DFT-B3LYP, NPA-, and QTAIM-Based Study of the Physical Properties of [M(II)(H2O)2(15-crown-5)] (M = Mn, Fe, Co, Ni, Cu, Zn) Complexes

Facile Access to Cationic Methylstannylenes and Silylenes Stabilized by E-Pt Bonding and their Methyl Group Transfer Reactivity

We describe a family of cationic methylstannylene and chloro- and azidosilylene organoplatinum(II) complexes supported by a neutral, binucleating ligand. Methylstannylenes MeSn:+ are stabilized by coordination to PtII and are formed by facile Me group transfer from dimethyl or monomethyl PtII complexes, in the latter case triggered by concomitant B-H, Si-H, and H2 bond activation that involves hydride transfer from Sn to Pt. A cationic chlorosilylene complex was obtained by formal HCl elimination and Cl- removal from HSiCl3 under ambient conditions. The computational studies show that stabilization of cationic methylstannylenes and cationic silylenes is achieved through weak coordination to a neutral N-donor ligand binding pocket. The analysis of the electronic potentials, as well as the Laplacian of electron density, also reveals the differences in the character of Pt-Si vs. Pt-Sn bonding. We demonstrate the importance of a ligand-supported binuclear Pt/tetrel core and weak coordination to facilitate access to tetrylium-ylidene Pt complexes, and a transmetalation approach to the synthesis of MeSnII :+ derivatives.

Photophysical and biological aspects of α, β-unsaturated ketones: Experimental and in silico approach

In this work, four fluorinated α, β-unsaturated ketones named as 3-(3-bromophenyl)-1-(3-(trifluoromethyl)phenyl)prop-2-en-1-one (1), 3-(4-methoxyphenyl)-1-(3-(trifluoromethyl)phenyl) prop-2-en-1-one (2), 3-(3-bromo-5-chloro-2-hydroxyphenyl)-1-(3-(trifluoromethyl)phenyl) prop-2-en-1-one (3) and 3-(2-hydroxy-5-methylphenyl)-1-(3-(trifluoromethyl)phenyl)prop-2-en-1-one (4) were synthesized by Claisen-Schmidt reaction. The synthesized molecules were then characterized through ultraviolet-visible spectroscopy (UV-Vis), Fourier transform infrared (FTIR), 1 H-NMR, 13 C-NMR, and mass spectrometry. The antioxidant potential, Urease inhibition, and interaction of compounds 1-4 with Salmon sperm DNA were experimentally explored and supported by molecular docking studies. The synthesized compounds strongly interact with SS-DNA through intercalative mode. It was noticed that compound 1 served as potent Urease inhibitor while compound 4 as better antioxidant among synthesized compounds. Moreover, frontier molecular orbitals, nonlinear optical (NLO) properties, natural bond orbitals, molecular electrostatic potential, natural population analysis, and photophysical properties of synthesized compounds were accomplished through density functional theory and time-dependent density functional theory. The band gap of all the compounds have been worked out using Taucs method. In addition to that, a precise comparative account of UV and IR data obtained from theoretical and experimental findings showed good agreement between theoretical and experimental data. The findings of our studies reflected that compounds 1-4 possess better NLO properties than Urea standard and the band gap data also reflected their prospective use towards optoelectronic materials. The better NLO behavior of compounds was attributed to the noncentrosymmetric structure of synthesized compounds.

Assessment of Density Functional Theory Methods for the Structural Prediction of Transition and Post-Transition Metal-Nucleic Acid Complexes

Understanding the structure of metal-nucleic acid systems is important for many applications such as the design of new pharmaceuticals, metal detection platforms, and nanomaterials. Herein, we explore the ability of 20 density functional theory (DFT) functionals to reproduce the crystal structure geometry of transition and post-transition metal-nucleic acid complexes identified in the Protein Data Bank and Cambridge Structural Database. The environmental extremes of the gas phase and implicit water were considered, and analysis focused on the global and inner coordination geometry, including the coordination distances. Although gas-phase calculations were unable to describe the structure of 12 out of the 53 complexes in our test set regardless of the DFT functional considered, accounting for the broader environment through implicit solvation or constraining the model truncation points to crystallographic coordinates generally afforded agreement with the experimental structure, suggesting that functional performance for these systems is likely due to the models rather than the methods. For the remaining 41 complexes, our results show that the reliability of functionals depends on the metal identity, with the magnitude of error varying across the periodic table. Furthermore, minimal changes in the geometries of these metal-nucleic acid complexes occur upon use of the Stuttgart-Dresden effective core potential and/or inclusion of an implicit water environment. The overall top three performing functionals are ωB97X-V, ωB97X-D3(BJ), and MN15, which reliably describe the structure of a broad range of metal-nucleic acid systems. Other suitable functionals include MN15-L, which is a cheaper alternative to MN15, and PBEh-3c, which is commonly used in QM/MM calculations of biomolecules. In fact, these five methods were the only functionals tested to reproduce the coordination sphere of Cu²⁺-containing complexes. For metal-nucleic acid systems that do not contain Cu²⁺, ωB97X and ωB97X-D are also suitable choices. These top-performing methods can be utilized in future investigations of diverse metal-nucleic acid complexes of relevance to biology and material science.

The inorganic chemistry of the cobalt corrinoids - an update

The inorganic chemistry of the cobalt corrinoids, derivatives of vitamin B₁₂, is reviewed, with particular emphasis on equilibrium constants for, and kinetics of, their axial ligand substitution reactions. The role the corrin ligand plays in controlling and modifying the properties of the metal ion is emphasised. Other aspects of the chemistry of these compounds, including their structure, corrinoid complexes with metals other than cobalt, the redox chemistry of the cobalt corrinoids and their chemical redox reactions, and their photochemistry are discussed. Their role as catalysts in non-biological reactions and aspects of their organometallic chemistry are briefly mentioned. Particular mention is made of the role that computational methods - and especially DFT calculations - have played in developing our understanding of the inorganic chemistry of these compounds. A brief overview of the biological chemistry of the B₁₂-dependent enzymes is also given for the reader's convenience.

Tetrel Bonding in Anion Recognition: A First Principles Investigation

Twenty-five molecule-anion complex systems [I₄Tt···X^-] (Tt = C, Si, Ge, Sn and Pb; X = F, Cl, Br, I and At) were examined using density functional theory (ωB97X-D) and ab initio (MP2 and CCSD) methods to demonstrate the ability of the tetrel atoms in molecular entities, I₄Tt, to recognize the halide anions when in close proximity. The tetrel bond strength for the [I₄C···X^-] series and [I₄Tt···X^-] (Tt = Si, Sn; X = I, At), was weak-to-moderate, whereas that in the remaining 16 complexes was dative tetrel bond type with very large interaction energies and short Tt···X close contact distances. The basis set superposition error corrected interaction energies calculated with the highest-level theory applied, [CCSD(T)/def2-TZVPPD], ranged from -3.0 to -112.2 kcal mol^-1. The significant variation in interaction energies was realized as a result of different levels of tetrel bonding environment between the interacting partners at the equilibrium geometries of the complex systems. Although the ωB97X-D computed intermolecular geometries and interaction energies of a majority of the [I₄Tt···X^-] complexes were close to those predicted by the highest level of theory, the MP2 results were shown to be misleading for some of these systems. To provide insight into the nature of the intermolecular chemical bonding environment in the 25 molecule-anion complexes investigated, we discussed the charge-density-based topological and isosurface features that emanated from the application of the quantum theory of atoms in molecules and independent gradient model approaches, respectively.

The Pnictogen Bond: The Covalently Bound Arsenic Atom in Molecular Entities in Crystals as a Pnictogen Bond Donor

In chemical systems, the arsenic-centered pnictogen bond, or simply the arsenic bond, occurs when there is evidence of a net attractive interaction between the electrophilic region associated with a covalently or coordinately bound arsenic atom in a molecular entity and a nucleophile in another or the same molecular entity. It is the third member of the family of pnictogen bonds formed by the third atom of the pnictogen family, Group 15 of the periodic table, and is an inter- or intramolecular noncovalent interaction. In this overview, we present several illustrative crystal structures deposited into the Cambridge Structure Database (CSD) and the Inorganic Chemistry Structural Database (ICSD) during the last and current centuries to demonstrate that the arsenic atom in molecular entities has a significant ability to act as an electrophilic agent to make an attractive engagement with nucleophiles when in close vicinity, thereby forming σ-hole or π-hole interactions, and hence driving (in part, at least) the overall stability of the system’s crystalline phase. This overview does not include results from theoretical simulations reported by others as none of them address the signatory details of As-centered pnictogen bonds. Rather, we aimed at highlighting the interaction modes of arsenic-centered σ- and π-holes in the rationale design of crystal lattices to demonstrate that such interactions are abundant in crystalline materials, but care has to be taken to identify them as is usually done with the much more widely known noncovalent interactions in chemical systems, halogen bonding and hydrogen bonding. We also demonstrate that As-centered pnictogen bonds are usually accompanied by other primary and secondary interactions, which reinforce their occurrence and strength in most of the crystal structures illustrated. A statistical analysis of structures deposited into the CSD was performed for each interaction type As···D (D = N, O, S, Se, Te, F, Cl, Br, I, arene’s π system), thus providing insight into the typical nature of As···D interaction distances and ∠R–As···D bond angles of these interactions in crystals, where R is the remainder of the molecular entity.

The Stibium Bond or the Antimony-Centered Pnictogen Bond: The Covalently Bound Antimony Atom in Molecular Entities in Crystal Lattices as a Pnictogen Bond Donor

A stibium bond, i.e., a non-covalent interaction formed by covalently or coordinately bound antimony, occurs in chemical systems when there is evidence of a net attractive interaction between the electrophilic region associated with an antimony atom and a nucleophile in another, or the same molecular entity. This is a pnictogen bond and are likely formed by the elements of the pnictogen family, Group 15, of the periodic table, and is an inter- or intra-molecular non-covalent interaction. This overview describes a set of illustrative crystal systems that were stabilized (at least partially) by means of stibium bonds, together with other non-covalent interactions (such as hydrogen bonds and halogen bonds), retrieved from either the Cambridge Structure Database (CSD) or the Inorganic Crystal Structure Database (ICSD). We demonstrate that these databases contain hundreds of crystal structures of various dimensions in which covalently or coordinately bound antimony atoms in molecular entities feature positive sites that productively interact with various Lewis bases containing O, N, F, Cl, Br, and I atoms in the same or different molecular entities, leading to the formation of stibium bonds, and hence, being partially responsible for the stability of the crystals. The geometric features, pro-molecular charge density isosurface topologies, and extrema of the molecular electrostatic potential model were collectively examined in some instances to illustrate the presence of Sb-centered pnictogen bonding in the representative crystal systems considered.

Synthesis of Ionizable Calix[4]arenes for Chelation of Selected Divalent Cations

Two sets of functionalised calix[4]arenes, either with a 1,3-crown ether bridge or with an open-chain oligo ether moiety in 1,3-position were prepared and further equipped with additional deprotonisable sulfonamide groups to establish chelating systems for selected cations Sr2+, Ba2+, and Pb2+ ions. To improve the complexation behaviour towards these cations, calix[4]arenes with oligo ether groups and modified crowns of different sizes were synthesized. Association constants were determined by UV/Vis titration in acetonitrile using the respective perchlorate salts and logK values between 3.2 and 8.0 were obtained. These findings were supported by the calculation of the binding energies exemplarily for selected complexes with Ba2+.

A Structural Diversity of Molecular Alkaline-Earth-Metal Polyphosphides: From Supramolecular Wheel to Zintl Ion

A series of molecular group 2 polyphosphides has been synthesized by using air-stable [Cp*Fe(η5 -P5 )] (Cp*=C5 Me5 ) or white phosphorus as polyphosphorus precursors. Different types of group 2 reagents such as organo-magnesium, mono-valent magnesium, and molecular calcium hydride complexes have been investigated to activate these polyphosphorus sources. The organo-magnesium complex [(Dipp BDI-Mg(CH3 ))2 ] (Dipp BDI={[2,6-i Pr2 C6 H3 NCMe]2 CH}- ) reacts with [Cp*Fe(η5 -P5 )] to give an unprecedented Mg/Fe-supramolecular wheel. Kinetically controlled activation of [Cp*Fe(η5 -P5 )] by different mono-valent magnesium complexes allowed the isolation of Mg-coordinated formally mono- and di-reduced products of [Cp*Fe(η5 -P5 )]. To obtain the first examples of molecular calcium-polyphosphides, a molecular calcium hydride complex was used to reduce the aromatic cyclo-P5 ring of [Cp*Fe(η5 -P5 )]. The Ca-Fe-polyphosphide is also characterized by quantum chemical calculations and compared with the corresponding Mg complex. Moreover, a calcium coordinated Zintl ion (P7 )3- was obtained by molecular calcium hydride mediated P4 reduction.

Metal-only Lewis Pairs of Rhodium with s, p and d-Block Metals

Metal-only Lewis pairs (MOLPs) in which the two metal fragments are solely connected by a dative M→M bond represent privileged architectures to acquire fundamental understanding of bimetallic bonding. This has important implications in many catalytic processes or supramolecular systems that rely on synergistic effects between two metals. However, a systematic experimental/computational approach on a well-defined class of compounds is lacking. Here we report a family of MOLPs constructed around the RhI precursor [(η5 -C5 Me5 )Rh(PMe3 )2 ] (1) with a series of s, p and d-block metals, mostly from the main group elements, and investigate their bonding by computational means. Among the new MOLPs, we have structurally characterized those formed by dative bonding between 1 and MgMeBr, AlMe3 , GeCl2 , SnCl2 , ZnMe2 and Zn(C6 F5 )2, as well as spectroscopically identified the ones resulting from coordination to MBArF (M=Na, Li; BArF - =[B(C6 H2 -3,5-(CF3 )2 )4 ]- ) and CuCl. Some of these compounds represent unique examples of bimetallic structures, such as the first unambiguous cases of Rh→Mg dative bonding or base-free rhodium bound germylene and stannylene species. Multinuclear NMR spectroscopy, including 103 Rh NMR, is used to probe the formation of Rh→M bonds. A comprehensive theoretical analysis of those provides clear trends. As anticipated, greater bond covalency is found for the more electronegative acids, whereas ionic character dominates for the least electronegative nuclei, though some degree of electron sharing is identified in all cases.

Quantum Chemical and Monte Carlo Simulation Studies on Inhibition Performance of Caffeine and Its Derivatives against Corrosion of Copper

Performance tests on caffeine’s corrosion inhibition properties and their derivatives against copper corrosion have been previously reported experimentally using gravimetric and electrochemical analyses. The test was able to measure the efficiency of their corrosion inhibition accurately. However, the caffeine and its derivatives’ structure patterns and coating mechanisms when interacting with metals during copper corrosion inhibition have not been explained in detail by experimental studies. In the present study, the theoretical density functional study (DFT), ab initio MP2, and Monte Carlo simulation approaches explain the problem. The geometrical and quantum chemical parameters of inhibitors were compared under normal and protonated conditions in the gas and aqueous environments. Theoretical studies can accurately determine the molecule’s geometrical parameters and successfully explain the quantum parameters of inhibitors. Molecular dynamics are applied to study the mechanism of interaction between inhibitors and metal surfaces in an explicit water molecule environment. The energy absorption of caffeine and its derivatives on metal surfaces was linear, with quantum parameters calculated from the density functional theory and an ab initio approach. Furthermore, these theoretical study results align with the previously reported experimental studies published by de Souza et al. The inhibition efficiency ranking of studied molecules preventing copper corrosion was caffeine > theobromine > theophylline. This theoretical approach is expected to bridge the gap in designing effective corrosion inhibitors.

Analysis of charge density in nonaaquagadolinium(III) trifluoromethanesulfonate - insight into GdIII-OH2 bonding

The experimental charge-density distribution in [Gd(H₂O)₉](CF₃SO₃)₃ has been analysed and compared with the theoretical density functional theory calculations. Although the Gd-OH₂ bonds are mainly ionic, a covalent contribution is detectable when inspecting both the topological parameters of these bonds and the natural bond orbital results. This contribution originates from small electron transfer from the lone pairs of oxygen atoms to empty 5d and 6s spin orbitals of Gd³⁺.

Structural, Spectroscopic, and Chemical Bonding Analysis of Zn(II) Complex [Zn(sal)](H2O): Combined Experimental and Theoretical (NBO, QTAIM, and ELF) Investigation

The Zn(II) complex of salen-like scaffold [Zn(sal)](H2O) was synthesized and characterized by elemental analysis, IR, UV–Vis, and 1H-NMR spectroscopic techniques. The structure of complex was confirmed by single crystal X-ray diffraction studies. In the complex, Zn (II) was placed in the inner N2O2 compartment of the salen scaffold in square planar geometry and crystallized in the monoclinic space group P21/n. DFT and TDDFT calculations were performed to reproduce the experimentally observed structural and spectroscopic (IR and UV–vis) findings. The bonding of the Zn(II) framework in the [Zn(sal)](H2O) complex was explored in depth. The theoretical approaches employed were perturbation theory within the context of the natural bond orbital (NBO) framework, and quantum theory of atoms in molecule (QTAIM) and electron localization function (ELF) analysis. The study begins by delineating the difference between the NBO and QTAIM approaches. This paper thus exhibits the supportive nature of NBO theory and QTAIM in discussion of the bonding in the [Zn(sal)](H2O) complex, when both the methodologies are used in combination.

A theoretical study on the antioxidant properties of methoxy-substituted chalcone derivatives: A case study of kanakugiol and pedicellin through their Fe (II and III) coordination ability

A theoretical study on the antioxidant properties of two chalcone derivatives, kanakugiol and pedicellin, is performed by considering their Fe[Formula: see text] and Fe[Formula: see text] coordination ability. The objective of the study is to elucidate the factors influencing the stability of the isolated conformers, the nature of the complexes, metal[Formula: see text]ligand stability, metal ion affinities (MIA) and electronic properties of the cations before and after coordination to the ligand. The study is performed using the B3LYP/6–311[Formula: see text]G(2d,p)//B3LYP/6–31[Formula: see text]G(d,p) method. The LANL2DZ pseudopotential is selected to describe the Fe[Formula: see text] ions. Time-dependent density functional theory (TDDFT) method is used to assess the electronic UV–Vis spectra of the isolated chalcones and their complexes with Fe[Formula: see text] ions. The results suggest that the preferred complexes are those in which the Fe ion is coordinated at the hydroxyl-methoxy and hydroxyl-keto sites for kanakugiol and methoxy-keto site for pedicellin. Both kanakugiol and pedicellin have potential to chelate iron ions as demonstrated by their high MIA values in vacuo and in water solution. However, the ability of pedicellin to chelate iron is slightly lower than that of kanakugiol, indicating that the presence of the hydroxyl group has an effect of enhancing the metal binding abilities of the chalcone derivatives. In all the complexes obtained in vacuo, kanakugiol and pedicellin exhibit the ability to reduce the Fe[Formula: see text] ion. In water solution (which mimics the environment in biological systems or studies performed in vivo), Fe[Formula: see text] is reduced to Fe[Formula: see text] upon coordination to the ligand while the oxidation number of Fe[Formula: see text] upon coordination to the ligand remains virtually unchanged.

Computational assessment of electron density in metallo-organic nickel pincer complexes for formation of PC bonds

Hydrophosphination is an atomically efficient method for introducing new carbon-phosphorous bonds in organic synthesis. New late-transition metal catalytic complexes are proposed to facilitate this process. These nickel-based complexes are analyzed using semiempirical (SE), Hartree-Fock (H-F), and density functional theory (DFT) models. H-F proves to be ineffective, while the SE approach has limited, qualitative use. DFT shows electron density at the metal center suitable for catalyzing bond formation in the proposed, reductive hydrophosphination mechanism. It also shows that the pincer complexes under investigation are relatively insensitive to solvent dielectric constant and to the chemical character of the monodentate ligand, both in terms of electron distribution and in terms of molecular orbital energies.

Mechanistic insights into the reductive dehydroxylation pathway for the biosynthesis of isoprenoids promoted by the IspH enzyme

Here, we report an integrated quantum mechanics/molecular mechanics (QM/MM) study of the bio-organometallic reaction pathway of the 2H+/2e- reduction of (E)-4-hydroxy-3-methylbut-2-enyl pyrophosphate (HMBPP) into the so called universal terpenoid precursors isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP), promoted by the IspH enzyme. Our results support the viability of the bio-organometallic pathway through rotation of the OH group of HMBPP away from the [Fe4S4] cluster at the core of the catalytic site, to become engaged in a H-bond with Glu126. This rotation is synchronous with π-coordination of the C2[double bond, length as m-dash]C3 double bond of HMBPP to the apical Fe atom of the [Fe4S4] cluster. Dehydroxylation of HMBPP is triggered by a proton transfer from Glu126 to the OH group of HMBPP. The reaction pathway is completed by competitive proton transfer from the terminal phosphate group to the C2 or C4 atom of HMBPP.

Ligand(s)-to-metal charge transfer as a factor controlling the equilibrium constants of late first-row transition metal complexes: revealing the Irving–Williams thermodynamical series

Ligand(s)-to-metal charge transfer obtained from QTAIM charges unravel the Irving–William series for the equilibrium constants of late first-row bivalent metal ions.

Phenylvinylcobalamin: an alkenylcobalamin featuring a ligand with a large trans influence

Cob(I)alamin reacts with phenylacetylene to produce two diastereomers in which the organic ligand is coordinated to the upper (β) and lower (α) face of the corrin ring, respectively. The isomers were separated chromatographically and characterised by ESI-MS and, in the case of the β isomer, by (1)H and (13)C NMR. Only the β isomer crystallised and its molecular structure, determined by X-ray diffraction, shows that the organic ligand coordinates Co(III) through the β carbon of the phenylvinyl ligand. The Co-C bond length is 2.004(8) Å while the Co-N bond length to the trans 5,6-dimethylbenzimidazole (dmbzm) base is 2.217(8) Å, one of the longest Co-Ndmbzm bond lengths known in an organocobalamin. Unlike benzylcobalamin (BzCbl), phenylvinylcobalamin (PhVnCbl) is stable towards homolysis. DFT calculations (BP86/TZVP) on model compounds of BzCbl and PhVnCbl show that the Co-C bond dissociation energy for homolysis to Co(II) and an organic radical in the former is 8 kcal mol(-1) lower than in the latter. An analysis of the electron density at the Co-C bond critical point using Bader's QTAIM approach shows that the Co-C bond in PhVnCbl is shorter, stronger and somewhat more covalent than that in BzCbl, and has some multiple bond character. Together with calculations that show that the benzyl radical is more stable than the phenylvinyl radical, this rationalises the stability of PhVnCbl compared to BzCbl. The phenylvinyl ligand has a large trans influence. The pKa for deprotonation of dmbzm and its coordination by the metal in β-PhVnCbl is 4.60 ± 0.01, one of the highest values reported to date in cobalamin chemistry. The displacement of dmbzm ligand by CN(-) in β-PhVnCbl occurs with log K = 0.7 ± 0.1; the trans influence order of C-donor ligands is therefore CN(-) < CCH < CHCH2 = PhVn < Me < Et.