Non-protein amino acids in peptide design

An overview of the use of non-protein amino acids in the design of conformationally well-defined peptides, based on work from the author’s laboratory, is discussed. The crystal structures of several designed oligopeptides illustrate the useα-aminoisobutyric acid (Aib) in the construction of helices, D-amino acids in the design of helix termination segments and^DPro-Xxx segments for nucleating ofβ-hairpin structures.β- andγ-amino acid residues have been used to expand the range of designed polypeptide structures. Dedicated to Professor C N R Rao on his 70th birthday     

Correction to: Elucidating the therapeutic activity of selective curcumin analogues: DFT-based reactivity analysis

Structural Chemistry - A Correction to this paper has been published: https://doi.org/10.1007/s11224-021-01788-w     

Elucidating the therapeutic activity of selective curcumin analogues: DFT-based reactivity analysis

Structural Chemistry - Density functional theory (DFT) has been employed to study the structure, stability and reactivity of curcumin and some of its important analogues by computing HOMO-LUMO...     

Environmental risk modelling under probability-normal interval-valued fuzzy number

In almost all the realistic circumstances, such as health risk assessment and uncertainty analysis of atmospheric dispersion, it is very essential to include all the information into modelling. The parameters associated to a particular model may include different kind of variability, imprecision and uncertainty. More often, it is seen that available informations are interpreted in probabilistic sense. Probability theory is a well-established theory to measure such kind of variability. However, not all of available information, data or model parameters affected by variability, imprecision and uncertainty can be handled by traditional probability theory. Uncertainty or imprecision may occur due to incomplete information or data, measurement errors or data obtained from expert judgement or subjective interpretation of available data or information. Thus, model parameters, data may be affected by subjective uncertainty. Traditional probability theory is inappropriate to represent them. Possibility theory and fuzzy set theory is another branch of mathematics which is used as a tool to describe the parameters with insufficient or vague knowledge. In this paper, an attempt has been made to combine probability knowledge and possibility knowledge and draw the uncertainty. The paper describes an algorithm for combining probability distribution and interval-valued fuzzy number and applied to environmental risk modelling with a case study. The primary aim of this paper is to propagate the proposed method. Computer codes are prepared for the proposed method using MATLAB.     

Pattern formation in dewetting poly(tert-butyl acrylate)/polyhedral oligomeric silsesquioxane (POSS) bilayer films

The surface morphology of dewetting poly(tert-butyl acrylate) (PtBA) and trisilanolphenyl-POSS (TPP) bilayers has been studied as a function of time at 95 degrees C. For short annealing times, only the upper nanoparticle (TPP) layer dewets from the underlying PtBA layer. The number and lateral dimensions of the holes in the upper TPP layer increase with increasing annealing times, forming interconnected rim structures. At later annealing times, scattered holes that reach down into the PtBA layer are observed among the interconnected rim structures. Fractal nanofiller (TPP)-rich aggregates are found at the bottom of the scattered holes.     

Host-guest supramolecular interactions in the coordination compounds of 4,4'-azobis(pyridine) with MnX2 (X = NCS–, NCNCN–, and PF6(–)): structural analyses and theoretical study

Three new Mn(II) coordination compounds {[Mn(NCNCN)(2)(azpy)]·0.5azpy}(n) (1), {[Mn(NCS)(2)(azpy)(CH(3)OH)(2)]·azpy}(n) (2), and [Mn(azpy)(2)(H(2)O)(4)][Mn(azpy)(H(2)O)(5)]·4PF(6)·H(2)O·5.5azpy (3) (where azpy = 4,4'-azobis(pyridine)) have been synthesized by self-assembly of the primary ligands, dicyanamide, thiocyanate, and hexafluorophosphate, respectively, together with azpy as the secondary spacer. All three complexes were characterized by elemental analyses, IR spectroscopy, thermal analyses, and single crystal X-ray crystallography. The structural analyses reveal that complex 1 forms a two-dimensional (2D) grid sheet motif. These sheets assemble to form a microporous framework that incorporates coordination-free azpy by host-guest π···π and C-H···N hydrogen bonding interactions. Complex 2 features azpy bridged one-dimensional (1D) chains of centrosymmetric [Mn(NCS)(2)(CH (3)OH)(2)] units which form a 2D porous sheet via a CH(3)···π supramolecular interaction. A guest azpy molecule is incorporated within the pores by strong H-bonding interactions. Complex 3 affords a 0-D motif with two monomeric Mn(II) units in the asymmetric unit. There exist π···π, anion···π, and strong hydrogen bonding interactions between the azpy, water, and the anions. Density functional theory (DFT) calculations, at the M06/6-31+G* level of theory, are used to characterize a great variety of interactions that explicitly show the importance of host-guest supramolecular interactions for the stabilization of coordination compounds and creation of the fascinating three-dimensional (3D) architecture of the title compounds.     

A computational approach to understanding the mechanism of aromatic bromination using quaternary ammonium tribromides

Quaternary ammonium tribromides (QATBs) have garnered interest for nearly a century now. Various types of tribromides have been synthesized over the years and their diverse applications have been extensively reported. However, despite the fact that these reagents are touted as safer alternatives to the very poisonous bromine, there is insufficient information on the structure of Br₃^? in QATB systems and there is still no clear explanation for how the tribromide ion (Br₃^?) participates in bromination reactions. This paper reports a through structural assessment of Br₃^?, followed by an attempt was made to fully understand the mechanistic behaviour of tribromide during bromination of aromatic compounds.     

Aggregation modes in sheets formed by protected beta-amino acids and beta-peptides

The crystal structures of four protected beta-amino acid residues, Boc-(S)-beta3-HAla-NHMe (1); Boc-(R)-beta3-HVal-NHMe (2); Boc-(S)-beta3-HPhe-NHMe (3); Boc-(S)-beta3-HPro-OH (6) and two beta-dipeptides, Boc-(R)-beta3-HVal-(R)-beta3-HVal-OMe (4); Boc-(R)-beta3-HVal-(S)-beta3-HVal-OMe (5) have been determined. Gauche conformations about the C(beta)-C(alpha) bonds (theta approximately +/-60 degrees) are observed for the beta3-HPhe residues in and all four beta3-HVal residues in the dipeptides and . Trans conformations (theta is approximately 180 degrees) are observed for beta3-HAla residues in both independent molecules in and for the beta3-HVal and beta3-HPro residues in and , respectively. In the cases of compounds , molecules associate in the crystals via intermolecular backbone hydrogen bonds leading to the formation of sheets. The polar strands formed by beta3-residues aggregate in both parallel (1,3,5) and antiparallel (2,4 fashion. Sheet formation accommodates both the trans and gauche conformations about the C(beta)-C(alpha) bonds.     

A New Family of Trinuclear Nickel(II) Complexes as Single‐Molecule Magnets

Three new trinuclear nickel (II) complexes with the general composition [Ni₃L₃(OH)(X)](ClO₄) have been prepared in which X=Cl^? ( 1 ), OCN^? ( 2 ), or N₃^? ( 3 ) and HL is the tridentate N,N,O donor Schiff base ligand 2‐[(3‐dimethylaminopropylimino)methyl]phenol. Single‐crystal structural analyses revealed that all three complexes have a similar Ni₃ core motif with three different types of bridging, namely phenoxido (μ₂ and μ₃), hydroxido (μ₃), and μ₂‐Cl ( 1 ), μ_1,1‐NCO ( 2 ), or μ_1,1‐N₃ ( 3 ). The nickel(II) ions adopt a compressed octahedron geometry. Single‐crystal magnetization measurements on complex 1 revealed that the pseudo‐three‐fold axis of Ni₃ corresponds to a magnetic easy axis, being consistent with the magnetic anisotropy expected from the coordination structure of each nickel ion. Temperature‐dependent magnetic measurements indicated ferromagnetic coupling leading to an S=3 ground state with 2J/k=17, 17, and 28 K for 1 , 2 , and 3 , respectively, with the nickel atoms in an approximate equilateral triangle. The high‐frequency EPR spectra in combination with spin Hamiltonian simulations that include zero‐field splitting parameters D_Ni/k=?5, ?4, and ?4 K for 1 , 2 , and 3 , respectively, reproduced the EPR spectra well after a anisotropic exchange term was introduced. Anisotropic exchange was identified as D_i,j/k=?0.9, ?0.8, and ?0.8 K for 1 , 2 , and 3 , respectively, whereas no evidence of single‐ion rhombic anisotropy was observed spectroscopically. Slow relaxation of the magnetization at low temperatures is evident from the frequency‐dependence of the out‐of‐phase ac susceptibilities. Pulsed‐field magnetization recorded at 0.5 K shows clear steps in the hysteresis loop at 0.5–1 T, which has been assigned to quantum tunneling, and is characteristic of single‐molecule magnets.