Electronic and relativistic contributions to ion-pairing in polyoxometalate model systems

Physical Chemistry Chemical Physics
Ion pairs and solubility related to ion-pairing in water influence many processes in nature and in synthesis including efficient drug delivery, contaminant transport in the environment, and self-assembly of materials in water. Ion pairs are difficult to observe spectroscopically because they generally do not persist unless extreme solution conditions are applied. Here we demonstrate two advanced techniques coupled with computational studies that quantify the persistence of ion pairs in simple solutions and offer explanations for observed solubility trends. The system of study, ([(CH3)4N]+,Cs)8[M6O19] (M = Nb,Ta), is a set of unique polyoxometalate salts whose water solubility increases with increasing ion-pairing, contrary to most ionic salts. The techniques employed to characterize Cs+ association with...  Read more

Tailoring Single Chain Polymer Nanoparticle Thermo-Mechanical Behavior by Cross-link Density

Soft Matter
Single chain polymer nanoparticles (SCPNs) are formed from intrachain cross-linking of a single polymer chain, making SCPN distinct from other polymer nanoparticles for which the shape is predefined before polymerization. The degree of cross-linking in large part determines the internal architecture of the SCPNs and therefore their mechanical and themomechanical properties. Here, we use molecular dynamics (MD) simulations to study thermomechanical behavior of individual SCPNs with different underlying structures by varying the degree of cross-linking and the degree of polymerization. We characterize the particles in terms of shape, structure, glass transition temperature, mobility and stress response to compressive loading. The results indicate that the constituent monomers of SCPNs become less mobile as the degree of cross-linking is increased corresponding to lower diffusivity and higher stress at a given temperature.Read more

Cyclometalated ruthenium complexes from naturally occurring quinones: Studies on their photophysical features, computational details and trypanocidal activity

New Journal of Chemistry
Phenazinic ligands and Ru(II)-based complexes were synthesized from natural products lapachol and lawsone and evaluated against T. cruzi, the etiological agent of Chagas disease. These new ruthenium compounds could provide promising trypanocidal drugs. Besides synthesis and trypanocidal activity, this paper reports photophysical features and computational details of the compounds. The fluorescent trypanocidal substances are promising derivatives for further studies aiming to find molecules active against parasites associated to neglected diseases.Read more

Discrete wavelet assisted correlation optimised warping of chromatograms: optimizing the computational time for correcting the drifts in peak positions

Analytical Methods
Correlation optimised warping (COW) has been the most favourite chromatographic peak alignment approach in recent years. After optimization of the two parameters, slack and segment length, COW works well in aligning the chromatograms. However, one of the serious disadvantages of COW is that it is computationally time consuming. Often several segment lengths and slack parameters need to be tested to find the optimum combination for achieving the alignment that makes the whole analysis take several hours. In the present work, it has been shown that with the application of wavelet analysis prior to alignment it is possible to provide the necessary computational economy to the COW algorithm.Read more

Magnetically recoverable Fe3O4@Au-coated nanoscale catalysts for A3-coupling reaction

Dalton Transactions
The utility of a novel Fe3O4@Au nanoparticles as magnetically separable and recyclable heterogeneous catalysts for the A3- coupling reaction of aldehydes, amines, and terminal alkynes to yield the corresponding propargylamines is demonstrated. Herein we present a comprehensive analysis of the experimentally observed trends in the conversions with computational analysis using LUMO density on molecular isosurfaces and the electrostatic potential (ESP) effects estimated using DFT calculations.Read more

Inhibition of MurA enzyme in Fusobacterium nucleatum by potential inhibitors identified through computational and in vitro approaches

Molecular BioSystems
Fusobacterium nucleatum plays a key role in several diseases such as periodontitis, gingivitis, appendicitis and inflammatory bowel disease (IBD). Development of antibiotic resistance by this bacterium demands for novel therapeutic intervention. Our recent work has reported UDP-N-acetylglucosamine 1-carboxyvinyltransferase (MurA) as one of the potential target proteins in F. nucleatum. In this study, we proposed two novel MurA inhibitors through in silico screening and evaluated their mode of inhibition by in vitro experiments. MurA structural arrangement (inside-out α/β barrel) is stabilized by L/FXXXG(A) motif-based interactions. The protein is maintained in open or substrate-free conformation due to repulsive forces between two parallelly arranged positive charged residues of domain I and II. In this conformation, we identified six best compounds that held key interactions with substrate binding pocket via structure based virtual screening of natural and chemical compound...  Read more

Stereoselective binding of agonists to the β2-adrenergic receptor: insights into molecular details and thermodynamics from molecular dynamics simulations

Molecular BioSystems
The β2-adrenergic receptor (β2-AR) is one of the most studied G-protein-coupled receptors. When interacting with ligand molecule, it exhibits the binding characteristic that is strongly dependent on ligand stereoconfiguration. In particular, many experimental and theoretical studies confirmed that stereoisomers of an important β2-AR agonist, fenoterol, are associated with diverse mechanisms of binding and activation of β2-AR. The objective of the present study was to explore the stereoselective binding of fenoterol to β2-AR through the application of the advanced computational methodology based on the enhanced-sampling molecular dynamics simulations and potentials of interactions tailored to investigate the stereorecogniction effects. The results remain in a very good, quantitative agreement with the experimental data (measured in the context of ligand-receptor affinities and their dependence on the temperature) which provides an additional validation for the applied...  Read more

Prediction of luciferase inhibitors by high-performance MIEC-GBDT approach based on interaction energetic patterns

Physical Chemistry Chemical Physics
High-throughput screening (HTS) is widely applied in many fields ranging from drug discovery to clinical diagnostics and toxicity assessment. The firefly luciferase is commonly used as a reporter to monitor the effect of chemical compounds on the activity of a specific target or pathway in HTS. However, the false positive rate of luciferase-based HTS is relatively high because many artifacts or promiscuous compounds that have direct interaction with the luciferase reporter enzyme are usually identified as active compounds (hits). Therefore, it is necessary to develop a rapid screening method to identify these compounds that can inhibit the luciferase activity directly. In this study, a virtual screening (VS) classification model called MIEC-GBDT was developed to distinguish luciferase inhibitors from non-inhibitors. The molecular interaction energy components (MIECs) calculated by the Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) free energy decomposition were used to...  Read more

Automatic generation of reaction energy databases from highly accurate atomization energy benchmark sets

Physical Chemistry Chemical Physics
In this contribution, we discuss how reaction energy benchmark sets can automatically be created from arbitrary atomization energy databases. As an example, over 11,000 reaction energies derived from the W4-11 database, as well as some relevant subsets are reported. Importantly, there is only very modest computational overhead involved in computing >11,000 reaction energies compared to 140 atomization energies, since the rate-determining step for either benchmark is performing the same 140 quantum chemical calculations. The performance of commonly used electronic structure methods for the new database is analyzed. This allows investigating the relationship between the performances for atomization and reaction energy benchmarks based on an identical set of molecules. The atomization energy is found to be a weak predictor for the overall usefulness of a method. The performance of density functional approximations in light of the number of empirically optimized parameters used in...  Read more

Charge transfer induced energy storage in CaZnOS:Mn – insight from experimental and computational spectroscopy

Physical Chemistry Chemical Physics
CaZnOS:Mn2+ is a rare-earth-free luminescent compound with an orange broadband emission at 612 nm, featuring pressure sensing capabilities, often explained by defect levels where energy can be stored. Despite recent efforts from experimental and theoretical points of view, the underlying luminescence mechanisms in this phosphor still lack a profound understanding. By the evaluation of thermoluminescence as a function of the charging wavelength, we probe the defect levels allowing energy storage. Multiple trap depths and trapping routes are found, suggesting predominantly local trapping close to Mn2+ impurities. We demonstrate that this phosphor shows mechanoluminescence which is unexpectedly stable at high temperature (up to 200 °C), allowing pressure sensing in a wide temperature range. Next, we correlate the spectroscopic results with a theoretical study of the electronic structure and stability of the Mn defects in CaZnOS. DFT...  Read more

Synthesis of 2-julolidin-imidazo[1,2-a]pyridines via Groebke-Blackburn-Bienaymé reaction and studies of optical properties

New Journal of Chemistry
A series of sixteen new 2-julolidin-imidazo[1,2-a]pyridine bound-type bis-heterocycles were synthesized in good to excellent yields (61-98%) via an MW-assisted Groebke-Blackburn-Bienaymé (GBB) reaction. Then, experimental studies were conducted to determine the luminescence properties of these compounds. Various high quantum yields were found. In fact, one product exhibited a quantum yield (86.6%) comparable to that of the reference compound rhodamine (94.8%). Finally, further computational studies were performed by means of TD-DFT to calculate their HOMO-LUMO distributions and theoretical absorption spectra. Good agreement between the experimental and computational results were obtained, which provides a rationalized explanation for the observed structure/property relationships.Read more

Estimation of conventional C-H∙∙∙π (arene), unconventional C-H∙∙∙π (chelate) and C-H∙∙∙π (thiocyanate) interactions in hetero-nuclear nickel-cadmium complexes with a compartmental Schiff base: Novel example of a diamine bridged hetero-polynuclear complex having NiO2Cd core

Dalton Transactions
Three new heteronuclear nickel(II)/cadmium(II) complexes, [(SCN)(Cl)Cd(L)Ni(DMF)2] (1), [(SCN)(CH3CO2)Cd(L)Ni(CH3OH)2] (2) and [(SCN)(Cl)Cd(L)Ni(NH2CH2CH2CH2NH2)]n (3) {where H2L = N,N'-bis(3-ethoxysalicylidene) propane-1,3-diamine is a potential hexadentate compartmental Schiff base}, have been synthesized and characterized by elemental analysis, IR, UV-Vis and fluorescence spectroscopy. The structures of the complexes have been confirmed by single crystal X-ray diffraction studies. In each complex, nickel(II) is placed in the inner N2O2 environment and cadmium(II) is placed in the outer O4 compartment of the compartmental Schiff base. Furthermore, the importance of unconventional C-H∙∙∙π (chelate) interactions in the solid state of complexes 1 and 2 have been described by means of DFT and MEP calculations and characterized using the NCI plot. All complexes show photoluminescence at room temperature upon the irradiation of ultraviolet light. The life times of excited states...  Read more

Highly selective synthesis of substituted (E)-alkenylsilatranes via catalytic trans-silylation and mechanistic implications

Dalton Transactions
A new route for the synthesis of functionalized alkenylsilatranes has been developed based on the ruthenium-catalyzed trans-silylation with olefins. This transformation allowed for the synthesis of new (E)-alkenylsilatranes in good yields and excellent selectivity. Experimental studies concerning reaction mechanism were carried out and the intermediate ruthenium-silatranyl complex was isolated and characterized. Moreover, detailed DFT calculations regarding the mechanism of silylative coupling catalytic cycle of silatranes catalyzed by [Ru]-H complexes were also performed.Read more

Topological landscapes of porous organic cages

We define a nomenclature for the classification of porous organic cage molecules, enumerating the 20 most probable topologies, 12 of which have been synthetically realised to date. We then discuss the computational challenges encountered when trying to predict the most likely topological outcomes from dynamic covalent chemistry (DCC) reactions of organic building blocks. This allows us to explore the extent to which comparing the internal energies of possible reaction outcomes is successful in predicting topology for a series of 10 different building block combinations.Read more

Umbrella Sampling Molecular Dynamics Simulations Reveal Concerted Ion Movement through G-Quadruplex DNA Channels

Physical Chemistry Chemical Physics
We have applied the umbrella sampling (US) method in all-atom molecular dynamics (MD) simulations to obtain potential of mean force (PMF) profiles for ion transport through three representative G-quadruplex DNA channels: [d(TG4T)]4, [d(G3T4G4)]2, and d[G4(T4G4)3]. The US MD results are in excellent agreement with those obtained previously with the adaptive biasing force (ABF) method. We then utilized the unique features in the US MD method to investigate multi-ion effects in [d(G3T4G4)]2 and discovered that the concerted ion movement is crucial for fully explaining the unusual experimental results on ion movement in this particular G-quadruplex system. We anticipate that these modern free-energy methods will be able to aid in silico design of G-quadruplex DNA as ion channels.Read more

Mechanism of degradation of nitrogenous heterocycle induced by a reductive radical: Decomposition of sym-triazine ring

Physical Chemistry Chemical Physics
The cyanuric-acid is one of major component of materials & chemicals and also the most important intermediate in the degradation processes of sym-triazine compounds in nature environment, as well as water treatment. However, the degradation mechanism of cyanuric-acid is still unclear in varieties of advanced oxidation processes (AOPs), where •OH is usually regarded as dominant radical. Here, combined density functional theory calculations with experimental observations, we unexpectedly show that sym-triazine ring structure is broken efficiently by the reductive free radicals -- hydrogen radicals (•H), rather than traditional •OH. The energy barrier of the cyanuric-acid reacting with •H to form the -NH2 group and break the sym-triazine ring is only 4.96 kcal/mol, which is clearly lower than that (13.32 kcal/mol) of the cyanuric-acid reacting with •OH. Our theoretical predictions are further confirmed by the experiments of γ photon irradiation, which shows when the •H...  Read more

Time-dependent Vibrational Spectral Analysis of First Principles Trajectory of Methylamine with Wavelet Transform

Physical Chemistry Chemical Physics
The fluctuation dynamics of amine stretch frequencies, hydrogen bonds, dangling N-D bonds, and orientation profile of amine group of methylamine (MA) are investigated at ambient condition by means of dispersion corrected density functional theory based first principles molecular dynamics (FPMD) simulations. Along with the dynamical properties, various equilibrium properties such as radial distribution functions, spatial distribution function, combined radial and angular distribution functions and hydrogen bonding were also calculated. The instantaneous stretching frequencies of amine groups were obtained by wavelet transform of trajectory obtained from FPMD simulations. The frequency-structure correlation reveals that amine stretching frequency is weakly correlated with nearest nitrogen-deuterium distance. The frequency-frequency correlation function has short time scale of at around 110 fs, and a longer time scale of about 1.15 ps. It is found that, the short time scale originates...  Read more

A coarse-grained model for assisting the investigation of the structure and dynamics of large nucleic acid species by Ion Mobility Spectrometry - Mass Spectrometry

Physical Chemistry Chemical Physics
Ion Mobility Spectrometry-Mass Spectrometry (IMS-MS) is a rapidly emerging tool for the investigation of nucleic acid structure and dynamics. IMS-MS determinations can provide valuable information regarding alternative topologies, folding intermediates, and conformational heterogeneities, which are not readily accessible to other analytical techniques. The leading strategies for data interpretation rely on computational and experimental approaches to correctly assign experimental observations to putative structures. A very effective strategy involves the application of molecular dynamics (MD) simulations to predict the structure of the analyte molecule, calculate its collision cross section (CCS), and then compare this computational value with the corresponding experimental data. While this approach works well for small nucleic acid species, analyzing larger nucleic acids of biological interest is hampered by the computational cost associated with capturing their extensive structure...  Read more

Diffusion of Active Dimers in a Couette Flow

Soft Matter
We study the 3D dynamics of an elastic dimer consisting of an active swimmer bound to a passive cargo, both suspended in a Couette flow. Using numerical simulations, we determine the diffusivity of such an active dimer in the presence of long-range hydrodynamic interactions for different values of its self-propulsion speed and the Couette flow. We observe that the effect of the hydrodynamic interactions is greatly enhanced under the condition that self-propulsion is strong enough to contrast the shear flow. The magnitude of the effect grows with the size of the dimer's constituents relative to their distance, which makes it appreciable under experimental conditions.Read more

From isolated to 2D Coordination Polymers based on 6-aminonicotinate and 3d-Metal Ions: Towards Field-Induced Single-Ion-Magnets

We report herein the synthesis, structural and chemical characterization of six new compounds consisting of 6-aminonicotinate (6ani) ligand and first-row transition metal ions, namely, [Mn2(μ-6ani)2(H2O)8](6ani)2 (1), [Co(6ani)(bipy)2(H2O)3](6ani)•5H2O (2), [M(μ-6ani)(6ani)(H2O)3]•2H2O [MII = Co (3), Ni (4)], and [M(μ-6ani)2]•H2O [MII = Co (5), Cu (6)] (where bipy = 4,4’-bipyridine). Compounds 1 and 2 consist of isolated dimeric and monomeric entities held together by supramolecular interactions governed by 6ani free anions. The rigid and low symmetry of 6ani ligands, in addition to their coordination as terminal and bridging ligands to octahedral metal geometries, gives rise to chiral 1D chains of compounds 3 and 4. 2D sql layers are established (5 and 6) when 6ani ligands act as ligands bridging the metal ions, which precludes the presence of water molecules in the framework. Despite the wide structural diversity observed, all architectures share the occurrence of...  Read more