Pressure-Dependent Structure of Methanol–Water Mixtures up to 1.2 GPa: Neutron Diffraction Experiments and Molecular Dynamics Simulations

Total scattering structure factors of per-deuterated methanol and heavy water, CD₃OD and D₂O, have been determined across the entire composition range as a function of pressure up to 1.2 GPa, by neutron diffraction. The largest variations due to increasing pressure were observed below a scattering variable value of 5 Å⁻¹, mostly as shifts in terms of the positions of the first and second maxima. Molecular dynamics computer simulations, using combinations of all-atom potentials for methanol and various water force fields, were conducted at the experimental pressures with the aim of interpreting neutron diffraction results. The peak-position shifts mentioned above could be qualitatively reproduced by simulations, although in terms of peak intensities, the accord between neutron diffraction and molecular dynamics was much less satisfactory. However, bearing in mind that increasing pressure must have a profound effect on repulsive forces between neighboring molecules, the agreement between experiment and computer simulation can certainly be termed as satisfactory. In order to reveal the influence of changing pressure on local intermolecular structure in these “simplest of complex” hydrogen-bonded liquid mixtures, simulated structures were analyzed in terms of hydrogen bond-related partial radial distribution functions and size distributions of hydrogen-bonded cyclic entities. Distinct differences between pressure-dependent structures of water-rich and methanol-rich composition regions were revealed.     

Role of Hydrogen Bond Defects for Cluster Formation and Distribution in Ionic Liquids by Means of Neutron Diffraction and Molecular Dynamics Simulations

Defects fundamentally govern the properties of all real materials. Correlating molecular defects to macroscopic quantities remains a challenge, particularly in the liquid phase. Herein, we report the influence of hydrogen bonds (HB) acting as defects in mixtures of non-hydroxyl-functionalized ionic liquids (ILs) with an increasing concentration of hydroxyl-functionalized ILs. We observed two types of HB defects: The conventional HBs between cation and anion (c–a), and the elusive HBs between cations (c–c) despite the repulsive Coulomb forces. We use neutron diffraction with isotopic substitution in combination with molecular dynamics simulations for measuring the geometry, strength, and distribution of mobile OH defects in the IL mixtures. In principle, this procedure allows relating the number and stability of defects to macroscopic properties such as diffusion, viscosity, and conductivity, which are of utmost importance for the performance of electrolytes in batteries and other electrical devices.     

The Double‐Faced Nature of Hydrogen Bonding in Hydroxy‐Functionalized Ionic Liquids Shown by Neutron Diffraction and Molecular Dynamics Simulations

We characterize the double‐faced nature of hydrogen bonding in hydroxy‐functionalized ionic liquids by means of neutron diffraction with isotopic substitution (NDIS), molecular dynamics (MD) simulations, and quantum chemical calculations. NDIS data are fit using the empirical potential structure refinement technique (EPSR) to elucidate the nearest neighbor H???O and O???O pair distribution functions for hydrogen bonds between ions of opposite charge and the same charge. Despite the presence of repulsive Coulomb forces, the cation–cation interaction is stronger than the cation–anion interaction. We compare the hydrogen‐bond geometries of both “doubly charged hydrogen bonds” with those reported for molecular liquids, such as water and alcohols. In combination, the NDIS measurements and MD simulations reveal the subtle balance between the two types of hydrogen bonds: The small transition enthalpy suggests that the elusive like‐charge attraction is almost competitive with conventional ion‐pair formation.     

Structure and Thermodynamics of Mg:Phosphate Interactions in Water: A Simulation Study

The association of Mg²⁺ and H₂PO₄^? in water can give insights into Mg:phosphate interactions in general, which are very widespread, but for which experimental data is surprisingly sparse. It is studied through molecular dynamics simulations (>100 ns) by using the polarizable AMOEBA force field, and the association free energy is computed for the first time. Explicit consideration of outer‐sphere and two types of inner‐sphere association provides considerable insight into the dynamics and thermodynamics of ion pairing. After careful assessment of the computational approximations, the agreement with experimental values indicates that the methodology can be extended to other inorganic and biological Mg:phosphate interactions in solution.     

Self-Assembly of NaOL-DDA Mixtures in Aqueous Solution: A Molecular Dynamics Simulation Study

The self-assembly behaviors of sodium oleate (NaOL), dodecylamine (DDA), and their mixtures in aqueous solution were systematically investigated by large-scale molecular dynamics simulations, respectively. The interaction mechanisms between the surfactants, as well as the surfactants and solvent, were revealed via the radial distribution function (RDF), cluster size, solvent-accessible surface area (SASA), hydrogen bond, and non-bond interaction energy. Results showed that the molecules more easily formed aggregates in mixed systems compared to pure systems, indicating higher surface activity. The SASA values of DDA and NaOL decreased significantly after mixing, indicating a tighter aggregation of the mixed surfactants. The RDF results indicated that DDA and NaOL strongly interacted with each other, especially in the mixed system with a 1:1 molar ratio. Compared to van der Waals interactions, electrostatic interactions between the surfactant molecules were the main contributors to the improved aggregation in the mixed systems. Besides, hydrogen bonds were found between NaOL and DDA in the mixed systems. Therefore, the aggregates in the mixed systems were much more compact in comparison with pure systems, which contributed to the reduction of the repulsive force between same molecules. These findings indicated that the mixed NaOL/DDA surfactants had a great potential in application of mineral flotation.     

Analysis of the Structure-Function-Dynamics Relationships of GALT Enzyme and of Its Pathogenic Mutant p.Q188R: A Molecular Dynamics Simulation Study in Different Experimental Conditions

The third step of the catabolism of galactose in mammals is catalyzed by the enzyme galactose-1-phosphate uridylyltransferase (GALT), a homodimeric enzyme with two active sites located in the proximity of the intersubunit interface. Mutations of this enzyme are associated to the rare inborn error of metabolism known as classic galactosemia; in particular, the most common mutation, associated with the most severe phenotype, is the one that replaces Gln188 in the active site of the enzyme with Arg (p.Gln188Arg). In the past, and more recently, the structural effects of this mutation were deduced on the static structure of the wild-type human enzyme; however, we feel that a dynamic view of the proteins is necessary to deeply understand their behavior and obtain tips for possible therapeutic interventions. Thus, we performed molecular dynamics simulations of both wild-type and p.Gln188Arg GALT proteins in the absence or in the presence of the substrates in different conditions of temperature. Our results suggest the importance of the intersubunit interactions for a correct activity of this enzyme and can be used as a starting point for the search of drugs able to rescue the activity of this enzyme in galactosemic patients.     

A Combined Experimental and Computational Study of Halogen and Hydrogen Bonding in Molecular Salts of 5-Bromocytosine

Although natural or artificial modified pyrimidine nucleobases represent important molecules with valuable properties as constituents of DNA and RNA, no systematic analyses of the structural aspects of bromo derivatives of cytosine have appeared so far in the literature. In view of the biochemical and pharmaceutical relevance of these compounds, six different crystals containing proton-transfer derivatives of 5-bromocytosine are prepared and analyzed in the solid-state by single crystal X-ray diffraction. All six compounds are organic salts, with proton transfer occurring to the N_imino atom of the pyridine ring. Experimental results are then complemented with Hirshfeld surface analysis to quantitively evaluate the contribution of different intermolecular interactions in the crystal packing. Furthermore, theoretical calculations, based on different arrangements of molecules extracted from the crystal structure determinations, are carried out to analyze the formation mechanism of halogen bonds (XBs) in these compounds and provide insights into the nature and strength of the observed interactions. The results show that the supramolecular architectures of the six molecular salts involve extensive classical intermolecular hydrogen bonds. However, in all but one proton-transfer adducts, weak to moderate XBs are revealed by C–Br^…O short contacts between the bromine atom in the fifth position, which acts as XB donor (electron acceptor). Moreover, the lone pair electrons of the oxygen atom of adjacent pyrimidine nucleobases and/or counterions or water molecules, which acts as XB acceptor (electron donor).     

核糖核酸酶Sa表面水和尿素分子的分布和动力学行为的分子动力学模拟

利用分子动力学模拟研究了在不同尿素浓度下,核糖核酸酶Sa(RNase Sa)表面水和尿素分子的分布和动力学行为。 结果表明,尿素分子可与RNase Sa酶形成较强的相互作用,并取代其表面的水分子而富集在蛋白质表面。 尿素分子更倾向与RNase Sa酶的疏水残基作用,与RNase Sa酶主链形成氢键的能力更强。 尿素分子的平动和转动远远慢于水分子的平动和转动。 RNase Sa酶表面水分子的平动和转动随着尿素浓度增加而逐渐变慢,但RNase Sa酶表面尿素分子的动力学并不依赖于尿素浓度变化。 本研究中明晰的RNase Sa酶表面水和尿素分子分布和动力学有助于理解水和尿素分子对蛋白质稳定性的影响。     

Freezing points and related properties of electrolyte solutions. II. Mixtures of lithium chloride and sodium chloride in water

The freezing points of aqueous lithium chloride and its mixtures with sodium chloride have been measured from 0.1 to 1.5m. From these measurements, calorimetric enthalpies of mixing, and osmotic coefficients of the pure salts at 298°K, osmotic and activity coefficients of the mixtures have been calculated up to 6.0m at 298°K. Excellent agreement with the literature values is found over the entire range of composition. This method of computation is considered to be superior to the analysis of only isopiestic results in the calculation of activity coefficients in mixed electrolytes.     

Dynamic Behavior of Rotation Transmission Nano-System in Helium Environment: A Molecular Dynamics Study

The molecular dynamics (MD) method is used to investigate the influence of the shielding gas on the dynamic behavior of the heterogeneous rotation transmission nano-system (RTS) built on carbon nanotubes (CNTs) and boron nitride nanotube (BNNT) in a helium environment. In the heterogeneous RTS, the inner CNT acts as a rotor, the middle BNNT serves as a motor, and the outer CNT functions as a stator. The rotor will be actuated to rotate by the motor due to the interlayer van der Waals effects and the end effects. The MD simulation results show that, when the gas density is lower than a critical range, a stable signal of the rotor will arise on the output and the rotation transmission ratio (RRT) of RTS can reach 1.0, but as the gas density is higher than the critical range, the output signal of the rotor cannot be stable due to the sharp drop of the RRT caused by the large friction between helium and the RTS. The greater the motor input signal of RTS, the lower the critical working helium density range. The results also show that the system temperature and gas density are the two main factors affecting the RTS transmission behavior regardless of the size of the simulation box. Our MD results clearly indicate that in the working temperature range of the RTS from 100 K to 600 K, the higher the temperature and the lower the motor input rotation frequency, the higher the critical working helium density range allows.     

NMR Studies of Mixed-Ligand Lanthanide (III) Complexes. Peculiarities of Molecular Structure, Dynamics and Paramagnetic Properties for Cerium Subgroup Chelates with Crown Ethers

The molecular structure, dynamics and paramagnetic properties of the complex cations [Ln(ptfa)₂ (18-crown-6)]⁺ in deuterated toluene were studied for Ln = La, Ce, Pr and Nd. The activation enthalpy values of 68 ± 5, 55 ± 15 and 60 ± 13 kJ mol^-1 for the 18-crown-6 conformationalinversion processes for the complexcations of Ce, Pr and Nd, respectively,were obtained. Quantitativeinvestigation of the lanthanide-induced chemical shifts shows a monotonic change of a spatial structure and magnetic susceptibility in comparison with the Bleaney predicted dependence. The free energy of molecular inversion activation for 18-crown-6 molecules in the complex cation [Ln(fod)₂(18-crown-6)]⁺ is 74 ± 9 kJ mol^-1 at 363 K, which is a little more than the value of the free energy of activation 64 ± 9 kJ mol^-1 at 363 K in the complex cation [Ln(ptfa)₂(18-crown-6)]⁺.     

Global Analysis of Plasmodium falciparum Dihydropteroate Synthase Variants Associated with Sulfadoxine Resistance Reveals Variant Distribution and Mechanisms of Resistance: A Computational-Based Study

The continual rise in sulfadoxine (SDX) resistance affects the therapeutic efficacy of sulfadoxine-pyrimethamine; therefore, careful monitoring will help guide its prolonged usage. Mutations in Plasmodium falciparum dihydropteroate synthase (Pfdhps) are being surveilled, based on their link with SDX resistance. However, there is a lack of continuous analyses and data on the potential effect of molecular markers on the Pfdhps structure and function. This study explored single-nucleotide polymorphisms (SNPs) in Pfdhps that were isolated in Africa and other countries, highlighting the regional distribution and its link with structure. In total, 6336 genomic sequences from 13 countries were subjected to SNPs, haplotypes, and structure-based analyses. The SNP analysis revealed that the key SDX resistance marker, A437G, was nearing fixation in all countries, peaking in Malawi. The mutation A613S was rare except in isolates from the Democratic Republic of Congo and Malawi. Molecular docking revealed a general loss of interactions when comparing mutant proteins to the wild-type protein. During MD simulations, SDX was released from the active site in mutants A581G and A613S before the end of run-time, whereas an unstable binding of SDX to mutant A613S and haplotype A437A/A581G/A613S was observed. Conformational changes in mutant A581G and the haplotypes A581G/A613S, A437G/A581G, and A437G/A581G/A613S were seen. The radius of gyration revealed an unfolding behavior for the A613S, K540E/A581G, and A437G/A581G systems. Overall, tracking such mutations by the continuous analysis of Pfdhps SNPs is encouraged. SNPs on the Pfdhps structure may cause protein–drug function loss, which could affect the applicability of SDX in preventing malaria in pregnant women and children.     

Molecular Dynamic Study of Mechanism Underlying Nature of Molecular Recognition and the Role of Crosslinker in the Synthesis of Salmeterol-Targeting Molecularly Imprinted Polymer for Analysis of Salmeterol Xinafoate in Biological Fluid

The rational preparation of molecularly imprinted polymers (MIPs) in order to have selective extraction of salmeterol xinafoate (SLX) from serum was studied. SLX is an acting β-adrenergic receptor agonist used in the treatment of asthma and has an athletic performance-enhancing effect. Molecular dynamics were used for the simulation of the SLX-imprinted pre-polymerization system, to determine the stability of the system. The computational simulation showed that SLX as a template, 4-hydroxyethyl methacrylate (HEMA) as a monomer, and trimethylolpropane trimethacrylate (TRIM) as a crosslinker in mol ratio of 1:6:20 had the strongest interaction in terms of the radial distribution functional. To validate the computational result, four polymers were synthesized using the precipitation polymerization method, and MIP with composition and ratio corresponding with the system with the strongest interaction as an MD simulation result showed the best performance, with a recovery of 96.59 ± 2.24% of SLX in spiked serum and 92.25 ± 1.12% when SLX was spiked with another analogue structure. Compared with the standard solid phase extraction sorbent C-18, which had a recovery of 79.11 ± 2.96%, the MIP showed better performance. The harmony between the simulation and experimental results illustrates that the molecular dynamic simulations had a significant role in the study and development of the MIPs for analysis of SLX in biological fluid.     

Minor Groove Binding between Norfloxacin and DNA Duplexes in Solution： A Molecular Dynamics Study

Quinolones,a series of nalidixic acid analogues,represent a class of extremely potent antibacterial drugs.Although the functional target of these agents such as norfloxacin has been identified as the enzyme DNA gyrase,the direct binding site of the drug is the DNA itself1.Interactions between quinolones and diversified DNA have been studied by several biochemical,spectroscopic and computational methods2-8.Shen et al.proposed a cooperative drug-DNA binding model.The essential feature of th…     

Approaching Dissolved Species in Ammonoacidic GaN Crystal Growth: A Combined Solution NMR and Computational Study

Solutions of gallium trihalides GaX₃ (X=F, Cl, Br, I) and their ammoniates in liquid ammonia were studied at ambient temperature under autogenous pressure by multinuclear (⁷¹Ga, ³⁵Cl, ⁸¹Br) NMR spectroscopy. To unravel the role of pH, the analyses were done both in absence and in presence of ammonium halides, which are employed as mineralizers during ammonoacidic gallium nitride crystal growth. While gallium trifluoride and its ammoniate were found to be too sparingly soluble to give rise to a NMR signal, the spectra of solutions of the heavier halides reveal the presence of a single gallium-containing species in all cases. DFT calculations and molecular dynamics simulations suggest the identification of this species as consisting of a [Ga(NH₃)₆]³⁺ cation and up to six surrounding halide anions, resulting in an overall trend towards negative complex charge. Quantitative ⁷¹Ga NMR studies on saturated solutions of GaCl₃ containing various amounts of additional NH₄Cl revealed a near linear increase of GaCl₃ solubility with mineralizer concentration of about 0.023 mol GaCl₃ per mol NH₄Cl at room temperature. These findings reflect the importance of Coulombic shielding for the inhibition of oligomerization and precipitation processes and help to rationalize both the low solubility of gallium halides in neutral ammonia solution and, in turn, the proliferating effect of the mineralizer during ammonoacidic gallium nitride formation.     

真空条件下β-环糊精和对-甲基苯酚包结物动态结构的分子动力学模拟

本文报道了真空状态下主体β-环糊精和客体对-甲基苯酚形成的包结物在一定时间间隔内动态微观结构的分子动力学模拟结果。研究表明，对-甲基苯酚在环糊精腔内的运动具较大的自由度，但由于存在范德华作用，其运动受到一定的限制，同时通过计算观察到包结前后主客体的某些微观结构和性质发生了较为明显的变化。本文还给出了计算得到的主客体包结物的时间平均构象。     

Hydrogen Adsorption and Diffusion in p‐tert‐Butylcalix[4]arene: An Experimental and Molecular Simulation Study

Experimental adsorption isotherms were measured and computer simulations were performed to determine the nature of the H₂ gas uptake in the low‐density p‐tert‐butylcalix[4]arene (tBC) phase. ¹H NMR peak intensity measurements for pressures up to 175 bar were used to determine the H₂ adsorption isotherm. Weak surface adsorption (up to ≈2 mass % H₂) and stronger adsorption (not exceeding 0.25 mass % or one H₂ per calixarene bowl) inside the calixarene phase were detected. The latter type of adsorbed H₂ molecule has restricted motion and shows a reversible gas adsorption/desorption cycle. Pulsed field gradient (PFG) NMR pressurization/depressurization measurements were performed to study the diffusion of H₂ in the calixarene phases. Direct adsorption isotherms by exposure of the calixarene phase to pressures of H₂ gas to ≈60 bar are also presented, and show a maximum H₂ adsorption of 0.4 H₂ per calixarene bowl. Adsorption isotherms of H₂ in bulk tBC have been simulated using grand canonical Monte Carlo calculations in a rigid tBC framework, and yield adsorptions of ≈1 H₂ per calixarene bowl at saturation. Classical molecular dynamics simulations with a fully flexible calixarene molecular force field are used to determine the guest distribution and inclusion energy of the H₂ in the solid with different loadings.