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Kuntar SP, Ghosh A, Ghanty TK. Theoretical prediction of donor-acceptor type novel complexes with strong noble gas-boron covalent bond. Phys Chem Chem Phys 2024; 26:4975-4988. [PMID: 38258349 DOI: 10.1039/d3cp02667a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The experimental identification of NgBeO molecules, followed by the recent theoretical exploration of super-strong NgBO+ (Ng = He-Rn) ions motivated us to investigate the stability of iso-electronic NgBNH+ (Ng = He-Rn) ions using various ab initio-based quantum chemical methods. The hydrogen-like chemical behavior of gold in small clusters and molecules also inspired us to study the nature of the bonding interactions in NgBNAu+ ions compared to that in NgBNH+ ions. The calculated Ng-B bond lengths in the predicted ions have been found to be much lower than the corresponding covalent limits, indicating a covalent Ng-B interaction in both the NgBNH+ and NgBNAu+ ions. In addition, the Ng-B bond dissociation energies are found to be in the range of 136.7-422.8 kJ mol-1 for NgBNH+ and 77.4-319.1 kJ mol-1 for NgBNAu+, implying the stable nature of the predicted ions. Interestingly, the Ng-B bond length (except for Ne) is the lowest reported to date together with the highest He-B and Ne-B binding energies considering all the neutral and cationic complexes containing Ng-B bonding motifs. Moreover, the natural bonding orbital (NBO) and electron density-based atoms-in-molecule (AIM) analysis reveal the covalent nature of the Ng-B bond in the predicted ions. Furthermore, the energy decomposition analysis together with the natural bond orbital in the chemical valence (EDA-NOCV) studies indicate that the orbital interaction energy is the main contributor to the total attraction energy in the Ng-B bonds. All the calculated results indicate the hydrogen-like chemical behavior of gold in the predicted NgBNM+ ions, showing further evidence of the concept of "gold-hydrogen analogy". Also, for comparison, the corresponding Cu and Ag analogs are investigated. All the computed results together with the experimental identification of the NgMX (Ng = Ar-Xe; M = Cu, Ag, Au; X = F, Cl), ArOH+, and NgBeO (Ng = Ar-Xe) systems clearly indicate that it may be possible to prepare and characterize the predicted NgBNM+ ions experimentally using suitable technique(s).
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Affiliation(s)
- Subrahmanya Prasad Kuntar
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400 094, India
- Bio-Science Group, Bhabha Atomic Research Centre, Mumbai 400 085, India.
| | - Ayan Ghosh
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400 094, India
- Laser and Plasma Technology Division, Beam Technology Development Group, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Tapan K Ghanty
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400 094, India
- Bio-Science Group, Bhabha Atomic Research Centre, Mumbai 400 085, India.
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2
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Wang D, Li P, Yan JL, Mao H, Liu L, Wang M, Chen M, Ye T, Chen Y. Assigning the stereochemical structures of aurantinin A and B with the assistance of biosynthetic investigations. Org Chem Front 2022. [DOI: 10.1039/d2qo01251k] [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
The stereochemistry of aurantinin was determined by spectroscopic and computational analysis with the assistance of biosynthetic studies. The latter method provided critical evidence for the assignment of the configuration of the 3-ketosugar moiety.
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Affiliation(s)
- Dacheng Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Pengwei Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jia-Lei Yan
- Innovation Center of Marine Biotechnology and Pharmaceuticals, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, Guangdong, China
| | - Huijin Mao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lilu Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Min Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Innovation Center of Marine Biotechnology and Pharmaceuticals, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, Guangdong, China
| | - Meng Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tao Ye
- Innovation Center of Marine Biotechnology and Pharmaceuticals, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, Guangdong, China
- State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Xili, Nanshan District, Shenzhen 518055, China
| | - Yihua Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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3
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Jana G, Pal R, Chattaraj PK. XNgNSi (X = HCC, F; Ng = Kr, Xe, Rn): A New Class of Metastable Insertion Compounds Containing Ng-C/F and Ng-N Bonds and Possible Isomerization therein. J Phys Chem A 2021; 125:10514-10523. [PMID: 34747606 DOI: 10.1021/acs.jpca.1c07677] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recently, astronomically important silaisocyanoacetylene (HCCNSi) possessing a large dipole moment has been detected for the first time with the help of crossed molecular beam experiments. Quantum chemical computations at higher levels of theory have also been performed to characterize the transient species. In this study, we have analyzed the equilibrium geometry, stability, reactivity, and energetics as well as the nature of bonding in the noble gas (Ng) inserted HCCNSi compound. We have also considered its F analogue to understand the influence of the most electronegative atom in the compound. Metastable behavior of the XNgNSi compounds (X = HCC, F; Ng = Kr-Rn) is examined by calculating thermochemical parameters like free energy change (ΔG) and zero-point-energy-corrected dissociation energy (D0) at 298 K for all possible two-body (2B) and three-body (3B) (both neutral as well as ionic) dissociation channels using coupled-cluster theory [CCSD(T)] in addition to density functional theory (DFT) as well as second order Møller-Plesset perturbation theory (MP2). The set of predicted compounds is found to be endergonic in nature, having high positive free energy change suggesting the thermochemical stability of the compounds except for the 2B Ng-release paths. Though thermodynamically feasible, they are kinetically protected with very high activation free energy barriers. Interestingly, the release of Ng from the parent moiety XNgNSi produces the XSiN isomer, by 180° flipping of the NSi moiety. This can also be seen in the dynamical simulation carried out with the help of atom-centered density matrix propagation (ADMP) technique at 2000K for 1 ps. The bonding in Ng-C, Ng-F, and Ng-N bonds of the studied compounds is analyzed and described with the aid of natural bond orbital (NBO), topological parameters computed using atoms-in-molecules theory (AIM), energy decomposition analysis (EDA), and adaptive natural density partitioning (AdNDP) methods. The natural charge distribution on the constituent atoms suggests that the compounds can be partitioned into both ways of representations, viz., neutral radical as well as ionic fragments. Lastly, the reactivity of the compounds is scrutinized using certain reactivity descriptors calculated within the domain of conceptual density functional theory (CDFT).
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Affiliation(s)
- Gourhari Jana
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai-400076, India
| | - Ranita Pal
- Advanced Technology Development Centre, Indian Institute of Technology Kharagpur, Kharagpur-721302, India
| | - Pratim Kumar Chattaraj
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai-400076, India.,Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur-721302, India
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4
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Lin WT, Shih YJ, Hsu TJ, Hu WP. Noble Gas in a Ring. Molecules 2021; 26:molecules26154677. [PMID: 34361829 PMCID: PMC8347956 DOI: 10.3390/molecules26154677] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 07/22/2021] [Accepted: 07/29/2021] [Indexed: 11/23/2022] Open
Abstract
We have designed a new type of molecule with a noble gas (Ng = Kr and Xe) atom in a six-membered ring. Their structures and stability have been studied by density functional theory and by correlated electronic structure calculations. The results showed that the six-membered ring is planar with very short Ng–O and Ng–N polar covalent bonds. The calculated energy barriers for all the unimolecular dissociation pathways are higher than 20 and 35 kcal/mol for Ng = Kr and Xe, respectively. The current study suggests that these molecules and their derivatives might be synthesized and observable at cryogenic conditions.
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Affiliation(s)
- Wei-Te Lin
- Department of Chemistry and Biochemistry, National Chung Cheng University, Chia-Yi 621, Taiwan; (W.-T.L.); (Y.-J.S.)
| | - Ya-Jyun Shih
- Department of Chemistry and Biochemistry, National Chung Cheng University, Chia-Yi 621, Taiwan; (W.-T.L.); (Y.-J.S.)
| | - Tzu-Jeng Hsu
- Department of Mechanical Engineering, Chung Yuan Christian University, Chung-Li 320, Taiwan;
| | - Wei-Ping Hu
- Department of Chemistry and Biochemistry, National Chung Cheng University, Chia-Yi 621, Taiwan; (W.-T.L.); (Y.-J.S.)
- Correspondence:
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5
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Santos GFN, Carvalho LC, Oliveira DAS, Rego DG, Bueno MA, Oliveira BG. The definitive challenge of forming uncommon pseudo‐π···H–F and C···H–F hydrogen bonds on cyclic and cubic nonpolar hydrocarbons. J PHYS ORG CHEM 2020. [DOI: 10.1002/poc.4098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | - Leila Cardoso Carvalho
- Centro das Ciências Exatas e das Tecnologias Universidade Federal do Oeste da Bahia Barreiras Brazil
| | | | - Danilo Guimarães Rego
- Centro das Ciências Exatas e das Tecnologias Universidade Federal do Oeste da Bahia Barreiras Brazil
| | - Mauro Alves Bueno
- Centro das Ciências Exatas e das Tecnologias Universidade Federal do Oeste da Bahia Barreiras Brazil
| | - Boaz Galdino Oliveira
- Centro das Ciências Exatas e das Tecnologias Universidade Federal do Oeste da Bahia Barreiras Brazil
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Pettersson P, Barth A. Correlations between the structure and the vibrational spectrum of the phosphate group. Implications for the analysis of an important functional group in phosphoproteins. RSC Adv 2020; 10:4715-4724. [PMID: 35495230 PMCID: PMC9049017 DOI: 10.1039/c9ra10366j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 01/17/2020] [Indexed: 12/02/2022] Open
Abstract
Density functional theory calculations were used to establish correlations between the structure and the vibrational spectrum of the phosphate group in model compounds for phosphorylated amino acids. The model compounds were acetyl phosphate, methyl phosphate, and p-tolyl phosphate, which represented the phosphorylated amino acids aspartyl phosphate, serine or threonine phosphate, and tyrosine phosphate, respectively. The compounds were placed in different environments consisting of one or several HF or H2O molecules, which modeled interactions of phosphorylated amino acids in the protein environment. The calculations were performed with the B3LYP functional and the 6-311++G(3df, 3pd) basis set. In general, the wavenumbers (or frequencies) of the stretching vibrations of the terminal P–O bonds correlated better with bond lengths of the phosphate group than with its bond angles. The best correlations were obtained with the shortest and the mean terminal P–O bond lengths with standard deviations from the trend line of only 0.2 pm. Other useful correlations were observed with the bond length difference between the shortest and longest terminal P–O bond and with the bond length of the bridging P–O bond. Vibrational frequencies of phosphate are sensitive to bond length changes on the sub-picometer scale.![]()
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Affiliation(s)
- Pontus Pettersson
- Department of Biochemistry and Biophysics
- Arrhenius Laboratories
- Stockholm University
- 10691 Stockholm
- Sweden
| | - Andreas Barth
- Department of Biochemistry and Biophysics
- Arrhenius Laboratories
- Stockholm University
- 10691 Stockholm
- Sweden
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7
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Borocci S, Grandinetti F, Nunzi F, Sanna N. Classifying the chemical bonds involving the noble-gas atoms. NEW J CHEM 2020. [DOI: 10.1039/d0nj01927e] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The Ng–X bonds are classified into covalent (Cov), and different types of non-covalent (nCov), or partially-covalent (pCov) interactions.
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Affiliation(s)
- Stefano Borocci
- Dipartimento per la Innovazione nei Sistemi Biologici
- Agroalimentari e Forestali (DIBAF)
- Università della Tuscia
- 01100 Viterbo
- Italy
| | - Felice Grandinetti
- Dipartimento per la Innovazione nei Sistemi Biologici
- Agroalimentari e Forestali (DIBAF)
- Università della Tuscia
- 01100 Viterbo
- Italy
| | - Francesca Nunzi
- Dipartimento di Chimica
- Biologia e Biotecnologie (DCBB)
- 8 06123 Perugia
- Italy
- Istituto di Scienze e Tecnologie Chimiche (SCITEC) “Giulio Natta” del CNR
| | - Nico Sanna
- Dipartimento per la Innovazione nei Sistemi Biologici
- Agroalimentari e Forestali (DIBAF)
- Università della Tuscia
- 01100 Viterbo
- Italy
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8
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Martini P, Kranabetter L, Goulart M, Rasul B, Gatchell M, Scheier P, Echt O. Atomic Gold Ions Clustered with Noble Gases: Helium, Neon, Argon, Krypton, and Xenon. J Phys Chem A 2019; 123:9505-9513. [PMID: 31621319 DOI: 10.1021/acs.jpca.9b06715] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
High-resolution mass spectra of helium droplets doped with gold and ionized by electrons reveal HenAu+ cluster ions. Additional doping with heavy noble gases results in NenAu+, ArnAu+, KrnAu+, and XenAu+ cluster ions. The high stability predicted for covalently bonded Ar2Au+, Kr2Au+, and Xe2Au+ is reflected in their relatively high abundance. Surprisingly, the abundance of Ne2Au+, which is predicted to have zero covalent bonding character and no enhanced stability, features a local maximum, too. The predicted size and structure of complete solvation shells surrounding ions with essentially nondirectional bonding depends primarily on the ratio σ* of the ion-ligand versus the ligand-ligand distance. For Au+ solvated in helium and neon, the ratio σ* is slightly below 1, favoring icosahedral packing in agreement with a maximum observed in the corresponding abundance distributions at n = 12. HenAu+ appears to adopt two additional solvation shells of Ih symmetry, containing 20 and 12 atoms, respectively. For ArnAu+, with σ* ≈ 0.67, one would expect a solvation shell of octahedral symmetry, in agreement with an enhanced ion abundance at n = 6. Another anomaly in the ion abundance at Ar9Au+ matches a local maximum in its computed dissociation energy.
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Affiliation(s)
- Paul Martini
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck , Technikerstr. 25 , A-6020 Innsbruck , Austria
| | - Lorenz Kranabetter
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck , Technikerstr. 25 , A-6020 Innsbruck , Austria
| | - Marcelo Goulart
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck , Technikerstr. 25 , A-6020 Innsbruck , Austria
| | - Bilal Rasul
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck , Technikerstr. 25 , A-6020 Innsbruck , Austria
- Department of Physics , University of Sargodha , 40100 Sargodha , Pakistan
| | - Michael Gatchell
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck , Technikerstr. 25 , A-6020 Innsbruck , Austria
- Department of Physics , Stockholm University , 106 91 Stockholm , Sweden
| | - Paul Scheier
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck , Technikerstr. 25 , A-6020 Innsbruck , Austria
| | - Olof Echt
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck , Technikerstr. 25 , A-6020 Innsbruck , Austria
- Department of Physics , University of New Hampshire , Durham , New Hampshire NH 03824 , United States
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9
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Saha R, Jana G, Pan S, Merino G, Chattaraj PK. How Far Can One Push the Noble Gases Towards Bonding?: A Personal Account. Molecules 2019; 24:E2933. [PMID: 31412650 PMCID: PMC6719121 DOI: 10.3390/molecules24162933] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 07/29/2019] [Accepted: 07/30/2019] [Indexed: 01/29/2023] Open
Abstract
Noble gases (Ngs) are the least reactive elements in the periodic table towards chemical bond formation when compared with other elements because of their completely filled valence electronic configuration. Very often, extreme conditions like low temperatures, high pressures and very reactive reagents are required for them to form meaningful chemical bonds with other elements. In this personal account, we summarize our works to date on Ng complexes where we attempted to theoretically predict viable Ng complexes having strong bonding to synthesize them under close to ambient conditions. Our works cover three different types of Ng complexes, viz., non-insertion of NgXY type, insertion of XNgY type and Ng encapsulated cage complexes where X and Y can represent any atom or group of atoms. While the first category of Ng complexes can be thermochemically stable at a certain temperature depending on the strength of the Ng-X bond, the latter two categories are kinetically stable, and therefore, their viability and the corresponding conditions depend on the size of the activation barrier associated with the release of Ng atom(s). Our major focus was devoted to understand the bonding situation in these complexes by employing the available state-of-the-art theoretic tools like natural bond orbital, electron density, and energy decomposition analyses in combination with the natural orbital for chemical valence theory. Intriguingly, these three types of complexes represent three different types of bonding scenarios. In NgXY, the strength of the donor-acceptor Ng→XY interaction depends on the polarizing power of binding the X center to draw the rather rigid electron density of Ng towards itself, and sometimes involvement of such orbitals becomes large enough, particularly for heavier Ng elements, to consider them as covalent bonds. On the other hand, in most of the XNgY cases, Ng forms an electron-shared covalent bond with X while interacting electrostatically with Y representing itself as [XNg]+Y-. Nevertheless, in some of the rare cases like NCNgNSi, both the C-Ng and Ng-N bonds can be represented as electron-shared covalent bonds. On the other hand, a cage host is an excellent moiety to examine the limits that can be pushed to attain bonding between two Ng atoms (even for He) at high pressure. The confinement effect by a small cage-like B12N12 can even induce some covalent interaction within two He atoms in the He2@B12N12 complex.
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Affiliation(s)
- Ranajit Saha
- Department of Chemistry and Centre for Theoretical Studies Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Gourhari Jana
- Department of Chemistry and Centre for Theoretical Studies Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Sudip Pan
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing 211816, China.
| | - Gabriel Merino
- Departamento de Física Aplicada, Centro de Investigación y de Estudios Avanzados, Unidad Mérida. Km 6 Antigua Carretera a Progreso. Apdo. Postal 73, Cordemex, Mérida 97310, Yuc., Mexico.
| | - Pratim Kumar Chattaraj
- Department of Chemistry and Centre for Theoretical Studies Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India.
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Sousa SF, Neves RP, Waheed SO, Fernandes PA, Ramos MJ. Structural and mechanistic aspects of S-S bonds in the thioredoxin-like family of proteins. Biol Chem 2018; 400:575-587. [DOI: 10.1515/hsz-2018-0319] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/22/2018] [Indexed: 02/06/2023]
Abstract
Abstract
Disulfide bonds play a critical role in a variety of structural and mechanistic processes associated with proteins inside the cells and in the extracellular environment. The thioredoxin family of proteins like thioredoxin (Trx), glutaredoxin (Grx) and protein disulfide isomerase, are involved in the formation, transfer or isomerization of disulfide bonds through a characteristic thiol-disulfide exchange reaction. Here, we review the structural and mechanistic determinants behind the thiol-disulfide exchange reactions for the different enzyme types within this family, rationalizing the known experimental data in light of the results from computational studies. The analysis sheds new atomic-level insight into the structural and mechanistic variations that characterize the different enzymes in the family, helping to explain the associated functional diversity. Furthermore, we review here a pattern of stabilization/destabilization of the conserved active-site cysteine residues presented beforehand, which is fully consistent with the observed roles played by the thioredoxin family of enzymes.
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Affiliation(s)
- Sérgio F. Sousa
- UCIBIO@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências , Universidade do Porto , Rua do Campo Alegre, s/n , 4169-007 Porto , Portugal
| | - Rui P.P. Neves
- UCIBIO@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências , Universidade do Porto , Rua do Campo Alegre, s/n , 4169-007 Porto , Portugal
| | - Sodiq O. Waheed
- UCIBIO@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências , Universidade do Porto , Rua do Campo Alegre, s/n , 4169-007 Porto , Portugal
| | - Pedro A. Fernandes
- UCIBIO@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências , Universidade do Porto , Rua do Campo Alegre, s/n , 4169-007 Porto , Portugal
| | - Maria João Ramos
- UCIBIO@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências , Universidade do Porto , Rua do Campo Alegre, s/n , 4169-007 Porto , Portugal
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11
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Jana G, Pan S, Merino G, Chattaraj PK. Noble Gas Inserted Metal Acetylides (Metal = Cu, Ag, Au). J Phys Chem A 2018; 122:7391-7401. [DOI: 10.1021/acs.jpca.8b05404] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gourhari Jana
- Department of Chemistry and Centre for Theoretical Studies, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Sudip Pan
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing, China
| | - Gabriel Merino
- Departamento de Física Aplicada, Centro de Investigación y de Estudios Avanzados, Unidad Mérida. Km 6 Antigua Carretera a Progreso. Apdo. Postal 73, Cordemex, 97310, Mérida, Yuc., México
| | - Pratim K. Chattaraj
- Department of Chemistry and Centre for Theoretical Studies, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India
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12
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Pan S, Jana G, Ravell E, Zarate X, Osorio E, Merino G, Chattaraj PK. Stable NCNgNSi (Ng=Kr, Xe, Rn) Compounds with Covalently Bound C-Ng-N Unit: Possible Isomerization of NCNSi through the Release of the Noble Gas Atom. Chemistry 2018; 24:2879-2887. [PMID: 29194873 DOI: 10.1002/chem.201705112] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Indexed: 11/07/2022]
Abstract
Although the noble gas (Ng) compounds with either Ng-C or Ng-N bonds have been reported in the literature, compounds containing both bonds are not known. The first set of systems having a C-Ng-N bonding unit is predicted herein through the analysis of stability and bonding in the NCNgNSi (Ng=Kr-Rn) family. While the Xe and Rn inserted analogues are thermochemically stable with respect to all dissociation channels, but for the one producing CNSiN and free Ng, NCKrNSi has another additional three-body dissociation channel, NCKrNSi→CN+Kr+NSi, which is exergonic by -9.8 kcal mol-1 at 298 K. This latter dissociation can be hindered by lowering the temperature. Moreover, the NCNgNSi→Ng+CNSiN dissociation is also kinetically prohibited by a quite high free energy barrier ranging from 25.2 to 39.3 kcal mol-1 , with a gradual increase in going from Kr to Rn. Therefore, these compounds are appropriate candidates for experimental realization. A detailed bonding analysis by employing natural bond orbital, electron density, energy decomposition, and adaptive natural density partitioning analyses indicates that both Ng-N and C-Ng bonds in the title compounds are covalent in nature. In fact, the latter analysis indicates the presence of delocalized 3c-3e σ-bond within the C-Ng-N moiety and a totally delocalized 5c-2e σ-bond in these compounds. This is an unprecedented bonding characteristic in the sense that the bonding pattern in Ng inserted compounds is generally represented as the presence of covalent bond in one side of Ng, and the ionic interaction in the other side. Further, the dissociation of Ng from NCNgNSi facilitates the formation of a higher energy isomer of NCNSi, CNSiN, which cannot be formed from bare NCNSi as such, because of the very high free energy barrier associated with the isomeric transformation. Therefore, in the presence of Ng atoms it might be possible to detect the high energy isomer.
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Affiliation(s)
- Sudip Pan
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing, P. R. China
| | - Gourhari Jana
- Department of Chemistry and Centre for Theoretical Studies, Indian Institute of Technology, Kharagpur, 721302, India
| | - Estefanía Ravell
- Departamento de Física Aplicada, Centro de Investigación y de Estudios Avanzados, Unidad Mérida, Km 6 Antigua Carretera a Progreso. Apdo. Postal 73, Cordemex, 97310, Mérida, Yuc., México
| | - Ximena Zarate
- Instituto de Ciencias Químicas Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, Av. Pedro de Valdivia 425, Santiago, Chile
| | - Edison Osorio
- Departamento de Ciencias Básicas, Universidad Católica Luis Amigó, SISCO, Transversal 51A #67B 90, Medellín, Colombia
| | - Gabriel Merino
- Departamento de Física Aplicada, Centro de Investigación y de Estudios Avanzados, Unidad Mérida, Km 6 Antigua Carretera a Progreso. Apdo. Postal 73, Cordemex, 97310, Mérida, Yuc., México
| | - Pratim K Chattaraj
- Department of Chemistry and Centre for Theoretical Studies, Indian Institute of Technology, Kharagpur, 721302, India
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13
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Gao K, Sheng L. Neutral noble gas compound with a xenon-metal double bond: A theoretical study of F2XeWF2. COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2017.10.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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14
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The influence of the dispersion corrections on the performance of DFT method in modeling HNgY noble gas molecules and their complexes. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2017.11.040] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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15
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Jana G, Pan S, Merino G, Chattaraj PK. MNgCCH (M = Cu, Ag, Au; Ng = Xe, Rn): The First Set of Compounds with M–Ng–C Bonding Motif. J Phys Chem A 2017; 121:6491-6499. [DOI: 10.1021/acs.jpca.7b04993] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gourhari Jana
- Department
of Chemistry and Centre for Theoretical Studies Indian Institute of Technology Kharagpur, 721302 Kharagpur, India
| | - Sudip Pan
- Department
of Chemistry and Centre for Theoretical Studies Indian Institute of Technology Kharagpur, 721302 Kharagpur, India
- Departamento
de Física Aplicada, Centro de Investigación y de Estudios
Avanzados, Unidad Mérida. Km 6 Antigua Carretera a Progreso.
Apdo. Postal 73, Cordemex, 97310, Mérida, Yucatan, México
| | - Gabriel Merino
- Departamento
de Física Aplicada, Centro de Investigación y de Estudios
Avanzados, Unidad Mérida. Km 6 Antigua Carretera a Progreso.
Apdo. Postal 73, Cordemex, 97310, Mérida, Yucatan, México
| | - Pratim K. Chattaraj
- Department
of Chemistry and Centre for Theoretical Studies Indian Institute of Technology Kharagpur, 721302 Kharagpur, India
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16
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Lei Y, Jiang W, Gao Y, Xu D, Wang B, Wang Z. First Principles Study of the Interaction of Rare Gases in a U@C60Fullerene. ChemistrySelect 2016. [DOI: 10.1002/slct.201601389] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Yanyu Lei
- Institute of Atomic and Molecular Physics; Jilin University; Changchun 130012 P. R. China
- Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy; Jilin University; Changchun 130012 P. R. China
| | - Wanrun Jiang
- Institute of Atomic and Molecular Physics; Jilin University; Changchun 130012 P. R. China
- Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy; Jilin University; Changchun 130012 P. R. China
| | - Yang Gao
- Institute of Atomic and Molecular Physics; Jilin University; Changchun 130012 P. R. China
- Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy; Jilin University; Changchun 130012 P. R. China
| | - Dexuan Xu
- Institute of Atomic and Molecular Physics; Jilin University; Changchun 130012 P. R. China
- Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy; Jilin University; Changchun 130012 P. R. China
| | - Bo Wang
- Institute of Atomic and Molecular Physics; Jilin University; Changchun 130012 P. R. China
- Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy; Jilin University; Changchun 130012 P. R. China
| | - Zhigang Wang
- Institute of Atomic and Molecular Physics; Jilin University; Changchun 130012 P. R. China
- Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy; Jilin University; Changchun 130012 P. R. China
- Institute of Theoretical Chemistry; Jilin University; Changchun 130012 P. R. China
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17
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GHARA MANAS, PAN SUDIP, DEB JYOTIRMOY, KUMAR ANAND, SARKAR UTPAL, CHATTARAJ PRATIMKUMAR. A computational study on structure, stability and bonding in Noble Gas bound metal Nitrates, Sulfates and Carbonates (Metal = Cu, Ag, Au). J CHEM SCI 2016. [DOI: 10.1007/s12039-016-1150-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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18
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Chen W, Chen GH, Wu D, Wang Q. BNg3F3: the first three noble gas atoms inserted into mono-centric neutral compounds - a theoretical study. Phys Chem Chem Phys 2016; 18:17534-45. [PMID: 27301893 DOI: 10.1039/c6cp01432a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Following the study of HXeOXeH and HXeCCXeH, in which two Xe atoms were inserted into H2O and C2H2 theoretically and experimentally, the structures and stability of BNg3F3 (Ng = Ar, Kr and Xe), in which three Ng atoms are inserted into BF3, have been explored theoretically using DFT and ab initio calculations. It is shown that BNg3F3 (Ng = Ar, Kr and Xe) with D3h symmetry are local minima with short B-Ng bond lengths of 1.966, 2.027 and 2.214 Å at the CCSD(T)/aug-cc-pVTZ/LJ18 level, which are close to their covalent limits. Note that although BNg3F3 (Ng = Kr and Xe) are energetically higher than the dissociation products 3Ng + BF3, they are still kinetically stable as metastable species with protecting barriers of 13.38 and 17.99 kcal mol(-1) for BKr3F3 and BXe3F3. Moreover, BKr3F3, the tri-Kr-inserted compound, even has comparable kinetic stability to HXeOXeH and HXeOXeF. In addition, upon the formation of BNg3F3, there is a large amount of charge transferred from B to Ng of at least 0.619 e. The calculated Wiberg Bond Indices (WBI) suggest that B-Ng bonds are naturally singly bonded; the large vibrational frequencies of B-Ng and Ng-F stretching modes and the negative Laplacian electron density of B-Ng bonds confirm further that BNg3F3 are stiff molecules with covalent B-Ng bonds. It should be noted that three Ng atoms inserted into mono-centric neutral molecules have not been reported previously. We hope that the present theoretical study may provide important evidence for the experimental synthesis of BNg3F3.
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Affiliation(s)
- Wei Chen
- Department of Chemistry, Shantou University, Shantou 515063, China.
| | - Guang-Hui Chen
- Department of Chemistry, Shantou University, Shantou 515063, China.
| | - Di Wu
- Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China
| | - Qiang Wang
- Department of Applied Chemistry, College of Science, Nanjing Tech University, Nanjing 211816, China
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19
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Russo MG, Sancho MI, Silva LMA, Baldoni HA, Venancio T, Ellena J, Narda GE. Looking for the interactions between omeprazole and amoxicillin in a disordered phase. An experimental and theoretical study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2016; 156:70-77. [PMID: 26654963 DOI: 10.1016/j.saa.2015.11.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 10/08/2015] [Accepted: 11/20/2015] [Indexed: 06/05/2023]
Abstract
In this paper, co-grinding mixtures of omeprazole-amoxicillin trihydrate (CGM samples) and omeprazole-anhydrous amoxicillin (CGMa samples) at 3:7, 1:1 and 7:3 molar ratios, respectively, were studied with the aim of obtaining a co-amorphous system and determining the potential intermolecular interactions. These systems were fully characterized by differential scanning calorimetry (DSC), FT-infrared spectroscopy (FTIR), X-ray powder diffraction (PXRD), scanning electron microscopy (SEM) and solid state Nuclear Magnetic Resonance (ssNMR). The co-grinding process was not useful to get a co-amorphous system but it led to obtaining the 1:1 CGMa disordered phase. Moreover, in this system both FTIR and ssNMR analysis strongly suggest intermolecular interactions between the sulfoxide group of omeprazole and the primary amine of amoxicillin anhydrous. The solubility measurements were performed in simulated gastric fluid (SGF) to prove the effect of the co-grinding process. Complementarily, we carried out density functional theory calculations (DFT) followed by quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analyses in order to shed some light on the principles that guide the possible formation of heterodimers at the molecular level, which are supported by spectroscopic experimental findings.
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Affiliation(s)
- Marcos G Russo
- Inorganic Chemistry, INTEQUI, National University of San Luis, Chacabuco and Pedernera-5700, San Luis, Argentina
| | - Matias I Sancho
- Physical Chemical Laboratory, National University of San Luis, Chacabuco and Pedernera-5700, San Luis, Argentina
| | - Lorena M A Silva
- Chemistry Department, Federal University of São Carlos, PO Box 676, 13565-905 São Carlos, Brazil
| | - Hector A Baldoni
- Institute of Applied Mathematics San Luis (IMASL-CONICET), National University of San Luis, Chacabuco and Pedernera-5700, San Luis, Argentina
| | - Tiago Venancio
- Chemistry Department, Federal University of São Carlos, PO Box 676, 13565-905 São Carlos, Brazil
| | - Javier Ellena
- Physics Institute of São Carlos, University of São Paulo, CP 369, 13560-970 São Carlos, SP, Brazil
| | - Griselda E Narda
- Inorganic Chemistry, INTEQUI, National University of San Luis, Chacabuco and Pedernera-5700, San Luis, Argentina.
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20
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Pan S, Ghara M, Ghosh S, Chattaraj PK. Noble gas bound beryllium chromate and beryllium hydrogen phosphate: a comparison with noble gas bound beryllium oxide. RSC Adv 2016. [DOI: 10.1039/c6ra20232b] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Two new beryllium based compounds, beryllium hydrogen phosphate and beryllium chromate are found to have remarkable noble gas binding ability, particularly for Ar–Rn atoms.
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Affiliation(s)
- Sudip Pan
- Department of Chemistry and Center for Theoretical Studies
- Indian Institute of Technology Kharagpur
- India
| | - Manas Ghara
- Department of Chemistry and Center for Theoretical Studies
- Indian Institute of Technology Kharagpur
- India
| | - Sreyan Ghosh
- Department of Chemistry and Center for Theoretical Studies
- Indian Institute of Technology Kharagpur
- India
| | - Pratim K. Chattaraj
- Department of Chemistry and Center for Theoretical Studies
- Indian Institute of Technology Kharagpur
- India
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21
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Zhang G, Li H, Weinhold F, Chen D. 3c/4e -type long-bonding competes with ω-bonding in noble-gas hydrides HNgY (Ng = He, Ne, Ar, Kr, Xe, Rn; Y = F, Cl, Br, I): a NBO/NRT perspective. Phys Chem Chem Phys 2016; 18:8015-26. [DOI: 10.1039/c5cp07965a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Novel resonance bonding for the HNgY molecule is demonstrated based on natural resonance theory analyses. Ng/Y affects the ω-bonding vs. long-bonding propensity in each of the HNgY molecules.
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Affiliation(s)
- Guiqiu Zhang
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Hong Li
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Frank Weinhold
- Department of Chemistry
- University of Wisconsin
- Madison
- USA
| | - Dezhan Chen
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
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22
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23
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Zhu C, Räsänen M, Khriachtchev L. Fluorinated noble-gas cyanides FKrCN, FXeCN, and FXeNC. J Chem Phys 2015; 143:074306. [DOI: 10.1063/1.4928649] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Cheng Zhu
- Department of Chemistry, University of Helsinki, P.O. Box 55, FI-00014 Helsinki, Finland
| | - Markku Räsänen
- Department of Chemistry, University of Helsinki, P.O. Box 55, FI-00014 Helsinki, Finland
| | - Leonid Khriachtchev
- Department of Chemistry, University of Helsinki, P.O. Box 55, FI-00014 Helsinki, Finland
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24
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Gao K, Sheng L. Theoretical investigation of HNgNH3(+) ions (Ng = He, Ne, Ar, Kr, and Xe). J Chem Phys 2015; 142:144301. [PMID: 25877572 DOI: 10.1063/1.4916648] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The equilibrium geometries, harmonic frequencies, and dissociation energies of HNgNH3(+) ions (Ng = He, Ne, Ar, Kr, and Xe) were investigated using the following method: Becke-3-parameter-Lee-Yang-Parr (B3LYP), Boese-Matrin for Kinetics (BMK), second-order Møller-Plesset perturbation theory (MP2), and coupled-cluster with single and double excitations as well as perturbative inclusion of triples (CCSD(T)). The results indicate that HHeNH3(+), HArNH3(+), HKrNH3(+), and HXeNH3(+) ions are metastable species that are protected from decomposition by high energy barriers, whereas the HNeNH3(+) ion is unstable because of its relatively small energy barrier for decomposition. The bonding nature of noble-gas atoms in HNgNH3(+) was also analyzed using the atoms in molecules approach, natural energy decomposition analysis, and natural bond orbital analysis.
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Affiliation(s)
- Kunqi Gao
- Department of Chemistry, Academy of Fundamental and Interdisciplinary Sciences, Harbin Institute of Technology, Harbin 150080, People's Republic of China
| | - Li Sheng
- Department of Chemistry, Academy of Fundamental and Interdisciplinary Sciences, Harbin Institute of Technology, Harbin 150080, People's Republic of China
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25
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Ghosh A, Dey S, Manna D, Ghanty TK. Noble-Gas-Inserted Fluoro(sulphido)boron (FNgBS, Ng = Ar, Kr, and Xe): A Theoretical Prediction. J Phys Chem A 2015; 119:5732-41. [PMID: 25928588 DOI: 10.1021/jp512520y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The possibility of the existence of a new series of neutral noble gas compound, FNgBS (where Ng = Ar, Kr, Xe), is explored theoretically through the insertion of a Ng atom into the fluoroborosulfide molecule (FBS). Second-order Møller-Plesset perturbation theory, density functional theory, and coupled cluster theory based methods have been employed to predict the structure, stability, harmonic vibrational frequencies, and charge distribution of FNgBS molecules. Through energetics study, it has been found that the molecules could dissociate into global minima products (Ng + FBS) on the respective singlet potential energy surface via a unimolecular dissociation channel; however, the sufficiently large activation energy barriers provide enough kinetic stability to the predicted molecules, which, in turn, prevent them from dissociating into the global minima products. Moreover, the FNgBS species are thermodynamically stable, owing to very high positive energies with respect to other two two-body dissociation channels, leading to FNg + BS and F(-) + NgBS(+), and two three-body dissociation channels, corresponding to the dissociation into F + Ng + BS and F(-) + Ng + BS(+). Furthermore, the Mulliken and NBO charge analysis together with the AIM results reveal that the Ng-B bond is more of covalent in nature, whereas the F-Ng bond is predominantly ionic in character. Thus, these compounds can be better represented as F(-)[NgBS](+). This fact is also supported by the detail analysis of bond length, bond dissociation energy, and stretching force constant values. All of the calculated results reported in this work clearly indicate that it might be possible to prepare and characterize the FNgBS molecules in cryogenic environment through matrix isolation technique by using a mixture of OCS/BF3 in the presence of large quantity of noble gas under suitable experimental conditions.
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Affiliation(s)
- Ayan Ghosh
- †Laser and Plasma Technology Division, Beam Technology Development Group, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Sourav Dey
- ‡Ramakrishna Mission Vidyamandira, Belur Math, West Bengal 711 202, India
| | - Debashree Manna
- §Theoretical Chemistry Section, Chemistry Group, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Tapan K Ghanty
- §Theoretical Chemistry Section, Chemistry Group, Bhabha Atomic Research Centre, Mumbai 400 085, India
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26
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Borocci S, Giordani M, Grandinetti F. Bonding Motifs of Noble-Gas Compounds As Described by the Local Electron Energy Density. J Phys Chem A 2015; 119:6528-41. [PMID: 25988571 DOI: 10.1021/acs.jpca.5b03043] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The bonding situation of some exemplary noble-gas (Ng) compounds, including HNg(+), HNgF, FNgO(-), Ng-HF, and NgBeO (Ng = He-Xe) was assayed by examining their local electron energy density H(r). In general, this function partitions the space of atomic species (neutral and ionic) into inner regions of negative values and outer regions of positive values. In the formation of chemical bonds, these atomic regions combine so to form a molecular H(r), Hmol(r), whose plotted form naturally shows the "covalent" and "noncovalent" regions of the molecular species and allows also the recognition of different types of noncovalent interactions such van der Waals, hydrogen, and ionic or partially ionic bonds. The qualitative assignment of the various bonding motifs is corroborated by the topological analysis of Hmol(r), which typically includes several critical points of rank 3 and variable signature. These points are, in particular, characterized here in terms of their bond degree (BD). From a previous definition (Espinosa J. Chem. Phys. 2002, 117, 5529-5542), this quantity is taken as the ratio between the energy density calculated at the critical point of H(r), H(rc), and the corresponding electron density ρ(rc): BD = -H(rc)/ρ(rc). Thus, the BD is positive for covalent interactions (H(rc) < 0) and negative for noncovalent interactions (H(rc) > 0). For structurally related species, the BD result, in general, positively correlated with the binding energies and is, therefore, a semiquantitative index of stability. The present study suggests the general validity of the Hmol(r) to effectively assay the bonding motifs of noble-gas compounds.
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Affiliation(s)
- Stefano Borocci
- Dipartimento per la Innovazione nei sistemi Biologici, Agroalimentari e Forestali (DIBAF), Università della Tuscia, L.go dell'Università, s.n.c., 01100 Viterbo, Italy.,Istituto per le Metodologie Chimiche del CNR, Via Salaria, Km 29.500, 00015 Monterotondo, RM, Italy
| | - Maria Giordani
- Dipartimento per la Innovazione nei sistemi Biologici, Agroalimentari e Forestali (DIBAF), Università della Tuscia, L.go dell'Università, s.n.c., 01100 Viterbo, Italy.,Istituto per le Metodologie Chimiche del CNR, Via Salaria, Km 29.500, 00015 Monterotondo, RM, Italy
| | - Felice Grandinetti
- Dipartimento per la Innovazione nei sistemi Biologici, Agroalimentari e Forestali (DIBAF), Università della Tuscia, L.go dell'Università, s.n.c., 01100 Viterbo, Italy.,Istituto per le Metodologie Chimiche del CNR, Via Salaria, Km 29.500, 00015 Monterotondo, RM, Italy
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27
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Pan S, Saha R, Chattaraj PK. On the stability of noble gas bound 1-tris(pyrazolyl)borate beryllium and magnesium complexes. NEW J CHEM 2015. [DOI: 10.1039/c5nj00983a] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
1-Tris(pyrazolyl)borate beryllium and magnesium cationic complexes are found to bind Ar–Rn atoms quite effectively.
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Affiliation(s)
- Sudip Pan
- Department of Chemistry and Centre for Theoretical Studies
- Indian Institute of Technology Kharagpur
- India
| | - Ranajit Saha
- Department of Chemistry and Centre for Theoretical Studies
- Indian Institute of Technology Kharagpur
- India
| | - Pratim K. Chattaraj
- Department of Chemistry and Centre for Theoretical Studies
- Indian Institute of Technology Kharagpur
- India
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28
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Foroutan-Nejad C, Vicha J, Marek R. Design of stereoelectronically promoted super lewis acids and unprecedented chemistry of their complexes. Chemistry 2014; 20:11584-90. [PMID: 25055748 DOI: 10.1002/chem.201402582] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Indexed: 11/12/2022]
Abstract
A new family of stereoelectronically promoted aluminum and scandium super Lewis acids is introduced on the basis of state-of-the-art computations. Structures of these molecules are designed to minimize resonance electron donation to central metal atoms in the Lewis acids. Acidity of these species is evaluated on the basis of their fluoride-ion affinities relative to the antimony pentafluoride reference system. It is demonstrated that introduced changes in the stereochemistry of the designed ligands increase acidity considerably relative to Al and Sc complexes with analogous monodentate ligands. The high stability of fluoride complexes of these species makes them ideal candidates to be used as weakly coordinating anions in combination with highly reactive cations instead of conventional Lewis acid-fluoride complexes. Further, the interaction of all designed molecules with methane is investigated. All studied acids form stable pentavalent-carbon complexes with methane. In addition, interactions of the strongest acid of this family with very weak bases, namely, H2, N2, carbon oxides, and noble gases were investigated; it is demonstrated that this compound can form considerably stable complexes with the aforementioned molecules. To the best of our knowledge, carbonyl and nitrogen complexes of this species are the first hypothetical four-coordinated carbonyl and nitrogen complexes of aluminum. The nature of bonding in these systems is studied in detail by various bonding analysis approaches.
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Affiliation(s)
- Cina Foroutan-Nejad
- National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5A4, 62500 Brno (Czech Republic).
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29
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Zhang M, Sheng L. Predicted organic compounds derived from rare gas atoms and formic acid. Phys Chem Chem Phys 2014; 16:196-203. [PMID: 24232663 DOI: 10.1039/c3cp52175c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Organic insertion compounds of rare gas atoms into formic acid were investigated at the MP2(full)/aug-cc-pVTZ level. There are two configuration isomers for each molecule based on the location of H atoms: trans- and cis-HCOORgH (Rg = Ar, Kr, Xe). Their structures, harmonic frequencies, and decomposition energies have been calculated using the above ab initio method. Using trans-HCOOXeH as an example, natural bond orbital (NBO) and atom-in-molecules (AIM) analyses were also carried out to explore the binding nature of the rare gas atoms. The formation mechanism of molecular orbitals is also presented in this paper. The presented results indicate that HCOOXeH and HCOOKrH are potential candidates for experimental observation.
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Affiliation(s)
- Min Zhang
- Department of Chemistry, Natural Science Research Center, Academy of Fundamental and Interdisciplinary Sciences, Harbin Institute of Technology, Harbin 150080, P. R. China.
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30
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Mondal S, Chandra Singh P. Noble gas induced surprisingly higher stability of π hydrogen bonded complex: comparative study of hydrogen bonded complexes of HKrCCH and HCCH with H2O, NH3, CH3OH and CH3NH2. RSC Adv 2014. [DOI: 10.1039/c3ra47427e] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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31
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Quantum chemical calculation of amino-substituted but-2-yne dications: Distonic and gitonic character? J PHYS ORG CHEM 2013. [DOI: 10.1002/poc.3232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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32
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Abstract
Rare-gas hydrides of the type HRgX (Rg = Xe or Rn and X = F, Cl, Br, or I) have been studied using Møller–Plesset and density functional theory methods. Six model core potentials and their associated basis sets were used, with relativistic effects included implicitly. The effects of polarization, correlating, and diffuse basis functions were investigated. Molecular geometries of the metastable hydrides and transition states along the decomposition pathway were computed together with corresponding energies of formation and decomposition. The results of quantum theory of atoms in molecules analysis further elucidate the interactions between atoms in HRgX species and confirm the results of analyses obtained from the natural bond orbitals approach.
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Affiliation(s)
- Amelia Fitzsimmons
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Mariusz Klobukowski
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
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33
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Affiliation(s)
- J. Peter Toennies
- a Max-Planck-Institut für Dynamik und Selbstorganisation , Göttingen , Germany
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34
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Chen JL, Yang CY, Lin HJ, Hu WP. Theoretical prediction of new noble-gas molecules FNgBNR (Ng = Ar, Kr, and Xe; R = H, CH3, CCH, CHCH2, F, and OH). Phys Chem Chem Phys 2013; 15:9701-9. [PMID: 23670409 DOI: 10.1039/c3cp50447f] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have computationally predicted a new class of stable noble-gas molecules FNgBNR (Ng = Ar, Kr, Xe; R = H, CH3, CCH, CHCH2, F, and OH). The FNgBNR were found to have compact structures with F-Ng bond lengths of 1.9-2.2 Å and Ng-B bond lengths of ~1.8 Å. The endoergic three-body dissociation energies of FNgBNH to F + Ng + BNH were calculated to be 12.8, 31.7, and 63.9 kcal mol(-1), for Ng = Ar, Kr, and Xe, respectively at the CCSD(T)/CBS level. The energy barriers of the exoergic two-body dissociation to Ng + FBNH were calculated to be 16.1, 24.0, and 33.2 kcal mol(-1) for Ng = Ar, Kr, and Xe, respectively. Our results showed that the dissociation energetics is relatively insensitive to the identities of the terminal R groups. The current study suggested that a wide variety of noble-gas containing molecules with different types of R groups can be thermally stable at low temperature, and the number of potentially stable noble-gas containing molecules would thus increase very significantly. It is expected some of the FNgBNR molecules could be identified in future experiments under cryogenic conditions in noble-gas matrices or in the gas phase.
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Affiliation(s)
- Jien-Lian Chen
- Department of Chemistry and Biochemistry, National Chung Cheng University, Chia-Yi, Taiwan
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Zhang M, Sheng L. Ab initio study of the organic xenon insertion compound into ethylene and ethane. J Chem Phys 2013; 138:114301. [PMID: 23534633 DOI: 10.1063/1.4795007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
This paper studies Xe-insertion ethylene and ethane compounds, i.e., HXeC2H3 and HXeC2H5. The structures, harmonic frequencies, and energetics for both molecules have been calculated at the MP2(full)/6-311++G(2d,2p) level. Our theoretical results predict the existence of HXeC2H3 and the instability of HXeC2H5. Natural bond orbital (NBO) analysis shows a strong ionic bond between the xenon atom and hydrocarbon radical. In addition, the interaction between the donor (Xe lone pair) and acceptor (the C-C antibonding orbital, i.e., π*(C-C)) increases the stability of HXeC2H3.
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Affiliation(s)
- Min Zhang
- Department of Chemistry, Natural Science Research Center, Academy of Fundamental and Interdisciplinary Sciences, Harbin Institute of Technology, Harbin 150080, People's Republic of China
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Peng CY, Yang CY, Sun YL, Hu WP. Theoretical prediction on the structures and stability of the noble-gas containing anions FNgCC- (Ng=He, Ar, Kr, and Xe). J Chem Phys 2013. [PMID: 23181302 DOI: 10.1063/1.4766326] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We have made high-level theoretical study on a new type of noble-gas (Ng) containing anions FNgCC(-). The calculated short Ng-CC bond lengths of 1.13, 1.77, 1.89, and 2.04 Å for Ng=He, Ar, Kr, and Xe, respectively, and the electron density distributions indicated strong covalent interactions between the Ng and CC induced by the polarizing fluoride ion. Except for FHeCC(-), the structures of all other FNgCC(-) were predicted to be linear. The intrinsic stability of the FNgCC(-) was studied by calculating the energies of the three-body dissociation reaction: FNgCC(-) → F(-) + Ng + CC and by calculating the energy barriers of the two-body dissociation reaction: FNgCC(-) → Ng + FCC(-). The results showed that FNgCC(-) (Ng=Ar, Kr, Xe) could be kinetically stable in the gas phase with the three-body dissociation energies of 17, 37, and 64 kcal/mol and two body-dissociation barriers of 22, 31, and 42 kcal/mol, respectively, at the coupled-cluster single double (triple)/aug-cc-pVQZ level of theory. The structures and the stability were also confirmed using the multi-reference CASPT2 calculation. Future experimental identification of the FNgCC(-) anions is expected under cryogenic conditions.
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Affiliation(s)
- Chia-Yu Peng
- Department of Chemistry and Biochemistry, National Chung Cheng University, Chia-Yi 62102, Taiwan
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Zou W, Nori-Shargh D, Boggs JE. On the Covalent Character of Rare Gas Bonding Interactions: A New Kind of Weak Interaction. J Phys Chem A 2012; 117:207-12. [DOI: 10.1021/jp3104535] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Wenli Zou
- Institute for Theoretical Chemistry, Chemistry and Biochemistry
Department, The University of Texas at Austin, Austin, Texas 78712-0165,
United States
| | - Davood Nori-Shargh
- Institute for Theoretical Chemistry, Chemistry and Biochemistry
Department, The University of Texas at Austin, Austin, Texas 78712-0165,
United States
- Department of Chemistry, Arak Branch, Islamic Azad University, Arak, Iran
| | - James E. Boggs
- Institute for Theoretical Chemistry, Chemistry and Biochemistry
Department, The University of Texas at Austin, Austin, Texas 78712-0165,
United States
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Wang X, Andrews L, Willmann K, Brosi F, Riedel S. Investigation of gold fluorides and noble gas complexes by matrix-isolation spectroscopy and quantum-chemical calculations. Angew Chem Int Ed Engl 2012; 51:10628-32. [PMID: 23001952 DOI: 10.1002/anie.201205072] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Indexed: 11/08/2022]
Abstract
Noble with a difference: Matrix-isolation experiments and quantum-chemical calculations have led to the characterization of two new compounds, namely first open-shell binary gold fluoride, AuF(2), and a NeAuF complex. Moreover, ArAuF, AuF(3), Au(2)F(6), and monomeric AuF(5) have been produced and identified under cryogenic conditions in neon and argon matrices.
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Affiliation(s)
- Xuefeng Wang
- Department of Chemistry, Tongji University, Shanghai 200092, China
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Wang X, Andrews L, Willmann K, Brosi F, Riedel S. Untersuchung von Goldfluoriden und ihren Edelgaskomplexen durch Matrixisolationsspektroskopie und quantenchemische Rechnungen. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201205072] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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40
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Bouchoux G, Rashad AM, Helal AI. Theoretical Investigation of Selenium Interferences in Inductively Coupled Plasma Mass Spectrometry. J Phys Chem A 2012; 116:9058-70. [DOI: 10.1021/jp304644u] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- G. Bouchoux
- Laboratoire des Mécanismes
Réactionnels, Département de Chimie, Ecole Polytechnique and CNRS, 91128 Palaiseau, France
| | - A. M. Rashad
- Central Laboratory for Elemental
and Isotopic Analysis, Nuclear Research Center, Atomic Energy Authority, Cairo 13759, Egypt
| | - A. I. Helal
- Central Laboratory for Elemental
and Isotopic Analysis, Nuclear Research Center, Atomic Energy Authority, Cairo 13759, Egypt
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Noble gas matrix effects on the equilibrium and transition structures of noble gas molecules: A theoretical study. COMPUT THEOR CHEM 2012. [DOI: 10.1016/j.comptc.2012.05.044] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Theoretical investigation of the noble gas molecular anions XAuNgX− and HAuNgX− (X = F, Cl, Br; Ng = Xe, Kr, Ar). Struct Chem 2012. [DOI: 10.1007/s11224-012-9978-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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43
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Pavanello M, Neugebauer J. Modelling charge transfer reactions with the frozen density embedding formalism. J Chem Phys 2011; 135:234103. [DOI: 10.1063/1.3666005] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Singh PC. C–H⋯O/N hydrogen bonded complexes of FKrCCH are stronger than FCCH complexes: Effect of rare gas insertion. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.09.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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45
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Kozuch S, Martin JML. DSD-PBEP86: in search of the best double-hybrid DFT with spin-component scaled MP2 and dispersion corrections. Phys Chem Chem Phys 2011; 13:20104-7. [DOI: 10.1039/c1cp22592h] [Citation(s) in RCA: 318] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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