Study on the cooperativity of hydrogen bonds between H2Y and HX (X = F, Cl, Br; Y = O, S, Se)

The structure characteristics, interaction energies, cooperative energies of the complexes between chalcogen hydrides ( H 2 Y ) and halogen hydrides (HX) have been studied theoretically at the MP2 level with aug-cc-pVTZ basis set in this paper. The conclusions show that there are strong interactions between H 2 Y and HX. The stability of the complex is decided by the electronegativity of the negatively charged atom. The cooperativity is observed in the two or three hydrogen bonds of each trimer structures in title system. The values of the cooperative energies and the cooperative contributions all illustrate that the cooperativity is of great importance in these complexes. The "atoms in molecules" (AIM) analyses show that the complexes in title system are mainly electrostatic interactions (closed-shell interactions) in character. For H ⋯ O bonds in H 2 O ⋯ HF ⋯ H 2 O , H 2 O ⋯ HBr ⋯ H 2 O and HF ⋯ H 2 O ⋯ HF , the 1 < |Vc|/Gc < 2 and -Gc < Hc < 0 indicate the interactions in these compounds are between closed-shell interaction and opened-shell interaction.

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Can THF hydrogen bond to glycine as strong as water?

Canadian Journal of Chemistry ◽

10.1139/cjc-2016-0604 ◽

2017 ◽

Vol 95 (6) ◽

pp. 664-673 ◽

Cited By ~ 1

Author(s):

Damanjit Kaur ◽

Geetanjali Chopra ◽

Rajinder Kaur

Keyword(s):

Hydrogen Bond ◽

Electrostatic Interactions ◽

Density Functional ◽

Dominant Role ◽

Basis Set ◽

Hydrogen Bond Donor ◽

Orbital Theory ◽

Interaction Terms ◽

Stability Of Complexes ◽

The Stability

Hydrogen bond complexation between glycine and THF and between glycine and water involving four lowest-energy glycine conformers have been studied. The complexes have been investigated in the gas phase at the ab initio molecular orbital theory (MP2) with aug-cc-pVDZ basis set and density functional theory (B3LYP) with aug-cc-pVTZ basis set. Bader’s theory of atoms in molecules (AIM), natural bond orbital (NBO), and symmetry adapted perturbation theory (SAPT) analyses are employed to elucidate the interaction characteristics in the complexes. The premise that the hydrogen bond donor ability of the O–H group of the carboxyl group dominates the interaction between glycine and THF and between glycine and water is confirmed. It is found that in comparison with water, THF binds more strongly to glycine. The quantum studies indicate that contribution of N–H···O and C–H···O hydrogen bonds in the complexes, although lower in magnitude to O–H···O interactions, play an important role in the stability of complexes. The blue and red shifts in the stretching frequencies of the hydrogen bond donors X–H (X = O, C, N) have also been related to stabilization energies. Decomposition of the stabilization energy based on the SAPT method clearly indicates the dominant role of the electrostatic interactions in all the complexes under study; however, induction and dispersion interaction terms are relatively higher in glycine–THF complexes.

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Abinitio interpretation of conformer stabilization through bonding in the acetyl derivatives of two representative heterocyclic methine bases

Canadian Journal of Chemistry ◽

10.1139/v95-158 ◽

1995 ◽

Vol 73 (8) ◽

pp. 1287-1293 ◽

Cited By ~ 4

Author(s):

Kathleen M. Gough ◽

Janice Millington

Keyword(s):

Internal Rotation ◽

Closed Shell ◽

Theoretical Explanation ◽

Atoms In Molecules ◽

Basis Set ◽

Basis Sets ◽

Side Chain ◽

Derivatives Of ◽

Favorable Structure ◽

Oxygen Interaction

Abinitio calculations (STO-3G and 3-21G* basis sets) have been performed on 2 and 3 to determine the most favorable structure and to provide an estimate of the barrier to internal rotation of the acyl group. The Z configuration is preferred in 2, the E configuration in 3, with calculated barriers to internal rotation of 79.9 and 68.7 kJ/mol, respectively, at the 3-21G* level. The wave functions from the 3-21G* calculations are analyzed with the theory of atoms in molecules. The identification of bond critical points characteristic of a closed shell interaction establishes the existence of a weak bond between [Formula: see text] in 2 and between [Formula: see text] in 3, for the preferred configurations. The energy required to break this bond as well as the loss of extended conjugation throughout the hetero ring and its side chain are responsible for the asymmetry in the barrier. These findings provide a theoretical explanation for experimental observations on this class of molecules in which one conformer is preferred to any other and only one crystal structure is identified. Keywords: nonbonded sulfur–oxygen interaction, closed shell interaction, hydrogen bonding, 3-21G* basis set, theory of atoms in molecules.

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A Theoretical Study of Hydrogen-Bonded Complexes of Ethylene Glycol, Thioglycol and Dithioglycol with Water

Asian Journal of Chemistry ◽

10.14233/ajchem.2022.23487 ◽

2021 ◽

Vol 34 (1) ◽

pp. 169-182

Author(s):

Ruchi Kohli ◽

Rupinder Preet Kaur

Keyword(s):

Hydrogen Bond ◽

Charge Transfer ◽

Hydrogen Bonds ◽

Ethylene Glycol ◽

Structural Parameters ◽

Intermolecular Hydrogen Bond ◽

Basis Set ◽

Interaction Energies ◽

Orbital Theory ◽

Hydrogen Bond Formation

In the present study, a theoretical analysis of hydrogen bond formation of ethylene glycol, thioglycol, dithioglycol with single water molecule has been performed based on structural parameters of optimized geometries, interaction energies, deformation energies, orbital analysis and charge transfer. ab initio molecular orbital theory (MP2) method in conjunction with 6-31+G* basis set has been employed. Twelve aggregates of the selected molecules with water have been optimized at MP2/6-31+G* level and analyzed for intramolecular and intermolecular hydrogen bond interactions. The evaluated interaction energies suggest aggregates have hydrogen bonds of weak to moderate strength. Although the aggregates are primarily stabilized by conventional hydrogen bond donors and acceptors, yet C-H···O, S-H···O, O-H···S, etc. untraditional hydrogen bonds also contribute to stabilize many aggregates. The hydrogen bonding involving sulfur in the aggregates of thioglycol and dithioglycol is disfavoured electrostatically but favoured by charge transfer. Natural bond orbital (NBO) analysis has been employed to understand the role of electron delocalizations, bond polarizations, charge transfer, etc. as contributors to stabilization energy.

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Insights into the Intramolecular Properties ofη6-Arene-Ru-Based Anticancer Complexes Using Quantum Calculations

Journal of Chemistry ◽

10.1155/2013/892052 ◽

2013 ◽

Vol 2013 ◽

pp. 1-14

Author(s):

Adebayo A. Adeniyi ◽

Peter A. Ajibade

Keyword(s):

Hydrogen Bonds ◽

Dft Method ◽

Closed Shell ◽

Noncovalent Interaction ◽

Anticancer Activities ◽

Atomic Properties ◽

Anticancer Complexes ◽

Network Of Hydrogen Bonds ◽

The Stability ◽

Half Sandwich

The factors that determine the stability and the effects of noncovalent interaction on theη6-arene ruthenium anticancer complexes are determined using DFT method. The intramolecular and intra-atomic properties were computed for two models of these half-sandwich ruthenium anticancer complexes and their respective hydrated forms. The results showed that the stability of these complexes depends largely on the network of hydrogen bonds (HB), strong nature of charge transfer, polarizability, and electrostatic energies that exist within the complexes. The hydrogen bonds strength was found to be related to the reported anticancer activities and the activation of the complexes by hydration. The metal–ligand bonds were found to be closed shell systems that are characterised by high positive Laplacian values of electron density. Two of the complexes are found to be predominantly characterised by LMCT while the other two are predominately characterised by MLCT.

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Intrinsic Stacking Interactions of Natural and Artificial Nucleobases

10.26434/chemrxiv.11400405 ◽

2019 ◽

Author(s):

Drew P. Harding ◽

Laura J. Kingsley ◽

Glen Spraggon ◽

Steven Wheeler

Keyword(s):

Gas Phase ◽

Electrostatic Interactions ◽

Density Functional ◽

Molecular Descriptors ◽

Stacking Interactions ◽

Interaction Energies ◽

Functional Theory ◽

Binding Partner ◽

Heavy Atoms ◽

Wide Range

The intrinsic (gas-phase) stacking energies of natural and artificial nucleobases were explored using density functional theory (DFT) and correlated ab initio methods. Ranking the stacking strength of natural nucleobase dimers revealed a preference in binding partner similar to that seen from experiments, namely G > C > A > T > U. Decomposition of these interaction energies using symmetry-adapted perturbation theory (SAPT) showed that these dispersion dominated interactions are modulated by electrostatics. Artificial nucleobases showed a similar stacking preference for natural nucleobases and were also modulated by electrostatic interactions. A robust predictive multivariate model was developed that quantitively predicts the maximum stacking interaction between natural and a wide range of artificial nucleobases using molecular descriptors based on computed electrostatic potentials (ESPs) and the number of heavy atoms. This model should find utility in designing artificial nucleobase analogs that exhibit stacking interactions comparable to those of natural nucleobases. Further analysis of the descriptors in this model unveil the origin of superior stacking abilities of certain nucleobases, including cytosine and guanine.

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Performance of Electronic Structure Methods for the Description of Hückel-Möbius Interconversions in Extended π-Systems

10.26434/chemrxiv.10564115 ◽

2019 ◽

Author(s):

Tatiana Woller ◽

Ambar Banerjee ◽

Nitai Sylvetsky ◽

Xavier Deraet ◽

Frank De Proft ◽

...

Keyword(s):

Electronic Structure ◽

Basis Set ◽

Dft Methods ◽

Molecular Switching ◽

Wide Range ◽

Electronic Structure Methods ◽

Explicitly Correlated ◽

Relative Errors ◽

The Stability ◽

Basis Set Expansion

Expanded porphyrins provide a versatile route to molecular switching devices due to their ability to shift between several π-conjugation topologies encoding distinct properties. Taking into account its size and huge conformational flexibility, DFT remains the workhorse for modeling such extended macrocycles. Nevertheless, the stability of Hückel and Möbius conformers depends on a complex interplay of different factors, such as hydrogen bonding, p···p stacking, steric effects, ring strain and electron delocalization. As a consequence, the selection of an exchange-correlation functional for describing the energy profile of topological switches is very difficult. For these reasons, we have examined the performance of a variety of wavefunction methods and density functionals for describing the thermochemistry and kinetics of topology interconversions across a wide range of macrocycles. Especially for hexa- and heptaphyrins, the Möbius structures have a pronouncedly stronger degree of static correlation than the Hückel and figure-eight structures, and as a result the relative energies of singly-twisted structures are a challenging test for electronic structure methods. Comparison of limited orbital space full CI calculations with CCSD(T) calculations within the same active spaces shows that post-CCSD(T) correlation contributions to relative energies are very minor. At the same time, relative energies are weakly sensitive to further basis set expansion, as proven by the minor energy differences between MP2/cc-pVDZ and explicitly correlated MP2-F12/cc-pVDZ-F12 calculations. Hence, our CCSD(T) reference values are reasonably well-converged in both 1-particle and n-particle spaces. While conventional MP2 and MP3 yield very poor results, SCS-MP2 and particularly SOS-MP2 and SCS-MP3 agree to better than 1 kcal mol-1 with the CCSD(T) relative energies. Regarding DFT methods, only M06-2X provides relative errors close to chemical accuracy with a RMSD of 1.2 kcal mol-1. While the original DSD-PBEP86 double hybrid performs fairly poorly for these extended p-systems, the errors drop down to 2 kcal mol-1 for the revised revDSD-PBEP86-NL, again showing that same-spin MP2-like correlation has a detrimental impact on performance like the SOS-MP2 results.

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Cooperation/Competition between Halogen Bonds and Hydrogen Bonds in Complexes of 2,6-Diaminopyridines and X-CY3 (X = Cl, Br; Y = H, F)

Symmetry ◽

10.3390/sym13050766 ◽

2021 ◽

Vol 13 (5) ◽

pp. 766

Author(s):

Barbara Bankiewicz ◽

Marcin Palusiak

Keyword(s):

Complex Formation ◽

Hydrogen Bonds ◽

Dft Calculations ◽

Electrostatic Interactions ◽

Dipole Moments ◽

Main Role ◽

Halogen Bonds ◽

Topological Parameters ◽

Leading Role ◽

The Impact

The DFT calculations have been performed on a series of two-element complexes formed by substituted 2,6-diaminopyridine (R−PDA) and pyridine (R−Pyr) with X−CY3 molecules (where X = Cl, Br and Y = H, F). The primary aim of this study was to examine the intermolecular hydrogen and halogen bonds in the condition of their mutual coexistence. Symmetry/antisymmetry of the interrelation between three individual interactions is addressed. It appears that halogen bonds play the main role in the stabilization of the structures of the selected systems. However, the occurrence of one or two hydrogen bonds was associated with the favourable geometry of the complexes. Moreover, the impact of different substituent groups attached in the para position to the aromatic ring of the 2,6-diaminopyridine and pyridine on the character of the intermolecular hydrogen and halogen bonds was examined. The results indicate that the presence of electron-donating substituents strengthens the bonds. In turn, the presence of electron-withdrawing substituents reduces the strength of halogen bonds. Additionally, when hydrogen and halogen bonds lose their leading role in the complex formation, the nonspecific electrostatic interactions between dipole moments take their place. Analysis was based on geometric, energetic, and topological parameters of the studied systems.

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

Molecules ◽

10.3390/molecules25143294 ◽

2020 ◽

Vol 25 (14) ◽

pp. 3294 ◽

Cited By ~ 2

Author(s):

Sławomir J. Grabowski

Keyword(s):

Hydrogen Bonds ◽

Molecular Hydrogen ◽

Spectroscopic Properties ◽

Lewis Base ◽

Basis Set ◽

Orbital Method ◽

Topological Parameters ◽

Theoretical Approaches ◽

Strength Of Interaction ◽

Moller Plesset

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.

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Exo-bonded six-membered heterocycle in the crystal structures of RE7Co2Ge4(RE = La–Nd)

Dalton Transactions ◽

10.1039/c6dt03302d ◽

2016 ◽

Vol 45 (46) ◽

pp. 18522-18531 ◽

Cited By ~ 2

Author(s):

Siméon Ponou ◽

Sven Lidin

Keyword(s):

Crystal Structures ◽

Strong Interactions ◽

The Stability ◽

Membered Heterocycle

The stability of the heterocyclic {Co4Ge6} clusters in RE7Co2Ge4(RE = La–Nd) is determined by strong interactions with the surrounding RE atoms in the structures.

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