1
|
Inducing high exo selectivity in Diels-Alder reaction by dimethylborane substituent: a DFT study. Sci Rep 2022; 12:22225. [PMID: 36564456 PMCID: PMC9789069 DOI: 10.1038/s41598-022-26685-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
In this work, the role of Lewis acid-base (LAB) interaction on the stereoselectivity of the Diels-Alder (DA) reaction has been studied by DFT in gas and solution (dichloromethane) phases. The calculations were performed at the B3LYP/6-311G++ (d, p) level. Two different series of DA reactions were investigated: (1)-three mono-substituted cyclopentadienes + dimethyl(vinyl)borane; (2)-five α,β-unsaturated carbonyl compounds + cyclopenta-2,4-dien-1-yldimethylborane. The reacting diene and dienophile pairs were chosen to restrict LAB interaction to the exo reaction pathway. It was found that in some of the examined cases, the favorable LAB interaction is so strong that it can lead to a completely exo-selective DA reaction. Furthermore, a novel multistep synthetic method was hypothesized for preparing exo cycloadduct with near 100% stereoselectivity. Our results can open up new avenues toward the rational design of exo-selective DA reactions for synthesizing novel bioorganic compounds.
Collapse
|
2
|
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
|
3
|
Kotena ZM, Fattahi A. Computational insight into networking H‐bonds in open and cyclic forms of glucose. J PHYS ORG CHEM 2021. [DOI: 10.1002/poc.4285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
| | - Alireza Fattahi
- Department of Chemistry Sharif University of Technology Tehran Iran
| |
Collapse
|
4
|
Shang XY, An HY, Zhang T, Lin JH, Hao F, Yu DH, Xiao JC, Li TD. Evaluating and understanding the affinity of metal ions to water and ammonia using density functional theory calculation. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.138398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
5
|
Farrokhpour H, Khoshkhou S. A TD-DFT study of the excited dissociative electronic states of the DNA nucleobases bound to Li . SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 244:118862. [PMID: 32927359 DOI: 10.1016/j.saa.2020.118862] [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: 05/09/2020] [Revised: 08/13/2020] [Accepted: 08/17/2020] [Indexed: 06/11/2023]
Abstract
In this work, the first and second dissociative potential curves of adenineLi+ (ADLi+), guanineLi+ (GUALi+), cytosineLi+(CYTLi+), and thymineLi+ (THYLi+) complexes, related to the dissociation of their LiO and LiN bonds, have been calculated in the gas phase and water, separately. For this purpose, the fifteen excited potential curves, in order of increasing energy, were calculated for each complex and the dissociative potential curves were distinguished from them considering the conical intersection points. The time-dependent density functional theory (TD-DFT) method employing the M06-2X functional was used for the calculations. It was observed that the electron transfer from the DNA base to the Li+ took place during the dissociation of complexes in the gas phase. The electrostatic field of water blocked this charge transfer and led to the excited DNA base and Li+ in its ground state. The vertical excitation energy for the desorption of the Li fragment as a neutral and cation species from the DNA bases was determined. The effect of the interaction site of Li+ on the dissociative potential curves was also investigated.
Collapse
Affiliation(s)
- H Farrokhpour
- Department of Chemistry, Isfahan University of Technology, Isfahan 84156-83111, Iran.
| | - S Khoshkhou
- Department of Chemistry, Isfahan University of Technology, Isfahan 84156-83111, Iran
| |
Collapse
|
6
|
Synthesis and characterization of Cd (L-Proline)2 complex using vibrational spectroscopy and quantum chemical calculation. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.128972] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
7
|
Taherinia D, Mahmoodi MM, Fattahi A. Theoretical investigation of the effect of hydrogen bonding on the stereoselectivity of the Diels–Alder reaction. NEW J CHEM 2021. [DOI: 10.1039/d1nj01373d] [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
Here, we report the computational prediction of high exo selectivities in a series of Diels–Alder reactions with H-bonding interaction.
Collapse
Affiliation(s)
- Davood Taherinia
- Department of Chemistry, Sharif University of Technology, Tehran 11155-9516, Iran
| | - M. Mohsen Mahmoodi
- Department of Chemistry, Sharif University of Technology, Tehran 11155-9516, Iran
| | - Alireza Fattahi
- Department of Chemistry, Sharif University of Technology, Tehran 11155-9516, Iran
| |
Collapse
|
8
|
Borah B, Devi TG. Characterization of Zn (l-Proline)2 complex using spectroscopic techniques and DFT analysis. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
9
|
Kotena ZM, Fattahi A. Comparison of acidity and metal ion affinity of D-Glucosamine and N-acetyl-D-glucosamine, a DFT study. J Mol Graph Model 2020; 98:107612. [PMID: 32302939 DOI: 10.1016/j.jmgm.2020.107612] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 03/06/2020] [Accepted: 03/27/2020] [Indexed: 11/28/2022]
Abstract
The derivatives of glucose such as glucosamine (β-D-GlcN) and N-acetyl-D-β-glucosamine (GlcNAc) are significant in several biological systems. D-GlcN has been used widely to treat osteoarthritis in humans and animal models as well as GlcNAc has been proposed as a treatment for autoimmune diseases. The DFT/B3LYP/6-311++G (d,p) method as well as QTAIM and NBO analyses were used to the acidity values of D-GlcN and GlcNAc sugars and their complexes with alkali ions in the gas phase. The Li+, Na+ and K+ prefer bi-dentate chelate in these complexes. The computed results indicate that metal ion affinity (MIA) in GlcNAc is higher than that in D-GlcN. There are direct correlations between the MIA values of D-GlcN and GlcNAc sugars and the atomic numbers of Li, Na, and K. The calculated acidity values for GlcNAc at C2-NH and C6-HO6 sites are 331 and 333 kcal mol-1, respectively. Whereas the calculated acidity values for D-GlcN at C2-NH and C6-HO6 sites are 365 and 372 kcal mol-1, respectively. The AIM and NBO analyses indicate the presence of intramolecular H-bonds in GlcNAc sugar in both its neutral form and conjugate base; whereas D-GlcN indicates intramolecular H-bonds in only its conjugate base.
Collapse
Affiliation(s)
| | - Alireza Fattahi
- Department of Chemistry, Sharif University of Technology, P.O. Box 11365-9516, Tehran, Iran.
| |
Collapse
|
10
|
Rejeeth C, Sharma A, Nipun Babu V, Gautam R. Label-free colorimetric detection of serum cysteine using Ag-NP probes in the presence of Be 2+ ions. NEW J CHEM 2020; 44:9018-9024. [DOI: 10.1039/d0nj00967a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Amino acids play a crucial role in a variety of significant metabolic processes and their homeostasis is essential for cell growth and survival.
Collapse
Affiliation(s)
- Chandrababu Rejeeth
- School of Biomedical Engineering
- Med-X Research Institute
- Shanghai Jiao Tong University
- Shanghai 200030
- P. R. China
| | - Alok Sharma
- State Key Laboratory of Oncogenes and Related Genes
- Institute for Personalized Medicine
- School of Biomedical Engineering
- Shanghai Jiao Tong University
- Shanghai 200030
| | | | - Rahul Gautam
- Jian Pei Medical Imaging Research Center
- Hangzhou 311140
- P. R. China
| |
Collapse
|
11
|
Modeling of neotame and fructose thermochemistry: Comparison with mono and divalent metal ions by Computational and experimental approach. Sci Rep 2019; 9:18414. [PMID: 31804530 PMCID: PMC6895154 DOI: 10.1038/s41598-019-54626-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 11/18/2019] [Indexed: 11/25/2022] Open
Abstract
The metal complexes can demonstrate various interesting biological activities in the human body. However, the role of certain metal ions for specific cell activities is still subject to debate. This study is aimed at comparing the thermochemical properties of neotame (artificial sweetener) and α, β-fructose in gas phase and water medium. The interaction of α and β-fructose, neotame with monovalent and divalent metal ions was studied and comprehended by density functional theory (DFT) using B3LYP functional, 6–311 + G (d, p) and D3 basis set. Metal ion affinities (MIA) values depicted that ionic radius of metal ions played an important role in the interaction of α, β-fructose and neotame. The ∆G parameter was calculated to predict and understand the interaction of metal ions with α and β-fructose, neotame. The results suggested that the presence of hydroxyl groups and oxygen atoms in sugar molecules acted as preferred sites for the binding and interaction of mono and divalent ions. For the first time computational study has been introduced in the present study to review the progress in the application of metal binding with sugar molecules especially with neotame. Moreover, voltammetric behaviour of neotame-Zn2+ was studied using cyclic and differential pulse voltammetry. The obtained results suggest that the peak at −1.13 V is due to the reduction of Zn2+ in 0.1 M phosphate buffer medium at pH 5.5. Whereas, addition of 6-fold higher concentration of neotame to the ZnCl2.2H2O resulted in a new irreversible cathodic peak at −0.83, due to the reduction of neotame-Zn2+ complex. The Fourier transform infrared spectroscopy (FTIR) results indicates that the β-amino group (-NH) and carboxyl carbonyl (-C = O) groups of neotame is participating in the chelation process, which is further supported by DFT studies. The findings of this study identify the efficient chelation factors as major contributors into metal ion affinities, with promising possibilities to determine important biological processes in cell wall and glucose transmembrane transport.
Collapse
|
12
|
Liu D, Thomas T, Gong H, Li F, Li Q, Song L, Azhagan T, Jiang H, Yang M. A mechanism of alkali metal carbonates catalysing the synthesis of β-hydroxyethyl sulfide with mercaptan and ethylene carbonate. Org Biomol Chem 2019; 17:9367-9374. [PMID: 31621741 DOI: 10.1039/c9ob01816f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The reaction of β-hydroxyethylation is essential to the current practice of organic chemistry. Here, we proposed a new and green route to synthesize 2-hydroxyethyl n-alkyl sulfide with n-alkyl mercaptan and ethylene carbonate (EC) in the presence of alkali carbonates as catalysts and revealed the mechanism by experiments and theoretical calculations. The reaction reported proceeds rapidly with high yields when it is performed at 120 °C and the catalytic loading is ∼1 mol%. This protocol is applicable to other mercaptans to synthesize the corresponding β-hydroxyethyl sulfide. Density functional theory-based calculations show the energy profile for the reaction pathway. The rate-determining step is the ring-opening of EC. A negatively charged O atom of alkali carbonates approaches the S atom of -SH under the influence of hydrogen bonds. An activated S atom that carries more negative charge serves as a nucleophilic reagent and assists in the ring-opening of EC by reducing the Mayer bond orders of the C1-O1 bond in EC. Alkali cations also contribute to the C1-O1 bond cleavage. The energy barrier for the ring-opening of EC decreases with the decrease of electronegativity of alkali cations. Subsequent transference of a H atom leads to the formation of β-hydroxyethyl sulfide, the dissociation of CO2 and the reduction of K2CO3.
Collapse
Affiliation(s)
- Dongliang Liu
- College of Chemistry, Chemical Engineering and Environment Engineering, Liaoning Shihua University, Fushun 113001, China.
| | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Shuai Z, Li AY. Excited States of Weak Interacting Complexes of Formaldehyde and Alkali Metal Ions. J STRUCT CHEM+ 2018. [DOI: 10.1134/s0022476618050086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
14
|
Dmitrieva OA, Fedotova MV, Buchner R. Evidence for cooperative Na+ and Cl− binding by strongly hydrated l-proline. Phys Chem Chem Phys 2017; 19:20474-20483. [DOI: 10.1039/c7cp04335j] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Strongly hydrated l-proline cooperatively binds Na+ and Cl− ions in aqueous solution.
Collapse
Affiliation(s)
- Olga A. Dmitrieva
- G.A. Krestov Institute of Solution Chemistry
- Russian Academy of Sciences
- 153045 Ivanovo
- Russian Federation
| | - Marina V. Fedotova
- G.A. Krestov Institute of Solution Chemistry
- Russian Academy of Sciences
- 153045 Ivanovo
- Russian Federation
| | - Richard Buchner
- Institut für Physikalische und Theoretische Chemie
- Universität Regensburg
- 93040 Regensburg
- Germany
| |
Collapse
|
15
|
Jami-Alahmadi Y, Linford BD, Fridgen TD. Distinguishing Isomeric Peptides: The Unimolecular Reactivity and Structures of (LeuPro)M+ and (ProLeu)M+ (M = Alkali Metal). J Phys Chem B 2016; 120:13039-13046. [DOI: 10.1021/acs.jpcb.6b09588] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Yasaman Jami-Alahmadi
- Department of Chemistry, Memorial University, St. John’s, Newfoundland A1N 4T8, Canada
| | - Bryan D. Linford
- Department of Chemistry, Memorial University, St. John’s, Newfoundland A1N 4T8, Canada
| | - Travis D. Fridgen
- Department of Chemistry, Memorial University, St. John’s, Newfoundland A1N 4T8, Canada
| |
Collapse
|
16
|
Kang N, Lin F, Zhao W, Lombardi JP, Almihdhar M, Liu K, Yan S, Kim J, Luo J, Hsiao BS, Poliks M, Zhong CJ. Nanoparticle–Nanofibrous Membranes as Scaffolds for Flexible Sweat Sensors. ACS Sens 2016. [DOI: 10.1021/acssensors.6b00414] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
| | | | | | | | - Mihdhar Almihdhar
- Department
of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Kai Liu
- Department
of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | | | | | | | - Benjamin S. Hsiao
- Department
of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | | | | |
Collapse
|
17
|
Khalili B, Rimaz M. Interaction of l-proline with group IIB (Zn2+, Cd2+, Hg2+) metal cations in the gas and aqueous phases: a quantum computational study. CAN J CHEM 2016. [DOI: 10.1139/cjc-2015-0616] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The gas and aqueous phase complexation geometries, electronic interactions, and metal ion affinities of Zn2+, Cd2+, and Hg2+ metal cations with the two most stable conformations of l-proline complexes were studied. The complexes were optimized by density functional theory (B3LYP) using the 6-311++G(d,p) orbital basis set and relativistic pseudopotentials for the metal cations. The interactions of the metal cations at different nucleophilic sites of l-proline were considered as were three modes of interactions including salt bridged, charge solvated 1, and charge solvated 2, which are indicative of binding in a bidentate manner through the carboxylate group, carbonyl and hydroxyl oxygen, and carbonyl oxygen and the nitrogen atom of l-proline. All of the coordination patterns were characterized by both charge transfer and ionic interactions between l-proline and the metal cation. The metal ion affinity (MIA) and interaction energy were also computed for all of the complexes at both the gas and aqueous phases. Results showed that the order of MIA at the gas and aqueous phases are different. MIA order at the gas phase was in the order of Zn2+ > Hg2+ > Cd2+ whereas at the aqueous phase, the order of Zn2+ > Cd2+ > Hg2+ was obtained for MIA. The infrared stretching vibrational modes of the N–H and O–H groups of free l-proline were compared with l-proline–M2+ in both CS1 and CS2 coordination patterns at the gas phase and results showed a considerable shift to lower frequency during complexation process.
Collapse
Affiliation(s)
- Behzad Khalili
- Department of Chemistry, Faculty of Sciences, University of Guilan, P.O. Box 41335-1914 Rasht, Iran
| | - Mehdi Rimaz
- Department of Chemistry, Payame Noor University, P.O. Box 19395-3697, Tehran, Iran
| |
Collapse
|
18
|
An insight into the interaction of L-proline with the transition metal cations Fe(2+), Co(2+), Ni(2+): a gas phase theoretical study. J Mol Model 2015; 22:11. [PMID: 26676722 DOI: 10.1007/s00894-015-2865-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 11/15/2015] [Indexed: 10/22/2022]
Abstract
The interaction of Fe(2+), Co(2+), and Ni(2+) with L-proline has been studied. Three modes of interaction have been considered: salt bridged (SB), involving binding in a bi-dentate manner through the carboxylate group of L-proline, charge solvated 1 (CS1) involving carbonyl and hydroxyl oxygen, and charge solvated 2 (CS2) involving carbonyl oxygen and the lone pair of the nitrogen atom. All calculations including geometry optimization, metal ion affinities (MIAs), and frequency calculations of the binding structures of Fe(2+), Co(2+), and Ni(2+) to L-proline were calculated using the hybrid density functional theory (DFT-B3LYP) method. All three cations were found to bind preferentially in a zwitterionic (SB) coordination pattern with the metal ion affinity in the order Ni(2+) ˃ Co(2+) ˃ Fe(2+) in all binding forms. The nature of the binding interaction between metal cations and L-proline was found to be mainly electrostatic. Comparison of the infrared vibrations of the C=O, the N-H and the O-H groups of free L-proline with L-proline-M(2+) in both CS1 and CS2 complex structures indicated a considerable shift to lower frequency during complexation. In order to gain more insight into the nature of the interaction of L-proline with group VIIIB metal ions, comparison of the interaction of L-proline with other cations such as (Li(+), Na(+), K(+), Be(2+), Mg(2+), and Ca(2+)) was made. Graphical Abstract L-proline with the transition metal cations Fe(2+), Co(2+), Ni(2.)
Collapse
|
19
|
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
|
20
|
Alahmadi YJ, Gholami A, Fridgen TD. The protonated and sodiated dimers of proline studied by IRMPD spectroscopy in the N-H and O-H stretching region and computational methods. Phys Chem Chem Phys 2015; 16:26855-63. [PMID: 25375752 DOI: 10.1039/c4cp03104k] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
IRMPD spectroscopy and computational chemistry techniques have been used to determine that the proton- and sodium-bound dimers of proline exist as a mixture of a number of different structures. Simulated annealing computations were found to be helpful in determining the unique structures of the protonated and sodiated dimers, augmenting chemical intuition. The experimental and computational results are consistent with the proton-bound dimer of N-protonated proline bound to zwitterionic proline. There was no spectroscopic evidence in the 3200-3800 cm(-1) region for a canonical structure which is predicted to have a weak N-H stretch at about 3440 cm(-1). A well resolved band at 1733 cm(-1) from a previous spectroscopic study (DOI: 10.1021/ja068715a ) was reassigned from a high energy canonical isomer to the C=O stretch of a lower energy zwitterionic structure. This band is a free carboxylate C=O stretch where protonated proline is hydrogen bonded to the other carboxylate oxygen which is also involved in an intramolecular hydrogen bond. Fifteen structures of the sodium bound proline dimer were computed to be within 10 kJ mol(-1) of Gibbs energy and eight structures were within 5 kJ mol(-1). None of these structures can be ruled out based on the experimental IRMPD spectrum. They all have an N-H stretching band predicted in a position that agrees with the experimental spectrum. However, only structures where one of the proline monomers is in the canonical form and having a free O-H bond can produce the band at ∼3600 cm(-1).
Collapse
|
21
|
Zhang Q, Meng XJ. The mechanisms of α- H and proton transfers of glycine induced by Mg2+. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2015. [DOI: 10.1142/s021963361550008x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A MP2/6-31++G(d,p)//B3LYP/6-31++G(d,p) method was used to investigate the mechanisms of α- H and proton transfers of glycine induced by Mg 2+. Eight complexes were obtained, six of which were neutral and the other two were zwitterionic. Among them, the zwitterion with a binding energy of 159.4 kcal/mol was the most stable structure. Conformation transformations of the complexes caused by the rotation of single bond and the transfers of α- H and proton were completed via seven transition states. The inductive effect of Mg 2+ made the electron cloud of glycine deviate to Mg 2+, which activated the covalent bond involving the transferred proton. The neutral complex can be turned into the zwitterionic one by the transfers of both carboxyl hydrogen and α- H , and the energy barrier of each reaction was less than 9.2 kcal/mol. After the transfer of α- H , a delocalized π bond was formed in glycine skeleton and the α- C atom took 0.19 positive charges. So the chemical activity of the glycine enhanced, and glycine was readily available for addition and nucleophilic substitution reactions. The path from the most stable glycine conformer G1 to the zwitterionic conformation I is G1 → G1–G3 → G3 → G3–G4 → G4 → G2–G4 → G2 → VI → I–VI → I, and the highest energy barrier of this path is 9.2 kcal/mol.
Collapse
Affiliation(s)
- Qing Zhang
- Department of Chemistry, Tangshan Normal University, Tangshan 063000, P. R. China
| | - Xiang-Jun Meng
- Department of Chemistry, Tangshan Normal University, Tangshan 063000, P. R. China
| |
Collapse
|
22
|
Kowalska-Baron A. Theoretical study of the complexes of tyrosine and tryptophan with biologically important metal cations in aqueous solutions. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2015.01.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
23
|
Despotović I. Complexation of some alkali and alkaline earth metal cations by macrocyclic compounds containing four pyridine subunits – a DFT study. NEW J CHEM 2015. [DOI: 10.1039/c5nj00459d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Tetradentate pyridine-based macrocyclic compounds offer useful ligands capable of efficient and selective complexation of M = Li+, Na+, K+, Be2+, Mg2+and Ca2+.
Collapse
Affiliation(s)
- Ines Despotović
- Quantum Organic Chemistry Group
- Department of Organic Chemistry and Biochemistry
- Ruđer Bošković Institute
- Zagreb 10000
- Croatia
| |
Collapse
|
24
|
DFT study on foscarnet as an antiviral drug: Conformer analysis, gas phase acidity, metal ion affinity and influence of metal complexation on gas phase acidity. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2014.09.075] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
25
|
Meng L, Lin Z. Complexations of alkali/alkaline earth metal cations with gaseous glutamic acid. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.04.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
26
|
Moghaddam MB, Fridgen TD. IRMPD Spectroscopic Study of Microsolvated [Na(GlyAla)]+ and [Ca(GlyAla–H)]+ and the Blue Shifting of the Hydrogen-Bonded Amide Stretch with Each Water Addition. J Phys Chem B 2013; 117:6157-64. [DOI: 10.1021/jp402217g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Maryam B. Moghaddam
- Department
of Chemistry, Memorial University, St. John’s, Newfoundland
and Labrador, Canada A1B 3X7 Canada
| | - Travis D. Fridgen
- Department
of Chemistry, Memorial University, St. John’s, Newfoundland
and Labrador, Canada A1B 3X7 Canada
| |
Collapse
|
27
|
Armentrout PB, Citir M, Chen Y, Rodgers MT. Thermochemistry of Alkali Metal Cation Interactions with Histidine: Influence of the Side Chain. J Phys Chem A 2012; 116:11823-32. [DOI: 10.1021/jp310179c] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- P. B. Armentrout
- Department of Chemistry, University of Utah, 315 South 1400 East,
Room 2020, Salt Lake City, Utah 84112, United States
| | - Murat Citir
- Department of Chemistry, University of Utah, 315 South 1400 East,
Room 2020, Salt Lake City, Utah 84112, United States
| | - Yu Chen
- Department of Chemistry, Wayne State University, Detroit, Michigan
48202, United States
| | - M. T. Rodgers
- Department of Chemistry, Wayne State University, Detroit, Michigan
48202, United States
| |
Collapse
|
28
|
Crestoni ME, Chiavarino B, Scuderi D, Di Marzio A, Fornarini S. Discrimination of 4-hydroxyproline diastereomers by vibrational spectroscopy of the gaseous protonated species. J Phys Chem B 2012; 116:8771-9. [PMID: 22764742 DOI: 10.1021/jp302382p] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydroxylation of proline is a prominent oxidative post-translational modification (oxPTM) in animals, characterized by site specificity and stereochemical control. The presence of this irreversible modification and the ensuing generation of a chiral center have been assayed in (2S,4R)-4-hydroxyproline and (2S,4S)-4-hydroxyproline forming the protonated species by electrospray ionization and sampling them by infrared multiple photon dissociation (IRMPD) spectroscopy. IRMPD spectra, recorded both in the 950-1950 cm(-1) (using the CLIO free electron laser) and in the 3200-3700 cm(-1) [using a tabletop parametric oscillator/amplifier (OPO/OPA) laser] regions, have been interpreted by comparison with the absorbance spectra of the lowest energy structures calculated at MP2/6-311+G** level of theory. Remarkable spectral differences have emerged in the fingerprint region, pointing to the unambiguous discrimination between S,R and S,S diastereomers. The main differences arise from the position of the carbonyl stretching mode, a signature of nonzwitterionic structures, moving from 1750 cm(-1) for the S,R form to 1770 cm(-1) for the S,S diastereomer. Furthermore, a well-defined band associated with the NH(2) wagging mode at 1333 cm(-1) is a distinct mark of the S,S isomer. Each gaseous protonated epimer comprises a population of at least three conformers, stabilized by intramolecular hydrogen bonds linking the two hydrogens of protonated secondary amine group with the 4-hydroxy substituent and with an oxygen atom of the carboxylic group, respectively. Interestingly, a tendency to adopt either C(4)-exo (up) or C(4)-endo (down) pyrrolidine puckering upon proline 4(R)- or 4(S)-hydroxylation, respectively, is observed here. The same bias is found in neutral hydroxyprolines and in collagen model peptides. In the protonated species under examination, this bias originates chirality-induced vibrational features revealed by IRMPD spectroscopy.
Collapse
Affiliation(s)
- Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma La Sapienza, P. le A. Moro 5, I-00185 Roma, Italy.
| | | | | | | | | |
Collapse
|
29
|
Theoretical study on the interaction of glutathione with group IA (Li+, Na+, K+), IIA (Be2+, Mg2+, Ca2+), and IIIA (Al3+) metal cations. Struct Chem 2012. [DOI: 10.1007/s11224-012-0031-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
|
30
|
Wu X, Yang G, Zu Y, Zhou L. Molecular dynamics studies of β-hairpin folding with the presence of the sodium ion. Comput Biol Chem 2012; 38:1-9. [PMID: 22487489 DOI: 10.1016/j.compbiolchem.2012.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Revised: 01/20/2012] [Accepted: 02/14/2012] [Indexed: 11/19/2022]
Abstract
Metal ions are ubiquitous in protein systems and play a significant role during their folding processes. Nineteen independent structures were determined for the Na(+)/β-hairpin interacting systems, and their folding pathways are different. (i) For Na(S47), the turn is rapidly shaped with the help of Na(+) and acts as the folding nucleus for the rest regions. Two intermediate states are observed and the resulted structure is the most folded. (ii) For Na(B41), Na(B52), Na(B54), Na(S55) and Na(B56), the inclusive Na(+) ions are anchored by β-strands. The local structures around the Na(+) ions and the turn regions fold simultaneously and serve as two independent folding nuclei. (iii) The other systems have no folding nuclei and correspond to low-folded structures. Long-range electrostatic interactions contribute a lot to the folding, especially from the four negatively charged residues (Glu42, Asp46, Asp47 and Glu56). The initial positions of the Na(+) ions are largely responsible for the different folding behaviors. The interactions with sidechain- rather than backbone-O atoms generally lead to more compact structures. Another factor affecting the folding is whether the O atoms are associated with native H-bonds, and those involved show decreased affinities to metal ions. The addition of water solvent does not induce obvious folding and conformational transitions to the Na(+)/β-hairpin interacting systems.
Collapse
Affiliation(s)
- Xiaomin Wu
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, PR China
| | | | | | | |
Collapse
|
31
|
TAVASOLI ELHAM, FATTAHI ALIREZA. DFT STUDY OF BOND ENERGIES AND ATTACHMENT SITES OF SAMPLE DIVALENT CATIONS (Mg2+, Ca2+, Zn2+) TO HISTIDINE IN THE GAS PHASE. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633609004642] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In view of better understanding interactions of amino acids and peptides with metallic cations in the isolated state, the model system histidine– M 2+ ( M 2+ = Mg 2+, Ca 2+, Zn 2+) has been studied theoretically. The computations have been performed with the help of the density functional theory (DFT) and the B3LYP functional. The extended basis set was the standard 6-311++G**. All the molecular complexes obtained by the interaction between several energetically low-lying tautomers/conformers/zwitterions of histidine and the cations on different binding sites were considered. Our study shows that complexes of histidine with Mg 2+, Ca 2+, Zn 2+ are rather similar. In the isolated state, the most stable form corresponds to a tridentate complex in which the cation interacts with oxygen and two nitrogen atoms: one from the terminal NH 2 and one from the imidazole ring. All computations indicate that the metal ion affinity (MIA) decreases on going from Zn 2+ to Mg 2+ and Ca 2+, for the considered amino acid. This indicates that histidine prefers to bind to the transition metal cation rather than alkali earth metals. The influence of theses cations on the acidity of histidine were also considered. As expected, upon metal complexation, proton dissociation of histidine becomes much more favorable, that is, its acidity becomes much less endothermic.
Collapse
Affiliation(s)
- ELHAM TAVASOLI
- Department of Chemistry, Sharif University of Technology, P. O. Box 11365-9516, Tehran, Iran
| | - ALIREZA FATTAHI
- Department of Chemistry, Sharif University of Technology, P. O. Box 11365-9516, Tehran, Iran
| |
Collapse
|
32
|
TAVASOLI ELHAM, FATTAHI ALIREZA. DFT STUDY ON GAS-PHASE INTERACTION BETWEEN HISTIDINE AND ALKALI METAL IONS (Li+, Na+, K+); AND INFLUENCE OF THESE IONS ON HISTIDINE ACIDITY. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633609004812] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The gas-phase metal affinities of histidine Li +, Na + and K + ions have been determined theoretically employing the hybrid B3LYP exchange–correlation functional and using 6-311++G** basis sets. All computations indicate that the metal ion affinity decreases on going from Li + to Na + and K + for the considered amino acid. Different types of M + coordinations on several histidine conformers/tautomers were considered in detail. The optimized structures indicate that Li + and Na + prefer a tri-dentate coordination, bonding with a nitrogen atom of imidazole ring ( N τ), – NH 2, and an oxygen atom of a carbonyl, while in the K +-histidine lowest-energy conformer, the cation appears to be bi-coordinated to both oxygen atoms of the zwitterionic form by the energy values not too far from that of tri-coordination. We also performed the DFT calculations for proton dissociation energy of histidine both in the presence and absence of alkali metal ions. Our results also reveal that the acidity of histidine dramatically increases upon metal ion complexation.
Collapse
Affiliation(s)
- ELHAM TAVASOLI
- Department of Chemistry, Sharif University of Technology, P.O. Box: 11365-9516, Tehran, Iran
| | - ALIREZA FATTAHI
- Department of Chemistry, Sharif University of Technology, P.O. Box: 11365-9516, Tehran, Iran
| |
Collapse
|
33
|
Effect of regular hydration on gas phase structural stability of [zwitterionic alanine+M+] (M+=Li+, Na+, K+) complexes: A quantum chemical study. Chem Phys 2011. [DOI: 10.1016/j.chemphys.2010.11.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
34
|
|
35
|
Shankar R, Kolandaivel P, Senthilkumar L. Interaction studies of cysteine with Li+, Na+, K+, Be2+, Mg2+, and Ca2+ metal cation complexes. J PHYS ORG CHEM 2010. [DOI: 10.1002/poc.1786] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
36
|
Armentrout PB, Armentrout EI, Clark AA, Cooper TE, Stennett EMS, Carl DR. An Experimental and Theoretical Study of Alkali Metal Cation Interactions with Cysteine. J Phys Chem B 2010; 114:3927-37. [DOI: 10.1021/jp911219u] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- P. B. Armentrout
- Department of Chemistry, University of Utah, 315 S. 1400 E. Rm 2020, Salt Lake City, Utah
| | - Erin I. Armentrout
- Department of Chemistry, University of Utah, 315 S. 1400 E. Rm 2020, Salt Lake City, Utah
| | - Amy A. Clark
- Department of Chemistry, University of Utah, 315 S. 1400 E. Rm 2020, Salt Lake City, Utah
| | - Theresa E. Cooper
- Department of Chemistry, University of Utah, 315 S. 1400 E. Rm 2020, Salt Lake City, Utah
| | - Elana M. S. Stennett
- Department of Chemistry, University of Utah, 315 S. 1400 E. Rm 2020, Salt Lake City, Utah
| | - Damon R. Carl
- Department of Chemistry, University of Utah, 315 S. 1400 E. Rm 2020, Salt Lake City, Utah
| |
Collapse
|
37
|
Ye SJ, Armentrout PB. Guided ion beam and theoretical studies of sequential bond energies of water to sodium cysteine cation. Phys Chem Chem Phys 2010; 12:13419-33. [DOI: 10.1039/c0cp00302f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
38
|
Yang ZW, Wu XM, Zhou LJ, Yang G. A proline-based neuraminidase inhibitor: DFT studies on the zwitterion conformation, stability and formation. Int J Mol Sci 2009; 10:3918-3930. [PMID: 19865525 PMCID: PMC2769147 DOI: 10.3390/ijms10093918] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2009] [Accepted: 09/02/2009] [Indexed: 12/25/2022] Open
Abstract
The designs of potent neuraminidase (NA) inhibitors are an efficient way to deal with the recent "2009 H1N1" influenza epidemic. In this work, density functional calculations were employed to study the conformation, stability and formation of the zwitterions of 5-[(1R,2S)-1-(acetylamino)-2-methoxy-2-methylpentyl]-4-[(1Z)-1-propenyl]-(4S,5R)-d-proline (BL), a proline-based NA inhibitor. Compared to proline, the zwitterion stability of BL is enhanced by 1.76 kcal mol(-1) due to the introduction of functional groups. However, the zwitterion of BL will not represent a local minimum on the potential energy surface until the number of water molecules increases up to two (n = 2). With the addition of two and three water molecules, the energy differences between the zwitterions and corresponding canonical isomers were calculated at 3.13 and -1.54 kcal mol(-1), respectively. The zwitterions of BL are mainly stabilized by the H-bonds with the water molecules, especially in the case of three water molecules where the carboxyl-O atoms are largely coordination-saturated by three H-bonds of medium strengths, causing the zwitterion stability even superior to the canonical isomer. With the presence of two and three water molecules, the energy barriers for the conversion processes from the canonical isomers to the zwitterions are equal to 4.96 and 3.13 kcal mol(-1), respectively. It indicated that the zwitterion formation is facile to take place with addition of two molecules and further facilitated by more water molecules. Besides, the zwitterion formation of BL is finished in a single step, different from other NA inhibitors. Owing to the above advantages, BL is a good NA inhibitor candidate and more attention should be paid to explorations of BL-based drugs.
Collapse
Affiliation(s)
- Zhi-Wei Yang
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, China; E-Mails: (Z.-W.Y.); (X.-M.W.); (L.-J.Z.)
| | - Xiao-Min Wu
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, China; E-Mails: (Z.-W.Y.); (X.-M.W.); (L.-J.Z.)
| | - Li-Jun Zhou
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, China; E-Mails: (Z.-W.Y.); (X.-M.W.); (L.-J.Z.)
| | - Gang Yang
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, China; E-Mails: (Z.-W.Y.); (X.-M.W.); (L.-J.Z.)
- Institute of Theoretical Chemistry, Shandong University, Jinan 250100, China
| |
Collapse
|
39
|
Wu R, McMahon TB. Structures, energetics, and dynamics of gas phase ions studied by FTICR and HPMS. MASS SPECTROMETRY REVIEWS 2009; 28:546-585. [PMID: 19353714 DOI: 10.1002/mas.20223] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Both Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) and high-pressure mass spectrometry (HPMS) are very powerful tools in the field of gas phase ion chemistry. Many experimental method developments based on FTICR-MS and HPMS are summarized, including the coupling of a high-pressure external ion source to a FTICR mass spectrometer, blackbody infrared radiative dissociation (BIRD), coupling laser desorption ionization with HPMS, infrared multiple photon dissociation (IRMPD), radiative association and bimolecular routes to gas phase cluster ion formation. An abundance of thermochemical data, such as proton affinities, gas phase acidities, methyl cation affinities and metal cation affinities, have been obtained. Some of these data are the basis of the standard data listed in the NIST thermochemical databases. Ion-molecule interactions, energetics, reactivities, and structures of molecules have been extensively investigated using the methods developed based on HPMS and FTICR mass spectrometric techniques.
Collapse
Affiliation(s)
- Ronghu Wu
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | | |
Collapse
|
40
|
Lee GY. Interaction of Proline with Cu+and Cu2+Ions in the Gas PhaseGab Yong Lee*Department of Life Chemistry, Catholic University of Daegu, Gyeongsan 712‐702, Korea(Received March 3, 2009)INTRODUCTIONCopper ions are the most important transitionmetals involved in several biological processes ofliving systems, including oxidation, dioxygentransport, and charge transfer.1 The study of interactionsbetween the metal ion and amino acids hasattracted considerable attention from experimental2-6and theoretical6-11 viewpoints. Thermochemicalinformation on interactions between the metal ion and biological. JOURNAL OF THE KOREAN CHEMICAL SOCIETY-DAEHAN HWAHAK HOE JEE 2009. [DOI: 10.5012/jkcs.2009.53.3.257] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
41
|
Fei W, Rai AK, Lu Z, Lin Z. Structural stabilities of metalated histidines in gas phase and existence of gaseous zwitterionic histidine conformers. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2008.10.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
42
|
Dunbar RC, Steill JD, Polfer NC, Oomens J. Dimeric Complexes of Tryptophan with M2+ Metal Ions. J Phys Chem A 2009; 113:845-51. [DOI: 10.1021/jp8087176] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Robert C. Dunbar
- FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439MN Nieuwegein, The Netherlands, Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106, and Department of Chemistry, The University of Florida, Gainesville, Florida 32611
| | - Jeffrey D. Steill
- FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439MN Nieuwegein, The Netherlands, Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106, and Department of Chemistry, The University of Florida, Gainesville, Florida 32611
| | - Nick C. Polfer
- FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439MN Nieuwegein, The Netherlands, Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106, and Department of Chemistry, The University of Florida, Gainesville, Florida 32611
| | - Jos Oomens
- FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439MN Nieuwegein, The Netherlands, Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106, and Department of Chemistry, The University of Florida, Gainesville, Florida 32611
| |
Collapse
|
43
|
Rashidian M, Fattahi A. Comparison of thermochemistry of aspartame (artificial sweetener) and glucose. Carbohydr Res 2009; 344:127-33. [DOI: 10.1016/j.carres.2008.09.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2007] [Revised: 08/25/2008] [Accepted: 09/01/2008] [Indexed: 11/16/2022]
|
44
|
Drayss MK, Blunk D, Oomens J, Schäfer M. Infrared Multiple Photon Dissociation Spectroscopy of Potassiated Proline. J Phys Chem A 2008; 112:11972-4. [DOI: 10.1021/jp809111b] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Miriam K. Drayss
- Institute for Organic Chemistry, University Cologne, Greinstraβe 4, 50939 Köln, Germany, and FOM-Institute for Plasmaphysics, Rijnhuizen, Edisonbaan 14, NL-3439 MN Nieuwegein, The Netherlands
| | - Dirk Blunk
- Institute for Organic Chemistry, University Cologne, Greinstraβe 4, 50939 Köln, Germany, and FOM-Institute for Plasmaphysics, Rijnhuizen, Edisonbaan 14, NL-3439 MN Nieuwegein, The Netherlands
| | - Jos Oomens
- Institute for Organic Chemistry, University Cologne, Greinstraβe 4, 50939 Köln, Germany, and FOM-Institute for Plasmaphysics, Rijnhuizen, Edisonbaan 14, NL-3439 MN Nieuwegein, The Netherlands
| | - Mathias Schäfer
- Institute for Organic Chemistry, University Cologne, Greinstraβe 4, 50939 Köln, Germany, and FOM-Institute for Plasmaphysics, Rijnhuizen, Edisonbaan 14, NL-3439 MN Nieuwegein, The Netherlands
| |
Collapse
|
45
|
Atkins CG, Rajabi K, Gillis EAL, Fridgen TD. Infrared Multiple Photon Dissociation Spectra of Proton- and Sodium Ion-Bound Glycine Dimers in the N−H and O−H Stretching Region. J Phys Chem A 2008; 112:10220-5. [DOI: 10.1021/jp805514b] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Chad G. Atkins
- Department of Chemistry, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada A1N 4T8
| | - Khadijeh Rajabi
- Department of Chemistry, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada A1N 4T8
| | - Elizabeth A. L. Gillis
- Department of Chemistry, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada A1N 4T8
| | - Travis D. Fridgen
- Department of Chemistry, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada A1N 4T8
| |
Collapse
|
46
|
Ye SJ, Clark AA, Armentrout PB. Experimental and Theoretical Investigation of Alkali Metal Cation Interactions with Hydroxyl Side-Chain Amino Acids. J Phys Chem B 2008; 112:10291-302. [DOI: 10.1021/jp800861j] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- S. J. Ye
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112
| | - A. A. Clark
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112
| | - P. B. Armentrout
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112
| |
Collapse
|
47
|
Bush MF, Oomens J, Saykally RJ, Williams ER. Effects of Alkaline Earth Metal Ion Complexation on Amino Acid Zwitterion Stability: Results from Infrared Action Spectroscopy. J Am Chem Soc 2008; 130:6463-71. [DOI: 10.1021/ja711343q] [Citation(s) in RCA: 147] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Matthew F. Bush
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Jos Oomens
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Richard J. Saykally
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Evan R. Williams
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| |
Collapse
|
48
|
Polfer NC, Oomens J, Dunbar RC. Alkali Metal Complexes of the Dipeptides PheAla and AlaPhe: IRMPD Spectroscopy. Chemphyschem 2008; 9:579-89. [DOI: 10.1002/cphc.200700700] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
49
|
Wu R, McMahon TB. Stabilization of Zwitterionic Structures of Amino Acids (Gly, Ala, Val, Leu, Ile, Ser and Pro) by Ammonium Ions in the Gas Phase. J Am Chem Soc 2008; 130:3065-78. [DOI: 10.1021/ja076685l] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ronghu Wu
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | - Terry B. McMahon
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| |
Collapse
|
50
|
Sang-Aroon W, Ruangpornvisuti V. Conformational analysis of alkali metal complexes of anionic species of aspartic acid, their interconversion and deprotonation: A DFT investigation. J Mol Graph Model 2008; 26:982-90. [PMID: 17884644 DOI: 10.1016/j.jmgm.2007.08.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2007] [Revised: 08/10/2007] [Accepted: 08/14/2007] [Indexed: 11/27/2022]
Abstract
Gas-phase geometry-optimized structures of aspartate complexes of anionic species (Hasp(-)) with lithium, sodium and potassium metal cations and transition-state structures for their interconversions were obtained using the density functional theory computations at the B3LYP/6-311++G(d,p) level of theory. The metal ion affinities of Hasp(-) species and deprotonation energies of [Hasp-M] complexes, M=Li+, Na+ and K+, and their conformers were obtained. Relative energies of the [Hasp-M] complex conformers, reaction energies, thermodynamic properties, rate and equilibrium constants of their complexation are reported. Binding energies of the most stable complexes with Li+, Na+ and K+ are -168.53, -133.34 and -117.68kcal/mol, respectively. The most stable complex conformer as a tri-coordinated form for aspartate complex with Li(+) and bi-coordinated form for aspartate complexes with Na+ and K+ were found.
Collapse
Affiliation(s)
- Wichien Sang-Aroon
- Supramolecular Chemistry Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | | |
Collapse
|