Gauge-including Atomic Orbitals Research Articles

Synthesis, crystal structure, Hirshfeld surface analysis, spectral characterization, and quantum computational evaluation of (E)-2-(((4-bromophenyl)imino)methyl)-6-methylphenol

A newly synthesized compound, (E)-2-(((4-bromophenyl)imino)methyl)-6-methylphenol (C14H12BrNO), is analyzed in detail for structural clarification by experimental X-ray, Fourier transform IR, 1H and 13C NMR, and UV–vis spectral data along with theoretical quantum chemical computations. For the theoretical computations, the density functional theory B3LYP functional and 6–311++G (d,p) basis set were used in the gas phase, and the harmonic vibrational wavenumbers were assigned with the help of the potential energy distribution. The theoretical NMR spectra were obtained with the gauge-including atomic orbital (GIAO) method and for the UV–vis spectrum time-dependent density functional theory based on the integral equation formalism polarizable continuum model (IEFPCM) was used. By Hirshfeld surface analysis, the most important contributions were obtained for the crystal packing, and the possible contact points were determined. In addition, frontier molecular orbital (highest occupied molecular orbital–lowest unoccupied molecular orbital), molecular electrostatic potential, and nonlinear optical analyses were performed for the calculated optimized structure. Finally, molecular docking between (E)-2-(((4-bromophenyl)imino)methyl)-6-methylphenol and two different receptors (ubiquinol-cytochrome c reductase [Protein Data Bank ID 1BE3] and glucan endo-1,6-β-glucosidase [Protein Data Bank ID 5NGL]) was studied. From the results, (E)-2-(((4-bromophenyl)imino)methyl)-6-methylphenol was determined to be a good ubiquinol-cytochrome c reductase inhibitor because of its binding energy and affinity for protein active sites.

The identification of alkaloids from the stems of Picrasma quassioides via computer-assisted structure elucidation and quantum chemical calculations

Four new alkaloids (1-4) and one known alkaloid were isolated from the stems of Picrasma quassioides. The structures of these isolated compounds were elucidated by spectroscopic analyses, a combination of computer-assisted structure elucidation software (ACD/Structure Elucidator) and gauge-including atomic orbital (GIAO) calculation of 1 D NMR data. All compounds were evaluated for their cytotoxic activities against hepatocellular carcinoma HepG2 and Hep3B cells. However, they did not show obvious inhibitory activities.

GIAO versus GIPAW: Comparison of Methods To Calculate 11B NMR Shifts of Icosahedral Closo-Heteroboranes toward Boron-Rich Borides.

In this work, we perform first-principle density functional theory calculations with the Perdew-Burke-Ernzerhof (PBE) exchange correlation functional to compare the results of the gauge-including atomic orbital (GIAO) method with the gauge-including projector-augmented wave (GIPAW) approach for isotropic 11B nuclear magnetic resonance shifts. GIPAW had been used successfully for the theoretical calculation of nuclear magnetic parameters of 11B species in strong ionic solid-phase compounds such as borates but had been applied very rarely to structures where boron is mainly involved in complex covalent bonding situations, for example, in icosahedra of boron-rich borides. Thus, we investigate the accuracy of both well-known methods and reliability of the effective treatment of core electrons on a test set containing 16 experimentally known closo-(hetero)dodecaboranes. In general, we find very good agreement between GIAO and GIPAW when compared to experimental observations. However, accidental degeneracies of the shift values are better predicted by GIPAW. The optimized molecular geometries on the PBE level agree well with gaseous electron diffraction data and lead to theoretical isotropic chemical 11B shifts with root-mean-square errors of 2.1 and 1.0 ppm depending on the used model of converting absolute shieldings to chemical shifts. The comparison with results from hybrid functionals (B3LYP, B3LYP-D2, and PBE0) shows a minor improvement in accuracy, which is in agreement with 13C shifts of sp3-hybridized species. In order to prove the reliability of the conversion parameters obtained by PBE, we report the calculated 11B shifts of 1,2-, 1,7-, and 1,12-PCB10H11 with GIAO and GIPAW to our knowledge for the first time. Additionally, Bader's analysis is carried out on the converged electron density for all boron species within the molecular test set, yielding no simple direct relation between charge and isotropic shifts.

An Efficient Coupled-Perturbed Kohn-Sham Implementation of NMR Chemical Shift Computations with Local Hybrid Functionals and Gauge-Including Atomic Orbitals.

Nuclear shielding calculations for local hybrid (LH) functionals with position-dependent exact-exchange admixtures within a coupled-perturbed Kohn-Sham (CPKS) framework have been implemented into the Turbomole code using efficient seminumerical integration techniques to deal with two-electron integrals. When using gauge-including atomic orbitals, LHs generate additional terms within the "pre-loop" section of the CPKS scheme compared to global hybrid (GH) functionals, related to perturbed electron-repulsion integrals. These terms have been implemented and tested in detail, together with dependencies on grid sizes and integral screening procedures. Even with relatively small grids, a seminumerical treatment of GHs reproduces analytical GH results with high accuracy while improving scaling with system and basis-set sizes significantly. The extra terms generated by LHs in the pre-loop part increase the scaling of that contribution slightly, but the advantages compared to the analytical scheme are largely retained, in particular for the typically large basis sets used in NMR shift calculations, allowing for a very efficient computational scheme. An initial comparison of four first-generation LHs based on LDA exchange for a shielding test set of 15 small main-group molecules against high-level CCSD(T) benchmark data indicates a substantial reduction of the systematically underestimated shieldings compared to semilocal functionals or GHs for non-hydrogen nuclei when a so-called t-LMF is used to control the position dependence of the exact-exchange admixture. In contrast, proton shieldings are underestimated with this LMF, while an LH with a so-called s-LMF performs much better. These results are discussed in the context of experience for other properties, and they suggest directions for further improvements of LHs regarding nuclear shieldings.

Calculation of the EPR g-tensor from auxiliary density functional theory.

The working equations for the calculation of the electron paramagnetic resonance (EPR) g-tensor within the framework of the auxiliary density functional theory (ADFT) are presented. The scheme known as gauge including atomic orbitals (GIAOs) is employed to treat the gauge origin problem. This ADFT-GIAO formulation possesses an inherent high computational performance, allowing for the calculation of the EPR g-tensor of molecules containing some hundreds of atoms in reasonable computational time employing moderate computational resources. The effect of the use of a gauge independent auxiliary density on the quality of the g-tensor calculation for the evaluation of the exchange-correlation contribution is analyzed in this work. The best agreement with the experiment is obtained with the BLYP functional (Becke 1988 exchange and Lee-Yang-Parr correlation) in combination with a double-ζ basis set, in particular aug-cc-pVDZ. Furthermore, models of endohedral fullerenes N@Cn, with n = {60, 70, 100, 180, 240}, were used for benchmarking its computational performance.

Reduced graphene oxide contains a minimum of six oxygen atoms for higher dipolar strength: A DFT study

The present work focused on the reduced graphene oxide contains a minimum of six oxygen atoms for the higher dipolar strength. The ionization potential and electron affinity decreased only for the six oxygen atoms based graphene. The six oxygen atoms based graphene have the highest dipole moment. The reduced graphene has 0.25 eV bandgap, which is very suitable for electron transfer. The six oxygen atoms based graphene leads to the least gauge including atomic orbital (GIAO) rotational tensor; however, it has the highest isotropic polarizability difference, diamagnetic susceptibility tensor difference, paramagnetic susceptibility tensor difference, and total susceptibility. The C-C bond length has increased only for the six oxygen atoms based graphene.

Synthesis, Spectroscopic Properties, Quantum Chemical Calculations, and Biological Activities of 2-{[5-(2-Fluorophenyl)-4-(4-methylphenyl)-4H-1,2,4-triazol-3-yl]sulfanyl}-1-[3-methyl-3-(2,4,6-trimethylphenyl)-cyclobutyl]ethan-1-one

2-{[5-(2-Fluorophenyl)-4-(4-methylphenyl)-4H-1,2,4-triazol-3-yl]sulfanyl}-1-[3-methyl-3-(2,4,6-trimethylphenyl)cyclobutyl]ethanone was synthesized and characterized by spectral techniques and quantum chemical calculations. The molecular geometry, vibrational frequencies, and gauge-including atomic orbital (GIAO) 1H and 13C NMR chemical shifts of the title compound in the ground state were calculated using the density functional method (B3LYP) with the 6–311G(d, p) basis set, and its electronic absorption spectra were calculated by the TD-DFT method based on the B3LYP/6-311G(d, p) level optimized structure in ethanol by using the PCM model. The calculated results showed that the optimized geometry well reproduces the theoretical vibrational frequencies, and the calculated chemical shifts were in a good agreement with the experimental values. The energetic behavior of the title compound was examined using the B3LYP method with the 6-311G(d, p) basis set in the framework of the Onsager and polarizable continuum model (PCM). In addition, DFT calculations of frontier molecular orbitals were carried out at the B3LYP/6-311G(d, p) level of theory. The title compound showed antibacterial and antioxidant activities at different levels.

Synthesis, Structural Characterization, Spectroscopic Properties, and Theoretical Investigation of Siderol Acetate

In the present study, siderol acetate (1) was synthesized from siderol isolated from endemic Sideritis species, then its chemical structure was determined by using various spectroscopic methods (FT-IR, 1H NMR, and 13C NMR). The geometrical parameters, vibrational frequencies and gauge including atomic orbital (GIAO) 1H and 13C NMR chemical shift values for siderol acetate in the ground state have been calculated using the Density Functional Theory (DFT) and Hartree–Fock (HF) methods with the 6-31G(d) basis set. The calculated vibrational frequencies and 1H and 13C NMR chemical shifts have been compared with experimental values. A combined study based on NMR data and quantum-mechanical calculations using DFT/GIAO indicate that 1 is the correct structure of the title molecule.

Interactions in inclusion complex of β-cyclodextrin/l-Metheonine: DFT computational studies

In the present work, the host–guest complexation between l-Metheonine/β-Cyclodextrin was investigated using the DFT/B97-D3/6-31G (d) level of the theory. The results obtained clearly indicate that the Orientation B (the carboxylic group of l-Metheonine points toward the primary hydroxyl of β-CD) is energetically favored than that one of the Orientation A (the carboxylic group of l-Metheonine points toward the secondary hydroxyl of β-CD). The energy decomposition analysis, thermodynamic parameters, HOMO, LUMO, the global reactivity descriptors and non covalent interactions-reduced density gradient analysis of the two complexes were calculated and interpreted. The QAIM theory has been used to examine the properties of the bond critical points. Finally, the 1H nuclear magnetic resonance (NMR) chemical shift of the complexes was studied using the Gauge-Including Atomic Orbital (GIAO) method and compared with experimental values. The structures of inclusion complexes of l-Metheonine@β-CD.

On the magnetic properties of nanodiamonds: Electronic g-tensor calculations.

The electronic g-tensor calculations are carried out for various paramagnetic defects introduced into hydrogenated diamond nanocrystal C35H36, showing that such a system can be successfully used to model magnetic properties of nanodiamonds (NDs) with paramagnetic centers containing no vacancies. In addition, it is revealed that, depending on the geometric positions in ND, paramagnetic centers of the same type produce noticeable variations of the g-tensor values. A side-by-side comparison of the performance of effective nuclear charge and spin-orbit mean field (SOMF) approaches indicates that the latter is more sensitive to the quality of basis sets, especially concerning diffuse functions, the inclusion of which is found to be nonbeneficial. What is more, the SOMF method also exhibits a much more pronounced gauge-origin dependence. Compared to electronic charge centroid, spin centers (SCs) demonstrate a superior suitability as gauge origins, providing a better agreement with diamagnetic and paramagnetic contributions of g-tensor obtained employing gauge-including atomic orbitals (GIAOs). Therefore, SCs can be recommended for the g-tensor calculations of NDs whenever GIAOs are not available.

Chemical constituents of the root bark of Ulmus davidiana var. japonica and their potential biological activities

The root bark of Ulmus davidiana var. japonica (Ulmaceae), commonly known as yugeunpi, has been used as a traditional Korean medicine for the treatment of gastroenteric and inflammatory disorders. As part of continuing projects to discover bioactive natural products from traditional medicinal plants with pharmacological potential, phytochemical investigation of the root bark of this plant was carried out. This led to the successful isolation of a new chromane derivative (1) and 22 known compounds: catechin derivatives (2–5), megastigmane glycoside (6), dihydrochalcone glycosides (7 and 8), flavanone glycosides (9 and 10), coumarins (11 and 12), lignan derivatives (13–17), and phenolic compounds (18–23). The structure of the new compound (1) was determined with 1D and 2D NMR spectroscopy and HR-ESIMS, and its absolute configurations were achieved by chemical reactions and the gauge-including atomic orbital (GIAO) NMR chemical shifts calculations. All the isolated compounds were evaluated for their potential biological activities including neuro-protective, anti-neuroinflammatory, and anti-Helicobacter pylori activities. Among the isolates, compounds 1, 8, and 20 displayed stronger potency by causing a greater increase in the production and the activity of nerve growth factor (NGF) in C6 glioma cells (147.04 ± 4.87, 206.27 ± 6.70, and 143.70 ± 0.88%, respectively), whereas compounds 11, 14, and 19 inhibited nitric oxide (NO) production in lipopolysaccharide (LPS)-stimulated murine microglial cells (IC50 of 18.72, 12.31, and, 21.40 µM, respectively). In addition, compounds 1, 11, 18, and 20 showed anti-H. pylori activity with MIC values of 25 or 50 µM against two strains of H. pylori 51 and 43504. These findings provide scientific evidence that supports the traditional usage of U. davidiana var. japonica root bark in the treatment of gastroenteric and inflammatory disorders.

Structural, spectroscopic, Hirshfeld surface and charge distribution analysis of 3-(1H-imidazole-1-yl)-1-phenylpropan-1-ol complemented by molecular docking predictions: An integrated experimental and computational approach

The optimized structure of title compound 3-(1H-imidazole-1-yl)-1-phenylpropan-1-ol (3HIP) was predicted according to the density functional theory (DFT) using the B3LYP method with 6-311G (d,p) basis set. Computed structural parameters of 3HIP were compared with X-ray diffraction data. Recorded and computed wavenumbers were assigned according to the total energy distribution (TED) using VEDA software. The natural bond orbital (NBO) analysis was used to characterize intramolecular rehybridization and delocalization of the electron density within the title molecule. Predictions of the NMR (1H and 13C) chemical shift assignments obtained by applying the gauge including atomic orbital (GIAO) approach were consistent with the corresponding experimental values. Ultraviolet-visible spectra of the title compound were simulated and validated experimentally. A molecular electrostatic potential (MEP) diagram visualized the electrophilic and nucleophilic sites of the 3HIP molecule. Hirshfeld surface analysis assessed the potential interactions of each atom inside the 3HIP molecule. Moreover, molecular docking analysis simulated the potential binding site pose of 3HIP within the active site of its target protein. The resulting 3HIP–target protein model can provide guidance for the development of new potent antifungal treatments.

Synthesis, characterization and structural computational investigation of novel Zn(II) phthalocyanines containing peripheral anthracene moieties

New zinc(II) phthalocyanines (ZnPc-I and ZnPc-II) containing four peripheral anthracene pendant groups were synthesized by cyclotetramerization of (E)-4-(3-(4-((anthracen-9-yl-methylene)amino)phenoxy)propoxy)phthalonitrile and 4-(3-(4-((anthracen-9-ylmethyl)amino)phenoxy)propoxy)phthalonitrile. All compounds were characterized using a combination of analytical and spectroscopic techniques such 1H, [Formula: see text]C NMR, FT-IR, UV-vis and MS spectral data. The molecular geometry and gauge including atomic orbital (GIAO) 1H and [Formula: see text]C chemical shift values of the compounds in the ground state have also been calculated using B3LYP with the 6–31G([Formula: see text] basis set. The chemical shift of the optimized molecular structure is compared with the experimental chemical shift values.

Structural and spectroscopic characterization and DFT studies of 2-amino-1,10-phenanthrolin-1-ium chloride

A versatile synthetic building block, 2-amino-1,10-phenanthrolin-1-ium chloride (L∙HCl) was synthesized and characterized by IR, 1H and 13C NMR DEPT analysis, UV/Vis and single-crystal X-ray diffraction technique. The molecular geometry, vibrational wavenumbers and gauge including atomic orbital (GIAO), 1H and 13C NMR chemical shifts values of the title compound in the ground state were obtained by using density functional theory (DFT/B3LYP) method with 6-311++G(d,p) basis set and compared with the experimental data. Electronic absorption spectrum of the salt was determined using the time-dependent density functional theory (TD-DFT) method at the same level. In the NMR and electronic absorption spectra calculations, the effect of solvent on the theoretical parameters was included using the default model with DMSO as solvent. The obtained theoretical parameters agree well with the experimental findings.

Density Functional Theory and Single Crystal X-ray Studies on Some Bis-Chalcone Derivatives

The three bis-chalcone compounds, (2E,6E)-2,6-bis(3-chlorobenzylidene)cyclohexanone (1), (2E,6E)-2,6-bis(2,3-dichlorobenzylidene)cyclohexanone (2) and (2E,5E)-2,5-bis(2,6-dichloro benzylidene) cyclopentanone (3), were studied with theoretical and single-crystal X-ray diffraction (XRD) methods. The molecular geometric parameters, frontier molecular orbitals, MEP, normal mode frequencies and the corresponding vibrational assignments, gauge-including atomic orbital (GIAO) 1H-NMR, 13C-NMR chemical shift values of the bis-chalcone compounds in the ground state have been calculated using the density functional (B3LYP) methods with 6-311G (d,p) basis set. These molecules demonstrate apparently a long and flat shape. Each molecule adopt an (E) configuration about the central olefinic bonds. The most important feature is stacking mode in the molecules. The calculated results reveal that the optimized geometries can well reproduce the crystal structure. The theoretical vibrational frequencies and 1H-NMR and 13C-NMR chemical shift values show good agreement with the experimental data.

Cholesterol thiosalicylate, a novel cholesterol conjugate its synthesis experimental studies conformational analysis chemical reactivity intermolecular interaction and first order hyperpolarizability

In the present work 10,13-dimethyl-17-(6-methylheptan-2-yl)-tetradecahydro-1H-cyclopentaphenanthren-3-yl-2-mercaptobenzoate (2) was synthesized from Cholesterol (1), isolated as a major component from chloroform extract of Allamandaviolacea.The synthesized compound (2) has been characterized with the help of 1H, 13C, UV, FT-IR spectroscopy. The molecular geometry of synthesized compound was calculated by Density functional theory (DFT) with B3LYP functional and 631G (d,p) basis set in ground state.1H and 13C NMR chemical shifts were calculated in ground state by using Gauge-Including Atomic Orbital (GIAO) approach and these values were correlated with experimental observations. The electronic properties such as HOMO and LUMO energies were calculated using time dependentDensity Functional Theory (TD-DFT). The strength and intra molecular interactions were analyzed by AIM (Atom in molecule) approaches. Global reactivity descriptors were calculated to study the reactive sites within molecule. The vibrational wavenumbers were calculated using DFT method and assigned with the help of potential energy distribution (PED). Dipole moment, polarizability and first hyperpolarizability values have been determined to explain the nonlinear optical (NLO) property of the synthesized compounds. Molecular electrostatic potential (MEP) and conformational analysis has also been performed. The local reactivity descriptors Fukui functions (fk+, fk–), local softness's (sk+, sk–) and electrophilicity indices (ωk+, ωk–) determined the reactive sites within molecule

Transition-Dipole Moments for Electronic Excitations in Strong Magnetic Fields Using Equation-of-Motion and Linear Response Coupled-Cluster Theory.

An implementation of transition-dipole moments at the equation-of-motion coupled-cluster singles-doubles (EOM-CCSD) and CCSD linear response (LR) levels of theory for the treatment of atoms and molecules in strong magnetic fields is presented. The presence of a finite magnetic field leads, in general, to a complex wave function and a gauge-origin dependence, necessitating a complex computer code together with the use of gauge-including atomic orbitals. As in the field-free case, for EOM-CC, the evaluation of transition-dipole moments consists of setting up the one-electron transition-density matrix (TDM) which is then contracted with dipole-moment integrals. In the case of CC-LR, the evaluation proceeds with a modified TDM but additionally requires a second contribution accounting for the amplitude response which is missing in EOM-CC theory for properties. We present a selected set of transitions for the sodium atom and investigate the LiH molecule in both a parallel as well as a perpendicular magnetic field. The dependence of excited-state energies and transition moments on the magnetic-field strength is discussed with a focus on magnetic-field-induced avoided crossings. Additionally, the differences between field-dependent EOM-CCSD and CCSD-LR transition moments are investigated.

An Example of Polynomial Expansion: The Reaction of 3(5)-Methyl-1H-Pyrazole with Chloroform and Characterization of the Four Isomers.

The reaction in phase-transfer catalyzed conditions of 3(5)-methyl-1H-pyrazole with chloroform affords four isomers 333, 335, 355 and 555 in proportions corresponding to the polynomial expansion (a + b)3, with a = 0.6 and b = 0.4, a and b being 3-methyl and 5-methyl proportions. The up (u) and down (d) conformation of the pyrazolyl rings with regard to the Csp3–H atom was established by X-ray crystallography and by 1H-, 13C- and 15N-NMR in solution combined with gauge-including atomic orbitals (GIAO)/B3LYP/6-311++G(d,p) calculations. A comparison with other X-ray structures of tris-pyrazolylmethanes was carried out.

Linear and sublinear scaling computation of the electronic g-tensor at the density functional theory level.

We present an efficient and low-scaling implementation of a density functional theory based method for the computation of electronic g-tensors. It allows for an accurate description of spin-orbit coupling effects by employing the spin-orbit mean-field operator. Gauge-origin independence is ensured by the use of gauge-including atomic orbitals. Asymptotically linear scaling with molecule size is achieved with an atomic orbital based formulation, integral screening methods, and sparse linear algebra. In addition, we introduce an ansatz that exploits the locality of the contributions to the g-tensor for molecules with local spin density. For such systems, sublinear scaling is obtained by restricting the magnetic field perturbation to the relevant subspaces of the full atomic orbital space; several criteria for selecting these subspaces are discussed and compared. It is shown that the computational cost of g-tensor calculations with the local approach can fall below the cost of the self-consistent field calculation for large molecules. The presented methods thus enable efficient, accurate, and gauge-origin independent computations of electronic g-tensors of large molecular systems.

Density functional theories study of the interactions between host β-Cyclodextrin and guest 8-Anilinonaphthalene-1-sulfonate: Molecular structure, HOMO, LUMO, NBO, QTAIM and NMR analyses

In the present work, a quantum chemical calculation of energies, geometric parameters, frontier molecular orbitals, thermodynamic parameters, for inclusion complex of host β-Cyclodextrin and guest 8-Anilinonaphthalene-1-sulfonate (1,8-ANS@β-CD) have been investigated using the following functionals, B3LYP, M06-2X and WB97X-D with the split valence double zeta 6-31G(d) basis set in both gas and aqueous phases. The results indicate that the orientation in which the guest molecule points toward the primary hydroxyls of the hydrophobic cavity of β-CD is energetically preferred and exhibited a good agreement with the experimental results. NBO and QTAIM analysis are carried out in order to understand various second-order interactions between the filled orbital of one subsystem and vacant orbital of another subsystem. The 1H nuclear magnetic resonance (NMR) chemical shift of the complexes was studied using the Gauge-Including Atomic Orbital (GIAO) method and compared with experimental values.