Red Circularly Polarized Luminescence from Dimeric H-Aggregates of Acridine Orange by Chiral Induction.

Understanding the mechanism of chirality transfer from a chiral surface to an achiral molecule is essential for designing molecular systems with tunable chiroptical properties. These aspects are explored herein using l- and d-isomers of alkyl valine amphiphiles, which self-assemble in water as nanofibers possessing a negative surface charge. An achiral chromophore, acridine orange, upon electrostatic binding on these surfaces displays mirror-imaged bisignated circular dichroism and red-emitting circularly polarized luminescence signals with a high dissymmetry factor. Experimental and computational investigations establish that the chiroptical properties emerge from surface-bound asymmetric H-type dimers of acridine orange, further supported by fluorescence lifetime imaging studies. Specifically, atomistic molecular dynamics simulations show that the experimentally observed chiral signatures have their origin in van der Waals interactions between acridine orange dimers and the amphiphile head groups as well as in the extent of solvent exposure of the chromophore.

Liquid-Vapor Interface of Aqueous Ethylene Glycol Solutions: A Molecular Dynamics Study.

While the organic constituent in an aqueous binary solution enriches its liquid-vapor (l-v) interface, the extent of enrichment can depend nonlinearly on its mole fraction. A microscopic quantification and rationalization of this behavior are crucial to understand the dependence of properties such as surface tension and evaporation rate of the solution on its composition. Extensive all-atom molecular dynamics simulations of aqueous ethylene glycol (EG) solutions show that the composition of the solution at the l-v interface deviates the most from that in the bulk solution at an EG mole fraction of 0.3. The population of EG molecules with their central C-C dihedral in the gauche conformation was found to be higher at the l-v interface than that in the bulk solution to facilitate the orientation of its hydrophobic methyl groups toward the vapor phase. Free energy calculations reveal that in dilute EG solutions, an EG molecule is most stable at the l-v interface. The behavior of vapor pressure in aqueous EG solutions is ideal and follows Raoult's law, while in contrast, the aqueous solution of dimethyl sulfoxide does not. A rationale for the same is provided through the orientational distribution of interfacial water molecules in the respective solutions.

Noncovalent interaction guided selectivity of haloaromatic isomers in a flexible porous coordination polymer.

Porous, supramolecular structures exhibit preferential encapsulation of guest molecules, primarily by means of differences in the order of (noncovalent) interactions. The encapsulation preferences can be for geometry (dimension and shape) and the chemical nature of the guest. While geometry-based sorting is relatively straightforward using advanced porous materials, designing a "chemical nature" specific host is not. To introduce "chemical specificity", the host must retain an accessible and complementary recognition site. In the case of a supramolecular, porous coordination polymer (PCP) [Zn(o-phen)(ndc)] (o-phen: 1,10-phenanthroline, ndc: 2,6-naphthalenedicarboxylate) host, equipped with an adaptable recognition pocket, we have discovered that the preferential encapsulation of a haloaromatic isomer is not only for dimension and shape, but also for the "chemical nature" of the guest. This selectivity, i.e., preference for the dimension, shape and chemical nature, is not guided by any complementary recognition site, which is commonly required for "chemical specificity". Insights from crystal structures and computational studies unveil that the differences in the different types of noncovalent host-guest interaction strengths, acting in a concerted fashion, yield the unique selectivity.

Lipase A from Bacillus subtilis: Substrate Binding, Conformational Dynamics, and Signatures of a Lid.

Protein-ligand binding studies are crucial for understanding the molecular basis of biological processes and for further advancing industrial biocatalysis and drug discovery. Using computational modeling and molecular dynamics simulations, we investigated the binding of a butyrate ester substrate to the lipase A (LipA) enzyme of Bacillus subtilis. Besides obtaining a close agreement of the binding free energy with the experimental value, the study reveals a remarkable reorganization of the catalytic triad upon substrate binding, leading to increased essential hydrogen bond populations. The investigation shows the distortion of the oxyanion hole in both the substrate-bound and unbound states of LipA and highlights the strengthening of the same in the tetrahedral intermediate complex. Principal component analysis of the unbound ensemble reveals the dominant motion in LipA to be the movement of Loop-1 (Tyr129-Arg142) between two states that cover and uncover the active site, mirroring that of a lid prevalent in several lipases. This lid-like motion of Loop-1 is also supported by its tendency to spontaneously open up at an oil-water interface. Overall, this study provides valuable insights into the impact of substrate binding on the structure, flexibility, and conformational dynamics of the LipA enzyme.

Understanding the Anomalous Diffusion of Water in Aqueous Electrolytes Using Machine Learned Potentials.

The diffusivity of water in aqueous cesium iodide solutions is larger than that in neat liquid water and vice versa for sodium chloride solutions. Such peculiar ion-specific behavior, called anomalous diffusion, is not reproduced in typical force field based molecular dynamics (MD) simulations due to inadequate treatment of ion-water interactions. Herein, this hurdle is tackled by using machine learned atomic potentials (MLPs) trained on data from density functional theory calculations. MLP based atomistic MD simulations of aqueous salt solutions reproduce experimentally determined thermodynamic, structural, dynamical, and transport properties, including their varied trends in water diffusivities across salt concentration. This enables an examination of their intermolecular structure to unravel the microscopic underpinnings of the differences in their transport properties. While both ions in CsI solutions contribute to the faster diffusion of water molecules, the competition between the heavy retardation by Na ions and the slight acceleration by Cl ions in NaCl solutions reduces their water diffusivity.

Supramolecular Polymerization of a Pyrene-Substituted Diamide and Its Ensemble of Kinetically Trapped Configurations.

The prevalence of kinetically accessible states in supramolecular polymerization pathways has been exploited to control the growth of the polymer and thereby to obtain niche morphologies. Yet, these pathways themselves are not easily amenable for experimental delineation but could potentially be understood through molecular dynamics (MD) simulations. Herein, we report an extensive investigation of the self-assembly of pyrene-substituted diamide (PDA) monomers in solution, conducted using atomistic MD simulations and advanced sampling methods. We characterize such kinetic and thermodynamic states as well as the transition pathways and free energy barriers between them. PDA forms a dimeric segment with the N- to C-termini vectors of the diamide moieties arranged either in parallel or anti-parallel fashion. This characteristic, combined with the molecule's torsional flexibility and pyrene-solvent interactions, presents an ensemble of molecular configurations contributing to the kinetic state in the polymerization pathway. While this ensemble primarily comprises short oligomers containing a mix of anti-parallel and parallel dimeric segments, the thermodynamic state of the assembly is a right-handed polymer featuring parallel ones only. Our work thus offers an approach by which the landscape of any specific supramolecular polymerization can be deconstructed.

Structurally Induced Chirality of an Achiral Chromophore on Self-Assembled Nanofibers: A Twist Makes It Chiral.

The surface domains of self-assembled amphiphiles are well-organized and can perform many physical, chemical, and biological functions. Here, we present the significance of chiral surface domains of these self-assemblies in transferring chirality to achiral chromophores. These aspects are probed using l- and d-isomers of alkyl alanine amphiphiles which self-assemble in water as nanofibers, possessing a negative surface charge. When bound on these nanofibers, positively charged cyanine dyes (CY524 and CY600), each having two quinoline rings bridged by conjugated double bonds, show contrasting chiroptical features. Interestingly, CY600 displays a bisignated circular dichroic (CD) signal with mirror-image symmetry, while CY524 is CD silent. Molecular dynamics simulations reveal that the model cylindrical micelles (CM) derived from the two isomers exhibit surface chirality and the chromophores are buried as monomers in mirror-imaged pockets on their surfaces. The monomeric nature of template-bound chromophores and their binding reversibility are established by concentration- and temperature-dependent spectroscopies and calorimetry. On the CM, CY524 displays two equally populated conformers with opposite sense, whereas CY600 is present as two pairs of twisted conformers in each of which one is in excess, due to differences in weak dye-amphiphile hydrogen bonding interactions. Infrared and NMR spectroscopies support these findings. Reduction of electronic conjugation caused by the twist establishes the two quinoline rings as independent entities. On-resonance coupling between the transition dipoles of these units generates bisignated CD signals with mirror-image symmetry. The results presented herein provide insight on the little-known structurally induced chirality of achiral chromophores through transfer of chiral surface information.

Revisiting the Burden Borne by Fumarase: Enzymatic Hydration of an Olefin.

Fumarate hydratase (FH) is a remarkable catalyst that decreases the free energy of the catalyzed reaction by 30 kcal mol-1, much larger than most exceptional enzymes with extraordinary catalytic rates. Two classes of FH are observed in nature: class-I and class-II, which have different folds, yet catalyze the same reversible hydration/dehydration reaction of the dicarboxylic acids fumarate/malate, with equal efficiencies. Using class-I FH from the hyperthermophilic archaeon Methanocaldococcus jannaschii (Mj) as a model along with comparative analysis with the only other available class-I FH structure from Leishmania major (Lm), we provide insights into the molecular mechanism of catalysis in this class of enzymes. The structure of MjFH apo-protein has been determined, revealing that large intersubunit rearrangements occur across apo- and holo-protein forms, with a largely preorganized active site for substrate binding. Site-directed mutagenesis of active site residues, kinetic analysis, and computational studies, including density functional theory (DFT) and natural population analysis, together show that residues interacting with the carboxylate group of the substrate play a pivotal role in catalysis. Our study establishes that an electrostatic network at the active site of class-I FH polarizes the substrate fumarate through interactions with its carboxylate groups, thereby permitting an easier addition of a water molecule across the olefinic bond. We propose a mechanism of catalysis in FH that occurs through transition-state stabilization involving the distortion of the electronic structure of the substrate olefinic bond mediated by the charge polarization of the bound substrate at the enzyme active site.

Endobronchial lesion in an adolescent with hemoptysis biopsy or not to biopsy?

An 11-year-old girl was brought with complaints of recurrent massive hemoptysis. A computerized tomography (CT) of the chest showed ground glass opacities on the right lower lobe, and a CT angiography showed hypertrophied right pulmonary artery. Flexible bronchoscopy revealed a sessile friable lesion in the right lower lobe, raising suspicion of either a tumor or a vascular malformation. An endobronchial ultrasound (EBUS) revealed a cystic lesion in the submucous plane, with vascularity noted on Doppler mode. This confirmed the diagnosis of bronchial Dieulafoy disease. A bronchial angiography revealed a vascular malformation overlying the lesion with a bronchopulmonary shunt, which was ligated. This case demonstrates the importance of EBUS in endobronchial lesions, to avoid biopsy of a vascular malformation.

Conformer Selection Upon Dilution with Water: The Fascinating Case of Liquid Ethylene Glycol Studied via Molecular Dynamics Simulations.

The aqueous solution of ethylene glycol (EG) is a binary liquid mixture that displays rich conformational and structural behaviour, which has not yet been adequately explored through atomistic molecular dynamics simulations. Herein, employing an accurate force field for EG, several physical properties of this solution are calculated to be in quantitative agreement with experimental data. While 79 % of molecules in neat liquid EG exist with their central OCCO dihedral in the gauche state, this fraction increases to 89 % in the dilute aqueous solution, largely in response to the increase in the static dielectric constant of the solution from that of neat liquid EG. The increase in gauche conformers increases the mean dipole moment of EG molecules in the solution which is additionally contributed by specific conformational states of the two terminal HOCC dihedral angles.

Molecular simulations explain the exceptional thermal stability, solvent tolerance and solubility of protein-polymer surfactant bioconjugates in ionic liquids.

Proteins complexed electrostatically with polymer surfactants constitute a viscous liquid by themselves, called the solvent-free protein liquid (SFPL). A solution of SFPL in a room temperature ionic liquid (PS-IL) offers the protein hyperthermal stability, higher solubility and greater IL tolerance. A generic understanding of these protein-polymer systems is obtained herein through extensive atomistic molecular dynamics simulations of three different enzymes (lipase A, lysozyme and myoglobin) under various conditions. Along with increased intra-protein hydrogen bonding, the surfactant coating around the proteins imparts greater thermal stability, and also aids in screening protein-IL interactions, endowing them IL tolerance. The reduced surface polarity of the protein-polymer bioconjugate and hydrogen bonding between the ethylene glycol groups of the surfactant and the IL cation contribute to the facile solvation of the protein in its PS-IL form. The results presented here rationalize several experimental observations and will aid in the improved design of such hybrid materials for sustainable catalysis.

Tailoring a robust Al-MOF for trapping C2H6 and C2H2 towards efficient C2H4 purification from quaternary mixtures.

Light hydrocarbon separation is considered one of the most industrially challenging and desired chemical separation processes and is highly essential in polymer and chemical industries. Among them, separating ethylene (C2H4) from C2 hydrocarbon mixtures such as ethane (C2H6), acetylene (C2H2), and other natural gas elements (CO2, CH4) is of paramount importance and poses significant difficulty. We demonstrate such separations using an Al-MOF synthesised earlier as a non-porous material, but herein endowed with hierarchical porosity created under microwave conditions in an equimolar water/ethanol solution. The material possessing a large surface area (793 m2 g-1) exhibits an excellent uptake capacity for major industrial hydrocarbons in the order of C2H2 > C2H6 > CO2 > C2H4 > CH4 under ambient conditions. It shows an outstanding dynamic breakthrough separation of ethylene (C2H4) not only for a binary mixture (C2H6/C2H4) but also for a quaternary combination (C2H4/C2H6/C2H2/CO2 and C2H4/C2H6/C2H2/CH4) of varying concentrations. The detailed separation/purification mechanism was unveiled by gas adsorption isotherms, mixed-gas adsorption calculations, selectivity estimations, advanced computer simulations such as density functional theory (DFT), grand canonical Monte Carlo (GCMC) and ab initio molecular dynamics (AIMD), and stepwise multicomponent dynamic breakthrough experiments.

Gate Opening without Volume Change Triggers Cooperative Gas Interactions, Underpins an Isotherm Step in Metal-Organic Frameworks.

Three halogenated metal-organic frameworks (MOFs) reported recently exhibited a second step in their CO2 gas adsorption isotherms. The emergence of halogen-bonding interactions beyond a threshold gas pressure between the framework halogen and the CO2 guest was conjectured to be the underlying reason for the additional step in the isotherm. Our investigation employing periodic density functional theory calculations did not show significant interactions between the halogen and CO2 molecules. Further, using a combination of DFT-based ab initio molecular dynamics and grand canonical Monte Carlo simulations, we find that the increased separation of framework nitrate pairs facing each other across the pore channel enables the accommodation of an additional CO2 molecule which is further stabilized by cooperative interactions─an observation that facilely explains the second isotherm step. The increased separation between the nitrate groups can occur without any lattice expansion, consistent with experiments. The results point to a structural feature to achieve this isotherm step in MOFs that neither possess large pores nor exhibit large-scale structural changes such as breathing.

Insights into substrate behavior in a solvent-free protein liquid to rationalize its reduced catalytic rate.

When proteins are engineered with a polymer surfactant coating on their surface, they can form a liquid phase by themselves, without the need for a solvent, such as, say, water. However, such solvent-free protein liquids (SFPL), despite their capability to function at temperatures above those in aqueous solutions, exhibit much reduced catalytic rates. A comprehensive understanding of the nature of substrates in such liquids is crucial to reason out the reduced catalytic activity of enzymes as SFPL media, and thus identify the means to improve the same. Employing atomistic molecular dynamics simulations of lipase A from Bacillus subtilis in its SFPL form, we demonstrate that at low concentrations, the substrate molecules are located mostly in the hydrophilic layer of the surfactant shell that ensheaths the enzyme; substrates in this SFPL are present in various conformations with similar propensities as in the aqueous solution. Slower translational diffusion and reorientational dynamics, as well as the reduced tendency of a substrate molecule to closely interact with the enzymes in the SFPL medium have been identified herein as the contributing factors for the reduced activity of enzymes in this hybrid liquid. At high concentrations of substrates corresponding to those used in in vitro experiments, the formation of an enzyme-substrate complex is observed. Microscopic insights reported here can aid in the choice of surfactants to improve the catalytic rate of enzymes in SFPL.

Liquid ethylene glycol: prediction of physical properties, conformer population and interfacial enrichment with a refined non-polarizable force field.

Periodic density functional theory based molecular dynamics simulations confirm the fraction of molecules in neat liquid ethylene glycol with their central OCCO dihedral in the trans conformation to be 21% at ambient conditions, while the rest are gauche conformers. Using this result as a benchmark, two non-polarizable force fields are developed herein to reproduce the conformer populations in the liquid, an important aspect inadequately addressed in several generic force fields. The mean dipole moment of a molecule in the liquid is estimated to be about 40% enhanced over its value in the gas phase, a feature discerned via AIMD simulations and fairly reproduced by our force fields. They are also shown to quantitatively predict all the physical properties of the liquid. Molecules present at the liquid-vapor interface of ethylene glycol are oriented with their methylene groups pointing towards the vapor phase, a requirement that enriches the interface with gauche conformers, in line with polarized sum frequency generation spectroscopy results.

Structural basis for the hyperthermostability of an archaeal enzyme induced by succinimide formation.

Stability of proteins from hyperthermophiles (organisms existing under boiling water conditions) enabled by a reduction of conformational flexibility is realized through various mechanisms. A succinimide (SNN) arising from the post-translational cyclization of the side chains of aspartyl/asparaginyl residues with the backbone amide -NH of the succeeding residue would restrain the torsion angle Ψ and can serve as a new route for hyperthermostability. However, such a succinimide is typically prone to hydrolysis, transforming to either an aspartyl or ß-isoaspartyl residue. Here, we present the crystal structure of Methanocaldococcus jannaschii glutamine amidotransferase and, using enhanced sampling molecular dynamics simulations, address the mechanism of its increased thermostability, up to 100°C, imparted by an unexpectedly stable succinimidyl residue at position 109. The stability of SNN109 to hydrolysis is seen to arise from its electrostatic shielding by the side-chain carboxylate group of its succeeding residue Asp110, as well as through n → π∗ interactions between SNN109 and its preceding residue Glu108, both of which prevent water access to SNN. The stable succinimidyl residue induces the formation of an α-turn structure involving 13-atom hydrogen bonding, which locks the local conformation, reducing protein flexibility. The destabilization of the protein upon replacement of SNN with a Φ-restricted prolyl residue highlights the specificity of the succinimidyl residue in imparting hyperthermostability to the enzyme. The conservation of the succinimide-forming tripeptide sequence (E(N/D)(E/D)) in several archaeal GATases strongly suggests an adaptation of this otherwise detrimental post-translational modification as a harbinger of thermostability.

A Dynamic Chemical Clip in Supramolecular Framework for Sorting Alkylaromatic Isomers using Thermodynamic and Kinetic Preferences.

Adsorptive chemical separation is at the forefront of future technologies, for use in chemical and petrochemical industries. In this process, a porous adsorbent selectively allows a single component from a mixture of three or more chemical components to be adsorbed or permeate. To separate the unsorted chemicals, a different adsorbent is needed. A unique adsorbent which can recognize and separate each of the chemicals from a mixture of three or more components is the necessity for the next generation porous materials. In this regard, we demonstrate a "dynamic chemical clip" in a supramolecular framework capable of thermodynamic and kinetics-based chemical separation. The dynamic space, featuring a strong preference for aromatic guests through π-π and C-H⋅⋅⋅π interactions and adaptability, can recognize the individual chemical isomers from mixtures and separate those based on thermodynamic and kinetic factors. The liquid-phase selectivity and separation of the aromatic isomers are possible by the adaptability of the "chemical clip" and here we elucidate the prime factors in a combinatorial approach involving crystallographic evidence and detailed computational studies.

Efficient Parametrization of Force Field for the Quantitative Prediction of the Physical Properties of Ionic Liquid Electrolytes.

The prediction of transport properties of room-temperature ionic liquids from nonpolarizable force field-based simulations has long been a challenge. The uniform charge scaling method has been widely used to improve the agreement with the experiment by incorporating the polarizability and charge transfer effects in an effective manner. While this method improves the performance of the force fields, this prescription is ad hoc in character; further, a quantitative prediction is still not guaranteed. In such cases, the nonbonded interaction parameters too need to be refined, which requires significant effort. In this work, we propose a three-step semiautomated refinement procedure based on (1) atomic site charges obtained from quantum calculations of the bulk condensed phase; (2) quenched Monte Carlo optimizer to shortlist suitable force field candidates, which are then tested using pilot simulations; and (3) manual refinement to further improve the accuracy of the force field. The strategy is designed in a sequential manner with each step improving the accuracy over the previous step, allowing the users to invest the effort commensurate with the desired accuracy of the refined force field. The refinement procedure is applied on N,N-diethyl-N-methyl-N-(2-methoxyethyl)ammonium bis(trifluoromethanesulfonyl)imide (DEME-TFSI), a front-runner as an electrolyte for electric double-layer capacitors and single-molecule-based devices. The transferability of the refined force field is tested on N,N-dimethyl-N-ethyl-N-methoxyethoxyethylammonium bis(trifluoromethanesulfonyl)imide (N112,2O2O1-TFSI). The refined force field is found to be better at predicting both structural and transport properties compared to the uniform charge scaling procedure, which showed a discrepancy in the X-ray structure factor. The refined force field showed quantitative agreement with structural (density and X-ray structure factor) and transport properties-diffusion coefficients, ionic conductivity, and shear viscosity over a wide temperature range, building a case for the wide adoption of the procedure.

An atomistic view of solvent-free protein liquids: the case of Lipase A.

Solvent-free enzymes hold the promise of being able to deliver higher activity at elevated temperatures by virtue of them being not limited by the boiling point of the solvent. They have been realized in the liquid phase through a polymer surfactant coating on the protein surface. However, a clear understanding of intermolecular interactions, structure, dynamics, and the behaviour of the minuscule amount of water present in the solvent-free protein liquid is essential to enhance the activity of these biofluids. Using atomistic molecular dynamics simulations, we demonstrate that the scaled spatial correlations between proteins in the hybrid liquid phase of Lipase A enzymes are comparable to the inter-particle correlations in a noble gas fluid. The hydrophilic region of the surfactants forms a coronal layer around each enzyme which percolates throughout the liquid, while the hydrophobic parts are present as disjointed clusters. Inter-surfactant interactions, determined to be attractive and in the range of -200 to -300 kcal mol-1, stabilize the liquid state. While the protein retains its native state conformational dynamics in the solvent-free form, the fluxionality of its side chains is much reduced; at 333 K, the latter is found to be equivalent to that of the enzyme in an aqueous solution at 249 K. Despite the sluggishness of the solvent-free enzyme, some water molecules exhibit high mobility and transit between enzymes primarily via the interspersed hydrophilic regions. These microscopic insights offer ideas to improve substrate diffusion in the liquid to enable the enhancement of catalytic activity.

Fluorocarbon-Functionalized Superhydrophobic Metal-Organic Framework: Enhanced CO2 Uptake via Photoinduced Postsynthetic Modification.

The design and synthesis of porous materials for selective capture of CO2 in the presence of water vapor is of paramount importance in the context of practical separation of CO2 from the flue gas stream. Here, we report the synthesis and structural characterization of a photoresponsive fluorinated MOF {[Cd(bpee)(hfbba)]·EtOH}n (1) constructed by using 4,4'-(hexafluoroisopropylidene)bis(benzoic acid) (hfbba), Cd(NO3)2, and 1,2-bis(4-pyridyl)ethylene (bpee) as building units. Due to the presence of the fluoroalkyl -CF3 functionality, compound 1 exhibits superhydrophobicity, which is validated by both water vapor adsorption and contact angle measurements (152°). The parallel arrangement of the bpee linkers makes compound 1 a photoresponsive material that transforms to {[Cd2(rctt-tpcb)(hfbba)2]·2EtOH}n (rctt-tpcb = regio cis,trans,trans-tetrakis(4-pyridyl)cyclobutane; 1IR) after a [2 + 2] cycloaddition reaction. The photomodified framework 1IR exhibits increased uptake of CO2 in comparison to 1 under ambient conditions due to alteration of the pore surface that leads to additional weak electron donor-acceptor interactions with the -CF3 groups, as examined through periodic density functional theory calculations. The enhanced uptake is also aided by an expansion of the pore window, which contributes to increasing the rotational entropy of CO2, as demonstrated through force field based free energy calculations.