Atom Of Amino Group Research Articles

Density Functional Theory Computation and Machine Learning Studies of Interaction between Au3 Clusters and 20 Natural Amino Acid Molecules.

The optimal adsorption sites and the binding energies of neutral Au3 clusters with 20 natural amino acids under the gas phase and water solvation were systematically investigated based on density functional theory (DFT) calculations. The calculation results showed that in the gas phase Au3 tends to bind with N atoms of amino groups in amino acids, except methionine, which tends to bind with Au3 through S atoms. Under water solvation, Au3 clusters tended to bind to N atoms of amino groups and N atoms of side chain amino groups in amino acids. However, methionine and cysteine bind more strongly to the gold atom through the S atom. Based on the binding energy data of Au3 clusters and 20 natural amino acids under water solvation calculated by DFT, a machine learning model (gradient boosted decision tree) was proposed to predict the optimal binding Gibbs free energy (ΔG) of the interaction between Au3 clusters and amino acids. The main factors affecting the strength of the interaction between Au3 and amino acids were uncovered by the feature importance analysis.

Synthesis, characterization, thermal studies, electrochemical behavior, antimicrobial, docking studies, and computational simulation of triazole‐thiol metal complexes

AbstractIn this study, we elucidate the structure and molecular properties of triazole‐thiol derivative (HL) which is confirmed via B3LYP/6‐31G(d) for DFT and HF basis set. Triazole‐thiol (HL) was conjugated with several metal ions to afford stable metal complexes. Consequently, confirmed via intensive physicochemical analysis including FT‐IR spectra, elemental analysis, electronic, 1H‐NMR, TGA, and DTA. The explanation of the thermal cracking of these metal complexes has been estimated. The FT‐IR of these complexes indicated the presence of triazole‐thiol ligand (HL) as chelated coordinated through the N atom of amino group and S atom of SH moiety. Furthermore, Fe(III) complex and Ni(II) adopt octahedral stereochemistry, while the Cu(II) complex is trigonal bipyramidal, and Cd(II) complex is square planar. Thermal investigation maintained the chemical formulation of these metal complexes and exhibited that they decompose in many stages dependent on the kind of ligand and geometry of complexes. Moreover, the HL and metal complexes were exhibited antimicrobial evaluation against bacterial and fungal strains and showed higher activity comparable HL. Additionally, the theoretical docking stimulation of the ligand HL and metal complexes with different proteins showed different in energy affinity with shortage bond length with metal complexes and confirmed the experimental biological results. Eventually, the electrochemical features were explored utilizing cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS).

In English

The structure and energy characteristics of structures formed during arginine adsorption on silica surface from aqueous solution were studied by the density functional theory (B3LYP) method using a valence-split basis set 6-31++G(d,p) within the continuous solvent model (PCM) and supermolecular approximation. The equilibrium structural and energy parameters of the protonated arginine molecule in the gas phase dependent on the location of the hydrogen atom are considered including those of two possible zwitterions. The structure of the arginine ion Н2А+, which is formed when a proton attaches to a molecule or zwitterion of a given amino acid, has been elucidated. To determine the deprotonation constant of the carboxyl group in an acidic medium, the complexes of the arginine molecule (AH32+) in the state with undissociated and deprotonated carboxyl groups are considered. The simulation of the acid medium was performed by taking into account the interaction with two hydrated HCl ion pairs, which provided the protonation of the a-amino group and the nitrogen atom of amino group within the guanidine group. In the study on the interaction of an arginine molecule with silica surface in an aqueous medium, complexes containing a Si8O12(OH)7O– ion with a deprotonated silanol group, six water molecules, and an arginine molecule with a deprotonated carboxyl group were considered. It has been found that the arginine molecule is most likely to be adsorbed on slica surface with formation of hydrogen bonds between the hydrogen atoms of the a-amino group and the oxygen atom of the deprotonated silanol group. In this case, the formation of a hydrogen bond between the oxygen atom of the carboxyl group and the hydrogen atom of the neighboring silanol group is possible. Slightly less likely is adsorption of arginine molecules due to interaction of the guanidine group with silanol groups of the surface. According to the calculated data, the adsorption of the zwitterionic form of the arginine molecule from the aqueous solution is equally likely to occur due to interaction of silanol groups of silica surface with both the carboxyl group and the guanidine group.

A 3D nickel(II) coordination polymer constructed by mixed- ligand strategy: synthesis, crystal structure and sensing of Hg(II) ion

A new N-containing coordination polymer, namely, [Ni(L)(dpa)·2.5H2O]n (1) (H2L = 4,4'-azanediyldibenzoic acid, dpa = 4,4’-dipyridylamine) has been constructed under hydrothermal conditions. Structural analysis reveals that complex 1 exhibits a 3D 4-connected binodal net. With functional amino group, complex 1 is developed to detect heavy metal ions by colorimetric method. Notably, 1 can selectively detect Hg2+ and it is free from the interference of other metal ions. The linear range for Hg2+ detection is 0.1 to 0.5 mL. XPS shows that the N atoms of amino groups in 1 are responsible for the Hg2+ detection.

The structural aspects of the copper(II) binding by the His-analogue of somatostatin

In this paper we report on the coordination abilities of the somatostatin analogue towards copper(II) ions. The investigated peptide belongs to the group of peptide hormones having a cyclic structure formed by a disulfide bridge. In the case of somatostatin, the disulfide bride is formed between Cys1 and Cys14. The studied analogue is characterized by the replacement of both Cys residues by His residues. Potentiometric and spectroscopic studies allow us to characterize the coordination abilities of the ligand. The studied peptide is much more effective in metal ion binding in comparison with simple peptides with an XaaXaaHis motif. The structure of the complex, obtained using theoretical calculations, allows us to explain the high efficiency in metal ion binding of the investigated peptide. In both investigated complexes the Cu(II) ion is bound by two amide nitrogen atoms, an amino group atom and a nitrogen of a third imidazole ring in a square planar position. The metal ion is located in close proximity to aromatic amino acid residues, which can influence the stability of the considered binding mode.

Crystal structure of hexakis-(N-methylthiourea) bismuth(III) triperchlorate

A bismuth(III) complex of N-methylthiourea (Mtu, C2H6N2S) [Bi(C2H6N2S)6](ClO4)3 has been synthesized, and its crystal structure has been determined. The structure is built of octahedral Bi(Mtu)63+ cations and ClO4− anions. Sulfur atoms are coordinated to bismuth(III) (at axis 2) at octahedron vertices (Bi-S, 2.7670(8), 2.8142(8), and 2.8315(8) A); angles SBiS vary from 82.26(3)° to 96.13(2)°. The presence of amino groups and oxygen atoms in the structure results in the emergence of numerous hydrogen bonds (HBs). All H atoms of amino groups are involved in HBs; one of them is bound to the sulfur atom. One of the oxygen atoms of ClO4− anions does not participate in HBs.

Mechanisms and kinetics of chelating reaction between novel chitosan derivatives and Zn(II)

Modified chitosan such as chitosan alpha-ketoglutaric acid (KCTS) and hydroxamated chitosan alpha-ketoglutaric acid (HKCTS) are successfully prepared. The resulting polymers were characterized by 13C NMR and X-ray diffraction (XRD), respectively. A adsorption system was applied to study the adsorption of Zn(II) ion onto chitosan derivatives. The isothermal sorption kinetics of chitosan derivatives for Zn(II) ion has been investigated. The kinetics experimental data correlated well with the second-order kinetic model, indicating that the chemical sorption was the rate-limiting step. The adsorption mechanism of chitosan derivatives with Zn(II) was studied by Fourier transform infrared spectroscopy (FT-IR) and X-ray photoelectron spectroscopy (XPS). The results indicated that the nitrogen in amino group and the oxygen in carboxyl group of KCTS were coordination atoms. N atom of amino group, O atom of hydroxamic acid and O atom of carbonyl group in HKCTS coordinated with Zn(II).

Extended planarity and π delocalization in triazine-based derivatives

Substituents bearing amino groups in positions 2, 4 and 6 of sym-triazines (1,3,5-triazines) share the planarity of the corresponding aromatic triazine moiety to different extent. In these systems, π-electron delocalization also ranges over adjacent N atoms of amino groups. The origin of both chemical features is attributed to the stabilization of the HOMO. Negligible inversion barriers were found, rotational barriers increasing as the exo amino groups become planar. Rigid rotor harmonic oscillator approximation for lower frequency vibrations makes Gibbs free energy inversion barriers unreliable. Natural population analysis shows a direct relationship between the planarity of the exo amino groups and the donor–acceptor interaction involving the exo nitrogen lone pair and the vicinal CN ring antibonding orbital.

Syntheses and Structural Researches of Nine-Coordinated (NH4)[EuIII(Edta)(H2O)3] · H2O and (NH4)3[EuIII(Ttha)] · 5H2O1

The crystal and molecular structures of the (NH4)[EuIII(Edta)(H2O)3] · H2O (I); Edta4– is an ethylenediaminetetraacetate anion) and (NH4)3[EuIII(Ttha)] · 5H2O (II); Ttha6– is a triethylenetetraminehexaacetate anion) complexes have been determined by single-crystal X-ray structure analysis. The crystal of complex I is orthorhombic with Fdd2 space group. The crystal data are as follows: a = 1.9505(8) nm, b = 3.5445(14) nm, c = 1.2442(5) nm, V = 8.602(6) nm3, Z = 16, M = 531.29, p = 1.579 g cm–3, μ = 2.970 mm–1, and F(OOO) = 3924. The final R and wR values are 0.0378 and 0.1030 for 2799 (I > 2.0σ(I)) unique reflections, and 0.0495 and 0.1072 for all 6237 reflections, respectively. The nine-coordinated [EuIII(Edta)(H2O)3]– complex anion has a pseudo-monocapped square antiprismatic structure in which the nine coordinated atoms, two N and four O are from one Edta ligand and three O atoms from water molecules. The crystal of complex II is monoclinic with P21/c space group. The crystal data are as follows: a = 1.0387(3) nm, b = 1.2737(4) nm, c = 2.3031(7) nm, β = 90.870(5)°, V = 3.047(2) nm3, Z = 4, M = 784.58, C 51.83, H 4.32, N 115.12. ρ = 1.710 g cm–3, μ = 2.143 mm–1 and F(000) = 1608. The final R and wR are 0.0400 and 0.0720 for 5909 (I > 2.0σ(I)) unique reflections, and 0.0747 and 0.0799 for all 13825 reflections, respectively. The nine-coordinated [EuIII(Ttha)]3– complex anion has a pseudo-monocapped square antiprismatic structure in which the Ttha acts as an ninedentate ligand with four N atoms of amino groups and five O atoms of carboxylic groups actually, in addition, there is a non-coordinated free carboxylic group in the structure.

Coordinate Structures of PrIII, GdIII, TmIII, and YbIIIComplexes with Nitrilotriacetic Acids

The crystal and molecular structures of the [PrIII(nta)(H2O)2]·H2O (nta = nitrilotriacetic acids), K3[GdIII(nta)2(H2O)]·6H2O, and K3[YbIII(nta)2]·5H2O complexes have been determined by single-crystal X-ray structure analyses. In [PrIII(nta)(H2O)2]·H2O, the PrIIINO8 part forms a nine-coordinate pseudo-monocapped square antiprismatic structure in which one N and three O atoms are from one nta ligand in the same molecule, three O atoms from another nta ligand in the neighboring molecule and two O atoms from two coordinate water molecules. In K3[GdIII(nta)2(H2O)]·6H2O, the [GdIII(nta)2(H2O)3- complex anion has a nine-coordinate pseudo-monocapped square antiprismatic structure in which each nta acts as a tetradentate ligand with one N atom of the amino group and three O atoms of the carboxylic groups. In K3[YbIII(nta)2]·5H2O, each nta also acts as a tetradentate ligand with one N atom of amino group and three O atoms of the carboxylic groups, but the [YbIII(nta)2 3- complex anion has an eight-coordinate structure with a distorted square antiprismatic prism. All the results including those for [TmIII(nta)(H2O)2]·2H2O confirm the inferences on the coordinate structures and coordination numbers of rare earth metal complexes with the nta ligand.

Syntheses and structural researches of nine-coordinate (NH 4) 2[Er III(Httha)]·6H 2O and ten-coordinate (CH 3NH 3) 3[Nd III(ttha)]·CH 3NH 2·4H 2O

The crystal and molecular structures of the (NH 4) 2[Er III(Httha)]·6H 2O (ttha=triethylenetetraminehexaacetic acid) and (CH 3NH 3) 3[Nd III(ttha)]·CH 3NH 2·4H 2O complexes have been determined by single-crystal X-ray structure analyses. The crystal of the (NH 4) 2[Er III(Httha)]·6H 2O complex belongs to monoclinic crystal system and P2(1)/ c space group. The crystal data are as follows: a=1.0324(4) nm, b=1.2745(4) nm, c=2.3170(8) nm, β=91.014°, V=3.0482(18) nm 3, Z=4, M=800.84, D c =1.743 g cm −3, μ=2.839 mm −1 and F(000)=1624. The final R and wR values are 0.0261 and 0.0696 for 5384 [ I>2.0 σ( I)] unique reflections, and 0.0329 and 0.0719 for all 12442 reflections, respectively. The complex [Er III(Httha)] 2− anion has a nine-coordinate pseudo-monocapped square antiprismatic structure in which the nine coordinate atoms, four N and five O are from one ttha ligand. The crystal of the (CH 3NH 3) 3[Nd III(ttha)]·CH 3NH 2·4H 2O complex belongs to triclinic system and P 1 ̄ space group. The crystal data are as follows: a=1.0772(3) nm, b=1.2194(4) nm, c=1.4505(4) nm, α=105.502(4)°, β=98.225(5)°, γ=99.906(5)°, V=1.7723(9) nm 3, Z=2, M=831.98, D c =1.559 g cm −3, μ=1.542 mm −1 and F(000)=862. The final R and wR are 0.0291 and 0.0786 for 6224 [ I>2.0 σ( I)] unique reflections, and 0.0348 and 0.0823 for all 7398 reflections, respectively. The complex [Nd III(ttha)] 3− anion has a ten-coordination structure with distorted bicapped square antiprismatic prism in which the ttha acts as a decadentate ligand with four N atoms of amino groups and six O atoms of carboxylic groups.