Halide Ligated Iron Porphines: A DFT+U and UB3LYP Study

Mean Value Ensemble Hubbard-U Correction for Spin-Crossover Molecules

High-throughput searches for spin-crossover molecules require Hubbard-U corrections to common density functional exchange-correlation (XC) approximations. However, the U_eff values obtained from linear response or based on previous studies overcorrect the spin-crossover energies. We demonstrate that employing a linearly mixed ensemble average spin state as the reference configuration for the linear response calculation of U_eff resolves this issue. Validation on a commonly used set of spin-crossover complexes shows that these ensemble U_eff values consistently are smaller than those calculated directly on a pure spin state, irrespective of whether that be low- or high-spin. Adiabatic crossover energies using this methodology for a generalized gradient approximation XC functional are closer to the expected target energy range than with conventional U_eff values. Based on the observation that the U_eff correction is similar for different complexes that share transition metals with the same oxidation state, we devise a set of recommended averaged U_eff values for high-throughput calculations.

NiFe-mixed metal porphyrin aerogels as oxygen evolution reaction catalysts in alkaline electrolysers

Aerogels are a very interesting group of materials owing to their unique physical and chemical properties. In the context of electrocatalysis, the focus has been on their physical properties, and they have been used primarily as catalyst supports so far. In this work, we synthesized porphyrin aerogels containing Ni and NiFe mixed metal materials and studied them as catalysts for the oxygen evolution reaction (OER). Different Ni : Fe ratios were synthesized and studied in electrochemical cells, and DFT calculations were conducted in order to gain insight into their behavior. The activity trends were dependent on the metal ratios and differ from known NiFeOOH materials due to the change in the oxidation states of the metals to higher numbers. Herein, we show that Ni and Fe have a synergistic effect on the OER, despite being structurally separated. They are connected electronically, though, through a large organic aromatic system that facilitates electron sharing between them. Among the mixed metal porphyrin aerogels, the best ratio was found to be Ni : Fe = 35 : 65, in contrast to oxide/oxyhydroxide materials in which a ratio of 80 : 20 was found to be ideal.

Multi-Oxyanion Detection by an Organic Field-Effect Transistor with Pattern Recognition Techniques and Its Application to Quantitative Phosphate Sensing in Human Blood Serum

We herein report an organic field-effect transistor (OFET) based chemical sensor for multi-oxyanion detection with pattern recognition techniques. The oxyanions ubiquitously play versatile roles in biological systems, and accessing the chemical information they provide would potentially facilitate fundamental research in diagnosis and pharmacology. In this regard, phosphates in human blood serum would be a promising indicator for early case detection of significant diseases. Thus, the development of an easy-to-use chemical sensor for qualitative and quantitative detection of oxyanions is required in real-world scenarios. To this end, an extended-gate-type OFET has been functionalized with a metal complex consisting of 2,2'-dipicolylamine and a copper(II) ion (CuII-dpa), allowing a compact chemical sensor for oxyanion detection. The OFET combined with a uniform CuII-dpa-based self-assembled monolayer (SAM) on the extended-gate gold electrode shows a cross-reactive response, which suggests a discriminatory power for pattern recognition. Indeed, the qualitative detection of 13 oxyanions (i.e., hydrogen monophosphate, pyrophosphate, adenosine monophosphate, adenosine diphosphate, adenosine triphosphate, terephthalate, phthalate, isophthalate, malonate, oxalate, lactate, benzoate, and acetate) has been demonstrated by only using a single OFET-based sensor with linear discriminant analysis, which has shown 100% correct classification. The OFET has been further applied to the quantification of hydrogen monophosphate in human blood serum using a support vector machine (SVM). The multiple predictions of hydrogen monophosphate at 49 and 89 μM have been successfully realized with low errors, which indicates that the OFET-based sensor with pattern recognition techniques would be a practical sensing platform for medical assays. We believe that a combination of the OFET functionalized with the SAM-based recognition scaffold and powerful pattern recognition methods can achieve multi-analyte detection from just a single sensor.

Theoretical analysis of pressure induced spin crossover phenomenon in a di-nuclear Fe(II) molecular complex

We have studied a Fe-based di-nuclear molecular complex having the chemical formula [{Fe(bpp)(NCS)₂}₂([Formula: see text]'-bipy)]·2MeOH (where bpp  =  [Formula: see text]-bis(pyrazol-3-yl) pyridine and [Formula: see text]'-bipy  =  [Formula: see text]'-bipyridine, 1) using density functional theory and model Hamiltonian approach. Our study provides insight to the pressure driven spin-crossover (SCO) phenomena observed experimentally in these systems. Upon increasing the pressure, the spin state of Fe(II) cation gradually changes from a high spin state (S  =2) to a low spin (LS) state (S  =0) accompanied by volume contraction. The gradual increase in pressure shrinks Fe-N bond length and also causes angular deviation of the FeN₆ octahedron leading to full conversion to the LS state without global structural phase transition. We have carried out exact diagonalization study of an effective single site Hamiltonian and confirmed the importance of intramolecular interaction for SCO phenomena. We have investigated the cooperativity of the observed SCO phenomena. We have also studied the effect of Co doping on the spin state of Fe and find that the spin state of Fe has a subtle dependency on the concentration of dopant atoms. Excess Co doping pave the way towards the possibility of an intermediate spin state for Fe and can give rise to a bistable spin transition process.

Theoretical Study on Electronic Structural Properties of Catalytically Reactive Metalloporphyrin Intermediates

Metalloporphyrins have attracted great attention in the potential application of biomimetic catalysis. Especially, they were widely investigated as green catalysts in the chemical oxidation of various hydrocarbons through the catalytic activation of molecular oxygen. The structural properties of active central metal ions were reported to play a decisive role in catalytic activity. However, those delicate structural changes are difficult to be experimentally captured or elucidated in detail. Herein, we explored the electronic structural properties of metalloporphyrins (metal porphyrin (PMII, PMIIICl)) and their corresponding catalytically active intermediates (metal(III)-peroxo(PMIII-O2), metal(III)-hydroperoxo(PMIII-OH), and metal(IV)-oxo(PMIV=O), (M=Fe, Mn, and Co)) through the density functional theory method. The ground states of these intermediates were determined based on the assessment of relative energy and the corresponding geometric structures of ground states also further confirmed the stability of energy. Furthermore, our analyses of Mulliken charges and frontier molecular orbitals revealed the potential catalytic behavior of reactive metalloporphyrin intermediates.

Interfacial Spin Manipulation of Nickel-Quinonoid Complex Adsorbed on Co(001) Substrate

We studied the structural, electronic, and magnetic properties of a recently synthesized Ni(II)-quinonoid complex upon adsorption on a magnetic Co(001) substrate. Our density functional theory + U (DFT+U) calculations predict that the molecule undergoes a spin-state switching from low-spin S = 0 in the gas phase to high-spin S ≈ 1 when adsorbed on the Co(001) surface. A strong covalent interaction of the quinonoid rings and surface atoms leads to an increase of the Ni–O(N) bond lengths in the chemisorbed molecule that support the spin-state switching. Our DFT+U calculations show that the molecule is ferromagnetically coupled to the substrate. The Co surface–Ni center exchange mechanism was carefully investigated. We identified an indirect exchange interaction via the quinonoid ligands that stabilizes the molecule’s spin moment in ferromagnetic alignment with the Co surface magnetization.

3D pharmacophore-based virtual screening, docking and density functional theory approach towards the discovery of novel human epidermal growth factor receptor-2 (HER2) inhibitors

Human epidermal growth factor receptor 2 (HER2) is one of the four members of the epidermal growth factor receptor (EGFR) family and is expressed to facilitate cellular proliferation across various tissue types. Therapies targeting HER2, which is a transmembrane glycoprotein with tyrosine kinase activity, offer promising prospects especially in breast and gastric/gastroesophageal cancer patients. Persistence of both primary and acquired resistance to various routine drugs/antibodies is a disappointing outcome in the treatment of many HER2 positive cancer patients and is a challenge that requires formulation of new and improved strategies to overcome the same. Identification of novel HER2 inhibitors with improved therapeutics index was performed with a highly correlating (r=0.975) ligand-based pharmacophore model (Hypo1) in this study. Hypo1 was generated from a training set of 22 compounds with HER2 inhibitory activity and this well-validated hypothesis was subsequently used as a 3D query to screen compounds in a total of four databases of which two were natural product databases. Further, these compounds were analyzed for compliance with Veber's drug-likeness rule and optimum ADMET parameters. The selected compounds were then subjected to molecular docking and Density Functional Theory (DFT) analysis to discern their molecular interactions at the active site of HER2. The findings thus presented would be an important starting point towards the development of novel HER2 inhibitors using well-validated computational techniques.

A convenient procedure for the synthesis of fluoro-iron(III) complexes of common synthetic porphyrinates

We report here an improved method for the preparation of fluoro-iron(III) porphyrinate complexes. Treatment of [ Fe 2( P )2(μ- O )] (P = tetraphenylporphyrinate {TPP}, tetra-p-tolylporphyrinate {TTP}, or octaethylporphyrinate {OEP}) or [ Fe ( OH )( OH 2)( TMP )] (TMP = tetramesitylporphyrinate) with the commercially available fluorinating agent, Et 3 N ·3 HF , in dichloromethane affords the desired [ FeF ( P )] complexes in a straightforward fashion and in good yield while avoiding the use of aqueous hydrofluoric acid. All fluoro-iron(III) complexes have been completely characterized by a series of different spectroscopic techniques including cyclic voltammetry. Reaction of a representative complex, [ FeF ( OEP )], with various chloride reagents demonstrates that halide exchange with chloride is facile, but only proceeds at an appreciable rate in the presence of proton sources. Unexpectedly, treatment of [ FeF ( OEP )] with NOBF 4 did not to lead formation of an oxidized species, but rather to formation of the { Fe – NO }6 complex, [ Fe ( NO )( OEP )]( BF 4).

Cytochrome P450 compound I in the plane wave pseudopotential framework: GGA electronic and geometric structure of thiolate-ligated iron(IV)-oxo porphyrin

The cytochromes P450 constitute a ubiquitous family of metalloenzymes, catalyzing manifold reactions of biological and synthetic importance via a thiolate-ligated iron-oxo (IV) porphyrin radical species denoted compound I (Cpd I). Experimental investigations have implicated this intermediate in a broad spectrum of biophysically interesting phenomena, further augmenting the importance of a Cpd I model system. Ab initio molecular dynamics, including Car-Parrinello and path integral methods, conjoin electronic structure theory with finite temperature simulation, affording tools most valuable to approach such enzymes. These methods are typically driven by density functional theory (DFT) in a plane-wave pseudopotential framework; however, existing studies of Cpd I have been restricted to localized Gaussian basis sets. The appropriate choice of density functional and pseudopotential for such simulations is accordingly not obvious. To remedy this situation, a systematic benchmarking of thiolate-ligated Cpd I is performed using several generalized-gradient approximation (GGA) functionals in the Martins-Troullier and Vanderbilt ultrasoft pseudopotential schemes. The resultant electronic and structural parameters are compared to localized-basis DFT calculations using GGA and hybrid density functionals. The merits and demerits of each scheme are presented in the context of reproducing existing experimental and theoretical results for Cpd I.

A combination of receptor-based pharmacophore modeling & QM techniques for identification of human chymase inhibitors

Inhibition of chymase is likely to divulge therapeutic ways for the treatment of cardiovascular diseases, and fibrotic disorders. To find novel and potent chymase inhibitors and to provide a new idea for drug design, we used both ligand-based and structure-based methods to perform the virtual screening(VS) of commercially available databases. Different pharmacophore models generated from various crystal structures of enzyme may depict diverse inhibitor binding modes. Therefore, multiple pharmacophore-based approach is applied in this study. X-ray crystallographic data of chymase in complex with different inhibitors were used to generate four structure-based pharmacophore models. One ligand-based pharmacophore model was also developed from experimentally known inhibitors. After successful validation, all pharmacophore models were employed in database screening to retrieve hits with novel chemical scaffolds. Drug-like hit compounds were subjected to molecular docking using GOLD and AutoDock. Finally four structurally diverse compounds with high GOLD score and binding affinity for several crystal structures of chymase were selected as final hits. Identification of final hits by three different pharmacophore models necessitates the use of multiple pharmacophore-based approach in VS process. Quantum mechanical calculation is also conducted for analysis of electrostatic characteristics of compounds which illustrates their significant role in driving the inhibitor to adopt a suitable bioactive conformation oriented in the active site of enzyme. In general, this study is used as example to illustrate how multiple pharmacophore approach can be useful in identifying structurally diverse hits which may bind to all possible bioactive conformations available in the active site of enzyme. The strategy used in the current study could be appropriate to design drugs for other enzymes as well.

Importance of many-body effects in the Kernel of hemoglobin for ligand binding

We propose a mechanism for binding of diatomic ligands to heme based on a dynamical orbital selection process. This scenario may be described as bonding determined by local valence fluctuations. We support this model using linear-scaling first-principles calculations, in combination with dynamical mean-field theory, applied to heme, the kernel of the hemoglobin metalloprotein central to human respiration. We find that variations in Hund's exchange coupling induce a reduction of the iron 3d density, with a concomitant increase of valence fluctuations. We discuss the comparison between our computed optical absorption spectra and experimental data, our picture accounting for the observation of optical transitions in the infrared regime, and how the Hund's coupling reduces, by a factor of 5, the strong imbalance in the binding energies of heme with CO and O(2) ligands.

A GGA+U approach to effective electronic correlations in thiolate-ligated iron-oxo (IV) porphyrin

High-valent oxo-metal complexes exhibit correlated electronic behavior on dense, low-lying electronic state manifolds, presenting challenging systems for electronic structure methods. Among these species, the iron-oxo (IV) porphyrin denoted Compound I occupies a privileged position, serving a broad spectrum of catalytic roles. The most reactive members of this family bear a thiolate axial ligand, exhibiting high activity toward molecular oxygen activation and substrate oxidation. The default approach to such systems has entailed the use of hybrid density functionals or multi-configurational/multireference methods to treat electronic correlation. An alternative approach is presented based on the GGA+U approximation to density functional theory, in which a generalized gradient approximation (GGA) functional is supplemented with a localization correction to treat on-site correlation as inspired by the Hubbard model. The electronic structure of thiolate-ligated iron-oxo (IV) porphyrin and corresponding Coulomb repulsion U are determined both empirically and self-consistently, yielding spin-distributions, state level splittings, and electronic densities of states consistent with prior hybrid functional calculations. Comparison of this detailed electronic structure with model Hamiltonian calculations suggests that the localized 3d iron moments induce correlation in the surrounding electron gas, strengthening local moment formation. This behavior is analogous to strongly correlated electronic systems such as Mott insulators, in which the GGA+U scheme serves as an effective single-particle representation for the full, correlated many-body problem.

Electronic structure, spin-states, and spin-crossover reaction of heme-related Fe-porphyrins: a theoretical perspective

The electronic structures, spin-states, and geometrical parameters of tetra-, penta-, and hexa-coordinated iron-porphyrins are investigated applying density functional theory (DFT) based calculations, utilizing the plane-wave pseudopotential as well as localized basis set approaches. The splitting of the spin multiplet energies are investigated applying various functionals including recently developed hybrid meta-GGA (M06 family) functionals. Almost all of the hybrid functionals accurately reproduce the experimental ground state spins of the investigated Fe-porphyrins. However, the energetic ordering of the spin-states and the energies between them are still an issue. The widely used B3LYP provides consistent results for all chosen systems. The GGA+U functionals are found to be equally competent. After assessing the performance of various functionals in spin-state calculations, the potential energy surfaces of the oxygen binding process by heme is investigated. This reveals a "double spin-crossover" feature for the lowest energy reaction path that is consistent with previous CASPT2 calculations but predicting a lowest energy singlet state. The calculations have hence captured the spin-crossover as well as spin-flip processes. These are driven by the intra-atomic orbital polarization on the central metal atom due to the atomic and orbitals rearrangements. The nature of the chemical bonding and a molecular orbital analysis are also performed for the geometrically simple but electronic structurally complicated system tetra-coordinated planar Fe porphyrin in comparison to the penta-coordinated systems. This analysis explains the observed paradoxical appearance of certain peaks in the local density of states (DOS).