Effect of solvents on intra- and inter-molecular interactions of oligothiophenes

CONTEXT

Oligothiophenes have long been used as model compounds to understand the chemistry of polythiophenes. Herein, we have some quantum chemical calculations and intra- and inter-molecular interaction calculations of a series of oligothiophenes such as terthiophene, quintetthiophene, sevensthiophene, terthiophene-terthiophene, terthiophene-water, terthiophene-methanol, and terthiophene-chloroform performed by time-dependent density functional theory (TD-DFT), density functional theory (DFT), and Multiwfn: a multifunctional wavefunction analyzer. The UV-vis spectra, HOMO-LUMO energies, NBO analysis, MEP, molecular structures, and electronic properties were computed using DFT/TD-DFT at the level of B3LYP/6-31+ G (d,p) and described. The nature of molecular interactions between terthiophene and solvents like water, methanol, and chloroform were also investigated using non-covalent interaction index (NCI), reduced density gradient (RDG), localized orbital locator (LOL), and electron localization function (ELF) topological analyses. Besides, Fukui functions and energy of population density-of-states were computed using the same method. The calculation results show that there are some changes in the terthiophene with the addition of solvent to the medium.

METHODS

DFT calculations were performed using the Gaussian 09 software and GaussView 5.0 visulation program. Multiwfn software is used to calculate the reduced density gradient (RDG) scatterplots, non-covalent interactions (NCI), ELF, LOL, Fukui analysis, and energy of population density-of-states of oligothiophenes.

A Comprehensive Study of N-Butyl-1H-Benzimidazole

Imidazole derivatives have found wide application in organic and medicinal chemistry. In particular, benzimidazoles have proven biological activity as antiviral, antimicrobial, and antitumor agents. In this work, we experimentally and theoretically investigated N-Butyl-1H-benzimidazole. It has been shown that the presence of a butyl substituent in the N position does not significantly affect the conjugation and structural organization of benzimidazole. The optimized molecular parameters were performed by the DFT/B3LYP method with 6-311++G(d,p) basis set. This level of theory shows excellent concurrence with the experimental data. The non-covalent interactions that existed within our compound N-Butyl-1H-benzimidazole were also analyzed by the AIM, RDG, ELF, and LOL topological methods. The color shades of the ELF and LOL maps confirm the presence of bonding and non-bonding electrons in N-Butyl-1H-benzimidazole. From DFT calculations, various methods such as molecular electrostatic potential (MEP), Fukui functions, Mulliken atomic charges, and frontier molecular orbital (HOMO-LUMO) were characterized. Furthermore, UV-Vis absorption and natural bond orbital (NBO) analysis were calculated. It is shown that the experimental and theoretical spectra of N-Butyl-1H-benzimidazole have a peak at 248 nm; in addition, the experimental spectrum has a peak near 295 nm. The NBO method shows that the delocalization of the aσ-electron from σ (C1-C2) is distributed into antibonding σ* (C1-C6), σ* (C1-N26), and σ* (C6-H11), which leads to stabilization energies of 4.63, 0.86, and 2.42 KJ/mol, respectively. Spectroscopic investigations of N-Butyl-1H-benzimidazole were carried out experimentally and theoretically to find FTIR vibrational spectra.

The DOLFIN method: a novel laparoscopic Billroth-I gastroduodenostomy for gastric cancer with duodenal invasion

BACKGROUND

Laparoscopic Billroth-I gastroduodenostomy using a delta-shaped anastomosis is safe and feasible. However, it is often difficult to perform in patients who have a short posterior wall of the duodenum. Thus, we have developed a new method named duodenal overlap functional anastomosis with linear stapler (DOLFIN). We hereby report the technical details of the new method and our preliminary experience performing it.

METHODS

After the completion of lymphadenectomy, the duodenum was transected craniocaudally with an endoscopic linear stapler. The hepatoduodenal mesentery was dissected approximately 4 cm along the duodenal bulb, and the anastomosis between the posterior wall of the stomach and the lesser curvature of the duodenum was created. The common entry hole was then transected using an endoscopic linear stapler, and the anastomosis was finally completed.

RESULTS

There were 36 patients with gastric cancer who underwent laparoscopic distal gastrectomy (LDG) or robotic distal gastrectomy (RDG) with B-I reconstruction using DOLFIN. There were no postoperative complications classified as C-D grade 3 or more and complications related to anastomosis, such as anastomotic leak or stenosis.

CONCLUSIONS

Our DOLFIN gastroduodenostomy can be performed safely. In addition, it results in good postoperative outcomes. A long-term comparative study is required to further evaluate the clinical usefulness of this method.

Interaction of 5-fluorouracil anticancer drug with nucleobases: insight from DFT, TD-DFT, and AIM calculations

In this study, the interaction of 5-fluorouracil (5FU) drug with adenine (A), guanine(G), cytosine(C), uracil (U), and thymine (T) nucleobases of DNA and RNA are surveyed at the ωB97XD/LANL2DZ, M06-2X/6-31G (d, p), MPW1PWQ1/6-31G(d, p), PBEPBE/6-31(d, p) and ωB97XD/6-31G(d, p) levels of density functional theory (DFT). The considered complexes of 5FU drug with nucleobases are optimized at the above level of theories. Max Force and RMS of optimization criteria are 0.00035 (Ha), and 0.0003 respectively. From optimized structures, the adsorption energy, thermodynamic parameters in gas and solvent media, quantum theory atom in molecule (QTAIM), electron localized function (ELF), and reduced density gradient (RDG) are calculated at ωB97XD/LANL2DZ and M06-2X/6-31G (d, p) level of DFT theory. The QTAIM, ELF, and RDG results confirm that the nature of bonding between 5FU drug with A, C, G, U, and T nucleobases is electrostatic or hydrogen bond type. The adsorption and thermodynamic energy results demonstrate that the interaction of the 5FU drug with C and G nucleobases is stronger than other nucleobases. The results of this study can be suggested the mechanism of interaction of the 5FU drug with nucleobases of DNA and RNA.Communicated by Ramaswamy H. Sarma.

Density functional theory-based analyses on selective gas separation by β-PVDF-supported ionic liquid membranes

Finding proper candidates for polymer-supported ionic liquid (IL)-based gas separating membranes is a challenge. The current article elucidates the quantum chemical perspective of the selective gas adsorption efficiency, from a mixture of CO₂, CO, CH₄, and H₂, of α- and β-polyvinylidene fluoride (PVDF)-supported imidazolium- and pyridinium-based six ionic liquid membranes. Although IL-based membrane efficiency mainly depends on the gas solubility of ILs, IL/support binding and gas adsorption on the support material are also studied to describe the overall gas adsorption properties of the PVDF/IL complexes. β-PVDF exhibits better binding with the ILs, and better gas affinity, thus, qualified as a more suitable membrane component as compared to α-PVDF. Dispersion-corrected density functional calculations are performed to provide a detailed insight into the energetic interactions, nonbonding intermolecular interactions based on symmetry adapted perturbation theory (SAPT), natural bond orbitals (NBO), Bader's quantum theory of atoms in molecules (QTAIM), reduced density gradient (RDG), frontier orbital interactions, density of states (DOS), and thermochemical analyses of the gas-adsorbed systems. Gas molecules interact with the membrane components through weak hydrogen bonds and exhibit low interaction energies, indicating physisorption of the gases. Gas adsorption energies are more negative than the mutual interaction energies of the gas molecules, ensuring effective gas adsorption by the membrane components. All the β-PVDF/IL systems have shown the highest and lowest affinity for CO2 and H2, respectively, leading to effective separation of CO₂ and H₂ from the other gases.

Quantum chemical calculation, performance of selective antimicrobial activity using molecular docking analysis, RDG and experimental (FT-IR, FT-Raman) investigation of 4-[{2-[3-(4-chlorophenyl)-5-(4-propan-2-yl) phenyl)-4, 5-dihydro- 1H- pyrazol-1-yl]-4-oxo-1, 3- thiazol-5(4H)-ylidene} methyl] benzonitrile

The research received a great deal of worldwide attention due to the nature of interpretation before the experimental process. Based on the systematic process the structure of thiazole -pyrazole compound 4-[{2-[3-(4-chlorophenyl)-5-(4-propan-2-yl) phenyl)-4, 5-dihydro- 1H- pyrazol-1-yl]-4-oxo-1, 3- thiazol-5(4H)-ylidene} methyl] benzonitrile [CPTBN] was investigated. In the first level, the spectral statistics on experimental FT-IR and FT- Raman was reported. At the next level, geometrical parameters was theoretically acquired from density functional theory (DFT) using B3LPY/6-31G and 6-311G basis set. The computed Wavenumber were collected and compared with the experimental data. The vibrational modes were interpreted in terms of potential energy distribution (PED) results. The FMO, MEP, and NBO analysis further validated the electrophilic and nucleophilic interaction in the molecular systems. Two grams-positive bacteria: staphylococcus aureus, Bacillus subtilis and two gram-negative bacteria: Esherichia coli, Pseudomonas aeruginosa was performed for antibacterial activity. Two fungal strain Candida albicans and Aspergillus Niger was carried out against a ligand using anti-fungal activity. The molecular docking analysis explores the antimicrobial and selective potential inhibitory nature of the binding molecule. Besides, RDG and ELF analysis were also performed to show the nature of interactions between the molecule.

Speculative assessment, molecular composition, PDOS, topology exploration (ELF, LOL, RDG), ligand-protein interactions, on 5-bromo-3-nitropyridine-2-carbonitrile

Computational calculations of 5-bromo-3-nitropyridine-2-carbonitrile (5B3N2C) on molecular structure and on energy are implemented using the 6-311++G(d,p) basis set by DFT/B3LYP method. The UV-Vis spectrum of 5B3N2C was obtained by TD-DFT with chloroform as a solvent. The analysis of molecular electrostatic potential (MEP) and frontier molecular orbital (FMO) were used to evaluate, the entire electron density and organic reactive sites of 5B3N2C. The electron-hole conversions were conjointly deliberated. Donor-acceptor interactions (NBO) analysis examines the intra-and intermolecular charge transfer, hyper conjugate interaction of the compound. The orbital molecular contributions are evaluated by density of states (DOS and PDOS). To discern the reactivity of the molecule, topology analyses were done. The biological prominence of the 5B3N2C molecule was investigated in a pertinent study of molecular docking with target protein 3CEJ exhibiting the centromere associated protein inhibitor property. Molecular Dynamics simulations were done to assess the stability of the complex. 5B3N2C physiochemical parameters were also compared to those of widely viable medications Ispinesib and Lonafarnib.

Effective adsorption of A-series chemical warfare agents on graphdiyne nanoflake: a DFT study

Chemical warfare agents (CWAs) are highly poisonous and their presence may cause diverse effects not only on living organisms but also on environment. Therefore, their detection and removal in a short time span is very important. In this regard, here the utility of graphdiyne (GDY) nanoflake is studied theoretically as an electrochemical sensor material for the hazardous CWAs including A-230, A-232, and A-234. Herein, we explain the phenomenon of adsorption of A-series CWAs on GDY nanoflake within the density functional theory (DFT) framework. The characterisation of adsorption is based on optimised geometries, BSSE-corrected energies, SAPT0, RDG, FMO, CHELPG charge transfer, QTAIM and UV-Vis analyses. The calculated counterpoise adsorption energies for reported complexes range from - 13.70 to - 17.19 kcal mol^-1. These adsorption energies show that analytes are physiosorbed onto GDY which usually takes place through noncovalent interactions. The noncovalent adsorption of CWAs on GDY is also attributed by the SAPT0, RDG and QTAIM analyses. These properties also reveal that dispersion factors dominate in the complexes among many noncovalent components (exchange, induction, electrostatic, steric and repulsion). In order to estimate the sensitivity of GDY, the %sensitivity and average energy gap variations are quantitatively measured by energies of HOMO and LUMO orbitals. In terms of adsorption affinity of GDY, UV-Vis analysis, CHELPG charge transfer and DOS analyses depict an appreciable response towards these toxic CWAs. Graphical abstract.

Theoretical prediction of the impact sensitivities of energetic C-nitro compounds

In order to design high-energetic and insensitive explosives, the frontier orbital energy gaps, surface electrostatic potentials, nitro group charges, bond dissociation energies (BDEs) of the C-NO₂ trigger bonds, and intermolecular interactions obtained by the M06-2X/6-311++G(2d,p) method were quantitatively correlated with the experimental drop hammer potential energies of 10 typical C-nitro explosives. The changes of several information-theoretic quantities (ITQs) in the density functional reactivity theory were discussed upon the formation of complexes. The BDEs in the explosives with six-membered ring are larger than those with five-membered ring. The frontier orbital energy gaps of the compounds with benzene ring are larger than those with N-heterocycle. The models involving the intermolecular interaction energies and the energy gaps could be used to predict the impact sensitivity of the C-nitro explosives, while those involving ΔS_S, ΔI_F, and ΔS_GBP are invalid. With the more and more ITQs, the further studies are needed to seek for a good correlation between impact sensitivity measurements and ITQs for the energetic C-nitro compounds. The origin of sensitivity was revealed by the reduced density gradient method.

Molecular docking studies, structural and spectroscopic properties of monomeric and dimeric species of benzofuran-carboxylic acids derivatives: DFT calculations and biological activities

Structural optimization, molecular docking analysis, electronic and vibrational properties have been investigated for the 1-benzofuran-2-carboxylic acid (2BF) and 1-benzofuran-3-carboxylic acid (3BF) using DFT/B3LYP/6-311++G(d,p) level of theory. The theoretical parameters have a very good consistency with the experimental ones. The weak intermolecular interactions were analyzed by different tool such as: Hirshfeld surfaces, topological analysis and natural bond orbital studies. The nonlinear optical properties have been investigated. Molecular electrostatic potential and frontier molecular orbitals (FMOs) analysis have been carried out to understand the reactivity of the molecule. In addition, TD-DFT calculation is initiated to simulate the UV-vis absorption spectrum and to determine several important electronic properties like HOMO-LUMO gap energy and electronic transitions. The complete vibrational assignments and the force constants were reported for monomer and dimers of both acids. The biological activities of the tow acids have been studied via molecular docking analysis. The later calculations prove that the studied acids have an inhibitor effect against cancer and microbial diseases.

Intermolecular hydrogen bond interactions in the thiourea/water complexes (Thio-(H2O)n) (n = 1, …, 5): X-ray, DFT, NBO, AIM, and RDG analyses

This study aims to experimentally and theoretically examine the nature and energy of intermolecular bond interactions between thiourea and water molecules using natural bond orbital (NBO), non-linear optical (NLO), atoms in molecules (AIM), and reduced density gradient (RDG) analyses based on the quantum chemical approach and spectroscopic analysis on X-ray and FTIR. Geometry optimizations of Thio-(H₂O)_1-5 complexes were carried out in the gas phase by B3LYP/6-311++G(d,p) level of density functional theory. The nature of the molecular interactions between the water and thiourea through hydrogen bonding has been investigated using RDG and AIM methods. NBO analysis shows that the Thio-(H₂O)₅ complex has higher stabilization energy values than the other complexes. The non-linear optical properties, such as dipole moment (μ), the polarizability (α₀), and the first hyperpolarizability (β_tot), and thermodynamic functions, such as entropy (S), specific heat capacity (C_v), and thermal energy (E), were calculated using the same method. It was observed that thermodynamic parameters, polarizability, and the first hyperpolarizability increased with the number of water molecules. X-ray diffraction analysis confirmed that thiourea is single crystal, and the thiourea/water complexes are crystalline in nature. Besides, the infrared spectrum shows the existence of water molecules and it is used to get details of the structure of the complex.

The mechanism of the excited-state proton transfer of Salicylaldehyde azine and 2,2'-[1,4-Phenylenebis{(E)- nitrilomethylidyne}] bisphenol: Via single or double proton transfer

The Salicylaldehyde azine (H₂SA) and 2,2'-[1,4-Phenylenebis{(E)-nitrilomethylidyne}] bisphenol (H₂SPA) with double proton transfer characteristics were synthesized recently (Phys. Chem. Chem. Phys., 2018, 20, 23,762). However, the detailed theoretical interpretation of proton transfer (PT) mechanism is inadequate. In the present work, density functional theory (DFT) and time-density functional theory (TDDFT) are employed to study the proton transfer mechanism of H₂SA and H₂SPA in detail. Bond parameters, infrared (IR) spectra and frontier molecular orbitals (FMOs) calculated by PBE0/TZVP method indicate the strength of hydrogen bond is enhanced in S₁ state, which can be visualized by the reduced density gradient (RDG) analysis. The potential energy surfaces (PESs) of H₂SA and H₂SPA are also constructed. The small barriers indicate that both the single proton transfer and double proton transfer of H₂SA and H₂SPA are more likely to occur in the S₁ state. In addition, the properties of H₂SA and H₂SPA after chelation with Li⁺ have also been theoretically characterized. According to the calculated fluorescence spectra of compounds (H₂SA-Li⁺ and H₂SPA-Li⁺), it was found that only the planar structure of H₂SA-Li⁺ can form metallogel, which verified the experimental results.

The novel excited state intramolecular proton transfer broken by intermolecular hydrogen bonds in HOF system

2-(4-(Dimethylamino)phenyl)-3-hydroxy-6,7-dimethoxy-4Hchromen-4-one (HOF) was synthesized in experiment (Wang et al., Sensor. Actuat. B-Chem. 277 (2018) 484), and its photophysical and photochemical properties was reported. However the corresponding full theoretical interpretation of mechanisms is inadequate. In the present research, the intermolecular hydrogen bond structure of HOF-methanol complex (HOF-2M) was found, and mechanism of alcohols monitoring of HOF was deeply studied using the density functional theory (DFT) and time-dependent density functional theory (TDDFT). The enhancing mechanism of the excited state hydrogen bond is verified by analyzing the hydrogen bond parameters, infrared spectra and frontier molecular orbitals. Importantly, the reduced density gradient visual analysis and topological quantificational analysis confirm that the intramolecular hydrogen bond of HOF is broken by strong intermolecular hydrogen bonds of HOF-2M using the Atoms-In-Molecule theory. The obtained absorption and emission spectra are found to agree well with the experimental results and the complete quenched keto-emission in methanol and ethanol solvents provide a suitable sensing mechanism for detecting alcohols. The reaction path of the excited state intramolecular proton transfer for HOF is explained in detail through the constructed potential energy curves.

Theoretical insights into the hydrogen bonding interaction in the complexation of epinephrine with uracil

The present study is aimed at probing the hydrogen bonding interaction between epinephrine and uracil by means of density functional theory calculations concerning their complexation's geometries, interaction energies, and vibrational frequencies. Geometry optimization was carried out giving 19 stable geometries of epinephrine-uracil complex with interaction energies in a range of - 21.51 to - 62.37 kJ mol^-1 using the basis set superposition error (BSSE) correction. The analysis of structure and vibration shows that the hydrogen bonding elongates the length of corresponding bond O(N)-H and decreases the symmetric stretching vibrational frequency, which indicates red-shifted H-bonding interactions in all the geometries. Additionally, the analysis with theories of natural bond orbital (NBO), atoms in molecules (AIM), and the reduced density gradient (RDG) of hydrogen bonding properties and characteristics of the 19 geometries suggests that the hydrogen bonding in all the optimized structures of epinephrine-uracil complex is kind of a closed-shell interaction and mainly electrostatic dominant.

Theoretical explanation for the pharmaceutical incompatibility through the cooperativity effect of the drug-drug intermolecular interactions in the phenobarbital∙∙∙paracetamol∙∙∙H2O complex

In order to reveal the essence of the pharmaceutical incompatibility, the cooperativity effects of the drug-drug intermolecular π∙∙∙π and H∙∙∙O H-bonding interactions involving hydration were evaluated in the phenobarbital∙∙∙paracetamol∙∙∙H₂O complex at the M06-2X/6-311++G** and MP2/6-311++G** levels. The thermodynamic cooperativity effects were also investigated by the statistical thermodynamic method. The results show that the π∙∙∙π stacking ternary complexes with the moderate anti-cooperativity effects are dominant in controling the aggregation process of phenobarbital, paracetamol, and H₂O, as is confirmed by the atoms-in-molecules (AIM) and reduced density gradient (RDG) analyses. Therefore, it can be inferred that the anti-cooperativity effect plays an important role in forming the pharmaceutical incompatibility, and thus a deduction on the formation process of the pharmaceutical incompatibility between phenobarbital and paracetamol, with the hydration effect, is given. Several valuable models that relate the features of molecular surface electrostatic potentials or their statistical parameters, such as the surface areas, average values ([Formula: see text]), variances ([Formula: see text], [Formula: see text] and [Formula: see text]), and product of [Formula: see text] and electrostatic balance parameter (ν) ([Formula: see text]ν), to the values of the cooperativity effects were predicted. The formation of the pharmaceutical incompatibility is a thermodynamic cooperativity process driven by the enthalpy change. Graphical abstract Anti-cooperativity effect plays an important role in forming the pharmaceutical incompatibility.

Nonbonding interaction analyses on PVDF/[BMIM][BF4] complex system in gas and solution phase

The present study provides a detailed quantum chemical description of the physicochemical interactions between poly-vinylidene fluoride (PVDF) and 1-butyl-3-methyl-imidazolium tetrafluoro borate ([BMIM][BF₄]) ionic liquid (IL). Geometry optimization and frequency calculations are carried out for four monomer units of α- and β-PVDF, [BMIM][BF₄], and PVDF/[BMIM][BF₄] using dispersion corrected density functional theory. The effects of solvation on the systems under study are demonstrated for three polar aprotic solvents, namely tetra-hydrofuran (THF), acetone, and n,n-dimethyl formamide (DMF) using the integral equation formalism polarizable continuum model (IEFPCM). Calculated negative solvation free energy values suggest solution phase stability of the systems under study. Binding and interaction energies for β-PVDF/IL are found higher in magnitude than those for α-PVDF/IL. The nonbonding interaction phenomenon of β-PVDF/[BMIM][BF₄] is elucidated on the basis of natural bond orbital (NBO), Bader's quantum theory of atoms in molecules (QTAIM), delocalization indices, Hirshfeld surface, and reduced density gradient (RDG) analyses. Both anions and cations of ionic liquids are found to show weak van der Waals interaction with PVDF molecule but the anion ([BF₄]^-)/PVDF interaction is found to be stronger than cation ([BMIM]⁺)/PVDF interaction. Inter-unit C-H⋯F type hydrogen bonds are found to show improper (causing blue shifts in vibrational frequencies) nature. Frontier molecular orbital analysis is carried out, and different chemical parameters like electronegativity, chemical potential, chemical hardness and softness, and electrophilicity index are calculated using Koopmans' theorem. Thermochemical calculations are also performed, and the variation in different standard thermodynamic parameters with temperature is formulated. Graphical abstract (a) Hirshfeld surface mapped onto electron density and (b) NCI isosurfaces showing inter-unit interactions of β-PVDF/[BMIM][BF₄].

Application of terahertz spectroscopy and theoretical calculation in dimethylurea isomers investigation

The characteristic absorption spectra of two structural isomers of dimethylurea(DMU) in 0.6-1.8 THz region have been measured using terahertz time-domain spectroscopy (THZ-TDS) at room temperature. Significant differences have been found between their terahertz spectra and implied that the THZ-TDS is an effective means of identifying structural isomers. To simulate their spectra, calculations on single molecule and cluster of 1,1-DMU and 1,3-DMU were performed, and we found that the cluster calculations using DFT-D3 method are better to predict the experimental spectra. Using the normal mode as displacements in redundant internal coordinates and the GaussView program, most observed THz vibrational modes are assigned to bending and rocking modes related to the intermolecular hydrogen bonding interactions, and twisting mode of ethyl groups. The different spectral features of two isomers mainly arise from different intermolecular hydrogen bonds resulting from different atom arrangements in molecules and different molecule arrangements in crystals. Using the reduced-density-gradient (RDG) analysis, the positions and types of intermolecular hydrogen bonding interactions in 1,1-DMU and 1,3-DMU crystals are visualized. Therefore, we can confirm that THz-TDS can be used as an effective means for the recognition of structural isomers and detection of intermolecular hydrogen bonding interactions in these crystals.