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Khera M, Kaur N, Goel N. First-Principles Characterization of Noncovalent Interactions in the Enantioselective Oxetane Ring Opening via SPHENOL-Based Chiral Phosphoric Acid Catalyst. J Org Chem 2024. [PMID: 39146239 DOI: 10.1021/acs.joc.4c01022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
The asymmetric ring-opening reaction of 3,3-substituted oxetanes catalyzed by chiral phosphoric acid (CPA) derived from a newly developed SPHENOL (2,2',3,3'-tetrahydro-1,1'-spirobi[phenalene]-9,9'-diol) framework was investigated by performing density functional calculations. The plausible transition states were traced by considering the oxetane activation mode. The energy profiles obtained for various substrates provide a rational understanding of the reaction at the atomic level. The truncation models help to attribute the reaction initiation and origin of enantioselectivity to three types of noncovalent interactions between the catalyst and the substrate. The Quantum theory of atoms in molecules (QTAIM), Noncovalent Interactions (NCI) Plots, and Wiberg Bond Index (WBI) provide conclusive evidence of the origin of stereoselectivity for the intramolecular desymmetrization of the five substrates considered here. The current study establishes that the SPHENOL-derived CPA catalyst forges enantioselective desymmetrization of 3,3-substituted oxetanes with higher enantiomeric excess in comparison to previously known SPINOL- and BINOL-derived CPA catalysts.
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Affiliation(s)
- Mayank Khera
- Computational and Theoretical Chemistry Group, Department of Chemistry & Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India
- Department of Applied Science, Chandigarh College of Engineering, CGC-Jhanjheri, Mohali 140307, India
| | - Navjot Kaur
- Faculty of Science, SGT University, Gurugram 122505, India
| | - Neetu Goel
- Computational and Theoretical Chemistry Group, Department of Chemistry & Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India
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Ortega DE, Cortés-Arriagada D. Atmospheric microplastics and nanoplastics as vectors of primary air pollutants - A theoretical study on the polyethylene terephthalate (PET) case. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 318:120860. [PMID: 36521720 DOI: 10.1016/j.envpol.2022.120860] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 12/09/2022] [Accepted: 12/10/2022] [Indexed: 06/17/2023]
Abstract
Polyethylene terephthalate (PET) microplastics and nanoplastics are ubiquitously present in the atmosphere as atmospheric and airborne forms (PET-aMPs). Using first-principles calculations, we analyze the uptake of primary air pollutants onto PET-aMPs, focusing on their stabilities, adsorption mechanisms, and thermochemistry. The results show that PET-aMPs are selective for the spontaneous adsorption of CO, CO2, NO, N2O, NO2, NH3, and SO2, reaching stable adsorption energies of 6-20 kcal/mol per molecule, with comparable uptake ability than carbon-based materials, metals/metalloids, and metal oxide surfaces. Then, PET-aMPs become a vector for coexisting air pollutants in the atmosphere, which adsorb by inner or outer adsorption depending on the molecular polarity (dipole moment) and atomic constitution (electronegativity) of gaseous molecules. Also, atmospheric H2O and O2 are not competitive molecules, and ozone could enhance adsorption due to surface oxidation and structure breakdown. The interplay of electrostatic (46-61%) and dispersion forces (21-58%) drives the adsorption mechanism, where low-polar pollutants display almost a balanced electrostatic vs. dispersion contribution, while high polar molecules display a higher electrostatic stabilization. The outer adsorption is reached by strong dispersion, hydrogen bonding, and dipole-dipole-induced pairs, while lone-pair-π interactions appear in the inner adsorption regime. These results expand the understanding of the hazards and risks of atmospheric and airborne microplastics/nanoplastics, their impacts, co-transport ability, and interaction with the environment.
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Affiliation(s)
- Daniela E Ortega
- Centro Integrativo de Biología y Química Aplicada (CIBQA), Universidad Bernardo O'Higgins, General Gana 1702, Santiago, 8370854, Chile.
| | - Diego Cortés-Arriagada
- Programa Institucional de Fomento a La Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, Ignacio Valdivieso 2409, San Joaquín, Santiago, 8940577, Chile.
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3
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Ansari M, Rajaraman G. Comparative oxidative ability of mononuclear and dinuclear high-valent iron-oxo species towards the activation of methane: does the axial/bridge atom modulate the reactivity? Dalton Trans 2023; 52:308-325. [PMID: 36504243 DOI: 10.1039/d2dt02559k] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Over the years, mononuclear FeIVO species have been extensively studied, but the presence of dinuclear FeIVO species in soluble methane monooxygenase (sMMO) has inspired the development of biomimic models that could activate inert substrates such as methane. There are some successful attempts; particularly the [(Por)(m-CBA) FeIV(μ-N)FeIV(O)(Por˙+)]- species has been reported to activate methane and yield decent catalytic turnover numbers and therefore regarded as the closest to the sMMO enzyme functional model, as no mononuclear FeIVO analogues could achieve this feat. In this work, we have studied a series of mono and dinuclear models using DFT and ab initio DLPNO-CCSD(T) calculations to probe the importance of nuclearity in enhancing the reactivity. We have probed the catalytic activities of four complexes: [(HO)FeIV(O)(Por)]- (1), [(HO)FeIV(O)(Por˙+)] (2), μ-oxo dinuclear iron species [(Por)(m-CBA)FeIV(μ-O)FeIV(O) (Por˙+)]- (3) and N-bridged dinuclear iron species [(Por)(m-CBA)FeIV(μ-N)FeIV(O)(Por˙+)]- (4) towards the activation of methane. Additionally, calculations were performed on the mononuclear models [(X)FeIV(O)(Por˙+)]n {X = N 4a (n = -2), NH 4b (n = -1) and NH24c (n = 0)} to understand the role of nuclearity in the reactivity. DFT calculations performed on species 1-4 suggest an interesting variation among them, with species 1-3 possessing an intermediate spin (S = 1) as a ground state and species 4 possessing a high-spin (S = 2) as a ground state. Furthermore, the two FeIV centres in species 3 and 4 are antiferromagnetically coupled, yielding a singlet state with a distinct difference in their electronic structure. On the other hand, species 2 exhibits a ferromagnetic coupling between the FeIV and the Por˙+ moiety. Our calculations suggest that the higher barriers for the C-H bond activation of methane and the rebound step for species 1 and 3 are very high in energy, rendering them unreactive towards methane, while species 2 and 4 have lower barriers, suggesting their reactivity towards methane. Studies on the system reveal that model 4a has multiple FeN bonds facilitating greater reactivity, whereas the other two models have longer Fe-N bonds and less radical character with steeper barriers. Strong electronic cooperativity is found to be facilitated by the bridging nitride atom, and this cooperativity is suppressed by substituents such as oxygen, rendering them inactive. Thus, our study unravels that apart from enhancing the nuclearity, bridging atoms that facilitate strong cooperation between the metals are required to activate very inert substrates such as methane, and our results are broadly in agreement with earlier experimental findings.
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Affiliation(s)
- Mursaleem Ansari
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India.
| | - Gopalan Rajaraman
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India.
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Association Complexes of Calix[6]arenes with Amino Acids Explained by Energy-Partitioning Methods. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27227938. [PMID: 36432040 PMCID: PMC9699162 DOI: 10.3390/molecules27227938] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/09/2022] [Accepted: 11/09/2022] [Indexed: 11/18/2022]
Abstract
Intermolecular complexes with calixarenes are intriguing because of multiple possibilities of noncovalent binding for both polar and nonpolar molecules, including docking in the calixarene cavity. In this contribution calix[6]arenes interacting with amino acids are studied with an additional aim to show that tools such as symmetry-adapted perturbation theory (SAPT), functional-group SAPT (F-SAPT), and systematic molecular fragmentation (SMF) methods may provide explanations for different numbers of noncovalent bonds and of their varying strength for various calixarene conformers and guest molecules. The partitioning of the interaction energy provides an easy way to identify hydrogen bonds, including those with unconventional hydrogen acceptors, as well as other noncovalent bonds, and to find repulsive destabilizing interactions between functional groups. Various other features can be explained by energy partitioning, such as the red shift of an IR stretching frequency for some hydroxy groups, which arises from their attraction to the phenyl ring of calixarene. Pairs of hydrogen bonds and other noncovalent bonds of similar magnitude found by F-SAPT explain an increase in the stability of both inclusion and outer complexes.
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Dutta D, Sharma P, Gomila RM, Frontera A, Barcelo-Oliver M, Verma AK, Gogoi M, Bhattacharyya MK. Solvent driven structural topologies involving unconventional O H(methanol)⋯π contact and anti-cooperative HB⋯anion-π⋯HB assemblies with unusual enclathration of dual guest (H2O)4 cores in Mn(II) and Ni(II) coordination compounds: Antiproliferative evaluation and theoretical studies. Polyhedron 2021. [DOI: 10.1016/j.poly.2021.115503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Kazim M, Guan L, Chopra A, Sun R, Siegler MA, Lectka T. Switching a HO···π Interaction to a Nonconventional OH···π Hydrogen Bond: A Completed Crystallographic Puzzle. J Org Chem 2020; 85:9801-9807. [PMID: 32633510 DOI: 10.1021/acs.joc.0c01121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this article, we present crystallographic and spectroscopic evidence of a tunable system wherein a HO···π interaction switches incrementally to a nonconventional OH···π hydrogen bonding (HB) interaction. More specifically, we report the synthesis of substituted forms of model system 1 to study the effects of aryl ring electronic density on the qualitative characteristics of OH···π hydrogen bonds therein. The OH stretch in experimental infrared data, in agreement with density-functional theory (DFT) calculations, shows continuous red-shifts as the adjacent ring becomes more electron rich. For example, the OH stretch of an amino-substituted analogue is red-shifted by roughly 50 cm-1 compared to the same stretch in the CF3 analogue, indicating a significantly stronger HB interaction in the former. Moreover, DFT calculations (ωB97XD/6-311+G**) predict that increasing electronic density on the adjacent top ring reduces the aryl π-OH σ* energy gap with a concomitant enhancement of the OH n-π* energy gap. Consequently, a dominant π-σ* interaction in the amino substituted analogue locks the system in the in-form while a favorable n-π* interaction reverses the orientation of the oxygen-bound hydrogen in its protonated form. Additionally, the 1H NMR data of various analogues reveal that stronger OH···π interactions in systems with electron-rich aromatic rings slow exchange of the alcoholic proton, thereby revealing coupling with the geminal proton. Finally, X-ray crystallographic analyses of a spectrum of analogues clearly visualize the three distinct stages of "switch"-starting with exclusive HO···π, to partitioned HO···π/OH···π, and finally to achieving exclusive OH···π forms. Furthermore, the crystal structure of the amino analogue reveals an interesting feature in which an extended HB network, involving two conventional (NH···O) and two nonconventional (OH···π) HBs, dimerizes and anchors the molecule in the unit cell.
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Affiliation(s)
- Muhammad Kazim
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Liangyu Guan
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States.,Calibr-A Division of Scripps Research, 11119 N Torrey Pines Rd, La Jolla, San Diego, California 92037, United States
| | - Anant Chopra
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Roy Sun
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Maxime A Siegler
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Thomas Lectka
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
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7
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de Souza GLC, Peterson KA. Probing the ionization potentials of the formaldehyde dimer. J Chem Phys 2020; 152:194305. [PMID: 33687222 DOI: 10.1063/5.0009658] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
In this work, we present a computational investigation on the ionization potentials (IPs) of the formaldehyde dimer, (H2CO)2. Twelve lowest lying IPs (corresponding to the entire valence orbitals) for both C2h and Cs symmetry conformers have been computed at the coupled cluster level of theory using large correlation consistent basis sets with extrapolation to the complete basis set limit and consideration of core electron correlation effects. Specifically, the equation-of-motion ionization potential coupled-cluster with single and double (EOMIP-CCSD) excitations method with the aug-cc-pVXZ and aug-cc-pCVXZ (X = T, Q, and 5) basis sets combined with the Feller-Peterson-Dixon approach was employed, as well as CCSD with perturbative triples [CCSD(T)] with the aug-cc-pVTZ basis sets. In general, excellent agreement was observed from the comparison between the results obtained through the use of these approaches. In addition, the IPs for the formaldehyde monomer were also obtained using such methodologies and the results compared with existing experimental data; excellent agreement was also observed in this case. To the best of our knowledge, this work represents the first of its kind to determine the IPs for all these systems using a high level theory approach and is presented to motivate experimental investigations, e.g., studies involving photoionization, particularly for the formaldehyde dimer. The equilibrium binding energy of the C2h dimer is calculated in this work at the CCSD(T)/aug-cc-pVTZ level of theory to be -4.71 kcal/mol. At this same level of theory, the equilibrium isomerization energy between C2h and Cs conformers is 0.76 kcal/mol (Cs conformer being more stable).
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Affiliation(s)
- Gabriel L C de Souza
- Departamento de Química, Universidade Federal de Mato Grosso, Cuiabá, Mato Grosso 78060-900, Brazil
| | - Kirk A Peterson
- Department of Chemistry, Washington State University, Pullman, Washington 99164, USA
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8
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Veljković DŽ. Strong CH/O interactions between polycyclic aromatic hydrocarbons and water: Influence of aromatic system size. J Mol Graph Model 2018; 80:121-125. [PMID: 29331729 DOI: 10.1016/j.jmgm.2017.12.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 12/19/2017] [Accepted: 12/21/2017] [Indexed: 10/18/2022]
Abstract
Energies of CH/O interactions between water molecule and polycyclic aromatic hydrocarbons with a different number of aromatic rings were calculated using ab initio calculations at MP2/cc-PVTZ level. Results show that an additional aromatic ring in structure of polycyclic aromatic hydrocarbons significantly strengthens CH/O interactions. Calculated interaction energies in optimized structures of the most stable tetracene/water complex is -2.27 kcal/mol, anthracene/water is -2.13 kcal/mol and naphthalene/water is -1.97 kcal/mol. These interactions are stronger than CH/O contacts in benzene/water complex (-1.44 kcal/mol) while CH/O contacts in tetracene/water complex are even stronger than CH/O contacts in pyridine/water complexes (-2.21 kcal/mol). Electrostatic potential maps for different polycyclic aromatic hydrocarbons were calculated and used to explain trends in the energies of interactions.
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Affiliation(s)
- Dušan Ž Veljković
- Department of Chemistry, University of Belgrade, Studentski trg 12-16, Belgrade, Serbia.
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9
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Guan L, Holl MG, Pitts CR, Struble MD, Siegler MA, Lectka T. Through-Space Activation Can Override Substituent Effects in Electrophilic Aromatic Substitution. J Am Chem Soc 2017; 139:14913-14916. [DOI: 10.1021/jacs.7b09792] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Liangyu Guan
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Maxwell Gargiulo Holl
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Cody Ross Pitts
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Mark D. Struble
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Maxime A. Siegler
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Thomas Lectka
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
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10
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Maier JM, Li P, Vik EC, Yehl CJ, Strickland SMS, Shimizu KD. Measurement of Solvent OH−π Interactions Using a Molecular Balance. J Am Chem Soc 2017; 139:6550-6553. [DOI: 10.1021/jacs.7b02349] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Josef M. Maier
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Ping Li
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Erik C. Vik
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Christopher J. Yehl
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Sharon M. S. Strickland
- Department
of Biology, Chemistry, and Physics, Converse College, Spartanburg, South Carolina 29302, United States
| | - Ken D. Shimizu
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
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Affiliation(s)
- A. Subha Mahadevi
- Centre for Molecular Modelling, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, India 500607
| | - G. Narahari Sastry
- Centre for Molecular Modelling, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, India 500607
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12
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Marchione D, McCoustra MRS. Non-covalent interaction of benzene with methanol and diethyl ether solid surfaces. Phys Chem Chem Phys 2016; 18:20790-801. [DOI: 10.1039/c6cp01787h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We have investigated the interactions involved at the interface of binary, layered ices (benzene on methanol and on diethyl ether) by means of laboratory experiments and ab initio calculations on model clusters.
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13
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Dong XY, Li X, Li B, Zhu YY, Zang SQ, Tang MS. Water sandwiched by a pair of aromatic rings in a proton-conducting metal–organic framework. Dalton Trans 2016; 45:18142-18146. [DOI: 10.1039/c6dt03632e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Water–benzene interactions are investigated in a metal–organic framework incorporating strong H-bond nets which contribute to distinct proton conduction.
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Affiliation(s)
- Xi-Yan Dong
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou 450001
- China
- College of Chemistry and Chemical Engineering
| | - Xue Li
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou 450001
- China
| | - Bo Li
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou 450001
- China
| | - Yan-Yan Zhu
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou 450001
- China
| | - Shuang-Quan Zang
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou 450001
- China
| | - Ming-Sheng Tang
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou 450001
- China
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14
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15
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A theoretical investigation of the competition between hydrogen bonding and lone pair⋯π interaction in complexes of TNT with NH3. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2015.04.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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16
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Struble MD, Holl MG, Coombs G, Siegler MA, Lectka T. Synthesis of a Tight Intramolecular OH···Olefin Interaction, Probed by IR, 1H NMR, and Quantum Chemistry. J Org Chem 2015; 80:4803-7. [DOI: 10.1021/acs.joc.5b00470] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mark D. Struble
- Department
of Chemistry, New Chemistry Building, Johns Hopkins University, 3400
North Charles Street, Baltimore, Maryland 21218 United States
| | - Maxwell Gargiulo Holl
- Department
of Chemistry, New Chemistry Building, Johns Hopkins University, 3400
North Charles Street, Baltimore, Maryland 21218 United States
| | - Gavin Coombs
- Department
of Chemistry, New Chemistry Building, Johns Hopkins University, 3400
North Charles Street, Baltimore, Maryland 21218 United States
| | - Maxime A. Siegler
- Department
of Chemistry, New Chemistry Building, Johns Hopkins University, 3400
North Charles Street, Baltimore, Maryland 21218 United States
| | - Thomas Lectka
- Department
of Chemistry, New Chemistry Building, Johns Hopkins University, 3400
North Charles Street, Baltimore, Maryland 21218 United States
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Hussain HB, Wilson KA, Wetmore SD. Serine and Cysteine π-Interactions in Nature: A Comparison of the Frequency, Structure, and Stability of Contacts Involving Oxygen and Sulfur. Aust J Chem 2015. [DOI: 10.1071/ch14598] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Despite many DNA–protein π-interactions in high-resolution crystal structures, only four X–H···π or X···π interactions were found between serine (Ser) or cysteine (Cys) and DNA nucleobase π-systems in over 100 DNA–protein complexes (where X = O for Ser and X = S for Cys). Nevertheless, 126 non-covalent contacts occur between Ser or Cys and the aromatic amino acids in many binding arrangements within proteins. Furthermore, Ser and Cys protein–protein π-interactions occur with similar frequencies and strengths. Most importantly, due to the great stability that can be provided to biological macromolecules (up to –20 kJ mol–1 for neutral π-systems or –40 kJ mol–1 for cationic π-systems), Ser and Cys π-interactions should be considered when analyzing protein stability and function.
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18
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Mitoraj MP, Janjić GV, Medaković VB, Veljković DŽ, Michalak A, Zarić SD, Milčić MK. Nature of the water/aromatic parallel alignment interactions. J Comput Chem 2014; 36:171-80. [DOI: 10.1002/jcc.23783] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 10/05/2014] [Accepted: 10/17/2014] [Indexed: 11/06/2022]
Affiliation(s)
- Mariusz P. Mitoraj
- Faculty of Chemistry; Department of Theoretical Chemistry; Jagiellonian University; R. Ingardena 3, 30-060 Krakow Poland
| | - Goran V. Janjić
- Institute of Chemistry, Technology and Metallurgy, University of Belgrade; Njegoševa 12 11000 Belgrade Serbia
| | - Vesna B. Medaković
- Department of Chemistry; University of Belgrade; Studentski trg 12-16 11000 Belgrade Serbia
| | - Dušan Ž. Veljković
- Department of Chemistry; University of Belgrade; Studentski trg 12-16 11000 Belgrade Serbia
| | - Artur Michalak
- Faculty of Chemistry; Department of Theoretical Chemistry; Jagiellonian University; R. Ingardena 3, 30-060 Krakow Poland
| | - Snežana D. Zarić
- Department of Chemistry; University of Belgrade; Studentski trg 12-16 11000 Belgrade Serbia
- Department of Chemistry; Texas A & M University at Qatar; P.O. Box 23874 Doha Qatar
| | - Miloš K. Milčić
- Department of Chemistry; University of Belgrade; Studentski trg 12-16 11000 Belgrade Serbia
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Janjić GV, Malkov SN, Zivković MV, Zarić SD. What are preferred water-aromatic interactions in proteins and crystal structures of small molecules? Phys Chem Chem Phys 2014; 16:23549-53. [PMID: 25271703 DOI: 10.1039/c4cp00929k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The distribution of water molecules around aromatic rings in the protein structures and crystal structures of small molecules shows quite a small number of the strongest OH-π interactions, a larger number of parallel interactions, and the largest number of the weakest CH-O interactions.
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Affiliation(s)
- Goran V Janjić
- Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Njegoševa 12, P.O. Box 473, Belgrade, Serbia
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Vojislavljević-Vasilev DZ, Janjić GV, Medaković VB, Blagojević JP, Zarić SD. Parallel water/aromatic interactions of non-coordinated and coordinated water. Chemphyschem 2014; 15:2386-96. [PMID: 24840235 DOI: 10.1002/cphc.201402004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 03/19/2014] [Indexed: 11/07/2022]
Abstract
The parallel interactions of non-coordinated and coordinated water molecules with an aromatic ring were studied by analyzing data in the Cambridge structural database (CSD) and by using quantum chemical calculations. The CSD data show that water/aromatic contacts prefer parallel to OH/π interactions, which indicates the importance of parallel interactions. The results reveal the influence of water coordination to a metal ion; the interactions of aqua complexes are stronger. Coordinated water molecules prefer a parallel-down orientation in which one OH bond is parallel to the aromatic ring, whereas the other OH bond points to the plane of the ring. The interactions of aqua complexes with parallel-down water/benzene orientation are as strong as the much better known OH/π orientations. The strongest calculated interaction energy is -14.89 kcal mol(-1) . The large number of parallel contacts in crystal structures and the quite strong interactions indicate the importance of parallel orientation in water/benzene interactions.
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Veljković DŽ, Medaković VB, Andrić JM, Zarić SD. C–H/O interactions of nucleic bases with a water molecule: a crystallographic and quantum chemical study. CrystEngComm 2014. [DOI: 10.1039/c4ce00595c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The C–H/O interactions of nucleic bases are substantially stronger than the C–H/O interactions of benzene and pyridine. These results can be very important for molecular recognition of DNA and RNA.
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Affiliation(s)
- D. Ž. Veljković
- Department of Chemistry
- University of Belgrade
- 11000 Belgrade, Serbia
| | - V. B. Medaković
- Department of Chemistry
- University of Belgrade
- 11000 Belgrade, Serbia
| | - J. M. Andrić
- Innovation Center
- Department of Chemistry
- 11000 Belgrade, Serbia
| | - S. D. Zarić
- Department of Chemistry
- University of Belgrade
- 11000 Belgrade, Serbia
- Department of Chemistry
- Texas A&M University at Qatar
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