Low Energy Packing Research Articles

Layered Hexaphenylbenzene (HPB) derivatives with pseudo-2D structure for high-performance Li ion batteries

Herein, we have synthesized a series of hexaphenylbenzene (HPB) derivatives: HPB-H, HPB-COOCH3 and HPB-COOH that differs in functional groups attached to the periphery of the outer benzene rings. Among them, the HPB with carboxyl functional group (HPB-COOH) as LIB anode shows a superior capacity of 997.4 mAh g−1 and better rate performance than HPB and HPB-COOCH3. Such superior anode properties can be attributed to the fact that HPB-COOH has a layered morphology, a pseudo-2D structure, lower LUMO energy, and higher electron conductivity, compared with that of HPB-COOCH3 and HPB-H, respectively. Moreover, low energy packing with transport channels is beneficial for Li ions diffusion during the lithiation and extraction processes. Furthermore, HPB-COOH shows excellent cycling stability presumably due to its layered molecular packing structures. Our work paves the way for the design synthesis of novel organic molecules with suitable electrochemical redox-active groups and layered hierarchical structure to achieve high capacity, good rate performance, and high cyclic stability for next generation Li ion batteries (LIBs).

Robust Stability of Multicomponent Membranes: The Role of Glycolipids

We present the multicomponent functionalized free energies that characterize the low-energy packings of amphiphilic molecules within a membrane through a correspondence to connecting orbits within a reduced dynamical system. To each connecting orbits we associate a manifold of low energy membrane-type configurations parameterized by a large class of admissible interfaces. The normal coercivity of the manifolds is established through criteria depending solely on the structure of the associated connecting orbit. We present a class of examples that arise naturally from geometric singular perturbation techniques, focusing on a model that characterizes the stabilizing role of cholesterol-like glycolipids within phospholipid membranes.

Crystal structure prediction could have helped the experimentalists with polymorphism in benzamide

Benzamide was the first molecular material for which polymorphism was reported, as long as 176 years ago. Unfortunately, due to very similar cell metrics leading to massive peak overlap, the metastable form reported by Liebig escaped structural characterisation by XRD until recently. With the help of crystal structure prediction this old riddle of ‘Liebig's’ polymorph of benzamide could have been solved many years earlier. Performing state of the art crystal structure prediction runs applying a commercial suite of programs (Cerius2 and the MS Modeling) identified both the metastable and the thermodynamically stable phase reported by Liebig as low energy packings.

Interactions between two β-sheets energetics of β/β packing in proteins

The analysis of the interactions between regularly folded segments of the polypeptide chain contributes to an understanding of the energetics of protein folding. Conformational energy-minimization calculations have been carried out to determine the favorable ways of packing two right-twisted beta-sheets. The packing of two five-stranded beta-sheets was investigated, with the strands having the composition CH3CO-(L-Ile)6-NHCH3 in one beta-sheet and CH3CO-(L-Val)6-NHCH3 in the other. Two distinct classes of low-energy packing arrangements were found. In the class with lowest energies, the strands of the two beta-sheets are aligned nearly parallel (or antiparallel) with each other, with a preference for a negative orientation angle, because this arrangement corresponds to the best complementary packing of the two twisted saddle-shaped beta-sheets. In the second class, with higher interaction energies, the strands of the two beta-sheets are oriented nearly perpendicular to each other. While the surfaces of the two beta-sheets are not complementary in this arrangement, there is good packing between the corner of one beta-sheet and the interior part of the surface of the other, resulting in a favorable energy of packing. Both classes correspond to frequently observed orientations of beta-sheets in proteins. In proteins, the second class of packing is usually observed when the two beta-sheets are covalently linked, i.e. when a polypeptide strand passes from one beta-sheet to the other, but we have shown here that a large contribution to the stabilization of this packing arrangement arises from noncovalent interactions.

Interactions between an α-helix and a β-sheet: Energetics of [formula omitted] packing in proteins

Conformational energy computations have been carried out to determine the favorable ways of packing a right-handed α-helix on a right-twisted antiparallel or parallel β-sheet. Co-ordinate transformations have been developed to relate the position and orientation of the α-helix to the β-sheet. The packing was investigated for a CH 3CO-( L-Ala) 16-NHCH 3 α-helix interacting with five-stranded β-sheets composed of CH 3CO-( L-Val) 6-NHCH 3 chains. All internal and external variables for both the α-helix and the β-sheet were allowed to change during energy minimization. Four distinct classes of low-energy packing arrangements were found for the α-helix interacting with both the parallel and the antiparallel β-sheet. The classes differ in the orientation of the axis of the α-helix relative to the direction of the strands of the right-twisted β-sheet. In the class with the most favorable arrangement, the α-helix is oriented along the strands of the β-sheet, as a result of attractive non-bonded side-chain-side-chain interactions along the entire length of the α-helix. A class with nearly perpendicular orientation of the helix axis to the strands is also of low energy, because it allows similarly extensive attractive interactions. In the other two classes, the helix is oriented diagonally relative to the strands of the β-sheet. In one of them, it interacts with the convex surface near the middle of the saddle-shaped twisted β-sheet. In the other, it is oriented along the concave diagonal of the β-sheet and, therefore, it interacts only with the corner regions of the sheet, so that this packing is energetically less favorable. The packing arrangements involving an antiparallel and a parallel β-sheet are generally similar, although the antiparallel β-sheet has been found to be more flexible. The major features of 163 observed α β packing arrangements in 37 proteins are accounted for in terms of the computed structural preferences. The energetically most favored packing arrangement is similar to the right-handed βαβ crossover structure that is observed in proteins; thus, the preference for this connectivity arises in large measure from this energetically favorable interaction.

A simple method for the calculation of low energy packings of α-helices—A threshold approximation. I. The use of the method to estimate the effects of amino acid substitutions, deletions and insertions in globins

A simple method is developed for computing low energy packings in alpha-helical proteins. This method is based on a simplified representation of a protein molecule in which the backbone of the alpha-helix is represented by a cylinder and the side chains of the amino acids by hard spheres. The energy function includes hydrophobic, electrostatic and Van der Waals' interactions. This method is used to compute low energy packings of an assembly of the alpha-helices of a globin molecule. The effect of mutations, deletions and insertions of a single amino acid resulting in drastic distortion of the spatial structure of sperm whale myoglobin was studied. The results demonstrated that these events can produce a breakdown of the spatial structure of the protein molecule.

The effects of mutations, deletions and insertions of single amino acids on the three-dimensional structure of globins

Using the method of calculation of low energy packings of α-helices, we studied the effects of mutations, deletions and insertions of amino acids on the structure of sperm whale myoglobin. It was found that these events can cause complete breakdown of this structure.