Rapid approximate calculation of water binding free energies in the whole hydration domain of (bio)macromolecules

The evaluation of water binding free energies around solute molecules is important for the thermodynamic characterization of hydration or association processes. Here, a rapid approximate method to estimate water binding free energies around (bio)macromolecules from a single molecular dynamics simulation is presented. The basic idea is that endpoint free‐energy calculation methods are applied and the endpoint quantities are monitored on a three‐dimensional grid around the solute. Thus, a gridded map of water binding free energies around the solute is obtained, that is, from a single short simulation, a map of favorable and unfavorable water binding sites can be constructed. Among the employed free‐energy calculation methods, approaches involving endpoint information pertaining to actual thermodynamic integration calculations or endpoint information as exploited in the linear interaction energy method were examined. The accuracy of the approximate approaches was evaluated on the hydration of a cage‐like molecule representing either a nonpolar, polar, or charged water binding site and on α‐ and β‐cyclodextrin molecules. Among the tested approaches, the linear interaction energy method is considered the most viable approach. Applying the linear interaction energy method on the grid around the solute, a semi‐quantitative thermodynamic characterization of hydration around the whole solute is obtained. Disadvantages are the approximate nature of the method and a limited flexibility of the solute. © 2016 Wiley Periodicals, Inc.     

Layered Black Phosphorus: Strongly Anisotropic Magnetic,Electronic, and Electron‐Transfer Properties

Layered elemental materials, such as black phosphorus, exhibit unique properties originating from their highly anisotropic layered structure. The results presented herein demonstrate an anomalous anisotropy for the electrical, magnetic, and electrochemical properties of black phosphorus. It is shown that heterogeneous electron transfer from black phosphorus to outer‐ and inner‐sphere molecular probes is highly anisotropic. The electron‐transfer rates differ at the basal and edge planes. These unusual properties were interpreted by means of calculations, manifesting the metallic character of the edge planes as compared to the semiconducting properties of the basal plane. This indicates that black phosphorus belongs to a group of materials known as topological insulators. Consequently, these effects render the magnetic properties highly anisotropic, as both diamagnetic and paramagnetic behavior can be observed depending on the orientation in the magnetic field.     

Two New Retigerane‐Type Sesterterpenoids from the Lichen Leprocaulon microscopicum

Two new sesterterpenes, 1 and 2 , have been isolated from the lichen Leprocaulon microscopicum. In addition to classic chromatographic methods, a liquid‐liquid chromatography technique, namely centrifugal partition chromatography (CPC) was applied for the purification of compound 2 . The structures were determined by analyses of mass spectrometry and 1D‐ and 2D‐NMR data. The relative configuration of the isolated compounds was assigned on the basis of 2D‐NOESY experiments. The two compounds possess a rare pentacyclic carbon skeleton typical for lichen metabolism, and quite unusual in the vegetal kingdom.     

Atomic Resolution Insight into Sac7d Protein Binding to DNA and Associated Global Changes by Molecular Dynamics Simulations

Sac7d is a small, thermostable protein that induces large helical deformations in DNA upon association. Starting from multiple initial placements of the unbound Sac7d structure relative to a B‐DNA oligonucleotide, molecular dynamics (MD) simulations were employed to directly follow several successful binding events at atomic resolution that resulted in structures in close agreement with the native complex geometry. The final native complex formed rapidly within tenths of nanoseconds and included simultaneous large‐scale kinking, groove opening, twisting, and intercalation in the target DNA. The simulations indicate that the complex formation process involves initial non‐native contacts that helped in reaching the final bound state, with residues intercalated at the center of the kinked DNA. It was also possible to identify several long‐lived trapped intermediate states of the binding process and to follow sliding processes of Sac7d along the DNA minor groove.     

Structural verification of a tetrahydrotetrazole compound

Tetrahydrotetrazoles are five‐membered‐ring heterocycles containing four contiguous saturated nitrogen atoms. Very few examples of such compounds have been reported in the literature. Our previous attempt at the synthesis of a member of this class of compound suggested that the N—N bonds may be more labile than expected. This finding raised the question as to whether the structures of any of the previously reported tetrahydrotetrazoles had been properly assigned. We have reproduced the synthesis of a reported tetrahydrotetrazole, namely 1,2‐di‐tert‐butyl 3‐phenyl‐1H,2H,3H,10bH‐[1,2,3,4]tetrazolo[5,1‐a]isoquinoline‐1,2‐dicarboxylate, C₂₅H₃₀N₄O₄, and have now confidently confirmed its structure via X‐ray crystallography. However, while sufficiently stable in the crystal phase, we discovered that it remains very labile in solution (having a half‐life of only 15 min at 20 °C in CDCl₃). A tentative reaction pathway for its dissociation based on ¹H NMR spectral evidence is provided.     

On Electrostatics,Covalency, and Chemical Dashes: Physical Interactions versus Chemical Bonds

The increasing availability of real-space interaction energies between quantum atoms or fragments that provide a chemically intuitive decomposition of intrinsic bond energies into electrostatic and covalent terms [see, for instance, Chem. Eur. J. 2018 , 24, 9101] provides evidence for differences between the physicist's concept of interaction and the chemist's concept of a bond. Herein, it is argued that, for the former, all types of interactions are treated equally, whereas, for the latter, only the covalent short-range interactions have actually been used to build intuition about chemical graphs and chemical bonds. This has led to the bonding role of long-range Coulombic terms in molecular chemistry being overlooked. Simultaneously, blind consideration of electrostatic terms in chemical bonding parlance may lead to confusion. The relationship between these concepts is examined herein, and some notes of caution on how to merge them are proposed.     

Quantitative analysis of backbone dynamics in a crystalline protein from nitrogen-15 spin-lattice relaxation

A detailed analysis of nitrogen-15 longitudinal relaxation times in microcrystalline proteins is presented. A theoretical model to quantitatively interpret relaxation times is developed in terms of motional amplitude and characteristic time scale. Different averaging schemes are examined in order to propose an analysis of relaxation curves that takes into account the specificity of MAS experiments. In particular, it is shown that magic angle spinning averages the relaxation rate experienced by a single spin over one rotor period, resulting in individual relaxation curves that are dependent on the orientation of their corresponding carousel with respect to the rotor axis. Powder averaging thus leads to a nonexponential behavior in the observed decay curves. We extract dynamic information from experimental decay curves, using a diffusion in a cone model. We apply this study to the analysis of spin-lattice relaxation rates of the microcrystalline protein Crh at two different fields and determine differential dynamic parameters for several residues in the protein.     

Magnesium Dibromide‐Linked Plumbylene Molecules

The reaction of PbCl₂ with the Grignard compound RMgBr (R = 2,4,6‐Et₃C₆H₂) furnishes orange red crystals of the adduct R₂Pb…MgBr₂(thf)₄…PbR₂ ( 4 ), in which two plumbylene molecules are linked through contacts with the bromine atoms of the MgBr₂(thf)₄ molecule. The unusual bonding situation in 4 is reflected by a strictly linear Br–Mg–Br framework, a short Pb…Br separation of 296.4(2) pm, and an Mg–Br…Pb angle of 136.84(7)?.