The components of the radial correlation energy density are calculated and analyzed for the atoms from He to Ar. The components include the nucleus-electron potential correlation energy density, the kinetic correlation energy density and the electron-electron potential correlation energy density. The necessary correlated one and two-electron density matrices are obtained from the Extrapolated-Full-Configuration-Interaction (exFCI) wave function where the reference wave function is restricted Hartree-Fock (RHF) or restricted open-shell Hartree-Fock (ROHF) depending on whether the atom is closed or open-shell. The accuracy associated with integrating the HF and exFCI energy density components, and the correlation energy density components, is evaluated on the SG-1 and SG-2 atomic grids. The SG-1 grid provides atomic energies that are accurate to about 1 kJ mol-1, with the exception of the kinetic energy. The SG-2 grid is required for the analysis of atomic kinetic energies and more subtle energetic effects. There is also a significant amount of integration error cancellation in the correlation energy densities. The radial correlation energy densities display notable shell structure, and there is a substantial difference between the alpha and beta-electron correlation energy densities for the open-shell atoms.

Molecular dynamics (MD) simulation was used to study the interactions of two immune proteins of HLA-Cw4-beta 2m-KIR2DL1 complex with small peptide QYDDAVYKL (nine amino acids) in an aqueous solution. This study aims to gain detailed information about the conformational changes and the dynamics of the complex. The parameters and force field for performing the MD simulations needed to calibrate the complex structure were examined and identified. The non-bonded interactions (electrostatic and van der Waals contributions), H-bond formation, and salt bridges between the ligand HLA-Cw4 and the receptor KIR2DL1, were estimated using the obtained MD simulation. The surface area buried due to binding was calculated to get insight into the causes of the specificity of the receptor to the ligand and to explain the mutations experiment. The study concluded that beta 2-microglobulin, one part of the complex, is not directly interacting with the peptide at the groove; therefore, it could be neglected from simulation. Our results showed that beta 2-microglobulin does not have any significant effect on the dynamics of the 3D-structure of the complex. This project will help optimize candidate drug design, a small peptide that disrupts the interaction, for the optimal biological effect.

The current world's life-threatening illnesses have amplified multidrug resistance infections, bringing about immune system mayhem, thus, the quest for novel antimicrobial compounds with a broad spectrum of action. Four Ni(II) complexes, [Ni(YB)Cl]& sdot;2H2O (C1), [Ni(YB)Br]& sdot;H2O (C2), [Ni(YB)NO3]& sdot;3H2O (C3), [Ni(YB)COOCH3]& sdot; 2H2O (C4) [HYB = 4-[(1E)-N-{2-[(Z)-(4-methoxybenzylidene)amino]ethyl}ethanimidoyl]benzene-1,3-diol], were synthesized. Analytical techniques like CHNS analysis, UV-Vis, FT-IR, molar conductance, XRD, 1H NMR, and TGA/DTA were utilized for characterization. The calculated EHOMO - ELUMO energy gap and global reactivity descriptors of the compounds were performed by DFT calculations. The energy gap (Delta E) = EHOMO - EHOMO for the studied compounds HYB, C3, C4, C1, and C2 were found to be 1.736, 1.243, 1.221 1.217, and 1.193 eV respectively. The chelated complexes exhibited higher DPPH radical scavenging power than the corresponding free HYB ligand. Amongst the complexes, C2 displayed the highest scavenging ability (IC50 = 2.59 +/- 1.21 mu M). Antimicrobial activities of the synthesized compounds were validated against bacterial strains: gram (+) E. faecalis and S. aureus; gram (-) P. aeruginosa and K. pneumoniae; and fungi: C. neoformans and C. albicans. C2 exhibited the most inhibition (MIC = 390.6 mu g/mL) against P. aeruginosa and E. faecalis, while C1 acted as the most effective compound (MIC = 48.83 mu g/mL) against the fungi strains. The docking study illustrated the highest binding affinity of -7.30 kcal/mol by C2 with P. aeruginosa (PDB: 8BN6), and C1 for the C. neoformans with -6.04 kcal/mol (PDB ID: 7T08) binding sites. Potential binding modes around the receptor's active sites were predicted by the in silico molecular docking studies.

At the nanoscale level, several biological processes take place, owing to the potential that engineered nanomaterials might interrelate with bio-molecules and cellular procedures. This study aimed to synthesize cadmium oxide nanoparticles via a one-step calcination process of tetradentate Schiff base-Cd(II) complex at different temperature ranges. The as-synthesized compounds were carried out via a viz UV–visible, elemental analysis, 1H NMR, molar conductivity, transmission electron microscopy (TEM), FT-IR spectroscopy, and X-ray diffraction (PXRD). The band gap energy and average particle sizes of the CdO particles are respectively (2.69 eV, 3.54 eV), 26.88 nm for CdO@250, and (3.20 eV, 3.57 eV), 25.67 nm for CdO@300, while CdO@350 exhibited the 3.78 eV and 28.42 nm values. The antioxidant accomplishments of the test samples through the scavenging activity of DPPH radicals showed CdO@300 to possess (IC50 = 5.18 ± 0.56 µg/mL). Similarly, the as-synthesized CdO nanoparticles exhibited higher antibacterial activities against S. aureus and E. coli as compared to the corresponding Cd-HMB and ligand (HMB), while ciprofloxacin acted as a standard antibiotic. Furthermore, HMB and its complex Cd-HMB were docked against the DNA gyrase enzymes of S. aureus (PDB IDs: 5CDQ) and E. coli (PDB IDs: 6F86) as receptors. The binding sites docking results showed that the binding energies of HMB and Cd-HMB to 5CDQ ranged from − 3.44 to − 4.99 kcal/mol and from − 6.45 to − 6.64 kcal/mol, while the binding energies related to the target 6F86 are in the ranges of (− 3.64, − 4.76) kcal/mol and (− 6.08, − 6.09) kcal/mol respectively. Therefore, the significant antioxidant and antibacterial activities of the ligand (HMB), Cd-HMB, and CdO NPs review the broad application prospects of these compounds as therapeutic agents for wide-ranging biomedical applications.

In this study, trivalent metal complexes of the category: [M(L)(H 2 O) n Cl y ] obtained from the interaction of metal 3 + ion salts with organic N, N, O -Schiff base ( HL ) (where: HL = 4-{( Z )-((2-{( E )-((2-hydroxyphenyl)meth- ylidene)amino}ethyl)imino)methyl}-2-methoxyphenol; n, y = 1 or 2 and M = Ti(III), Fe(III), Ru(III), Cr(III) and Al(III)) were synthesized and characterized viz molar conductance, FT-IR, and UV - Vis spectroscopies, elemental analyses, thermal analyses (TGA and DTA), and UV - Vis spectroscopy, theoretical calculations. A distorted octahedral structure around the metal ions was proposed based on the obtained experimental and calculated data. Thermal examination of the complexes signposts the step-by-step disintegration to give the final decomposition product as metal oxides. Moreover, DFT calculations were executed utilizing the B3LYP/LANL2DZ theory level, which revealed that the synthesized metal (III) complexes were more stable than the free ligand ( HL ). The value of Delta E for HL is 4.60 eV while the related values for the complexes of Cr(III) ( C1 ), Ru(III) ( C2 ), Fe (III) ( C3 ), Al(III) ( C4 ), and Ti(III) ( C5 ) are respectively 2.59, 3.68, 3.15, 1.64, and 2.75 eV. Scavenging abilities of DPPH and ABTS radicals by the test compounds revealed promising antioxidant behavior. It was observed that the compounds are proficient DPPH radical scavengers in a dose-dependent configuration. Ru(III); IC 50 = 1.69 +/- 2.68 mu M for DPPH and Ti(III); IC 50 = 8.70 +/- 2.78 mu M for ABTS performed best. Similarly, the complexes demonstrated higher antimicrobial activities compared to HL against the designated strains, while ciprofloxacin acted as a standard antibiotic. Furthermore, the ligand and its most effective complexes C2 and C5 were docked against the targets S. aureus DNA gyrase ( 2XCT ), S. pneumoniae DNA gyrase ( 5BOD ), and E . coli DNA gyrase ( 5L3J ). The binding sites were evaluated and the docking results showed that the studied molecules bind to the targets through classical O - H ... O and/or N - H ... O hydrogen bonds, as well as via hydrophobic contacts.

A boronic acid catalyzed carbon–carbon and carbon–nitrogen bond-forming reaction for the functionalization of various π-activated alcohols has been developed. Ferrocenium boronic acid hexafluoroantimonate salt was identified as an effective catalyst in the direct deoxygenative coupling of alcohols with a variety of potassium trifluoroborate and organosilane nucleophiles. In a comparison between these two classes of nucleophiles, the use of organosilanes leads to higher reaction yields, increased diversity of the alcohol substrate scope, and high E/Z selectivity. Furthermore, the reaction proceeds under mild conditions and yields up to 98%. Computational studies provide a rationalization for a mechanistic pathway for the retention of E/Z stereochemistry when E or Z alkenyl silanes are used as nucleophiles. This methodology is complementary to existing methodologies for deoxygenative coupling reactions involving organosilanes, and it is effective with a variety of organosilane nucleophile sub-types, including allylic, vinylic, and propargylic trimethylsilanes.

The Δ natural orbital (ΔNO) two-electron density matrix (2-RDM) and energy expression are derived from a multideterminantal wave function. The approximate ΔNO 2-RDM is combined with an on-top density functional and a double-counting correction to capture electron correlation. A trust-region Newton's method optimization algorithm for the simultaneous optimization of ΔNO orbitals and occupancies is introduced and compared to the previous iterative diagonalization algorithm. The combination of ΔNO and two different on-top density functionals, Colle-Salvetti (CS) and Opposite-spin exponential cusp and Fermi-hole correction (OF), is assessed on small hydrogen clusters and compared to density functional, single-reference coupled-cluster, and multireference perturbation theory (MRMP2) methods. The ΔNO-CS and ΔNO-OF methods outperform the single-reference methods and are comparable to MRMP2. However, there is a distinct qualitative error in the ΔNO potential energy surface for H4 compared to the exact. This discrepancy is explained through analysis of the ΔNO orbitals, occupancies, and the two-electron density.

The solid-state structure of the new compound μ-oxido-bis[dichloridotris(tetrahydrofuran-κO)titanium(III)], [Ti2Cl4O(C4H8O)6], at 150 K has been determined. The crystal has monoclinic (C2/c) symmetry and the complex features C2 symmetry about the bridging O atom. Positional disorder is evident in one of the three tetrahydrofuran environments. A post-Hartree-Fock computational analysis indicates that the complex has nearly degenerate triplet and singlet spin states, with the former favoured slightly by ca 2 kJ mol-1.

Three new measures of relative electron motion are introduced: equimomentum, antimomentum, and momentum-balance. The equimomentum is the probability that two electrons have the exact same momentum, whereas the antimomentum is the probability that their momenta are the exact opposite. Momentum-balance (MB) is the difference between the equimomentum and antimomentum and, therefore, indicates if equal or opposite momentum is more probable in a system of electrons. The equimomentum, antimomentum, and MB densities are also introduced, which are the local contribution to each quantity. The MB and MB density of the extrapolated-full configuration interaction wave functions of atoms of the first three rows of the periodic table are analyzed, with a particular focus on contrasting the correlated motion of electrons with opposite-spin and parallel-spin. Coulomb correlation between opposite-spin electrons leads to a higher probability of equimomentum, whereas Fermi correlation between parallel-spin electrons leads to a higher probability of antimomentum. The local contribution to MB, given an electron is present, is a minimum at the nucleus and generally increases as the distance from the nucleus increases. There are also interesting similarities between the effects of Fermi correlation and Coulomb correlation (of opposite-spin electrons) on MB.

Molecular dynamics (MD) simulation was used to study the interactions of two immune proteins of HLA-Cw4-β2m-KIR2DL1 complex with small peptide QYDDAVYKL (nine amino acids) in an aqueous solution. This study aims to gain a detailed information about the conformational changes and the dynamics of the complex. The right parameters and force field for performing the MD simulations that was needed to calibrate the complex structure were determined. The non-bonded interactions (Electrostatic and van der Waals contributions), H-bond formation, and salt bridges between the ligand HLA-Cw4 and the receptor KIR2DL1 were estimated using the obtained MD trajectories. The buried surface area due to binding was calculated to get insight into the causes of specificity of receptor to ligand and explains mutations experiment. The study concluded that β2-microglobulin, one part of the complex, is not directly interacting with the peptide at the groove; therefore, it could be neglected from simulation. Our results showed that β2-microglobulin does not have any significant effect on the dynamics of the 3D-structure of the complex. This project will help in understanding to optimize candidate drug design, a small peptide that disrupts the interaction, for the optimal biological effect.

The NO method for static correlation is combined with second-order Mller-Plesset perturbation theory (MP2) and coupled-cluster singles and doubles (CCSD) to account for dynamic correlation. The MP2 and CCSD expressions are adapted from nite-temperature CCSD, which includes orbital occupancies and vacancies, and expanded orbital summations. Correlation is partitioned with the aid of damping factors incorporated into the MP2 and CCSD residual equations. Potential energy curves for a selection of diatomics are in good agreement with extrapolated full conguration interaction results (exFCI), and on par with conventional multireference approaches.

The reaction of the anti-Criegee intermediate (anti-CI) of β-pinene with prevalent atmospheric species has been investigated using quantum-chemical calculations. The calculations predict that the ozone addition to CI occurs with a Gibbs energy of activation (ΔG‡) of 77 kJ mol−1. The CI reaction with CH4, C2H6, NH3, and chlorinated ethanes is not energetically favored and has high barriers in the range of 253 to 362 kJ mol−1. The more probable reaction with SO2 forms a secondary ozonide (SOZ) intermediate with a barrier of 9 kJ mol−1, while the ΔG‡ to dissociation is 101 kJ mol−1. Among the reactions studied, the one with $$ \dot{\mathrm{N}} $$ O had the lowest ΔG‡ for its rate-determining step. The ΔG‡ values of the first step addition of O3, NH3, SO2, and $$ \dot{\mathrm{N}} $$ O do not exceed 84 kJ mol−1. In contrast to previous predictions, the $$ \dot{\mathrm{N}} $$ O reaction with the CI did not proceed through cyclic adduct formation. The findings agree with previous studies which found that CIs act as oxidizing agents, converting SO2 to SO3, and $$ \dot{\mathrm{N}} $$ O to $$ \dot{\mathrm{N}} $$ O2. Thus, the CIs of biogenic compounds should be added to the list of atmospheric oxidizing agents along with O3, NO3, and OH radicals.

The ozonolysis of sabinene has been computationally studied at multiple levels of theory. The reaction proceeds through the so-called Criegee mechanism via the formation of a primary ozonide with two different conformations that dissociate into non-interconvertible zwitterionic Criegee intermediate (syn and anti) conformers and a carbonyl compound. The results show that the decomposition of the Criegee intermediate proceeds through different dissociation pathways. Possible pathways involve the formation of a vinyl hydroperoxide or a dioxirane ester. An alternative novel pathway that does not involve Criegee intermediate formation, but rather epoxide formation, is also investigated. The dissociation of the anti-Criegee intermediate to sabina ketone and OH radicals via the vinyl hydroperoxide pathway is more favorable than the analogous syn-Criegee intermediate dissociation. The calculations show that, between the two competing channels (the ester and vinyl hydroperoxide pathways), the ester pathway is more probable, particularly from the syn-Criegee intermediate. Furthermore, the reactions have been studied in the presence of H2O as a spectator molecule. Interestingly, it had a negligible effect on the energy barrier of the syn-ozone addition as it stabilized all the stationary points. All reactions were found to be strongly exothermic, except in the case of the dissociation of the syn-Criegee intermediate through the vinyl hydroperoxide pathway, where the reaction is endothermic.

The bimolecular reactions of methyl vinyl ketone oxide (MVK-OO) with H2O, H2S, NH3, their dimer forms, and CH3NH2, have been studied. The reactions of (H2O)(2) and (NH3)(2) exhibit an effect of reducing the free energies of activation (Delta G double dagger); a catalytic behavior. The former energy barriers decrease by 20 kJ mol(-1) while the latter by 14 kJ mol(-1). In contrast, additional molecules in H2S reactions increase the calculated Delta G double dagger values by 22 kJ mol(-1). The calculations of MVK-OO + CH3NH2 predict Delta G double dagger = 26 kJ mol(-1), lower than the catalyzed reactions of H2O, H2S, and NH3. Additional molecules in CH3NH2 reactions lead to negligible effects on the energy, except for the (CH3NH2 center dot center dot center dot H2O) reaction, where Delta G double dagger is reduced by 10 kJ mol(-1). The formation of a carbonyl hydroperoxide (via MVK-OO + HCO2H) is predicted to be the least favorable pathway with Delta G double dagger values in the range of 61-69 kJ mol(-1).

A computational study of the formation of secondary ozonide (SOZ) from the Criegee intermediates (CIs) of sabinene, including hydration reactions with H2O and 2H2O, was performed. All of the geometries were optimized at the B3LYP and M06-2X with several basis sets. Further single-point energy calculation at the CCSD(T) was performed. Two major pathways of SOZ formation suggest that it is mainly formed from the sabinene CI and formaldehyde rather than sabina ketone and formaldehyde-oxide. However, in both pathways, the activation energies are within a range of ±5 kJ mol-1. Furthermore, the hydration reactions of the anti-CI with H2O and 2H2O showed that the role of the second water molecule is a mediator (catalyst) in this reaction. The dimer hydration reaction has lower activation energies than the monomer by 60 and 69 kJ mol-1, at the M06-2X/6-31G(d) and CCSD(T)+CF levels of the theory, respectively. A novel water-mediated vinyl hydroperoxide (VHP) channel from both the monomer and dimer has been investigated. The results indicate that the direct nonmediated VHP formation and dissociation is interestingly more possible than the water-mediated VHP. The density functional theory calculations show that the monomer is faster than the dimer by roughly 22 kJ mol-1. Further, the infrared spectrum of sabina ketone was calculated at B3LYP/6-311+G(2d,p); the calculated carbonyl stretching of 1727 cm-1 is in agreement with the experimental range of 1700-1800 cm-1.

Separate, one-parameter, on-top density functionals are derived for the short-range dynamic correlation between opposite and parallel-spin electrons, in which the electron-electron cusp is represented by an exponential function. The combination of both functionals is referred to as the Opposite-spin exponential-cusp and Fermi-hole correction (OF) functional. The two parameters of the OF functional are set by fitting the ionization energies and electron affinities, of the atoms He to Ar, predicted by ROHF in combination with the OF functional to the experimental values. For ionization energies, the overall performance of ROHF-OF is better than completely renormalized coupled-cluster [CR-CC(2,3)] and better than, or as good as, conventional density functional methods. For electron affinities, the overall performance of ROHF-OF is less impressive. However, for both ionization energies and electron affinities of third row atoms, the mean absolute error of ROHF-OF is only 3 kJ mol-1.

The relative momentum of electron pairs in atoms and small molecules is examined through calculation of the p1 · p2 probability distribution. The likelihood of aligned or antialigned momenta between paired electrons is determined from the calculated distributions. Coulomb correlation aligns the momenta of electron pairs, and the amount of alignment varies when considering momenta in specific directions in three-dimensional space. A static electric field is found to have competing effects on momentum alignment parallel and perpendicular to the electric field. However, the net effect of the electric field on alignment is significantly smaller than the effect of Coulomb correlation. Recent experimental advances suggest that such a correlation of electron momenta can now be measured directly using attosecond spectroscopic tools.

Magnetic monopoles are hypothesised elementary particles connected by Dirac strings that behave like infinitely thin solenoids (Dirac 1931 Proc. R. Soc. A 133 60). Despite decades of searching, free magnetic monopoles and their Dirac strings have eluded experimental detection, although there is substantial evidence for deconfined magnetic monopole quasiparticles in spin ice materials (Castelnovo et al 2008 Nature 326 411). Here we report the detection of a hierarchy of unequally-spaced magnetic excitations via high resolution inelastic neutron spectroscopic measurements on the quantum spin ice candidate [Formula: see text] [Formula: see text] [Formula: see text]. These excitations are well-described by a simple model of monopole pairs bound by a linear potential (Coldea et al Science 327 177) with an effective tension of 0.642(8) K [Formula: see text] at 1.65 K. The success of the linear potential model suggests that these low energy magnetic excitations are direct spectroscopic evidence for the confinement of magnetic monopole quasiparticles in the quantum spin ice candidate [Formula: see text] [Formula: see text] [Formula: see text].