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Mahapatra N, Chandra S, Ramanathan N, Sundararajan K. Structural Elucidation of N 2O Clusters at Low Temperatures: Exemplary Framework Stabilized by π-Hole-Driven N···O and N···N Pnicogen Bonding Interactions. J Phys Chem A 2024; 128:4623-4637. [PMID: 38867592 DOI: 10.1021/acs.jpca.4c01103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
N2O is a classic prototype, in which central nitrogen is sufficiently electropositive with a positive potential of 20 kcal mol-1 in magnitude to qualify it as a possible pnicogen. This was applied to a test with N2O clusters using ab initio calculations in association with various molecular topographic tools. The structure of the energetically dominant and N2O dimer was in favor of a perpendicular geometry, where the central nitrogen atom of the N2O submolecule assumed a near 90° angle with the adjacent N═O and/or N═N moiety, which provides the affirmation of central nitrogen as a possible π-hole-driven pnicogen. The terminal nitrogen and oxygen atoms of N2O continue to act as conventional electron donors (Lewis bases) with a negative potential. Overall, predominant π-hole-driven N···O and N···N pnicogen bonding interactions were observed to stabilize N2O clusters. Furthermore, N2O clusters (dimers and trimers) were synthesized at low temperatures in an Ar matrix using molecular beam (effusive and supersonic expansion) experiments. The geometries of these clusters were characterized by probing infrared spectroscopy with corroboration from ab initio computational methods. In addition to our previously investigated nitromethane and nitrobenzene systems, N2O also makes it to a pnicogen bonder's club with the central nitrogen as a π-hole-driven pnicogen.
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Affiliation(s)
- Nandalal Mahapatra
- Materials Chemistry & Metal Fuel Cycle Group, Indira Gandhi Center for Atomic Research, Kalpakkam 603102, Tamil Nadu, India
- Indira Gandhi Center for Atomic Research, A CI of Homi Bhabha National Institute, Kalpakkam603102, Tami Nadu, India
| | - Swaroop Chandra
- Materials Chemistry & Metal Fuel Cycle Group, Indira Gandhi Center for Atomic Research, Kalpakkam 603102, Tamil Nadu, India
- Indira Gandhi Center for Atomic Research, A CI of Homi Bhabha National Institute, Kalpakkam603102, Tami Nadu, India
| | - Nagarajan Ramanathan
- Materials Chemistry & Metal Fuel Cycle Group, Indira Gandhi Center for Atomic Research, Kalpakkam 603102, Tamil Nadu, India
- Indira Gandhi Center for Atomic Research, A CI of Homi Bhabha National Institute, Kalpakkam603102, Tami Nadu, India
| | - Kalyanasundaram Sundararajan
- Materials Chemistry & Metal Fuel Cycle Group, Indira Gandhi Center for Atomic Research, Kalpakkam 603102, Tamil Nadu, India
- Indira Gandhi Center for Atomic Research, A CI of Homi Bhabha National Institute, Kalpakkam603102, Tami Nadu, India
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Definition of the Pnictogen Bond: A Perspective. INORGANICS 2022. [DOI: 10.3390/inorganics10100149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
This article proposes a definition for the term “pnictogen bond” and lists its donors, acceptors, and characteristic features. These may be invoked to identify this specific subset of the inter- and intramolecular interactions formed by elements of Group 15 which possess an electrophilic site in a molecular entity.
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Mahapatra N, Chandra S, Ramanathan N, Sundararajan K. Experimental proof for σ and π-hole driven dual pnicogen bonding in phosphoryl chloride-nitromethane heterodimers: A combined matrix isolation infrared and ab initio computational studies. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.132045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Varadwaj PR, Varadwaj A, Marques HM, Yamashita K. The Phosphorus Bond, or the Phosphorus-Centered Pnictogen Bond: The Covalently Bound Phosphorus Atom in Molecular Entities and Crystals as a Pnictogen Bond Donor. Molecules 2022; 27:molecules27051487. [PMID: 35268588 PMCID: PMC8911988 DOI: 10.3390/molecules27051487] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/16/2022] [Accepted: 02/16/2022] [Indexed: 02/07/2023] Open
Abstract
The phosphorus bond in chemical systems, which is an inter- or intramolecular noncovalent interaction, occurs when there is evidence of a net attractive interaction between an electrophilic region associated with a covalently or coordinately bonded phosphorus atom in a molecular entity and a nucleophile in another, or the same, molecular entity. It is the second member of the family of pnictogen bonds, formed by the second member of the pnictogen family of the periodic table. In this overview, we provide the reader with a snapshot of the nature, and possible occurrences, of phosphorus-centered pnictogen bonding in illustrative chemical crystal systems drawn from the ICSD (Inorganic Crystal Structure Database) and CSD (Cambridge Structural Database) databases, some of which date back to the latter part of the last century. The illustrative systems discussed are expected to assist as a guide to researchers in rationalizing phosphorus-centered pnictogen bonding in the rational design of molecular complexes, crystals, and materials and their subsequent characterization.
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Affiliation(s)
- Pradeep R. Varadwaj
- Department of Chemical System Engineering, School of Engineering, University of Tokyo 7-3-1, Tokyo 113-8656, Japan; (A.V.); (K.Y.)
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa;
- Correspondence:
| | - Arpita Varadwaj
- Department of Chemical System Engineering, School of Engineering, University of Tokyo 7-3-1, Tokyo 113-8656, Japan; (A.V.); (K.Y.)
| | - Helder M. Marques
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa;
| | - Koichi Yamashita
- Department of Chemical System Engineering, School of Engineering, University of Tokyo 7-3-1, Tokyo 113-8656, Japan; (A.V.); (K.Y.)
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Redox-initiated polymerization of N-vinylcarbazole based on carbon dots for modification and beyond. POLYMER 2022. [DOI: 10.1016/j.polymer.2022.124601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Is nitrogen in ammonia an elusive electron acceptingpnicogen in a predominantly phosphorus bonded PCl3:NH3 dimer? Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2021.139192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Sruthi P, Ramanathan N, Sundararajan K. Pentavalent P…N phosphorus bonding in the heterodimers of POCl3…nitrogen bases: Evidence from matrix isolation infrared spectroscopy and Ab initio computations. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130638] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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de Azevedo Santos L, Hamlin TA, Ramalho TC, Bickelhaupt FM. The pnictogen bond: a quantitative molecular orbital picture. Phys Chem Chem Phys 2021; 23:13842-13852. [PMID: 34155488 PMCID: PMC8297534 DOI: 10.1039/d1cp01571k] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 06/03/2021] [Indexed: 02/06/2023]
Abstract
We have analyzed the structure and stability of archetypal pnictogen-bonded model complexes D3PnA- (Pn = N, P, As, Sb; D, A = F, Cl, Br) using state-of-the-art relativistic density functional calculations at the ZORA-M06/QZ4P level. We have accomplished two tasks: (i) to compute accurate trends in pnictogen-bond strength based on a set of consistent data; and (ii) to rationalize these trends in terms of detailed analyses of the bonding mechanism based on quantitative Kohn-Sham molecular orbital (KS-MO) theory in combination with a canonical energy decomposition analysis (EDA) and Voronoi deformation density (VDD) analyses of the charge distribution. We have found that pnictogen bonds have a significant covalent character stemming from strong HOMO-LUMO interactions between the lone pair of A- and σ* of D3Pn. As such, the underlying mechanism of the pnictogen bond is similar to that of hydrogen, halogen, and chalcogen bonds.
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Affiliation(s)
- Lucas de Azevedo Santos
- Department of Theoretical Chemistry, Amsterdam Institute for Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands. and Department of Chemistry, Institute of Natural Sciences, Universidade Federal de Lavras, 37200-900, Lavras, MG, Brazil
| | - Trevor A Hamlin
- Department of Theoretical Chemistry, Amsterdam Institute for Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.
| | - Teodorico C Ramalho
- Department of Chemistry, Institute of Natural Sciences, Universidade Federal de Lavras, 37200-900, Lavras, MG, Brazil and Center for Basic and Applied Research, University Hradec Kralove, Hradec Kralove, Czech Republic
| | - F Matthias Bickelhaupt
- Department of Theoretical Chemistry, Amsterdam Institute for Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands. and Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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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: 2.5] [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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Ibrahim MAA, Saad SMA, Al-Fahemi JH, Mekhemer GAH, Ahmed SA, Shawky AM, Moussa NAM. External electric field effects on the σ-hole and lone-pair hole interactions of group V elements: a comparative investigation. RSC Adv 2021; 11:4022-4034. [PMID: 35424345 PMCID: PMC8694126 DOI: 10.1039/d0ra09765a] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 12/31/2020] [Indexed: 11/21/2022] Open
Abstract
σ-hole and lone-pair (lp) hole interactions of trivalent pnicogen-bearing (ZF3) compounds were comparatively scrutinized, for the first time, under field-free and external electric field (EEF) conditions. Conspicuously, the sizes of the σ-hole and lp-hole were increased by applying an EEF along the positive direction, while the sizes of both holes decreased through the reverse EEF direction. The MP2 energetic calculations of ZF3⋯FH/NCH complexes revealed that σ-holes exhibited more impressive interaction energies compared to the lp-holes. Remarkably, the strengths of σ-hole and lp-hole interactions evolved with the increment of the positive value of the considered EEF; i.e., the interaction energy increased as the utilized EEF value increased. Unexpectedly, under field-free conditions, nitrogen-bearing complexes showed superior strength for their lp-hole interactions than phosphorus-bearing complexes. However, the reverse picture was exhibited for the interaction energies of nitrogen- and phosphorus-bearing complexes interacting within lp-holes by applying the high values of a positively directed EEF. These results significantly demonstrate the crucial influence of EEF on the strength of σ-hole and lp-hole interactions, which in turn leads to an omnipresent enhancement for variable fields, including biological simulations and material science.
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Affiliation(s)
- Mahmoud A A Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University Minia 61519 Egypt
| | - Sherif M A Saad
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University Minia 61519 Egypt
| | - Jabir H Al-Fahemi
- Chemistry Department, Faculty of Applied Sciences, Umm Al-Qura University Makkah 21955 Saudi Arabia
| | - Gamal A H Mekhemer
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University Minia 61519 Egypt
| | - Saleh A Ahmed
- Chemistry Department, Faculty of Applied Sciences, Umm Al-Qura University Makkah 21955 Saudi Arabia
- Chemistry Department, Faculty of Science, Assiut University Assiut 71516 Egypt
| | - Ahmed M Shawky
- Science and Technology Unit (STU), Umm Al-Qura University Makkah 21955 Saudi Arabia
- Central Laboratory for Micro-analysis, Minia University Minia 61519 Egypt
| | - Nayra A M Moussa
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University Minia 61519 Egypt
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Suryaprasad B, Chandra S, Ramanathan N, Sundararajan K. Pentavalent P…π phosphorus bonding with associated Cl…π halogen bonding in influencing the geometry of POCl3-Phenylacetylene heterodimers: Evidence from matrix isolation infrared spectroscopy and ab initio computations. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129288] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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