Journal of Molecular Modeling

Theoretical studies of a new ion-pair receptor, meso-octamethylcalix[4]pyrrole (OMCP), and its interactions with the halide anions F−, Cl−, and Br− and the cesium halides CsF, CsCl, and CsBr have been performed. Geometries, binding energies, and binding enthalpies were evaluated with the restricted hybrid Becke three-parameter exchange functional (B3LYP) method using the 6-31+G(d) basis set and relativistic effective core potentials. The optimized geometric structures were used to perform natural bond orbital (NBO) analysis. The two typical types of hydrogen bonds, N–H…X− and C–H…X−, were investigated. The results indicate that hydrogen bonding interactions are dominant, and that the halide anions (F−, Cl−, and Br−) offer lone pair electrons to the σ*(N–H) or σ*(C–H) antibonding orbitals of OMCP. In addition, electrostatic interactions between the lone pair electrons of the halide anion and the LP* orbitals of Cs+ as well as cation–π interactions between the metal ion and π-orbitals of the pyrrole rings have important roles to play in the Cs+•OMCP•X− complexes. The current study further demonstrates that this easy-to-make OMCP host compound functions as not only an anion receptor but also an ion-pair receptor.

Electrostatic potentials and average local ionization energies on the molecular surfaces of 19 phenols, 17 benzoic acids and their respective conjugate bases were computed at the HF/STO-5G(d)//B3LYP/6-311G(d,p) level. Good correlations were found between pK as and the V S,max values of the neutral acids and the V S,min and % MathType!Translator!2!1!AMS LaTeX.tdl!TeX -- AMS-LaTeX! % MathType!MTEF!2!1!+- % feaafeart1ev1aaatCvAUfeBSn0BKvguHDwzZbqefeKCPfgBGuLBPn % 2BKvginnfarmWu51MyVXgatuuDJXwAK1uy0HwmaeHbfv3ySLgzG0uy % 0Hgip5wzaebbnrfifHhDYfgasaacH8YjY-vipgYlH8Gipec8Eeeu0x % Xdbba9frFj0-OqFfea0dXdd9vqaq-JfrVkFHe9pgea0dXdar-Jb9hs % 0dXdbPYxe9vr0-vr0-vqpWqaaeaabiGaciaacaqabeaadaqadqaaaO % qaaiqadMeagaqeamaaBaaaleaacaqGtbGaaeilaiaab2gacaqGPbGa % aeOBaaqabaaaaa!3D93! $$ \bar{I}_{{{\text{S,min}}}} $$ of the conjugate bases for both sets of molecules. V S,max is the most positive value of the electrostatic potential on the molecular surface and is an indicator of the ease with which the phenols and benzoic acids lose their acidic hydrogens. V S,min and % MathType!Translator!2!1!AMS LaTeX.tdl!TeX -- AMS-LaTeX! <![CDATA[% MathType!MTEF!2!1!+- % feaafeart1ev1aaatCvAUfeBSn0BKvguHDwzZbqefeKCPfgBGuLBPn % 2BKvginnfarmWu51MyVXgatuuDJXwAK1uy0HwmaeHbfv3ySLgzG0uy % 0Hgip5wzaebbnrfifHhDYfgasaacH8YjY-vipgYlH8Gipec8Eeeu0x % Xdbba9frFj0-OqFfea0dXdd9vqaq-JfrVkFHe9pgea0dXdar-Jb9hs % 0dXdbPYxe9vr0-vr0-vqpWqaaeaabiGaciaacaqabeaadaqadqaaaO % qaaiqadMeagaqeamaaBaaaleaacaqGtbGaaeilaiaab2gacaqGPbGa % aeOBaaqabaaaaa!3D93! $$ \bar{I}_{{{\text{S,min}}}} $$ are the minimum values of the electrostatic potential and the local ionization energy computed on the molecular surface; the V S,min and % MathType!Translator!2!1!AMS LaTeX.tdl!TeX -- AMS-LaTeX! <![CDATA[% MathType!MTEF!2!1!+- % feaafeart1ev1aaatCvAUfeBSn0BKvguHDwzZbqefeKCPfgBGuLBPn % 2BKvginnfarmWu51MyVXgatuuDJXwAK1uy0HwmaeHbfv3ySLgzG0uy % 0Hgip5wzaebbnrfifHhDYfgasaacH8YjY-vipgYlH8Gipec8Eeeu0x % Xdbba9frFj0-OqFfea0dXdd9vqaq-JfrVkFHe9pgea0dXdar-Jb9hs % 0dXdbPYxe9vr0-vr0-vqpWqaaeaabiGaciaacaqabeaadaqadqaaaO % qaaiqadMeagaqeamaaBaaaleaacaqGtbGaaeilaiaab2gacaqGPbGa % aeOBaaqabaaaaa!3D93! $$ \bar{I}_{{{\text{S,min}}}} $$ of the conjugate bases of the phenoxides and benzoates are indicative, respectively, of the tendencies of electrophiles to approach the anions (V S,min) and to react with the anions ( % MathType!Translator!2!1!AMS LaTeX.tdl!TeX -- AMS-LaTeX! <![CDATA[% MathType!MTEF!2!1!+- % feaafeart1ev1aaatCvAUfeBSn0BKvguHDwzZbqefeKCPfgBGuLBPn % 2BKvginnfarmWu51MyVXgatuuDJXwAK1uy0HwmaeHbfv3ySLgzG0uy % 0Hgip5wzaebbnrfifHhDYfgasaacH8YjY-vipgYlH8Gipec8Eeeu0x % Xdbba9frFj0-OqFfea0dXdd9vqaq-JfrVkFHe9pgea0dXdar-Jb9hs % 0dXdbPYxe9vr0-vr0-vqpWqaaeaabiGaciaacaqabeaadaqadqaaaO % qaaiqadMeagaqeamaaBaaaleaacaqGtbGaaeilaiaab2gacaqGPbGa % aeOBaaqabaaaaa!3D93! $$ \bar{I}_{{{\text{S,min}}}} $$ ) to reform the original acids. The correlations observed between the computed molecular surface quantities, taken as single parameters, and the experimental pK a values ranged from R=0.938 to R=0.970 for the two classes of compounds. Figure Correlation between pK a and the computed V S,max of the benzoic acids listed in Table 2. The linear correlation coefficient is 0.970

This work aims to find the most suitable method that is practically applicable for the calculation of 31P NMR chemical shifts of Pt(II) complexes. The influence of various all-electron and ECP basis sets, DFT functionals, and solvent effects on the optimized geometry was tested. A variety of combinations of DFT functionals BP86, B3LYP, PBE0, TPSSh, CAM-B3LYP, and ωB97XD with all-electron basis sets 6-31G, 6-31G(d), 6-31G(d,p), 6-311G(d,p), and TZVP and ECP basis sets SDD, LanL2DZ, and CEP-31G were used. Chemical shielding constants were then calculated using BP86, PBE0, and B3LYP functionals in combination with the TZ2P basis. The magnitude of spin-orbit interactions was also evaluated.

In recent years, there has been a growing interest in developing bacterial peptide deformylase (PDF) inhibitors as novel antibiotics. The purpose of the study is to generate a three-dimensional (3D) pharmacophore model by using diverse PDF inhibitors which is useful for designing of potential antibiotics. Twenty one structurally diverse compounds were considered for the generation of quantitative pharmacophore model using HypoGen of Catalyst, further model was validated using 78 compounds. Pharmacophore model demonstrated the importance of two acceptors, one donor and one hydrophobic feature toward the biological activity. The inhibitors were also docked into the binding site of PDF to comprehend the structural insights of the active site. Combination of ligand and structure based methods were used to find the potential antibiotics.

The current study belongs to a series of investigations of polycyclic aromatic compounds containing intramolecular hydrogen bonds. Close proximity of the coupled aromatic system and hydrogen bridges gives rise to resonance-assisted hydrogen bonding phenomena. Substituted naphthols are ideally suited for this kind of investigation. The parent compound, 1-hydroxy-8-methoxy-3-methylnaphthalene, and its derivative, 1-bromo-5-hydroxy-4-isopropoxy-7-methylnaphthalene, both with known crystal structure, are investigated. Car-Parrinello molecular dynamics (CPMD) is chosen as a theoretical background for this study. Gas phase and solid state simulations are carried out. The effect of Grimme’s dispersion corrections is also included. The report presents time evolution of structural parameters, spectroscopic signatures based on the CPMD simulations, and comparison with available experimental data. We show that the proton transfer phenomena do not occur within the simulations, which is consistent with evaluation based on the acidity of the donor and acceptor sites. The effects of the substitution in the aromatic system and change of the environment (gas vs. condensed phase) are of similar magnitude.

The conformational preferences of three azadipeptides Ac-Pro-azaXaa-NHMe [Xaa = Asn (1), Asp (2), Ala (3)] have been carried out in gas phase and solution (water) using the density functional method B3LYP/6–311 +  + G(d,p) to explore the effect of the change of side chain of azaamino acids at the i + 2 position on the stability of these components. The most stable conformations of compounds (1), (2), and (3) have an amid bond oriented trans, trans, and cis, respectively, in gas phase, whereas the orientation of amid bond in water solvent of compounds (2) and (3) has changed to cis and trans, respectively. We have also noticed the importance of backbone-side chain hydrogen bonds in the stabilization of the β turn motif in gas phase since this motif is more stable in the case of compounds (1) and (2) and less stable in the case of compound (3) in which these hydrogen bonds are absent. Furthermore, the βII(βII′) turn structure is more stable than βI turn for all conformations of the three compounds in gas phase, while it is not true in the case of some conformations in solution. Moreover, the stability of β turn increases from azaAsn to azaAsp which could be due to the side chain’s basic nature of azaAsn. In general, hydrogen bonds were found to play a key role in the stabilization of these compounds since most of conformers are lower in energy when they have more than two hydrogen bond interactions while conformations with one or no hydrogen bonds are higher in energy and thus less stable.