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Low-band-gap and thermally stable conjugated polymers developed using a dual acceptor–acceptor strategy and the addition of S and F atoms.

Rhodamine B benzoisothiazole-spirolactam as multi-stimuli fluorescent switch manifesting ethanol-responsiveness, photo responsiveness, and acidochromism.

Tetracyanoquinodimethane (TCNQ) on reaction with primary/secondary amines sequels in mono/di-substituted TCNQ adducts known as diaminodicyanoquinodimethanes (DADQ’s) possessing astounding optical or non-linear optical characteristics. Crucially, the subtle choice of amine contributes to the outcome of molecular material aspects. Herein, we present a comprehensive investigation of 7,7-bis(N,N-diethylethylenediamino)-8,8-dicyanoquinodimethane (BDEDDQ); manifesting the impact of ethyl group (existing on the di-substituted nitrogen of N,N-diethylethylenediamine (DEED)); on the crystal structure, optical property and thermal stability. Crystallography study revealed supramolecular self-assemblies among molecular dipoles emanating fluorescence enhancement in the solid state compared to solutions. Quantum yields were primarily ~0.2 to 0.4% in solutions and ~56% in the solid. Stokes shift was noticed to be more in solutions (~90 nm) than solid (~67 nm), suggesting excess vibrational relaxations in solutions. Differential scanning calorimetry revealed ~182 °C as the melting temperature. The heat capacity of solid was found to be 5.03 mJs−1. Thermogravimetric analysis conveyed single stage decomposition process initiated by the two amine side chains. Scanning electron microscopy of films prepared by drop casting solutions imparted divergent morphological features, due to different rates of evaporation accompanied by varied growth kinetics. Accordingly, in this paper we have demonstrated the utilization of simple N,N-diethylethylenediamine (DEED) to successfully generate a noteworthy blue emissive molecular material exhibiting semiconducting feature besides reasonable thermal stability.

Metalloenzymes are ubiquitous in nature catalyzing a number of crucial biochemical processes in animal and plant kingdoms. For better adaptation to the relative abundance of different metal ions in different cellular fluids, many of these enzymes exhibit metal promiscuity. The microbial enzyme DapE, an essential enzyme for bacterial growth and survival and a potentially safe target for antibiotics, continues to show enzyme activity when the two zinc ions in its active site are replaced by other transition metal ions. The effect of metal-ion substitution at the second metal-binding site of DapE on its substrate affinity and catalytic efficiency is investigated by QM/MM treatment of the enzyme-substrate complex, by modelling the enzyme with Mn(II), Co(II), Ni(II), or Cu(II) ion in place of Zn(II) at its second metal-binding site, while retaining Zn(II) ion at the first metal-binding site. On the basis of substrate binding energy and activation energy barrier for the chemical catalysis, it is found that Zn-Mn DapE shows poor binding affinity as well as inefficient chemical catalysis. Although Zn-Cu and Zn-Ni DapEs show activation energy barriers comparable to that of wild-type Zn-Zn DapE, their weaker substrate affinity renders these mixed-metal enzymes less efficient. On the other hand, Zn-Co DapE is found to outperform the naturally occurring Zn-Zn DapE, both in terms of substrate affinity and chemical catalysis. The observed metal promiscuity may have played an important role in the survival of bacteria even in those cellular media where Zn ions are in limited supply. Metal nonspecificity in the catalysis of DapE enzyme allows bacteria to thrive in different cellular media.

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.

Tetracyanoquinodimethane (TCNQ) is known to react with various amines to generate substituted TCNQ derivatives with remarkable optical and nonlinear optical characteristics. The choice of amine plays a crucial role in the outcome of molecular material attributes. Especially, mono/di-substituted TCNQ’s possessing strong fluorescence in solutions than solids are deficient. Furthermore, cation recognition in the solid-state TCNQ derivatives is yet undetermined. In this article, we present solution-enhanced fluorescence and exclusive solid-state recognition of K+ ion achieved through the selection of 4-(4-aminophenyl)morpholin-3-one (APM) having considerable π-conjugation and carbonyl (C=O) functionality, particularly in the ring. TCNQ when reacted with APM, in a single-step reaction, resulted in two well-defined distinct compounds, namely, 7,7-bis(4-(4-aminophenyl)morpholin-3-ono)dicyanoquinodimethane (BAPMDQ [1], yellow) and 7,7,8-(4-(4-aminophenyl)morpholin-3-ono)tricyanoquinodimethane (APMTQ [2], red), with increased fluorescence intensity in solutions than their solids. Crystal structure investigation revealed extensive C–H−π interactions and strong H-bonding in [1], whereas moderate to weak interactions in [2]. Surprisingly, simple mechanical grinding during KBr pellet preparation with [1, 2] triggered unidentified cation recognition with a profound color change (in ∼1 min) detected by the naked eye, accompanied by a drastic enhancement of fluorescence, proposed due to the presence of carbonyl functionality, noncovalent intermolecular interactions, and molecular assemblies in [1, 2] solids. Cation recognition was also noted with various other salts as well (KCl, KI, KSCN, NH4Cl, NH4Br, etc.). Currently, the recognition mechanism of K+ ion in [1, 2] is demonstrated by the strong electrostatic interaction of K+ ion with CO and simultaneously cation−π interaction of K+ with the phenyl ring of APM, supported by experimental and computational studies. Computational analysis also revealed that a strong cation−π interaction occurred between the K+ ion and the phenyl ring (APM) in [2] than in [1] (ΔGbinding calculated as ∼16.3 and ∼25.2 kcal mol–1 for [1] and [2], respectively) providing additional binding free energy. Thus, both electrostatic and cation−π interactions lead to the recognition. Scanning electron microscopy of drop-cast films showed microcrystalline “roses” in [1] and micro/nano “aggregates” in [2]. Optical band gap (∼3.565 eV) indicated [1, 2] as wide-band-gap materials. The current study demonstrates fascinating novel products obtained by single-pot reaction, resulting in contrasting optical properties in solutions and experiencing cation recognition capability exclusively in the solid state.

The reaction between 2,5-bis(diphenylphosphinomethyl)pyrrole and Me3SiN3 gave the new pyrrole-based bis(phosphinimine) L1H in an excellent yield. L1H reacts with [CuCl(COD)]2, AgBF4, or AgOTf to give the corresponding two-coordinate mononuclear ionic complex formulated as [M{(L1H)-κ2N,N}]+[X]- where M = Cu and Ag; X = [CuCl2], BF4 or OTf. Their single crystal X-ray diffraction studies confirmed the two-coordinate geometry formed by the chelate bonding mode of L1H. These 10-membered metalacycles exhibit planar chirality and were also characterized by spectroscopic methods. In addition, in all three structures, there exists a hitherto unknown π-interaction between the pyrrole ring atoms and metal, represented as η2-(Cα-N) in the copper(i) complex, and η3-(Cα-N-Cα') in the silver(i) complexes. These weak interactions were supported by DFT calculations in terms of their electron densities, non-covalent interaction plots and the decrease in the aromaticity of the pyrrole ring.

A series of organometallic complexes [Cl(dppe)2 Ru-C≡C-(3-R-C4 H2 S)-C≡C-Ru(dppe)2 Cl] (3-R-C4 H2 S=3-substituted thienyl moiety; R=-H, -C2 H5 , -C3 H7 , -C4 H9 , -C6 H13 , -OMe, -CN in 5 a-5 g respectively) have been synthesized by systematic variation of 3-substituents at the thienylethynyl bridging unit. The diruthenum(II) wire-like complexes (5 a-5 g) have been achieved by the reaction of thienylethynyl bridging units, HC≡C-(3-R-C4 H2 S)-C≡CH (4 a-4 g) with cis-[Ru(dppe)2 Cl2 ]. The wire-like diruthenium(II) complexes undergo two consecutive electrochemical oxidation processes in the potential range of 0.0 - 0.8 V. Interestingly, the wave separation between the two redox waves is greatly influenced by the substituents at the 3-position of the thienylethynyl. Thus, the substitution on 3-position of the thienylethynyl bridging unit plays a pivotal role for tuning the electronic properties. To understand the electronic behavior, density functional theory (DFT) calculations of the selected diruthenium wire-like complexes (5 a-5 e) with different alkyl appendages are performed. The theoretical data demonstrate that incorporation of alkyl groups to the thienylethynyl entity leaves unsymmetrical spin densities, thus affecting the electronic properties. The voltammetric features of the other two Ru(II) alkynyl complexes 5 f and 5 g (with -OMe and -CN group respectively) show an apparent dependence on the electronic properties. The electronic properties in the redox conjugate, (5 a+ ) with Kc of 3.9×106 are further examined by UV-Vis-NIR and FTIR studies, showing optical responses in NIR region along with changes in "-Ru-C≡C-" vibrational stretching frequency. The origin of the observed electronic transition has been assigned based on time-dependent DFT (TDDFT) calculations.

The detection of fluoride ions in a competitive environment often poses several challenges. In this work, we have designed and synthesized a coumarin functionalized fluorescein dyad (R3) which represents an ideal through bond energy transfer (TBET) fluorophore with the coumarin unit as donor and fluorescein unit as acceptor. The bichromophoric dyad demonstrates the detection of fluoride ions in the parts per billion (ppb) concentration level (22.8 ppb) with high selectivity via a TBET emission signal at 548 nm with a diagnostic bright yellow colour fluorescence output. Based on UV-visible, fluorescence, 1H NMR and DFT studies, it is shown that the fluoride ion induces the opening of the spirolactam ring of the fluorescein moiety and provides a π-conjugation link between the donor and acceptor units enabling a TBET phenomenon with a larger pseudo-Stokes shift of 172 nm. To the best of our knowledge, this is the first report where the fluoride ion is detected via a TBET signal between the coumarin and fluorescein units in a bichromophoric dyad.

The valence shell photoelectron spectrum of OsO4 has been calculated from the wave functions of the ejected photoelectrons responsible for the formation of the lowest five cationic states, whose vertical ionization energies have been estimated using the equation of motion coupled cluster with singles and doubles (EOM-CCSD) and multi-configurational self consistent field (MCSCF) based methods. These non-relativistic states when coupled via the spin–orbit operator result in the spin–orbit states, which are compared with the results from synchrotron measurements. The lowest three cationic states could be described by both the EOM-CCSD and MCSCF based methods, whereas the multi-reference character of the closely spaced fourth and fifth cationic states was suitably described by the latter method. The photoelectron spectral intensities of different ionization channels, calculated using the Dyson orbital formalism within the sudden approximation, reproduced the experimental spectrum by capturing all of its essential features, including the detailed vibronic structure of the first band, which shows the presence of fundamental, overtone and combination bands of a1 and e modes. The kinetic energy dependence of the photoionization parameters, such as the photoionization cross section and asymmetry parameters, has been calculated for each of the photoionization channels and the complex interplay of multiple partial waves that define the wave function of the ejected electron at different photon energies has been analyzed to explain the resonance structures observed in the experimental cross section profiles.

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.

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

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 M

2,4-Dienones undergo visible-light-promoted, photocatalyst-free dimerization in neat conditions to provide cyclohexene derivatives stereoselectively through cascade rearrangement pathways, whereas regioselective E → Z isomerization of the more dienophilic double bond takes place exclusively in nitromethane. On the basis of intermediate isolation and computational DFT studies, the dimerization reaction is proposed to proceed via s-trans to s-cis isomerization/regioselective E → Z isomerization/Diels-Alder cycloaddition.

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.

Amyloid polymorphism has emerged as an important topic of research in recent years to identify the particular species responsible for several neurodegenerative disorders, whereas the concept is overlooked in the case of the simplest building block, that is, l-phenylalanine (l-Phe) self-assembly. Here, we report the first evidence of l-Phe polymorphism and the conversion of metastable helical fibrillar to thermodynamically stable rodlike crystalline morphologies with increasing time and temperature. Furthermore, only the fibrillar l-Phe polymorph shows a significant modulation of the model membrane. In addition, the l-Phe molecules prefer to arrange in a multilayered rodlike fashion than in a lateral arrangement, which reduces the membrane binding ability of the l-Phe polymorph due to the decrease in the partial charge of the N-terminal of l-Phe units. The present work exemplifies a different approach to understanding l-Phe self-assembly and provides an effective strategy for the therapy of phenylketonuria by scrutinizing the discrete membrane activity of different l-Phe polymorphs.

Lipoxygenases are non-heme iron containing enzymes that catalyze oxygenation of poly-unsaturated fatty acids in different animal and plant species with extremely high regio- and stereospecificity. Nature employs 8-lipoxygenase to produce 8R-hydroperoxide from the oxygenation of arachidonic acid. A single-point L434F mutation of 8-lipoxygenase alters the regio- and stereospecificity of the final products, with a product ratio of 66 : 34 for 8R- and 12S-hydroperoxide, respectively. A molecular level explanation of this flipped regiospecificity is presented in this work on the basis of molecular dynamics simulations and transition network analysis of oxygen migration in the protein matrix. Phe434 is shown to exist in two conformations, the so-called open and closed conformations. In the closed conformation, the phenyl group of Phe434 shields the C8 site of the substrate, thereby preventing access of the oxygen molecule to this site, which leads to a quenching of the 8R-product. On the other hand, both closed and open conformations of Phe434 allow the oxygen molecule to approach the pro-S face of the C12 site of the substrate, which enhances the propensity of the 12S-hydroperoxide.

Accurate treatment of electron correlation and spin-orbit coupling is essential for understanding the electronic structure and spectroscopy of high-spin, open-shell transition metal dihalides. The experimental photoelectron spectra of MnX2, X = Cl, Br, I, have been interpreted on the basis of multi-configurational ab initio electronic structure calculations. The intensity of the photoelectron bands have been calculated from the norms of the Dyson orbitals, which represent the transition probability to a particular ionic state from a given starting state. The present study provides a detailed account of the contribution of the one- and two-electron transitions in the experimental photoelectron spectra of the title molecules and outlines the nature of the photoelectron bands in terms of the closely spaced quintet and septet states of the cationic species.

The perils of antimicrobial drug resistance can be overcome by finding novel antibiotic targets and corresponding small molecule inhibitors. Microbial enzyme DapE is a promising antibiotic target due to its importance to the bacterial survival. The potency of L-Captopril, a well known angiotensin-converting enzyme inhibitor, as an inhibitor of DapE enzyme has been evaluated by analyzing its binding modes and binding affinity towards DapE enzyme. L-Captopril is found to bind the metal centers of DapE enzyme either via its thiolate group or through its carboxylate group. While the latter binding mode is found to be thermodynamically favorable, the former binding mode, also seen in the crystal structure, is kinetically favored. To optimize the binding affinity of the inhibitor towards DapE enzyme, a series of L-Captopril-based inhibitors have been modelled by changing the side groups of L-Captopril. The introduction of a bipolar functional group at the C4 position of the pyrrolidine ring of L-Captopril and the substitution of the thiol group with a carboxylate group, have been shown to provide excellent enzyme affinity that supersedes the binding affinity of DapE enzyme towards its natural substrate, thus making this molecule a potential inhibitor with great promise.

In the search for a low molecular weight organo gelator, sodium-4-oxo-4-((11-phenoxyundecyl)oxy)but-2-enoate (PUDMS) was designed and synthesized using phenol, 11-bromoundecanol, and maleic anhydride as starting materials. The maleate based amphiphile entrap hydrocarbon solvents like cyclohexane, hexane, and heptane in the presence of 25 μL water, interestingly in pure solvents no gelation was observed. Among the hydrocarbon solvents, cyclohexane shows excellent gelation with lowest critical gelation concentration (0.44 mg/mL) value with higher gelation number (8005) in an optimal water volume of 25 μL. The organogels were characterized by various conventional techniques such as rheology, DSC, FE-SEM, and XRD. The dynamic mechanical strength is independent of the angular frequency ranging between 0.1 Hz to 12 Hz irrespective of the organic solvent used, though cyclohexane showed little higher magnitude in the storage modulus (G') value. The microstructure observed by the FE-SEM study suggested PUDMS has emulsified morphology for cyclohexane and hexane solvent where as sheet like structure observed for heptane. Further, the bilayer thickness for the gel network structure was calculated from XRD studies. The pH-induced release of vitamin B 12 from the vitamin B 12 -loaded PUDMS organogel, showing potential application in pH-triggered nutraceutical release.

The mechanism of the catalytic hydrolysis of N-succinyl diaminopimelic acid (SDAP) by the microbial enzyme DapE in its wild-type (wt) form as well as three of its mutants (E134D, H67A, and H349A) is investigated employing a hybrid quantum mechanics/molecular mechanics (QM/MM) method coupled with molecular dynamics (MD) simulations, wherein the time evolution of the atoms of the QM and MM regions are obtained from the forces acting on the individual atoms. The free-energy profiles along the reaction coordinates of this multistep hydrolysis reaction process are explored using a combination of equilibrium and nonequilibrium (umbrella sampling) QM/MM-MD simulation techniques. In the enzyme-substrate complexes of wt-DapE and the E134D mutant, nucleophilic attack is found to be the rate-determining step involving a barrier of 15.3 and 21.5 kcal/mol, respectively, which satisfactorily explains the free energy of activation obtained from kinetic experiments in wt-DapE-SDAP (15.2 kcal/mol) and the 3 orders of magnitude decrease in the catalytic activity due to E134D mutation. The catalysis is found to be quenched in the H67A and H349A mutants of DapE due to conformational rearrangement in the active site induced by the absence of the active site His residues that prohibits activation of the catalytic water molecule.

Linear or near linear bicoordinated mononuclear Co(II) complexes are studied as potential single molecule magnets due to the strong spin-orbit constant of Co(II) and its low coordination number that retains the metal orbital angular momentum unquenched. The spin-orbit coupled unquenched orbital angular momentum of the metal center upon interaction with ligand field produces strong magnetic anisotropy. The role of ligand environment, structural distortion and conformational change on the magnetic anisotropy of the Co(II) complexes are investigated employing ab initio electronic structure calculations. The zero-field splitting parameters, g-tensors, and the transition magnetic moment matrix elements among the Kramer's pairs are evaluated to obtain the effective anisotropy barriers (Ueff) and mechanism of relaxation of magnetization in a series of Co(II) complexes, where the estimated values of Ueff range between 394 cm-1 to 974 cm-1, representing the largest effective anisotropy barrier reported for transition metal complexes. The calculations reveal that the ligand field strength, structural distortion and conformational changes not only affect the magnetic anisotropy barrier but also significantly alter the mechanism of relaxation of magnetic moments.

In the search for single molecule magnets, metal ions are considered pivotal towards achieving large magnetic anisotropy barriers. In this context, the influence of ligands with heavy elements, showing large spin-orbit coupling, on magnetic anisotropy barriers was investigated using a series of Mn(ii)-based complexes, in which the metal ion did not have any orbital contribution. The mixing of metal and ligand orbitals was achieved by explicitly correlating the metal and ligand valence electrons with CASSCF calculations. The CASSCF wave functions were further used for evaluating spin-orbit coupling and zero-field splitting parameters for these complexes. For Mn(ii) complexes with heavy ligand atoms, such as Br and I, several interesting inter-state mixings occur via the spin-orbit operator, which results in large magnetic anisotropy in these Mn(ii) complexes.

The valence shell photoelectron spectrum of OsO4 has been calculated from the wave functions of the ejected photoelectrons responsible for the formation of the lowest five cationic states, whose vertical ionization energies have been estimated using the equation of motion coupled cluster with singles and doubles (EOM-CCSD) and multi-configurational self consistent field (MCSCF) based methods. These non-relativistic states when coupled via the spin-orbit operator result in the spin-orbit states, which are compared with the results from synchrotron measurements. The lowest three cationic states could be described by both the EOM-CCSD and MCSCF based methods, whereas the multi-reference character of the closely spaced fourth and fifth cationic states was suitably described by the latter method. The photoelectron spectral intensities of different ionization channels, calculated using the Dyson orbital formalism within the sudden approximation, reproduced the experimental spectrum by capturing all of its essential features, including the detailed vibronic structure of the first band, which shows the presence of fundamental, overtone and combination bands of a1 and e modes. The kinetic energy dependence of the photoionization parameters, such as the photoionization cross section and asymmetry parameters, has been calculated for each of the photoionization channels and the complex interplay of multiple partial waves that define the wave function of the ejected electron at different photon energies has been analyzed to explain the resonance structures observed in the experimental cross section profiles.

Lipoxygenases (lox's) are a group of non-heme iron containing enzymes that catalyze oxygenation of polyunsaturated fatty acids with precise regio- and stereoselectivities. The origin of regio- and stereospecific catalysis by 8-lox is explored in its wild-type (wt) form and in three mutants (Arg185Ala, Ala592Met, and Ala623His). The catalytic action of this enzyme progresses in two steps, namely, hydrogen abstraction from one double allylic carbon atom of substrate followed by oxygen insertion at the resulting prochiral carbon radical of the substrate. It is shown that the positional specificity of the hydrogen abstraction is a result of conformational dynamics of the bound substrate. While the C10 atom of the substrate is found to be the most probable site of hydrogen abstraction in the wt-lox, hydrogen abstraction from C13 is more favorable in the mutants. The present study discovers the presence of an interconnected network of a three-channel migration pathway operating in the protein matrix for efficient oxygen transport. Each migration channel is bestowed with a pocket at the peripheral region of protein as an oxygen access site, which transfers the oxygen to the active site through a well-connected migration path on a time scale of a few hundred picoseconds. By a careful geometric analysis of the oxygen pockets near the substrate binding cleft, the present study identifies the launching sites for oxygenation at the prochiral carbon centers C8, C11, C12, and C15 and the stereochemistry (

(PMe3)2FeCl3 is an Fe(III) complex that exists in the intermediate-spin ground state in a distorted trigonal bipyramidal geometry. An electronic state with high-spin configuration lies in close vic...

The Renner vibronic-coupling problem in

Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur-721 302, West Bengal, India E-mail: mishra@chem.iitkgp.ac.in Manuscript received online 22 April 2019, revised and accepted 08 May 2019 In the era of ever-increasing anti-microbial resistance, drug re-purposing offers a faster and economic route to the discovery of novel antibiotics. L-Captopril, a widely used angiotensin-converting enzyme inhibitor, has shown inhibitory action towards the microbial enzyme DapE, which is a potential antibiotic target. In this work, a series of biased and unbiased QM/MM-MD simulations has been carried out to investigate the catalytic hydrolysis of L-captopril along a general acid-base hydrolysis mechanism. The QM/MM-MD simulations not only provide an accurate estimation of free energy of activation, but also account for the corrections to the free energy arising from conformational dynamics of the enzyme-substrate complexes. The nucleophilic attack of the hydroxyl ion on the carbonyl group of L-captopril, was found to be the rate-determining step of the catalyzed hydrolysis reaction, which involved activation energy barrier of 15.6 and 13.1 kcal/mol, for the O- and S-coordinated conformations of L-captopril, respectively. Comparing these activation energy barriers with the barriers obtained for the hydrolysis of the natural substrate of DapE enzyme, it is concluded that the catalytic activation of L-captopril by DapE is as efficient as the activation of its natural substrate. Unlike the natural substrate, the activation of L-captopril by DapE yields side products that interrupt the crucial lysine biosynthetic pathway in bacteria.

A series of heterobimetallic wire-like organometallic complexes [(tpy-C6H4-R)(PPh3)2Ru–C≡C–Fc]+ (tpy-C6H4-R = 4′-(aryl)-2,2′:6′,2′′-terpyridyl, Fc = [(η5-Cp)2Fe], R = -H, -Me, -F, -NMe2 in complexes 5–8, respectively) featuring ferrocenyl and 4′-(aryl)-2,2′:6′,2′′-terpyridyl ruthenium(II) complexes as redox active metal termini, have been synthesized. Various spectroscopic tools, such as multinuclear NMR, IR spectra, HRMS, CHN analyses, and single crystal X-ray crystallography have been utilized to characterize the heterobimetallic complexes. The electrochemical and UV–vis–NIR spectroscopic studies have been investigated to evaluate the electronic delocalization across the molecular backbones of the Ru(II)–Fe(II) heterobinuclear organometallic dyads. Electrochemical studies reveal two well-separated reversible redox waves as a result of successive oxidation of the ferrocenyl and Ru(II) redox centers. The spin density distribution analyses reveal that the initial oxidation process is associated with the Fe...

Raman spectroscopy is an effective tool to detect conformational changes and secondary structures of biological molecules. The amide-I band representing the amide carbonyl (C=O) stretching, with smaller contributions of C–N stretching and N–H bending is a signature band for protein secondary structure conformation. We have simulated the Raman spectra of insulin by a hybrid quantum-mechanics and molecular-mechanics (QM/MM) method with an aim to provide an accurate description of the amide-I band. To fulfil this aim we have considered three different QM/MM models with increasingly accurate description of the electrostatic environment for tyrosine (TYR), phenylalanine (PHE) and cystine (CYS) residues of insulin. All three models successfully describe the experimental Raman spectral features associated with the vibrational modes of the amino acid side chains. However, an accurate simulation of the amide-I band is achieved only in one of the three models, where the peptide backbone atoms together with ...

SummaryDevelopment of disease-modifying therapeutics is urgently needed for treating Alzheimer disease (AD). AD is characterized by toxic β-amyloid (Aβ) peptides produced by β- and γ-secretase-mediated cleavage of the amyloid precursor protein (APP). β-secretase inhibitors reduce Aβ levels, but mechanism-based side effects arise because they also inhibit β-cleavage of non-amyloid substrates like Neuregulin. We report that β-secretase has a higher affinity for Neuregulin than it does for APP. Kinetic studies demonstrate that the affinities and catalytic efficiencies of β-secretase are higher toward non-amyloid substrates than toward APP. We show that non-amyloid substrates are processed by β-secretase in an endocytosis-independent manner. Exploiting this compartmentalization of substrates, we specifically target the endosomal β-secretase by an endosomally targeted β-secretase inhibitor, which blocked cleavage of APP but not non-amyloid substrates in many cell systems, including induced pluripotent stem cell (iPSC)-derived neurons. β-secretase inhibitors can be designed to specifically inhibit the Alzheimer process, enhancing their potential as AD therapeutics without undesired side effects.

The reaction of three copper(II) carboxylate (R = Me, Ph and H in RCO2−) salts in MeOH with H3L resulted three [Cu4] aggregates: [Cu4(μ4-O)(μ-H2L)2(μ1,3-O2CCH3)4] (1), [Cu4(μ4-O)(μ-H2L)2(μ1,3-O2CPh)(PhCO2)3]⋅H2O (2⋅H2O), and [Cu4(μ3-OH)2(μ-H2L)2(μ1,1-HCO2)2(HCO2)2]⋅2H2O (3⋅2H2O). Three different carboxylate groups showing varying coordination modes were responsible for the self-aggregation of two ligand bound [Cu2(H2L)]3+ units. The [Cu4O] and [Cu4(OH)2] cores were generated from water-derived oxido and hydroxido nucleating groups to provide quasi-tetrahedral and partial-dicubane topologies. In complexes 1 and 2⋅2H2O the μ1,3 bridging mode of the carboxylate bridges were responsible for the entrapment of μ4-O unit, whereas μ1,1 bridge by formato groups resulted in trapping of two μ3-OH units in complex 3⋅2H2O. Complex 3⋅2H2O is the first reported example of a μ1,1-formato bridged [Cu4] aggregate. Long range van der Waals forces, in presence of hydrogen bonding interactions, also play significant role in the [Cu4] aggregation process. These have been analyzed by DFT calculations and Hirshfeld surface analysis.

The valence shell photoelectron spectrum of ICN has been simulated using the equation-of-motion coupled-cluster method to calculate the ionization energies and the norms of the Dyson orbitals to describe the intensity of the photoelectron bands. The simulated spectrum not only reproduces the position and intensity of the four main bands observed in the experimental photoelectron spectrum, but the vibronic structure present in the individual photoelectron bands is also reproduced to a reasonable extent. The agreement between the experimental and simulated vibronic structures at higher energies corresponding to the A and B states is particularly noteworthy. Additionally, the photoionization cross section and asymmetry parameter have been calculated for the ionization of four outermost valence molecular orbitals in the photon energy range of 0–50 eV. The computed asymmetry parameters are found to provide a qualitative description of the corresponding experimental measurements. The shape-resonance seen in the experimental asymmetry parameters and the trends seen in the calculated cross section for the four ionization channels have been explained by the partial wave analysis of the contribution of the individual angular momentum channels to the photoelectron.

The amyloid cascade hypothesis dealing with the senile plaques is until date thought to be one of the causative pathways leading to the pathophysiology of Alzheimer's disease (AD). Though many aggregation inhibitors of misfolded amyloid beta (Aβ42) peptide have failed in clinical trials, there are some positive aspects of the designed therapeutic peptides for diseases involving proteinaceous aggregation. Here, we evaluated a smart design of side chain tripeptide (Leu-Val-Phe)-based polymeric inhibitor addressing the fundamental hydrophobic amino acid stretch "Lys-Leu-Val-Phe-Phe-Ala" (KLVFFA) of the Aβ42 peptide. The in vitro analyses performed through the thioflavin T (ThT) fluorescence assay, infrared spectroscopy, isothermal calorimetry, cytotoxicity experiments, and so on evinced a promising path towards the development of new age AD therapeutics targeting the inhibition of misfolded Aβ42 peptide fibrillization. The in silico simulations done contoured the mechanism of drug action of the present block copolymer as the competitive inhibition of aggregate-prone hydrophobic stretch of Aβ42. Graphical abstract The production of misfolded Aβ42 peptide from amyloid precursor protein initiates amyloidosis pathway which ends with the deposition of fibrils via the oligomerization and aggregation of Aβ42 monomers. The side chain tripeptide-based PEGylated polymer targets these Aβ42 monomers and oligomers inhibiting their aggregation. This block copolymer also binds and helps degrading the preformed fibrils of Aβ42.

Organometallic molecular wires with π-conjugation along their molecular backbones are of considerable interest for application in molecular-scale electronics. In this regard, thienylethynyl-based π-conjugated oligomers of three, five and seven thienylethynyl units with -C[triple bond, length as m-dash]C-H termini have been successfully synthesized through stepwise Pd(0)/Cu(i)-catalyzed Sonogashira coupling. The corresponding highly soluble diruthenium(ii) diacetylide complexes (O1-Ru2, O3-Ru2, O5-Ru2 and O7-Ru2, respectively) have been prepared by the reaction of cis-Ru(dppe)2Cl2 and NaPF6 in DCM with the corresponding rigid rod-like thienylethynyl oligomers with one, three, five and seven thienylethynyl π-conjugated segments containing alkynyl termini (O1, O3, O5 and O7). These Ru(ii)-Cl capped diacetylide complexes have been further functionalized by incorporating a phenylacetynyl moiety to afford [Ru(ii)-C[triple bond, length as m-dash]C-Ph]-capped diacetylide organometallic wires (O1-Ru2-Ph, O3-Ru2-Ph, O5-Ru2-Ph and O7-Ru2-Ph). The photophysical properties of the highly soluble thienylethynyl-based oligomers and Ru(ii)-organometallic wires have been explored to understand their electronic properties. Electrochemical studies of the binuclear ruthenium(ii)-alkynyl complexes showed highly interesting results, revealing long-range electrochemical communication between the two remote Ru(ii) termini connected even with five and seven thienylethynyl units. DFT computational studies further support the long range electrochemical communication between the redox active metal termini through heavy participation of the thienylethynyl bridge in the corresponding mono-oxidized mixed valence species of the organometallic wire-like complexes.

In this article Quantum mechanical (QM) calculations by Density Functional Theory (DFT) have been performed of all amino acids present in bovine insulin. Simulated Raman spectra of those amino acids are compared with their experimental spectra and the major bands are assigned. The results are in good agreement with experiment. We have also verified the DFT results with Quantum mechanical molecular mechanics (QM/MM) results for some amino acids. QM/MM results are very similar with the DFT results. Although the theoretical calculation of individual amino acids are feasible, but the calculated Raman spectrum of whole protein molecule is difficult or even quite impossible task, since it relies on lengthy and costly quantum-chemical computation. However, we have tried to simulate the Raman spectrum of whole protein by adding the proportionate contribution of the Raman spectra of each amino acid present in this protein. In DFT calculations, only the contributions of disulphide bonds between cysteines are included but the contribution of the peptide and hydrogen bonds have not been considered. We have recorded the Raman spectra of bovine insulin using micro-Raman set up. The experimental spectrum is found to be very similar with the resultant simulated Raman spectrum with some exceptions.

In the fight against bacterial infections and antibiotic resistance, the dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase (DapE) is a potentially safe target enzyme. The role of the Glu134, His67, and His349 residues in the binding and hydrolysis of N-succinyl-l,l-diaminopimelic acid (SDAP) is investigated by employing molecular dynamics simulation and hybrid quantum mechanical-molecular mechanical (MM) calculations of the E134D, H67A, and H349A mutants of DapE. The free energy of substrate binding obtained from the MM-Poisson-Boltzmann surface area approach correctly reproduced the experimentally observed ordering of substrate affinity, that is, E134DwtH67AH349A. The mechanism of catalytic action by the E134D mutant is elucidated by structurally and energetically characterizing the intermediates and the transition states along the reaction pathway. The rate-determining step in the general acid-base hydrolysis reaction by the E134D mutant is found to be the nucleophilic attack step, which involves an activation energy barrier 10 kcal/mol greater than that in the wild-type (wt)-DapE. This explains the 3 orders of magnitude decrease in the experimentally determined k