AcquaAlta: a directional approach to the solvation of ligand-protein complexes

Water molecules mediating polar interactions in ligand-protein complexes can substantially contribute to binding affinity and specificity. To account for such water molecules in computer-aided drug design, we performed an extensive search in the Cambridge Structural Database (CSD) to identify the geometrical criteria defining interactions of water molecules with ligand and protein. In addition, with ab initio calculations the propensity of ligand hydration was evaluated. Based on this information, we developed an algorithm (AcquaAlta) to reproduce water molecules bridging polar interactions between ligand and protein moieties. This approach was validated with 20 crystal structures and yielded a match of 76% between experimental and calculated water positions. When water molecules establishing only weak interactions with the protein were neglected, the match could be improved to 88%. Supported by a pharmacophore-based alignment tool, the solvation algorithm was then applied to the docking of oligopeptides to the periplasmic oligopeptide binding protein A (OppA). Calculated waters based on the crystal poses matched an average of 66% of the experimental waters. With water molecules calculated based on the docked ligands, the average match with the experimental waters dropped to 53%.     

A method for calculating the Gibbs energies of hydrophobic effects and specific interactions of nonelectrolytes in aqueous solutions

The thermodynamic characteristics of hydrophobic hydration, the Gibbs energies of hydrophobic effect, were calculated. The method for calculations was based on the division of the Gibbs energy of hydration into contributions of nonspecific interactions, specific interactions between solutes and solvents (if they exist), and hydrophobic effect. In the absence of specific interactions between solutes and water, the Gibbs energy of hydrophobic effect depended linearly on the characteristic molecular volume of the solute for substances with different structures and properties. The universality of this dependence allows the suggestion to be made that it remains valid also in the presence of specific interactions. This allows the Gibbs energy of specific interactions in water to be determined for a wide range of compounds, in particular, for aliphatic alcohols.     

A DFT study of the interaction between microhydrated anions and naphthalendiimides

The characteristics of the interaction of anions with naphthalendiimides, the basic structural motif of a newly synthesized anion channel based on anion···π interactions, are studied by computational methods. Stable complexes are formed with bromide, chloride, fluoride or hydroxide anions, which exhibit strong anion···π interactions in the gas phase. Following the sequence of the polarizing power of the anions, hydroxide and fluoride complexes are the most strongly interacting. The presence of a small number of water molecules strongly affects the anion···π interactions, especially for hydroxide and fluoride complexes, so the differences in interaction strength among the anions drop significantly. The calculations suggest that a small number of water molecules can be crucial to reducing dehydration cost and contributing to stabilizing interactions with the naphthalendiimide units.     

The nature of thermodynamic compatibility of components of aqueous solutions of starch and cellulose carboxymethyl derivatives

The Gibbs free energy, enthalpy, and entropy of mixing of starch and carboxymethyl derivatives of starch and cellulose with water were determined by sorption and calorimetry methods at 25°C throughout the entire range of compositions. The contributions due to the equilibrium intermolecular interactions and relaxation of a metastable glassy structure were separated. The relaxation of the metastable structure taking place during physical adsorption of the first portions of water on polymers makes a negative contribution to all thermodynamic functions of mixing. The contribution of equilibrium interactions, which includes pair nonviolent interactions of units and water molecules and electrostatic interactions of ions, is positive for the enthalpy and entropy of mixing. In this case, the positive entropy values exceed those of enthalpy, which is responsible for the thermodynamic compatibility. Thermodynamic analysis of the processes of dissolution of starch, carboxymethyl starch and carboxymethyl cellulose sodium salts showed that, contrary to the popular point of view, the compatibility of polysaccharides and their derivatives with water is based not on the enthalpy, but entropy nature and is strengthened additionally owing to relaxation of the metastable glassy structure of polymers.     

Rationalizing cellulose (in)solubility: reviewing basic physicochemical aspects and role of hydrophobic interactions

Despite being the world’s most abundant natural polymer and one of the most studied, cellulose is still challenging researchers. Cellulose is known to be insoluble in water and in many organic solvents, but can be dissolved in a number of solvents of intermediate properties, like N-methylmorpholine N-oxide and ionic liquids which, apparently, are not related. It can also be dissolved in water at extreme pHs, in particular if a cosolute of intermediate polarity is added. The insolubility in water is often referred to strong intermolecular hydrogen bonding between cellulose molecules. Revisiting some fundamental polymer physicochemical aspects (i.e. intermolecular interactions) a different picture is now revealed: cellulose is significantly amphiphilic and hydrophobic interactions are important to understand its solubility pattern. In this paper we try to provide a basis for developing novel solvents for cellulose based on a critical analysis of the intermolecular interactions involved and mechanisms of dissolution.     

Dual-scale modeling of benzene adsorption onto Ni(111) and Au(111) surfaces in explicit water.

We present a multiscale modeling approach for studying interactions of organic molecules with metal surfaces in explicit water. The approach is based on combining adsorption energies of isolated molecules on transition metal surfaces calculated by ab initio density functional methods and classical molecular dynamics simulations using atomistically detailed force fields. The interaction of benzene with Ni(111) and Au(111) surfaces was studied. It is shown that a strong affinity of water for the hydrophilic surfaces makes benzene adsorption on Au thermodynamically unfavorable, while on Ni there is no preference. The work presented here serves as a first step in modeling the interactions of larger organic molecules with metal surfaces.     

Induction and stabilization of liquid crystal order in H-bond complexes containing non-mesogenic species

A new approach to create mesomorphic ordered systems is discussed. It is based on the idea to use noncovalent interactions in the designing of thermotropic structures by modelling lyotropic liquid crystal (LC) when the water interlayer is changed by appropriate solid substances that are able to interact with the polar part of an amphiphilic molecule without any strong change in the intermolecular interactions between the non-polar “tails”.     

Bacterial interactions and transport in unsaturated porous media

The convection-dispersion transport model, which can well define solute transport, has been introduced to describe bacterial transport. Due to different interaction natures within the porous media, bacterial transport in the subsurface, especially in the vadose zone is a complex scenario. When transported in the vadose zone, bacteria may be captured on the media surface, at the air–water interface, or at the media–air–water three-phase interface depending upon the predominant interactions of concerned bacteria within the pore system. In this study, transport of Echerichia coli, Pseudomonas fluorescens and Bacillus subtilis in silica sand under water unsaturated conditions was investigated using column experiments. Bacterial interactions within the system were characterized based on bacterial and media surface thermodynamic properties, which were determined independently by means of contact angle measurements. These calculated interactions provided solid evidence of the bacterial retention mechanisms in the pore system, which served as the bases for suitable assumptions of bacterial transport modeling. The micro-scale interaction investigations helped eliminate uncertainties arising with bacterial transport modeling.     

Infrared and molecular-dynamics studies of the rotational dynamics of water highly diluted in supercritical CO2

Far-infrared (FIR) and mid-infrared (MIR) profiles of D2O infinitely dilute in supercritical CO2 have been studied using molecular-dynamics simulations. For this purpose, we have proposed an intermolecular potential model taking implicitly into account electron donor-acceptor (EDA) interactions between water and CO2 evaluated from ab initio calculations of the intermolecular potential-energy surface (IPS). Interaction-induced dipole mechanisms have been also taken into account in addition to the water permanent dipole to evaluate the simulated FIR profiles of water and CO2 polarizable molecules. They were found to play a minor role in the genesis of the FIR profiles of water/CO2 under supercritical conditions. The analysis of the reorientational dynamics of D2O shows that the rotational dynamics of water is weakly anisotropic due to the EDA interactions which affect more specifically the reorientational motions of the C2 symmetry axis of solute. These results have been used to assess the contribution of the vibrational relaxation in the experimental mid-infrared profiles associated with the nu1 symmetric and nu3 antisymmetric stretching and nu2 bending modes of D2O. It was found that the rotational dynamics mainly contribute to the broadening of the infrared (IR) profiles. Nevertheless, the vibrational processes play a role in the frequency shifts of the band centers and the relative intensity enhancements of the nu1 and nu3 modes of D2O. In particular, the EDA interactions between water and CO2 lead to the appearance of a well-defined IR band of the nu1 mode of D2O. Finally, a comparison with another model taking only into account dipole-quadrupole electrostatic interactions between water and CO2 molecules clearly reveals that EDA interactions have to be considered to reproduce both MIR and FIR measurements. From this point of view CO2 can be classified on a hydrophilic solvent scale based upon the solubility criterion as an intermediate solvent between "inert" xenon and carbon tetrachloride.     

Modeling of the water network at protein-RNA interfaces

Water plays an important role in the mediation of biomolecular interactions. Thus, accurate prediction and evaluation of water-mediated interactions is an important element in the computational design of interfaces involving proteins, RNA, and DNA. Here, we use an algorithm (WATGEN) to predict the locations of interfacial water molecules for a data set of 224 protein-RNA interfaces. The accuracy of the prediction is validated against water molecules present in the X-ray structures of 105 of these complexes. The complexity of the water networks is deconvoluted through definition of the characteristics of each water molecule based on its bridging properties between the protein and RNA and on its depth in the interface with respect to the bulk solvent. This approach has the potential for scoring the water network for incorporation into the computational design of protein-RNA complexes.     

基于喹啉和三唑环的开链冠醚对金属离子的选择传感

本文通过Click化学反应合成了一种含喹啉基和三唑基的开链冠醚, 考察和比较了主体化合物对镉等金属离子的荧光传感和选择性键合行为, 并通过荧光和核磁等手段研究了溶剂对其荧光传感的影响.     

Molecular explanation for why talc surfaces can be both hydrophilic and hydrophobic

While individual water molecules adsorb strongly on a talc surface (hydrophilic behavior), a droplet of water beads up on the same surface (hydrophobic behavior). To rationalize this dichotomy, we investigated the influence of the microscopic structure of the surface and the strength of adhesive (surface-water) interactions on surface hydrophobicity. We have shown that at low relative humidity, the competition between adhesion and the favorable entropy of being in the vapor phase determines the surface coverage. However, at saturation, it is the competition between adhesion and cohesion (water-water interactions) that determines the surface hydrophobicity. The adhesive interactions in talc are strong enough to overcome the unfavorable entropy, and water adsorbs strongly on talc surfaces. However, they are too weak to overcome the cohesive interactions, and water thus beads up on talc surfaces. Surprisingly, even talc-like surfaces that are highly adhesive do not fully wet at saturation. Instead, a water droplet forms on top of a strongly adsorbed monolayer of water. Our results imply that the interior of hydrophobic zeolites suspended in water may contain adsorbed water molecules at pressures much lower than the intrusion pressure.     

Charged-cell periodic DFT simulations via an impurity model based on density embedding: Application to the ionization potential of liquid water

Calculations of charged systems in periodic boundary conditions (PBC) are problematic because there are spurious interactions between the charges in different periodic images that can affect the physical picture. In addition, the intuitive limit of Coulomb interactions decaying to zero as the interacting charges are placed at infinite separation no longer applies, and for example total energies become undefined. Leveraging subsystem density functional theory (also known as density embedding) we define an impurity model that embeds a finite neutral or charged subsystem within an extended (infinite) surrounding subsystem. The combination of the impurity model and a consistent choice of the Coulomb reference provides us with an algorithm for evaluating the ionization potential (IP) in extended systems. We demonstrate our approach in a pilot calculation of the IP of liquid water, based on a configuration from a prior ab initio molecular dynamics (AIMD) simulation of liquid water (Genova et al., J. Chem. Phys. 2016, 144, 234105). The calculations with the impurity model capture the broadening on the ionization energies introduced by the interactions between the water molecules. Furthermore, the calculated average IP value (10.5 eV) compare favorably to experiments (9.9-10.06 eV) and very recent simulations based on the GW approximation (10.55 eV), while at the same time outperforming density embedding calculations carried out with a naïve handling of the electrostatic interactions (about 7 eV).     

MICROEMULSION MODEL EXPERIMENTAL AND THEORETICAL DIAGRAMS INFLUENCE OF BENDING ENERGY.

A stability model for quaternary microemulsion is presented and then applied to interpret experimental results obtained for the system Water-Decane-Pentanol-Betaine. It is based on the pseudophases model and thus the composition of interface as well as its variations are taken into account. The free enthalpy function contains four terms ; i-the entropy of dispersion ; ii-the water/oil interactions with a screening term ; in- the interface/oil and interface/water interactions; iiii- the bending energy. The parameters associated with the j-screening term, jj- interface/oil, interface/water interactions and spontaneous curvature, are related to the interface composition. The importance of the screening term is demonstrated. The effect of different terms and parameters upon phase behaviour is analysed. A very good agreement between experimental and calculated diagrams is obtained ; the study leads, in particular, to the conclusion that the bending constant is of the order of RT.     

Long-range Lennard-Jones and electrostatic interactions in interfaces: application of the isotropic periodic sum method

Molecular dynamics (MD) simulations of heptane/vapor, hexadecane/vapor, water/vapor, hexadecane/water, and dipalmitoylphosphatidylcholine (DPPC) bilayers and monolayers are analyzed to determine the accuracy of treating long-range interactions in interfaces with the isotropic periodic sum (IPS) method. The method and cutoff (rc) dependences of surface tensions, density profiles, water dipole orientation, and electrostatic potential profiles are used as metrics. The water/vapor, heptane/vapor, and hexadecane/vapor interfaces are accurately and efficiently calculated with 2D IPS (rc=10 A). It is demonstrated that 3D IPS is not practical for any of the interfacial systems studied. However, the hybrid method PME/IPS [Particle Mesh Ewald for electrostatics and 3D IPS for Lennard-Jones (LJ) interactions] provides an efficient way to include both types of long-range forces in simulations of large liquid/vacuum and all liquid/liquid interfaces, including lipid monolayers and bilayers. A previously published pressure-based long-range LJ correction yields results similar to those of PME/IPS for liquid/liquid interfaces. The contributions to surface tension of LJ terms arising from interactions beyond 10 A range from 13 dyn/cm for the hexadecane/vapor interface to approximately 3 dyn/cm for hexadecane/water and DPPC bilayers and monolayers. Surface tensions of alkane/vapor, hexadecane/water, and DPPC monolayers based on the CHARMM lipid force fields agree very well with experiment, whereas surface tensions of the TIP3P and TIP4P-Ew water models underestimate experiment by 16 and 11 dyn/cm, respectively. Dipole potential drops (DeltaPsi) are less sensitive to long-range LJ interactions than surface tensions. However, DeltaPsi for the DPPC bilayer (845+/-3 mV proceeding from water to lipid) and water (547+/-2 mV for TIP4P-Ew and 521+/-3 mV for TIP3P) overestimate experiment by factors of 3 and 5, respectively, and represent expected deficiencies in nonpolarizable force fields.     

The role of low levels of water in the electrochemical oxidation of α-tocopherol (vitamin E) and other phenols in acetonitrile

The phenol, α-tocopherol, can be electrochemically oxidised in a -2e(-)/-H(+) process to form a diamagnetic cation that is long-lived in dry organic solvents such as acetonitrile and dichloromethane, but in the presence of water quickly reacts to form a hemiketal. Variable scan rate cyclic voltammetry experiments in acetonitrile with carefully controlled amounts of water between 0.010 M-0.6 M were performed in order to determine the rate of reaction of the diamagnetic cation with water. The water content of the solvent was accurately determined by Karl Fischer coulometric titrations and the voltammetric data were modelled using digital simulation techniques. The oxidation peak potential of α-tocopherol measured during cyclic voltammetry experiments was found to shift to less positive potentials as increasing amounts of water (0.01-0.6 M) were added to the acetonitrile, which was interpreted based on hydrogen-bonding interactions between the phenolic hydrogen atom and water. Several other phenols were examined and they displayed similar voltammetric features to α-tocopherol, suggesting that interactions of phenols with trace amounts of water were a common occurrence in acetonitrile. The H-bonding interactions of α-tocopherol with water were also examined via NMR and UV-vis spectroscopies, with the voltammetric and spectroscopic studies extended to include other coordinating solvents (dimethyl sulfoxide and pyridine).     

Water-silica force field for simulating nanodevices

Amorphous silica is an inorganic material that is central for many nanotechnology applications, such as nanoelectronics, microfluidics, and nanopore sensors. To use molecular dynamics (MD) simulations to study the behavior of biomolecules interacting with silica, we developed a force field for amorphous silica surfaces based on their macroscopic wetting properties that is compatible with the CHARMM force field and TIP3P water model. The contact angle of a water droplet on a silica surface served as a criterion to tune the intermolecular interactions. The resulting force field was used to study the permeation of water through silica nanopores, illustrating the influence of the surface topography and the intermolecular parameters on permeation kinetics. We find that minute modeling of the amorphous surface is critical for MD studies, since the particular arrangement of surface atoms controls sensitively electrostatic interactions between silica and water.     

固体NMR研究PAA/PEO共混物中氢键相互作用与结构演化

分子间相互作用是决定材料结构和性能的关键因素之一,而如何在分子水上实现对复杂相互作用分子的检测仍然是一个挑战性课题。本工作首先在不同p H值条下以聚丙烯酸/聚环氧乙烷(PAA/PEO)的混合水溶液制备了系列的固体薄膜,然后采用多种基于连续相调制多脉冲技术的一维和二维~1H多脉冲去耦(CRAMPS)固体NMR新技术,并结合高分辨~(13)C交叉极化魔角旋转(CPMAS)、~(23)Na多量子(MQ)等多核固体NMR实验,对PAA/PEO聚合物共混物的微观结构和动力学进行了原位和系统的研究。通过不同类型的~1H高分辨CRAMPS实验检测到共混物中包含多种不同类型质子:通过氢键相互作用形成二聚体的COOH基团、自由COOH基团、与水结合的COOH基团和主链基团。随着p H值的升高,除主链质子外,大部分其它区域的信号都明显降低,这是由于PAA与PEO以及水的氢键作用减弱所致。这些CRAMPS NMR技术也被用来阐明不同p H值制备的样品中不同基团的分子运动性。此外,二维~1H-~1H自旋交换NMR实验提供了关于聚合物PAA与PEO大分子链间、以及水与聚合物的相互作用。~1H自旋扩散实验表明,在这些共混物中明显存在相微观相分离的结构,并且测定的分散相区尺寸约为17 nm。~(23)Na MQMAS实验揭示了在共混物中存在两种类型~(23)Na位,一种是自由的钠离子,另一种是与大分子相互作用的Na离子。特别是通过~1H-检测的~(23)Na-~1H CPMAS实验揭示了Na~+离子的位置远离PEO而与PAA临近。上述这些SSNMR实验结果在分子水平上提供了氢键相互作用对PAA/PEO共混物微观结构和动力学影响的详细信息,可以获得不同p H值对PAA与PEO的氢键作用、相容性、微观结构、水-聚合物相互作用和不同组分分子运动性的影响。在上述核磁共振研究的基础上,我们提出了一种新的PAA/PEO共混物的结构模型,该模型首次成功地揭示了不同的p H值对PAA/PEO共混物中微观结构和动力学的影响。本工作清楚地表明,固态核磁共振是在分子水平上研究具有复杂相互作用的多相聚合物材料的有力工具。本文的研究工作对于探索检测聚合物弱相互作用的新方法和发展基于氢键相互作用的聚合物新材料的开发具有重要意义。     

A Triptycene‐Based Approach to Solubilising Carbon Nanotubes and C60

We describe herein the synthesis of a triptycene‐based surfactant designed with the ability to solubilise single‐walled carbon nanotubes (SWNTs) and C₆₀ in water through non‐covalent interactions. Furthermore, an amphiphilic naphthalene‐based surfactant with the same ability to solubilise SWNTs and C₆₀ has also been prepared. The compounds synthesised were designed with either two ionic or non‐ionic tails to ensure a large number of supramolecular interactions with the solvent, thereby promoting strong solubilisation. The surfactants produced stable suspensions in which the SWNTs are dispersed and the surfactant/SWNT complexes formed are stable for more than one year. UV/Vis/NIR absorption spectroscopy, TEM and AFM were employed to probe the solubilisation properties of the dispersion of surfactants and SWNTs in water.