Molecules

Research

14 pages, 1953 KiB

Open AccessArticle

Rotational Spectroscopy Meets Quantum Chemistry for Analyzing Substituent Effects on Non-Covalent Interactions: The Case of the Trifluoroacetophenone-Water Complex

by Juncheng Lei, Silvia Alessandrini, Junhua Chen, Yang Zheng, Lorenzo Spada, Qian Gou, Cristina Puzzarini and Vincenzo Barone

Molecules 2020, 25(21), 4899; https://doi.org/10.3390/molecules25214899 - 23 Oct 2020

Cited by 10 | Viewed by 2880

Abstract

The most stable isomer of the 1:1 complex formed by 2,2,2-trifluoroacetophenone and water has been characterized by combining rotational spectroscopy in supersonic expansion and state-of-the-art quantum-chemical computations. In the observed isomer, water plays the double role of proton donor and acceptor, thus forming [...] Read more.

The most stable isomer of the 1:1 complex formed by 2,2,2-trifluoroacetophenone and water has been characterized by combining rotational spectroscopy in supersonic expansion and state-of-the-art quantum-chemical computations. In the observed isomer, water plays the double role of proton donor and acceptor, thus forming a seven-membered ring with 2,2,2-trifluoroacetophenone. Accurate intermolecular parameters featuring one classical O-H···O hydrogen bond and one weak C-H···O hydrogen bond have been determined by means of a semi-experimental approach for equilibrium structure. Furthermore, insights on the nature of the established non-covalent interactions have been unveiled by means of different bond analyses. The comparison with the analogous complex formed by acetophenone with water points out the remarkable role played by fluorine atoms in tuning non-covalent interactions. Full article

(This article belongs to the Special Issue Spectroscopic Aspects of Noncovalent Interactions)

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17 pages, 2197 KiB

Open AccessFeature PaperArticle

Molecular Hydrogen as a Lewis Base in Hydrogen Bonds and Other Interactions

by Sławomir J. Grabowski

Molecules 2020, 25(14), 3294; https://doi.org/10.3390/molecules25143294 - 20 Jul 2020

Cited by 8 | Viewed by 2680

Abstract

The second-order Møller–Plesset perturbation theory calculations with the aug-cc-pVTZ basis set were performed for complexes of molecular hydrogen. These complexes are connected by various types of interactions, the hydrogen bonds and halogen bonds are most often represented in the sample of species analysed; [...] Read more.

The second-order Møller–Plesset perturbation theory calculations with the aug-cc-pVTZ basis set were performed for complexes of molecular hydrogen. These complexes are connected by various types of interactions, the hydrogen bonds and halogen bonds are most often represented in the sample of species analysed; most interactions can be classified as σ-hole and π-hole bonds. Different theoretical approaches were applied to describe these interactions: Quantum Theory of ‘Atoms in Molecules’, Natural Bond Orbital method, or the decomposition of the energy of interaction. The energetic, geometrical, and topological parameters are analysed and spectroscopic properties are discussed. The stretching frequency of the H-H bond of molecular hydrogen involved in intermolecular interactions is considered as a parameter expressing the strength of interaction. Full article

(This article belongs to the Special Issue Spectroscopic Aspects of Noncovalent Interactions)

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16 pages, 2197 KiB

Open AccessArticle

Dimerization of Acetic Acid in the Gas Phase—NMR Experiments and Quantum-Chemical Calculations

by Ondřej Socha and Martin Dračínský

Molecules 2020, 25(9), 2150; https://doi.org/10.3390/molecules25092150 - 04 May 2020

Cited by 15 | Viewed by 5872

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)

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15 pages, 1441 KiB

Open AccessArticle

Nature of the Interaction of Pyridines with OCS. A Theoretical Investigation

by Sumitra Bhattarai, Dipankar Sutradhar, Asit K. Chandra and Therese Zeegers-Huyskens

Molecules 2020, 25(2), 416; https://doi.org/10.3390/molecules25020416 - 19 Jan 2020

Cited by 8 | Viewed by 2880

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)

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15 pages, 4371 KiB

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

by Dragoș Dăbuleanu, Antonio Bauzá, Joaquín Ortega-Castro, Eduardo C. Escudero-Adán, Pablo Ballester and Antonio Frontera

Molecules 2020, 25(2), 285; https://doi.org/10.3390/molecules25020285 - 10 Jan 2020

Cited by 3 | Viewed by 3304

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)

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14 pages, 1662 KiB

Open AccessFeature PaperArticle

Isolation of a Halogen-Bonded Complex Formed between Methane and Chlorine Monofluoride and Characterisation by Rotational Spectroscopy and Ab Initio Calculations

by Anthony C. Legon, David G. Lister, John H. Holloway, Devendra Mani and Elangannan Arunan

Molecules 2019, 24(23), 4257; https://doi.org/10.3390/molecules24234257 - 22 Nov 2019

Cited by 2 | Viewed by 3607

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 k_σ

≅

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 r_e(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 D_e

≅

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)

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15 pages, 1120 KiB

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

by Mariusz Michalczyk, Wiktor Zierkiewicz, Rafał Wysokiński and Steve Scheiner

Molecules 2019, 24(18), 3329; https://doi.org/10.3390/molecules24183329 - 12 Sep 2019

Cited by 32 | Viewed by 2733

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)

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14 pages, 2308 KiB

Open AccessArticle

N^…C and S^…S Interactions in Complexes, Molecules, and Transition Structures HN(CH)SX:SCO, for X = F, Cl, NC, CCH, H, and CN

by Janet E. Del Bene, Ibon Alkorta and José Elguero

Molecules 2019, 24(18), 3232; https://doi.org/10.3390/molecules24183232 - 05 Sep 2019

Cited by 3 | Viewed by 2202

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 C_s 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 S^…S 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 N^…C and S^…S bonds in these two systems. Full article

(This article belongs to the Special Issue Spectroscopic Aspects of Noncovalent Interactions)

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12 pages, 830 KiB

Open AccessArticle

Effects of Halogen, Chalcogen, Pnicogen, and Tetrel Bonds on IR and NMR Spectra

by Jia Lu and Steve Scheiner

Molecules 2019, 24(15), 2822; https://doi.org/10.3390/molecules24152822 - 02 Aug 2019

Cited by 39 | Viewed by 3565

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)

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