Accurate integration over atomic regions bounded by zero‐flux surfaces

The approach for the integration over a region covered by zero‐flux surface is described. This approach based on the surface triangulation technique is efficiently realized in a newly developed program TWOE . The elaborated method is tested on several atomic properties including the source function. TWOE results are compared with those produced by using well‐known existing programs. Absolute errors in computed atomic properties are shown to range usually from 10^?6 to 10^?5 au. The demonstrative examples prove that present realization has perfect convergence of atomic properties with increasing size of angular grid and allows to obtain highly accurate data even in the most difficult cases. It is believed that the developed program can be bridgehead that allows to implement atomic partitioning of any desired molecular property with high accuracy. © 2012 Wiley Periodicals, Inc.     

FEW: A workflow tool for free energy calculations of ligand binding

In the later stages of drug design projects, accurately predicting relative binding affinities of chemically similar compounds to a biomolecular target is of utmost importance for making decisions based on the ranking of such compounds. So far, the extensive application of binding free energy approaches has been hampered by the complex and time‐consuming setup of such calculations. We introduce the free energy workflow (FEW) tool that facilitates setup and execution of binding free energy calculations with the AMBER suite for multiple ligands. FEW allows performing free energy calculations according to the implicit solvent molecular mechanics (MM‐PB(GB)SA), the linear interaction energy, and the thermodynamic integration approaches. We describe the tool's architecture and functionality and demonstrate in a show case study on Factor Xa inhibitors that the time needed for the preparation and analysis of free energy calculations is considerably reduced with FEW compared to a fully manual procedure. © 2013 Wiley Periodicals, Inc.     

QMX: A versatile environment for hybrid calculations applied to the grafting of Al2Cl3Me3 on a silica surface

We present a new software to easily perform QM:MM and QM:QM' calculations called QMX. It follows the subtraction scheme and it is implemented in the Atomic Simulation Environment (ASE). Special attention is paid to couple molecular calculations with periodic boundaries approaches. QMX inherits the flexibility and versatility of the ASE package: any combination of methods namely force field, semiempirical, first principle, and ab initio, can be used as hybrid potential energy surface (PES). Its ease of use is demonstrated by considering the adsorption of Al₂Cl₃Me₃ on silica surface and by combining different levels of theory (from standard DFT to MP2 calculations) for the so‐called High Level cluster with standard PW91 density functional theory calculations for the Low Level environment. It is shown that the High Level cluster must contain the silanol group close to the aluminum atoms. The bridging adsorption is favored by 58 kJ mol^?1 at the MP2:PW91 level with respect to the terminal position. Using large clusters at the MP2:PW91 level, it is shown that PW91 calculations are sufficient for structure optimization but that embedded methods are required for accurate energy profiles. © 2013 Wiley Periodicals, Inc.     

Comparative assessment of computational methods for the determination of solvation free energies in alcohol‐based molecules

The determination of differences in solvation free energies between related drug molecules remains an important challenge in computational drug optimization, when fast and accurate calculation of differences in binding free energy are required. In this study, we have evaluated the performance of five commonly used polarized continuum model (PCM) methodologies in the determination of solvation free energies for 53 typical alcohol and alkane small molecules. In addition, the performance of these PCM methods, of a thermodynamic integration (TI) protocol and of the Poisson–Boltzmann (PB) and generalized Born (GB) methods, were tested in the determination of solvation free energies changes for 28 common alkane‐alcohol transformations, by the substitution of an hydrogen atom for a hydroxyl substituent. The results show that the solvation model D (SMD) performs better among the PCM‐based approaches in estimating solvation free energies for alcohol molecules, and solvation free energy changes for alkane‐alcohol transformations, with an average error below 1 kcal/mol for both quantities. However, for the determination of solvation free energy changes on alkane‐alcohol transformation, PB and TI yielded better results. TI was particularly accurate in the treatment of hydroxyl groups additions to aromatic rings (0.53 kcal/mol), a common transformation when optimizing drug‐binding in computer‐aided drug design. © 2013 Wiley Periodicals, Inc.     

Synthesis and Properties of Oval‐Shaped Iron Oxide/Ethylene Glycol Mesostructured Nanosheets

We have demonstrated a new and facile bottom‐up protocol for the effective synthesis of oval‐shaped iron oxide/ethylene glycol (FeO_x/EG) mesostructured nanosheets. Deprotonated ethylene glycol molecules are intercalated into iron oxide layers to form an interlayer distance of 10.6 Å. These materials display some peculiar magnetic properties, such as the low Morin temperature T_M and ferromagnetism below this T_M value. CdSe/ZnS nanoparticles can be loaded onto these mesostructured nanosheets to produce nanocomposites that combine both magnetic and fluorescence functions. In addition, iron oxide/propanediol (or butanediol) mesostructured materials with increased interlayer distances can also be synthesized. The developed synthetic strategy may be extended toward the creation of other ultrathin mesostructured nanosheets.     

Epoxide Opening versus Silica Condensation during Sol–Gel Hybrid Biomaterial Synthesis

Hybrid organic–inorganic solids represent an important class of engineering materials, usually prepared by sol–gel processes by cross‐reaction between organic and inorganic precursors. The choice of the two components and control of the reaction conditions (especially pH value) allow the synthesis of hybrid materials with novel properties and functionalities. 3‐Glycidoxypropyltrimethoxysilane (GPTMS) is one of the most commonly used organic silanes for hybrid‐material fabrication. Herein, the reactivity of GPTMS in water at different pH values (pH 2–11) was deeply investigated for the first time by solution‐state multinuclear NMR spectroscopic and mass spectrometric analysis. The extent of the different and competing reactions that take place as a function of the pH value was elucidated. The NMR spectroscopic and mass spectrometric data clearly indicate that the pH value determines the kinetics of epoxide hydrolysis versus silicon condensation. Under slighly acidic conditions, the epoxy‐ring hydrolysis is kinetically more favourable than the formation of the silica network. In contrast, under basic conditions, silicon condensation is the main reaction that takes place. Full characterisation of the formed intermediates was carried out by using NMR spectroscopic and mass spectrometric analysis. These results indicate that strict control of the pH values allows tuning of the reactivity of the organic and inorganic moities, thus laying the foundations for the design and synthesis of sol–gel hybrid biomaterials with tuneable properties.     

Functional Monomers and Polymers. 145. Synthetic Application Based on the Tautomerism of Polymer-Bound Purine and Pyrimidine Bases

Polymer-bound alkylthiopurine and -pyrimidine bases were prepared and used as the polymeric reagents for the reactions of nitrile, olefin, and enone formation. The corresponding low molecular weight compounds were also prepared for comparison. Differences in the reactivity of these reagents were related to the change in tautomerism of the purine and pyrimidine moieties.     

Controlled Click‐Assembly of Well‐Defined Hetero‐Bifunctional Cubic Silsesquioxanes and Their Application in Targeted Bioimaging

A general procedure for the assembly of hetero‐bifunctional cubic silsesquioxanes with diverse functionality and a perfectly controlled distribution of functional groups on the inorganic framework has been developed. The method is based on a two‐step sequence of mono‐ and hepta‐functionalization through the ligand‐accelerated copper(I)‐catalyzed azide–alkyne cycloaddition of a readily available octaazido cubic silsesquioxane. The stoichiometry of the reactants and the law of binomial distribution essentially determine the selectivity of the key monofunctionalization reaction when a copper catalyst with strong donor ligands is used. The methodology has been applied to the preparation of a set of bifunctional nano‐building‐blocks with orthogonal reactivity for the controlled assembly of precisely defined hybrid nanomaterials and a fluorescent multivalent probe for application in targeted cell‐imaging. The inorganic cage provides an improved photostability to the covalently attached dye as well as a convenient framework for the 3D multivalent display of the pendant epitopes. Thus, fluorescent bioprobes based on well‐defined cubic silsesquioxanes offer interesting advantages over more conventional fully organic analogues and ill‐defined hybrid nanoparticles and promise to become powerful tools for the study of cell biology and for biomedical applications.     

Silica/Silicone Nanofilament Hybrid Coatings with Almost Perfect Superhydrophobicity

A facile method for the preparation of silica/silicone nanofilament hybrid coatings with almost perfect superhydrophobicity (contact angle=179.8° and sliding angle=1.3°) is presented. The coatings are obtained by dip‐coating of silica nanoparticles, followed by chemical vapor deposition of silicone nanofilaments. Predominant growth of silicone nanofilaments onto aggregated silica nanoparticles generates a two‐tier structure. The effect of silica nanoparticle size on the growth of silicone nanofilaments, along with their anti‐wetting properties and transparency are investigated in detail. Surface roughness and anti‐wetting properties can be simply regulated by controlling the size of silica nanoparticles.