molecules-logo

Journal Browser

Journal Browser

Special Issue "Spectroscopic Aspects of Noncovalent Interactions"

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Physical Chemistry".

Deadline for manuscript submissions: closed (30 June 2020).

Special Issue Editors

Dr. Wiktor Zierkiewicz
Website
Guest Editor
Wrocław University of Science and Technology, Wroclaw, Poland
Interests: My scientific research is focused on investigations using quantum chemical computational methods of selected properties of complexes stabilized by noncovalent interactions assigned to the following types: hydrogen, halogen, chalcogen, pnicogen, tetrel, aerogen, or triel bond.
Prof. Dr. Steve Scheiner
Website
Guest Editor
Department of Chemistry and Biochemistry, Utah State University, Logan, UT, USA
Interests: Noncovalent bonds with particular emphasis on H-bonds and proton transfers occurring within them, halogen, chalcogen, pnicogen, and tetrel bonds. The applications of these bonds to biochemical structure and function is of special interest.
Special Issues and Collections in MDPI journals

Special Issue Information

Dear colleagues,

The replacement of the bridging H atom in H-bonds by a variety of other, more electronegative, atoms has led to a great deal of accumulating information concerning the related noncovalent bonds, generally known as halogen, chalcogen, pnicogen, and tetrel bonds. The newly acquired information from quantum chemical calculations has a natural overlap with experimental information in the area of spectral data. This Special Issue is dedicated to this overlap with the hope that computational and experimental studies can find a mutual synergy, act as a check on one another, and together provide profound insights into the fundamental nature of all of these interactions.

Dr. Wiktor Zierkiewicz
Prof. Dr. Steve Scheiner
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2000 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Noncovalent bonds
  • H-bonds
  • Halogen bonds
  • Chalcogen bonds
  • Pnicogen bonds
  • Tetrel bonds
  • IR and Raman spectra
  • NMR spectra

Published Papers (7 papers)

Order results
Result details
Select all
Export citation of selected articles as:

Research

Open AccessArticle
Dimerization of Acetic Acid in the Gas Phase—NMR Experiments and Quantum-Chemical Calculations
Molecules 2020, 25(9), 2150; https://doi.org/10.3390/molecules25092150 - 04 May 2020
Abstract
Due to the nature of the carboxylic group, acetic acid can serve as both a donor and acceptor of a hydrogen bond. Gaseous acetic acid is known to form cyclic dimers with two strong hydrogen bonds. However, trimeric and various oligomeric structures have [...] Read more.
Due to the nature of the carboxylic group, acetic acid can serve as both a donor and acceptor of a hydrogen bond. Gaseous acetic acid is known to form cyclic dimers with two strong hydrogen bonds. However, trimeric and various oligomeric structures have also been hypothesized to exist in both the gas and liquid phases of acetic acid. In this work, a combination of gas-phase NMR experiments and advanced computational approaches were employed in order to validate the basic dimerization model of gaseous acetic acid. The gas-phase experiments performed in a glass tube revealed interactions of acetic acid with the glass surface. On the other hand, variable-temperature and variable-pressure NMR parameters obtained for acetic acid in a polymer insert provided thermodynamic parameters that were in excellent agreement with the MP2 (the second order Møller–Plesset perturbation theory) and CCSD(T) (coupled cluster with single, double and perturbative triple excitation) calculations based on the basic dimerization model. A slight disparity between the theoretical dimerization model and the experimental data was revealed only at low temperatures. This observation might indicate the presence of other, entropically disfavored, supramolecular structures at low temperatures. Full article
(This article belongs to the Special Issue Spectroscopic Aspects of Noncovalent Interactions)
Show Figures

Graphical abstract

Open AccessArticle
Nature of the Interaction of Pyridines with OCS. A Theoretical Investigation
Molecules 2020, 25(2), 416; https://doi.org/10.3390/molecules25020416 - 19 Jan 2020
Abstract
Ab initio calculations were carried out to investigate the interaction between para-substituted pyridines (X-C5H4N, X=NH2, CH3, H, CN, NO2) and OCS. Three stable structures of pyridine.OCS complexes were detected at the MP2=full/aug-cc-pVDZ [...] Read more.
Ab initio calculations were carried out to investigate the interaction between para-substituted pyridines (X-C5H4N, X=NH2, CH3, H, CN, NO2) and OCS. Three stable structures of pyridine.OCS complexes were detected at the MP2=full/aug-cc-pVDZ level. The A structure is characterized by N…S chalcogen bonds and has binding energies between −9.58 and −12.24 kJ/mol. The B structure is bonded by N…C tetrel bond and has binding energies between −10.78 and −11.81 kJ/mol. The C structure is characterized by π-interaction and has binding energies between −10.76 and −13.33 kJ/mol. The properties of the systems were analyzed by AIM, NBO, and SAPT calculations. The role of the electrostatic potential of the pyridines on the properties of the systems is outlined. The frequency shift of relevant vibrational modes is analyzed. Full article
(This article belongs to the Special Issue Spectroscopic Aspects of Noncovalent Interactions)
Show Figures

Graphical abstract

Open AccessFeature PaperArticle
Synthesis, X-ray Characterization and Density Functional Theory (DFT) Studies of Two Polymorphs of the α,α,α,α, Isomer of Tetra-p-Iodophenyl Tetramethyl Calix[4]pyrrole: On the Importance of Halogen Bonds
Molecules 2020, 25(2), 285; https://doi.org/10.3390/molecules25020285 - 10 Jan 2020
Abstract
This manuscript reports the improved synthesis of the α,α,α,α isomer of tetra-p-iodophenyl tetra-methyl calix[4]pyrrole and the X-ray characterization of two solvate polymorphs. In the solid state, the calix[4]pyrrole receptor adopts the cone conformation, including one acetonitrile molecule in its aromatic cavity [...] Read more.
This manuscript reports the improved synthesis of the α,α,α,α isomer of tetra-p-iodophenyl tetra-methyl calix[4]pyrrole and the X-ray characterization of two solvate polymorphs. In the solid state, the calix[4]pyrrole receptor adopts the cone conformation, including one acetonitrile molecule in its aromatic cavity by establishing four convergent hydrogen bonds between its nitrogen atom and the four pyrrole NHs of the former. The inclusion complexes pack into rods, displaying a unidirectional orientation. In turn, the rods form flat 2D-layers by alternating the orientation of their p-iodo substituents. The 2D layers stack on top of another, resulting in a head-to-head and tail-to-tail orientation of the complexes or their exclusive arrangement in a head-to-tail geometry. The dissimilar stacking of the layers yields two solvate polymorphs that are simultaneously present in the structures of the single crystals. The ratio of the two polymorph phases is regulated by the amount of acetonitrile added to the chloroform solutions from which the crystals grow. Halogen bonding interactions are highly relevant in the crystal lattices of the two polymorphs. We analyzed and characterized these interactions by means of density functional theory (DFT) calculations and several computational tools. Remarkably, single crystals of a solvate containing two acetonitrile molecules per calix[4]pyrrole were obtained from pure acetonitrile solution. Full article
(This article belongs to the Special Issue Spectroscopic Aspects of Noncovalent Interactions)
Show Figures

Graphical abstract

Open AccessFeature PaperArticle
Isolation of a Halogen-Bonded Complex Formed between Methane and Chlorine Monofluoride and Characterisation by Rotational Spectroscopy and Ab Initio Calculations
Molecules 2019, 24(23), 4257; https://doi.org/10.3390/molecules24234257 - 22 Nov 2019
Cited by 1
Abstract
A halogen-bonded complex formed between methane and chlorine monofluoride has been isolated in the gas phase before the reaction between the components and has been characterised through its rotational spectrum, which is of the symmetric-top type but only exhibits K = 0 type [...] Read more.
A halogen-bonded complex formed between methane and chlorine monofluoride has been isolated in the gas phase before the reaction between the components and has been characterised through its rotational spectrum, which is of the symmetric-top type but only exhibits K = 0 type transitions at the low effective temperature of the pulsed-jet experiment. Spectroscopic constants for two low-lying states that result from internal rotation of the CH4 subunit were detected for each of the two isotopic varieties H4C···35ClF and H4C···37ClF and were analysed to show that ClF lies on the symmetry axis with Cl located closer than F to the C atom, at the distance r0(C···Cl) 3.28 Å and with an intermolecular stretching force constant kσ 4 N m−1. Ab initio calculations at the explicitly correlated level CCSD(T)(F12c)/cc-pVTZ-F12 show that in the equilibrium geometry, the ClF molecule lies along a C3 axis of CH4 and Cl is involved in a halogen bond. The Cl atom points at the nucleophilic region identified on the C3 axis, opposite the unique C–H bond and somewhere near the C atom and the tetrahedron face centre, with re(C···Cl) = 3.191 Å. Atoms-in-molecules (AIM) theory shows a bond critical point between Cl and C, confirming the presence of a halogen bond. The energy that is required to dissociate the complex from the equilibrium conformation into its CH4 and ClF components is only De 5 kJ mol−1. A likely path for the internal rotation of the CH4 subunit is identified by calculations at the same level of theory, which also provide the variation of the energy of the system as a function of the motion along that path. The barrier to the motion along the path is only 20 cm−1. Full article
(This article belongs to the Special Issue Spectroscopic Aspects of Noncovalent Interactions)
Show Figures

Graphical abstract

Open AccessFeature PaperArticle
Theoretical Studies of IR and NMR Spectral Changes Induced by Sigma-Hole Hydrogen, Halogen, Chalcogen, Pnicogen, and Tetrel Bonds in a Model Protein Environment
Molecules 2019, 24(18), 3329; https://doi.org/10.3390/molecules24183329 - 12 Sep 2019
Cited by 3
Abstract
Various types of σ-hole bond complexes were formed with FX, HFY, H2FZ, and H3FT (X = Cl, Br, I; Y = S, Se, Te; Z = P, As, Sb; T = Si, Ge, Sn) as Lewis acid. In order [...] Read more.
Various types of σ-hole bond complexes were formed with FX, HFY, H2FZ, and H3FT (X = Cl, Br, I; Y = S, Se, Te; Z = P, As, Sb; T = Si, Ge, Sn) as Lewis acid. In order to examine their interactions with a protein, N-methylacetamide (NMA), a model of the peptide linkage was used as the base. These noncovalent bonds were compared by computational means with H-bonds formed by NMA with XH molecules (X = F, Cl, Br, I). In all cases, the A–F bond, which lies opposite the base and is responsible for the σ-hole on the A atom (A refers to the bridging atom), elongates and its stretching frequency undergoes a shift to the red with a band intensification, much as what occurs for the X–H bond in a H-bond (HB). Unlike the NMR shielding decrease seen in the bridging proton of a H-bond, the shielding of the bridging A atom is increased. The spectroscopic changes within NMA are similar for H-bonds and the other noncovalent bonds. The C=O bond of the amide is lengthened and its stretching frequency red-shifted and intensified. The amide II band shifts to higher frequency and undergoes a small band weakening. The NMR shielding of the O atom directly involved in the bond rises, whereas the C and N atoms both undergo a shielding decrease. The frequency shifts of the amide I and II bands of the base as well as the shielding changes of the three pertinent NMA atoms correlate well with the strength of the noncovalent bond. Full article
(This article belongs to the Special Issue Spectroscopic Aspects of Noncovalent Interactions)
Show Figures

Graphical abstract

Open AccessArticle
NC and SS Interactions in Complexes, Molecules, and Transition Structures HN(CH)SX:SCO, for X = F, Cl, NC, CCH, H, and CN
Molecules 2019, 24(18), 3232; https://doi.org/10.3390/molecules24183232 - 05 Sep 2019
Abstract
Ab initio Møller–Plesset perturbation theory (MP2)/aug’-cc-pVTZ calculations have been carried out in search of complexes, molecules, and transition structures on HN(CH)SX:SCO potential energy surfaces for X = F, Cl, NC, CCH, H, and CN. Equilibrium complexes on these surfaces have C1 symmetry, [...] Read more.
Ab initio Møller–Plesset perturbation theory (MP2)/aug’-cc-pVTZ calculations have been carried out in search of complexes, molecules, and transition structures on HN(CH)SX:SCO potential energy surfaces for X = F, Cl, NC, CCH, H, and CN. Equilibrium complexes on these surfaces have C1 symmetry, but these have binding energies that are no more than 0.5 kJ·mol–1 greater than the corresponding Cs complexes which are vibrationally averaged equilibrium complexes. The binding energies of these span a narrow range and are independent of the N–C distance across the tetrel bond, but they exhibit a second-order dependence on the S–S distance across the chalcogen bond. Charge-transfer interactions stabilize all of these complexes. Only the potential energy surfaces HN(CH)SF:SCO and HN(CH)SCl:SCO have bound molecules that have short covalent N–C bonds and significantly shorter SS chalcogen bonds compared to the complexes. Equation-of-motion coupled cluster singles and doubles (EOM-CCSD) spin-spin coupling constants 1tJ(N–C) for the HN(CH)SX:SCO complexes are small and exhibit no dependence on the N–C distance, while 1cJ(S–S) exhibit a second-order dependence on the S–S distance, increasing as the S–S distance decreases. Coupling constants 1tJ(N–C) and 1cJ(S–S) as a function of the N–C and S–S distances, respectively, in HN(CH)SF:SCO and HN(CH)SCl:SCO increase in the transition structures and then decrease in the molecules. These changes reflect the changing nature of the NC and SS bonds in these two systems. Full article
(This article belongs to the Special Issue Spectroscopic Aspects of Noncovalent Interactions)
Show Figures

Graphical abstract

Open AccessArticle
Effects of Halogen, Chalcogen, Pnicogen, and Tetrel Bonds on IR and NMR Spectra
Molecules 2019, 24(15), 2822; https://doi.org/10.3390/molecules24152822 - 02 Aug 2019
Cited by 4
Abstract
Complexes were formed pairing FX, FHY, FH2Z, and FH3T (X = Cl, Br, I; Y = S, Se, Te; Z = P, As, Sb; T = Si, Ge, Sn) with NH3 in order to form an A⋯N noncovalent [...] Read more.
Complexes were formed pairing FX, FHY, FH2Z, and FH3T (X = Cl, Br, I; Y = S, Se, Te; Z = P, As, Sb; T = Si, Ge, Sn) with NH3 in order to form an A⋯N noncovalent bond, where A refers to the central atom. Geometries, energetics, atomic charges, and spectroscopic characteristics of these complexes were evaluated via DFT calculations. In all cases, the A–F bond, which is located opposite the base and is responsible for the σ-hole on the A atom, elongates and its stretching frequency undergoes a shift to the red. This shift varies from 42 to 175 cm−1 and is largest for the halogen bonds, followed by chalcogen, tetrel, and then pnicogen. The shift also decreases as the central A atom is enlarged. The NMR chemical shielding of the A atom is increased while that of the F and electron donor N atom are lowered. Unlike the IR frequency shifts, it is the third-row A atoms that undergo the largest change in NMR shielding. The change in shielding of A is highly variable, ranging from negligible for FSnH3 all the way up to 1675 ppm for FBr, while those of the F atom lie in the 55–422 ppm range. Although smaller in magnitude, the changes in the N shielding are still easily detectable, between 7 and 27 ppm. Full article
(This article belongs to the Special Issue Spectroscopic Aspects of Noncovalent Interactions)
Show Figures

Graphical abstract

Back to TopTop