Gauge-including Atomic Orbital Approach Research Articles

11B NMR Chemical Shift Predictions via Density Functional Theory and Gauge-Including Atomic Orbital Approach: Applications to Structural Elucidations of Boron-Containing Molecules.

11B nuclear magnetic resonance (NMR) spectroscopy is a useful tool for studies of boron-containing compounds in terms of structural analysis and reaction kinetics monitoring. A computational protocol, which is aimed at an accurate prediction of 11B NMR chemical shifts via linear regression, was proposed based on the density functional theory and the gauge-including atomic orbital approach. Similar to the procedure used for carbon, hydrogen, and nitrogen chemical shift predictions, a database of boron-containing molecules was first compiled. Scaling factors for the linear regression between calculated isotropic shielding constants and experimental chemical shifts were then fitted using eight different levels of theory with both the solvation model based on density and conductor-like polarizable continuum model solvent models. The best method with the two solvent models yields a root-mean-square deviation of about 3.40 and 3.37 ppm, respectively. To explore the capabilities and potential limitations of the developed protocols, classical boron–hydrogen compounds and molecules with representative boron bonding environments were chosen as test cases, and the consistency between experimental values and theoretical predictions was demonstrated.

Isolation and identification of two novel compounds from Marsdenia roylei and their quantum chemical calculations

Two new compounds 1 (Methyl 26-di-deoxy-6-methyl-β-D-allohexopyranoside) and 3 (3, 11, 12, 20 tetra-O-acetyl-pregn-5-ene-14β-ol) have been isolated from the chloroform-soluble extract of the whole plant of Marsdenia roylei (family: Asclepiadaceae) and their structures were determined by 1D, 2D NMR and ESI–MS as well as by chemical modification. We have calculated the molecular geometries, local reactivity descriptors by the density functional theory with B3LYP functional with basis set 6-311G+(d,2p) of 1, 3 and 4 (deacylated 3). The 1H and 13C NMR chemical shifts of 1, 3 and 4 were calculated using Gauge-Including Atomic Orbital approach and these values are correlated with the experimental observations.

Theoretical calculations, cytotoxic evaluation, and molecular docking studies of 4-(1-adamantyl)-5-[2-(3-hydroxynapthyl)]-2H-1,2,4-triazole-3(4H)-thione as a novel chemotherapeutic agent

In this work, we report combined experimental and theoretical studies on molecular structure, vibrational spectra, and NBO analysis of 4-(1-adamantyl)-5-[2-(3-hydroxynapthyl)]-2H-1,2,4-triazole-3(4H)-thione. The density functional theoretical computations were performed at B3LYP/6-311G+(d,p) levels to derive the optimized geometry, vibrational wavenumbers with FT-IR intensity, HOMO–LUMO energies, and several thermodynamic properties in ground state. 1H-NMR chemical shifts were also studied using gauge-including atomic orbital approach, which were found in good agreement with the experimental values. The delocalization of electron density various constituents of the molecule has been discussed with the aid of natural bond orbital analysis and the calculated HOMO–LUMO energies show that the charge transfer occurs within the molecule. Finally, the title compound was also evaluated for its in vitro anticancer activity against MCF-7 cancer line and inhibition activity of new 1,2,4-triazole with the protein BRCA2, is simulated by using AutoDock Vina software. Docking of synthesized compound against BRCA2, forget enzyme for MCF-7 cancer cell agent was achieved to explore the interactions of discovered hits within the amino acid residues of enzyme binding pocket.

Synthesis and DFT studies of structural and some spectral parameters of nickel(II) complex with 2-(2-hydroxybenzoyl)-N-(1-adamantyl) hydrazine carbothioamide

An efficient synthesis of the novel 2-(2-hydroxybenzoyl)-N-(1-adamantyl) hydrazine carbothioamide and its Ni(II) complex are described. Quantum chemical calculations including molecular geometry and vibrational frequencies were carried out for the structures to explain stability and geometry using both density functional (DFT/B3LYP) with 6-311+G(d,p) and LANL2DZ basis sets. 1H-NMR chemical shifts were also studied using a gauge-including atomic orbital approach (GIAO), and were found to be in good agreement with the experimental values. The Mulliken charges and HOMO–LUMO orbital energies were calculated and analyzed. The calculated HOMO–LUMO energies show that the charge transfer occurs within the molecule. The maximum positive atomic charge was obtained for C11 and the presence of a large negative charge on O (46) and O (45) for the ligand suggested the bonding of the Ni(II) ion with oxygen atoms. The chemical structures of the compounds were established by elemental analysis, FT-IR, 1H-NMR, 13C-NMR, UV–Vis spectra, magnetic moments, and thermal analyses. The electronic spectra and magnetic measurement studies revealed that the structure of complex is octahedral. Additionally, the cytotoxic effects of the obtained ligand and its complex were determined by using PC3 prostate cancer cell cultures. The results indicated that the ligand showed distinctly better activity than the complex.

Elucidation of Structural Restraints for Phosphate Residues with Different Hydrogen Bonding and Ionization States

Solid state NMR spectroscopy and gauge including atomic orbital (GIAO) theoretical calculations were employed to establish structural restraints (ionization, hydrogen bonding, spatial arrangement) for O-phosphorylated l-threonine derivatives in different ionization states and hydrogen bonding strengths. These structural restraints are invaluable in molecular modeling and docking procedures for biological species containing phosphoryl groups. Both the experimental and the GIAO approach show that 31P delta ii chemical shift tensor parameters are very sensitive to the ionization state. The negative values found for the skew kappa are typical for -2 phosphates. The distinct span Omega values reflect the change of strength of hydrogen bonding. For species in the -1 ionization state, engaged in very strong hydrogen bonds, Omega is smaller than for a phosphate group involved in weak hydrogen bonding. For phosphates in the -2 ionization state, Omega is significantly smaller compared to -1 species, although the kappa for -1 samples never reaches negative values. For -1 phosphate residues, in the case when 1H one pulse and/or combined rotation and multiple pulse spectroscopy (CRAMPS) sequences fail and assignment of proton chemical shift is ambiguous, a combination of 1H-(13)C and 1H-(31)P 2D heteronuclear correlation (HETCOR) correlations is found to be an excellent tool for the elucidation of 1H isotropic chemical shifts. In addition, a 2D strategy using 1H-(1)H double quantum filter (DQF) correlations [a back-to-back (BABA) sequence in this work] is useful for analyzing the topology of hydrogen bonding. In the case of a multicenter phosphorus domain, 2D 31P-(31)P proton driven spin diffusion experiments give information about the spatial arrangement of the phosphate residues.

Temperature Dependence of 1H and 17O NMR Shifts of Water: Entropy Effect

Density functional theory together with statistical thermodynamics based on the equilibrium constants method and concept of orientational entropy were applied to reproduce the temperature dependences of 1H and 17O nuclear magnetic resonance (NMR) chemical shifts in liquid water. Despite a rather simple theoretical model, a satisfactory agreement between calculated NMR quantities and corresponding experimental data was found. By using only a single adjustable parameter of arbitrary directionality, we succeeded to imitate the first-order temperature effect for both (1H and 17O) NMR signals in the neat water. 1H and 17O magnetic shielding tensors of water molecules in various water clusters have been calculated using the density functional theory. The full geometry optimization was performed using Becke's three-parameter hybrid method and the Lee–Yang–Parr correlation functional (B3LYP) combined with 6-311++G** basis set. Magnetic shielding tensors have been calculated using the modified hybrid functional of Perdew, Burke and Ernzerhof, and the gauge-including atomic orbital approach was applied to ensure gauge invariance of the results. Solvent effects were taken into account by the polarized continuum model.

Determination of the Orientation and Dynamics of Ergosterol in Model Membranes Using Uniform 13C Labeling and Dynamically Averaged 13C Chemical Shift Anisotropies as Experimental Restraints

A new strategy was established to determine the average orientation and dynamics of ergosterol in dimyristoylphosphatidylcholine model membranes. It is based on the analysis of chemical shift anisotropies (CSAs) averaged by the molecular dynamics. Static 13C CSA tensors were computed by quantum chemistry, using the gauge-including atomic-orbital approach within Hartree-Fock theory. Uniformly 13C-labeled ergosterol was purified from Pichia pastoris cells grown on labeled methanol. After reconstitution into dimyristoylphosphatidylcholine lipids, the complete 1H and 13C assignment of ergosterol’s resonances was performed using a combination of magic-angle spinning two-dimensional experiments. Dynamically averaged CSAs were determined by standard side-band intensity analysis for isolated 13C resonances (C 3 and ethylenic carbons) and by off-magic-angle spinning experiments for other carbons. A set of 18 constraints was thus obtained, from which the sterol’s molecular order parameter and average orientation could be precisely defined. The validity of using computed CSAs in this strategy was verified on cholesterol model systems. This new method allowed us to quantify ergosterol’s dynamics at three molar ratios: 16 mol % (Ld phase), 30 mol % (Lo phase), and 23 mol % (mixed phases). Contrary to cholesterol, ergosterol’s molecular diffusion axis makes an important angle (14°) with the inertial axis of the rigid four-ring system.

Nuclear magnetic shielding constants in the CC2 model

Test calculations of nuclear magnetic shielding constants in the CC2 model are performed using the gauge-including atomic orbital approach. Absolute shielding constants are reported for reprsentative first-row hydrides, a few multiply bonded molecules and some challenging cases. The performance of CC2 is analyzed by comparison with experimental data and results from calculations employing more sophisticated treatments of electron correlation. In most cases, CC2 shieldings and chemical shifts are close to those obtained at second-order perturbation theory, despite the fact that the CC2 model includes an approximate treatment of orbital relaxation effects at the correlated level.

GIAO-MBPT(3) and GIAO-SDQ-MBPT(4) calculations of nuclear magnetic shielding constants

The gauge-including atomic orbital approach for the calculation of NMR chemical shifts has been implemented at third- and fourth-order many-body perturbation theory with the latter restricted to single, double, and quadruple excitations. Results obtained for HF, H 2O, NH 3, CH 4, CO, N 2, HCN, and F 2 suggest that higher-order effects in the perturbative treatment of electron correlation are important for the accurate theoretical prediction of nuclear magnetic shielding constants.

Functional counterpoise corections for the NMR chemical shift in a model dimeric water system

Perturbed Hartree-Fock calculations in the gauge including atomic orbital approach (GIAO) with the 6-311G (d, p) basis have been carried out on a model dimeric water system to assess the importance of functional counterpoise corrections to the theoretically calculated chemical shift and shift anisotropy changes upon association. The basis set superposition error (bsse) found for the shift properties is found to be theoretically significant in this system for only the anisotropies of the oxygen and hydrogen atoms of those water molecules acting as proton acceptors, a result that can be understood in terms of the effect on the water lone pair orbitals by the donor water ghost orbitals. The results suggest that counterpoise corrections may be necessary when treating hydrogen bonded species with medium size basis sets.