Conformational Dynamics in Corynebacterium glutamicum Diaminopimelate Epimerase: Insights from Ligand Parameterization, Atomistic Simulation, and Markov State Modeling.

The microbial enzyme diaminopimelate epimerase (DapF), a vital enzyme in the lysine biosynthetic pathway, catalyzes the conversion of L, L-diaminopimelate (L, L-DAP) to D, L-diaminopimelate (D, L-DAP) using a catalytic cysteine dyad with one cysteine in thiol state and another in thiolate. Under oxidizing conditions, the catalytic cysteines of apo DapF form a disulfide bond that alters the structure and function of DapF. Given its potential as a target for antimicrobial resistance treatments, understanding DapF's functional dynamics is imperative. In the present work, we employ microsecond-scale all-atom molecular dynamics simulations of product-bound DapF and apo-DapF under oxidized and reduced conditions. We employ a polarized charge model for the ligand and the active site residues, which was necessary to preserve the electrostatic environment in the active site and retain the ligand in the active site. The product-bound DapF and apo-DapF in oxidized and reduced conditions exhibit a closed, semi-open, and open conformation, respectively, as identified using the internal coordinates of the dimeric enzyme and the principal component analysis. The conformational switch is guided by the dynamic catalytic (DC) loop, loop II, and loop III movements in the active site. The time scale of the close-to-open conformational transition is estimated to be 0.8 µs through Markov state modeling (MSM) and transition path theory (TPT). The present study explains the role of various active site residues and loops in ligand binding and protein dynamics in the DapF enzyme under different redox conditions. Such information will be helpful in future inhibitor design studies targeting the DapF enzyme.

Ab initio calculation of magnetic anisotropy and thermal spin transition in the variable temperature crystal conformations of [Co(terpy)2]2.

The structure-property correlation of [Co(terpy)2]2+, which shows a spin crossover at 270 K, has been computationally investigated based on its variable temperature crystal structures. Among the employed DFT functionals, only the re-parametrized hybrid B3LYP* functional could describe the correct spin transition temperature. Explicit consideration of metal-ligand sigma bonding with dynamic electron correlation is found to be necessary for an accurate determination of the SCO temperature with multi-reference calculations. The metal-ligand axial bond distances are found to be the most significant internal coordinates in deciding SCO. A small structural change along the axial distance causes a change in the t2g orbital splitting pattern and a reorientation of the magnetization axes at the SCO temperature. The complex shows an unusual triaxial magnetic anisotropy, with an easy axis of magnetization developing at higher temperatures. The strong coupling of low-frequency wagging motion of the two terpyridine ligands with the spin states of the complex provides an effective pathway for the relaxation of magnetization, resulting in a small magnetic anisotropy barrier.

Hückel molecular orbital theory on a quantum computer: A scalable system-agnostic variational implementation with compact encoding.

Hückel molecular orbital (HMO) theory provides a semi-empirical treatment of the electronic structure in conjugated π-electronic systems. A scalable system-agnostic execution of HMO theory on a quantum computer is reported here based on a variational quantum deflation (VQD) algorithm for excited state quantum simulation. A compact encoding scheme is proposed here that provides an exponential advantage over the direct mapping and allows for quantum simulation of the HMO model for systems with up to 2n conjugated centers with n qubits. The transformation of the Hückel Hamiltonian to qubit space is achieved by two different strategies: an iterative refinement transformation and the Frobenius-inner-product-based transformation. These methods are tested on a series of linear, cyclic, and hetero-nuclear conjugated π-electronic systems. The molecular orbital energy levels and wavefunctions from the quantum simulation are in excellent agreement with the exact classical results. However, the higher excited states of large systems are found to suffer from error accumulation in the VQD simulation. This is mitigated by formulating a variant of VQD that exploits the symmetry of the Hamiltonian. This strategy has been successfully demonstrated for the quantum simulation of C60 fullerene containing 680 Pauli strings encoded on six qubits. The methods developed in this work are easily adaptable to similar problems of different complexity in other fields of research.

Design, Synthesis, and Characterization of Organometallic BODIPY-Ru(II) Dyads: Redox and Photophysical Properties with Singlet Oxygen Generation Capability†.

A series of Ru(II)-acetylide complexes (Ru1, Ru2, and Ru1m) with alkynyl-functionalized borondipyrromethene (BODIPY) conjugates were designed by varying the position of the linker that connects the BODIPY unit to the Ru(II) metal center through acetylide linkage at either the 2-(Ru1) and 2,6-(Ru2) or the meso-phenyl (Ru1m) position of the BODIPY scaffold. The Ru(II) organometallic complexes were characterized by various spectroscopic methods, including nuclear magnetic resonance (NMR) spectroscopy, infrared (IR) spectroscopy, CHN, and high-resolution mass spectrometry (HRMS) analyses. The Ru(II)-BODIPY conjugates exhibit fascinating electrochemical and photophysical properties. All BODIPY-Ru(II) complexes exhibit strong absorption (εmax = 29,000-72,000 M-1 cm-1) in the visible region (λmax = 502-709 nm). Fluorescence is almost quenched for Ru1 and Ru2, whereas Ru1m shows the residual fluorescence of the corresponding BODIPY core at 517 nm. The application of the BODIPY-Ru(II) dyads as nonporphyrin-based triplet photosensitizers was explored by a method involving the singlet oxygen (1O2)-mediated photo-oxidation of diphenylisobenzofuran. Effective π-conjugation between the BODIPY chromophore and Ru(II) center in the case of Ru1 and Ru2 was found to be necessary to improve intersystem crossing (ISC) and hence the 1O2-sensitizing ability. In addition, electrochemical studies indicate electronic interplay between the metal center and the redox-active BODIPY in the BODIPY-Ru(II) dyads.

Functionalized Carbon Nano-Onions as a Smart Drug Delivery System for the Poorly Soluble Drug Carmustine for the Management of Glioblastoma.

The drug delivery system for transporting anticancer agents to targeted tissues in the body is a challenging issue. In search of a suitable biocompatible carrier having controlled and sustained drug release properties of poorly soluble drugs, carbon nano-onions (CNOs) were loaded with an anticancer drug, bis-chloroethyl nitrosourea (BCNU/carmustine). CNOs being autofluorescent, drug-loaded functionalized CNOs (f-CNO-BCNU) can be detected in vivo. Transmission electron microscopy (TEM) and differential light scattering (DLS) techniques were used to analyze the sizes of these f-CNOs. The molecular study revealed that the f-CNO-BCNU readily and noncovalently binds with the folate receptors present on the cancer cell surface in excess. Computer modeling and molecular dynamics simulation followed by binding free energy calculation shows f-CNOs have -29.9 kcal/mol binding free energy, and it noncovalently binds the receptor FRα using loop dynamics of three essential loops present in the protein along with polar stabilization interactions provided by Asp55 and Glu86 residues present in the active site. The f-CNO effectively decreased cancer cell viability with a low IC50 value (the concentration that led to 50% killing of the cells). The cell-based Franz diffusion assay was performed to study the drug release profile. The f-CNO-BCNUs also decreased the mitochondrial membrane potential of U87 cells, increased reactive oxygen species release, and caused a loss of mitochondrial membrane integrity. The f-CNOs also increased the percentage of apoptotic cells observed by the Annexin V assay. Based on observed results, it can be concluded that the f-CNO-BCNU efficiently targets the cancer cells, enhances the bioavailability of carmustine, and can be used as a smart chemotherapeutic agent. This strategy offers better patient compliance and greater bioavailability of the drug.

2-Anilidomethylpyridine-Derived Three-Coordinate Zinc Hydride: The Journey Unveils Anilide Backbone's Reactive Nature.

Low-coordinate heteroleptic zinc hydrides are catalytically important but rare and synthetically challenging. We herein report three-coordinate monomeric zinc hydride on a 2-anilidomethylpyridine framework (NNL). The synthetic success comes through systematically screening a few different routes from different precursors. During the process, the ligand's anilide backbone interestingly appears to be more reactive than Zn's terminal site to electrophilic Lewis and Brønsted acids. The proligand NNLH reacts with [Zn{N(SiMe3)2}2] and ZnEt2 to give [(NNL)ZnA] (A = N(SiMe3)2 (1), Et(2)). Both are inert to PhSiH3 and H2 but react with HBpin only through the internal Zn-Nanilide bond to give the borylated ligand NNLBpin (3). The reactions of 1 and 2 with Ph3EOH (E = C, Si) afford a series of divergent compounds like [(NNLH)Zn(OSiPh3)2] (4), [Zn3(OSiPh3)4Et2] (5), and [EtZn(OCPh3)] (6). But in all cases, it is invariably the Zn-Nanilide bond protonated by the -OH with equal or higher preference than the terminal Zn-N or Zn-C bonds. A DFT analysis rationalizes the origin of such a reactivity pattern. Realizing that an acid-free route might be the key, reacting [(NNL)Li] with ZnBr2 gives [(NNL)Zn(µ-Br)]2 (7), which on successively treating with KOSiPh3 and PhSiH3 gives the desired [(NNL)ZnH] (8) as a three-coordinate monomer with a terminal Zn-H bond. Estimating the ligand steric in 8 shows the openness in Zn's coordination sphere, a desired criterion for efficient catalysis. This and a positive influence of the pyridyl sidearm is reflected in 8's superior activity in hydroborating PhC(O)Me by HBpin in comparison to Jones' two-coordinate anilido zinc hydride.

The interplay of vibronic and spin-orbit coupling in the fluorescence quenching in trans-dithionated PDI.

Organic chromophores such as the thionated derivatives of perylene diimides (PDIs) show prolonged triplet-excited state lifetimes in contrast to their pristine parent PDI molecule, which shows near unity fluorescence quantum yield. The excited state dynamics in the trans-dithionated PDI (S2-PDI) are studied here. Unlike PDI, the photo absorbing ππ* state of S2-PDI is in close proximity to quasi-degenerate nπ* states. The latter exhibits an interesting vibronic problem leading to the breaking of orbital symmetry mediated through non-totally symmetric vibrations. The time-dependent quantum dynamics are studied with a diabatic model Hamiltonian involving three singlet and three triplet states coupled via 22 vibrational modes. A combined effect of multiple internal-conversion and inter-system crossing (ISC) pathways leads to population transfer from the 1ππ* state to the 3ππ* state via the nπ* states, with an overall ISC rate of 0.70 ps that compares well with the experimental value. The calculated absorption spectra for PDI and S2-PDI reproduce the essential vibronic features in the observed experimental spectra. The dominant vibronic progressions are found to have significant contributions from the vinyl stretching modes of the PDI core.

Benchmarking of different optimizers in the variational quantum algorithms for applications in quantum chemistry.

Classical optimizers play a crucial role in determining the accuracy and convergence of variational quantum algorithms; leading algorithms use a near-term quantum computer to solve the ground state properties of molecules, simulate dynamics of different quantum systems, and so on. In the literature, many optimizers, each having its own architecture, have been employed expediently for different applications. In this work, we consider a few popular and efficacious optimizers and assess their performance in variational quantum algorithms for applications in quantum chemistry in a realistic noisy setting. We benchmark the optimizers with critical analysis based on quantum simulations of simple molecules, such as hydrogen, lithium hydride, beryllium hydride, water, and hydrogen fluoride. The errors in the ground state energy, dissociation energy, and dipole moment are the parameters used as yardsticks. All the simulations were carried out with an ideal quantum circuit simulator, a noisy quantum circuit simulator, and finally a noisy simulator with noise embedded from the IBM Cairo quantum device to understand the performance of the classical optimizers in ideal and realistic quantum environments. We used the standard unitary coupled cluster ansatz for simulations, and the number of qubits varied from two starting from the hydrogen molecule to ten qubits in hydrogen fluoride. Based on the performance of these optimizers in the ideal quantum circuits, the conjugate gradient, limited-memory Broyden-Fletcher-Goldfarb-Shanno bound, and sequential least squares programming optimizers are found to be the best-performing gradient-based optimizers. While constrained optimization by linear approximation (COBYLA) and Powell's conjugate direction algorithm for unconstrained optimization (POWELL) perform most efficiently among the gradient-free methods, in noisy quantum circuit conditions, simultaneous perturbation stochastic approximation, POWELL, and COBYLA are among the best-performing optimizers.

Excited State Photophysics of Curcumin and its Modulation in Alkaline Non-Aqueous Medium.

Curcumin, a well-known medicinal pigment, has seen limited applications in biology despite having great potential as a therapeutic drug. Deprotonation is one of the possible ways to enhance solubility of curcumin in polar solvent. Here, we have explored the effect of deprotonation on the ultrafast dynamics of this biomolecule with the help of the time-resolved fluorescence spectroscopic measurements using the femtosecond fluorescence upconversion technique. The excited state photophysics of fully deprotonated curcumin significantly differs from that of neutral curcumin. We have observed that the completely deprotonated curcumin not only has higher quantum yield, but also higher excited state lifetime and slower solvation dynamics in comparison to neutral curcumin. We propose solvation dynamics and intramolecular charge transfer as the excited state processes associated with the radiative decay of the completely deprotonated molecule, while ruling out the possibility of excited state proton exchange or proton transfer. Our results are well supported by time-dependent density-functional theory calculations. Lastly, we have also demonstrated the possibility of modulating the ultrafast dynamics of fully deprotonated curcumin using non-aqueous alkaline binary solvent mixtures. We believe our results will provide significant physical insight towards unveiling the excited state dynamics of this molecule.

Spin-state energetics and magnetic anisotropy in penta-coordinated Fe(III) complexes with different axial and equatorial ligand environments.

The penta-coordinated trigonal-bi-pyramidal (TBP) Fe(III) complex (PMe2Ph)2FeCl3 shows a reduced magnetic anisotropy in its intermediate-spin (IS) state as compared to its methyl-analog (PMe3)2Fe(III)Cl3. In this work, the ligand environment in (PMe2Ph)2FeCl3 is systematically altered by replacing the axial -P with -N and -As, the equatorial -Cl with other halides, and the axial methyl group with an acetyl group. This has resulted in a series of Fe(III) TBP complexes modelled in their IS and high-spin (HS) states. Lighter ligands -N and -F stabilize the complex in the HS state, while the magnetically anisotropic IS state is stabilized by -P and -As at the axial site, and -Cl, -Br, and -I at the equatorial site. Larger magnetic anisotropies appear for complexes with nearly degenerate ground electronic states that are well separated from the higher excited states. This requirement, largely controlled by the d-orbital splitting pattern due to the changing ligand field, is achieved with a certain combination of axial and equatorial ligands, such as -P and -Br, -As and -Br, and -As and -I. In most cases, the acetyl group at the axial site enhances the magnetic anisotropy compared to its methyl counterpart. In contrast, the presence of -I at the equatorial site compromises the uniaxial type of anisotropy of the Fe(III) complex leading to an enhanced rate of quantum tunneling of magnetization.

Energy Storage Application of Conducting Polymers Featuring Dual Acceptors: Exploring Conjugation and Flexible Chain Length Effects.

Solution-processable conducting polymers (CPs) are a compelling alternative to inorganic counterparts because of their potential for tuning chemical properties and creating flexible organic electronics. CPs, which typically comprise either only an electron donor (D) or its alternative combinations with an electron acceptor (A), exhibit charge transfer behavior between the units, resulting in an electrical conductivity suitable for utilization in electronic devices and for energy storage applications. However, the energy storage behavior of CPs with a sequence of electron acceptors (A-A), has rarely been investigated, despite their promising lower band gap and higher charge carrier mobility. Utilizing the aforesaid concept herein, four CPs featuring benzodithiophenedione (BDD), and diketopyrrolepyrrole (DPP) are synthesized. Among them, the BDDTH-DPPEH polymer exhibited the highest specific capacitance of 126.5 F g-1 at a current density of 0.5 A g-1 in an organic electrolyte over a wide potential window of -0.6-1.4 V. Notably, the supercapacitor properties of the polymeric electrode materials improved with increasing conjugation length by adding thiophene donor units and shortening the alkyl chain lengths. Furthermore, a symmetric supercapacitor device fabricated using BDDTH-DPPEH exhibited a high-power density of 4000 W kg-1 and an energy density of 31.66 Wh kg-1 .

The coordinated action of the enzymes in the L-lysine biosynthetic pathway and how to inhibit it for antibiotic targets.

BACKGROUND: Antimicrobial resistance is a global health issue that requires immediate attention in terms of new antibiotics and new antibiotic targets. The l-lysine biosynthesis pathway (LBP) is a promising avenue for drug discovery as it is essential for bacterial growth and survival and is not required by human beings. SCOPE OF REVIEW: The LBP involves a coordinated action of fourteen different enzymes distributed over four distinct sub-pathways. The enzymes involved in this pathway belong to different classes, such as aspartokinase, dehydrogenase, aminotransferase, epimerase, etc. This review provides a comprehensive account of the secondary and tertiary structure, conformational dynamics, active site architecture, mechanism of catalytic action, and inhibitors of all enzymes involved in LBP of different bacterial species. MAJOR CONCLUSIONS: LBP offers a wide scope for novel antibiotic targets. The enzymology of a majority of the LBP enzymes is well understood, although these enzymes are less widely studied in the critical pathogens (according to the 2017 WHO report) that require immediate attention. In particular, the enzymes in the acetylase pathway, DapAT, DapDH, and Aspartokinase in critical pathogens have received little attention. High throughput screening for inhibitor design against the enzymes of lysine biosynthetic pathway is rather limited, both in number and in the extent of success. GENERAL SIGNIFICANCE: This review can serve as a guide for the enzymology of LBP and help in identifying new drug targets and designing potential inhibitors.

Spirocyclic rhodamine B benzoisothiazole derivative: a multi-stimuli fluorescent switch manifesting ethanol-responsiveness, photo responsiveness, and acidochromism.

Multi-stimuli fluorescent switching materials have been extensively employed in chemistry, biochemistry, physics, and materials science. Although rhodamine-based spirolactams have been specifically considered for metal ion sensing by photoluminescence, only some of them manifest photochromic behavior, and further development of rhodamine B (RHB)-based photochromic materials is required. RHB and its cyclic amides are advantageous in various sensing applications owing to their colorimetric responses to external stimulation. Hence, the current work reports a novel multifunctional active molecular material (3',6'-bis(diethylamino))-2-(5-nitrobenzo[c]isothiazol-3-yl)spiro[isoindoline-1,9'-xanthen]-3-one (RHBIT) by linking rhodamine B with 3-amino,5-nitro[2,1]benzoisothiazole (ANB) in a facile synthetic pathway; that perceives both emission color change and switching between off-on states. RHBIT shows acidochromism, photochromism, and pH sensitivity accompanied by unique ethanol responsiveness, with potential applications in anti-counterfeiting and drug delivery. Notably, RHBIT is highly acid sensitive and reverts to the ring-closed form on treatment with triethylamine (base), visible with the naked eye amidst colorless-pink-colorless transformations. On short UV irradiation, RHBIT provides a two-fold rise in the lifetime for the ring-open form in CHCl3 and DCM compared to the spirolactam (closed form). DFT and TDDFT studies provide electronic characterization for the absorption spectra of the open and closed forms. Using the photoresponsive feature of RHBIT, an information protection application has been enacted via a rewritable platform.

Deciphering the role of the two metal-binding sites of DapE enzyme via metal substitution.

DapE is a microbial metalloenzyme that hosts two Zn ions in its active site, although it shows catalytic activity with varying efficiency when the Zn ions in one or both of its metal-binding sites (MBS) are replaced by other transition-metal ions. The metal-ion promiscuity of DapE is believed to be a microbial strategy to overcome the homeostatic regulation of Zn ions by the mammalian host. Here, a hybrid QM/MM study is performed on a series of mixed-metal DapEs, where the Zn ion in the first MBS (MBS-1) is substituted by Mn, Co, Ni, and Cu ions, while the MBS-2 is occupied by Zn(II). The substrate binding affinity and the mechanism of catalytic action are estimated by optimizing the intermediates and the transition states with hybrid QM/MM method. Comparison of the binding affinity of the MBS-1 and MBS-2 substituted DapEs reveals that the MBS-1 substitution does not affect the substrate binding affinity in the mixed-metal DapEs, while a strong metal specificity was observed in MBS-2 substituted DapEs. On the contrary, the activation energy barriers show a high metal specificity at MBS-1 compared to MBS-2. Taken together, the QM/MM studies indicate that MBS-2 leads the substrate binding process, while MBS-1 steers the catalytic activity of the DapE enzyme.

Ligands-induced open-close conformational change during DapE catalysis: Insights from molecular dynamics simulations.

The microbial enzyme DapE plays a critical role in the lysine biosynthetic pathway and is considered as a potentially safe antibiotic target. In this study, atomistic simulations are employed to identify the modes of essential dynamics that define the conformational response of the enzyme to ligand binding and unbinding. The binding modes and the binding affinities of the products to the DapE enzyme are estimated from the MM-PBSA method, and the residues contributing to the ligand binding are identified. Various structural analyses and the principal component analysis of the molecular dynamics trajectories reveal that the removal of products from the active site causes a significant change in the overall enzyme structure. Both Cartesian and dihedral principal component analyses are used to characterize the structural changes in terms of domain unfolding and domain twisting motions. In the most dominant mode, that is, the domain unfolding motion, the two catalytic domains move away from the two dimerization domains of the dimeric enzyme, representing a closed-to-open conformational change. The conformational changes are initiated by the coordinated movement of three loops (Asp75-Pro82, Gly240-Asn244, and Thr347-Glu353) that trigger a domain-level movement. From multiple short trajectories, the time constant associated with the domain opening motion is estimated as 43.6 ns. Physiologically, this close-to-open conformational change is essential for the regeneration of the initial state of the enzyme for the subsequent cycle of catalytic action and provides the apo enzyme enough flexibility for efficient substrate binding.

Self-Assembling Behaviour of Perylene, Perylene Diimide, and Thionated Perylene Diimide Deciphered through Non-Covalent Interactions.

The π-conjugated supramolecular polymers (SMP) have gained vast popularity in materials chemistry and biomedicine due to their spectacular self-assembling behaviour. A detailed account of the electronic structure and bonding through quantum theory of atoms-in-molecules, non-covalent interactions, and energy decomposition analysis (EDA) in the oligomers of perylene, perylene diimide (PDI), and thionated-PDI (t-PDI) is presented. The oligomers of all three molecules show a slip angle of θ≈62° thus forming H-aggregates. The stacking pattern in perylene oligomers prefers a slip-stacked brick-layer order, while the bulkier PDI and t-PDI prefer a parallel step-wise pattern in their oligomers. Successive addition of monomers leads to a consequent rise in the association energy, although to a much greater extent in PDI and t-PDI than in perylene. While the major contribution to this association energy comes from the dispersion interactions in all three systems, the steric interactions in t-PDI quench the cooperativity in its SMP formation. A detailed analysis of the non-covalent interactions reveals the presence of π-π, π-hole⋅⋅⋅O=C, and π-hole⋅⋅⋅S=C electrostatic interactions playing a crucial role in the self-assembly process, which can be further implemented on developing force field-based methods for understanding the self-assembling mechanism in higher degree of oligomers.

Transition Metal Phthalocyanines as Redox Mediators in Li-O2 Batteries: A Combined Experimental and Theoretical Study of the Influence of 3d Electrons in Redox Mediation.

Redox mediation is an innovative strategy for ensuring efficient energy harvesting from metal-oxygen systems. This work presents a systematic exploratory analysis of first-row transition-metal phthalocyanines as solution-state redox mediators for lithium-oxygen batteries. Our findings, based on experiment and theory, convincingly demonstrate that d5 (Mn), d7 (Co), and d8 (Ni) configurations function better compared to d6 (Fe) and d9 (Cu) in redox mediation of the discharge step. The d10 configuration (Zn) and non-d analogues (Mg) do not show any redox mediation because of the inability of binding with oxygen. The solution-state discharge product, transition-metal bound Li2O2, undergoes dissociation and oxidation in the charging step of the battery, thus confirming a bifunctional redox mediation. Apart from the reaction pathways predicted based on thermodynamic considerations, density functional theory calculations also reveal interesting effects of electrochemical perturbation on the redox mediation mechanisms and the role of the transition-metal center.

Identification of potential inhibitors against FemX of Staphylococcus aureus: A hierarchial in-silico drug repurposing approach.

Staphylococcus aureus causes a wide range of common diseases in both community-acquired and hospital-acquired environments. The treatment becomes challenging due to the emergence of multi-drug resistant strains such as Methicillin-Resistant Staphylococcus aureus (MRSA). This study aims to find some drugs that can be used in repurposing. Virtual screening has been performed against S. aureus FemX using 1,918 FDA-approved drugs, which provides the top 10 drugs with good binding affinity. These drugs are re-docked to understand their interaction patterns with FemX. Docking study shows a high score for three drugs, Lumacaftor, Dihydroergocornine and Olaparib, and they are selected for molecular dynamics and quantum mechanical analysis. Molecular dynamics calculation shows that drug-FemX forms a stable structure compared to apo-FemX. Besides, the free energy landscape reveals that drug-protein complexes possess a single global minimum indicating their thermodynamic stability. MM/GBSA calculations show that Lumacaftor, Dihydroergocornine and Olaparib have the binding free energy of -30.03, -19.22 and -16.54 kcal/mol, respectively. The analysis of the wavefunctions from quantum chemical calculations reveals the presence of non-covalent interactions between drug and receptor, dominated by aromatic π-π interactions. The drug-receptor interaction energy estimated from quantum mechanical methods suggests an important role of dispersion interactions in stabilizing the drug molecules with FemX. The hierarchy of computational methods of increasing accuracy employed in this work finds Lumacaftor to be the most potent inhibitor against FemX.

Spin-vibronic coupling in the quantum dynamics of a Fe(III) trigonal-bipyramidal complex.

The presence of a high density of excited electronic states in the immediate vicinity of the optically bright state of a molecule paves the way for numerous photo-relaxation channels. In transition-metal complexes, the presence of heavy atoms results in a stronger spin-orbit coupling, which enables spin forbidden spin-crossover processes to compete with the spin-allowed internal conversion processes. However, no matter how effectively the states cross around the Franck-Condon region, the degree of vibronic coupling, of both relativistic and non-relativistic nature, drives the population distribution among these states. One such case is demonstrated in this work for the intermediate-spin Fe(III) trigonal-bipyramidal complex. A quantum dynamical investigation of the photo-deactivation mechanism in the Fe(III) system is presented using the multi-configurational time-dependent Hartree approach based on the vibronic Hamiltonian whose coupling terms are derived from the state-averaged complete active space self-consistent field/complete active space with second-order perturbation theory (CASPT2) calculations and spin-orbit coupling of the scalar-relativistic CASPT2 states. The results of this study show that the presence of a strong (non-relativistic) vibronic coupling between the optically bright intermediate-spin state and other low-lying states of the same spin-multiplicity overpowers the spin-orbit coupling between the intermediate-spin and high-spin states, thereby lowering the chances of spin-crossover while exhibiting ultrafast relaxation among the intermediate-spin states. In a special case, where the population transfer pathway via the non-relativistic vibronic coupling is blocked, the probability of the spin-crossover is found to increase. This suggests that a careful modification of the complex by incorporation of heavier atoms with stronger relativistic effects can enhance the spin-crossover potential of Fe(III) intermediate-spin complexes.

Pomegranate peel polyphenols prophylaxis against SARS-CoV-2 main protease by in-silico docking and molecular dynamics study.

Pomegranate peel, the waste product generated from pomegranate fruit, has prophylactic properties, such as antimicrobial, anti-malarial, and controls respiratory infections and influenza. Based on the previous literature and need of the hour, molecular docking was performed to evaluate the inhibitory effects of major pomegranate peel polyphenols against COVID-19. Among the 44 studied compounds, 37 polyphenols show interaction with the catalytic dyad of the Mpro protease and 18 polyphenols have a higher binding affinity than that of the Mpro protease inhibitor (N3), indicating their high probability of binding at ACE2: SARS-CoV-2 interface. Furthermore, several polyphenols studied in this work are found to have higher binding affinity as compared to those of hydroxychloroquine, lopinavir, nelfinavir, and curcumin, some of which have been earlier tested against COVID-19. Further, molecular dynamics simulations (200 ns) for Mpro-polyphenols including pelargonidin3-glucoside, quercetin3-O-rhamnoside, cyanidin3-glucoside and punicalin revealed highly stable complexes with less conformational fluctuations and similar degree of compactness. Estimation of total number of intermolecular hydrogen bonds and binding free energy confirmed the stability of these Mpro-polyphenol complexes over Mpro-curcumin complex. Based on the greater binding affinity of polyphenols of pomegranate peel towards Mpro as compared to that of curcumin, pomegranate peel may be considered in any herbal medicinal formulation or may be incorporated into daily diets for prevention of COVID-19.Communicated by Ramaswamy H. Sarma.