Mononuclear half-sandwich nd7 metallo drug complexes based on bidentate N∩N dendritic scaffolds: DFT (B3LYP; BP86 and B3PW91) examination

Through an use of three functionals (B3PW91, B3LYP and BP86) associated to a generic basis set LanL2DZ for transition metals (as well as halogen atoms) and 6-311+G (d,p) for others atoms, an examination of the bonding properties of a series of mononuclear half-sandwich nd⁷ transition metal (anticancer) complexes based on N∩N dendritic scaffolds (L) has been done. Collectively, complexes studied have adopted the piano-stool environment. An examination of the performance of each functional has shown that for the most reliable geometrical analysis of Metal-Nitrogen and Metal-Halogen bonds, the B3LYP and B3PW91 functionalities are suitable respectively. Regardless of the halogen ligand adopted, the B3LYP metal-nitrogen bond lengths are the most widely overestimated. A correlation has been built between the retained charge on each divalent transition metal cation and its metal ion affinity (MIA). Topological examinations reveal the higher instability of metal-N bonds compared to metal-X ones (X = Cl and Br). By the mean of the energy decomposition analysis, a predominant electrostatic character of metal … halogen and [LCP]^- … [MX]⁺ interaction has been demonstrated. The transition metal atom … (hydrophobic) surface (Cp*) interaction is most pronounced for the chloride rhodium complexes of rhodium (combined with (E)-N-(pyridin-2-ylmethylene) Propan-1-amine and 2,2'- dipyridylketone ligands and iridium combined with 2,2'- dipyridylketone ligand. The charge decomposition analysis displays the weakening of the [Formula: see text] bonds in the studied complexes.

DFT/B3LYP and BP86 examination of mononuclear half-sandwich nd7 metallo drug complexes based on N∩O dendritic scaffolds

In this paper, we have explored the bonding properties of a series of mononuclear half-sandwich nd⁷ anticancer complexes based on N∩O dendritic scaffolds (L) using two functionals (B3LYP and BP86) with generic basis set (LanL2DZ for transition metals (as well as halogen atoms) and 6-311 + G (d,p) for others atoms. The geometry optimization of structures have led to the adoption of the piano-stool environment and the formation of kings of intermolecular hydrogen bonding: CH … X (Cl,Br) (2.619-2.954) and CH...O (2.266-2.973 Å) interaction. The metal (M)-bromine bond distances have shown to be significantly higher than metal-chlorine ones. In chloride complexes, salicylaldimine ligand-Co²⁺ (-3097.15 kJ/mol) and salicylaldimine ligand-Ir²⁺ (-3436.78 kJ/mol) interactions are stronger. Except for cobalt complexes, the interaction energies are underestimated by B3LYP functional, by contrast B3LYP HOMO-LUMO gaps obtained are highly greater. The metal ion affinity (MIA) is increasing in the order: Ir⁺²<Rh⁺²<Co⁺² for both halogen ligands adopted, exception for picolinate and salicylaldimine ligands. Our results also show that the metal … oxygen, metal … nitrogen and metal … halogen interactions are closed-shell interaction. From the contribution of the ΔE_orb term in the ranges 4.06-98.61% (X = Cl) and 10.29-99.87% (X = Br), the nature of the [Formula: see text] … X^- interaction turned out to be mainly dependent on the transition metal and halogen atom involved. The smallest back-donation observed for chloride complexes corresponding to the highest barrier to the formation of [MLCP^∗]-X bond traduces that the fact that chloride complexes are the least reactive. In the majority of cases, larger donation is obtained compared to back-donation showing that the possibility of [Formula: see text] [Formula: see text] charge separation can be expected. For α rings of chloride complexes, B3LYP HOMA indexes are higher than those estimated by PB86 functional. Conversely, opposite results were found for their bromide counterparts.

Label-free colorimetric detection of serum cysteine using Ag-NP probes in the presence of Be2+ ions

Amino acids play a crucial role in a variety of significant metabolic processes and their homeostasis is essential for cell growth and survival.

Insights into the origin of the excited transitions in graphene quantum dots interacting with heavy metals in different media

Exploring graphene quantum dots (GQDs) is an attractive way to design novel optical and electrochemical sensors for fast and reliable detection of toxic heavy metals (HMs), such as Cd, Hg and Pb.

Interaction of l-proline with group IIB (Zn2+, Cd2+, Hg2+) metal cations in the gas and aqueous phases: a quantum computational study

The gas and aqueous phase complexation geometries, electronic interactions, and metal ion affinities of Zn2+, Cd2+, and Hg2+ metal cations with the two most stable conformations of l-proline complexes were studied. The complexes were optimized by density functional theory (B3LYP) using the 6-311++G(d,p) orbital basis set and relativistic pseudopotentials for the metal cations. The interactions of the metal cations at different nucleophilic sites of l-proline were considered as were three modes of interactions including salt bridged, charge solvated 1, and charge solvated 2, which are indicative of binding in a bidentate manner through the carboxylate group, carbonyl and hydroxyl oxygen, and carbonyl oxygen and the nitrogen atom of l-proline. All of the coordination patterns were characterized by both charge transfer and ionic interactions between l-proline and the metal cation. The metal ion affinity (MIA) and interaction energy were also computed for all of the complexes at both the gas and aqueous phases. Results showed that the order of MIA at the gas and aqueous phases are different. MIA order at the gas phase was in the order of Zn2+ > Hg2+ > Cd2+ whereas at the aqueous phase, the order of Zn2+ > Cd2+ > Hg2+ was obtained for MIA. The infrared stretching vibrational modes of the N–H and O–H groups of free l-proline were compared with l-proline–M2+ in both CS1 and CS2 coordination patterns at the gas phase and results showed a considerable shift to lower frequency during complexation process.

First-principles data set of 45,892 isolated and cation-coordinated conformers of 20 proteinogenic amino acids

We present a structural data set of the 20 proteinogenic amino acids and their amino-methylated and acetylated (capped) dipeptides. Different protonation states of the backbone (uncharged and zwitterionic) were considered for the amino acids as well as varied side chain protonation states. Furthermore, we studied amino acids and dipeptides in complex with divalent cations (Ca²⁺, Ba²⁺, Sr²⁺, Cd²⁺, Pb²⁺, and Hg²⁺). The database covers the conformational hierarchies of 280 systems in a wide relative energy range of up to 4 eV (390 kJ/mol), summing up to a total of 45,892 stationary points on the respective potential-energy surfaces. All systems were calculated on equal first-principles footing, applying density-functional theory in the generalized gradient approximation corrected for long-range van der Waals interactions. We show good agreement to available experimental data for gas-phase ion affinities. Our curated data can be utilized, for example, for a wide comparison across chemical space of the building blocks of life, for the parametrization of protein force fields, and for the calculation of reference spectra for biophysical applications.

An insight into the interaction of L-proline with the transition metal cations Fe(2+), Co(2+), Ni(2+): a gas phase theoretical study

The interaction of Fe(2+), Co(2+), and Ni(2+) with L-proline has been studied. Three modes of interaction have been considered: salt bridged (SB), involving binding in a bi-dentate manner through the carboxylate group of L-proline, charge solvated 1 (CS1) involving carbonyl and hydroxyl oxygen, and charge solvated 2 (CS2) involving carbonyl oxygen and the lone pair of the nitrogen atom. All calculations including geometry optimization, metal ion affinities (MIAs), and frequency calculations of the binding structures of Fe(2+), Co(2+), and Ni(2+) to L-proline were calculated using the hybrid density functional theory (DFT-B3LYP) method. All three cations were found to bind preferentially in a zwitterionic (SB) coordination pattern with the metal ion affinity in the order Ni(2+) ˃ Co(2+) ˃ Fe(2+) in all binding forms. The nature of the binding interaction between metal cations and L-proline was found to be mainly electrostatic. Comparison of the infrared vibrations of the C=O, the N-H and the O-H groups of free L-proline with L-proline-M(2+) in both CS1 and CS2 complex structures indicated a considerable shift to lower frequency during complexation. In order to gain more insight into the nature of the interaction of L-proline with group VIIIB metal ions, comparison of the interaction of L-proline with other cations such as (Li(+), Na(+), K(+), Be(2+), Mg(2+), and Ca(2+)) was made. Graphical Abstract L-proline with the transition metal cations Fe(2+), Co(2+), Ni(2.)

Interactions of Zn(II) with single and multiple amino acids. Insights from density functional and ab initio calculations

Calculations were performed to study the interactions of metal ions (M) with (multiple) amino acids (AA) and fill the gap between single AA and proteins. A complete conformational search results in nine and eleven ZnGly isomers at B3P86 and MP2 levels, respectively, and four populated conformers of glycine are responsible for production of these isomers. For all M, the isomers via the OO and NO binding modes are the main constituents, and the OO mode is favored by stronger electrostatic interactions. Binding with more glycines causes larger structural distortions, improves relative stabilities of monodentate binding isomers and generates new binding modes (e.g. ZnB(III) via only the hydroxyl group). The scaling factor of Zn(Gly)(n) structures, the ratio of its binding affinity versus the sum of comprising ZnGly isomers, is linear with glycine number (n), and the linear relationship may not be altered by mutations of glycines and M. It thus allows to estimate M(AA)(n) binding affinities (n ≥ 2) from the comprising MAA structures and analyze their structures with kinetic methods. The DFT and MP2 results become comparable by increasing metal coordination, e.g. the ZnB(III) versus ZnA(I) (zwitterionic) relative energy differs by 41.9 kcal mol(-1) at B3P86 and MP2 levels and is close by addition of three water molecules (4.1 kcal mol(-1)). The presence of water solvent improves the relative stabilities of monodentate binding isomers and results in a broader conformational distribution.