiency and versatile methodology toward diverse supported MOF coating-based stationary phases to achieve high-efficiency chromatographic separation was first reported based on the immobilized cysteine (Cys)-triggered in situ growth (ICISG) strategy. As a proof-of-concept demonstration, four types of MOF crystals consisting of different ligands and metal ions (Zn2+, Cu2+, Fe3+, and Zr4+) were conveniently and firmly grown on a Cys-modified capillary using the ICISG strategy and employed as the functional stationary phase for electrochromatographic separation. A broad variety of neutral, acidic, and basic compounds were all separated in a highly efficient manner on the developed four MOF-coated columns. The maximum theoretical plate number for Cys-MIL-100(Fe)@capillary was close to 1.0 × 105 plates/m, and the intraday, interday, and column-to-column repeatabilities of retention times for the four MOF-modified columns were all less than 5.25%. More interestingly, the diversified separation performance of the developed MOF-coated columns indicated that the preparation strategy and the skeletal structure of the MOF coating-based stationary phases have a significant influence on the electrochromatographic separation performance and column capacity. Benefiting from the strong universality and high applicability of the developed ICISG strategy, the present study provides an effective route to facilitate the design and fabrication of novel functional MOF-based chromatographic stationary phases.
Collapse
Affiliation(s)
- Baian Ji
- School of Pharmacy, Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Gaoyi Yi
- School of Pharmacy, Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Yuanqi Gui
- School of Pharmacy, Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Jiale Zhang
- School of Pharmacy, Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Wenwen Long
- School of Pharmacy, Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Mingyue You
- School of Pharmacy, Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Zhining Xia
- School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Qifeng Fu
- School of Pharmacy, Southwest Medical University, Luzhou, Sichuan 646000, China
| |
Collapse
|
10
|
Wang M, Akamatsu H, Dabo I, Sasaki K. Environmental impact of amino acids on the release of selenate immobilized in hydrotalcite: Integrated interpretation of experimental and density-functional theory study. CHEMOSPHERE 2021; 274:129927. [PMID: 33979939 DOI: 10.1016/j.chemosphere.2021.129927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/26/2021] [Accepted: 02/07/2021] [Indexed: 06/12/2023]
Abstract
The environmental impact of amino acids on the release of SeO42- immobilized into hydrotalcite (Mg2Al-LDH) which belongs to the layered double hydroxides (LDHs) family was investigated by experimental study and the observed layer structure of hydrotalcite was verified through density-functional theory (DFT) calculations. Glycine, l-cysteine, and l-aspartic acid, which have smaller molecular sizes, can release SeO42- largely due to intercalation, unstabilization of Mg2Al-LDH and simple dissolution, while l-tryptophan and l-phenylalanine caused limited SeO42- release due to their larger sizes and aromaticity. XRD patterns for the solid residues after intercalation of amino acids revealed that the layer distance of Mg2Al-LDH was partially expanded. The main peaks and shoulder features corresponding to d003 diffraction were well explained by DFT simulations using glycine as a model: the layer spacing of the main peak is responsible for the remaining SeO42- and singly stacked glycine molecule and the layer spacing of the shoulder peak was well explained by doubly stacked glycine molecules. Hydrogen bonds between amino acids and hydroxyl ions in the metallic layers of Mg2Al-LDH were responsible for the stable configuration of the intercalated Mg2Al-LDH. This study indicates potential limitations to the stability of low-level radioactive wastes of 79Se in repositories which are affected by smaller molecules of amino acids released through degradation of organic matters in the pedosphere.
Collapse
Affiliation(s)
- Mengmeng Wang
- Department of Earth Resources Engineering, Kyushu University, Fukuoka, 819-0395, Japan.
| | - Hirofumi Akamatsu
- Department of Applied Chemistry, Kyushu University, Fukuoka, 819-0395, Japan.
| | - Ismaila Dabo
- Department of Materials Science and Engineering, The Pennsylvania State University, University Park, PA, 16802, United States.
| | - Keiko Sasaki
- Department of Earth Resources Engineering, Kyushu University, Fukuoka, 819-0395, Japan.
| |
Collapse
|
11
|
Taylor C, Schönberger N, Laníková A, Patzschke M, Drobot B, Žídek L, Lederer F. Investigation of the structure and dynamics of gallium binding to high-affinity peptides elucidated by multi-scale simulation, quantum chemistry, NMR and ITC. Phys Chem Chem Phys 2021; 23:8618-8632. [PMID: 33876023 DOI: 10.1039/d1cp00356a] [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
Gallium (as Ga3+) is a Group IIIa metal and its recovery from wastewaters has become increasingly important for its reuse. The use of peptides for recycling offers a low-cost and environmentally-friendly option but the structural characteristics of peptides likely to bind Ga3+ are largely unknown. Multiple computational methods, coupled with experimental verification via NMR and Isothermal Calorimetry (ITC), were used to establish that Ga3+ binds with high affinity to peptide sequences and to elucidate the structural characteristics that contributed. It was demonstrated that peptide pre-organisation is key to Ga3+ binding and that a favourable binding position is necessarily governed by the size and shape of the electrostatic environment as much as individual electrostatic interactions with peptide residues themselves. Given favourable conditions, Ga3+ retrieved plausible binding positions involving both charged and uncharged residues that greatly increases the range of bonding possibilities with other peptide sequences and offers insights for binding other metals. The addition of pH buffer substantially improved the affinity of Ga3+ and a structural role for a buffer component was demonstrated.
Collapse
Affiliation(s)
- Corey Taylor
- Department of Chemistry of the f-elements, Institute of Resource Ecology (IRE), Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany.
| | | | | | | | | | | | | |
Collapse
|
12
|
Tong C, Shi F, Tong X, Shi S, Ali I, Guo Y. Shining natural flavonols in sensing and bioimaging. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116222] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
13
|
Simon Claude NN, Didier TFA, Baruch AA, Joseph ZM, Luc MM, Désiré BM. DFT/B3LYP and BP86 examination of mononuclear half-sandwich nd 7 metallo drug complexes based on N∩O dendritic scaffolds. J Mol Graph Model 2021; 104:107830. [PMID: 33444980 DOI: 10.1016/j.jmgm.2020.107830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/25/2020] [Accepted: 12/28/2020] [Indexed: 11/25/2022]
Abstract
In this paper, we have explored the bonding properties of a series of mononuclear half-sandwich nd7 anticancer complexes based on N∩O dendritic scaffolds (L) using two functionals (B3LYP and BP86) with generic basis set (LanL2DZ for transition metals (as well as halogen atoms) and 6-311 + G (d,p) for others atoms. The geometry optimization of structures have led to the adoption of the piano-stool environment and the formation of kings of intermolecular hydrogen bonding: CH … X (Cl,Br) (2.619-2.954) and CH...O (2.266-2.973 Å) interaction. The metal (M)-bromine bond distances have shown to be significantly higher than metal-chlorine ones. In chloride complexes, salicylaldimine ligand-Co2+ (-3097.15 kJ/mol) and salicylaldimine ligand-Ir2+ (-3436.78 kJ/mol) interactions are stronger. Except for cobalt complexes, the interaction energies are underestimated by B3LYP functional, by contrast B3LYP HOMO-LUMO gaps obtained are highly greater. The metal ion affinity (MIA) is increasing in the order: Ir+2<Rh+2<Co+2 for both halogen ligands adopted, exception for picolinate and salicylaldimine ligands. Our results also show that the metal … oxygen, metal … nitrogen and metal … halogen interactions are closed-shell interaction. From the contribution of the ΔEorb term in the ranges 4.06-98.61% (X = Cl) and 10.29-99.87% (X = Br), the nature of the [Formula: see text] … X- interaction turned out to be mainly dependent on the transition metal and halogen atom involved. The smallest back-donation observed for chloride complexes corresponding to the highest barrier to the formation of [MLCP∗]-X bond traduces that the fact that chloride complexes are the least reactive. In the majority of cases, larger donation is obtained compared to back-donation showing that the possibility of [Formula: see text] [Formula: see text] charge separation can be expected. For α rings of chloride complexes, B3LYP HOMA indexes are higher than those estimated by PB86 functional. Conversely, opposite results were found for their bromide counterparts.
Collapse
Affiliation(s)
- Ndika Ngomb Simon Claude
- Department of Chemistry, Faculty of Science, University of Douala, P.O. Box 24157, Douala, Cameroon
| | - Tamafo Fouegue Aymard Didier
- Department of Chemistry, Higher Teacher Training College Bertoua, University of Ngaoundere, P.O Box. 652, Bertoua, Cameroon
| | - Ateba Amana Baruch
- Department of Chemistry, Faculty of Science, University of Douala, P.O. Box 24157, Douala, Cameroon
| | - Zobo Mfomo Joseph
- Department of Forestry and Wood Engineering, University of Douala, Advanced Training College for Technical Education, Douala, Cameroon
| | - Mbaze Meva'a Luc
- Department of Chemistry, Faculty of Science, University of Douala, P.O. Box 24157, Douala, Cameroon
| | - Bikele Mama Désiré
- Department of Chemistry, Faculty of Science, University of Douala, P.O. Box 24157, Douala, Cameroon.
| |
Collapse
|
14
|
Petrushenko I, Shipitsin N, Petrushenko K. Cation-π interactions of inorganic benzenes with Li, Na, and Mg cations: Theoretical insights. INORG CHEM COMMUN 2020. [DOI: 10.1016/j.inoche.2020.108043] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
15
|
Interaction of (G4)2 and (X4)2 DNA quadruplexes with Cu+, Ag+ and Au+ metal cations: a quantum chemical calculation on structural, energetic and electronic properties. Struct Chem 2019. [DOI: 10.1007/s11224-019-01421-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
16
|
Pitchumani Violet Mary C, Shankar R, Vijayakumar S. Theoretical insights into the metal chelating and antimicrobial properties of the chalcone based Schiff bases. MOLECULAR SIMULATION 2019. [DOI: 10.1080/08927022.2019.1573370] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
| | - R. Shankar
- Department of Physics, Bharathiar University, Coimbatore, India
| | - S. Vijayakumar
- Department of Medical Physics, Bharathiar University, Coimbatore, India
| |
Collapse
|
17
|
Saranya V, Shankar R, Vijayakumar S. Structural exploration of viral matrix protein 40 interaction with the transition metal ions (Ag+ and Cu2+). J Biomol Struct Dyn 2018; 37:2875-2896. [DOI: 10.1080/07391102.2018.1498803] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- V. Saranya
- Department of Physics, Bharathiar University, Coimbatore, India
| | - R. Shankar
- Department of Physics, Bharathiar University, Coimbatore, India
| | - S. Vijayakumar
- Department of Medical Physics, Bharathiar University, Coimbatore, India
| |
Collapse
|
18
|
Subashini G, Saravanan A, Shyamsivappan S, Arasakumar T, Mahalingam V, Shankar R, Mohan PS. A versatile “on-off-on” quinoline pyrazoline hybrid for sequential detection of Cu2+ and S− ions towards bio imaging and tannery effluent monitoring. Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2018.08.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
|
19
|
Manawi Y, Kochkodan V, Mahmoudi E, Johnson DJ, Mohammad AW, Atieh MA. Characterization and Separation Performance of a Novel Polyethersulfone Membrane Blended with Acacia Gum. Sci Rep 2017; 7:15831. [PMID: 29158521 PMCID: PMC5696536 DOI: 10.1038/s41598-017-14735-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 10/13/2017] [Indexed: 12/07/2022] Open
Abstract
Novel polyethersulfone (PES) membranes blended with 0.1-3.0 wt. % of Acacia gum (AG) as a pore-former and antifouling agent were fabricated using phase inversion technique. The effect of AG on the pore-size, porosity, surface morphology, surface charge, hydrophilicity, and mechanical properties of PES/AG membranes was studied by scanning electron microscopy (SEM), Raman spectroscopy, contact angle and zeta potential measurements. The antifouling -properties of PES/AG membranes were evaluated using Escherichia coli bacteria and bovine serum albumine (BSA). The use of AG as an additive to PES membranes was found to increase the surface charge, hydrophilicity (by 20%), porosity (by 77%) and permeate flux (by about 130%). Moreover, PES/AG membranes demonstrated higher antifouling and tensile stress (by 31%) when compared to pure PES membranes. It was shown that the prepared PES/AG membranes efficiently removed lead ions from aqueous solutions. Both the sieving mechanism of the membrane and chelation of lead with AG macromolecules incorporated in the membrane matrix contributed to lead removal. The obtained results indicated that AG can be used as a novel pore-former, hydrophilizing and antifouling agent, as well as an enhancer to the mechanical and rejection properties of the PES membranes.
Collapse
Affiliation(s)
- Yehia Manawi
- Qatar Environment and Energy Research Institute (QEERI), Hamad bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
- College of Science and Engineering, Hamad Bin Khalifa University, Qatar Foundation, PO Box, 5825, Doha, Qatar
| | - Viktor Kochkodan
- Qatar Environment and Energy Research Institute (QEERI), Hamad bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
- College of Science and Engineering, Hamad Bin Khalifa University, Qatar Foundation, PO Box, 5825, Doha, Qatar
| | - Ebrahim Mahmoudi
- Department of Chemical and Process Engineering, Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan, Malaysia
| | - Daniel J Johnson
- College of Engineering, Swansea University, Bay campus Swansea, SA1 8PP, Wales, United Kingdom
| | - Abdul Wahab Mohammad
- Department of Chemical and Process Engineering, Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan, Malaysia
| | - Muataz Ali Atieh
- Qatar Environment and Energy Research Institute (QEERI), Hamad bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar.
- College of Science and Engineering, Hamad Bin Khalifa University, Qatar Foundation, PO Box, 5825, Doha, Qatar.
| |
Collapse
|
20
|
Baburkin PO, Komarov PV, Malyshev MD, Khizhnyak SD, Pakhomov PM. Computer simulation of structuring in aqueous L-cysteine–silver-nitrate solutions under the action of initiating salt. COLLOID JOURNAL 2017. [DOI: 10.1134/s1061933x17050039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
21
|
Khizhnyak SD, Komarov PV, Ovchinnikov MM, Zherenkova LV, Pakhomov PM. Mechanism of gelation in low-concentration aqueous solutions of silver nitrate with l-cysteine and its derivatives. SOFT MATTER 2017; 13:5168-5184. [PMID: 28664947 DOI: 10.1039/c7sm00772h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We discuss the results of experimental studies of the processes of gelation in aqueous solutions of silver nitrate with l-cysteine and its derivatives. We focus on understanding what determines if these small molecules will self-assemble in water at their extremely low concentration to form a gel. A mechanism of gel formation in a cysteine-silver solution (CSS) is proposed. The analysis of the results indicates that filamentary aggregates of a gel network are formed via interaction of NH3+ and C(O)O- groups that belong to neighboring silver mercaptide (SM) aggregates. In turn, formation of sulphur-silver bonds between silver mercaptide molecules is responsible for self-assembling these molecules into SM aggregates which can be considered as supramonomers. Free polar groups located on the surfaces of the aggregates can form hydrogen bonds with water molecules, which explains the unique ability of CSS hydrogels to trap water at low concentrations of low-molecular-weight hydrogelators.
Collapse
Affiliation(s)
- Svetlana D Khizhnyak
- Department of Physical Chemistry and General Physics, Tver State University, Tver, 170100, Russia
| | - Pavel V Komarov
- Department of Physical Chemistry and General Physics, Tver State University, Tver, 170100, Russia and Institute of Organoelement Compounds, Russian Academy of Sciences, Moscow, 119991, Russia.
| | | | - Lubov V Zherenkova
- Department of Physical Chemistry and General Physics, Tver State University, Tver, 170100, Russia
| | - Pavel M Pakhomov
- Department of Physical Chemistry and General Physics, Tver State University, Tver, 170100, Russia
| |
Collapse
|
22
|
Latrous L, Salpin JY, Haldys V, Léon E, Correia C, Lamsabhi AM. Gas-phase interactions of organotin compounds with cysteine. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:1006-1015. [PMID: 27428725 DOI: 10.1002/jms.3812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 07/02/2016] [Accepted: 07/12/2016] [Indexed: 06/06/2023]
Abstract
The gas-phase interactions of cysteine with di-organotin and tri-organotin compounds have been studied by mass spectrometry experiments and quantum calculations. Positive-ion electrospray spectra show that the interaction of di- and tri-organotins with cysteine results in the formation of [(R)2 Sn(Cys-H)]+ and [(R)3 Sn(Cys)]+ ions, respectively. MS/MS spectra of [(R)2 Sn(Cys-H)]+ complexes are characterized by numerous fragmentation processes, notably associated with elimination of NH3 and (C,H2 ,O2 ). Several dissociation routes are characteristic of each given organic species. Upon collision, both the [(R)3 Sn(Gly)]+ and [(R)3 Sn(Cys)]+ complexes are associated with elimination of the intact amino acid, leading to the formation of [(R)3 Sn]+ cation. But for the latter complex, two additional fragmentation processes are observed, associated with the elimination of NH3 and C3 H4 O2 S. Calculations indicate that the interaction between organotins and cysteine is predominantly electrostatic but also exhibits a considerable covalent character, which is slightly more pronounced in tri-organotin complexes. A preferred bidentate interaction of the type -η2 -S-NH2 , with sulfur and the amino group, is observed. As for the [(R)3 Sn(Cys)]+ complexes, their stability is due to the combination of the hydrogen bond taking place between the amino group and the sulfur lone pair and the interaction between the carboxylic oxygen atom and the metal. Copyright © 2016 John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- Latifa Latrous
- Laboratoire de Chimie Analytique et Electrochimie Campus Universitaire, Faculté des Sciences de Tunis, Université de Tunis El Manar, 2092, Tunis, Tunisia.
| | - Jean-Yves Salpin
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Université d'Evry Val d'Essonne, Bâtiment Maupertuis-Boulevard François Mitterrand, 91025, Evry, France
- CNRS-UMR 8587, Evry, France
| | - Violette Haldys
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Université d'Evry Val d'Essonne, Bâtiment Maupertuis-Boulevard François Mitterrand, 91025, Evry, France
- CNRS-UMR 8587, Evry, France
| | - Emmanuelle Léon
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Université d'Evry Val d'Essonne, Bâtiment Maupertuis-Boulevard François Mitterrand, 91025, Evry, France
- CNRS-UMR 8587, Evry, France
| | - Catarina Correia
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Université d'Evry Val d'Essonne, Bâtiment Maupertuis-Boulevard François Mitterrand, 91025, Evry, France
- CNRS-UMR 8587, Evry, France
| | - Al Mokhtar Lamsabhi
- Departamento de Química, Ciencias, M-13, Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC Cantoblanco, 28049, Madrid, Spain
| |
Collapse
|
23
|
Pitchumani Violet Mary C, Shankar R, Vijayakumar S, Kolandaivel P. Interaction studies of human prion protein (HuPrP109–111: methionine-lysine-histidine) tripeptide model with transition metal cations. J Mol Graph Model 2016; 69:111-26. [DOI: 10.1016/j.jmgm.2016.08.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 08/05/2016] [Accepted: 08/31/2016] [Indexed: 01/09/2023]
|
24
|
Roffe GW, Boonseng S, Baltus CB, Coles SJ, Day IJ, Jones RN, Press NJ, Ruiz M, Tizzard GJ, Cox H, Spencer J. A synthetic, catalytic and theoretical investigation of an unsymmetrical SCN pincer palladacycle. ROYAL SOCIETY OPEN SCIENCE 2016; 3:150656. [PMID: 27152207 PMCID: PMC4852630 DOI: 10.1098/rsos.150656] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 03/02/2016] [Indexed: 06/05/2023]
Abstract
The SCN ligand 2-{3-[(methylsulfanyl)methyl]phenyl}pyridine, 1, has been synthesized starting from an initial Suzuki-Miyaura (SM) coupling between 3-((hydroxymethyl)phenyl)boronic acid and 2-bromopyridine. The C-H activation of 1 with in situ formed Pd(MeCN)4(BF4)2 has been studied and leads to a mixture of palladacycles, which were characterized by X-ray crystallography. The monomeric palladacycle LPdCl 6, where L-H = 1, has been synthesized, and tested in SM couplings of aryl bromides, where it showed moderate activity. Density functional theory and the atoms in molecules (AIM) method have been used to investigate the formation and bonding of 6, revealing a difference in the nature of the Pd-S and Pd-N bonds. It was found that S-coordination to the metal in the rate determining C-H bond activation step leads to better stabilization of the Pd(II) centre (by 13-28 kJ mol(-1)) than with N-coordination. This is attributed to the electron donating ability of the donor atoms determined by Bader charges. The AIM analysis also revealed that the Pd-N bonds are stronger than the Pd-S bonds influencing the stability of key intermediates in the palladacycle formation reaction pathway.
Collapse
Affiliation(s)
- Gavin W. Roffe
- Department of Chemistry, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QJ, UK
| | - Sarote Boonseng
- Department of Chemistry, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QJ, UK
| | - Christine B. Baltus
- School of Science, University of Greenwich at Medway, University of Greenwich, Chatham ME4 4TB, UK
| | - Simon J. Coles
- UK National Crystallography Service, School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
| | - Iain J. Day
- Department of Chemistry, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QJ, UK
| | - Rhiannon N. Jones
- Department of Chemistry, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QJ, UK
| | - Neil J. Press
- Novartis Pharmaceuticals UK Ltd, Horsham RH12 5AB, UK
| | - Mario Ruiz
- School of Science, University of Greenwich at Medway, University of Greenwich, Chatham ME4 4TB, UK
| | - Graham J. Tizzard
- UK National Crystallography Service, School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
| | - Hazel Cox
- Department of Chemistry, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QJ, UK
| | - John Spencer
- Department of Chemistry, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QJ, UK
- School of Science, University of Greenwich at Medway, University of Greenwich, Chatham ME4 4TB, UK
| |
Collapse
|
25
|
First-principles data set of 45,892 isolated and cation-coordinated conformers of 20 proteinogenic amino acids. Sci Data 2016; 3:160009. [PMID: 26881946 PMCID: PMC4755128 DOI: 10.1038/sdata.2016.9] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 01/15/2016] [Indexed: 11/24/2022] Open
Abstract
We present a structural data set of the 20 proteinogenic amino acids and their amino-methylated and acetylated (capped) dipeptides. Different protonation states of the backbone (uncharged and zwitterionic) were considered for the amino acids as well as varied side chain protonation states. Furthermore, we studied amino acids and dipeptides in complex with divalent cations (Ca2+, Ba2+, Sr2+, Cd2+, Pb2+, and Hg2+). The database covers the conformational hierarchies of 280 systems in a wide relative energy range of up to 4 eV (390 kJ/mol), summing up to a total of 45,892 stationary points on the respective potential-energy surfaces. All systems were calculated on equal first-principles footing, applying density-functional theory in the generalized gradient approximation corrected for long-range van der Waals interactions. We show good agreement to available experimental data for gas-phase ion affinities. Our curated data can be utilized, for example, for a wide comparison across chemical space of the building blocks of life, for the parametrization of protein force fields, and for the calculation of reference spectra for biophysical applications.
Collapse
|
26
|
Lesslie M, Lau JKC, Lawler JT, Siu KWM, Steinmetz V, Maître P, Hopkinson AC, Ryzhov V. Cysteine Radical/Metal Ion Adducts: A Gas-Phase Structural Elucidation and Reactivity Study. Chempluschem 2016; 81:444-452. [DOI: 10.1002/cplu.201500558] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Indexed: 12/22/2022]
Affiliation(s)
- Michael Lesslie
- Department of Chemistry and Biochemistry; Northern Illinois University; DeKalb IL 60115 USA
| | - Justin Kai-Chi Lau
- Department of Chemistry and Centre for Research in Mass Spectrometry; York University; Toronto ON M3J 1P3 Canada
- Department of Chemistry and Biochemistry; University of Windsor; Windsor ON N9B 3P4 Canada
| | - John T. Lawler
- Department of Chemistry and Biochemistry; Northern Illinois University; DeKalb IL 60115 USA
| | - K. W. Michael Siu
- Department of Chemistry and Centre for Research in Mass Spectrometry; York University; Toronto ON M3J 1P3 Canada
- Department of Chemistry and Biochemistry; University of Windsor; Windsor ON N9B 3P4 Canada
| | - Vincent Steinmetz
- Laboratoire de Chimie Physique; Université Paris-Sud; UMR8000 CNRS; 91405 Orsay France
| | - Philippe Maître
- Laboratoire de Chimie Physique; Université Paris-Sud; UMR8000 CNRS; 91405 Orsay France
| | - Alan C. Hopkinson
- Department of Chemistry and Centre for Research in Mass Spectrometry; York University; Toronto ON M3J 1P3 Canada
| | - Victor Ryzhov
- Department of Chemistry and Biochemistry; Northern Illinois University; DeKalb IL 60115 USA
| |
Collapse
|
27
|
Umadevi P, Senthilkumar L. Metal-interacted histidine dimer: an ETS-NOCV and XANES study. RSC Adv 2016. [DOI: 10.1039/c6ra01264g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We have analyzed the metal coordination in a histidine dimer, hydrated with a water molecule, based on the extended transition state scheme with the theory of natural orbitals for chemical valence (ETS-NOCV).
Collapse
Affiliation(s)
- P. Umadevi
- Department of Physics
- Bharathiar University
- Coimbatore
- India
| | | |
Collapse
|
28
|
Mahalingam M, Irulappan M, Kasirajan G, Palathurai Subramaniam M, Ramasamy S, Unnisa N. Synthesis of bisbenzimidazo quinoline fluorescent receptor for Fe2+ ion in the aqueous medium – An experimental and theoretical approach. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2015.06.070] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
29
|
An insight into hydration structure of sodium glycinate from ab initio quantum chemical study. J Mol Model 2015; 21:234. [PMID: 26271732 DOI: 10.1007/s00894-015-2781-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 07/30/2015] [Indexed: 10/23/2022]
Abstract
The hydration structure of sodium glycinate (Na(+)GL(-)) is probed by the Monte-Carlo multiple minimum (MCMM) method combined with quantum mechanical (QM) calculations at the MP2/6-311++G(d,p) level. In the gas phase, the energy of [Na(+)GL(-)]β is more than 30 kJ mol(-1) higher than [Na(+)GL(-)]α. With higher degrees of hydration, our results indicate that the most stable conformers of [Na(+)GL(-)]∙(H2O)8 were derived from [Na(+)GL(-)]β instead of [Na(+)GL(-)]α. The stable conformers determined by the conductor-like polarizable continuum model (CPCM) also show that [Na(+)GL(-)]β is more stable than [Na(+)GL(-)]α in the liquid phase. By analyzing the hydration process, water…water hydrogen bonding interaction will be more preferable than ion…water interaction as the number of water molecules increases. According to the electronic density at the bond critical point on the Na-X bonds (X = O1, O2, N) in the low-energy conformers, Na(+)GL(-) will be dissociated as Na(+) and GL(-) in the bulk water, which is not predicted by the CPCM model. The structure features and the charge redistribution of Na(+)GL(-) will provide a physical explanation for the weakening Na-O1 interaction.
Collapse
|
30
|
Tedsana W, Tuntulani T, Ngeontae W. A circular dichroism sensor for Ni2+ and Co2+ based on l-cysteine capped cadmium sulfide quantum dots. Anal Chim Acta 2015; 867:1-8. [DOI: 10.1016/j.aca.2014.12.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 11/28/2014] [Accepted: 12/02/2014] [Indexed: 02/02/2023]
|
31
|
Prakash M, Chambaud G, Al-Mogren MM, Hochlaf M. Role of size and shape selectivity in interaction between gold nanoclusters and imidazole: a theoretical study. J Mol Model 2014; 20:2534. [PMID: 25488624 DOI: 10.1007/s00894-014-2534-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 11/17/2014] [Indexed: 11/26/2022]
Abstract
We present a theoretical study on the structure, stability, spectra and electronic properties of imidazole (Im) adsorbed on gold nanoclusters (Aun, n = 2, 4, 6, 8, 10, and 20). These computations were performed using various density functional theories with and without inclusion of Grimme's (D3) dispersion correction. For small clusters, we also carried out wavefunction-based ab initio (MP2 and SCS-MP2) computations for comparison. Vibrational, atoms in molecules (AIM) and natural bond orbital (NBO) analyses clearly reveal the occurrence of charge transfer (CT) through covalent (N1-Au) and noncovalent interactions that play important roles in the stability of the Im@Aun complexes with anchor assisted H-bonds (Cα-H · Au). Therefore, gold clusters can act as H-bond acceptors with biomolecules for development of new materials and applications. Our study establishes also the ability and reliability of PBE0 and M05-2X functionals compared to B3LYP and PBE for an accurate description of covalent and noncovalent interactions between Im and gold clusters since they lead to close agreement with MP2. Finally, we show that the Au8 cluster may be viewed as large enough to mimic the 3D gold surface.
Collapse
Affiliation(s)
- Muthuramalingam Prakash
- Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR, Université Paris-Est, 8208 CNRS, 5 bd Descartes, 77454, Marne-la-Vallée, France
| | | | | | | |
Collapse
|
32
|
Umadevi P, Senthilkumar L. Influence of metal ions (Zn2+, Cu2+, Ca2+, Mg2+and Na+) on the water coordinated neutral and zwitterionicl-histidine dimer. RSC Adv 2014. [DOI: 10.1039/c4ra08155b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
|
33
|
Zhou C, Ye H, Nishiumi T, Qin H, Chen C. l-Histidine enhances stability of hemoglobin concentrates by coordinating with free iron. Food Res Int 2014. [DOI: 10.1016/j.foodres.2014.04.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
34
|
Shankar R, Radhika R, Thangamani D, Senthil Kumar L, Kolandaivel P. Theoretical studies on interaction of anticancer drugs (dacarbazine, procarbazine and triethylenemelamine) with normal (AT and GC) and mismatch (GG, CC, AA and TT) base pairs. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.913098] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
35
|
Vázquez M, Vélez D, Devesa V. More on the in vitro characterization of the intestinal absorption of methylmercury. Chem Res Toxicol 2014; 27:942-3. [PMID: 24844764 DOI: 10.1021/tx500164w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- M Vázquez
- Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC) , Avenida Agustín Escardino 7, 46980 Paterna, Valencia, Spain
| | | | | |
Collapse
|
36
|
Qin P, Lü W, Qin W, Zhang W, Xie H. Theoretical studies on complexes of calcium ion with amino acids. Chem Res Chin Univ 2014. [DOI: 10.1007/s40242-014-3303-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
37
|
Keerthana S, Kolandaivel P. Study of mutation and misfolding of Cu-Zn SOD1 protein. J Biomol Struct Dyn 2013; 33:167-83. [DOI: 10.1080/07391102.2013.865104] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
38
|
Hurtado M, Monte M, Lamsabhi AM, Yáñez M, Mó O, Salpin JY. Modeling Interactions between an Amino Acid and a Metal Dication: Cysteine-Calcium(II) Reactions in the Gas Phase. Chempluschem 2013; 78:1124-1133. [DOI: 10.1002/cplu.201300166] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Indexed: 11/11/2022]
|
39
|
Density functional theory investigation of cocaine water complexes. J Mol Model 2013; 19:3411-25. [PMID: 23686284 DOI: 10.1007/s00894-013-1866-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 04/21/2013] [Indexed: 10/26/2022]
Abstract
Twenty cocaine-water complexes were studied using density functional theory (DFT) B3LYP/6-311++G** level to understand their geometries, energies, vibrational frequencies, charge transfer and topological parameters. Among the 20 complexes, 12 are neutral and eight are protonated in the cocaine-water complexes. Based on the interaction energy, the protonated complexes are more stable than the neutral complexes. In both complexes, the most stable structure involves the hydrogen bond with water at nitrogen atom in the tropane ring and C=O groups in methyl ester. Carbonyl groups in benzoyl and methyl ester is the most reactive site in both forms and it is responsible for the stability order. The calculated topological results show that the interactions involved in the hydrogen bond are electrostatic dominant. Natural bond orbital (NBO) analysis confirms the presence of hydrogen bond and it supports the stability order. Atoms in molecules (AIM) and NBO analysis confirms the C-H···O hydrogen bonds formed between the cocaine-water complexes are blue shifted in nature.
Collapse
|
40
|
Kesharwani MK, Sahu D, Desai K, Ganguly B. In silico studies toward the recognition of fluoride ion by novel bicyclic diborane receptors and tuning through remote substituent effects. Theor Chem Acc 2013. [DOI: 10.1007/s00214-013-1358-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
41
|
Jurinovich S, Degano I, Mennucci B. A Strategy for the Study of the Interactions between Metal–Dyes and Proteins with QM/MM Approaches: the Case of Iron–Gall Dye. J Phys Chem B 2012; 116:13344-52. [DOI: 10.1021/jp3083002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sandro Jurinovich
- Dipartimento di Chimica
e Chimica Industriale, Università di Pisa, Via Risorgimento 35, Pisa
56126, Italy
| | - Ilaria Degano
- Dipartimento di Chimica
e Chimica Industriale, Università di Pisa, Via Risorgimento 35, Pisa
56126, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica
e Chimica Industriale, Università di Pisa, Via Risorgimento 35, Pisa
56126, Italy
| |
Collapse
|
42
|
Maksić ZB, Kovačević B, Vianello R. Advances in Determining the Absolute Proton Affinities of Neutral Organic Molecules in the Gas Phase and Their Interpretation: A Theoretical Account. Chem Rev 2012; 112:5240-70. [DOI: 10.1021/cr100458v] [Citation(s) in RCA: 154] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Zvonimir B. Maksić
- Quantum Organic
Chemistry Group, Department of Organic
Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička 54, HR-10000 Zagreb, Croatia
| | - Borislav Kovačević
- Quantum Organic
Chemistry Group, Department of Organic
Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička 54, HR-10000 Zagreb, Croatia
| | - Robert Vianello
- Quantum Organic
Chemistry Group, Department of Organic
Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička 54, HR-10000 Zagreb, Croatia
| |
Collapse
|
43
|
Zhou C, Wang H, Chen Y, Chen C. Effect of l-cysteine and lactose on color stability of porcine red blood cell during freeze-drying and powder storage. Food Sci Biotechnol 2012. [DOI: 10.1007/s10068-012-0087-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
|
44
|
Shankar R, Kolandaivel P, Senthil kumar L. Coordination and binding properties of zwitterionic glutathione with transition metal cations. Inorganica Chim Acta 2012. [DOI: 10.1016/j.ica.2012.01.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
|
45
|
|
46
|
Shakourian-Fard M, Nasiri M, Fattahi A, Vafaeezadeh M. Influence of the water molecules (n = 1–6) on the interaction between Li+, Na+, K+ cations and indole molecule as tryptophan amino acid residue. Struct Chem 2011. [DOI: 10.1007/s11224-011-9930-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
|