Calculating The Acidity of Silica Supported Alkyl Sulfonic Acids Considering the Matrix Effect: A Dft Study

Abstract

Density functional theory (DFT) was used to investigate the acidity of the various silica alkyl sulfonic acids. In this regard, cluster models with various alkyl spacer lengths were selected to mimic the surface of silica gel. The effects of distance from the surface and the role of hydrogen bond (H–bond) on the ΔH_acidity values of these catalysts were investigated. DFT calculations revealed that a notable gap of ΔH_acidity values exists between the structures considering lateral hydrogen bonding with the surface of the silica HB structure and the structures with omitted surface interactions (non-HB structures). Natural bonding orbital (NBO) and quantum theory of atoms in molecules (QTAIM) analyses were carried out to obtain detailed information about the nature of the H–bonds.     

An improved theoretical approach to the empirical corrections of density functional theory

An empirical correction to density functional theory (DFT) has been developed in this study. The approach, called correlation corrected atomization–dispersion (CCAZD), involves short- and long-range terms. Short-range correction consists of bond (1,2-) and angle (1,3-) interactions, which remedies the deficiency of DFT in describing the proto-branching stabilization effects. Long-range correction includes a Buckingham potential function aiming to account for the dispersion interactions. The empirical corrections of DFT were parameterized to reproduce reported ΔH _f values of the training set containing alkane, alcohol and ether molecules. The ΔH _f of the training set molecules predicted by the CCAZD method combined with two different DFT methods, B3LYP and MPWB1K, with a 6-31G* basis set agreed well with the experimental data. For 106 alkane, alcohol and ether compounds, the average absolute deviations (AADs) in ΔH _f were 0.45 and 0.51 kcal/mol for B3LYP- and MPWB1K-CCAZD, respectively. Calculations of isomerization energies, rotational barriers and conformational energies further validated the CCAZD approach. The isomerization energies improved significantly with the CCAZD treatment. The AADs for 22 energies of isomerization reactions were decreased from 3.55 and 2.44 to 0.55 and 0.82 kcal/mol for B3LYP and MPWB1K, respectively. This study also provided predictions of MM4, G3, CBS-QB3 and B2PLYP-D for comparison. The final test of the CCAZD approach on the calculation of the cellobiose analog potential surface also showed promising results. This study demonstrated that DFT calculations with CCAZD empirical corrections achieved very good agreement with reported values for various chemical reactions with a small basis set as 6-31G*.     

2-(4-取代-苯基)-3-异噻唑啉酮抗菌活性的定量构效关系研究

用密度泛函理论和逐步回归分析方法对22种新合成的2-(4-取代-苯基)-3-异噻唑啉酮化合物进行了结构与抗菌活性研究. 通过对平衡几何构型、前线轨道组成和Mulliken电荷分布的分析得出: S(1), N(2)原子是该类化合物的主要活性部位, 且5位氯取代的化合物抗菌活性较好. 通过回归分析, 筛选了影响抗菌活性的主要因素, 建立了定量构效关系方程. 结果表明, 硫原子的亲核前线电子密度、3D-Balaban指数、S(1)-N(2) Wiberg键级和Schultz分子价拓扑指数是影响异噻唑啉酮类化合物抗大肠杆菌活性的主要因素, 所得模型对化合物抗菌活性有较好的预报能力.     

Experimental and Theoretical Charge Density Study on Di‐2‐pyrazylamine (Hdpza) Molecule in Crystal

Electron density distribution of Di‐2‐pyrazylamine ( Hdpza ) is studied both by single‐crystal X‐ray diffraction method at 100K and theoretical calculation. Structural determination reveals that Hdpza molecules crystalize in a syn‐anti conformation with an intramolecular C? H?N hydrogen bond between two pyrazine rings and then gather together via two intermolecular N? H?N and C? H?N hydrogen interaction and π? π stacking interaction between pyrazine rings. Charge density analysis is made in terms of deformation density (Δπ), Laplacian distribution and topological analysis of total electron density based on multipole model and theoretical calculation. The agreement between experiment and theory is good. The topological properties at bond critical points of C? C and C? N bonds reveal a covalent bond character, and those of intermolecular interactions, such as hydrogen bonds and π? π stacking interactions, reveal a closed‐shell interaction. The potential energy curve of Hdpza molecule shows that the syn‐anti conformation is the most stable one (global minima) than the other two of syn‐syn and anti‐anti conformations.     

N,N′‐Dicyclohexyl‐N‐[4‐(1H‐indol‐3‐yl)butanoyl]urea

The title compound, C₂₅H₃₅N₃O₂, is a novel urea derivative. Pairs of intermolecular N—H...O hydrogen bonds join the molecules into centrosymmetric R₂²(12) and R₂²(18) dimeric rings, which are alternately linked into one‐dimensional polymeric chains along the [010] direction. The parallel chains are connected via C—H...O hydrogen bonds to generate a two‐dimensional framework structure parallel to the (001) plane. The title compound was also modelled by solid‐state density functional theory (DFT) calculations. A comparison of the molecular conformation and hydrogen‐bond geometry obtained from the X‐ray structure analysis and the theoretical study clearly indicates that the DFT calculation agrees closely with the X‐ray structure.     

N—O键解离焓的密度泛函理论研究

在高精度计算方法G3和G3B3的基础上,比较了密度泛函理论(DFT)十几种方法对N—O键解离焓(BDE)相对于实验值的计算精度,发现用B3P86方法计算15种化合物N—O键的BDE,均方根误差最小,仅为6.36kJ·mol-1,计算值与实验值的线性相关系数为0.991.在此基础上,用该方法分别计算了非芳香化合物及芳香化合物的N—O键BDE.通过自然键轨道分析,发现部分N—O键的BDE与N—O键的键长、原子电荷密度及键级之间存在定量关系.此外,在B3P86方法的基础上预测了几种典型的杂环芳香化合物N—O键BDE值.     

Nonconventional C–H···Cu Interaction Between Copper Cun Clusters (n = 3–20) and Aromatic Compounds

The present study examines bonding patterns between copper Cu_n clusters (n?=?3–20) and aromatic compounds (benzene, phenol, and benzaldehyde) using a density-functional theory (DFT) approach. Hirshfeld population, natural bond orbital (NBO), molecular orbitals, and quantum theory of atoms in molecules (QTAIM) analyses suggested the formation of two types of interactions Cu–arene and C–H···Cu, in the complexation of copper clusters by an aromatic compound.

     

一种双功能异噁唑酰腙的晶体结构、电子光谱、抑菌活性及其量化计算

以水杨醛和5-甲基-4-异噁唑甲酰肼为原料,于中温混合溶剂热体系中合成出标题化合物水杨醛-5-甲基-4-异噁唑甲酰腙[C12H11O3N3,3],用单晶X-射线衍射(XRD)、紫外及荧光和热重分析等实验方法对其进行了表征。结果表明,晶体属正交晶系,Pna21空间群。晶胞参数:a=1.28783(6)nm,b=1.13108(6)nm,c=0.86535(4)nm,V=1.2605nm3,Z=4。标题物3的水溶液在486nm处呈现一强蓝色荧光发射峰,可归属于激发态分子内质子转移电荷发光;同时,标题物3对枯草芽孢杆菌、铜绿脓杆菌、大肠杆菌和金黄色葡萄球菌等都有明显的抑菌活性;分子的静电势图(EPM)再现其具有较强的广谱抗菌活性。     

Density functional and multiconfigurational ab initio study of the ground and excited states of Os2

Multiconfigurational ab initio methods predict that the ⁵Π_u state as the ground state instead of the ⁷Δ_u state. Although multiconfigurational perturbation theory correctly predicts the ground state, they overestimate the bond dissociation energy (BDE). Only multireference configuration interaction method can reasonably calculate the BDE. The spin‐orbit effect on the spectroscopic constants is not significant. The results calculated by density functional theory (DFT) vary significantly depending on the selection of a DFT functional. No DFT functional gives the same energy ordering as calculated by the second‐order multiconfigurational perturbation theory (CASPT2). The old generalized gradient approximations functionals are well suited for predicting the ground state and calculating the bond length and the vibrational frequency of Os₂. According to the CASPT2 calculation, the ground state of Os₂ has a quadruple bond. © 2014 Wiley Periodicals, Inc.     

New Method for the Temperature‐ Programmed Desorption (TPD) of Ammonia Experiment for Characterization of Zeolite Acidity: A Review

In this review, a method for the temperature‐programmed desorption (TPD) of ammonia experiment for the characterization of zeolite acidity and its improvement by simultaneous IR measurement and DFT calculation are described. First, various methods of ammonia TPD are explained, since the measurements have been conducted under the concepts of kinetics, equilibrium, or diffusion control. It is however emphasized that the ubiquitous TPD experiment is governed by the equilibrium between ammonia molecules in the gas phase and on the surface. Therefore, a method to measure quantitatively the strength of the acid site (?H upon ammonia desorption) under equilibrium‐controlled conditions is elucidated. Then, a quantitative relationship between ?H and H₀ function is proposed, based on which the acid strength ?H can be converted into the H₀ function. The identification of the desorption peaks and the quantitative measurement of the number of acid sites are then explained. In order to overcome a serious disadvantage of the method (i.e., no information is provided about the structure of acid sites), the simultaneous measurement of IR spectroscopy with ammonia TPD, named IRMS‐TPD (infrared spectroscopy/mass spectrometry–temperature‐programmed desorption), is proposed. Based on this improved measurement, Brønsted and Lewis acid sites were differentiated and the distribution of Brønsted OH was revealed. The acidity characterized by IRMS‐TPD was further supported by the theoretical DFT calculation. Thus, the advanced study of zeolite acidity at the molecular level was made possible. Advantages and disadvantages of the ammonia TPD experiment are discussed, and understanding of the catalytic cracking activity based on the derived acidic profile is explained.     

Interaction of a C-F bond with the π-system of a C═C bond or "head on" with a proximate C-H bond

We describe the synthesis and preliminary study of two molecules, in which a fluorine atom is positioned proximately above the π-orbitals of a C═C bond or else wherein a C-F bond interacts in a "head on" fashion with a proximate C-H bond. The spectroscopic characteristics of these unusual interactions are documented, X-ray crystallographic analyses are reported, and theoretical calculations are employed to support the observed spectroscopy.     

Synthesis,characterization, crystal structure determination and computational study of the high-spin iron(II) 2-cyanopyrazine complex trans-[Fe(pzCN)4Cl2]

A new mononuclear high-spin complex, trans-[Fe(pzCN)₄Cl₂] (1), was prepared from the reaction of FeCl₂.4H₂O and 2-cyanopyrazine (pzCN) in acetonitrile as a solvent. Suitable crystals of this complex for crystal structure determination were collected by slow evaporation of the produced pale orange solution. Complex 1 was characterized by elemental analysis (CHN), spectral methods (IR and UV–Vis), and single-crystal X-ray diffraction. The X-ray structural analysis indicated that the iron(II) is six-coordinated in an octahedral configuration by four N atoms from four 2-cyanopyrazine ligands and two chloride anions. Furthermore, the average of Fe–N bond lengths is 2.284(1)Å. It is well known that in the high-spin iron(II) phenanthroline and bipyridine complexes, the Fe–N bond lengths are around 2.2 Å. So, due to the Fe–N bond length in this complex, the iron(II) is unambiguously high-spin. The experimental evaluations on 1 have been complemented theoretically by the density functional theory (DFT) and TD-DFT calculations. The character of the Fe–N and Fe–Cl bonds was investigated using quantum theory of atoms in molecules. Additionally, electron delocalization and hyper-conjugative interactions of the synthesized complex were evaluated by natural bond orbital calculations.

     

Synthesis,characterization, antimicrobial activity, 3D-QSAR,DFT, and molecular docking of some ciprofloxacin derivatives and their copper(II) complexes

Six new derivatives of ciprofloxacin compounds and their copper(II) complexes were synthesized, characterized by spectroscopic methods (ultraviolet–visible [UV–vis], Fourier transform infrared [FTIR], nuclear magnetic resonance [NMR], mass spectrometry [MS], and electron paramagnetic resonance [EPR]), and tested for antibacterial activities against gram-negative and gram-positive bacteria. The data showed that ciprofloxacin derivatives act as bidentate ligands and the metal ions coordinate through the pyridone carbonyl and the carboxylate oxygen atoms. Tetragonally distorted octahedral ligand fields were assumed for all complexes based on their spectral studies. Copper(II) complexes of the synthesized ciprofloxacin derivatives revealed higher antibacterial activities against gram-positive and gram-negative bacterial species than the parent ciprofloxacin antibiotic. Furthermore, three-dimensional quantitative structure–activity relationship (3D-QSAR) models were evaluated by studying 30 antibiotic compounds of the quinolone class. Density function theory (DFT) calculations were applied to evaluate the optimized geometrical structures using the B3LYP method and 6-311G(d,p) basis set. The 3D-QSAR study revealed that there are eight optimum parameters that give the best predictive modulation with good reliability (R² = 0.996, F = 12.004, sigma = 0.426). In silico molecular docking was also performed on the derivatives, and the results revealed the presence of two types of interactions between the Escherichia coli and the derivatives, H-bonding and Van der Waals interactions, and an effective inhibition at the docked site.     

Pharmacophore generation,atom-based 3D-QSAR and molecular dynamics simulation analyses of pyridine-3-carboxamide-6-yl-urea analogues as potential gyrase B inhibitors

DNA gyrase subunit B (GyrB) is an attractive drug target for the development of antibacterial agents with therapeutic potential. In the present study, computational studies based on pharmacophore modelling, atom-based QSAR, molecular docking, free binding energy calculation and dynamics simulation were performed on a series of pyridine-3-carboxamide-6-yl-urea derivatives. A pharmacophore model using 49 molecules revealed structural and chemical features necessary for these molecules to inhibit GyrB. The best fitted model AADDR.13 was generated with a coefficient of determination (r²) of 0.918. This model was validated using test set molecules and had a good r² of 0.78. 3D contour maps generated by the 3D atom-based QSAR revealed the key structural features responsible for the GyrB inhibitory activity. Extra precision molecular docking showed hydrogen bond interactions with key amino acid residues of ATP-binding pocket, important for inhibitor binding. Further, binding free energy was calculated by the MM-GBSA rescoring approach to validate the binding affinity. A 10 ns MD simulation of inhibitor #47 showed the stability of the predicted binding conformations. We identified 10 virtual hits by in silico high-throughput screening. A few new molecules were also designed as potent GyrB inhibitors. The information obtained from these methodologies may be helpful to design novel inhibitors of GyrB.     

Biomimetic complexes of Mn(II), Fe(III), Co(II), and Ni(II) with 1,10-phenanthroline and a salen type ligand: tailored synthesis,characterization, DFT,enzyme kinetics,and antibacterial screening

Abstract

A symmetrical tetradentate Schiff base, o-HACPHENEN, was prepared by condensation of 1,2-bis(ethylenediamine) with o-hydroxyacetophenone in 1:2 molar ratio. The Schiff base ligand and 1,10-phenanthroline were used for the tailored synthesis of four mixed-ligand complexes, [Mn(o-HACPHENEN)(1,10-phen)] (1), [Fe(o-HACPHENEN)(1,10-phen)]Cl (2), [Co(o-HACPHENEN)(1,10-phen)] (3), and [Ni(o-HACPHENEN)(1,10-phen)] (4). The ligand and complexes were characterized on the basis of elemental analyses, ESI-MS, molar conductance, electronic, FT-IR, ¹H-NMR, and ¹³C-NMR spectra. DFT study was used to optimize the geometry of the investigated compounds. Using Gaussian09 molecular modeling, HOMO-LUMO study, bond lengths, bond angles, molecular electrostatic potential map (MEP), and Mulliken charge were also evaluated. Complexes displayed remarkable catalase-like activity in the disproportion reactions of hydrogen peroxide. The kinetics of the activity were investigated and data are fitted in Lineweaver Burk plot, revealing Michaelis Menten behavior. The catalase activity of ligand and complexes were found in the order 1 > 2 > 4 > 3 > o-HACPHENEN. Compounds were screened for their antibacterial activity against gram-negative bacteria Escherichia coli in comparison to standard drugs. Complexes were more potent than Schiff base. The MIC of complexes was also studied.     

A Combined Experimental and Theoretical Electron Density Study of Intra‐ and Intermolecular Interactions in Thiourea S,S‐Dioxide

The thiourea S,S‐dioxide molecule is recognized as a zwitterion with a high dipole moment and an unusually long C? S bond. The molecule has a most interesting set of intermolecular interactions in the crystalline state—a relatively strong O???H? N hydrogen bond and very weak intermolecular C???S and N???O interactions. The molecule has C_s symmetry, and each oxygen atom is hydrogen‐bonded to two hydrogen atoms with O???H? N distances of 2.837 and 2.826 Å and angles of 176.61 and 158.38°. The electron density distribution is obtained both from Xray diffraction data at 110 K and from a periodic density functional theory (DFT) calculation. Bond characterization is made in terms of the analysis of topological properties. The covalent characters of the C? N, N? H, C? S, and S? O bonds are apparent, and the agreement on the topological properties between experiment and theory is adequate. The features of the Laplacian distributions, bond paths, and atomic domains are comparable. In a systematic approach, DFT calculations are performed based on a monomer, a dimer, a heptamer, and a crystal to see the effect on the electron density distribution due to the intermolecular interactions. The dipole moment of the molecule is enhanced in the solid state. The typical values of ρ_b and H_b of the hydrogen bonds and weak intermolecular C???S and N???O interactions are given. All the interactions are verified by the location of the bond critical point and its associated topological properties. The isovalue surface of Laplacian charge density and the detailed atomic graph around each atomic site reveal the shape of the valence‐shell charge concentration and provide a reasonable interpretation of the bonding of each atom.     

The geometry of intermolecular interactions in some crystalline fluorine-containing organic compounds

The propensity of C-F groups to form C-F H-C interactions with C-H groups on other molecules has been analyzed. Crystal structures of molecules containing only carbon, hydrogen, and fluorine, but no oxygen, nitrogen, or other hydrogen-bond-forming elements, were chosen for an initial study in which the intermolecular interactions in crystal-structure determinations of polycyclic aromatic hydrocarbons and their analogous fluoro derivatives were analyzed. It is found that C-F H-C interactions occur, but they are weak, as judged by the intermolecular distances and the angles involved. In a study of crystal structures of molecules containing other elements in addition to carbon, hydrogen, and fluorine, it was found that when an oxygen atom is in a neighboring position on an interacting molecule, a C-O group is more likely than a C-F group to form a linear interaction to the hydrogen atom of a C-H group. Thus, in spite of the high electronegativity of the fluorine atom, a C-F group competes unfavorably with a C-O^–, C-OH, or C=O group to form a hydrogen bond to an O-H, N-H, or C-H group. It is found, however, particularly for polycyclic aromatic hydrocarbons with substituted CF₃ groups that, in the absence of other functional groups that can form stronger interactions, C-F H-C interactions may serve to align molecules and give a different crystal packing from that in the pure hydrocarbon (where fluorine is replaced by hydrogen). Thus, C-F H-X (X = C, N, O) interactions are very weak, much weaker than C=O H-X interactions, but they cannot be ignored in predictions of modes of molecular packing in complexes and in crystals.     

Conformations and intermolecular interactions pattern in solid chloroxylenol and triclosan (API of anti‐infective agents and drugs). A 35Cl NQR, 1H‐14 N NQDR,X‐ray and DFT/QTAIM study

Two antibacterial and antifungal agents, chloroxylenol (4‐chloro‐3,5‐dimethyl‐phenol) and triclosan (5‐chloro‐2‐(2’,4’‐dichlorophenoxy)‐phenol), were studied experimentally in solid state with an X‐ray, ³⁵Cl‐nuclear quadrupole resonance (NQR) and ¹⁷O‐nuclear quadrupole double resonance (NQDR) spectroscopies and, theoretically, with the density functional theory/quantum theory of atoms in molecules (DFT/QTAIM). The crystallographic structure of triclosan, which crystallises in space group P3₁ with one molecule in the asymmetric unit [a = 12.64100(10), b = 12.64100(10), c = 6.71630(10) Å], was solved with an X‐ray and refined to a final R‐factor of 2.81% at room temperature. The NQR frequencies of ³⁵Cl and ¹⁷O were detected with the help of the density functional theory (DFT) assigned to particular chlorine and oxygen sites in the molecules of both compounds. The NQR frequencies at ³⁵Cl sites in chloroxylenol and triclosan were found to be more differentiated than frequencies at the ¹⁷O site. The former better describes the substituent withdrawing effects connected to π‐electron delocalization within the benzene rings and the influence of temperature; whereas, those at the ¹⁷O site provide more information on O‐H bond and intermolecular interactions pattern. The conformation adopted by diphenyl ether of triclosan in solid state was found to be typical of diphenyl ethers, but the opposite to those adopted when it was bound to different inhibitors. According to an X‐ray study, temperature had no effect on the conformation of the diphenyl ring of triclosan, which was the same at 90 K and at room temperature (RT). The scattering of NQR frequencies reproduced by the DFT under assumption of the X‐ray data at 90 K and RT is found to be a good indicator of the quality of resolution of the crystallographic structure. Copyright © 2012 John Wiley & Sons, Ltd.     

Bio-conjugated N-(2-hydroxy-1-naphthaldehyde)-glucosamine Cu(II) complex: Bacterial sensitivity and superoxide dismutase-like activity

Abstract

Bacterial sensitivity and super-oxide dismutase (SOD) activity of sugar Schiff base complexes represent great fascinating areas of research. Under such curiosity, herein a new glucosamine Schiff base Cu(II) complex of N-(2-hydroxy-1-naphthaldehyde)-glucosamine is reported. The compound has been characterized on the basis of various physicochemical techniques in association with density functional theory (DFT) approach. Becke-3-Lee-Yang-Parr (B3LYP)/Los Alamos National Laboratory 2 Double Z (LanL2DZ) specified of Cu atom and 6311G/B3LYP for all other atoms were applied for the theoretical analysis. From the study, experimental observations and theoretical outcomes have been found in close agreement with one another. A suitable square planar geometry has been suggested for the complex. Moreover, the Schiff base ligand and its metal complex were screened for the broad spectrum antibacterial sensitivity and SOD activity. Streptococcus pyogenes, Bacillus subtilis, Escherichia coli, Klebsiella pneumoniae and Salmonella typhus were the bacterial strains selected for the antimicrobial tests. From the measurement of inhibition zones, it is clear that the model compound is not so much bactericidal against the selected microbes. However, due to well-pronounced results obtained under SOD assay, the complex could be suggested for in vivo practice for detoxification of superoxide species.