Features of the pnictogen bonds formed by neighboring nitro groups in crystals

Features of the pnictogen bonds formed by neighboring nitro groups in crystals

Автор: Sobalev S.A., Matveychuk Yu.V., Bartashevich E.V.

Журнал: Вестник Южно-Уральского государственного университета. Серия: Химия @vestnik-susu-chemistry

Рубрика: Физическая химия

Статья в выпуске: 4 т.11, 2019 года.

Бесплатный доступ

Features of pnictogen O…N bonds were considered from the point of view of analyzing various geometric orientations of the neighboring nitro groups NO2…NO2 observed in molecular crystals. The “idealized” orientation for a pnictogen bond, where the nucleophilic fragment of the atom O of one nitro group was directed to the electrophilic site of the atom N of the other one, and the “stacking” orientation, which was characterized by the parallel stacking of nitro groups, differ in the features of the electron density and electrostatic potential distribution between O and N atoms. The applied electronic criterion, obtained with the use of quantum chemical calculations with periodic boundary conditions, confirmed that for the considered O…N interactions the necessary condition for their classification as pnictogen bonds was met.

Еще

Pnictogen bond, nitro group, electrostatic potential, electron density, laplacian of the electron density

Короткий адрес: https://sciup.org/147233148

IDR: 147233148   |   DOI: 10.14529/chem190408

Список литературы Features of the pnictogen bonds formed by neighboring nitro groups in crystals

  • Legon A.C. Tetrel, Pnictogen and Chalcogen Bonds Identified in the Gas Phase before they had Names: A Systematic Look at Non-Covalent Interactions. Phys. Chem. Chem. Phys., 2017, vol. 19, no. 23, pp. 14884-14896. DOI: 10.1039/c7cp02518a
  • Cavallo G, Metrangolo P., Pilati T., Resnati, G., Terraneo, G. Naming Interactions from the Electrophilic Site. Cryst. Growth Des., 2014, vol. 14, no. 6, pp. 2697-2702. DOI: 10.1021/cg5001717
  • Desiraju G.R., Ho P.S., Kloo L., Legon A.C., Marquardt R., Metrangolo P., Politzer P.A., Resnati G., Rissanen K. Definition of the halogen bond. Pure Appl. Chem., 2013, vol. 85, no. 8, pp. 1711-1713.
  • Reed A.E., Curtiss L.A., Weinhold F. Intermolecular Interactions from a Natural Bond Orbital, Donor-Acceptor Viewpoint. Chem. Rev., 1988, vol. 88, no. 6, pp. 899-926. DOI: 10.1021/cr00088a005
  • Bader R.F.W. Atoms in Molecules: A Quantum Theory, Clarendon Press, 1990. vol. 22, 438 p.
  • Grice M.E., Murray J.S., Politzer P. Calculated Surface Electrostatic Potentials of Molecular Sieve Models Containing SiO4, A1O4 and PO4 Units. J. Mol. Graphics., 1994, vol. 12, no. 3, pp. 169-171.
  • Becke A.D., Edgecombe K.E. A Simple Measure of Electron Localization in Atomic and Molecular Systems. J. Chem. Phys., 1990. vol. 92, no. 9, pp. 5397-5403.
  • DOI: 10.1063/1.458517
  • Silvi B., Savin A. Classification of Chemical Bonds Based on Topological Analysis of Electron Localization Functions, Nature, 1994, vol. 371, no. 6499, pp. 683-686.
  • DOI: 10.1038/371683a0
  • Sanchez-Sanz G., Trujillo C., Alkorta I., Elguero J. Electron Density Shift Description of Non-Bonding Intramolecular Interactions. Comput. Theor. Chem., 2012, vol. 991, no. 3, pp. 124-133.
  • DOI: 10.1016/j.comptc.2012.04.007
  • Johnson E.R., Keinan S., Mori-Sanchez P., Contreras-Garcia J., Cohen A.J., Yang W. Revealing Non-Covalent Interaction. J. Am. Chem. Soc., 2010. vol. 132, no. 18, pp. 6498-6506.
  • DOI: 10.1021/ja100936w
  • Politzer P., Murray J.S. An Overview of Strengths and Directionalities of Noncovalent Interactions: σ-Holes and ρ-Holes. Crystals, 2019, vol. 9, no. 3, p. 165.
  • DOI: 10.3390/cryst9030165
  • Sanchez-Sanz G., Trujillo C., Alkorta I., Elguero J. Intramolecular Pnicogen Interactions in Phosphorus and Arsenic Analogues of Proton Sponges. Phys. Chem. Chem. Phys., 2014, vol. 16, no. 30. pp. 15900-15909.
  • DOI: 10.1039/c4cp01072h
  • Sanchez-Sanz G., Trujillo C., Alkorta I., Elguero J. Competition between Intramolecular Hydrogen and Pnictogen Bonds in Protonated Systems. Theor. Chem. Acc., 2016, vol. 135, no. 5, p. 140.
  • DOI: 10.1007/s00214-016-1895-8
  • Sanchez-Sanz G., Trujillo C., Alkorta I., Elguero J. Modulating Intramolecular P···N Pnictogen Interactions. Phys. Chem. Chem. Phys., 2016, vol. 18, no. 13, pp. 9148-9160.
  • DOI: 10.1039/c6cp00227g
  • Bader R.F.W. Atoms in Molecules: A Quantum Theory. Oxford University Press, New York, 1990, 458 p.
  • Bader R.F.W. A quantum theory of molecular structure and its applications. Chem. Rev., 1991, vol. 91, no. 5, pp. 893-928.
  • DOI: 10.1021/cr00005a013
  • Bader R.F.W. A Bond Path: A Universal Indicator of Bonded Interactions. J. Phys. Chem. A, 1998, vol. 102, no. 37, pp. 7314-7323.
  • DOI: 10.1021/jp981794v
  • Popelier P.L.A. Atoms in Molecules. An Introduction. Harlow, Addison Wesley Longman, 2000, 188 p.
  • Matta C.F., Boyd R.J. The Quantum Theory of Atoms in Molecules. Wiley-VCH, Weinheim, 2007, vol. 46, no. 36, 567 p.
  • Bader R.F.W. Bond Paths Are Not Chemical Bonds. J. Phys. Chem. A, 2009, vol. 113, no. 38, pp. 10391-10396.
  • Bader R.F.W. Definition of Molecular Structure: By Choice or by Appeal to Observation? J. Phys. Chem. A, 2010, vol. 114, no. 28, pp. 7431-7444.
  • Fanfrik J., Zierkiewicz W., Svec P., Ruzickova Z., Rezac J., Michalczyk M., Ruzicka A., Michalska D., Hobza P. Pnictogen Bonding in Pyrazine·PnX5 (Pn = P, As, Sb and X = F, Cl, Br) complexes. J. Mol. Model., 2017, vol. 23, no. 11, p. 328.
  • DOI: 10.1007/s00894-017-3502-x
  • Fanfrik J., Hnyk D. Dihalogen and Pnictogen Bonding in Crystalline Icosahedral Phosphaboranes. Crystals, 2018, vol. 8, no. 10. p. 390.
  • DOI: 10.3390/cryst8100390
  • Joshi P.R., 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., 2015, vol. 119, no. 14, pp. 3440-3451.
  • DOI: 10.1021/jp511156d
  • Scilabra P., Terraneo G., Resnati G. Fluorinated Elements of Group 15 as Pnictogen Bond Donor Sites. J. Fluor. Chem., 2017, vol. 203, no. 11, pp. 62-74.
  • DOI: 10.1016/j.jfluchem.2017.10.002
  • Bauza A., Sharko A.V., Senchyk G.A., Rusanov E.B., Frontera A., Domasevitch K.V. π-Hole Interactions at Work: Crystal Engineering with Nitro-Derivatives. CrystEngComm., 2017, vol. 19, no. 14, pp. 1933-1937.
  • DOI: 10.1039/C7CE00267J
  • Bauza A., Mooibroek T.J., Frontera A. Directionality of π-Holes in Nitro Compounds. Chem. Comm., 2015, vol. 51, no. 8, pp. 1491-1493.
  • DOI: 10.1039/C4CC09132A
  • Legon A.C. Tetrel, Pnictogen and Chalcogen Bonds Identified in the Gas Phase before they had Names: A Systematic Look at Non-Covalent Interactions. Phys. Chem. Chem. Phys., 2017, vol. 19, no. 23, pp. 14884-14896.
  • DOI: 10.1039/c7cp02518a
  • Cavallo G, Metrangolo P., Pilati T., Resnati, G., Terraneo, G. Naming Interactions from the Electrophilic Site. Cryst. Growth Des., 2014, vol. 14, no. 6, pp. 2697-2702.
  • DOI: 10.1021/cg5001717
  • Desiraju G.R., Ho P.S., Kloo L., Legon A.C., Marquardt R., Metrangolo P., Politzer P.A., Resnati G., Rissanen K. Definition of the halogen bond. Pure Appl. Chem., 2013, vol. 85, no. 8, pp. 1711-1713.
  • Reed A.E., Curtiss L.A., Weinhold F. Intermolecular Interactions from a Natural Bond Orbital, Donor-Acceptor Viewpoint. Chem. Rev., 1988, vol. 88, no. 6, pp. 899-926.
  • DOI: 10.1021/cr00088a005
  • Bader R.F.W. Atoms in Molecules: A Quantum Theory, Clarendon Press, 1990. vol. 22, 438 p.
  • Grice M.E., Murray J.S., Politzer P. Calculated Surface Electrostatic Potentials of Molecular Sieve Models Containing SiO4, A1O4 and PO4 Units. J. Mol. Graphics., 1994, vol. 12, no. 3, pp. 169-171.
  • Becke A.D., Edgecombe K.E. A Simple Measure of Electron Localization in Atomic and Molecular Systems. J. Chem. Phys., 1990. vol. 92, no. 9, pp. 5397-5403.
  • DOI: 10.1063/1.458517
  • Silvi B., Savin A. Classification of Chemical Bonds Based on Topological Analysis of Electron Localization Functions, Nature, 1994, vol. 371, no. 6499, pp. 683-686.
  • DOI: 10.1038/371683a0
  • Sanchez-Sanz G., Trujillo C., Alkorta I., Elguero J. Electron Density Shift Description of Non-Bonding Intramolecular Interactions. Comput. Theor. Chem., 2012, vol. 991, no. 3, pp. 124-133.
  • DOI: 10.1016/j.comptc.2012.04.007
  • Johnson E.R., Keinan S., Mori-Sanchez P., Contreras-Garcia J., Cohen A.J., Yang W. Revealing Non-Covalent Interaction. J. Am. Chem. Soc., 2010. vol. 132, no. 18, pp. 6498-6506.
  • DOI: 10.1021/ja100936w
  • Politzer P., Murray J.S. An Overview of Strengths and Directionalities of Noncovalent Interactions: σ-Holes and ρ-Holes. Crystals, 2019, vol. 9, no. 3, p. 165.
  • DOI: 10.3390/cryst9030165
  • Sanchez-Sanz G., Trujillo C., Alkorta I., Elguero J. Intramolecular Pnicogen Interactions in Phosphorus and Arsenic Analogues of Proton Sponges. Phys. Chem. Chem. Phys., 2014, vol. 16, no. 30. pp. 15900-15909.
  • DOI: 10.1039/c4cp01072h
  • Sanchez-Sanz G., Trujillo C., Alkorta I., Elguero J. Competition between Intramolecular Hydrogen and Pnictogen Bonds in Protonated Systems. Theor. Chem. Acc., 2016, vol. 135, no. 5, p. 140.
  • DOI: 10.1007/s00214-016-1895-8
  • Sanchez-Sanz G., Trujillo C., Alkorta I., Elguero J. Modulating Intramolecular P···N Pnictogen Interactions. Phys. Chem. Chem. Phys., 2016, vol. 18, no. 13, pp. 9148-9160.
  • DOI: 10.1039/c6cp00227g
  • Bader R.F.W. Atoms in Molecules: A Quantum Theory. Oxford University Press, New York, 1990, 458 p.
  • Bader R.F.W. A quantum theory of molecular structure and its applications. Chem. Rev., 1991, vol. 91, no. 5, pp. 893-928.
  • DOI: 10.1021/cr00005a013
  • Bader R.F.W. A Bond Path: A Universal Indicator of Bonded Interactions. J. Phys. Chem. A, 1998, vol. 102, no. 37, pp. 7314-7323.
  • DOI: 10.1021/jp981794v
  • Popelier P.L.A. Atoms in Molecules. An Introduction. Harlow, Addison Wesley Longman, 2000, 188 p.
  • Matta C.F., Boyd R.J. The Quantum Theory of Atoms in Molecules. Wiley-VCH, Weinheim, 2007, vol. 46, no. 36, 567 p.
  • Bader R.F.W. Bond Paths Are Not Chemical Bonds. J. Phys. Chem. A, 2009, vol. 113, no. 38, pp. 10391-10396.
  • Bader R.F.W. Definition of Molecular Structure: By Choice or by Appeal to Observation? J. Phys. Chem. A, 2010, vol. 114, no. 28, pp. 7431-7444.
  • Fanfrik J., Zierkiewicz W., Svec P., Ruzickova Z., Rezac J., Michalczyk M., Ruzicka A., Michalska D., Hobza P. Pnictogen Bonding in Pyrazine·PnX5 (Pn = P, As, Sb and X = F, Cl, Br) complexes. J. Mol. Model., 2017, vol. 23, no. 11, p. 328.
  • DOI: 10.1007/s00894-017-3502-x
  • Fanfrik J., Hnyk D. Dihalogen and Pnictogen Bonding in Crystalline Icosahedral Phosphaboranes. Crystals, 2018, vol. 8, no. 10. p. 390.
  • DOI: 10.3390/cryst8100390
  • Joshi P.R., 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., 2015, vol. 119, no. 14, pp. 3440-3451.
  • DOI: 10.1021/jp511156d
  • Scilabra P., Terraneo G., Resnati G. Fluorinated Elements of Group 15 as Pnictogen Bond Donor Sites. J. Fluor. Chem., 2017, vol. 203, no. 11, pp. 62-74.
  • DOI: 10.1016/j.jfluchem.2017.10.002
  • Bauza A., Sharko A.V., Senchyk G.A., Rusanov E.B., Frontera A., Domasevitch K.V. π-Hole Interactions at Work: Crystal Engineering with Nitro-Derivatives. CrystEngComm., 2017, vol. 19, no. 14, pp. 1933-1937.
  • DOI: 10.1039/C7CE00267J
  • Bauza A., Mooibroek T.J., Frontera A. Directionality of π-Holes in Nitro Compounds. Chem. Comm., 2015, vol. 51, no. 8, pp. 1491-1493.
  • DOI: 10.1039/C4CC09132A
  • Bauza A., Mooibroek T.J., Frontera A. NO3- Anions Can Act as Lewis Acid in the Solid State. Nat. Commun., 2017, vol. 8, no. 2, p. 14522.
  • DOI: 10.1038/ncomms14522
  • Bauza A., Frontera A., Mooibroek T.J. π-Hole Interactions Involving Nitro Compounds: Directionality of Nitrate Esters. Crys. Growth Des., 2016, vol. 16, no. 9, pp. 5520-5524.
  • DOI: 10.1021/acs.cgd.6b00989
  • Wang Y., Li X., Zeng Y. Theoretical Insights into the p-Hole Interactions in the Complexes Containing Triphosphorus Hydride (P3H3) and Its Derivatives. Acta Cryst., 2017, vol. B73, no. 2, pp. 195-202.
  • DOI: 10.1107/S2052520616019223
  • Trujillo C., Sanchez-Sanz G., Alkorta I., Elguero J. Halogen, Chalcogen and Pnictogen Interactions in (XNO2)2 Homodimers (X = F, Cl, Br, I). New J. Chem., 2015, vol. 39, no. 9, pp. 6791-6802.
  • DOI: 10.1039/C5NJ00600G
  • Montisci F., Lanza A., Casati N., Macchi P. Testing Soft Donor-Acceptor Intermolecular Interactions with High Pressure. Acta Cryst. A., 2016, vol. 72, no. 8, p. 400.
  • DOI: 10.1107/S205327331609416X
  • Montisci F., Lanza A., Casati N., Macchi P. NO2···NO2 Contacts under Compression: Testing the Forces in Soft Donor-Acceptor Interactions. Cryst. Growth Des., 2018, vol. 18, no. 12, pp. 7579-7589.
  • DOI: 10.1021/acs.cgd.8b01392
  • Dovesi R., Saunders V.R., Roetti C. CRYSTAL14 User's Manual. Torino: University of Torino, 2014, 382 p.
  • Kostenetskiy P., Semenikhina P. SUSU Supercomputer Resources for Industry and Fundamental Science. Chelyabinsk: Global Smart Industry Conference (GloSIC), 2018, pp. 1-7.
  • Schmidt M.W., Baldridge K.K., Boatz J.A., Elbert S.T., Gordon M.S., Jensen J.H., Koseki S., Matsunaga N., Nguyen K.A., Su S., Windus T.L., Dupuis M., Montgomery Jr J.A. General Atomic and Molecular Electronic Structure System. J. Comp. Chem., 1993, vol. 14, no. 11, pp. 1347-1363.
  • DOI: 10.1002/jcc.540141112
  • Gatti C., Casassa S. Topond14 User's Manual, Torino: University of Torino, 2014, 53 p.
  • Groom C.R., Bruno I.J., Lightfoot M.P. The Cambridge Structural Database. Acta Cryst. B., 2016, vol. 72, no. 4, pp. 171-179.
  • DOI: 10.1107/S2052520616003954
  • Bartashevich E.V., Mukhitdinova S.E., Yushina I.D., Tsirelson V.G. Electronic Criterion for Categorizing the Chalcogen and Halogen Bonds: Sulfur-Iodine Interactions in Crystals. Acta Cryst. B., 2019, vol. 75, pp. 117-126.
  • DOI: 10.1107/S2052520618018280
  • Bartashevich E.V., Yushina I.D., Kropotina K.K., Muhitdinova S.E., Tsirelson V.G. Testing the Tools for Revealing and Characterizing the Iodine-Iodine Halogen Bond in Crystals. Acta Cryst. B., 2017, vol. 73, pp. 217-226.
  • DOI: 10.1107/S2052520617002931
Еще
Статья научная
QR-код для установки приложения SciUp Наведите камеру и скачайте бесплатное приложение SciUp