Net charge changes in the calculation of relative ligand‐binding free energies via classical atomistic molecular dynamics simulation

The calculation of binding free energies of charged species to a target molecule is a frequently encountered problem in molecular dynamics studies of (bio‐)chemical thermodynamics. Many important endogenous receptor‐binding molecules, enzyme substrates, or drug molecules have a nonzero net charge. Absolute binding free energies, as well as binding free energies relative to another molecule with a different net charge will be affected by artifacts due to the used effective electrostatic interaction function and associated parameters (e.g., size of the computational box). In the present study, charging contributions to binding free energies of small oligoatomic ions to a series of model host cavities functionalized with different chemical groups are calculated with classical atomistic molecular dynamics simulation. Electrostatic interactions are treated using a lattice‐summation scheme or a cutoff‐truncation scheme with Barker–Watts reaction‐field correction, and the simulations are conducted in boxes of different edge lengths. It is illustrated that the charging free energies of the guest molecules in water and in the host strongly depend on the applied methodology and that neglect of correction terms for the artifacts introduced by the finite size of the simulated system and the use of an effective electrostatic interaction function considerably impairs the thermodynamic interpretation of guest‐host interactions. Application of correction terms for the various artifacts yields consistent results for the charging contribution to binding free energies and is thus a prerequisite for the valid interpretation or prediction of experimental data via molecular dynamics simulation. Analysis and correction of electrostatic artifacts according to the scheme proposed in the present study should therefore be considered an integral part of careful free‐energy calculation studies if changes in the net charge are involved. © 2013 The Authors Journal of Computational Chemistry Published by Wiley Periodicals, Inc.     

TiS2 and ZrS2 single‐ and double‐wall nanotubes: First‐principles study

Hybrid density functional theory has been applied for investigations of the electronic and atomic structure of bulk phases, nanolayers, and nanotubes based on titanium and zirconium disulfides. Calculations have been performed on the basis of the localized atomic functions by means of the CRYSTAL‐2009 computer code. The full optimization of all atomic positions in the regarded systems has been made to study the atomic relaxation and to determine the most favorable structures. The different layered and isotropic bulk phases have been considered as the possible precursors of the nanotubes. Calculations on single‐walled TiS₂ and ZrS₂ nanotubes confirmed that the nanotubes obtained by rolling up the hexagonal crystalline layers with octahedral 1T morphology are the most stable. The strain energy of TiS₂ and ZrS₂ nanotubes is small, does not depend on the tube chirality, and approximately obeys to D^–2 law (D is nanotube diameter) of the classical elasticity theory. It is greater than the strain energy of the similar TiO₂ and ZrO₂ nanotubes; however, the formation energy of the disulfide nanotubes is considerably less than the formation energy of the dioxide nanotubes. The distance and interaction energy between the single‐wall components of the double‐wall nanotubes is proved to be close to the distance and interaction energy between layers in the layered crystals. Analysis of the relaxed nanotube shape using radial coordinate of the metal atoms demonstrates a small but noticeable deviation from completely cylindrical cross‐section of the external walls in the armchair‐like double‐wall nanotubes. © 2013 Wiley Periodicals, Inc.     

Interaction between ions and substituted buckybowls: A comprehensive computational study

Complexes formed by substituted buckybowls derived from corannulene and sumanene with sodium cation or chloride anion have been computationally studied by using a variety of methods. Best results have been obtained with the SCS‐MP2 method extrapolated to basis set limit, which reproduces the highest‐level values obtained with the MP2.X method. All bowls form stable complexes with chloride anion, with stabilities ranging from ?6 kcal/mol in the methylated corannulene derivative to ?45 kcal/mol in the CN‐substituted sumanene. The opposite trend is observed in sodium complexes, going from deeply attractive complexes with the methylated derivatives (?36 kcal/mol with sumanene derivative) to slightly repulsive ones in the CN‐substituted bowls (2 kcal/mol in the corannulene derivative). Anion complexes are stabilized by large electrostatic interactions combined with smaller though significant dispersion and induction contributions. Conversely, cation complexes are stabilized by large induction contributions capable of holding together the bowl and the cation even in cases where the electrostatic interaction is repulsive. The effect of substitution is mainly reflected on changes in the molecular electrostatic potential of the bowl and, thus, in the electrostatic contribution to the interaction. Therefore, the variations in the stability of the complexes on substitution could be roughly predicted just considering the changes in the electrostatic interaction. However, other contributions also register changes mainly as a consequence of displacements on the position of the ion at the minimum, so the accurate prediction of the stability of this kind of complexes requires going further than the electrostatic approach. © 2014 Wiley Periodicals, Inc.     

Computer‐assisted design and synthesis of molecularly imprinted polymers for the simultaneous determination of six carbamate pesticides from environmental water

The computer‐assisted design and synthesis of molecularly imprinted polymers for the simultaneous capture of six carbamate pesticides from environmental water are reported in this work. The quantum mechanical computational approach was employed to design the molecularly imprinted polymers with carbofuran as template. The interaction energies between the template molecule and different functional monomers in various solvents were calculated to assist in the selection of the functional monomer and porogen. The optimised molecularly imprinted polymer was subsequently used as a class‐selective sorbent in solid‐phase extraction for pre‐concentration and determination of carbamates from environmental water. The parameters influencing the extraction efficiency of the molecularly imprinted solid‐phase extraction procedure were systematically investigated to facilitate the class‐selective extraction. For the proposed method, linearity was observed over the range of 2–500 ng/mL with the correlation coefficient ranging from 0.9760 to 1.000. The limits of detection ranged from 0.2 to 1.2 ng/mL, and the limit of quantification was 4 ng/mL. These results confirm that computer‐assisted design is an effective evaluation tool for molecularly imprinted polymers synthesis, and that molecularly imprinted solid‐phase extraction can be applied to the simultaneous analysis of carbamates in environmental water.     

Highly Selective Dimerization and Trimerization of Isobutene to Linearly Linked Products by Using Nickel Catalysts

The unique linear linkage of isobutene to generate highly valuable C₈ precursors for plasticizers is feasible by using special nickel catalysts. (4‐Cyclooctene‐1‐yl)(1,1,1,5,5,5‐hexafluoro‐2,4‐acetylacetonato)nickel and aluminum‐alkyl‐activated nickel acetylacetonates produce isobutene dimers with high selectivities of up to 95 %. Moreover, selectivity for the head‐to‐head products (2,5‐dimethylhexenes) is remarkably high at up to 99 %. Additionally, novel C₁₂ isobutene trimers are also formed with a very high selectivity of up to 99 % for the linear linkage. The trimer structure (2,5,8‐trimethylnonenes) reflects the stepwise characteristic of the reaction mechanism. Pathways of insertion and activation and the deactivation processes of the catalyst are discussed in detail.     

A Theoretical Study on the Structure,Intramolecular Interactions,and Detonation Performance of Hydrazinium Dinitramide

The structures of hydrazinium dinitramide (HDN) in the gas phase and in aqueous solution have been studied at different levels of theory by using quantum chemistry. The intramolecular hydrogen‐bond interactions in HDN were studied by employing the quantum theory of atoms in molecules (QTAIM), as well as those in ammonium dinitramide (ADN), hydrazinium nitroformate (HNF), and ammonium nitroformate (ANF) for comparison. The results showed that HDN possessed the strongest hydrogen bonds, with the largest hydrogen‐bond energy (?47.95 kJ mol^?1) and the largest total hydrogen‐bond energy (?60.29 kJ mol^?1). In addition, the charge transfer between the cation and the anion, the binding energy, the energy difference between the frontier orbitals, and the second‐order perturbation energy of HDN were all the largest among the investigated compounds. These strongest intramolecular interactions accounted for the highest decomposition temperature of HDN among all four compounds. The IR spectra in the gas phase and in aqueous solution were very different and showed the significant influence of the solvent. The UV spectrum showed the strongest absorption at about 253 nm. An orbital‐interaction diagram demonstrated that the transition of electrons mainly happened inside the anion of HDN. The detonation velocity (D=8.34 km s^?1) and detonation pressure (P=30.18 GPa) of HDN were both higher than those of ADN (D=7.55 km s^?1 and P=24.83 GPa). The composite explosive HDN/CL‐20 with the weight ratio w_CL?20/w_HDN=0.388:0.612 showed the best performance (D=9.36 km s^?1, P=39.82 GPa), which was close to that of CL‐20 (D=9.73 km s^?1, P=45.19 GPa) and slightly better than that of the composite explosive ADN/CL‐20 (w_CL?20/w_ADN=0.298:0.702, D=9.34 km s^?1, P=39.63 GPa).     

Multiple Reaction Pathways Operating in the Mechanism of Vinylogous Mannich‐Type Reaction Activated by a Water Molecule

A systematic search for reaction pathways for the vinylogous Mannich‐type reaction was performed by the artificial force induced reaction method. This reaction affords δ‐amino‐γ‐butenolide in one pot by mixing 2‐trimethylsiloxyfuran, imine, and water under solvent‐free conditions. Surprisingly, the search identified as many as five working pathways. Among them, two concertedly produce anti and syn isomers of the product. Another two give an intermediate, which is a regioisomer of the main product. This intermediate can undergo a retro‐Mannich reaction to give a pair of intermediates: an imine and 2‐furanol. The remaining pathway directly generates this intermediate pair. The imine and 2‐furanol easily react with each other to afford the product. Thus, all of these stepwise pathways finally converge to give the main product. The rate‐determining step of all five (two concerted and three stepwise) pathways have a common mechanism: concerted Si? O bond formation through the nucleophilic attack of a water molecule on the silicon atom followed by proton transfer from the water molecule to the imine. Therefore, these five pathways have comparable barriers and compete with each other.     

On the Size Evolution of Monolayer‐Protected Gold Clusters during Ligand Place‐Exchange Reactions: The Effect of Solvents

Ligand place‐exchange (LPE) reactions are extensively applied for the post‐functionalization of monolayer‐protected gold clusters (MPCs) by using excessive incoming ligands to displace initial ones. However, the modified MPCs are often enlarged or degraded; this results in ill‐defined size‐dependent properties. The growth of MPCs essentially involves an unprotected surface that is subsequently has gold atoms added or is fused with other gold cores owing to collision. Reported herein is a guideline for the selection of solvents to suppress unwanted MPC growth. Favorable solvents are those with significant affinity to gold or with low solubility for desorbed ligands because these properties retard LPE reactions and minimize the time available for unprotected gold cores. This finding provides a general and convenient approach to regulate the size of functionalized MPCs.     

Formation of Periodic γ‐Turns in α/β‐Hybrid Peptides: DFT and NMR Experimental Evidence

Hybrid peptidic oligomers comprising natural and unnatural amino acid residues that can exhibit biomolecular folding and hydrogen‐bonding mimicry have attracted considerable interest in recent years. While a variety of hybrid peptidic helices have been reported in the literature, other secondary structural patterns such as γ‐turns and ribbons have not been well explored so far. The present work reports the design of novel periodic γ‐turns in the oligomers of 1:1 natural‐α/unnatural trans‐β‐norborenene (TNAA) amino acid residues. Through DFT, NMR, and MD studies, it is convincingly shown that, in the mixed conformational pool, the heterogeneous backbone of the hybrid peptides preferentially adopt periodic 8‐membered (pseudo γ‐turn)/7‐membered (inverse γ‐turn) hydrogen bonds in both polar and non‐polar solvent media. It is observed that the stereochemistry and local conformational preference of the β‐amino acid building blocks have a profound influence on accessing the specific secondary fold. These findings may be of significant relevance for the development of molecular scaffolds that facilitate desired positioning of functional side‐chains.     

Nucleophile‐Dependent Regio‐ and Stereoselective Ring Opening of 1‐Azoniabicyclo[3.1.0]hexane Tosylate

1‐[(1R)‐(1‐Phenylethyl)]‐1‐azoniabicyclo[3.1.0]hexane tosylate was generated as a stable bicyclic aziridinium salt from the corresponding 2‐(3‐hydroxypropyl)aziridine upon reaction with p‐toluenesulfonyl anhydride. This bicyclic aziridinium ion was then treated with various nucleophiles including halides, azide, acetate, and cyanide in CH₃CN to afford either piperidines or pyrrolidines through regio‐ and stereoselective ring opening, mediated by the characteristics of the applied nucleophile. On the basis of DFT calculations, ring‐opening reactions under thermodynamic control yield piperidines, whereas reactions under kinetic control can yield both piperidines and pyrrolidines depending on the activation energies for both pathways.