Slow Molecular Motions in Ionic Liquids Probed by Cross‐Relaxation of Nuclear Spins During Overhauser Dynamic Nuclear Polarization

Solution‐state Overhauser dynamic nuclear polarization (ODNP) at moderate fields, performed by saturating the electron spin resonance (ESR) of a free radical added to the sample of interest, is well known to lead to significant NMR signal enhancements in the steady state, owing to electron–nuclear cross‐relaxation. Here it is shown that under conditions which limit radical access to the molecules of interest, the time course of establishment of ODNP can provide a unique window into internuclear cross‐relaxation, and reflects relatively slow molecular motions. This behavior, modeled mathematically by a three‐spin version of the Solomon equations (one unpaired electron and two nuclear spins), is demonstrated experimentally on the ¹⁹F/¹H system in ionic liquids. Bulky radicals in these viscous environments turn out to be just the right setting to exploit these effects. Compared to standard nuclear Overhauser effect (NOE) work, the present experiment offers significant improvement in dynamic range and sensitivity, retains usable chemical shift information, and reports on molecular motions in the sub‐megahertz (MHz) to tens of MHz range—motions which are not accessed at high fields.     

Molecular dynamics of hydrophilic poly(propylene imine) dendrimers in aqueous solutions by 1H NMR relaxation

The local dynamics of three poly(propylene imine) dendrimers with hydrophilic triethylenoxy methyl ether terminal groups were studied in D₂O by the measurement of the ¹H NMR relaxation times, which were treated with the Lipari–Szabo model‐free approach. The results showed that the overall mobility increased with temperature and decreased with increasing dendrimer size. An Arrhenius trend was observed for both overall and local motions. The activation energy of overall tumbling increased from 11.3 to 17.5 kJ/mol with the dendrimer size. The local mobility decreased from the outer part to the inner part of the dendrimer and with the dendrimer size. The spatial restriction of local motions decreased with increasing temperature up to 55 °C and remained constant above 55 °C. Local motions were more restricted when the dendrimer size increased. The results showed that the hydrophilic end groups of the dendrimers were located preferentially at the periphery of the molecules and were extended in the aqueous environment. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 2969–2975, 2003     

Simultaneous measurements of T1 and T2 during fast polymerization reaction using continuous wave‐free precession NMR method

Continuous wave‐free precession (CWFP) pulse sequence employing time domain nuclear magnetic resonance spectroscopy (TD‐NMR) was used to measure longitudinal (T₁) and transverse relaxation times (T₂), during the cure of a commercial epoxy resin (Araldite^TM) with a 10‐min solidification time. The intensity of the NMR signal after the first pulse and in the CWFP regime were used to monitor the concentration of the monomers, and the relaxation times were used to monitor the chain mobility. The main advantage of CWFP over the standard methods to measure relaxation times, inversion recovery (inv‐rec) for T₁ and Carr‐Purcell‐Meiboom‐Gill (CPMG) for T₂, is that the measurement of both relaxation times can be performed in a fast and single NMR experiment and, therefore, using a single reaction batch. CWFP is also as fast as the CPMG measurement but at least fivefold faster than the method to obtain T₁ using null point approximation in the inv‐rec method. Therefore, the CWFP sequence can be used as a fast and general method to measure relaxation times in polymerization reactions, even with fast solidification time. As a TD‐NMR technique, CWFP can be employed in any low‐cost bench top TD‐NMR equipment commonly used in an academic or industrial laboratory. Copyright © 2012 John Wiley & Sons, Ltd.     

Aqueous solutions of sodium methylsulfate by Raman scattering,NMR, ultrasound,and density measurements

Dynamic properties of sodium methylsulfate were investigated by means of NMR and Raman spectroscopies. The concentration dependence of the spin-lattice relaxation times of²³Na in aqueous solutions of sodium methylsulfate show no detectable specific interactions between sodium and methylsulfate ions. Raman band profiles of the S-O stretching mode of methylsulfate ion in aqueous solution show asymmetry above about 3.0 mol-dm^–3. Furthermore, the proton spin-lattice relaxation rates of the methylsulfate ion in D₂O increase linearly up to about 3.0 mol-dm^–3, but above this concentration they deviate from linearity.These experimental results indicate that dynamic properties of methylsulfate ion are affected by ion-water interactions. Raman band asymmetry is attributed to the non-uniformity of the distribution of water molecules around the methylsulfate ion. This interpretation is supported by the theory developed by Knapp and Fischer. The distortion of the distribution of water molecules around ions is also discussed on the basis of the overlap of the hydration layer around methylsulfate ion which is estimated by the measurement of sound velocity and density.     

Correlation between Dynamic Heterogeneity and Local Structure in a Room‐Temperature Ionic Liquid: A Molecular Dynamics Study of [bmim][PF6]

The complex dynamics of a room‐temperature ionic liquid, 1‐n‐butyl‐3‐methylimidazolium hexafluorophosphate ([bmim][PF₆]), is studied using equilibrium classical molecular dynamics simulations in the temperature range of 250–450 K. The activation energies for the self‐diffusion of ions are around 30–34 kJ mol^?1, with that of the anion a little higher than that for the cation. The electrical conductivity of the liquid is calculated and good agreement with experiments is obtained. Structural relaxation is studied through the decay of coherent (total density–density correlation) and incoherent (self part of density–density correlation) intermediate scattering functions over a range of temperatures and wave vectors relevant to the system. The relaxation data are used to identify and characterize two processes, α and β. The dependence of the two relaxation times on temperature and wave vector is obtained. The dynamical heterogeneity of the ions determined through the non‐Gaussian parameter indicates the motion of the cation to be more heterogeneous than that of the anion. The faster ones among the cations are coordinated to faster anions, while slower cations are surrounded predominantly by slower anions. Thus, the dynamical heterogeneity in this ionic liquid is shown to have structural signatures.     

Molecular dynamics of cis‐1‐(2‐hydroxy‐5‐ methylphenyl)ethanone oxime and N‐(2‐hydroxy‐4‐methylphenyl)acetamide in solution studied by NMR spectroscopy

The formation of hydrogen bonds and molecular dynamics for the molecules cis‐1‐(2‐hydroxy‐5‐methylphenyl)ethanone oxime ( I ) and N‐(2‐hydroxy‐4‐methylphenyl)acetamide ( II ) have been investigated in solution using NMR. The results confirm the formation of O? H···O, O? H···N and O···H? N type inter‐ and intramolecular hydrogen bonds. Spin‐lattice relaxation times (T₁), activation energy of molecular dynamics and energy of intramolecular hydrogen bonds have been determined. Copyright © 2010 John Wiley & Sons, Ltd.     

Dynamics of Electronically Excited Metal Atoms (Zn and Cd) in Rare Gas Matrices: Simulation of Multiple-band Emission using Molecular Dynamics with Quantum Transitions

Molecular dynamics with quantum transitions approach is employed to simulate the spectroscopic characteristics of the ¹P₁↔¹S₀ transitions in atomic zinc and cadmium in order to gain insight into the excited state behavior of these atoms isolated in solid rare gases neon, argon, and krypton. The absorption and emission spectra are simulated. Non-radiative processes play a fundamental role in the transfer of population among the three electronic states initially accessed in absorption. Three distinct relaxation pathways were identified. Two of these are related to the dynamical modes described in previous works [McCaffrey and Kerins, J. Chem. Phys. 106 , 7885 (1997); Kerins and McCaffrey, J. Chem. Phys. 109 , 3131 (1998)] in which the system evolves to form a square planar configuration around the metal atom. The third distinct pathway involves motion on a hexagonal close packed plane. The temperature dependence of complex formation was also determined for the three relaxation pathways.     

Molecular Mechanisms on the Selectivity Enhancement of Ascorbic Acid,Dopamine, and Uric Acid by Serine Oligomers Decoration on Graphene Oxide: A Molecular Dynamics Study

The selectivity in the simultaneous detection of ascorbic acid (AA), dopamine (DA), and uric acid (UA) has been an open problem in the biosensing field. Many surface modification methods were carried out for glassy carbon electrodes (GCE), including the use of graphene oxide and amino acids as a selective layer. In this work, molecular dynamics (MD) simulations were performed to investigate the role of serine oligomers on the selectivity of the AA, DA, and UA analytes. Our models consisted of a graphene oxide (GO) sheet under a solvent environment. Serine tetramers were added into the simulation box and were adsorbed on the GO surface. Then, the adsorption of each analyte on the mixed surface was monitored from MD trajectories. It was found that the adsorption of AA was preferred by serine oligomers due to the largest number of hydrogen-bond forming functional groups of AA, causing a 10-fold increase of hydrogen bonds by the tetraserine adsorption layer. UA was the least preferred due to its highest aromaticity. Finally, the role of hydrogen bonds on the electron transfer selectivity of biosensors was discussed with some previous studies. AA radicals received electrons from serine through hydrogen bonds that promoted oxidation reaction and caused the negative shifts and separation of the oxidation potential in experiments, as DA and UA were less affected by serine. Agreement of the in vitro and in silico results could lead to other in silico designs of selective layers to detect other types of analyte molecules.     

A low molecular weight gel formed by cationic surfactant 1-dodecylpyridinium bromide in acetone/water: its characterisation and implication for enzyme immobilisation

A novel cationic surfactant-based gelling system is presented in this report. The cationic surfactant 1-dodecylpyridinium bromide (DPB) in the mixture of acetone and water can form gels without additive. The gel structure and the gelation mechanism were studied using techniques of rheology, microscopy, FT-IR and ¹H NMR spectroscopy. The present results indicate that the DPBs in acetone/water driven by hydrogen bonding, van der Waals force and other non-covalent interactions can self-assemble into rod-like fibers, and the fibers intertwined into a three-dimensional network. Laccase and horseradish peroxidase entrapped in the gel are biologically and/or electrochemically active. In addition, the present gel does not swell in the hydrophobic ionic liquid [Bmim]PF₆, showing its great promise in green biocatalysis and biotransformation.     

From Myricetin to the Discovery of Novel Natural Human ENPP1 Inhibitors: A Virtual Screening,Molecular Docking,Molecular Dynamics Simulation,and MM/GBSA Study

It was recently revealed that naturally occurring myricetin can inhibit ectonucleotidase ectonucleotide pyrophosphatase/phosphodiesterase 1 (ENPP1), which, in turn, can treat ischemic cardiac injury. However, due to myricetin’s poor druggability, its further developments are relatively limited, which necessitates the discovery of novel ENPP1-inhibiting myricetin analogs as alternatives. In this study, the binding model of myricetin with ENPP1 was elucidated by molecular docking and molecular dynamics studies. Subsequently, virtual screening on the self-developed flavonoid natural product database (FNPD), led to the identification of two flavonoid glycosides (Cas No: 1397173-50-0 and 1169835-58-8), as potential ENPP1 inhibitors. Docking scores and MM/GBSA binding energies predicted that they might have higher inhibitory effects than myricetin. This study provides a strong foundation for the future development of ischemic cardiac injury drugs.     

The Dynamics of the Neuropeptide Y Receptor Type 1 Investigated by Solid-State NMR and Molecular Dynamics Simulation

We report data on the structural dynamics of the neuropeptide Y (NPY) G-protein-coupled receptor (GPCR) type 1 (Y1R), a typical representative of class A peptide ligand GPCRs, using a combination of solid-state NMR and molecular dynamics (MD) simulation. First, the equilibrium dynamics of Y1R were studied using ¹⁵N-NMR and quantitative determination of ¹H-¹³C order parameters through the measurement of dipolar couplings in separated-local-field NMR experiments. Order parameters reporting the amplitudes of the molecular motions of the C-H bond vectors of Y1R in DMPC membranes are 0.57 for the Cα sites and lower in the side chains (0.37 for the CH₂ and 0.18 for the CH₃ groups). Different NMR excitation schemes identify relatively rigid and also dynamic segments of the molecule. In monounsaturated membranes composed of longer lipid chains, Y1R is more rigid, attributed to a higher hydrophobic thickness of the lipid membrane. The presence of an antagonist or NPY has little influence on the amplitude of motions, whereas the addition of agonist and arrestin led to a pronounced rigidization. To investigate Y1R dynamics with site resolution, we conducted extensive all-atom MD simulations of the apo and antagonist-bound state. In each state, three replicas with a length of 20 μs (with one exception, where the trajectory length was 10 μs) were conducted. In these simulations, order parameters of each residue were determined and showed high values in the transmembrane helices, whereas the loops and termini exhibit much lower order. The extracellular helix segments undergo larger amplitude motions than their intracellular counterparts, whereas the opposite is observed for the loops, Helix 8, and termini. Only minor differences in order were observed between the apo and antagonist-bound state, whereas the time scale of the motions is shorter for the apo state. Although these relatively fast motions occurring with correlation times of ns up to a few µs have no direct relevance for receptor activation, it is believed that they represent the prerequisite for larger conformational transitions in proteins.     

Hydroxamic Acids as PARP-1 Inhibitors: Molecular Design and Anticancer Activity of Novel Phenanthridinones

Poly(ADP-ribose)polymerase-1 (PARP-1) is a promising target for antitumor agents. This study presents the first evidence of hydroxamic acids as efficient PARP inhibitors. Molecular docking and molecular dynamics simulations revealed that N−O substituted phenanthridinones form a complex interplay with PARP-1. A series of cyclic aryl hydroxamic acids, N-(benzyloxy)- and N-(hydroxy)phenanthridinones, were prepared through a ligand-free methodology from N-(benzyloxy)benzamides using dual C−H/N−H bond activation. Three of the computed hit compounds exhibited significant activity in cell-based and enzymatic assays, inhibiting PARP-1 in the low-nanomolar range. The antiproliferative activity of all prepared compounds and the reference compounds PJ34 and Olaparib was evaluated in cancer cells (HepG2, BxPC3, MDA-MD-231, and HeLa) and in noncancer cell lines (NIH 3T3 and HEK 293). An N-(benzyloxy)- and an N-(hydroxy)phenanthridinone showed the most promising properties as leads for developing therapeutics with a submicromolar activity window. The study highlights the potential utility of this scaffold for PARP inhibitors and the importance of target-specific design to minimize toxicity and side effects.     

Molecular recognition of aminoglycoside antibiotics by bacterial defence proteins: NMR study of the structural and conformational features of streptomycin inactivation by Bacillus subtilis aminoglycoside-6-adenyl transferase

The molecular recognition of streptomycin by Bacillus subtilis aminoglycoside-6-adenyl transferase has been analysed by a combination of NMR techniques and molecular dynamic simulations. This protein inactivates streptomycin by transferring an adenyl group to position six of the streptidine moiety. Our combined approach provides valuable information about the bioactive conformation for both the antibiotic and ATP and shows that the molecular recognition process for streptomycin involves a conformational selection phenomenon. The binding epitope for both ligands has also been analysed by 1D-STD experiments. Finally, the specificity of the recognition process with respect to the aminoglycoside and to the nucleotide has been studied.     

The Hunt for the Closed Conformation of the Fruit-Ripening Enzyme 1-Aminocyclopropane-1-carboxylic Oxidase: A Combined Electron Paramagnetic Resonance and Molecular Dynamics Study

1-Aminocyclopropane-1-carboxylic oxidase (ACCO) is a non-heme iron(II)-containing enzyme involved in the biosynthesis of the phytohormone ethylene, which regulates fruit ripening and flowering in plants. The active conformation of ACCO, and in particular that of the C-terminal part, remains unclear and open and closed conformations have been proposed. In this work, a combined experimental and computational study to understand the conformation and dynamics of the C-terminal part is reported. Site-directed spin-labeling coupled to electron paramagnetic resonance (SDSL-EPR) spectroscopy was used. Mutagenesis experiments were performed to generate active enzymes bearing two paramagnetic labels (nitroxide radicals) anchored on cysteine residues, one in the main core and one in the C-terminal part. Inter-spin distance distributions were measured by pulsed EPR spectroscopy and compared with the results of molecular dynamics simulations. The results reveal the existence of a flexibility of the C-terminal part. This flexibility generates several conformations of the C-terminal part of ACCO that correspond neither to the existing crystal structures nor to the modelled structures. This highly dynamic region of ACCO raises questions on its exact function during enzymatic activity.     

1-丁烯在MCM-22分子筛中的吸附与扩散：Monte Carlo与动力学模拟研究

采用巨正则Monte Carlo方法和分子动力学方法研究了1-丁烯在MCM-22分子筛中的吸附现象和扩散行为,得到了1-丁烯吸附在该分子筛孔道中的相互作用能和在不同孔道中的扩散轨迹和扩散系数.结果表明1-丁烯在MCM-22分子筛中主要存存两个相互作用能区间,1-丁烯优先吸附在十元环孔道中;1-丁烯的扩散和移动主要发生在十二元环超笼的中部,十元环孔道中的1-丁烯扩散速度明显小于十二元环超笼系统中的扩散速度.     

Effect of Na+ and Ca2+ Ions on a Lipid Langmuir Monolayer: An Atomistic Description by Molecular Dynamics Simulations

Studying the effect of alkali and alkaline‐earth metal cations on Langmuir monolayers is relevant from biophysical and nanotechnological points of view. In this work, the effect of Na⁺ and Ca²⁺ on a model of an anionic Langmuir lipid monolayer of dimyristoylphosphatidate (DMPA^?) is studied by molecular dynamics simulations. The influence of the type of cation on lipid structure, lipid–lipid interactions, and lipid ordering is analyzed in terms of electrostatic interactions. It is found that for a lipid monolayer in its solid phase, the effect of the cations on the properties of the lipid monolayer can be neglected. The influence of the cations is enhanced for the lipid monolayer in its gas phase, where sodium ions show a high degree of dehydration compared with calcium ions. This loss of hydration shell is partly compensated by the formation of lipid–ion–lipid bridges. This difference is ascribed to the higher charge‐to‐radius ratio q/r for Ca²⁺, which makes ion dehydration less favorable compared to Na⁺. Owing to the different dehydration behavior of sodium and calcium ions, diminished lipid–lipid coordination, lipid–ion coordination, and lipid ordering are observed for Ca²⁺ compared to Na⁺. Furthermore, for both gas and solid phases of the lipid Langmuir monolayers, lipid conformation and ion dehydration across the lipid/water interface are studied.     

Addition–fragmentation chain transfer: Molecular weight distributions and retardation in the system methyl methacrylate/methyl α‐(bromomethyl)acrylate

A detailed investigation of addition–fragmentation chain transfer (AFCT) in the free‐radical polymerization of methyl methacrylate (MMA) in the presence of methyl α‐(bromomethyl)acrylate (MBMA) was carried out to elucidate mechanistic details with efficient macromonomer synthesis as an underlying goal. Advanced modeling techniques were used in connection with the experimental work. Curve fitting of simulated and experimental molecular weight distributions with respect to the rate coefficient for addition of propagating radicals to MBMA (k_add) over 60–120 °C resulted in E_add = 21.7 kJ mol^?1 and A_add = 2.18 × 10⁶ M^?1 s^?1 and a very weak temperature dependence of the chain‐transfer constant (E_add ≈ E_p). The rate coefficient for fragmentation of adduct radicals at 60 °C was estimated as k_f ≈ 39 s^?1 on the basis of experimental data of the MMA conversion and the concentration of 2‐carbomethoxy‐2‐propenyl end groups. The approach developed is generic and can be applied to any AFCT system in which copolymerization does not occur and in which the resulting unsaturated end groups do not undergo further reactions. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 2640–2650, 2004     

Molecular mechanism of HIV-1 integrase-vDNA interactions and strand transfer inhibitor action: a molecular modeling perspective

Human immunodeficiency virus type 1 (HIV-1) integrase (IN) is an essential enzyme for splicing a viral DNA (vDNA) replica of its genome into host cell chromosomal DNA (hDNA) and has been recently recognized as a promising therapeutic target for developing anti-AIDS agents. The interaction between HIV-1 IN and vDNA plays an important role in the integration process of the virus. However, a detailed understanding about the mechanism of this interactions as well as the action of the anti-HIV drug raltegravir (RAL, approved by FDA in 2007) targeting HIV-1 IN in the inhibition of the vDNA strand transfer is still absent. In the present work, a molecular modeling study by combining homology modeling, molecular dynamics (MD) simulations with molecular mechanics Poisson-Boltzmann surface area (MM-PBSA), and molecular mechanics Generalized-Born surface area (MM-GBSA) calculations was performed to investigate the molecular mechanism of HIV-1 IN-vDNA interactions and the inhibition action of vDNA strand transfer inhibitor (INSTI) RAL. The structural analysis showed that RAL did not influence the interaction between vDNA and HIV-1 IN, but rather targeted a special conformation of HIV-1 IN to compete with host DNA and block the function of HIV-1 IN by forcing the 3'-OH of the terminal A17 nucleotide away from the three catalytic residues (Asp64, Asp116, and Glu152) and two Mg(2+) ions. Thus, the obtained results could be helpful for understanding of the integration process of the HIV-1 virus and provide some new clues for the rational design and discovery of potential compounds that would specifically block HIV-1 virus replication.