Design of molecular switching and signaling based on proton transfer in 2-hydroxy Schiff bases: a computational study

Azo-hydrazone molecular switches: Synthesis and NMR conformational investigation

A series of five intramolecularly hydrogen-bonded arylhydrazone (aryl = phenol, p-nitrophenol, anisole, quinoline) derived molecular switches have been synthesized and characterized by NMR and HRMS techniques. It was found that the compounds exist as different isomers in solution. An investigation of both conformational and/or configurational changes of the azo-hydrazone compounds was carried out by 1D ¹ H- and ¹³ C- spectra, 2D NOESY, COSY, HSQC, and HMBC techniques. It was found that these stimuli-responsive molecular switches exist mainly in the E form by intramolecularly hydrogen bonded between NH and the pyridine nitrogen at equilibrium. Deprotonation of the neutral E form yields the E' deprotonated isomer. Prediction of ¹³ C-NMR chemical shifts was achieved by DFT quantum mechanical calculations. Anions have traditionally been difficult to calculate correctly, so calculations of the anion using different functionals, basis sets, and solvent effects are also included. Deuterium isotope effects on the ¹³ C-NMR chemical shifts were employed in the assignments and furthermore utilized as indicators of intramolecular hydrogen bonding. Studies in various organic solvents including CDCl₃ , CD₃ CN, and DMSO-d₆ were also performed aiming to monitor dynamic changes over several days. The effect of the hydrogen bonded solvents leads to Z forms.

A DFT mechanistic, thermodynamic and kinetic study on the reaction of 1, 3, 5-trihydroxybenzene and 2, 4, 6-trihydroxyacetophenone with •OOH in different media

A theoretical investigation on the reactions of 1, 3, 5-trihydroxybenzene (PG) and 2, 4, 6-trihydroxyacetophenone (ACPG) with •OOH has been performed with the aim of elucidating the peroxyl radical scavenging properties of PG and its acylated derivative. The study has considered the hydrogen atom transfer (HAT), the single electron transfer-proton transfer and the sequential proton loss-electron transfer mechanisms and determined the geometric, energetic and electronic properties of the reaction species as well as the kinetic parameters for the HAT mechanism. DFT/M06-2X, DFT/MPW1K and DFT/BHHLYP calculation methods have been utilized in combination with the 6-311++G(3df, 2p) basis set. The DFT methods were benchmarked using the CBS-QB3 method. Thermodynamic parameters such as bond dissociation enthalpy (BDE) and ionization energy suggest that the thermodynamically preferred mechanism is the HAT mechanism. The geometric, electronic and energetic parameters suggest that the preferred site for the abstraction of the free phenolic H atom in ACPG is the ortho position. Spin density and branching ratio values indicate that the most stable and preferable product formed is for the reaction of ACPG [Formula: see text] •OOH at the ortho position. The estimated rate constants obtained indicate that the reaction of ACPG [Formula: see text] •OOH is kinetically preferred to the reaction of PG [Formula: see text] •OOH, which is in agreement with experimental findings.

A DFT mechanistic and kinetic study on the reaction of phloroglucinol with •OH in different media: Hydrogen atom transfer versus oxidation

A theoretical study on the reaction of phloroglucinol with •OH has been performed with the aim of elucidating the geometric, energetic and kinetic properties of the reaction as well as identifying the preferred reaction pathway. Three reaction mechanisms have been considered, namely, direct hydrogen atom abstraction, addition–elimination mechanism in the absence and in the presence of a base catalyst and oxidation mechanism in the absence and in the presence of O2. The study has been performed using the DFT/M06[Formula: see text]2X, DFT/BHHLYP and DFT/MPW1K methods in conjunction with either the 6-31++G(d,p) or the 6-311++G(3df,2p) basis set. The energetic parameters are influenced by the type of function utilized and the media in which the calculation is done. The direct hydrogen abstraction mechanism provides the smallest branching ratio with respect to the •OH addition mechanisms. The PG + •OH reaction under atmospheric conditions saturated with O2 would predominantly form tetrahydroxybenzene; the predominant product within the biological system would largely depend on physiological conditions; under pH [Formula: see text] 7 and with oxygen dissolved within the biological system, the preferred product would be tetrahydroxybenzene; however, if the reaction takes place in some part of the biological system where the pH [Formula: see text] 7, the preferred product would be the phenoxyl radical.

Predicting substituent effects on activation energy changes by static catalytic fields

Catalytic fields illustrate topology of the optimal charge distribution of a molecular environment reducing the activation energy for any process involving barrier crossing, like chemical reaction, bond rotation etc. Until now, this technique has been successfully applied to predict catalytic effects resulting from intermolecular interactions with individual water molecules constituting the first hydration shell, aminoacid mutations in enzymes or Si→Al substitutions in zeolites. In this contribution, hydrogen to fluorine (H→F) substitution effects for two model reactions have been examined indicating qualitative applicability of the catalytic field concept in the case of systems involving intramolecular interactions.

Graphical abstract

Toward Exploring Novel Organic Materials: MP4-DFT Properties of 4-Amino-3-Iminoindene

Tautomerism links with many applications and remains an attracting feature in exploring novel systems. In this regard, properties of indene-based HNCCCN segments have not received any considerable attention. In this computational organic chemistry study, first, to calculate the proton transfer energy barrier at a reasonable cost, the study identified an accurate forth order Møller–Plesset perturbation theory-density functional theory (MP4-DFT) protocol equivalent to the outstanding pioneering benchmark calculations. The calculations illustrate that the two tautomers of the 4-amino-3-iminoindene nucleus are separated by a considerable energy barrier while featuring different molecular orbital characteristics; frontier orbital distribution, λmax, and energies, which are known basic requirements in molecular switching and logic circuit applications. The N-H/BH₂ substitution was found to have significant influence on the electronic structure of the skeleton. Similarities in the two tautomers and the boron derivative to properties of known molecular materials have been found.

Theoretical and experimental studies on three new coordination complexes of Co(II), Ni(II), and Cu(II) with 2,4-dichloro-6-{(E)-[(5-chloro-2 sulfanylphenyl)imino]methyl}phenol Schiff base ligand

Three mononuclear coordination complexes of Co(II), Ni(II), and Cu(II) have been synthesized from 2,4-dichloro-6-{(E)-[(5-chloro-2-sulfanylphenyl)imino]methyl}phenol ligand (H 2 L) obtained by simple condensation reaction of 3,5-dichloro-2-hydroxybenzaldehyde and 2-amino-4-chlorobenzenethiol and characterized by elemental analysis, spectral (FT-IR, electronic, and (1)H-NMR), molar conductance, thermal, SEM, PXRD, and fluorescence studies. The PXRD analysis and SEM-EDX micrographs show the crystalline nature of complexes. The domain size and the lattice strain of synthesized compounds have been determined according to Williamson-Hall plot. TG of the synthesized complexes illustrates the general decomposition pattern of the complexes. The ligand exhibits an interesting fluorescence property which is suppressed after complex formation. The Co(II) complex adopted a distorted octahedral configuration while Ni(II) and Cu(II) complexes showed square planar geometry around metal center. The geometry optimization, HOMO-LUMO, molecular electrostatic potential map (MEP), and spin density of synthesized compounds have been performed by density functional theory (DFT) method using B3LYP/6-31G and B3LYP/LANL2DZ as basis set. Graphical abstract Three new coordination complexes of Co(II), Ni(II) and Cu(II) with 2,4-dichloro-6-{(E)-[(5-chloro-2 sulfanylphenyl)imino]methyl}phenol Schiff base ligand.

Deuteration of Aromatic Rings under Very Mild Conditions through Keto-Enamine Tautomeric Amplification

We have discovered a surprising, mild method for deuteration of select aromatic compounds that is facilitated by a keto-enamine tautomeric intermediate. The mechanism of the reaction has been studied using kinetics experiments and detailed computational analysis. It was found that a chain of water molecules has a substantial role in lowering the activation barrier to the tautomerization-enhanced deuteration reaction. Our results demonstrate that tautomeric forms of aromatic molecules can be exploited to bring about enhanced reactivity.

Impact of proton transfer phenomena on the electronic structure of model Schiff bases: an AIM/NBO/ELF study

Understanding of the electronic structure evolution due to a proton dynamics is a key issue in biochemistry and material science. This paper reports on density functional theory calculations of Schiff bases containing short, strong intramolecular hydrogen bonds where the bridged proton is located: (i) at the donor site, (ii) strongly delocalized, and (iii) at the acceptor site. The mobility of the bridged proton and its influence on the molecular structure and properties of the chosen Schiff base derivatives have been investigated on the basis of Atoms in Molecules, Natural Bond Orbitals, and Electron Localization Function theories. It has been observed that the extent of the bridged proton delocalization is strongly modified by the steric and inductive effects present in the studied compounds introduced by various substituents. It has been shown that: (i) potential energy profiles for the proton motion are extremely dependent on the substitution of the aromatic ring, (ii) the topology of the free electron pairs present at the donor∕acceptor site, as well as their electron populations, are affected qualitatively by the bridged proton position, (iii) the distortion of the molecular structure due to the bridged proton dynamics includes the atomic charge fluctuations, which are in some cases non-monotonic, and (iv) topology of the ELF recognizes events of proton detachment from the donor and attachment to the acceptor. The quantitative and qualitative results shed light onto molecular consequences of the proton transfer phenomena.

Microwave assisted synthesis, crystal structure and modelling of cytotoxic dehydroacetic acid enamine: a natural alkaloid from Fusarium incarnatum (HKI0504)

Synthesis and modelling of DHA enamine, its co-crystal structure is presents four-molecules clusters joined by π-stacking like masonry walls.