Gauge-invariant Atomic Orbital Method Research Articles

Synthesis, structural analysis, and molecular docking of a novel 1,3,4-thiadiazole derivative: An experimental and molecular modeling studies

This study reports on the synthesis and characterization of a new thiadiazole derivative, (E)-N-(5-(2-nitrostyryl) -4-acetyl -4,5-dihydro -1,3,4-thiadiazol -2-yl) -N-phenylacetamide (ETDZ). The crystal structure was determined by single-crystal X-ray diffraction. ETDZ belongs to the monoclinic I2/a space group. The contribution of intermolecular interactions was assessed by Hirshfeld surface analysis and fingerprint plots. FT-IR, UV–Vis, and NMR (1H and 13C) techniques were used for spectroscopic characterization. The 1H and 13C NMR spectra were recorded in CDCl3 solvent. Density functional theory, employing the B3LYP functional and 6–311G(d,p) basis set in chloroform solvent, was used to calculate the structural and spectroscopic parameters of the molecule in the ground state. The vibrational wavenumbers were calculated and compared with the experimental FT-IR spectrum using the scaled quantum mechanics method. Isotropic chemical shifts were calculated using the Gauge invariant atomic orbital method. The calculated NMR chemical shifts and absorption wavelengths were compared with the experimental values, indicating good results from the DFT and TD-DFT methods. To get more information about charge transfer within the molecule, electronic properties such as HOMO and LUMO energies were studied using the DFT approach. The molecular electrostatic potential, frontier molecular orbital analysis, energy band gap, density of state, global chemical reactivity descriptors, and some thermodynamic functions were also calculated. Reduced density gradient and atom-in-molecule analysis were performed to investigate inter- and intra-non-covalent interactions. Molecular docking was carried out with the Eg5 kinesin protein, confirming the biological assets of the ETDZ ligand as a mitochondria disease and cancer agent.

AlCl3-Catalyzed Cascade Reactions of 1,2,3-Trimethoxybenzene and Adipoyl Chloride: Spectroscopic Investigations and Density Functional Theory Studies.

The reaction of 1,2,3-trimethoxybenzene with adipoyl chloride in the presence of AlCl3 gave two isomeric cyclopentene derivatives, 1,6-bis(2,3,4-trimethoxyphenyl)hexane-1,6-dione, and two demethylation products of aryl methyl ethers. The cyclopentene derivatives including unconjugated or conjugated enones are products formed in a cascade reaction resulting from first the Friedel-Crafts acylation reaction and then aldol condensation. All compounds were optimized by density functional theory calculated using two functional levels, B3LYP and M06-2X, with the 6-311+G(d,p) basis set. The structural properties were established, natural bond orbital analysis of donor-acceptor interactions was carried out, and charges on the atoms and quantum chemical reactivity identifiers were determined to compare the strength of the intramolecular hydrogen bonds formed and their stabilities. To compare the experimental 1H and 13C NMR chemical shifts with the calculated values, NMR chemical shift calculations were carried out using the gauge-invariant atomic orbital method.

Theoretical approach to the molecular structure, chemical reactivity, molecular orbital analysis, spectroscopic properties (IR, UV, NMR), and NBO analysis of deferiprone

In this investigation, the structural, electronic properties, 13C and 1H NMR parameters and the first hyperpolarizability of deferiprone are computed in the gas phase and various solvents at the M062X/6-311++G(d,p) level of theory. The solvent effect on the structural parameters, frontier orbital energies, 13C and 1H NMR parameters is also explored based on a polarizable continuum model. These consequences specify that the polarity of solvents affects the structures and spectroscopic properties of deferiprone. 1H and 13C NMR chemical shifts are evaluated by employing the gauge-invariant atomic orbital method. NBO analysis is exploited to examine the hybridization of atoms, atomic charges, and their second order stabilization energy within the molecule.

Computational study of osmabenzyne: The solvent effects on the structure and spectroscopic properties (IR, NMR)

In this article, the structural, electronic, and spectroscopic properties of osmabenzyne Os{≡CC(SiH3)=C(CH3)C(SiH3)=CH}Cl2(PH3)2 are explored in the gas phase and five solvents. The effects of solvents on the structural parameters, frontier orbital energies, and spectroscopic parameters of the complex are elucidated using the polarizable continuum model. The wavenumbers of selected IR-active vibrations in different solvents are obtained and correlated with the Kirkwood–Bauer–Magat equation. In addition, thermodynamic parameters of solvation are calculated for the complex. 1H and 13C NMR chemical shifts are estimated using the gauge-invariant atomic orbital method.

N-[4-(3-Methyl-3-phenyl-cyclobutyl)-thiazol-2-yl]-N′-pyridin-2-ylmethylene-chloro-acetic acid hydrazide: Synthesis and configurational assignment based on X-ray, 1H, and 13C NMR and theoretical calculations

In this study, quantum chemical calculations based on the density functional theory have been carried out to examine the effects of N-[4-(3-methyl-3-phenyl-cyclobutyl)-thiazol-2-yl]-N′-pyridin-2-ylmethylene- chloro-acetic acid hydrazide. The calculated values are compared with the experimental data available for these molecules as a mean of validation of our proposed chemistry model. Aided by normal coordinate analysis and potential energy distributions, a confident vibrational assignment of all fundamentals is proposed herein. Additional support is given by 1H and 13C NMR spectra recorded with the sample dissolved in CDCl3 and by predicted chemical shifts at the B3LYP/6-31G(d)/6-311G+(d) levels obtained using the gauge-invariant atomic orbital method. The calculated HOMO and LUMO energies also confirm that the charge transfer occurs within the molecule. Thiazole-based compounds are potential storehouse for exploiting CH···O and CH···N hydrogen bonding interactions for molecular self-assembly.

The spectroscopic and quantum chemical studies of 3,4-difluoroaniline

Spectroscopic and structural investigations of 3,4-difluoroaniline molecule are presented by using experimental (FT-IR, FT-Raman, 1H and 13C NMR, and UV–Vis) techniques and theoretical (DFT approach) calculations. FT-IR and FT-Raman spectra of 3,4-difluoroaniline molecule are recorded in the region 4000–400cm−1 and 3500–10cm−1 in the liquid phase, respectively. The NMR chemical shifts (1H and 13C) are recorded in chloroform-d solution. The UV absorption spectra of 3,4-difluoroaniline dissolved in ethanol and water are recorded in the range of 200–400nm. Experimental results are supported with the following theoretical calculations; the optimized geometry and vibrational (FT-IR and FT-Raman) spectra are carried out by DFT (B3LYP)/6-311++G(d,p) basis set calculations. The nuclear magnetic resonance spectra (1H and 13C NMR) are obtained by using the gauge-invariant atomic orbital method. Moreover, electronic characteristics, such as HOMO and LUMO energies, density of state diagrams, and molecular electrostatic potential surface are investigated. Nonlinear optical properties and thermodynamic features are also outlined theoretically. An excellent correlation of theoretical and experimental results provides a detailed description of the structural and physicochemical properties of the molecule. Thus, this work leads to a deep understanding of the characteristics of di-substituted aniline derivatives.

Synthesis and DFT calculation of a novel 5,17-di(2-antracenylazo)-25,27-di(ethoxycarbonylmethoxy)-26,28-dihydroxycalix[4]arene

In this study, 5,17-di(2-antracenylazo)-25,27-di(ethoxycarbonylmethoxy)-26,28-dihydroxycalix[4]arene has been synthesized from 2-aminoantracene and 25,27-dihydroxy-26,28-diethylacetate calix[4]arene. In order to identify the molecular structure and vibrational features of the prepared azocalix[4]arene, FT-IR and 1H NMR spectral data have been used. FT-IR spectrum of the studied molecule is recorded in the region 4000–400cm−1. 1H NMR spectrum is recorded for 0.1–0.2M solutions in DMSO-d6 solution. The molecular geometry, infrared spectrum are calculated by the density functional method employing B3LYP level with different basis sets, including 6-31G(d) and LanL2DZ. The chemical shifts calculation for 1H NMR of the title molecule is calculated by using by Gauge-Invariant Atomic Orbital method by utilizing the same basis sets. The total density of state, the partial density of state and the overlap population density of state diagram analysis are done via GaussSum 3.0 program. Frontier molecular orbital (HOMO–LUMO) and molecular electrostatic potential surface on the title molecule are carried out for various intramolecular interactions that are responsible for the stabilization of the molecule. The experimental results and theoretical calculations have been compared, and they are found to be in good agreement.

Spectroscopic analysis and charge transfer interaction studies of 4-benzyloxy-2-nitroaniline insecticide: A density functional theoretical approach

A widespread exploration on the intra-molecular charge transfer interaction through an efficient π-conjugated path from a strong electron-donor group (amino) to a strong electron-acceptor group (nitro) has been carried out using FTIR, FT-Raman, UV–Vis, fluorescence and NMR spectra on insecticide compound 4-benzyloxy-2-nitroaniline. Density functional theory method is used to determine optimized molecular geometry, harmonic vibrational wavenumbers and intensities using 6-311G(d,p) basis set by means of Gaussian 09W program suit. A comprehensive investigation on the sp2 to sp3 hybridization and non-planarity property has been performed. Natural bond orbital analysis is used to study the existence of C–H⋯O, N–H⋯O and C–H⋯π proper and improper hydrogen bonds. The HOMO and LUMO analysis reveals the possibility of charge transfer within the molecule. A complete assignment of the experimental absorption peaks in the ultraviolet region has also been performed. Isotropic chemical shifts of 13C, 1H, 15N and 18O NMR and nuclear spin–spin coupling constants have been computed using the gauge-invariant atomic orbital method. The biological activity of substituent amino and nitro groups are evident from the hydrogen bonds through which the target amino acids are linked to the drug as evidenced from molecular docking.

Single crystal, spectral, computational studies and in vitro cytotoxicity of 2-chloro-3-formylpyrido[2,1-a]isoquinoline-1-carbonitrile derivative

In the present work, comprehensive theoretical and experimental structural studies on 2-chloro-3-formyl-9,10-dimethoxy-4-oxo-6,7-dihydro-4H-pyrido[2,1-a]isoquinoline-1-carbonitrile (PQC) have been performed using spectral methods and X-ray crystallography. PQC crystallizes in monoclinic crystal system of P21/c space group with a=23.5106 (6)Å, b=17.7940 (4)Å, c=7.2843 (2)Å and β=90.1421 (9)°. The unit-cell is built by two molecules of different conformations. The two molecules are not coplanar and they are linked to each other through double intermolecular hydrogen bonds of different strength. Optimized molecular structure and harmonic vibrational frequencies have been investigated at DFT/B3LYP and HF level of theory combined with 6-31G(d) basis set. Stability, arises from hyperconjugative interactions, charge delocalization and H-bond, has been analyzed using natural bond orbital (NBO) analysis. Electronic structures were discussed by time-dependent density functional theory. Descriptions of frontier molecular orbitals and the relocation of the electron density were determined. 1H NMR chemical shifts were computed by using Gauge-invariant atomic orbital method in both gas and DMSO media, using the polarizable continuum model. The cytotoxicity assay was performed against three-cell lines, breast cancer (MCF7), colon Carcinoma (HCT) and human heptacellular Carcinoma (HepG2).

Comparison of the computational NMR chemical shifts of choline with the experimental data

One of the main biological markers of the presence of cancer in living patients is an over-expression of total choline (tCho), which is the sum of free choline and its derivatives. 1H Magnetic Resonance Spectroscopy, or H-MRS, enables the quantification of tCho via its proton spectra, and thus has the potential to be a diagnostic tool for the presence of cancer and an accurate early indicator of the response of cancer to treatment. However, it remains difficult to quantify individual choline derivatives, since they share a large structural similarity ((CH3)3-N+-CH2-CH2-O-), of which the strongest signal detectable by MRS is that of the choline "head group": the three methyl groups bonded to the nitrogen. This work used ACENet, a high performance computing system, to attempt to model the NMR parameters of choline derivatives, with the focus of this report being free choline. Optimized structures were determined using Density Functional Theory and the B3LYP electron correlation functional. The Polarizable Continuum Model was used to evaluate solvent effects. The Gauge-Invariant Atomic Orbital method was found to be the superior method for calculating the NMR parameters of cholines.

INVESTIGATION INTO THE REGIOCHEMISTRY OF SOME PYRAZOLES DERIVED FROM 1, 3-DIPOLAR CYCLOADDITION OF ACRYLONITRILE WITH SOME NITRILIMINES: THEORETICAL AND EXPERIMENTAL STUDIES

dipolar cycloaddition between acrylonitrile and two N-(4-substituted)phenyl-C-(4-chlorophenyl)nitrilimines which were generated in situ afforded the new pyrazoles. The regiochemistry and reactivity of these reactions has been investigated on the basis of density functional theory (DFT) -based reactivity indexes and activation energy calculations. The theoretical 13C NMR chemical shifts of the cycloadducts which were obtained by GIAO method were comparable with the observed values. the Diels-Alder (DA) reactions and the 1,3-DCs has grown from a fruitful interplay between theory and experiment 2-4. Two major factors i.e. the steric and electronic effects can influence the regioselectivity of these reactions 2. Although transition state theory remains the most widely used and the most rigorous approach for the study of the mechanism and the regiochemistry of these reactions, the localization of transition states is not always easier. Furthermore, transition state calculations are often very time-consuming when bulky substituents are present in reactive systems. Recently, reactivity descriptors based on the density functional theory (DFT), such as Fukui indexes, local softnesses and local electrophilicity, have been extensively used for the prediction of the regioselectivity. For instance, several treatments of 1,3-DC reactions of nitrilimines with various dipolarophiles can be found in the literature 5-8. In this context, we became interested in the reactivity of acrylonitrile 3 as dipolarophile towards two N-(4-substituted)phenyl-C-(4- chlorophenyl)nitrilimines 2 as dipoles which were generated in situ by base treatment of the corresponding hydrazonoyl chlorides 1 in order to synthesize the new 3-(4-chlorophenyl)-1-(4-nitrophenyl)-4,5-dihydro-1H-pyrazole-4- carbonitrile 4a and 1-(4-bromophenyl)-3-(4-chlorophenyl)-4,5-dihydro-1H- pyrazole-5-carbonitrile 5b (Scheme1). In addition, we found it worthwhile to analyze the regioselectivity of these 1,3-DC reactions by several theoretical approaches, namely, activation energy calculations and DFT-based reactivity indexes. Finally, the gauge-invariant atomic orbital (GIAO) method 9 was used to calculate NMR chemical shifts, to help the experimental cycloadduct determination, because it has shown to yield data comparable to those of the experiment 10.

13C NMR Studies of Hydrocarbon Guests in Synthetic Structure H Gas Hydrates: Experiment and Computation

(13)C NMR chemical shifts were measured for pure (neat) liquids and synthetic binary hydrate samples (with methane help gas) for 2-methylbutane, 2,2-dimethylbutane, 2,3-dimethylbutane, 2-methylpentane, 3-methylpentane, methylcyclopentane, and methylcyclohexane and ternary structure H (sH) clathrate hydrates of n-pentane and n-hexane with methane and 2,2-dimethylbutane, all of which form sH hydrates. The (13)C chemical shifts of the guest atoms in the hydrate are different from those in the free form, with some carbon atoms shifting specifically upfield. Such changes can be attributed to conformational changes upon fitting the large guest molecules in hydrate cages and/or interactions between the guests and the water molecules of the hydrate cages. In addition, powder X-ray diffraction measurements revealed that for the hexagonal unit cell, the lattice parameter along the a-axis changes with guest hydrate former molecule size and shape (in the range of 0.1 Å) but a much smaller change in the c-axis (in the range of 0.01 Å) is observed. The (13)C NMR chemical shifts for the pure hydrocarbons and all conformers were calculated using the gauge invariant atomic orbital method at the MP2/6-311+G(2d,p) level of theory to quantify the variation of the chemical shifts with the dihedral angles of the guest molecules. Calculated and measured chemical shifts are compared to determine the relative contribution of changes in the conformation and guest-water interactions to the change in chemical shift of the guest upon clathrate hydrate formation. Understanding factors that affect experimental chemical shifts for the enclathrated hydrocarbons will help in assigning spectra for complex hydrates recovered from natural sites.

Hyperfine switching triggered by resonant tunneling for the detection of a single nuclear spin qubit

A novel detection mechanism and a robust control of a single nuclear spin-flip by hyperfine interactions between the nuclear spin and tunneling electron spin are proposed on the basis of ab initio non-equilibrium Green's function calculations. The calculated relaxation times of the nuclear spin of proton in a nano-contact system, Pd(electrode)–H 2–Pd(electrode), show that ON/OFF switching of hyperfine interactions is effectively triggered by resonant tunneling mediated through the d-orbitals of Pd. The relaxation times at ON-resonance are ∼ 10 3 times faster than those at OFF-resonance, indicating that ON-resonance is suitable for the detection (read-out) of nuclear spin states. In addition, the effectiveness of bias voltage applications at OFF-resonance for selective operations on the proton qubit is demonstrated in the calculations of the resonant frequencies of proton using the gauge-invariant atomic orbital method.

Hyperfine switching triggered by resonant tunneling for the detection of a single nuclear spin qubit

Abstract A novel detection mechanism and a robust control of a single nuclear spin-flip by hyperfine interactions between the nuclear spin and tunneling electron spin are proposed on the basis of ab initio non-equilibrium Green's function calculations. The calculated relaxation times of the nuclear spin of proton in a nano-contact system, Pd(electrode)–H2–Pd(electrode), show that ON/OFF switching of hyperfine interactions is effectively triggered by resonant tunneling mediated through the d-orbitals of Pd. The relaxation times at ON-resonance are ∼ 10 3 times faster than those at OFF-resonance, indicating that ON-resonance is suitable for the detection (read-out) of nuclear spin states. In addition, the effectiveness of bias voltage applications at OFF-resonance for selective operations on the proton qubit is demonstrated in the calculations of the resonant frequencies of proton using the gauge-invariant atomic orbital method.

NMR shielding constants for hydrogen guest molecules in structure II clathrates

Proton NMR shielding constants and chemical shifts for hydrogen guests in small and large cages of structure II clathrates are calculated using density-functional theory and the gauge-invariant atomic-orbital method. Shielding constants are calculated at the B3LYP level with the 6-311++G(d,p) basis set. The calculated chemical shifts are corrected with a linear regression to reproduce the experimental chemical shifts of a set of standard molecules. The calculated chemical shifts of single hydrogen molecules in the small and large structure II cages are 4.94 and 4.84 ppm, respectively, which show that within the error range of the method the H2 guest molecules in the small and large cages cannot be distinguished. Chemical shifts are also calculated for double occupancy of the hydrogen guests in small cages, and double, triple, and quadruple occupancy in large cages. Multiple occupancy changes the chemical shift of the hydrogen guests by approximately 0.2 ppm. The relative effects of other guest molecules and the cage on the chemical shift are studied for the cages with multiple occupancies.

A study of peculiar tautomerism of pyrido62,3-c961,2,69thiadiazine 2,2-dioxide system

A systematic study of the tautomerism of 4-amino-1 H -pyrido[2,3- c ][1,2,6]thiadiazine 2,2-dioxide has been carried out. Thus, the relativity stability of the possible tautomers has been studied in the gas phase by ab initio and functional density theory (DFT) methods. The theoretical study in solution has been carried out using several continuum solvation models as self consistent reaction field (SCRF) and the Poisson-Boltzmann method. In addition, complexes with one or two molecules of water have been calculated in order to consider explicit solute–solvent interactions. These results have been compared with UV spectrophotometry data, giving good agreement between theoretical and experimental results in aqueous solution. Finally, the gauge invariant atomic orbital method (GIAO) for calculating magnetic absolute shielding with both the ab initio method (RHF/6-31G*) and density functional theory (B3LYP/6-31G*) have been applied to explore this method to study the tautomeric equilibrium in the pyrido[2,3- c ][1,2,6]thiadiazine 2,2-dioxide system.

A study of peculiar tautomerism of pyrido[2,3- c][1,2,6]thiadiazine 2,2-dioxide system

A systematic study of the tautomerism of 4-amino-1 H-pyrido[2,3- c][1,2,6]thiadiazine 2,2-dioxide has been carried out. Thus, the relativity stability of the possible tautomers has been studied in the gas phase by ab initio and functional density theory (DFT) methods. The theoretical study in solution has been carried out using several continuum solvation models as self consistent reaction field (SCRF) and the Poisson-Boltzmann method. In addition, complexes with one or two molecules of water have been calculated in order to consider explicit solute–solvent interactions. These results have been compared with UV spectrophotometry data, giving good agreement between theoretical and experimental results in aqueous solution. Finally, the gauge invariant atomic orbital method (GIAO) for calculating magnetic absolute shielding with both the ab initio method (RHF/6-31G*) and density functional theory (B3LYP/6-31G*) have been applied to explore this method to study the tautomeric equilibrium in the pyrido[2,3- c][1,2,6]thiadiazine 2,2-dioxide system.

Epoxides, Cyclic Sulfites, and Sulfate from Natural Pentacyclic Triterpenoids: Theoretical Calculations and Chemical Transformations

Several triterpenic derivatives, with the A-ring functionalized, were semisynthesized from oleanolic and maslinic acids. The reactivities of sulfites, sulfate, and epoxides in these triterpene compounds were investigated under different reaction conditions. Moreover, contracted A-ring triterpenes (five-membered rings) were obtained, by different treatments of the sulfate 7. From the epoxide 8, deoxygenated and halohydrin derivatives were semisynthesized with several nucleophiles. Ozonolysis and Beckmann reactions were used to yield 4-aza compounds, from five-membered ring olanediene triterpenes. The X-ray structure of sulfate 7 is given and compared with density functional theory geometries. Theoretical (13)C and (1)H chemical shifts (gauge-invariant atomic orbital method at the B3LYP/6-31G*//B3LYP/6-31G* level) and (3)J(H,H) coupling constants were calculated for compounds 5-9 and 34-36, identifying the (R)- or (S)-sulfur and alpha- or beta-epoxide configurations together with 4-aza or 3-aza structures.

AB INITIO CLUSTER CALCULATIONS OF THE CHEMICAL SHIFT TENSOR ON THE 31P NUCLEI IN THE RING CRYSTAL PHOSPHATES

The non-empirical quantum chemical calculations of the chemical shift tensor are used to predict the NMR spectrum form and to interpret the NMR spectrum obtained earlier. The calculated chemical shift tensors on the 31P nuclei for some crystal phosphates are presented in the present work. All calculations are carried out by GIAO (Gauge-Invariant Atomic Orbital) method using cluster approach. As the clusters the isolated ring fragment of the corresponding crystal structures are chosen. Considering such approach, the agreement between calculations and experimental results is good.

Hydrogen Bond Types, Binding Energies, and 1H NMR Chemical Shifts

Ab initio calculations at the MBPT(2)/(qzp,qz2p) level of theory were carried out using the gauge-invariant atomic orbital method to evaluate 1H NMR chemical shifts for the hydrogen-bonded proton i...