DFT STUDY OF THE PROTONATION AND DEPROTONATION ENTHALPIES OF BENZOXAZOLE, 1,2-BENZISOXAZOLE AND 2,1-BENZISOXAZOLE AND IMPLICATIONS FOR THE STRUCTURES AND ENERGIES OF THEIR ADDUCTS WITH EXPLICIT WATER MOLECULES

2013 ◽  
Vol 12 (07) ◽  
pp. 1350070 ◽  
Author(s):  
MWADHAM M. KABANDA ◽  
ENO E. EBENSO
Keyword(s):  
Hydrogen Bonds ◽  
Density Functional ◽  
Biologically Active ◽  
Basis Sets ◽  
Water Molecules ◽  
Intermolecular Hydrogen Bonds ◽  
Theoretical Approaches ◽  
Potential Applications ◽  
The Stability ◽  
Explicit Water

Benzoxazole, 1,2-benzisoxazole and 2,1-benzisoxazole are biologically active molecules with potential applications in drug design. Their interaction with aqueous medium in biological systems may be simulated by considering their interaction with explicit water molecules. Such studies provide information on the structures, energies and type of interactions stabilizing the resulting geometric systems. The objective of the current study was to utilize theoretical approaches to investigate the structures, stabilization energy and binding energy of benzoxazole–water, 1,2-benzisoxazole–water and 2,1-benzisoxazole–water complexes. The calculations were performed utilizing the density functional theory (DFT)/M06-2X/6-311 ++ G(d,p) method and the DFT/ωB97XD method with both the 6-311 ++ G(d,p) and the aug-cc-pVDZ basis sets. The results suggest that the stability of the different clusters depends on interrelated factors including the rings formed by intermolecular hydrogen bonds and the proton affinity (PA) or acidity of the atoms forming the intermolecular hydrogen bonds with the water molecules. A comparison across methods indicates that the results follow similar trends with different methods.

scholarly journals Microsolvation of Histidine—A Theoretical Study of Intermolecular Interactions Based on AIM and SAPT Approaches

Symmetry ◽  
2020 ◽  
Vol 12 (7) ◽  
pp. 1153
Author(s):  
Beata Kizior ◽  
Jarosław J. Panek ◽  
Aneta Jezierska
Keyword(s):  
Gas Phase ◽  
Density Functional ◽  
Heterocyclic Ring ◽  
Polarizable Continuum Model ◽  
Water Molecules ◽  
Implicit Solvent ◽  
Actual Interaction ◽  
The Stability ◽  
Explicit Water ◽  
The Impact

Histidine is unique among amino acids because of its rich tautomeric properties. It participates in essential enzymatic centers, such as catalytic triads. The main aim of the study is the modeling of the change of molecular properties between the gas phase and solution using microsolvation models. We investigate histidine in its three protonation states, microsolvated with 1:6 water molecules. These clusters are studied computationally, in the gas phase and with water as a solvent (Polarizable Continuum Model, PCM) within the Density Functional Theory (DFT) framework. The structural analysis reveals the presence of intra- and intermolecular hydrogen bonds. The Atoms-in-Molecules (AIM) theory is employed to determine the impact of solvation on the charge flow within the histidine, with emphasis on the similarity of the two imidazole nitrogen atoms—topologically not equivalent, they are revealed as electronically similar due to the heterocyclic ring aromaticity. Finally, the Symmetry-Adapted Perturbation Theory (SAPT) is used to examine the stability of the microsolvation clusters. While electrostatic and exchange terms dominate in magnitude over polarization and dispersion, the sum of electrostatic and exchange term is close to zero. This makes polarization the factor governing the actual interaction energy. The most important finding of this study is that even with microsolvation, the polarization induced by the presence of implicit solvent is still significant. Therefore, we recommend combined approaches, mixing explicit water molecules with implicit models.

scholarly journals SPECTRAL FEATURES AND HYDROGEN BOND STRUCTURE OF AQUEOUS SOLUTIONS OF ETHANOL

2021 ◽  
pp. 30-33
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonds ◽  
Aqueous Solutions ◽  
Gaseous Medium ◽  
Water Molecules ◽  
Structural Reorganization ◽  
Intermolecular Hydrogen Bonds ◽  
Method Of Molecular Dynamics ◽  
Combined Use ◽  
Structure Of Aqueous Solutions

The aim of this work is develop an approach that makes it possible to study the spectral properties and structure of intermolecular hydrogen bonds in aqueous solutions of ethanol formed in systems whose existence in a gaseous medium or an isolated state is practically impossible. This approach bases on the combined use of infrared spectroscopy and molecular dynamics (MD) methods. An analysis give the structural reorganization of water molecules depending on the concentration of ethanol alcohol. It has been shown that the method of molecular dynamics with classical force fields makes it possible to explicitly take into account the molecules of the solvent and solute, and, thus, to investigate hydrogen bonds in the system and to interpret with the experimental data obtained by vibrational spectroscopy.

Chitosan-Stabilized Oil-in-Water Nanoemulsions

2022 ◽  
pp. 44-58
Author(s):  
Viktoria Milkova
Keyword(s):  
Physicochemical Characteristics ◽  
Biological Properties ◽  
Precise Control ◽  
Theoretical Approaches ◽  
Natural Polysaccharide ◽  
Oil In Water ◽  
Degree Of Acetylation ◽  
Key Factor ◽  
Potential Applications ◽  
The Stability

Chitosan is a natural polysaccharide and emulsifier that can ensure a significant emulsion stability at suitable pH, ionic strength, composition, concentration, or thermal processing. The evaluation of the electrokinetic properties is a key factor in investigation of the stability of the nanoemulsions with a view to their potential applications in bionanotechnology. Consequently, the precise control over the physicochemical characteristics of chitosan (degree of acetylation, DA and molecular weight, Mw) can provide a high stability and specific biological properties of the developed functional structures. The chapter is focused on the interpretation of the electrokinetic response from nanoemulsion stabilized by adsorption of chitosan (as a polyelectrolyte or uncharged polymer) by using appropriate theoretical approaches.

Polymorphism in two biologically active dihydropyrimidinium hydrochloride derivatives: quantitative inputs towards the energetics associated with crystal packing

2014 ◽  
Vol 70 (4) ◽  
pp. 681-696 ◽  
Author(s):  
Piyush Panini ◽  
K. N. Venugopala ◽  
Bharti Odhav ◽  
Deepak Chopra
Keyword(s):  
Hydrogen Bonds ◽  
Intermolecular Interactions ◽  
Density Functional ◽  
Crystal Packing ◽  
Lattice Energy ◽  
Biologically Active ◽  
Two Dimensional ◽  
Energy Calculations ◽  
X Ray ◽  
Fingerprint Plots

A new polymorph belonging to the tetrahydropyrimidinium class of compounds, namely 6-(4-chlorophenyl)-5-(methoxycarbonyl)-4-methyl-2-(3-(trifluoromethylthio)phenylamino)-3,6-dihydropyrimidin-1-ium chloride, and a hydrate of 2-(3-bromophenylamino)-6-(4-chlorophenyl)-5-(methoxycarbonyl)-4-methyl-3,6-dihydropyrimidin-1-ium chloride, have been isolated and characterized using single-crystal X-ray diffraction (XRD). A detailed comprehensive analysis of the crystal packing in terms of the associated intermolecular interactions and a quantification of their interaction energies have been performed for both forms of the two different organic salts (AandB) using X-ray crystallography and computational methods such as density functional theory (DFT) quantum mechanical calculations, PIXEL lattice-energy calculations (with decomposition of total lattice energy into the Coulombic, polarization, dispersion and repulsion contribution), the calculation of the Madelung constant (the EUGEN method), Hirshfeld and two-dimensional fingerprint plots. The presence of ionic [N—H]+...Cl−and [C—H]+...Cl−hydrogen bonds mainly stabilizes the crystal packing in both formsAandB, while in the case ofB·H2O [N—H]+...Owaterand Owater—H...Cl−hydrogen bonds along with [N—H]+...Cl−and [C—H]+...Cl−provide stability to the crystal packing. The lattice-energy calculations from both PIXEL and EUGEN methods revealed that in the case ofA, form (I) (monoclinic) is more stable whereas forBit is the anhydrous form that is more stable. The analysis of the `Madelung mode' of crystal packing of two forms ofAandBand its hydrates suggest that differences exist in the position of the charged ions/atoms in the organic solid state. TheR/E(distance–energy) plots for all the crystal structures show that the molecular pairs in their crystal packing are connected with either highly stabilizing (due to the presence of organicR+and Cl−) or highly destabilizing Coulombic contacts. The difference in crystal packing and associated intermolecular interactions between polymorphs (in the case ofA) or the hydrates (in the case ofB) have been clearly elucidated by the analysis of Hirshfeld surfaces and two-dimensional fingerprint plots. The relative contributions of the various interactions to the Hirshfeld surface for the cationic (dihydropyrimidinium) part and anionic (chloride ion) part for the two forms ofAandBand its hydrate were observed to be different.

A DFT-D study on the stability and intramolecular interactions of the salts of 1,2,3- and 1,2,4-triazoles

2014 ◽  
Vol 92 (11) ◽  
pp. 1111-1117
Author(s):  
Xueli Zhang ◽  
Xuedong Gong
Keyword(s):  
Hydrogen Bonds ◽  
Density Functional ◽  
Energy Gap ◽  
Lattice Energy ◽  
Intramolecular Interactions ◽  
Dispersion Energy ◽  
Functional Theory ◽  
Formation Reaction ◽  
The Stability ◽  
Intramolecular Hydrogen

Nitrogen-rich 1,2,4-triazole (1) and 1,2,3-triazole (2) react as bases with the oxygen-rich acids HNO3 (a), HN(NO2)2 (b), and HClO4 (c) to produce energetic salts (1a, 1b, and 1c and 2a, 2b, and 2c, respectively) potentially applicable to composite explosives and propellants. In this study, these salts were studied with the dispersion-corrected density functional theory. For the isomers such as 1a and 2a, the more negative ΔrGm of the formation reaction leads to a higher thermally stable salt. The ability to form intramolecular hydrogen bonds predicted with the quantum theory of atoms in molecules has the order of 2 > 1. Different hydrogen bonds result in different second-order perturbation energies, redshifts in IR, and electron density differences. The charge transfer, binding energy, dispersion energy, lattice energy, and energy gap between frontier orbits in the salts of 1 are larger than those of 2, which is helpful for stabilizing the former, and 1 is more obviously stabilized than 2 by formation of salts. Different conformations of 1 and 2 hardly affect the frontier orbital distributions. Base 1 is a more preferred base than 2 to form salts.

A three-dimensional polycatenation framework:catena-poly[[diaquabis(4-{4-[4-(pyridin-4-yl)phenoxy]phenyl}pyridine)nickel(II)]-μ2-naphthalene-2,6-dicarboxylato]

2013 ◽  
Vol 69 (9) ◽  
pp. 1022-1025 ◽  
Author(s):  
Cui-Lian Guo ◽  
Xiao-Qiang Yao ◽  
Yong-Qiang Cheng ◽  
Yan Liu
Keyword(s):  
Three Dimensional ◽  
Water Molecules ◽  
Intermolecular Hydrogen Bonds ◽  
One Dimensional ◽  
Pyridine Ligands ◽  
Carboxylate Groups ◽  
Distorted Octahedral ◽  
Benzene Rings ◽  
The Stability ◽  
Coordinated Water

In the title compound, [Ni(C12H6O4)(C22H16N2O)2(H2O)2]n, the Ni2+cation resides on a centre of inversion in a slightly distorted octahedral [N2O4] environment. The two carboxylate groups of each naphthalene-2,6-dicarboxylate (NDC2−) ligand, which reside on centres of inversion, link the NiIIcations into a one-dimensional chain. Identical chains are linked by intermolecular hydrogen bonds between coordinated water molecules and the uncoordinated N atoms of 4-{4-[4-(pyridin-4-yl)phenoxy]phenyl}pyridine ligands to form (4,4)-topological sheets, and then the different sheets are interlocked in an inclined fashion to give a three-dimensional polycatenation network. The stability of the structure is further enhanced by π–π stacking interactions between pyridine and benzene rings.

Microsolvation of the formic acid dimer — (HCOOH)2(H2O)n clusters with n = 1, . . ., 5

2010 ◽  
Vol 88 (8) ◽  
pp. 736-743 ◽  
Author(s):  
Cara M. Nordstrom ◽  
Alaina J. McGrath ◽  
Ajit J. Thakkar
Keyword(s):  
Density Functional Theory ◽  
Perturbation Theory ◽  
Hydrogen Bonds ◽  
Formic Acid ◽  
Density Functional ◽  
Water Molecules ◽  
Spin Component ◽  
Functional Theory ◽  
Moller Plesset ◽  
Plesset Perturbation Theory

Density functional theory and spin-component-scaled Møller–Plesset perturbation theory calculations are used to examine the microsolvation of the formic acid dimer. The lowest energy structures with n water molecules consist of a n-water cluster, not necessarily of lowest energy, with two formic acid molecules attached to its surface by hydrogen bonds. The total number of hydrogen bonds does not correlate directly with relative stability.

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