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An X, Yang X, Li Q. Tetrel Bonds between Phenyltrifluorosilane and Dimethyl Sulfoxide: Influence of Basis Sets, Substitution and Competition. Molecules 2021; 26:molecules26237231. [PMID: 34885810 PMCID: PMC8658981 DOI: 10.3390/molecules26237231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 11/19/2021] [Accepted: 11/22/2021] [Indexed: 11/16/2022] Open
Abstract
Ab initio calculations have been performed for the complexes of DMSO and phenyltrifluorosilane (PTS) and its derivatives with a substituent of NH3, OCH3, CH3, OH, F, CHO, CN, NO2, and SO3H. It is necessary to use sufficiently flexible basis sets, such as aug’-cc-pVTZ, to get reliable results for the Si···O tetrel bonds. The tetrel bond in these complexes has been characterized in views of geometries, interaction energies, orbital interactions and topological parameters. The electron-donating group in PTS weakens this interaction and the electron-withdrawing group prominently strengthens it to the point where it exceeds that of the majority of hydrogen bonds. The largest interaction energy occurs in the p-HO3S-PhSiF3···DMSO complex, amounting to −122 kJ/mol. The strong Si···O tetrel bond depends to a large extent on the charge transfer from the O lone pair into the empty p orbital of Si, although it has a dominant electrostatic character. For the PTS derivatives of NH2, OH, CHO and NO2, the hydrogen bonded complex is favorable to the tetrel bonded complex for the NH2 and OH derivatives, while the σ-hole interaction prefers the π-hole interaction for the CHO and NO2 derivatives.
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Affiliation(s)
- Xiulin An
- College of Life Science, Yantai University, Yantai 264005, China;
| | - Xin Yang
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, China;
| | - Qingzhong Li
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, China;
- Correspondence:
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2
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Sanyal S, Esterhuysen C. Nature of halogen bond adducts of carbones with XCF3 (X = Cl, Br, I) species. Polyhedron 2021. [DOI: 10.1016/j.poly.2021.115107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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3
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Exploring pentavalent phosphorous bonding in phosphoryl chloride-halocarbon heterodimers at low temperatures and ab initio Computations. Chem Phys 2021. [DOI: 10.1016/j.chemphys.2021.111112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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4
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Chandra S, Suryaprasad B, Ramanathan N, Sundararajan K. Nitrogen as a pnicogen?: evidence for π-hole driven novel pnicogen bonding interactions in nitromethane-ammonia aggregates using matrix isolation infrared spectroscopy and ab initio computations. Phys Chem Chem Phys 2021; 23:6286-6297. [PMID: 33688865 DOI: 10.1039/d0cp06273a] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The role of nitrogen, the first member of the pnicogen group, as an electron donor in hypervalent non-covalent interactions has been established long ago, while observation of its electron accepting capability is still elusive experimentally, and remains quite intriguing, conceptually. In the light of minimal computational exploration of this novel class of pnicogen bonding so far, the present work provides experimental proof with unprecedented clarity, for the existence of N(acceptor)N(donor) interaction using the model nitromethane (NM) molecule with ammonia (AM) as a Lewis base in NM-AM aggregates. The NM-AM dimer, in which the nitrogen atom of NM (as a unique pnicogen) accepts electrons from AM (the traditional electron donor), was synthesized at low temperatures under isolated conditions within inert gas matrixes and was characterized using infrared spectroscopy. The experimental generation of the NM-AM dimer stabilized via NN interaction has strong corroboration from ab initio calculations. Furthermore, confirmation regarding the directional prevalence of this NN interaction over C-HN and N-HO hydrogen bonding is elucidated quantitatively by quantum theory of atoms in molecules (QTAIM), electrostatic potential mapping (ESP), natural bond orbital (NBO), non-covalent interaction (NCI) and energy decomposition (ED) analyses. The present study also allows the extension of σ-hole/π-hole driven interactions to the atoms of the second period, in spite of their low polarizability.
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Affiliation(s)
- Swaroop Chandra
- Homi Bhabha National Institute, Materials Chemistry & Metal Fuel Cycle Group, Indira Gandhi Center for Atomic Research, Kalpakkam - 603102, Tamil Nadu, India.
| | - B Suryaprasad
- Homi Bhabha National Institute, Materials Chemistry & Metal Fuel Cycle Group, Indira Gandhi Center for Atomic Research, Kalpakkam - 603102, Tamil Nadu, India.
| | - N Ramanathan
- Homi Bhabha National Institute, Materials Chemistry & Metal Fuel Cycle Group, Indira Gandhi Center for Atomic Research, Kalpakkam - 603102, Tamil Nadu, India.
| | - K Sundararajan
- Homi Bhabha National Institute, Materials Chemistry & Metal Fuel Cycle Group, Indira Gandhi Center for Atomic Research, Kalpakkam - 603102, Tamil Nadu, India.
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5
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Sruthi PK, Chandra S, Ramanathan N, Sundararajan K. Unusual blue to red shifting of C-H stretching frequency of CHCl 3 in co-operatively P⋯Cl phosphorus bonded POCl 3-CHCl 3 heterodimers at low temperature inert matrixes. J Chem Phys 2020; 153:174305. [PMID: 33167652 DOI: 10.1063/5.0031162] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Heterodimers of POCl3-CHCl3 were generated in Ne, Ar, and Kr matrixes at low temperatures and were studied using infrared spectroscopy. The remarkable role of co-operative pentavalent phosphorus bonding in the stabilization of the structure dictated by hydrogen bonding is deciphered. The complete potential energy surface of the heterodimer was scanned by ab initio and density functional theory computational methodologies. The hydrogen bond between the phosphoryl oxygen of POCl3 and C-H group of CHCl3 in heterodimers induces a blue-shift in the C-H stretching frequency within the Ne matrix. However, in Ar and Kr matrixes, the C-H stretching frequency is exceptionally red-shifted in stark contrast with Ne. The plausibility of the Fermi resonance by the C-H stretching vibrational mode with higher order modes in the heterodimers has been eliminated as a possible cause within Ar and Kr matrixes by isotopic substitution (CDCl3) experiments. To evaluate the influence of matrixes as a possible cause of red-shift, self-consistent Iso-density polarized continuum reaction field model was applied. This conveyed the important role of the dielectric matrixes in inducing the fascinating vibrational shift from blue (Ne) to red (Ar and Kr) due to the matrix specific transmutation of the POCl3-CHCl3 structure. The heterodimer produced in the Ne matrix possesses a cyclic structure stabilized by hydrogen bonding with co-operative phosphorus bonding, while in Ar and Kr the generation of an acyclic open structure stabilized solely by hydrogen bonding is promoted. Compelling justification regarding the dispersion force based influence of matrix environments in addition to the well-known dielectric influence is presented.
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Affiliation(s)
- P K Sruthi
- Homi Bhabha National Institute, Materials Chemistry and Metal Fuel Cycle Group, Indira Gandhi Centre for Atomic Research, Kalpakkam 603102, India
| | - Swaroop Chandra
- Homi Bhabha National Institute, Materials Chemistry and Metal Fuel Cycle Group, Indira Gandhi Centre for Atomic Research, Kalpakkam 603102, India
| | - N Ramanathan
- Homi Bhabha National Institute, Materials Chemistry and Metal Fuel Cycle Group, Indira Gandhi Centre for Atomic Research, Kalpakkam 603102, India
| | - K Sundararajan
- Homi Bhabha National Institute, Materials Chemistry and Metal Fuel Cycle Group, Indira Gandhi Centre for Atomic Research, Kalpakkam 603102, India
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6
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Abstract
The fundamental underpinnings of noncovalent bonds are presented, focusing on the σ-hole interactions that are closely related to the H-bond. Different means of assessing their strength and the factors that control it are discussed. The establishment of a noncovalent bond is monitored as the two subunits are brought together, allowing the electrostatic, charge redistribution, and other effects to slowly take hold. Methods are discussed that permit prediction as to which site an approaching nucleophile will be drawn, and the maximum number of bonds around a central atom in its normal or hypervalent states is assessed. The manner in which a pair of anions can be held together despite an overall Coulombic repulsion is explained. The possibility that first-row atoms can participate in such bonds is discussed, along with the introduction of a tetrel analog of the dihydrogen bond.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, USA
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7
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Chandra S, Suryaprasad B, Ramanathan N, Sundararajan K. Dominance of unique Pπ phosphorus bonding with π donors: evidence using matrix isolation infrared spectroscopy and computational methodology. Phys Chem Chem Phys 2020; 22:20771-20791. [PMID: 32909555 DOI: 10.1039/d0cp02880k] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Albeit the first account of hypervalentπ interactions has been reported with halogenπ interactions, the feasibility of their extension to other hypervalent atoms as possible Lewis acids is still open. In this work, the role of phosphorus as an acceptor from the π electron cloud (Pπ pnicogen or phosphorus bonding) in PCl3-C2H2 and PCl3-C2H4 heterodimers is explored, by combining matrix isolation infrared spectroscopy with ab initio and DFT computational methodologies. The respective potential energy surfaces of the PCl3-C2H2 and PCl3-C2H4 heterodimers reveal unique minima stabilized by a concert of reasonably strong to weak interactions, of which Pπ phosphorus bonding was energetically dominant. Heterodimers, trimers and tetramers bound primarily by this unique phosphorus bond were generated at low temperatures. The dominance of phosphorus bonding in the PCl3-C2H2 and PCl3-C2H4 heterodimers over other interactions (such as Hπ, HCl, HP, Clπ and lone pair-π interactions) was confirmed and substantiated using extended quantum theory of atoms in molecules, natural bond orbital, electrostatic potential mapping and energy decomposition analyses. The following inferences in correlation with results from non-covalent-interaction analysis offer a complete understanding of the nature of the Pπ phosphorus bonding interactions. The significance of electrostatic forces kinetically favoring the formation of phosphorus bonded heterodimers, in addition to thermodynamic stabilization, is demonstrated experimentally.
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Affiliation(s)
- Swaroop Chandra
- Homi Bhabha National Institute, Materials Chemistry & Metal Fuel Cycle Group, Indira Gandhi Center for Atomic Research, Kalpakkam - 603102, Tamil Nadu, India.
| | - B Suryaprasad
- Homi Bhabha National Institute, Materials Chemistry & Metal Fuel Cycle Group, Indira Gandhi Center for Atomic Research, Kalpakkam - 603102, Tamil Nadu, India.
| | - N Ramanathan
- Homi Bhabha National Institute, Materials Chemistry & Metal Fuel Cycle Group, Indira Gandhi Center for Atomic Research, Kalpakkam - 603102, Tamil Nadu, India.
| | - K Sundararajan
- Homi Bhabha National Institute, Materials Chemistry & Metal Fuel Cycle Group, Indira Gandhi Center for Atomic Research, Kalpakkam - 603102, Tamil Nadu, India.
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8
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Mahmudov KT, Gurbanov AV, Aliyeva VA, Resnati G, Pombeiro AJ. Pnictogen bonding in coordination chemistry. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2020.213381] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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9
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Synergistic and antagonistic interplay between tetrel bond and pnicogen bond in complexes involving ring compounds. J Mol Model 2019; 25:351. [DOI: 10.1007/s00894-019-4206-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 09/11/2019] [Indexed: 10/25/2022]
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10
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Sruthi PK, Sarkar S, Ramanathan N, Sundararajan K. Elusive hypervalent phosphorus⋯π interactions: evidence for paradigm transformation from hydrogen to phosphorus bonding at low temperatures. Phys Chem Chem Phys 2019; 21:12250-12264. [DOI: 10.1039/c9cp01925a] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
A paradigm transformation from hydrogen to phosphorus bonding is found to depend on the proton affinity of the interacting π-systems.
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Affiliation(s)
- P. K. Sruthi
- Materials Chemistry and Metal Fuel Cycle Group
- Homi Bhabha National Institute
- Indira Gandhi Centre for Atomic Research
- Kalpakkam-603 102
- India
| | - Shubhra Sarkar
- Materials Chemistry and Metal Fuel Cycle Group
- Homi Bhabha National Institute
- Indira Gandhi Centre for Atomic Research
- Kalpakkam-603 102
- India
| | - N. Ramanathan
- Materials Chemistry and Metal Fuel Cycle Group
- Homi Bhabha National Institute
- Indira Gandhi Centre for Atomic Research
- Kalpakkam-603 102
- India
| | - K. Sundararajan
- Materials Chemistry and Metal Fuel Cycle Group
- Homi Bhabha National Institute
- Indira Gandhi Centre for Atomic Research
- Kalpakkam-603 102
- India
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11
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Sánchez-Sanz G, Trujillo C. Improvement of Anion Transport Systems by Modulation of Chalcogen Interactions: The influence of solvent. J Phys Chem A 2018; 122:1369-1377. [DOI: 10.1021/acs.jpca.7b10920] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Goar Sánchez-Sanz
- Irish Centre of High-End Computing, Grand Canal
Quay, Dublin 2, Ireland
| | - Cristina Trujillo
- School
of Chemistry, Trinity Biomedical Sciences, Trinity College Dublin, 152−160 Pearse Street, Dublin 2, Ireland
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12
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Sruthi PK, Ramanathan N, Sarkar S, Sundararajan K. Pentavalent phosphorus as a unique phosphorus donor in POCl3 homodimer and POCl3–H2O heterodimer: matrix isolation infrared spectroscopic and computational studies. Phys Chem Chem Phys 2018; 20:22058-22075. [DOI: 10.1039/c8cp03937b] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Phosphorus, an important element among the pnicogen group, opens up avenues for experimental and computational explorations of its interaction in a variety of compounds.
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Affiliation(s)
- P. K. Sruthi
- Materials Chemistry & Metal Fuel Cycle Group
- Homi Bhabha National Institute, Indira Gandhi Centre for Atomic Research
- Kalpakkam 603 102
- India
| | - N. Ramanathan
- Materials Chemistry & Metal Fuel Cycle Group
- Homi Bhabha National Institute, Indira Gandhi Centre for Atomic Research
- Kalpakkam 603 102
- India
| | - Shubhra Sarkar
- Materials Chemistry & Metal Fuel Cycle Group
- Homi Bhabha National Institute, Indira Gandhi Centre for Atomic Research
- Kalpakkam 603 102
- India
| | - K. Sundararajan
- Materials Chemistry & Metal Fuel Cycle Group
- Homi Bhabha National Institute, Indira Gandhi Centre for Atomic Research
- Kalpakkam 603 102
- India
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13
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Krivdin LB. Calculation of 15N NMR chemical shifts: Recent advances and perspectives. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2017; 102-103:98-119. [PMID: 29157495 DOI: 10.1016/j.pnmrs.2017.08.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 08/21/2017] [Accepted: 08/21/2017] [Indexed: 06/07/2023]
Abstract
Recent advances in computation of 15N NMR chemical shifts are reviewed, concentrating mainly on practical aspects of computational protocols and accuracy factors. The review includes the discussion of the level of theory, the choice of density functionals and basis sets together with taking into account solvent effects, rovibrational corrections and relativistic effects. Computational aspects of 15N NMR are illustrated for the series of neutral and protonated open-chain nitrogen-containing compounds and nitrogen heterocycles, coordination and intermolecular complexes.
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Affiliation(s)
- Leonid B Krivdin
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033 Irkutsk, Russia.
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14
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Bagheri S, Masoodi HR, Akrami-Mohajeri AR. A theoretical survey of substituent effects on the properties of pnicogen and hydrogen bonds in cationic complexes of PH 4 + with substituted benzonitrile. J Mol Graph Model 2017; 77:64-71. [DOI: 10.1016/j.jmgm.2017.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 08/09/2017] [Accepted: 08/09/2017] [Indexed: 11/27/2022]
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15
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Esrafili MD, Mousavian P. The Key Role of Orbital Interaction in Cooperativity between B⋅⋅⋅N and Hydrogen/Lithium Bonding: An ab initio Study. ChemistrySelect 2017. [DOI: 10.1002/slct.201701309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Mehdi D. Esrafili
- Laboratory of Theoretical Chemistry; Department of Chemistry; University of Maragheh, P.O. Box: 5513864596; Maragheh Iran
| | - Parisasadat Mousavian
- Laboratory of Theoretical Chemistry; Department of Chemistry; University of Maragheh, P.O. Box: 5513864596; Maragheh Iran
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16
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Pnicogen bond interaction between PF2Y (Y = –C☰N, –N☰C) with NH3, CH3OH, H2O, and HF molecules. Struct Chem 2017. [DOI: 10.1007/s11224-017-0968-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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17
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Esrafili MD, Kiani H. Cooperativity between the hydrogen bonding and σ-hole interaction in linear NCX···(NCH)n=2–5 and O3Z···(NCH)n=2–5 complexes (X = Cl, Br; Z = Ar, Kr): a comparative study. CAN J CHEM 2017. [DOI: 10.1139/cjc-2016-0640] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Quantum chemical calculations are performed to investigate the cooperativity of hydrogen bonding with halogen or aerogen bonding interactions in linear NCX···(NCH)n=2–5 and O3Z···(NCH)n=2–5 clusters, where X = Cl, Br and Z = Ar, Kr. To understand the cooperativity mechanism in these systems, the corresponding binary NCX···NCH and O3Z···NCH complexes are also considered. The binding distances, interaction energies, and bonding properties of the NCX···(NCH)n=2–5 and O3Z···(NCH)n=2–5 clusters are analyzed in detail. It is found that the cooperative effects in the hydrogen bonding tend to strengthen X···N and Z···N interactions. For both NCX···(NCH)n and O3Z···(NCH)n clusters, a small bond shrinkage is observed from n = 4 to n = 5, which suggests that the cooperativity effects are almost saturated in the larger clusters (n > 5). As the size of the X or Z atom is increased, the magnitude of the cooperative energy in these systems is also increased, which is mainly ascribed to changes in electrostatic potentials and orbital interactions. Our results indicate that the cooperative effects lead to a substantial change in the 14N nuclear quadrupole coupling constants of the NCH molecule.
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Affiliation(s)
- Mehdi D. Esrafili
- Laboratory of Theoretical Chemistry, Department of Chemistry, University of Maragheh, Maragheh, Iran
- Laboratory of Theoretical Chemistry, Department of Chemistry, University of Maragheh, Maragheh, Iran
| | - Hossein Kiani
- Laboratory of Theoretical Chemistry, Department of Chemistry, University of Maragheh, Maragheh, Iran
- Laboratory of Theoretical Chemistry, Department of Chemistry, University of Maragheh, Maragheh, Iran
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Esrafili MD, Sadr-Mousavi A. Modulating of the pnicogen-bonding by a H⋯π interaction: An ab initio study. J Mol Graph Model 2017; 75:165-173. [PMID: 28595167 DOI: 10.1016/j.jmgm.2017.04.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 04/14/2017] [Accepted: 04/18/2017] [Indexed: 11/29/2022]
Abstract
An ab initio study of the cooperativity in XH2P⋯NCH⋯Z and XH2P⋯CNH⋯Z complexes (X=F, Cl, Br, CN, NC; Z=C2H2,C6H6) connected by pnicogen-bonding and H⋯π interactions is carried out by means of MP2 computational method. A detailed analysis of the structures, interaction energies and bonding properties is performed on these systems. For each set of the complexes considered, a favorable cooperativity is observed, especially in X=F and CN complexes. However, for a given X or Z, the amount of cooperativity effects in XH2P⋯CNH⋯Z complexes are more important than XH2P⋯NCH⋯Z counterparts. Besides, the influence of a H⋯π interaction on a P⋯N (C) bond is more pronounced than that of a P⋯N (C) bond on a H⋯π bond. The quantum theory of atoms in molecules shows that ternary complexes have increased electron densities at their bond critical points relative to the corresponding binary systems. The results also indicate that the strength of the P⋯N(C) and H⋯π interactions increases in the presence of the solvent.
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Affiliation(s)
- Mehdi D Esrafili
- Laboratory of Theoretical Chemistry, Department of Chemistry, University of Maragheh, P.O. Box: 5513864596, Maragheh, Iran.
| | - Asma Sadr-Mousavi
- School of Chemistry, University College of Science, University of Tehran, Tehran, Iran
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19
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Esrafili MD, Vakili M. The effect of hydrogen-bonding cooperativity on the strength and properties of σ-hole interactions: an ab initio study. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1292013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Mehdi D. Esrafili
- Laboratory of Theoretical Chemistry, Department of Chemistry, University of Maragheh, Maragheh, Iran
| | - Mahshad Vakili
- Young Researchers and Elite Club, Miyaneh Branch, Islamic Azad University, Miyaneh, Iran
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20
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Esrafili MD, Kiani H, Mohammadian-Sabet F. Tuning of carbon bonds by substituent effects: an ab initio study. Mol Phys 2016. [DOI: 10.1080/00268976.2016.1255800] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Mehdi D. Esrafili
- Laboratory of Theoretical Chemistry, Department of Chemistry, University of Maragheh, Maragheh, Iran
| | - Hossein Kiani
- Laboratory of Theoretical Chemistry, Department of Chemistry, University of Maragheh, Maragheh, Iran
| | - Fariba Mohammadian-Sabet
- Laboratory of Theoretical Chemistry, Department of Chemistry, University of Maragheh, Maragheh, Iran
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21
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Esrafili MD, Mohammadian-Sabet F, Solimannejad M. Single-electron aerogen bonds: Do they exist? Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.07.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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22
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Viana RB, Varela Jr JJG, Tello ACM, Savedra RML, da Silva ABF. The 1,2-hydrogen shift reaction for monohalogenophosphanes PH2X and HPX (X = F, Cl). Mol Phys 2016. [DOI: 10.1080/00268976.2016.1213438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Rommel B. Viana
- Departamento de Química e Física Molecular, Instituto de Química de São Carlos, Universidade de São Paulo (USP), São Carlos-SP, Brazil
| | - Jaldyr J. G. Varela Jr
- Laboratório de Química Quântica Computacional, Centro de Ciências Exatas e Tecnologia, Universidade Federal do Maranhão (UFMA), São Luís-MA, Brazil
| | - Ana C. M. Tello
- Departamento de Química e Física Molecular, Instituto de Química de São Carlos, Universidade de São Paulo (USP), São Carlos-SP, Brazil
| | - Ranylson M. L. Savedra
- Departamento de Química, Laboratório de Modelagem Molecular, Universidade de Lavras (UFLA), Lavras-MG, Brazil
| | - Albérico B. F. da Silva
- Departamento de Química e Física Molecular, Instituto de Química de São Carlos, Universidade de São Paulo (USP), São Carlos-SP, Brazil
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23
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Esrafili MD, Asadollahi S. Strengthening of the halogen-bonding by an aerogen bond interaction: substitution and cooperative effects in O3Z···NCX···NCY (Z = Ar, Kr, Xe; X = Cl, Br, I; Y = H, F, OH) complexes. Mol Phys 2016. [DOI: 10.1080/00268976.2016.1190470] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Mehdi D. Esrafili
- Laboratory of Theoretical Chemistry, Department of Chemistry, University of Maragheh, Maragheh, Iran
| | - Soheila Asadollahi
- Laboratory of Theoretical Chemistry, Department of Chemistry, University of Maragheh, Maragheh, Iran
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25
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Esrafili MD, Mohammadian-Sabet F, Vessally E. An ab initio study on the nature of σ-hole interactions in pnicogen-bonded complexes with carbene as an electron donor. Mol Phys 2016. [DOI: 10.1080/00268976.2016.1185547] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Mehdi D. Esrafili
- Department of Chemistry, Laboratory of Theoretical Chemistry, University of Maragheh, Maragheh, Iran
| | - Fariba Mohammadian-Sabet
- Department of Chemistry, Laboratory of Theoretical Chemistry, University of Maragheh, Maragheh, Iran
| | - Esmail Vessally
- Department of Chemistry, Payame Noor University, Tehran, Iran
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26
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Competition between chalcogen bond and halogen bond interactions in YOX4:NH3 (Y = S, Se; X = F, Cl, Br) complexes: An ab initio investigation. Struct Chem 2016. [DOI: 10.1007/s11224-016-0763-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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27
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Esrafili MD, Mohammadian-Sabet F. Substituent effects on geometry and bonding properties of asymmetric bifurcated pnicogen bonds: A theoretical study. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.02.060] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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28
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Esrafili MD, Asadollahi S. Cationic P⋯N interaction in XH 3 P + ⋯NCY complexes (X = H, F, CN, NH 2 , OH; Y = H, Li, F, Cl) and its cooperativity with hydrogen/lithium/halogen bond. J Mol Graph Model 2016; 64:131-138. [DOI: 10.1016/j.jmgm.2016.01.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 01/22/2016] [Accepted: 01/27/2016] [Indexed: 12/27/2022]
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29
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Tang Q, Li Q. Enhancing effect of metal coordination interaction on pnicogen bonding. J Mol Model 2016; 22:64. [DOI: 10.1007/s00894-016-2929-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2016] [Accepted: 02/04/2016] [Indexed: 10/22/2022]
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30
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31
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Wei Y, Li Q, Li W, Cheng J, McDowell SAC. Influence of the protonation of pyridine nitrogen on pnicogen bonding: competition and cooperativity. Phys Chem Chem Phys 2016; 18:11348-56. [PMID: 27055488 DOI: 10.1039/c6cp00551a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ab initio MP2/aug-cc-pVTZ calculations were performed to investigate the pnicogen-bonded complexes of PyZX2 (Py = pyridine, Z = P and As, X = H and F) and their protonated analogues.
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Affiliation(s)
- Yuanxin Wei
- The Laboratory of Theoretical and Computational Chemistry
- School of Chemistry and Chemical Engineering
- Yantai University
- Yantai 264005
- People's Republic of China
| | - Qingzhong Li
- The Laboratory of Theoretical and Computational Chemistry
- School of Chemistry and Chemical Engineering
- Yantai University
- Yantai 264005
- People's Republic of China
| | - Wenzuo Li
- The Laboratory of Theoretical and Computational Chemistry
- School of Chemistry and Chemical Engineering
- Yantai University
- Yantai 264005
- People's Republic of China
| | - Jianbo Cheng
- The Laboratory of Theoretical and Computational Chemistry
- School of Chemistry and Chemical Engineering
- Yantai University
- Yantai 264005
- People's Republic of China
| | - Sean A. C. McDowell
- Department of Biological and Chemical Sciences
- The University of the West Indies
- Cave Hill Campus
- Barbados
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32
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Quiñonero D, Bauzá A, Sánchez-Sanz G, Trujillo C, Alkorta I, Elguero J. Weak interactions within nitryl halide heterodimers. NEW J CHEM 2016. [DOI: 10.1039/c6nj01334a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nitryl halides (XNO2, X = F, Cl, Br and I) are versatile molecules that exhibit several types of interactions within XNO2:YNO2 heterodimers mainly governed by dispersion.
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Affiliation(s)
- David Quiñonero
- Departament de Química
- Universitat de les Illes Balears
- 07122 Palma de Mallorca
- Spain
| | - Antonio Bauzá
- Departament de Química
- Universitat de les Illes Balears
- 07122 Palma de Mallorca
- Spain
| | | | - Cristina Trujillo
- School of Chemistry
- Trinity Biomedical Sciences Institute
- Trinity College Dublin
- Dublin 2
- Ireland
| | - Ibon Alkorta
- Instituto de Química Médica
- CSIC
- E-28006 Madrid
- Spain
| | - José Elguero
- Instituto de Química Médica
- CSIC
- E-28006 Madrid
- Spain
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33
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Sánchez-Sanz G, Trujillo C, Alkorta I, Elguero J. Modulating intramolecular P⋯N pnictogen interactions. Phys Chem Chem Phys 2016; 18:9148-60. [DOI: 10.1039/c6cp00227g] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The strength of P⋯N intramolecular pnictogen interactions can be modulated, enhanced or diminished upon substitution of different electron withdrawing or donor groups.
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Affiliation(s)
| | - Cristina Trujillo
- School of Chemistry
- Trinity Biomedical Sciences Institute
- Trinity College Dublin
- Dublin 2
- Ireland
| | - Ibon Alkorta
- Instituto de Química Médica
- CSIC
- E-28006 Madrid
- Spain
| | - José Elguero
- Instituto de Química Médica
- CSIC
- E-28006 Madrid
- Spain
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34
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Ramanathan N, Sankaran K, Sundararajan K. PCl3–C6H6 heterodimers: evidence for P⋯π phosphorus bonding at low temperatures. Phys Chem Chem Phys 2016; 18:19350-8. [DOI: 10.1039/c6cp03825e] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A phosphorous trichloride (PCl3)–benzene (C6H6) heterodimer was generated in a low temperature N2 matrix and was characterized using infrared spectroscopy.
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Affiliation(s)
- N. Ramanathan
- Chemistry Group
- Indira Gandhi Center for Atomic Research
- Kalpakkam – 603102
- India
| | - K. Sankaran
- Chemistry Group
- Indira Gandhi Center for Atomic Research
- Kalpakkam – 603102
- India
| | - K. Sundararajan
- Chemistry Group
- Indira Gandhi Center for Atomic Research
- Kalpakkam – 603102
- India
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35
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LIU YANZHI, YUAN KUN, YUAN ZHAO, ZHU YUANCHENG, ZHAO XIANG. Theoretical exploration of pnicogen bond noncovalent interactions in HCHO⋯PH2X (X=CH3, H, C6H5, F, Cl, Br, and NO2) complexes. J CHEM SCI 2015. [DOI: 10.1007/s12039-015-0933-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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36
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Gas phase reaction of phosphorus trichloride and methanol: Matrix isolation infrared and DFT studies. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2015.07.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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37
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Esrafili MD, Mohammadian-Sabet F. Tuning tetrel bonds via cation–π interactions: anab initiostudy on concerted interaction in M+–C6H5XH3–NCY complexes (M = Li, Na, K; X = Si, Ge; Y = H, F, OH). Mol Phys 2015. [DOI: 10.1080/00268976.2015.1086498] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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38
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Bene JED, Alkorta I, Elguero J. Properties of cationic pnicogen-bonded complexes F4-nHnP+:N-base with H–P···N linear andn= 1–4. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1086835] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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39
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40
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Characterization of σ-hole interactions in 1:1 and 1:2 complexes of YOF2X (X = F, Cl, Br, I; Y = P, As) with ammonia: competition between halogen and pnicogen bonds. Struct Chem 2015. [DOI: 10.1007/s11224-015-0677-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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41
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Esrafili MD, Nurazar R, Mohammadian-Sabet F. Cooperative effects between tetrel bond and other σ–hole bond interactions: a comparative investigation. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1053550] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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42
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Del Bene JE, Alkorta I, Elguero J. Properties of Cationic Pnicogen-Bonded Complexes F4–nHnP+:N-Base with F–P···N Linear and n = 0–3. J Phys Chem A 2015; 119:5853-64. [DOI: 10.1021/acs.jpca.5b03035] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Janet E. Del Bene
- Department of Chemistry, Youngstown State University, Youngstown, Ohio 44555, United States
| | - Ibon Alkorta
- Instituto de Química Médica (IQM-CSIC), Juan de la
Cierva, 3, E-28006 Madrid, Spain
| | - José Elguero
- Instituto de Química Médica (IQM-CSIC), Juan de la
Cierva, 3, E-28006 Madrid, Spain
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43
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Azofra LM. Towards an understanding of the CO2-philicity in glycine: Deepening into the CO2:Aminoacid interactions. Chem Phys 2015. [DOI: 10.1016/j.chemphys.2015.03.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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44
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Joshi PR, Ramanathan N, Sundararajan K, Sankaran K. Evidence for Phosphorus Bonding in Phosphorus Trichloride–Methanol Adduct: A Matrix Isolation Infrared and ab Initio Computational Study. J Phys Chem A 2015; 119:3440-51. [DOI: 10.1021/jp511156d] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Prasad Ramesh Joshi
- Chemistry
Group, Indira Gandhi Center for Atomic Research, Kalpakkam 603102, Tamil Nadu, India
| | - N. Ramanathan
- Chemistry
Group, Indira Gandhi Center for Atomic Research, Kalpakkam 603102, Tamil Nadu, India
| | - K. Sundararajan
- Chemistry
Group, Indira Gandhi Center for Atomic Research, Kalpakkam 603102, Tamil Nadu, India
| | - K. Sankaran
- Chemistry
Group, Indira Gandhi Center for Atomic Research, Kalpakkam 603102, Tamil Nadu, India
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45
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Zhuo H, Li Q. Novel pnicogen bonding interactions with silylene as an electron donor: covalency, unusual substituent effects and new mechanisms. Phys Chem Chem Phys 2015; 17:9153-60. [PMID: 25758936 DOI: 10.1039/c5cp00187k] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An analogue of carbene, singlet silylene (H3P=N)2Si, was paired with the mono-substituted phosphines XH2Y (X = P, As, and Sb; Y = F, Cl, Br, and I) to form unconventional pnicogen-bonded complexes. All structures have Cs symmetry except the Sb complex, showing a deviation from this symmetry due to the coexistence of H···H interactions. The P and As complexes have different geometries from conventional pnicogen-bonded ones because the Y-X···Si line shows a large deviation from the molecular plane composed of two N atoms and one Si atom of (H3P=N)2Si. This deviation can be attributed to a new formation mechanism of the pnicogen bond due to the combined result of the LPSi→ BD*X-Y and LPX→ LP*Si orbital interactions. Generally, the pnicogen bond becomes stronger in the order of F < Cl < Br < I and weaker in the order of P > As > Sb, exhibiting an unexpected substitution effect and dependence on the nature of the pnicogen atom. These orders are inconsistent with the MEP on the X atom but can be better explained by the above orbital interactions. The Si···X interaction displays a character of covalent or partially covalent interaction, evidenced by the high interaction energy of -59.9 to -105.4 kJ mol(-1) as well as the negative energy density and the great charge transfer.
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Affiliation(s)
- Hongying Zhuo
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, People's Republic of China.
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46
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Ab initio study in the hydration process of metaphosphoric acid: the importance of the pnictogen interactions. Theor Chem Acc 2015. [DOI: 10.1007/s00214-015-1630-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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47
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Azofra LM, Alkorta I, Scheiner S. Chalcogen bonds in complexes of SOXY (X, Y = F, Cl) with nitrogen bases. J Phys Chem A 2015; 119:535-41. [PMID: 25547020 DOI: 10.1021/jp511828h] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
SOF2, SOFCl, and SOCl2 were each paired with a series of N bases. The potential energy surface of the binary complexes were characterized by MP2 calculations with double and triple-ξ basis sets, extrapolated to complete sets. The most stable configurations contained a S···N chalcogen bond with interaction energies as high as 6.8 kcal/mol. These structures are stabilized by a Nlp → σ*(S-Z) electron transfer (Z = O, F, Cl), complemented by Coulombic attraction of N to the σ-hole opposite the Z atom. N···S-F and N···S-Cl chalcogen bonds are stronger than N···S═O interactions. Formation of each chalcogen bond elongates all of the internal covalent bonds within SOXY, especially the S-Cl bond. Halogen-bonded (N···Cl-S) complexes were also observed, but these are more weakly bound, by less than 3 kcal/mol.
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Affiliation(s)
- Luis Miguel Azofra
- Instituto de Química Médica, CSIC , Juan de la Cierva, 3, E-28006 Madrid, Spain
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48
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Trujillo C, Sánchez-Sanz G, Alkorta I, Elguero J. Halogen, chalcogen and pnictogen interactions in (XNO2)2homodimers (X = F, Cl, Br, I). NEW J CHEM 2015. [DOI: 10.1039/c5nj00600g] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
XNO2(X = F, Cl, Br and I) homodimers present a large variety of interactions. A combination of pnictogen and chalcogen is stronger than single halogen bonds.
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Affiliation(s)
- Cristina Trujillo
- School of Chemistry
- Trinity Biomedical Sciences Institute
- Trinity College
- Dublin 2
- Ireland
| | - Goar Sánchez-Sanz
- School of Physics & Complex and Adaptive Systems Laboratory
- University College Dublin
- Dublin 4
- Ireland
| | - Ibon Alkorta
- Instituto de Química Médica
- CSIC
- E-28006 Madrid
- Spain
| | - José Elguero
- Instituto de Química Médica
- CSIC
- E-28006 Madrid
- Spain
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49
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Del Bene JE, Alkorta I, Elguero J. The Pnicogen Bond in Review: Structures, Binding Energies, Bonding Properties, and Spin-Spin Coupling Constants of Complexes Stabilized by Pnicogen Bonds. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2015. [DOI: 10.1007/978-3-319-14163-3_8] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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50
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Zhuo H, Li Q, Li W, Cheng J. The dual role of pnicogen as Lewis acid and base and the unexpected interplay between the pnicogen bond and coordination interaction in H3N⋯FH2X⋯MCN (X = P and As; M = Cu, Ag, and Au). NEW J CHEM 2015. [DOI: 10.1039/c4nj02051k] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ternary systems H3N⋯FH2X⋯MCN (X = P and As; M = Cu, Ag, and Au) as well as the corresponding pnicogen-bonded and coordination-bonded binary systems have been studied.
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Affiliation(s)
- Hongying Zhuo
- The Laboratory of Theoretical and Computational Chemistry
- School of Chemistry and Chemical Engineering
- Yantai University
- Yantai 264005
- People's Republic of China
| | - Qingzhong Li
- The Laboratory of Theoretical and Computational Chemistry
- School of Chemistry and Chemical Engineering
- Yantai University
- Yantai 264005
- People's Republic of China
| | - Wenzuo Li
- The Laboratory of Theoretical and Computational Chemistry
- School of Chemistry and Chemical Engineering
- Yantai University
- Yantai 264005
- People's Republic of China
| | - Jianbo Cheng
- The Laboratory of Theoretical and Computational Chemistry
- School of Chemistry and Chemical Engineering
- Yantai University
- Yantai 264005
- People's Republic of China
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