Predicting molecular structures: an application of the cutting angle method

The ability to predict molecular geometries has important applications in chemistry. Specific examples include the areas of protein space structure elucidation, the investigation of host–guest interactions, the understanding of properties of superconductors and of zeolites. This prediction of molecular geometries often depends on finding the global minimum or maximum of a function such as the potential energy. In this paper, we consider several well-known molecular conformation problems to which we apply a new method of deterministic global optimization called the cutting angle method. We demonstrate that this method is competitive with other global optimization techniques for these molecular conformation problems.

A new method for locating the global optimum : application of the cutting angle method to molecular structure prediction

Many problems in chemistry depend on the ability to identify the global minimum or maximum of a function. Examples include applications in chemometrics, optimization of reaction or operating conditions, and non-linear least-squares analysis. This paper presents the results of the application of a new method of deterministic global optimization, called the cutting angle method (CAM), as applied to the prediction of molecular geometries. CAM is shown to be competitive with other global optimization techniques for several benchmark molecular conformation problem. CAM is a general method that can also be applied to other computational problems involving global minima, global maxima or finding the roots of nonlinear equations.

Challenges of continuous global optimization in molecular structure prediction

The molecular geometry, the three dimensional arrangement of atoms in space, is a major factor determining the properties and reactivity of molecules, biomolecules and macromolecules. Computation of stable molecular conformations can be done by locating minima on the potential energy surface (PES). This is a very challenging global optimization problem because of extremely large numbers of shallow local minima and complicated landscape of PES. This paper illustrates the mathematical and computational challenges on one important instance of the problem, computation of molecular geometry of oligopeptides, and proposes the use of the Extended Cutting Angle Method (ECAM) to solve this problem.

ECAM is a deterministic global optimization technique, which computes tight lower bounds on the values of the objective function and fathoms those part of the domain where the global minimum cannot reside. As with any domain partitioning scheme, its challenge is an extremely large partition of the domain required for accurate lower bounds. We address this challenge by providing an efficient combinatorial algorithm for calculating the lower bounds, and by combining ECAM with a local optimization method, while preserving the deterministic character of ECAM.

Effect of solvent on ionic liquid dissolved regenerated antheraea assamensis silk fibroin

We report on the dissolution of semi-domestic silk type Antheraea assamensis using ionic liquids. We investigated the impact of different coagulating solvents, including isopropanol and water on the structure and the morphology of the regenerated silk. We found that the water regenerated silk film showed a high β-sheet content and a native silk-like XRD pattern.

PET imaging of tumours with a 64Cu labeled macrobicyclic cage amine ligand tethered to Tyr3-octreotate

The use of copper radioisotopes in cancer diagnosis and radionuclide therapy is possible using chelators that are capable of binding Cu(II) with sufficient stability in vivo to provide high tumour-to-background contrast. Here we report the design and synthesis of a new bifunctional chelator, 5-(8-methyl-3,6,10,13,16,19-hexaaza-bicyclo[6.6.6]icosan-1-ylamino)-5-oxopentanoic acid (MeCOSar), that forms copper complexes of exceptional stability by virtue of a cage amine (sarcophagine) ligand and a new conjugate referred to as SarTATE, obtained by the conjugation of MeCOSar to the tumour-targeting peptide Tyr(3)-octreotate. Radiolabeling of SarTATE with (64)Cu(II), a radioisotope suitable for positron emission tomography (PET), was fast (~20 min), easily performed at room temperature and consistently resulted in high radiochemical purity (>99%). In vitro and in vivo evaluation of (64)CuSarTATE demonstrated its high selectivity for tumour cells expressing somatostatin receptor 2 (sstr2). Biodistribution and PET imaging comparisons were made between (64)CuSarTATE and (64)Cu-labeled DOTA-Tyr(3)-octreotate ((64)CuDOTATATE). Both radiopharmaceuticals showed excellent uptake in sstr2-positive tumours at 2 h post-injection. While tumour uptake of (64)CuDOTATATE decreased significantly at 24 h, (64)CuSarTATE activity was retained, improving contrast at later time points. (64)CuSarTATE accumulated less than (64)CuDOTATATE in the non-target organs, liver and lungs. The uptake of (64)CuSarTATE in the kidneys was high at 2 h but showed significant clearance by 24 h. The new chemistry and pre-clinical evaluation presented here demonstrates that MeCOSar is a promising bifunctional chelator for Tyr(3)-octreotate that could be applied to a combined imaging and therapeutic regimen using a combination of (64)Cu- and (67)CuSarTATE complexes, owing to improved tumour-to-non-target organ ratios compared to (64)CuDOTATATE at longer time points.

Recent developments in electrospinning of nanofiber yarns

Nanofibers possess high surface area and excellent porosity. Though nanofibers can be produced by a variety of techniques, electrospinning stands distinct because of its simplicity and flexibility in processing different polymer materials, and ability to control fiber diameter, morphology, orientation, and chemical component. Nonetheless, electrospun nanofibers are predominantly produced in the form of randomly oriented fiber webs, which restrict their wide use. Converting nanofibers into twisted continuous bundles, i.e., nanofiber yarns, can improve their strength and facilitate their subsequent processes, but remains challenging to make. Nanofiber yarns also create enormous opportunities to develop well-defined three-dimensional nanofibrous architectures. This review article gives an overview of the state-of-the-art techniques for electrospinning of nanofiber yarns and control of nanofiber alignment. A detailed account on techniques to produce twisted/non-twisted short bundles and continuous yarns are discussed.

Probing the biophysical interaction between Neocarzinostatin toxin and EpCAM RNA aptamer

Neocarzinostatin (NCS) a potent DNA-damaging, anti-tumor toxin extracted from Streptomyces carzinostaticus that recognizes double-stranded DNA bulge and induces DNA damage. 2 Fluoro (2F) Modified EpCAM RNA aptamer is a 23-mer that targets EpCAM protein, expressed on the surface of epithelial tumor cells. Understanding the interaction between NCS and the ligand is important for carrying out the targeted tumor therapy. In this study, we have investigated the biophysical interactions between NCS and 2-fluro Modified EpCAM RNA aptamer using Circular Dichroism (CD) and Infra-Red (IR) spectroscopy. The aromatic amino acid residues spanning the β sheets of NCS are found to participate in intermolecular interactions with 2 F Modified EpCAM RNA aptamer. In-silico modeling and simulation studies corroborate with CD spectra data. Furthermore, it reinforces the involvement of C and D1 strand of NCS in intermolecular interactions with EpCAM RNA aptamer. This the first report on interactions involved in the stabilization of NCS-EpCAM aptamer complex and will aid in the development of therapeutic modalities towards targeted cancer therapy.

Simulation of oleuropein structural conformation in vacuum, water and triolein-water systems using molecular dynamics

Oleuropein, the main phenolic compound of olive leaves, exhibits a unique blend of biological activities and has been shown to locate itself at the oil-water (O/W) interface. This behavior could influence the physico-chemical properties of dispersed systems such as emulsions. In this work, we study the effect of the microenvironment (vacuum, water, and triolein-water) on the conformational preferences of oleuropein using molecular dynamics (MD) simulations at 300K for at least 30ns. The seven torsions that describe the flexible skeleton of oleuropein were monitored together with the distance between the glucose (Glu) and hydroxytyrosol (Hyd) moieties (dglu-hyd) of the molecule. The obtained trajectories demonstrated that oleuropein adopts different conformations that depend on the environment. The preferential conformers in each system were analyzed for their molecular geometry and internal energy. In vacuum, the oleuropein preferential conformation is tight with the glucose moiety in close proximity with the hydroxytyrosol moiety. In water, oleuropein preferential conformers presented large differences in their structural properties, varying from a close like U form, and a semi-opened form, to an opened form characterized by high fluctuations in dglu-hyd values. In a triolein-water system, oleuropein tends to adopt a more open form where the glucose moiety could be approximately aligned with the hydroxytyrosol and elenolic acid moieties. Based on a calculation at the HF/6-31G* level, these flexibilities of oleuropein required energy of 19.14kcal/mol in order to adopt the conformation between water and triolein-water system. A radial distribution function (RDF) analysis showed that specific hydroxyl groups of Hyd and Glu interact with water molecules, enabling us to understand the amphiphilic character of oleuropein at the triolein-water interface. MD calculations together with interfacial tension measurements revealed that the oleuropein binding at O/W interface is an enthalpy driven mechanism.

Molecular dynamics approach to the structural characterization and transport properties of poly(acrylonitrile)/N,N-dimethylformamide solutions

Poly(acrylonitrile) (PAN) in N,N-dimethylformamide (DMF) is a popular solution for producing large variety of polymer products. To precisely describe the behaviours of PAN and DMF in the synthesis processes, it is significant to call for more details about the structure, some thermodynamic and dynamical properties of PAN-DMF solutions. A PAN-DMF solution was simulated via molecular dynamics with an all-atom OPLS type potential in both the NPT and NVT ensembles. The simulation results were evaluated with quantum mechanical calculations (MP2/6-311 ++G(d,p) and counterpoise procedure) and were compared with available experimental results. The liquid structure was illustrated with pair correlation functions and transport and dynamics properties were calculated with the mean-square displacements MSD and the velocity autocorrelation functions. The strong H-bonds of C≡N « H-C=O, CH » O=C-H and CH2 O=C-H, with distances of 2.55 Å, 2.55 Å and 2.65 Å, respectively, were found. The largest interaction energy of - 7.157 kcal/mol between DMF molecules and PAN molecules was found at 4.9 Å center-of-mass distance. A potential profile of intermolecular interaction of DMF with PAN along the interaction distance was presented, clearly showing an increase of DMF vaporisation heat when it getting close to PAN molecules. This provided very useful information to analyse the vaporisation behaviours of DMF at the microscopic level, which is essential to comprehensively understand molecular rearrangements towards the design of synthetic processes. The impact of the presence of the PAN on the DMF solution properties were also benchmarked with pure DMF solution.

Molecular architecture of Aβ fibrils grown in cerebrospinal fluid solution and in a cell culture model of Aβ plaque formation

OBJECTIVES: The detailed structure of brain-derived Aβ amyloid fibrils is unknown. To approach this issue, we investigate the molecular architecture of Aβ(1-40) fibrils grown in either human cerebrospinal fluid solution, in chemically simple phosphate buffer in vitro or extracted from a cell culture model of Aβ amyloid plaque formation. METHODS: We have used hydrogen-deuterium exchange (HX) combined with nuclear magnetic resonance, transmission electron microscopy, seeding experiments both in vitro and in cell culture as well as several other spectroscopic measurements to compare the morphology and residue-specific conformation of these different Aβ fibrils. RESULTS AND CONCLUSIONS: Our data reveal that, despite considerable variations in morphology, the spectroscopic properties and the pattern of slowly exchanging backbone amides are closely similar in the fibrils investigated. This finding implies that a fundamentally conserved molecular architecture of Aβ peptide fold is common to Aβ fibrils.