Theoretical investigation of the proton affinities of benzazoles in the gas phase and in solution

The ground‐state equilibrium geometries of benzothiazole, benzoxazole, and benzimidazole were optimized at the density functional theory (DFT)/6‐31G** level of theory. Proton affinities on each of the possible sites in the studied series of compounds have been calculated at the DFT/6‐31G**/6‐311++G** level. The results indicate clearly that N‐site protonation is strongly favored over X‐site protonation (X = NH, O, S) for the series studied. Correlation of the computed proton affinities to the energy (E_HOMO) of the highest occupied MO in the gas phase and in solution has been explored and discussed. A comprehensive investigation of the effect of solvent on the process of protonation of the studied compounds has been performed. Different dielectric continuum models (i.e., Onsager, PCM, and IPCM) have been tested; their performance and range of applicability are reported and discussed. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

DFT conformational studies of alpha-maltotriose

Recent DFT optimization studies on alpha-maltose improved our understanding of the preferred conformations of alpha-maltose. The present study extends these studies to alpha-maltotriose with three alpha-D-glucopyranose residues linked by two alpha-[1-->4] bridges, denoted herein as DP-3's. Combinations of gg, gt, and tg hydroxymethyl groups are included for both "c" and "r" hydroxyl rotamers. When the hydroxymethyl groups are for example, gg-gg-gg, and the hydroxyl groups are rotated from all clockwise, "c", to all counterclockwise, "r", the minimum energy positions of the bridging dihedral angles (phi(H) and psi(H)) move from the region of conformational space of (-, -), relative to (0 degrees , 0 degrees), to a new position defined by (+, +). Further, it was found previously that the relative energies of alpha-maltose gg-gg-c and "r" conformations were very close to one another; however, the DP-3's relative energies between hydroxyl "c" or "r" rotamers differ by more than one kcal/mol, in favor of the "c" form, even though the lowest energy DP-3 conformations have glycosidic dihedral angles similar to those found in the alpha-maltose study. Preliminary solvation studies using COSMO, a dielectric solvation method, point to important solvent contributions that reverse the energy profiles, showing an energy preference for the "r" forms. Only structures in which the rings are in the chair conformation are presented here.     

A DFT and AIM analysis of the spin–spin couplings across the hydrogen bond in the 2‐fluorobenzamide and related compounds

In 1975 a large number of coupling constants were measured in 2‐fluorobenzamide labeled with ¹⁵N. Some of them were assigned to couplings through intramolecular N? H···F hydrogen bonds (HBs). These couplings change dramatically when CDCl₃ is replaced by DMSO‐d₆. In this theoretical paper we provide density functional theory (DFT) calculations that justify the existence of a weak HB in the absence of solvent, while solvents that act as HB acceptors break down the intramolecular hydrogen bond (IMHB) of 2‐fluorobenzamide. Atoms in molecules (AIM) analyses and Steiner‐Limbach plots were used to analyze the structure of the compounds. Copyright © 2009 John Wiley & Sons, Ltd.     

Mechanistic insight on (E)‐methyl 3‐(2‐aminophenyl)acrylate cyclization reaction by multicatalysis of solvent and substrate

The reaction mechanism of (E)‐methyl 3‐(2‐aminophenyl)acrylate ( A ) with phenylisothiocyanate ( B ) as well as the vital roles of substrate A and solvent water were investigated under unassisted, water‐assisted, substrate A ‐assisted, and water‐ A ‐assisted conditions. The reaction proceeds with four processes via nucleophilic addition, deprotonation and protonation, intramolecular cyclization with hydrogen transfer, and keto–enol tautomerization. According to the different H‐shift mode, two possible types of H‐shift P1 and P2 are carefully investigated to identify the most preferred pathway, differing in the ? NH₂ group deprotonation and ? CH group of A protonation processes. It is found that substrate A and water not only act as reactant and solvent, but also as catalyst, proton shuttle, and stabilizer in effectively lowering the energy barrier. Therefore, the results demonstrate that the strong donating and accepting ability of ? NH₂ group on A and the presence of bulk water are the keys to the title reaction proceed. © 2016 Wiley Periodicals, Inc.     

DFT calculations of amine‐imine tautomerism in some pyrimidine derivatives and their 1:1 and 1:2 complexes with water

Amine‐Imine tautomerization in 2‐amino‐pyrimidine (I), 2‐amino‐4,6‐dichloropyrimidine (II), 2‐amino‐4,6‐dimethylpyrimidine (III), and 2‐amino‐4,6‐dimethoxypyrimidine (IV) and their 1:1 and 1:2 H‐bonded complexes with water have been studied using the B3LYP/6‐31++G** method. Optimum molecular geometries, electronic properties, and energetics of these systems have been discussed. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

DFT study on the role of methanol solvent in Morita–Baylis–Hillman reaction

B3LYP/6‐311++G** calculations have been carried out to study the role of methanol solvent in the trimethylamine‐catalyzed Morita‐Baylis‐Hillman reaction between acraldehyde and formaldehyde with CPCM solvent method and supramolecular model with one explicit CH₃OH solvent molecule, respectively. The optimized geometries and energies of the reactant complexes, intermediates, transition states, and products of the two reaction channels (corresponding to the scenarios of syn‐ and anti‐acraldehyde, respectively) were obtained, and the relative energy profiles were completed. The results reveal that CH₃OH solvent molecules can stabilize the zwitterionic intermediates and largely reduce the barrier of H transfer process by taking part in the formation of the transition state in this process. C? C bond formation step is the rate‐determining step of the whole reaction cycle. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Protonation of 5‐methylhydantoin and its thio derivatives in the gas phase: A theoretical study

The gas phase proton affinities of 5‐methylhydantoin and its thio derivatives were theoretically studied through the use of high‐level density functional theory calculations. The structure of all possible tautomers and their conformers were optimized at the B3LYP/6‐311+(d,p) level of theory. Final energies were obtained at the B3LYP/6‐311+(2df,2p) level. The imidazolidone derivatives 5‐methyl‐2,4‐dioxo imidazolidine, 5‐methyl‐2‐oxo‐4‐thio imidazolidine, 5‐methyl‐2‐thio‐4‐oxo imidazolidine, and 5‐methyl‐2,4‐dithio imidazolidine possess moderately strong proton affinities. Protonation at sulfur would be larger than protonation at oxygen. The most stable protonated forms of 2O4O and 2S4O have the proton attached to the heteroatom in position 2, whereas protonation of 2O4S and 2S4S preferentially takes place at position 4. The barriers for proton migration between the different tautomers are rather large. The energy decomposition analysis analysis of the O? H⁺ and S? H⁺ interactions suggests that the bonding interactions come mainly from the covalent bond formation. The contribution of the Coulomb attraction is rather small. © 2012 Wiley Periodicals, Inc.     

Photo‐physical Properties of N‐methyl‐3,4‐fulleropyrrolidine and Its Derivatives: A DFT and TD‐DFT Investigation

A series of N‐methyl‐3,4‐fulleropyrrolidine (NMFP) derivatives were designed by selecting different π‐conjugated linkers and electron‐donating groups as D‐π‐A and D‐A systems. The optimised structures and photo‐physical properties of NMFP and its derivatives have been determined using density functional theory (DFT) and time‐dependent density functional theory (TD‐DFT) methods with the B3LYP functional and the 6‐31G basis set. According to the computation analysis, both the π‐conjugated linkers and the electron‐donating groups can influence the electronic and photo‐physical properties of the NMFP derivatives. Our calculated results demonstrated that the electron‐donating groups, with significant electron‐donating ability, had the tendency to increase the highest occupied molecular orbital (HOMO) energy. The π‐conjugated linkers with lower resonance energy decreased the lowest occupied molecular orbital (LUMO) energy and caused a significant decrease in the energy gap (E_g) between the E_HOMO and E_LUMO. A Natural Bond Orbital (NBO) analysis examines the effect of the electron‐donating group, π conjugated linker, and electron‐withdrawing group for these NMFP derivatives. For the NMFP derivatives, a projected density of state (PDOS) analysis demonstrated that the electron density of HOMO and LUMO are concentrated on the electron‐donating group and the π‐conjugated linker, respectively. A TD‐DFT/B3LYP calculation was performed to calculate the electronic absorption spectra of these NMFP derivatives. Both the electron‐donating group and the π‐conjugated linker contribute to the major absorption peaks, which are assigned as HOMO to LUMO transitions and are red‐shifted relative to those of non‐substituted NMFP.     

The structure of glibenclamide in the solid state

The structure of glibenclamide, 5‐chloro‐N‐(2‐{4‐[(cyclohexylamino)carbonyl] aminosulfonyl}phenyl) ethyl)‐2‐methoxybenzamide, an important antidiabetic drug, has been studied both in solution and in the solid state by a combination of NMR spectroscopy and theoretical calculations. The possibility that glibenclamide suffers a tautomerization under melting to afford a desmotrope was rejected. Copyright © 2012 John Wiley & Sons, Ltd.     

Experimental and theoretical electronic absorption spectra of 2,4‐diphenyl‐1,5‐benzothiazepine and its derivatives: Solvatochromic effect and time dependent density functional theory approach

Electronic spectra of 2,4‐diphenyl‐1,5‐benzothiazepine and some of its derivatives in 1,2‐dichloromethane and ethanol are investigated experimentally and theoretically using the time dependent density functional theory (TD‐DFT) method at the B3LYP/6‐311G** level of the theory. The origin of the spectrum of the parent compound is found to be an additive one. The observed ultra violet (UV) spectra in both solvents show two bands S1 in the range between 312–334 nm and S2 in the range between 248–272 nm. The solvent effect is investigated experimentally and theoretically and a blue shift is observed, which is explained in terms of a hydrogen bond model between the solvent and the most negative site of the solute (N atom). This theoretical model is robust in reproducing the experimental blue shift and calculating the hydrogen bond energy and hydrogen bond length. The extent of delocalization and charge transfer processes of the studied compounds is estimated and discussed in terms of natural bond orbital (NBO) analysis and second order perturbation interactions (E²) between donors and acceptors. The effect of substituents of the studied compounds in both solvents shows a noticeable red shift attributed to hyperconjugation effects of the π electron systems of the different moieties.     

Synthesis and Cytotoxicity of 6‐Pyrrolidinyl‐2‐(2‐Substituted Phenyl)‐4‐Quinazolinones

In our continuing search for potential anticancer candidates, 2‐(3‐methoxyphenyl)‐6‐pyrrolidinyl‐4‐quinazolinone ( JJC‐1 ) was selected as the lead compound. Starting 5‐pyrrolidinyl‐2‐aminobenzamide was prepared using standard methodology from 5‐chloro‐2‐nitrobenzoic acid by reaction with SOCl₂, NH₃, pyrrolidine, and H₂. The starting benzamide then was reacted with 2‐substituted benzaldehyde or benzoyl chloride in N,N‐dimethylacetamide (DMAC) in the presence of NaHSO₃ at 150 °C. Thermal cyclodehydration/dehydrogenation gave the target 6‐pyrrolidinyl‐2‐(2‐substituted phenyl)‐4‐quinazolinones ( 15–22 ). These target compounds were assayed for their cytotoxicity in vitro against six cancer cell lines, including human monocytic leukemia cells (U937), mouse monocytic leukemia cells (WEHI‐3), human hepatoma cells (HepG2, Hep3B) and human lung carcinoma cells (A549, CH27). Most of them exhibited significant cytotoxic effect toward U937 and WEHI‐3 cells, with EC₅₀ values ranging from 0.30 to 10.10 μM. Compound 19 was investigated further for its action mechanisms. Preliminary findings indicated that compound 19 induced G2/M arrest and apoptosis on U937 cells.     

A novel azocompound, 2‐(4‐phenylazoaniline)‐4‐phenylphenol: Spectroscopic and quantum‐chemical approach

A novel azocompound with two nonequivalents azo groups, 2‐(4‐phenylazoaniline)‐4‐phenylphenol, was synthesized and characterized by spectroscopic and computational analysis. An intramolecular hydrogen bonding (HB), ? O₁? H₁ ··· N₁? , involving the ? N₁?N₂? group and the proton in a neighbor hydroxyl moiety, was identified. It was found responsible for a characteristic π‐conjugated H₁? O₁? C₁₈?C₁₃? N₂?N₁? six‐membered cyclic fragment. It is worth noting that this azo group is involved in an azo‐hydrazo equilibrium, being the azo form the most stable one. This resonance‐assisted HB was characterized using the OH‐related infrared bands and the corresponding signals in ¹H NMR. In addition, conformational studies and geometrical and electronic parameter calculations were performed using the density functional theory, at B3LYP/6‐311++G** level. Bond and ring critical points were identified using the atoms in molecules theory, which allowed confirming the intramolecular HB. The second azo‐group cannot be involved in HB, but it also presents two stereoisomerics forms corresponding to cis (Z) and trans (E) configurations, with the later being the one with the lowest energy. © 2013 Wiley Periodicals, Inc.     

Periodicity in proton conduction along a H‐bonded chain. Application to biomolecules

Molecular complexes are constructed to simulate proton transfer channels of the influenza A virus and of the active site of carbonic anhydrase. These complexes consist of proton donor and acceptor groups connected by a chain of water molecules. Quantum chemical calculations on the methylimidazole(H⁺)? H₂O? CH₃COO^? model of the M2 virus channel indicate free translational motion of the water molecule between donor and acceptor, as well as concerted transfer of both H‐bond protons. The proton transfer barrier does not depend on the position of the bridged water molecule and varies linearly with the difference of electrostatic potentials between the donor and acceptor. When the water chain is elongated, and with various donor and acceptor models, periodicity appears in the H‐bond lengths and the progression of proton transfer in each link. This “wave” is shown to propagate along the chain, as it is driven by the displacement of a single proton. One can thereby estimate the velocity of the proton wave and proton conduction time. Computations are performed to examine the influence of immersing the system within a polarizable medium. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Comparative analysis of a full-electron basis set and pseudopotential for the iodine atom in DFT quantum-chemical calculations of iodine-containing compounds

A systematic study was performed to examine the possibilities of the B3LYP DFT method in a dgdzvp full-electron basis and of the method including a pseudopotential for iodine compounds. The full-electron basis generally gives better agreement for X-I bond lengths and reaction enthalpies of iodination of organic compounds and equally good agreement in calculations of the IR vibrations of the X-I bond length compared with the studies using the pseudopotential. The full-electron basis also allows adequate calculations of the quadrupole coupling constants of iodine atoms and is generally characterized by smaller computing times.     

不饱和类卡宾H_2C=CLiF的结构及氢迁移反应的DFT研究

用量子化学中的密度泛函DFT方法,在B3LYP/6-311G~*水平上研究了不饱和类 卡宾H_2C=CLiF的结构。结果表明,只有1种平衡结构是稳定的。对稳定的平衡结构 ,找到了分子内氢迁移反应的过渡态,并计算了不同温度下不饱和类卡宾 H_2C=CLiF的平均寿命τ,在200 K时,τ = 7.9 d,在300 K仅为τ = 2.4 s。     

Design,Synthesis, and Evaluation of 3‐((4‐(t‐Butyl)‐2‐(2‐benzylidenehydrazinyl)thiazol‐5‐yl)methyl)quinolin‐2(1H)‐ones as Neuraminidase Inhibitors

A series of novel 3‐((4‐(t‐butyl)‐2‐(2‐benzylidenehydrazinyl)thiazol‐5‐yl)methyl)quinolin‐2(1H)‐ones ( 7a – 7z ) were designed, synthesized and evaluated for their ability of inhibiting neuraminidase (NA) of in?uenza H1N1 virus. Some compounds displayed moderate influenza NA inhibitory activity. Compound 7l with the scaffold of 2‐(2‐(2‐methoxybenzylidene)hydrazinyl)thiazole was the best one, exhibiting moderate NA inhibitory activity with IC₅₀ of 44.66 µmol/L. Structure‐activity relationship showed that compounds with methoxy or hydroxy groups at the ortho position, fluorine and nitro groups at the meta position and chlorine and bromine groups at the para position of phenyl ring were more active. Docking study indicated that compound 7l has important interactions with some key residues (including Asp151, Glu119, Arg292, Tyr406, and Asn347) and binds to 430‐cavity adjacent to NA active site.     

Mechanism of Ethylene Migratory Insertion and Dimerization Catalyzed by δ‐Alkyl Platinum Complexes–A DFT Study

The mechanism of ethylene insertion reactions catalyzed by cationic δ‐alkyl platinum complexes has been studied at the B3LYP level of density functional theory. The initial steps of the reactions proceed via the coordination of ethylene to the reactants L₂Pt(II)R⁺, where L₂=none, (NH₃)₂, (CHNH)₂; R=H, CH₃, C₂H₅ in which ethylene coordinates strongly to the complexes PtCH⁺₃ and PtC₂H⁺₅ (coordination energies (CE) are 296.52 and 229.28 kJ/mol, respectively), while nitrogen‐containing ligands decrease the energies: Pt(NH₃)₂CH⁺₃ (CE: 180.04 kJ/mol), Pt(NH₃)₂C₂H⁺₅ (CE: 97.86 kJ/mol), Pt(CHNH)₂CH⁺₃ (CE : 176.31 kJ/mol) and Pt(CHNH)₂C₂H⁺₅ (CE: 91.00 kJ/mol). Moreover, ethylene insertion into the Pt‐alkyl bond, which is the rate‐determining step, is endothermic with barrier heights for L₂PtCH₃(C₂H₄)⁺ decreasing in the order: PtCH⁺₃ (164.18 kJ/mol)>(NH₃)₂ PtCH⁺₃ (129.95 kJ/mol)>(CHNH)₂ PtCH⁺₃ (115.27 kJ/mol), which has the same tendency for the ethyl case. The insertion product will continually undergo β‐hydride elimination, which is exothermic. On the other hand, the effects of solvent (dichloromethane, THF and benzene) are investigated with PCM method, but the inclusion of the effects in the computations only slightly affects the results. Beside that, a complete catalytic cycle for ethylene dimerization is studied in detail and the calculations agree well with known energetic and recognized tendencies.     

Electronic structures and reactivities of iodinating agents in the gas phase and in solutions: A density functional study

The electronic and spatial structures of a broad spectrum of neutral compounds with X-Hal (X = N, O, Cl; Hal = Cl, Br, I) bonds and their protonated forms and of different electronic states of triiodide cation, I₃ ⁺, were determined from density functional B3LYP/6 311G* quantum chemical calculations. The effects of the structure of these compounds on the parameters of electrophilic reactivity were revealed and the thermochemical characteristics of homolytic and heterolytic X-Hal bond dissociation and of iodine transfer in hydroxyl-containing solvents were calculated. Due to low homolytic bond dissociation energies of X-I, the formation of molecular iodine and triiodide cation I₃ ⁺ becomes thermodynamically favorable and the cation should act as iodinating agent alternative to acylhypoiodites and N-iodoimides. The solvation effects of MeOH and CH₂Cl₂ on the X-Hal bond homolysis and heterolysis were determined using the PCM model. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 8, pp. 1280–1288, August, 2006.