Optimal density-functional theory method for zinc-amino acid complexes determined by analyzing structural and Fourier-transform infrared spectroscopy data

Metal-amino acid complexes are important compounds for the human body. Their nutritional value and anticancer, antibacterial, and catalytic properties are the focus of several studies. Density functional theory (DFT) can be used to predict their properties by optimizing their structures and performing electron population analyses. However, conventional computational methods cannot adequately determine the parameters of polymeric metal-amino acid complexes. Therefore, intermolecular interactions of polymers must be considered to correctly predict the properties of metal-amino acid and related metal complexes. In this study, different DFT protocols were used to acquire the infrared spectra and determine interatomic distances of two zinc-amino acid complexes, Zn(Gly)2 and Zn(Met)2. The results were compared to spectroscopic and X-ray crystallographic data, revealing that the M06 and M06-L functionals and the 6-311++G(d,p) basis set produced the smallest computational errors. Our results provide a foundation for future theoretical studies on other metal-amino acid and metal-organic complexes.

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.

Influence of Number of Ligands and Point Group on the Electronic Structure of Co2+ Aqua-Complexes

The nucleation process of zeolitic imidazolate frameworks (ZIFs) is, to date, not yet completely understood, making the search for tailored materials very difficult. Recently, it has been shown that, during the formation process, the symmetry of the precursors is reduced by ligand elimination and substitution reactions. The octahedral precursors with simple ligands, such as water, methanol, and/or NO₃^-, are transformed to five- and finally four-coordinated complexes with imidazole ligands. This reduction of symmetry, caused both by the changing coordination environment and distortions from the perfect symmetry leading to another point group, will have a large influence on the electronic structure and more specifically on the d-orbital splitting. This, in turn, will affect the d-d electronic excitations, which can be followed using UV-vis spectroscopy and which can help to unravel the formation process. In this work, we systematically investigate how the lowering of the number of ligands affects the symmetry and thus the geometry and electronic structure of Co²⁺ complexes with six, five, and four aqua ligands. Therefore, we first resort to qualitative techniques, such as crystal field theory (CFT) and ligand field theory (LFT), which reveal that the orbital splitting is characteristic for the number of ligands. However, as these techniques are not capable of providing quantitative results without the use of experimental data as input, we perform various computational calculations. Both average of configuration (AOC) and unrestricted density functional theory (UDFT) are thoroughly investigated, and we will determine which technique is the best suited to properly describe the ground state of these systems. To investigate the dependency on the d-orbital occupation, we also investigated V²⁺, Mn²⁺, and Ni²⁺ hexa-aqua-complexes and compared them to the Co systems.

Definition of the Pnictogen Bond: A Perspective

This article proposes a definition for the term “pnictogen bond” and lists its donors, acceptors, and characteristic features. These may be invoked to identify this specific subset of the inter- and intramolecular interactions formed by elements of Group 15 which possess an electrophilic site in a molecular entity.

The Pnictogen Bond, Together with Other Non-Covalent Interactions, in the Rational Design of One-, Two- and Three-Dimensional Organic-Inorganic Hybrid Metal Halide Perovskite Semiconducting Materials, and Beyond

The pnictogen bond, a somewhat overlooked supramolecular chemical synthon known since the middle of the last century, is one of the promising types of non-covalent interactions yet to be fully understood by recognizing and exploiting its properties for the rational design of novel functional materials. Its bonding modes, energy profiles, vibrational structures and charge density topologies, among others, have yet to be comprehensively delineated, both theoretically and experimentally. In this overview, attention is largely centered on the nature of nitrogen-centered pnictogen bonds found in organic-inorganic hybrid metal halide perovskites and closely related structures deposited in the Cambridge Structural Database (CSD) and the Inorganic Chemistry Structural Database (ICSD). Focusing on well-characterized structures, it is shown that it is not merely charge-assisted hydrogen bonds that stabilize the inorganic frameworks, as widely assumed and well-documented, but simultaneously nitrogen-centered pnictogen bonding, and, depending on the atomic constituents of the organic cation, other non-covalent interactions such as halogen bonding and/or tetrel bonding, are also contributors to the stabilizing of a variety of materials in the solid state. We have shown that competition between pnictogen bonding and other interactions plays an important role in determining the tilting of the MX6 (X = a halogen) octahedra of metal halide perovskites in one, two and three-dimensions. The pnictogen interactions are identified to be directional even in zero-dimensional crystals, a structural feature in many engineered ordered materials; hence an interplay between them and other non-covalent interactions drives the structure and the functional properties of perovskite materials and enabling their application in, for example, photovoltaics and optoelectronics. We have demonstrated that nitrogen in ammonium and its derivatives in many chemical systems acts as a pnictogen bond donor and contributes to conferring stability, and hence functionality, to crystalline perovskite systems. The significance of these non-covalent interactions should not be overlooked, especially when the focus is centered on the rationale design and discovery of such highly-valued materials.

Molecular, Supramolecular Structures Combined with Hirshfeld and DFT Studies of Centrosymmetric M(II)-azido {M=Ni(II), Fe(II) or Zn(II)} Complexes of 4-Benzoylpyridine

The supramolecular structures of the three metal (II) azido complexes [Fe(4bzpy)4(N3)2]; 1, [Ni(4bzpy)4(N3)2]; 2 and [Zn(4bzpy)2(N3)2]n; 3 with 4-benzoylpyridine (4bzpy) were presented. All complexes contain hexa-coordinated divalent metal ions with a slightly distorted octahedral MN6 coordination sphere. Complexes 1 and 2 are monomeric with terminal azido groups while 3 is one-dimensional coordination polymer containing azido groups with μ(1,1) and μ(1,3) bridging modes of bonding. Hirshfeld analysis was used to quantitatively determine the different contacts affecting the molecular packing in the studied complexes. The most common interactions are the polar O…H and N…H interactions and the hydrophobic C…H contacts. The charges at the M(II) sites are calculated to be 1.004, 0.847, and 1.147 e for complexes 1–3, respectively. The degree of asymmetry is the highest in the case of the terminal azide in complexes 1 and 2 while was found the lowest in the μ(1,1) and μ(1,3) azide bonding modes in the Zn(II) complex 3. These facts were further explained in terms of atoms in molecules (AIM) topological parameters.

Tuning the Kinetic Inertness of Bi3+ Complexes: The Impact of Donor Atoms on Diaza-18-Crown-6 Ligands as Chelators for 213Bi Targeted Alpha Therapy

The radionuclide ²¹³Bi can be applied for targeted α therapy (TAT): a type of nuclear medicine that harnesses α particles to eradicate cancer cells. To use this radionuclide for this application, a bifunctional chelator (BFC) is needed to attach it to a biological targeting vector that can deliver it selectively to cancer cells. Here, we investigated six macrocyclic ligands as potential BFCs, fully characterizing the Bi³⁺ complexes by NMR spectroscopy, mass spectrometry, and elemental analysis. Solid-state structures of three complexes revealed distorted coordination geometries about the Bi³⁺ center arising from the stereochemically active 6s² lone pair. The kinetic properties of the Bi³⁺ complexes were assessed by challenging them with a 1000-fold excess of the chelating agent diethylenetriaminepentaacetic acid (DTPA). The most kinetically inert complexes contained the most basic pendent donors. Density functional theory (DFT) and quantum theory of atoms in molecules (QTAIM) calculations were employed to investigate this trend, suggesting that the kinetic inertness is not correlated with the extent of the 6s² lone pair stereochemical activity, but with the extent of covalency between pendent donors. Lastly, radiolabeling studies of ²¹³Bi (30-210 kBq) with three of the most promising ligands showed rapid formation of the radiolabeled complexes at room temperature within 8 min for ligand concentrations as low as 10^-7 M, corresponding to radiochemical yields of >80%, thereby demonstrating the promise of this ligand class for use in ²¹³Bi TAT.

Theoretical investigation of tetrahedral distortion of four-coordinate iron(II) centres in FePd(CN)4

The tetrahedral distortion of iron(ii) centres in the cyanide-bridged framework FePd(CN)4 was recently demonstrated experimentally. Here, we theoretically confirmed the electronically driven tetrahedral distortion of iron(ii) by comparing the density of states and total energies of FePd(CN)4 (d6) and ZnPd(CN)4 (d10). The calculation results suggested that a Jahn-Teller-like effect is caused on the tetrahedral geometry by the electronic effect of unequally occupied non-bonding 3d orbitals in the corresponding structure.

Metastable Dianions and Dications

A theoretical study of metastable dianions and dications has been carried out at the CCSD(T)//MP2 level. MX₃ ^2- and LX₄ ^2- (M=Li and Na, L=Be and Mg, X=F and Cl) have been considered as dianions, M₃ X²⁺ (M=Li and Na, X=F and Cl), YH₃ ²⁺ and ZH₄ ²⁺ (Y=F and Cl and Z=O, S) as dications. Minima structures are found in all cases, but they are less stable than the corresponding dissociated pair of mono-ions. The dissociation profile of the molecules in two mono-ions has been explored showing in all cases a maximum that prevent their spontaneous dissociation. The strength and nature of the chemical bond in the dianions and dications have been analyzed with the QTAIM, NBO and LMOEDA method and compared to the corresponding monoanions and monocations.

Hydrothermal growth of facet-tunable fluoride perovskite crystals KMF3 (M = Mg, Mn, Co, Ni and Zn)

A family of perovskite structure fluoride (KMF₃, M = Mg, Mn, Co, Ni, and Zn) single crystals has been grown with tuneable exposed facets via ligand substitution strategy in mild hydrothermal condition.

Coinage metal dimers as the noncovalent interaction acceptors: study of the σ-lump interactions

The ability of group 11 coinage metal dimers M₂ (M = Cu, Ag, Au) to favorably interact with different electron acceptors XCN (X = H, F, Cl, Br) was evaluated with the M06-L functional and the aug-cc-pVDZ basis sets (aug-cc-pVDZ-pp basis sets were used for copper, silver, and gold atoms). The metal dimers M₂ (M = Cu, Ag, Au) have negative regions of electrostatic potential (ESP) in the middle of the M-M bond, namely the σ-lumps. The positive ESP outside the X atom along the extension of the X-C bond in XCN (X = H, F, Cl, Br) could interact with the σ-lump of metal dimers to form the σ-lump interactions. When M remains unchanged, the σ-lump interactions between M₂ (M = Cu, Ag, Au) and XCN (X = F, Cl, Br) increase gradually in the order of F, Cl and Br. The electrostatic interactions are the dominant attractive interactions in the M₂XCN (X = F, Cl, Br) halogen-bonded interactions. The orbital interactions contribute more than the electrostatic interactions in the M₂HCN hydrogen-bonded interactions. Molecular graphs after orbital separation show that the π orbitals contribute the most to the σ-lump interactions; the σ and δ orbitals also have some contributions. Charge transfer occurs in the formation of the σ-lump interactions, mainly from the M-M bonding orbital of metal dimers to the X-C anti-bonding orbital. The M₂BrCN (M = Cu, Ag, Au) series complexes possess the largest charge transfer from donor to acceptor orbitals.

Halogen Bonding: A Halogen-Centered Noncovalent Interaction Yet to Be Understood

In addition to the underlying basic concepts and early recognition of halogen bonding, this paper reviews the conflicting views that consistently appear in the area of noncovalent interactions and the ability of covalently bonded halogen atoms in molecules to participate in noncovalent interactions that contribute to packing in the solid-state. It may be relatively straightforward to identify Type-II halogen bonding between atoms using the conceptual framework of σ-hole theory, especially when the interaction is linear and is formed between the axial positive region (σ-hole) on the halogen in one monomer and a negative site on a second interacting monomer. A σ-hole is an electron density deficient region on the halogen atom X opposite to the R–X covalent bond, where R is the remainder part of the molecule. However, it is not trivial to do so when secondary interactions are involved as the directionality of the interaction is significantly affected. We show, by providing some specific examples, that halogen bonds do not always follow the strict Type-II topology, and the occurrence of Type-I and -III halogen-centered contacts in crystals is very difficult to predict. In many instances, Type-I halogen-centered contacts appear simultaneously with Type-II halogen bonds. We employed the Independent Gradient Model, a recently proposed electron density approach for probing strong and weak interactions in molecular domains, to show that this is a very useful tool in unraveling the chemistry of halogen-assisted noncovalent interactions, especially in the weak bonding regime. Wherever possible, we have attempted to connect some of these results with those reported previously. Though useful for studying interactions of reasonable strength, IUPAC’s proposed “less than the sum of the van der Waals radii” criterion should not always be assumed as a necessary and sufficient feature to reveal weakly bound interactions, since in many crystals the attractive interaction happens to occur between the midpoint of a bond, or the junction region, and a positive or negative site.

Sigma-hole carbon-bonding interactions in carbon-carbon double bonds: an unnoticed contact

In this manuscript, we combine high-level ab initio calculations on some small complexes and a CSD survey to analyze the existence of unprecedented noncovalent carbon bonds in X₂C[double bond, length as m-dash]CH₂Y systems (Y = electron-rich atom or group). The methylene group is usually seen as a weak hydrogen bond donor when interacting with an electron-rich atom. However, we demonstrate that when the electron-rich atom is located equidistant from the two H atoms and along the C[double bond, length as m-dash]C bond a σ-hole noncovalent carbon-bonding interaction is established, instead of a bifurcated hydrogen bond, as derived from Atoms-in-Molecules (AIM) and Natural bond orbital (NBO) analyses. The physical nature of the interaction has been analyzed using the Symmetry Adapted Perturbation Theory (SAPT) method. The results indicate that electrostatics is very important followed by either the induction or dispersion terms in anionic and neutral complexes, respectively. In addition the CSD analysis reveals the existence of such interactions, giving reliability to our calculations, which are much more numerous for neutral than for anionic Y systems.

Revealing the Chemistry between Band Gap and Binding Energy for Lead-/Tin-Based Trihalide Perovskite Solar Cell Semiconductors

A relationship between reported experimental band gaps (solid) and DFT-calculated binding energies (gas) is established, for the first time, for each of the four ten-membered lead (or tin) trihalide perovskite solar cell semiconductor series examined in this study, including CH₃ NH₃ PbY₃ , CsPbY₃ , CH₃ NH₃ SnY₃ and CsSnY₃ (Y=I_(3-x) Br_x=1-3 , I_(3-x) Cl_x=1-3 , Br_(3-x) Cl _x=1-3 , and IBrCl). The relationship unequivocally provides a new dimension for the fundamental understanding of the optoelectronic features of solid-state solar cell thin films by using the 0 K gas-phase energetics of the corresponding molecular building blocks.

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.

Ammonia-modified Co(II) sites in zeolites: spin and electron density redistribution through the Co(II)-NO bond

Electronic factors essential for the bonding of a non-innocent NO ligand to ammonia-modified Co(2+) sites in cobalt-exchanged zeolites are examined for small cluster models using DFT and advanced correlated wave function calculations. The analysis of charge transfer processes between the NO ligand and the cobalt center involves two protocols: valence-bond expansion of the multiconfiguration CASSCF wave function (in terms of fragment-localized active orbitals) and spin-resolved natural orbitals for chemical valence (SR-NOCV). Applicability of SR-NOCV analysis to transition metal complexes involving non-innocent fragments is critically assessed and the approach based on the CASSCF wave function turns out to be much more robust and systematic for all studied models. It is shown that the character and direction of electron density redistribution through the Co-N-O bond, quantified by relative share of the Co(II)-NO(0), Co(III)-NO(-), and Co(I)-NO(+) resonance structures in the total wave function, fully rationalize the activation of the N-O bond upon NH3 co-ligation (evidenced by calculated and measured red-shift of the NO stretching frequency and commonly ascribed to enhanced backdonation). The huge red-shift of νN-O is attributed to an effective electron transfer between the ammonia-modified Co(ii) centers and the NO antibonding π*-orbitals (related to the increased share of the Co(III)-NO(-) form). Unexpectedly, the effect is stronger for the singlet complex with three NH3 ligands than for that with five NH3 ligands bound to the cobalt center. Our results also indicate that high-efficiency electron transfers between the Co(ii) center and the NO ligand may be enabled for the selected spin state and disabled for the other spin state of the adduct. This illustrates how the cobalt center may serve to fine-tune the electronic communication between the NO ligand and its binding site.

Can an entirely negative fluorine in a molecule, viz. perfluorobenzene, interact attractively with the entirely negative site(s) on another molecule(s)? Like liking like!

The study presents the possibility for the formation of attractive intermolecular interactions between various entirely negative Lewis bases, leading to the formation of the thirteen isolated binary complexes examined.

Noncovalent interactions determine the conformation of aurophilic complexes with 2-mercapto-4-methyl-5-thiazoleacetic acid ligands

The synthesis of three new gold(i) salts is reported. The intermolecular interactions stabilizing the aurophilic dimers are examined by several first principles interpretative techniques.

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.

Unusual bonding modes of perfluorobenzene in its polymeric (dimeric, trimeric and tetrameric) forms: entirely negative fluorine interacting cooperatively with entirely negative fluorine

The Laplacian of the charge density plot for the tetramer of perfluorobenzene, displaying the attraction between entirely negative fluorine atoms, as well as the windmill type intermolecular topology between those atoms.

Dynamic motion of an Lu pair inside a C76(Td) cage

The dynamic motion of an Lu pair inside a C₇₆(T_d) cage was investigated by relativistic density functional theory (DFT).

Significant evidence of C⋯O and C⋯C long-range contacts in several heterodimeric complexes of CO with CH3–X, should one refer to them as carbon and dicarbon bonds!

An illustrated example of a ‘dicarbon bond’ formed between a pair of two carbon atoms of the OC⋯CH₃–Cl₃intermolecular complex, one corresponding to the methylated carbon in 1,1,1-trichloro-ethane (CH₃–Cl₃) and one to the carbon in the carbon dioxide (CO) molecule.

Halogen bonding interaction of chloromethane with several nitrogen donating molecules: addressing the nature of the chlorine surface σ-hole

The small and positive σ-hole on the outermost extension of the C–Cl covalent bond in CH₃Cl can adequately form halogen bonded interactions with the RN series of thirteen other molecules, R = FC, ClC, BrC, CH₃C, HOC, HSC, PCC, P, CCl₃C, SiH₃C, NCC, CNC, and NaC.