International Journal of Molecular Sciences

Research

26 pages, 16372 KiB

Open AccessArticle

Halogen Bond via an Electrophilic π-Hole on Halogen in Molecules: Does It Exist?

by Pradeep R. Varadwaj

Int. J. Mol. Sci. 2024, 25(9), 4587; https://doi.org/10.3390/ijms25094587 - 23 Apr 2024

Viewed by 293

This study reveals a new non-covalent interaction called a π-hole halogen bond, which is directional and potentially non-linear compared to its sister analog (σ-hole halogen bond). A π-hole is shown here to be observed on the surface of halogen in halogenated molecules, which [...] Read more.

This study reveals a new non-covalent interaction called a π-hole halogen bond, which is directional and potentially non-linear compared to its sister analog (σ-hole halogen bond). A π-hole is shown here to be observed on the surface of halogen in halogenated molecules, which can be tempered to display the aptness to form a π-hole halogen bond with a series of electron density-rich sites (Lewis bases) hosted individually by 32 other partner molecules. The [MP2/aug-cc-pVTZ] level characteristics of the π-hole halogen bonds in 33 binary complexes obtained from the charge density approaches (quantum theory of intramolecular atoms, molecular electrostatic surface potential, independent gradient model (IGM-δg^inter)), intermolecular geometries and energies, and second-order hyperconjugative charge transfer analyses are discussed, which are similar to other non-covalent interactions. That a π-hole can be observed on halogen in halogenated molecules is substantiated by experimentally reported crystals documented in the Cambridge Crystal Structure Database. The importance of the π-hole halogen bond in the design and growth of chemical systems in synthetic chemistry, crystallography, and crystal engineering is yet to be fully explicated. Full article

(This article belongs to the Special Issue Noncovalent Interactions: New Developments in Experiment and Theory)

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15 pages, 2467 KiB

Open AccessArticle

Insight into the Binding of Argon to Cyclic Water Clusters from Symmetry-Adapted Perturbation Theory

by Carly A. Rock and Gregory S. Tschumper

Int. J. Mol. Sci. 2023, 24(24), 17480; https://doi.org/10.3390/ijms242417480 - 14 Dec 2023

Viewed by 577

Abstract

This work systematically examines the interactions between a single argon atom and the edges and faces of cyclic H

_{2}

O clusters containing three–five water molecules (Ar(H

_{2}

O)

_{n = 3 - 5}

). Full geometry optimizations and subsequent harmonic vibrational frequency [...] Read more.

This work systematically examines the interactions between a single argon atom and the edges and faces of cyclic H

_{2}

O clusters containing three–five water molecules (Ar(H

_{2}

O)

_{n = 3 - 5}

). Full geometry optimizations and subsequent harmonic vibrational frequency computations were performed using MP2 with a triple-

ζ

correlation consistent basis set augmented with diffuse functions on the heavy atoms (cc-pVTZ for H and aug-cc-pVTZ for O and Ar; denoted as haTZ). Optimized structures and harmonic vibrational frequencies were also obtained with the two-body–many-body (2b:Mb) and three-body–many-body (3b:Mb) techniques; here, high-level CCSD(T) computations capture up through the two-body or three-body contributions from the many-body expansion, respectively, while less demanding MP2 computations recover all higher-order contributions. Five unique stationary points have been identified in which Ar binds to the cyclic water trimer, along with four for (H

_{2}

O)

_{4}

and three for (H

_{2}

O)

_{5}

. To the best of our knowledge, eleven of these twelve structures have been characterized here for the first time. Ar consistently binds more strongly to the faces than the edges of the cyclic (H

_{2}

O)

_{n}

clusters, by as much as a factor of two. The 3b:Mb electronic energies computed with the haTZ basis set indicate that Ar binds to the faces of the water clusters by at least 3 kJ mol

^{- 1}

and by nearly 6 kJ mol

^{- 1}

for one Ar(H

_{2}

O)

_{5}

complex. An analysis of the interaction energies for the different binding motifs based on symmetry-adapted perturbation theory (SAPT) indicates that dispersion interactions are primarily responsible for the observed trends. The binding of a single Ar atom to a face of these cyclic water clusters can induce perturbations to the harmonic vibrational frequencies on the order of 5 cm

^{- 1}

for some hydrogen-bonded OH stretching frequencies. Full article

(This article belongs to the Special Issue Noncovalent Interactions: New Developments in Experiment and Theory)

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13 pages, 4032 KiB

Open AccessArticle

Intermolecular Interactions in 3-Aminopropyltrimethoxysilane, N-Methyl-3-aminopropyltrimethoxysilane and 3-Aminopropyltriethoxysilane: Insights from Computational Spectroscopy

by Mariela M. Nolasco, Stewart F. Parker, Pedro D. Vaz and Paulo J. A. Ribeiro-Claro

Int. J. Mol. Sci. 2023, 24(23), 16634; https://doi.org/10.3390/ijms242316634 - 23 Nov 2023

Viewed by 668

Abstract

In this work, a computational spectroscopy approach was used to provide a complete assignment of the inelastic neutron scattering spectra of three title alkoxysilane derivatives—3-aminopropyltrimethoxysilane (APTS), N-methyl-3-aminopropyltrimethoxysilane (MAPTS), and 3-aminopropyltriethoxysilane (APTES). The simulated spectra obtained from density functional theory (DFT) calculations exhibit a [...] Read more.

In this work, a computational spectroscopy approach was used to provide a complete assignment of the inelastic neutron scattering spectra of three title alkoxysilane derivatives—3-aminopropyltrimethoxysilane (APTS), N-methyl-3-aminopropyltrimethoxysilane (MAPTS), and 3-aminopropyltriethoxysilane (APTES). The simulated spectra obtained from density functional theory (DFT) calculations exhibit a remarkable match with the experimental spectra. The description of the experimental band profiles improves as the number of molecules considered in the theoretical model increases, from monomers to trimers. This highlights the significance of incorporating non-covalent interactions, encompassing classical NH···N, N–H···O, as well as C–H···N and C–H···O hydrogen bond contacts, to achieve a comprehensive understanding of the system. A distinct scenario emerges when considering optical vibrational techniques, infrared and Raman spectroscopy. In these instances, the monomer model provides a reasonable description of the experimental spectra, and no substantial alterations are observed in the simulated spectra when employing dimer and trimer models. This observation underscores the distinctive ability of neutron spectroscopy in combination with DFT calculations in assessing the structure and dynamics of molecular materials. Full article

(This article belongs to the Special Issue Noncovalent Interactions: New Developments in Experiment and Theory)

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13 pages, 3714 KiB

Open AccessArticle

Computational Insight into the Nature and Strength of the π-Hole Type Chalcogen∙∙∙Chalcogen Interactions in the XO₂∙∙∙CH₃YCH₃ Complexes (X = S, Se, Te; Y = O, S, Se, Te)

by Fengying Lei, Qingyu Liu, Yeshuang Zhong, Xinai Cui, Jie Yu, Zuquan Hu, Gang Feng, Zhu Zeng and Tao Lu

Int. J. Mol. Sci. 2023, 24(22), 16193; https://doi.org/10.3390/ijms242216193 - 10 Nov 2023

Viewed by 936

Abstract

In recent years, the non-covalent interactions between chalcogen centers have aroused substantial research interest because of their potential applications in organocatalysis, materials science, drug design, biological systems, crystal engineering, and molecular recognition. However, studies on π-hole-type chalcogen∙∙∙chalcogen interactions are scarcely reported [...] Read more.

In recent years, the non-covalent interactions between chalcogen centers have aroused substantial research interest because of their potential applications in organocatalysis, materials science, drug design, biological systems, crystal engineering, and molecular recognition. However, studies on π-hole-type chalcogen∙∙∙chalcogen interactions are scarcely reported in the literature. Herein, the π-hole-type intermolecular chalcogen∙∙∙chalcogen interactions in the model complexes formed between XO₂ (X = S, Se, Te) and CH₃YCH₃ (Y = O, S, Se, Te) were systematically studied by using quantum chemical computations. The model complexes are stabilized via one primary X∙∙∙Y chalcogen bond (ChB) and the secondary C−H∙∙∙O hydrogen bonds. The binding energies of the studied complexes are in the range of −21.6~−60.4 kJ/mol. The X∙∙∙Y distances are significantly smaller than the sum of the van der Waals radii of the corresponding two atoms. The X∙∙∙Y ChBs in all the studied complexes except for the SO₂∙∙∙CH₃OCH₃ complex are strong in strength and display a partial covalent character revealed by conducting the quantum theory of atoms in molecules (QTAIM), a non-covalent interaction plot (NCIplot), and natural bond orbital (NBO) analyses. The symmetry-adapted perturbation theory (SAPT) analysis discloses that the X∙∙∙Y ChBs are primarily dominated by the electrostatic component. Full article

(This article belongs to the Special Issue Noncovalent Interactions: New Developments in Experiment and Theory)

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17 pages, 3499 KiB

Open AccessArticle

New Insights into Acylhydrazones E/Z Isomerization: An Experimental and Theoretical Approach

by Sara Fernández-Palacios, Esther Matamoros, Isabel Morato Rojas, Juan T. López Navarrete, M. Carmen Ruiz Delgado, Yolanda Vida and Ezequiel Perez-Inestrosa

Int. J. Mol. Sci. 2023, 24(19), 14739; https://doi.org/10.3390/ijms241914739 - 29 Sep 2023

Viewed by 1012

Abstract

A family of acylhydrazones have been prepared and characterized with the aim of investigating their potential as information storage systems. Their well-established synthetic methodologies allowed for the preparation of seven chemically stable acylhydrazones in excellent yields that have been photophysically and photochemically characterized. [...] Read more.

A family of acylhydrazones have been prepared and characterized with the aim of investigating their potential as information storage systems. Their well-established synthetic methodologies allowed for the preparation of seven chemically stable acylhydrazones in excellent yields that have been photophysically and photochemically characterized. In addition, DFT and TD-DFT calculations have been performed to gain more insights into the structural, energetic and photophysical properties of the E/Z isomers. Our results reveal that E/Z configurational isomerization upon irradiation is highly dependent on the stabilization of the E or Z isomers due to the formation of intramolecular H bonds and the electronic/steric effects intrinsically related to their structures. In addition, Raman spectroscopy is also used to confirm the molecular structural changes after the formation of hydrogen bonds in the isomers. Full article

(This article belongs to the Special Issue Noncovalent Interactions: New Developments in Experiment and Theory)

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26 pages, 6005 KiB

Open AccessArticle

Photonics of Some Monomethine Cyanine Dyes in Solutions and in Complexes with Biomolecules

by Pavel G. Pronkin and Alexander S. Tatikolov

Int. J. Mol. Sci. 2023, 24(18), 13954; https://doi.org/10.3390/ijms241813954 - 11 Sep 2023

Viewed by 669

Abstract

In search of new probes for biomolecules, the spectral fluorescent study of four monomethine cyanine dyes (MCD), both unsymmetrical and symmetrical, has been carried out in different organic solvents, in aqueous buffer solutions, and in the presence of DNA and HSA. The complexation [...] Read more.

In search of new probes for biomolecules, the spectral fluorescent study of four monomethine cyanine dyes (MCD), both unsymmetrical and symmetrical, has been carried out in different organic solvents, in aqueous buffer solutions, and in the presence of DNA and HSA. The complexation of MCD with biomacromolecules leads to a steep growth of the fluorescence intensity. Complexes of MCD with dsDNA and HSA of various types were modeled in silico by molecular docking. Experiments on thermal dissociation of dsDNA in the presence of MCD showed the formation of intercalative complexes of MCD with DNA. Quenching of intrinsic fluorescence of HSA by MCD occurred with rate constants much higher than the diffusion limit, that is, in dye–HSA complexes. Effective constants of MCD complexation with the biomacromolecules were estimated. MCD 1 has the best characteristics as a possible fluorescent probe for dsDNA and can serve as a sensitive and selective probe for dsDNA in the presence of HSA. Photochemical properties of MCD complexed with DNA have been also studied. An increase in the quantum yield of the triplet states of MCD in complexes with DNA has been found, which may be important for using these dyes as potential candidates in photodynamic therapy. Full article

(This article belongs to the Special Issue Noncovalent Interactions: New Developments in Experiment and Theory)

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13 pages, 1445 KiB

Open AccessArticle

C∙∙∙O and Si∙∙∙O Tetrel Bonds: Substituent Effects and Transfer of the SiF₃ Group

by Zhihao Niu, Qiaozhuo Wu, Qingzhong Li and Steve Scheiner

Int. J. Mol. Sci. 2023, 24(15), 11884; https://doi.org/10.3390/ijms241511884 - 25 Jul 2023

Cited by 1 | Viewed by 752

Abstract

The tetrel bond (TB) between 1,2-benzisothiazol-3-one-2-TF₃-1,1-dioxide (T = C, Si) and the O atom of pyridine-1-oxide (PO) and its derivatives (PO-X, X = H, NO₂, CN, F, CH₃, OH, OCH₃, NH₂, and Li) [...] Read more.

The tetrel bond (TB) between 1,2-benzisothiazol-3-one-2-TF₃-1,1-dioxide (T = C, Si) and the O atom of pyridine-1-oxide (PO) and its derivatives (PO-X, X = H, NO₂, CN, F, CH₃, OH, OCH₃, NH₂, and Li) is examined by quantum chemical means. The Si∙∙∙O TB is quite strong, with interaction energies approaching a maximum of nearly 70 kcal/mol, while the C∙∙∙O TB is an order of magnitude weaker, with interaction energies between 2.0 and 2.6 kcal/mol. An electron-withdrawing substituent on the Lewis base weakens this TB, while an electron-donating group has the opposite effect. The SiF₃ group transfers roughly halfway between the N of the acid and the O of the base without the aid of cooperative effects from a third entity. Full article

(This article belongs to the Special Issue Noncovalent Interactions: New Developments in Experiment and Theory)

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14 pages, 3176 KiB

Open AccessArticle

A Study on the Interactions of Proteinase K with Myricetin and Myricitrin by Multi-Spectroscopy and Molecular Modeling

by Kefan Liu, Yubo Zhang, Wei Zhang, Liyan Liu and Zhan Yu

Int. J. Mol. Sci. 2023, 24(6), 5317; https://doi.org/10.3390/ijms24065317 - 10 Mar 2023

Cited by 1 | Viewed by 1201

Abstract

Myricetin (MYR) and myricitrin (MYT) are well recognized for their nutraceutical value, such as antioxidant, hypoglycemic, and hypotensive effects. In this work, fluorescence spectroscopy and molecular modeling were adopted to investigate the conformational and stability changes of proteinase K (PK) in the presence [...] Read more.

Myricetin (MYR) and myricitrin (MYT) are well recognized for their nutraceutical value, such as antioxidant, hypoglycemic, and hypotensive effects. In this work, fluorescence spectroscopy and molecular modeling were adopted to investigate the conformational and stability changes of proteinase K (PK) in the presence of MYR and MYT. The experimental results showed that both MYR and MYT could quench fluorescence emission via a static quenching mechanism. Further investigation demonstrated that both hydrogen bonding and van der Waals forces play significant roles in the binding of complexes, which is consistent with the conclusions of molecular modeling. Synchronous fluorescence spectroscopy, Förster resonance energy transfer, and site-tagged competition experiments were performed to prove that the binding of MYR or MYT to PK could alter its micro-environment and conformation. Molecular docking results revealed that either MYR or MYT spontaneously interacted with PK at a single binding site via hydrogen bonding and hydrophobic interactions, which is consistent with the results of spectroscopic measurements. A 30 ns molecular dynamics simulation was conducted for both PK-MYR and PK-MYT complexes. The calculation results showed that no large structural distortions or interaction changes occurred during the entire simulation time span. The average RMSD changes of PK in PK-MYR and PK-MYT were 2.06 and 2.15 Å, respectively, indicating excellent stability of both complexes. The molecular simulation results suggested that both MYR and MYT could interact with PK spontaneously, which is in agreement with spectroscopic results. This agreement between experimental and theoretical results indicates that the method herein could be feasible and worthwhile for protein–ligand complex studies. Full article

(This article belongs to the Special Issue Noncovalent Interactions: New Developments in Experiment and Theory)

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