Effect of an aliphatic spacer group on the adsorption mechanism on the colloidal silver surface of L‐proline phosphonodipeptides

A comparative study of molecular structures of five L ‐proline (L ‐Pro) phosphonodipeptides: L ‐Pro‐NH‐C(Me,Me)‐PO₃H₂ (P1), L ‐Pro‐NH‐C(Me,iPr)‐PO₃H₂ (P2), L ‐Pro‐L ‐NH‐CH(iBu)‐PO₃H₂ (P3), L ‐Pro‐L ‐NH‐CH(PA)‐PO₃H₂ (P4) and L ‐Pro‐L ‐NH‐CH(BA)‐PO₃H₂ (P5) has been carried out using Raman and absorption infrared techniques of molecular spectroscopy. The interpretation of the obtained spectra has been supported by density functional theory calculations (DFT) at the B3LYP; 6–31 + + G** level using Gaussian 2003 software. The surface‐enhanced Raman scattering (SERS) on Ag‐sol in aqueous solutions of these phosphonopeptides has also been investigated. The surface geometry of these molecules on a silver colloidal surface has been determined by observing the position and relative intensity changes of the Pro ring, amide, phosphonate and so‐called spacer (−R) groups vibrations of the enhanced bands in their SERS spectra. Results show that P4 and P5 adsorb onto the silver as anionic molecules mainly via the amide bond (∼1630, ∼1533, ∼1248, ∼800 and ∼565 cm⁻¹), Pro ring (∼956, ∼907 and ∼876 cm⁻¹) and carboxylate group (∼1395 and ∼909 cm⁻¹). Coadsorption of the imine nitrogen atom and PO group with the silver surface, possibly by formation of a weaker interaction with the metal, is also suggested by the enhancement of the bands at 1158 and 1248 cm⁻¹. P1, P2 and P3 show two orientations of their main chain on the silver surface resulting from different interactions of the  C CH₃,  NH and  CONH fragments with this surface. Bonding to the Ag surface occurs mainly through the imino atom (1166 cm⁻¹) for P2, while for P1 and P3 it occurs via the methyl group(s) (1194–1208 cm⁻¹). The amide group functionality (CONH) is practically not involved in the adsorption process for P1 and P2, whereas the C_s P bonds do assist in the adsorption. Copyright © 2008 John Wiley & Sons, Ltd.     

Density functional study of structural and electronic properties of Al<Subscript><Emphasis Type="Italic">n</Emphasis></Subscript>P (2 ≤ <Emphasis Type="Italic">n</Emphasis> ≤ 12) clusters

Low-lying equilibrium geometric structures of Phosphorus-doped aluminum cluster Al _n P (n = 2–12) clusters obtained by an all-electron linear combination of atomic orbital approach, within spin-polarized density functional theory, are reported. The binding energy, dissociation energy, and stability of these clusters are studied within the local spin density approximation (LSDA) and the three-parameter hybrid generalized gradient approximation (GGA) due to Becke-Lee-Yang-Parr (B3LYP). Ionization potentials, electron affinities, hardness, and static polarizabilities are calculated for the ground-state structures within the GGA. It is observed that symmetric structures with the P atom occupying a peripheral position are lowest-energy geometries of Al _n P (n = 2, 4–11), while the P impurities of Al₃P and Al₁₂P prefer to occupy internal sites in the aluminum clusters. Generalized gradient approximation extends bond lengths as compared to the LSDA lengths. The odd-even oscillations in the dissociation energy, the second differences in energy, the HOMO–LUMO gaps, the ionization potential, the electron affinity, and the hardness are more pronounced within both GGA and LSDA. The stability analysis based on the energies clearly shows the clusters with an even number of valence electrons are more stable than clusters with odd number of valence electrons.     

C, N CPMAS NMR and GIAO DFT calculations of stereoisomeric oxindole alkaloids from Cat's Claw (Uncaria tomentosa)

Oxindole alkaloids, isolated from the bark of Uncaria tomentosa [Willd. ex Schult.] Rubiaceae, are considered to be responsible for the biological activity of this herb. Five pentacyclic and two tetracyclic alkaloids were studied by solid-state NMR and theoretical GIAO DFT methods. The ¹³C and ¹⁵N CPMAS NMR spectra were recorded for mitraphylline, isomitraphylline, pteropodine (uncarine C), isopteropodine (uncarine E), speciophylline (uncarine D), rhynchophylline and isorhynchophylline. Theoretical GIAO DFT calculations of shielding constants provide arguments for identification of asymmetric centers and proper assignment of NMR spectra. These alkaloids are 7R/7S and 20R/20S stereoisomeric pairs. Based on the ¹³C CP MAS chemical shifts the 7S alkaloids (δ C3 70–71 ppm) can be easily and conveniently distinguished from 7R (δC3 74.5–74.9 ppm), also 20R (δC20 41.3–41.7 ppm) from the 20S (δC20 36.3–38.3 ppm). The epiallo-type isomer (3R, 20S) of speciophylline is characterized by a larger ¹⁵N MAS chemical shift of N4 (64.6 ppm) than the allo-type (3S, 20S) of isopteropodine (δN4 53.3 ppm). ¹⁵N MAS chemical shifts of N1–H in pentacyclic alkaloids are within 131.9–140.4 ppm.     

Hydration of copper(II) amino acids complexes

Hydration of the copper(II) bis‐complexes with glycine, serine, lysine, and aspartic acid was studied by DFT and MD simulation methods. The distances between copper(II) and water molecules in the 1st and 2nd coordination shells, the average number of water molecules and their mean residence times in the hydration shells were calculated. Good agreement was observed between the values obtained and those found by DFT and NMR relaxation methods. Influence of the functional groups of the ligands and the cis–trans isomerism of the complexes on the structural and dynamical parameters of the hydration shells was displayed and explained. Analysis of the MD trajectories reveals the competition for a copper(II) axial position between water molecules or water molecules and the functional chain groups of the ligands and confirms the suggestion on the pentacoordination of copper(II) in such complexes. MD simulations show that only one axial position of Cu(II) is basically occupied at each time step while in average the coordination number more than 5 is observed. © 2017 Wiley Periodicals, Inc.     

Macrocyclic Cr3+, Mn2+ and Fe3+ complexes of a mimic SOD moiety: Design,structural aspects,DFT, XRD,optical properties and biological activity

A novel SOD-like macrocycle “H₂DPD” and its trivalent chromium, iron and divalent manganese complexes have been isolated and characterized using the conventional tools. The macrocycle was prepared by 2:2 condensation of P-phenylenediamine with 5,5-dimethyl1,3-cyclohexanedione. IR and electronic spectral data suggested that H₂DPD coordinates to the metal ion as N₄ tetradentate donor with two Cl⁻ occupying the remaining two sites of the distorted octahedron. XRD spectrum of Cr³⁺ complex indicated that the complex crystallizes in a face-centered monoclinic structure with lattice parameters: a = 10.9380 Å; b = 12.4870 Å; c = 12.4600 Å, α = γ = 90° and β = 111.430 with space group P 1 21/c 1 (14). The energy gap (E_HOMO-E_LUMO), molecular electrostatic potential map (EPM) of title compounds, bond length, bond angle, as well as global and local reactivity were estimated using DFT method. The E_g values obtained from electronic spectra of Cr³⁺, Mn²⁺ and Fe³⁺ complexes were found to be 1.284, 1.220 and 1.138 eV, respectively which are in accordance with those evaluated by DFT revealing semiconductor nature. Also, the thermal degradation of all title compounds was carried out and the kinetic parameters were evaluated using Coats-Redfern and Horowitz-Metzger equations. Moreover, the compounds have screened for antibacterial as well as superoxide mimic activities. Cr³⁺ complex exhibited the most significant potent activity against all bacterial strains. With respect to SOD-like activity, the macrocycle showed the most remarkable SOD-like activity comparable to the standard drug, ascorbic acid.     

Synthesis,structural, spectroscopic,and thermal studies of some transition-metal complexes of a ligand containing the amino mercapto triazole moiety

A new series of transition-metal complexes of Schiff base ligand containing the amino mercapto triazole moiety ( HL ) was prepared. The Schiff base and its metal complexes were elucidated by different spectroscopic techniques (infrared [IR], ¹H nuclear magnetic resonance, UV–Visible, mass, and electron spin resonance [ESR]), and magnetic moment and thermal studies. Quantum chemical calculations have been carried out to study the structure of the ligand and some of its complexes. The IR spectra showed that the ligand is chelated with the metal ion in a neutral, tridentate, and bidentate manner using NOS and NO donors in complexes 1 – 6 , 10–12 , and 7 and 8 , respectively, whereas it behaves in a monobasic tridentate fashion using NOS donor sites in copper(II) nitrate complex ( 9 ). The magnetic moment and electronic spectra data revealed octahedral and square pyramidal geometries for complexes 2 , 11 , 12 , and 5 – 8 and 10 , respectively. However, the other complexes were found to have tetrahedral ( 4 ), trigonal bipyramidal ( 1 and 3 ), and square planar ( 9 ) structures. Thermal studies revealed that the chelates with different crystallized solvents undergo different types of interactions and the decomposition pathway ended with the formation of metal oxygen (MO) and metal sulfur (MS) as final products. The ESR spectrum of copper(II) complex 10 is axial in nature with hyperfine splitting with ²B_1g as a ground state. By contrast, complexes 7 and 8 undergo distortion around the Cu(II) center, affording rhombic ESR spectra. The HL ligand and some of its complexes were screened against two bacterial species. Data showed that complex 12 demonstrated a better antibacterial activity than HL ligand and other chelates.     

Interaction of moderately reactive molecules with organic superhalogens: a theoretical perspective

The interaction of four moderately reactive molecules (MRMs), benzene (BZ), water, ammonia and silicon dioxide, with three aromatic organic superhalogens (OSHs) has been investigated at the density functional theory (DFT) level. The strength of the interaction is analysed from the distortions in the structures of both the MRMs and OSHs after complexation and the calculated binding energy (BE) values between the two interacting moieties. The interaction becomes stronger as we move from BZ to H₂O to NH₃ and strongest for SiO₂ molecule. Contributions from different terms in total interaction energy have been examined by energy decomposition analysis (EDA). The charge flow values between MRMs and OSHs, and Mulliken spin density localised on the moderately reactive molecules have been evaluated to ensure whether the interaction is ionic or not. Atoms in Molecules (AIM) analysis has been performed to characterise the bonds formed between the two. Overall, our study gives a comprehensive account of the interaction between the moderately reactive molecules and three theoretically designed aromatic organic superhalogens, which will further motivate researchers in the field of superhalogen chemistry.