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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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Suryaprasad B, Chandra S, Ramanathan N, Sundararajan K. Unique Dispersion-Induced Tetrel Bond with Co-operative σ-hole-Induced Pnicogen Bond in the POCl 3-Acetone Heterodimer: Experimental Confirmation at Low Temperatures. J Phys Chem A 2022; 126:6637-6647. [PMID: 36126354 DOI: 10.1021/acs.jpca.2c04635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Both tetrel and pnicogen bonds are known to be induced through σ-/π-holes. This work reports computational and experimental evidence of the carbonyl carbon of acetone hosting a tetrel bond by dispersion rather electrostatic forces, for the first time, while phosphorus of POCl3 sustains pnicogen bonding via the σ-hole. Heterodimers of POCl3 with acetone (CH3COCH3) have been isolated within inert gas matrixes of Ar and N2 at 12 K. Characteristic vibrational bands at P═O stretching of POCl3 and C═O stretching of CH3COCH3 have been obtained in support of the computations. The potential energy surface has been traced computationally using ab initio and density functional methods. CH3COCH3 harboring such a tetrel bond, in itself, is quite intriguing. The interplay of these interactions has been comprehended by the quantum theory of atoms in molecules, natural bond orbital, energy decomposition, electrostatic potential mapping, and noncovalent interaction analyses.
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Affiliation(s)
- Bodda Suryaprasad
- Materials Chemistry and Metal Fuel Cycle Group, Indira Gandhi Centre for Atomic Research, Kalpakkam 603102, Tamilnadu, India.,Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
| | - Swaroop Chandra
- Materials Chemistry and Metal Fuel Cycle Group, Indira Gandhi Centre for Atomic Research, Kalpakkam 603102, Tamilnadu, India.,Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
| | - Nagarajan Ramanathan
- Materials Chemistry and Metal Fuel Cycle Group, Indira Gandhi Centre for Atomic Research, Kalpakkam 603102, Tamilnadu, India.,Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
| | - Kalyanasundaram Sundararajan
- Materials Chemistry and Metal Fuel Cycle Group, Indira Gandhi Centre for Atomic Research, Kalpakkam 603102, Tamilnadu, India.,Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
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3
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Hockey EK, Vlahos K, Howard T, Palko J, Dodson LG. Weakly Bound Complex Formation between HCN and CH 3Cl: A Matrix-Isolation and Computational Study. J Phys Chem A 2022; 126:3110-3123. [PMID: 35583384 DOI: 10.1021/acs.jpca.2c00716] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The matrix-isolated infrared spectrum of a hydrogen cyanide-methyl chloride complex was investigated in a solid argon matrix. HCN and CH3Cl were co-condensed onto a substrate held at 10 K with an excess of argon gas, and the infrared spectrum was measured using Fourier-transform infrared spectroscopy. Quantum chemical geometry optimization, harmonic frequency, and natural bonding orbital calculations indicate stabilized hydrogen- and halogen-bonded structures. The two resulting weakly bound complexes are both composed of one CH3Cl molecule bound to a (HCN)3 subunit, where the three HCN molecules are bound head-to-tail in a ring formation. Our study suggests that─in the presence of CH3Cl─the formation of (HCN)3 is promoted through complexation. Since HCN aggregates are an important precursor to prebiotic monomers (amino acids and nucleobases) and other life-bearing polymers, this study has astrophysical implications toward the search for life in space.
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Affiliation(s)
- Emily K Hockey
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Korina Vlahos
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Thomas Howard
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Jessica Palko
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Leah G Dodson
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
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4
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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: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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5
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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: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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6
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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: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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7
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Gopi R, Ramanathan N, Sundararajan K. The structure of benzonitrile-water complex as unveiled by matrix isolation infrared spectroscopy: Is it linear or cyclic at low temperatures? J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128636] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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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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9
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Ramanathan N, Sarkar S, Sankaran K, Sundararajan K. Photolysis of PCl 3
/POCl 3
with Oxygen Dopant Using 193 nm ArF Excimer at Low Temperatures: Oxygen Insertion through ‘Phosphadioxirane’ Pathway. ChemistrySelect 2019. [DOI: 10.1002/slct.201803318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Nagarajan Ramanathan
- Materials Chemistry and Metal Fuel Cycle group; Homi Bhabha National Institute; Indira Gandhi Centre for Atomic Research; Kalpkkam- 603102 India
| | - Shubhra Sarkar
- Materials Chemistry and Metal Fuel Cycle group; Homi Bhabha National Institute; Indira Gandhi Centre for Atomic Research; Kalpkkam- 603102 India
| | - Kannan Sankaran
- Materials Chemistry and Metal Fuel Cycle group; Homi Bhabha National Institute; Indira Gandhi Centre for Atomic Research; Kalpkkam- 603102 India
| | - Kalyanasundaram Sundararajan
- Materials Chemistry and Metal Fuel Cycle group; Homi Bhabha National Institute; Indira Gandhi Centre for Atomic Research; Kalpkkam- 603102 India
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10
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Sarkar S, Ramanathan N, Sundararajan K. Effect of Methyl Substitution on the N–H···O Interaction in Complexes of Pyrrole with Water, Methanol, and Dimethyl Ether: Matrix Isolation Infrared Spectroscopy and ab Initio Computational Studies. J Phys Chem A 2018; 122:2445-2460. [DOI: 10.1021/acs.jpca.8b00023] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shubhra Sarkar
- Materials Chemistry and Metal Fuel Cycle Group, Indira Gandhi Centre for Atomic Research, Kalpakkam 603 102, India
- Homi Bhabha National Institute, Kalpakkam 603 102, India
| | - N. Ramanathan
- Materials Chemistry and Metal Fuel Cycle Group, Indira Gandhi Centre for Atomic Research, Kalpakkam 603 102, India
- Homi Bhabha National Institute, Kalpakkam 603 102, India
| | - K. Sundararajan
- Materials Chemistry and Metal Fuel Cycle Group, Indira Gandhi Centre for Atomic Research, Kalpakkam 603 102, India
- Homi Bhabha National Institute, Kalpakkam 603 102, India
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11
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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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12
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Gopi R, Ramanathan N, Sundararajan K. Probing C-H⋯N interaction in acetylene-benzonitrile complex using matrix isolation infrared spectroscopy and DFT computations. Chem Phys 2017. [DOI: 10.1016/j.chemphys.2016.11.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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13
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Ramanathan N, Sundararajan K, Vidya K, Jemmis ED. Non-covalent C-Cl…π interaction in acetylene-carbon tetrachloride adducts: Matrix isolation infrared and ab initio computational studies. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2016; 157:69-78. [PMID: 26722673 DOI: 10.1016/j.saa.2015.12.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 11/23/2015] [Accepted: 12/14/2015] [Indexed: 06/05/2023]
Abstract
Non-covalent halogen-bonding interactions between π cloud of acetylene (C2H2) and chlorine atom of carbon tetrachloride (CCl4) have been investigated using matrix isolation infrared spectroscopy and quantum chemical computations. The structure and the energies of the 1:1 C2H2-CCl4 adducts were computed at the B3LYP, MP2 and M05-2X levels of theory using 6-311++G(d,p) basis set. The computations indicated two minima for the 1:1 C2H2-CCl4 adducts; with the C-Cl…π adduct being the global minimum, where π cloud of C2H2 is the electron donor. The second minimum corresponded to a C-H…Cl adduct, in which C2H2 is the proton donor. The interaction energies for the adducts A and B were found to be nearly identical. Experimentally, both C-Cl…π and C-H…Cl adducts were generated in Ar and N2 matrixes and characterized using infrared spectroscopy. This is the first report on halogen bonded adduct, stabilized through C-Cl…π interaction being identified at low temperatures using matrix isolation infrared spectroscopy. Atoms in Molecules (AIM) and Natural Bond Orbital (NBO) analyses were performed to support the experimental results. The structures of 2:1 ((C2H2)2-CCl4) and 1:2 (C2H2-(CCl4)2) multimers and their identification in the low temperature matrixes were also discussed.
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Affiliation(s)
- N Ramanathan
- Chemistry Group, Indira Gandhi Centre for Atomic Research, Kalpakkam 603 102, India
| | - K Sundararajan
- Chemistry Group, Indira Gandhi Centre for Atomic Research, Kalpakkam 603 102, India.
| | - K Vidya
- School of Chemistry, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala 695016, India
| | - Eluvathingal D Jemmis
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560 012, India.
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14
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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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15
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Ramanathan N, Brahmmananda Rao CVS, Sankaran K, Sundararajan K. Unraveling the Conformational Landscape of Triallyl Phosphate: Matrix Isolation Infrared Spectroscopy and Density Functional Theory Computations. J Phys Chem A 2015; 119:4017-31. [DOI: 10.1021/acs.jpca.5b00889] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- N. Ramanathan
- Chemistry
Group, Indira Gandhi Centre for Atomic Research, Kalpakkam 603 102, Tamil Nadu, India
| | | | - K. Sankaran
- Chemistry
Group, Indira Gandhi Centre for Atomic Research, Kalpakkam 603 102, Tamil Nadu, India
| | - K. Sundararajan
- Chemistry
Group, Indira Gandhi Centre for Atomic Research, Kalpakkam 603 102, Tamil Nadu, India
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16
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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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