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Bartkowiak W, Lipkowski P, Chołuj M. Molecular systems in spatial confinement: Variation of linear and nonlinear electrical response of molecules in the bond dissociation processes. Advances in Quantum Chemistry 2023. [DOI: 10.1016/bs.aiq.2023.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
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Chołuj M, Lipkowski P, Bartkowiak W. HeH + under Spatial Confinement. Molecules 2022; 27:molecules27248997. [PMID: 36558130 PMCID: PMC9787572 DOI: 10.3390/molecules27248997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/02/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022]
Abstract
In the present study, the influence of spatial confinement on the bond length as well as dipole moment, polarizability and (hyper)polarizabilities of HeH+ ion was analyzed. The effect of spatial confinement was modelled by cylindrically symmetric harmonic oscillator potential, that can be used to mimic high pressure conditions. Based on the conducted research it was found that the spatial confinement significantly affects the investigated properties. Increasing the confinement strength leads to a substantial decrease of their values. This work may be of particular interest for astrochemistry as HeH+ is believed to be the first compound to form in the Universe.
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Lipkowski P, Kozłowska J, Bartkowiak W. A Look at the Spatial Confining Effect on the Molecular Electrostatic Potential (MEP)-A Case Study of the HF and BrCN Molecules. Molecules 2021; 26:5924. [PMID: 34641468 PMCID: PMC8512269 DOI: 10.3390/molecules26195924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/28/2021] [Accepted: 09/28/2021] [Indexed: 11/16/2022] Open
Abstract
In this theoretical study, we report on the molecular electrostatic potential (MEP) of titled molecules confined by repulsive potentials of cylindrical symmetry mimicking a topology. Our calculations show that the spatial restriction significantly changes the picture of the MEP of molecules in a quantitative and qualitative sense. In particular, the drastic changes in the MEP as a function of the strength of spatial confinement are observed for the BrCN molecule. This preliminary study is the first step in the investigation of the behavior of the MEP of molecular systems under orbital compression.
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Affiliation(s)
| | | | - Wojciech Bartkowiak
- Department of Physical and Quantum Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wyb. Wyspiańskiego 27, PL-50370 Wrocław, Poland; (P.L.); (J.K.)
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Hetmańczyk Ł, Goremychkin EA, Waliszewski J, Vener MV, Lipkowski P, Tolstoy PM, Filarowski A. Spectroscopic Identification of Hydrogen Bond Vibrations and Quasi-Isostructural Polymorphism in N-Salicylideneaniline. Molecules 2021; 26:molecules26165043. [PMID: 34443632 PMCID: PMC8401763 DOI: 10.3390/molecules26165043] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 08/13/2021] [Accepted: 08/16/2021] [Indexed: 11/16/2022] Open
Abstract
The ortho-hydroxy aryl Schiff base 2-[(E)-(phenylimino)methyl]phenol and its deutero-derivative have been studied by the inelastic incoherent neutron scattering (IINS), infrared (IR) and Raman experimental methods, as well as by Density Functional Theory (DFT) and Density-Functional Perturbation Theory (DFPT) simulations. The assignments of vibrational modes within the 3500–50 cm−1 spectral region made it possible to state that the strong hydrogen bond in the studied compound can be classified as the so-called quasi-aromatic bond. The isotopic substitution supplemented by the results of DFT calculations allowed us to identify vibrational bands associated with all five major hydrogen bond vibrations. Quasi-isostructural polymorphism of 2-[(E)-(phenylimino)methyl]phenol (SA) and 2-[(E)-(phenyl-D5-imino)methyl]phenol (SA-C6D5) has been studied by powder X-ray diffraction in the 20–320 K temperature range.
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Affiliation(s)
- Łukasz Hetmańczyk
- Faculty of Chemistry, Jagiellonian University, 2 Gronostajowa Str., 30-387 Cracow, Poland;
| | - Eugene A. Goremychkin
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research 6 F. Joliot-Curie str., 141980 Dubna, Russia;
| | - Janusz Waliszewski
- Faculty of Physics, University of Bialystok, 1L Ciolkowskiego str., 15-245 Bialystok, Poland;
| | - Mikhail V. Vener
- Quantum Chemistry Department, Mendeleev University of Chemical Technology, Miusskaya Square 9, 125047 Moscow, Russia;
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii Prosp. 31, 119991 Moscow, Russia
| | - Paweł Lipkowski
- Department of Physical and Quantum Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańnskiego 27, 50-370 Wrocław, Poland;
| | - Peter M. Tolstoy
- Institute of Chemistry, St. Petersburg State University, Universitetskij pr. 26, 198504 Saint Petersburg, Russia
- Correspondence: (P.M.T.); (A.F.); Tel.: +48-71-375-7229 (A.F.)
| | - Aleksander Filarowski
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research 6 F. Joliot-Curie str., 141980 Dubna, Russia;
- Faculty of Chemistry, University of Wrocław 14 F. Joliot-Curie str., 50-383 Wrocław, Poland
- Correspondence: (P.M.T.); (A.F.); Tel.: +48-71-375-7229 (A.F.)
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Kozłowska J, Lipkowski P, Roztoczyńska A, Bartkowiak W. DFT and spatial confinement: a benchmark study on the structural and electrical properties of hydrogen bonded complexes. Phys Chem Chem Phys 2019; 21:17253-17273. [PMID: 31347634 DOI: 10.1039/c9cp02714a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
An extended set of 37 exchange correlation functionals, representing different DFT approximations, has been evaluated on a difficult playground represented by the dipole moment (μz), polarizability (αzz), first hyperpolarizability (βzzz), and the corresponding interaction-induced electrical properties (Δμz, Δαzz, Δβzzz) of spatially confined hydrogen bonded (HB) dimers. A two-dimensional harmonic oscillator potential was used to exert the effect of spatial restriction. The performance of DFT methods in predicting hydrogen bond lengths in the studied molecular complexes upon confinement has also been examined. The data determined using a high-level CCSD(T) method serve as a reference. The conducted analyses allow us to conclude that methods rooted in DFT constitute a precise tool for the calculation of μz and αzz as well as Δμz and Δαzz, as most of the tested functionals provide results affected by rather small relative errors. On the other hand, an accurate description of the nonlinear optical response of the studied HB systems remains a great challenge for most of the analyzed DFT functionals, both in vacuum and in the presence of an analytical confining potential. Some of the tested DFT methods are found to be prone to catastrophic failure in the prediction of βzzz as well as Δβzzz. The obtained results indicate that there is no great chasm in performance between functionals belonging to different DFT approximations or functionals including different amount of Hartree-Fock exchange when the values of dipole moment and first hyperpolarizability as well as the corresponding interaction-induced electrical properties are considered. However, a higher fraction of Hartree-Fock exchange improves the quality of predictions of αzz and Δαzz. Additionally, it has been shown that only three functionals from the examined set, namely B2PLYP, B3LYP and ωB97X-D, provide highly accurate structural parameters for the investigated systems. Of significant importance is the conclusion that the ωB97X-D functional, representing a modern and highly parametrized range-separated hybrid, demonstrates the most coherent behavior, showing rather small deviations from the reference data in the case of μz, αzz, Δμz and Δαzz as well as the structural parameters of the studied HB dimers. Moreover, our results indicate that the presence of spatial confinement has a rather small effect on the performance of DFT methods.
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Affiliation(s)
- Justyna Kozłowska
- Department of Physical and Quantum Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, PL-50370 Wrocław, Poland.
| | - Paweł Lipkowski
- Department of Physical and Quantum Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, PL-50370 Wrocław, Poland.
| | - Agnieszka Roztoczyńska
- Department of Physical and Quantum Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, PL-50370 Wrocław, Poland.
| | - Wojciech Bartkowiak
- Department of Physical and Quantum Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, PL-50370 Wrocław, Poland.
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Leen V, Laine M, Ngongo JM, Lipkowski P, Verbelen B, Kochel A, Dehaen W, Van der Auweraer M, Nadtochenko V, Filarowski A. Impact of the Keto–Enol Tautomeric Equilibrium on the BODIPY Chromophore. J Phys Chem A 2018; 122:5955-5961. [DOI: 10.1021/acs.jpca.8b03489] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Volker Leen
- Department of Chemistry, KU Leuven, Celestijnenlaan 200f−bus 02404, 3001 Leuven, Belgium
| | - Marina Laine
- Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie 14, 50-383, Wrocław, Poland
| | - Joseph Molisho Ngongo
- Faculty of Science, Université de Kinshasa, B.P. 190, Kinshasa XI, Democratic Republic of the Congo
| | - Paweł Lipkowski
- Department of Physical and Quantum Chemistry, Wrocław University of Technology, Wyb. Wyspianskiego 27, 50-370 Wrocław, Poland
| | - Bram Verbelen
- Department of Chemistry, KU Leuven, Celestijnenlaan 200f−bus 02404, 3001 Leuven, Belgium
| | - Andrzej Kochel
- Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie 14, 50-383, Wrocław, Poland
| | - Wim Dehaen
- Department of Chemistry, KU Leuven, Celestijnenlaan 200f−bus 02404, 3001 Leuven, Belgium
| | - Mark Van der Auweraer
- Department of Chemistry, KU Leuven, Celestijnenlaan 200f−bus 02404, 3001 Leuven, Belgium
| | - Viktor Nadtochenko
- N.N. Semenov Institute of Chemical Physics, RAS, Kosigin str. 4, 119991, Moscow, Russian Federation
| | - Aleksander Filarowski
- Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie 14, 50-383, Wrocław, Poland
- Department of Physics, Industrial University of Tyumen, 625-000, Tyumen, Russian Federation
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Kwocz A, Jan Panek J, Jezierska A, Hetmańczyk Ł, Pawlukojć A, Kochel A, Lipkowski P, Filarowski A. A molecular roundabout: triple cyclically arranged hydrogen bonds in light of experiment and theory. NEW J CHEM 2018. [DOI: 10.1039/c8nj04339f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
This paper dwells on the synthesis and diverse studies of cyclically arranged hydrogen bridges in tris-hydroxy aryl Schiff bases. Experimental (IINS, IR, Raman and X-ray) and theoretical (CPMD, DFTP and DFT) studies of tris-hydroxy aryl Schiff bases have been performed in the solid state.
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Affiliation(s)
- Agnieszka Kwocz
- Faculty of Chemistry
- University of Wrocław
- 50-383 Wrocław
- Poland
| | | | - Aneta Jezierska
- Faculty of Chemistry
- University of Wrocław
- 50-383 Wrocław
- Poland
| | - Łukasz Hetmańczyk
- Faculty of Chemistry
- Jagiellonian University
- 30-387 Kraków
- Poland
- Frank Laboratory of Neutron Physics
| | - Andrzej Pawlukojć
- Frank Laboratory of Neutron Physics
- Joint Institute for Nuclear Research
- 141980 Dubna
- Russia
- Institute of Nuclear Chemistry and Technology
| | - Andrzej Kochel
- Faculty of Chemistry
- University of Wrocław
- 50-383 Wrocław
- Poland
| | - Paweł Lipkowski
- Department of Physical and Quantum Chemistry
- Faculty of Chemistry
- Wrocław University of Science and Technology
- 50-370 Wrocław
- Poland
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Roztoczyńska A, Lipkowski P, Kozłowska J, Bartkowiak W. About the nature of halogen bond interaction under the spatial confinement. J Chem Phys 2017; 146:154304. [PMID: 28433010 DOI: 10.1063/1.4980033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Nowadays, much attention is put toward the description of noncovalent complexes exposed to the high pressure or embedded in confining environments. Such conditions may strongly modify the physical and chemical properties of molecular systems. This study focuses on the theoretical description of the confinement induced changes in geometry and energetic parameters of the halogen bonded FCl⋯CNF complex. A model analytical potential is applied to render the effect of orbital compression. In order to analyze the nature of halogen bond interaction, in the presence of spatial confinement, the supermolecular approach together with the symmetry-adapted perturbation theory is used. Furthermore, a thorough analysis of topological parameters, characterizing the halogen bond upon orbital compression, is performed within the quantum theory of atoms in molecules. The calculations are carried out using the ωB97x and CCSD(T) methods in connection with the aug-cc-pVTZ basis set. Among others, the obtained results indicate that the spatial confinement not only modifies the nature of halogen bond interaction but also induces the appearance of a completely new form of the studied FCl⋯CNF system.
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Affiliation(s)
- Agnieszka Roztoczyńska
- Department of Physical and Quantum Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, PL-50370 Wrocław, Poland
| | - Paweł Lipkowski
- Department of Physical and Quantum Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, PL-50370 Wrocław, Poland
| | - Justyna Kozłowska
- Department of Physical and Quantum Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, PL-50370 Wrocław, Poland
| | - Wojciech Bartkowiak
- Department of Physical and Quantum Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, PL-50370 Wrocław, Poland
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Roztoczyńska A, Kozłowska J, Lipkowski P, Bartkowiak W. Hydrogen bonding inside and outside carbon nanotubes: HF dimer as a case study. Phys Chem Chem Phys 2016; 18:2417-27. [PMID: 26701220 DOI: 10.1039/c5cp04153h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this theoretical work we analyze the noncovalent interactions of molecular complexes formed between the hydrogen bonded HF dimer and single-walled carbon nanotubes (SWCNTs) of different diameters. In particular, the interaction energies of: (i) spatially confined hydrogen fluoride molecules and (ii) HF dimer and the exterior or interior of SWCNTs are investigated. The computations are carried out in a supermolecular manner using the M06-2X exchange-correlation functional. In order to establish the influence of mutual orientation of the hydrogen fluoride dimer and molecular carbon cages on the analyzed energetic parameters energy scans are performed. Furthermore, changes in the charge distribution of the investigated endo- and exohedral complexes are studied employing the Natural Bond Orbital analysis. Among others, the position of the HF dimer with respect to the carbon cages proves to have a significant influence on the analyzed quantities. The results of our study also indicate that the HF dimer interacts stronger with the interior rather than the exterior of SWCNTs. Moreover, a substantial enhancement of the basis set superposition error is disclosed.
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Affiliation(s)
- Agnieszka Roztoczyńska
- Department of Physical and Quantum Chemistry, Wrocław University of Technology, Wybrzeże Wyspiańskiego 27, PL - 50370 Wrocław, Poland.
| | - Justyna Kozłowska
- Department of Physical and Quantum Chemistry, Wrocław University of Technology, Wybrzeże Wyspiańskiego 27, PL - 50370 Wrocław, Poland.
| | - Paweł Lipkowski
- Department of Physical and Quantum Chemistry, Wrocław University of Technology, Wybrzeże Wyspiańskiego 27, PL - 50370 Wrocław, Poland.
| | - Wojciech Bartkowiak
- Department of Physical and Quantum Chemistry, Wrocław University of Technology, Wybrzeże Wyspiańskiego 27, PL - 50370 Wrocław, Poland.
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Abstract
A boron-dipyrrin chromophore connected with an o-hydroxyaryl aldimine by a diazo bridge (BODIPY-Schiff dye) has been developed. The photophysical properties of the BODIPY-Schiff dye have been investigated with UV, steady-state, and time-resolved fluorimetry. The spectral features have been characterized with respect to density functional theory and time-dependent density functional theory. The conformational analysis of the studied compound has been accomplished both in the ground and excited states. A scheme of the processes occurring in the BODIPY-Schiff dye has been proposed.
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Affiliation(s)
- Aleksander Filarowski
- Faculty of Chemistry, University of Wroclaw , F. Joliot-Curie 14, 50-383 Wrocław, Poland
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Panek JJ, Jezierska-Mazzarello A, Lipkowski P, Martyniak A, Filarowski A. Comparison of resonance assisted and charge assisted effects in strengthening of hydrogen bonds in dipyrrins. J Chem Inf Model 2014; 54:86-95. [PMID: 24392989 DOI: 10.1021/ci400091f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This paper deals with the study of two types of hydrogen bonding: a quasi-aromatic hydrogen bonding in dipyrromethene and the ionic one in dipyrromethane. The study focuses on two phenomena-the proton transfer process and tautomeric equilibrium. Metric parameters and spectroscopic assignments have been calculated; this allowed a further comparison of spectral features calculated with four methods (Car-Parrinello molecular dynamics (CPMD), ab initio, density functional theory (DFT), and numerical calculation of anharmonic vibrational levels via a solution of the corresponding 1D Schrödinger equation). A significant dynamics of the bridged proton and bent vibration of pyrrole fragments in dipyrromethane have been exposed by the CPMD calculations. The prevailing of the ionic effect over the π-electronic coupling in the strengthening of the hydrogen bonding has been shown on the basis of the calculated structural, electron-topological, and spectral data as well as potential energy surface (PES). The analysis of the aromaticity and electronic state of pyrrole and chelate moieties depending on the tautomeric equilibrium by the quantum theory of atoms in molecules (QTAIM) method was conducted. The principle divergence in the behavior of aromaticity of the chelate chains in the analyzed compounds was demonstrated.
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Affiliation(s)
- Jarosław J Panek
- Faculty of Chemistry, University of Wrocław , F. Joliot-Curie 14, 50-383 Wrocław, Poland
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Lipkowski P, Kozłowska J, Roztoczyńska A, Bartkowiak W. Hydrogen-bonded complexes upon spatial confinement: structural and energetic aspects. Phys Chem Chem Phys 2014; 16:1430-40. [DOI: 10.1039/c3cp53583e] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Skwara B, Góra RW, Zaleśny R, Lipkowski P, Bartkowiak W, Reis H, Papadopoulos MG, Luis JM, Kirtman B. Electronic Structure, Bonding, Spectra, and Linear and Nonlinear Electric Properties of Ti@C28. J Phys Chem A 2011; 115:10370-81. [DOI: 10.1021/jp206331n] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Bartłomiej Skwara
- Theoretical Chemistry Group, Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wybrzeże Wyspiánskiego 27, 50-370 Wrocław, Poland
| | - Robert W. Góra
- Theoretical Chemistry Group, Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wybrzeże Wyspiánskiego 27, 50-370 Wrocław, Poland
| | - Robert Zaleśny
- Theoretical Chemistry Group, Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wybrzeże Wyspiánskiego 27, 50-370 Wrocław, Poland
| | - Paweł Lipkowski
- Theoretical Chemistry Group, Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wybrzeże Wyspiánskiego 27, 50-370 Wrocław, Poland
| | - Wojciech Bartkowiak
- Theoretical Chemistry Group, Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wybrzeże Wyspiánskiego 27, 50-370 Wrocław, Poland
| | - Heribert Reis
- Institute of Organic and Pharmaceutical Chemistry, The National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, 11635 Athens, Greece
| | - Manthos G. Papadopoulos
- Institute of Organic and Pharmaceutical Chemistry, The National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, 11635 Athens, Greece
| | | | - Bernard Kirtman
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
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15
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Abstract
The MP2/6-311++G(d,p) calculations were performed on several hydrogen-bonded systems. Different complexes were taken into account to analyze various types of hydrogen bonds, possessing different types of proton donors and proton acceptors as well as characterized by the broad range of the interaction energy. The Quantum Theory of Atoms in Molecules is applied. The results of the hybrid variational-perturbational approach are discussed. The unique properties of hydrogen bonds, where π-electrons act as the proton acceptor (X-H···π), are analyzed, and these interactions are compared with the other types of hydrogen bonds, mainly with C-H···Y interactions. It is shown that for X-H···π systems the ellipticity at the bond critical point of the proton···acceptor interaction is much greater than for the other types of hydrogen bonds. However, both X-H···π and C-H···Y interactions are characterized by the dominance of the dispersive energy.
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Affiliation(s)
- Sławomir J Grabowski
- Kimika Fakultatea, Euskal Herriko Unibertsitatea and Donostia International Physics Center (DIPC), Donostia, Euskadi, Spain.
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Wiśniewski Ł, Deperasińska I, Staszewska A, Stefanowicza P, Berski S, Lipkowski P, Szewczuka Z, Szemik-Hojniak A. Photophysical Properties of Dipeptides Containing Substituted 3-(Quinoxalin-6-yl) Alanine. Spectroscopic Studies and Theoretical Calculations. J Phys Chem A 2010; 114:9405-12. [DOI: 10.1021/jp911285u] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ł Wiśniewski
- Faculty of Chemistry, University of Wroclaw, Joliot-Curie 14 st, 50-383 Wroclaw, Poland
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Czyżnikowska Ż, Góra RW, Zaleśny R, Lipkowski P, Jarzembska KN, Dominiak PM, Leszczynski J. Structural Variability and the Nature of Intermolecular Interactions in Watson−Crick B-DNA Base Pairs. J Phys Chem B 2010; 114:9629-44. [DOI: 10.1021/jp101258q] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ż. Czyżnikowska
- Theoretical Chemistry Group, Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland; Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Jackson State University, 1400 J. R. Lynch St., Jackson, Mississippi 39217; and Department of Chemistry, Warsaw University, Pasteura 1, 02-093 Warsaw, Poland
| | - R. W. Góra
- Theoretical Chemistry Group, Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland; Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Jackson State University, 1400 J. R. Lynch St., Jackson, Mississippi 39217; and Department of Chemistry, Warsaw University, Pasteura 1, 02-093 Warsaw, Poland
| | - R. Zaleśny
- Theoretical Chemistry Group, Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland; Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Jackson State University, 1400 J. R. Lynch St., Jackson, Mississippi 39217; and Department of Chemistry, Warsaw University, Pasteura 1, 02-093 Warsaw, Poland
| | - P. Lipkowski
- Theoretical Chemistry Group, Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland; Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Jackson State University, 1400 J. R. Lynch St., Jackson, Mississippi 39217; and Department of Chemistry, Warsaw University, Pasteura 1, 02-093 Warsaw, Poland
| | - K. N. Jarzembska
- Theoretical Chemistry Group, Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland; Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Jackson State University, 1400 J. R. Lynch St., Jackson, Mississippi 39217; and Department of Chemistry, Warsaw University, Pasteura 1, 02-093 Warsaw, Poland
| | - P. M. Dominiak
- Theoretical Chemistry Group, Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland; Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Jackson State University, 1400 J. R. Lynch St., Jackson, Mississippi 39217; and Department of Chemistry, Warsaw University, Pasteura 1, 02-093 Warsaw, Poland
| | - J. Leszczynski
- Theoretical Chemistry Group, Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland; Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Jackson State University, 1400 J. R. Lynch St., Jackson, Mississippi 39217; and Department of Chemistry, Warsaw University, Pasteura 1, 02-093 Warsaw, Poland
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Czyżnikowska Ż, Kurzawa J, Zaleśny R, Lipkowski P, Bartkowiak W. Reinvestigation of electronic structure and electric properties of large betaine molecules: A combined long-range-corrected DFT and coupled-cluster study. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.08.056] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Czyżnikowska Ż, Lipkowski P, Góra RW, Zaleśny R, Cheng AC. On the Nature of Intermolecular Interactions in Nucleic Acid Base−Amino Acid Side-Chain Complexes. J Phys Chem B 2009; 113:11511-20. [DOI: 10.1021/jp904146m] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Ż. Czyżnikowska
- Theoretical Chemistry Group, Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland, and Department of Molecular Structure, Amgen Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139
| | - P. Lipkowski
- Theoretical Chemistry Group, Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland, and Department of Molecular Structure, Amgen Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139
| | - R. W. Góra
- Theoretical Chemistry Group, Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland, and Department of Molecular Structure, Amgen Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139
| | - R. Zaleśny
- Theoretical Chemistry Group, Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland, and Department of Molecular Structure, Amgen Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139
| | - A. C. Cheng
- Theoretical Chemistry Group, Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland, and Department of Molecular Structure, Amgen Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139
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Filarowski A, Koll A, Lipkowski P, Pawlukojć A. Inelastic neutron scattering and vibrational spectra of 2-(N-methyl-α-iminoethyl)-phenol and 2-(N-methyliminoethyl)-phenol: Experimental and theoretical approach. J Mol Struct 2008. [DOI: 10.1016/j.molstruc.2007.11.045] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Melikova S, Rutkowski K, Lipkowski P, Shchepkin D, Koll A. FTIR studies of HCl dissolved in liquid CO: Anharmonic effects in the weak OC…HCl complex. J Mol Struct 2007. [DOI: 10.1016/j.molstruc.2007.03.033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Lipkowski P, Grabowski SJ, Leszczynski J. Properties of the Halogen−Hydride Interaction: An ab Initio and “Atoms in Molecules” Analysis. J Phys Chem A 2006; 110:10296-302. [PMID: 16928121 DOI: 10.1021/jp062289y] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
X-Cl...H-Y interactions are analyzed by applying ab initio methods as well as the Bader theory. All calculations were performed using Pople's basis sets (6-311++G(2df,2pd) and 6-311++G(3df,3pd)) as well as the Dunning-type bases (aug-cc-pVDZ and aug-cc-pVTZ) within the MP2 method. For the complexes analyzed here, X-Cl and H-Y may be treated as a Lewis acid and a Lewis base, respectively. The Cl...H interactions are rather weak or at most moderate since, for the strongest interaction of the F3...HLi complex, the binding energy calculated at the MP2/6-311++G(3df,3pd) level of approximation amounts to -3.4 kcal/mol, and the H...Cl distance is equal to 2.65 A, less than the corresponding sum of van der Waals radii. These interactions may be classified as halogen-hydride interactions. However, some of the complexes analyzed, especially F3SiCl...HBeF and F3SiCl...HBeF, are very weakly bound, probably by typical van der Waals interactions.
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Affiliation(s)
- Paweł Lipkowski
- Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, Jackson, Mississippi 39217, USA
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Bartkowiak W, Lipkowski P. Hydrogen-bond effects on the electronic absorption spectrum and evaluation of nonlinear optical properties of an aminobenzodifuranone derivative that exhibits the largest positive solvatochromism. J Mol Model 2005; 11:317-22. [PMID: 16007436 DOI: 10.1007/s00894-005-0249-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2004] [Accepted: 01/25/2005] [Indexed: 11/26/2022]
Abstract
In this work, for the first time, a theoretical approach to describing the influence of hydrogen-bond formation on the electronic absorption spectrum and nonlinear optical properties of an aminobenzodifuranone derivative (ABF) that exhibits the largest positive solvatochromic shift compared to other known chromophores is given. The solvent effect was included via the supermolecule (SM) method. The calculations were performed for a strong low-lying (pi-->pi*) transition based on the configuration interaction singles (CIS) and time-dependent DFT (TDDFT) methods. The first-order hyperpolarizabilities (beta) were computed using the finite-field (FF) technique combined with the Hartree-Fock (HF) theory. Reasonable agreement between theory and experiment was obtained for the solvatochromic shifts of the ABF molecule. Moreover, it was found that H-bond formation strongly influences the NLO response of the systems investigated. [Figure: see text]. The interaction difference-density maps of the systems studied: a II--complex ABF with NFTB; b III--complex ABF with HMPA. The red color designates an increase of the electron density caused by the intermolecular interactions, whereas blue indicates a corresponding decrease of the electron density. The isodensity contours were plotted for +/-0.01 electron/bohr3 (DFT/B3LYP/6-31G(d,p)).
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Affiliation(s)
- Wojciech Bartkowiak
- Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wybrzeze Wyspiańskiego 27, 50-370, Wrocław, Poland.
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Hilpert K, Roszak S, Saloni J, Miller M, Lipkowski P, Leszczynski J. The Dimerization of SnCl2(g): Mass Spectrometric and Theoretical Studies. J Phys Chem A 2005; 109:1286-94. [PMID: 16833442 DOI: 10.1021/jp0460691] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The vaporization of SnCl2(s) was investigated in the temperature range between 382 and 504 K by the use of Knudsen effusion mass spectrometry. The Sn+, SnCl+, SnCl2+, Sn2Cl3+, and Sn2Cl4+ ions were detected in the mass spectrum of the equilibrium vapor. The SnCl2(g) and Sn2Cl4(g) gaseous species were identified, and their partial pressures were determined. The structure and vibrational properties of both species and corresponding fragmentation products were studied applying density functional theory and second-order Møller-Plesset perturbation theoretical approaches. Molecular parameters yielded thermodynamic functions by the use of statistical thermodynamics. The sublimation enthalpies of SnCl2(g) and Sn2Cl4(g) at 298 K resulting from the second- and third-law methods are evaluated as 130.9 +/- 6.2 kJ mol(-1) and 155.8 +/- 7.3 kJ mol(-1), respectively. The enthalpy changes of the dissociation reactions Sn2Cl4(g) = 2 SnCl2(g) were obtained as delta(d)H degrees(298) = 106.8 +/- 6.2 kJ mol(-1). The corresponding theoretical value amounts to 103.4 kJ mol(-1). The change of monomer properties due to the dimerization reaction is also discussed.
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Affiliation(s)
- K Hilpert
- Institute for Materials and Processes in Energy Systems, Research Center Jülich, 52425 Jülich, Germany
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Lipkowski P, Grabowski SJ, Robinson TL, Leszczynski J. Properties of the C−H···H Dihydrogen Bond: An ab Initio and Topological Analysis. J Phys Chem A 2004. [DOI: 10.1021/jp048562i] [Citation(s) in RCA: 221] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Paweł Lipkowski
- Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, Jackson, Mississippi 39217, Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wyb. Wyspiańskiego 27, 50−370 Wrocław, Poland, and Department of Crystallography and Crystal Chemistry, University of Łódź 90-236 Łódź, ul. Pomorska 149/153, Poland
| | - Sławomir J. Grabowski
- Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, Jackson, Mississippi 39217, Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wyb. Wyspiańskiego 27, 50−370 Wrocław, Poland, and Department of Crystallography and Crystal Chemistry, University of Łódź 90-236 Łódź, ul. Pomorska 149/153, Poland
| | - Teri L. Robinson
- Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, Jackson, Mississippi 39217, Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wyb. Wyspiańskiego 27, 50−370 Wrocław, Poland, and Department of Crystallography and Crystal Chemistry, University of Łódź 90-236 Łódź, ul. Pomorska 149/153, Poland
| | - Jerzy Leszczynski
- Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, Jackson, Mississippi 39217, Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wyb. Wyspiańskiego 27, 50−370 Wrocław, Poland, and Department of Crystallography and Crystal Chemistry, University of Łódź 90-236 Łódź, ul. Pomorska 149/153, Poland
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Lipkowski P, Koll A, Karpfen A, Wolschann P. Steric enhancement of the strength of intramolecular hydrogen bond in 3-Cl substituted 2-(N-dimethylaminomethyl) phenols. Chem Phys Lett 2003. [DOI: 10.1016/s0009-2614(03)00068-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Rutkowski K, Melikova S, Shchepkin D, Lipkowski P, Koll A. Higher-order transitions in the IR spectrum of the weak OC⋯HCl complex dissolved in liquid CO. Chem Phys Lett 2000. [DOI: 10.1016/s0009-2614(00)00716-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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