Low-energy electron scattering with the purine bases of DNA/RNA using the R-matrix method

R-matrix calculations on electron collisions with the purine bases found in DNA and RNA (i.e., adenine and guanine) are presented. Resonant anion states of these systems are identified by employing different approximation levels of ab initio theoretical methods, such as the static exchange, the static exchange plus polarization, and the close-coupling methods. The results are compared with other available calculations and experiments. All of these ab initio approximations, which we refer to as a scattering "model," give four shape resonances of (2)A' (π) symmetry within the energy range of 10 eV for both molecules. For adenine, the most sophisticated method, the close-coupling model, gives two very narrow (2)A' (σ) symmetry Feshbach-type resonances at energies above 5 eV. Quantitative results for the total elastic and electronic excitation cross sections are also presented.     

Different growth regimes on prepatterned surfaces: consistent evidence from simulations and experiments

Molecule deposition on a prepatterned substrate is a recently developed technique to generate desired structures of organic molecules on surfaces via self-organization. For the case of prepatterned stripes, the time-resolved process of structure formation is studied via lattice Monte Carlo simulations. By systematic variation of the interaction strength, three distinct growth regimes can be identified: localized growth, bulge formation, and cluster formation. All three growth regimes can be recovered in the experiment when choosing appropriate organic molecules. Some key microscopic observables, reflecting the properties of the structure formation, display a non-monotonous dependence on the interaction strength.     

An Efficient Approach for Preparing Giant Polypeptide Triblock Copolymers by Protein Dimerization

An efficient and convenient approach for preparing a giant polypeptide–poly(ethylene oxide) triblock copolymer architecture of defined structure and composition is reported. This copolymer consists of two long polypeptide chains derived from bovine serum albumin of distinct lengths with stabilizing poly(ethylene oxide) side‐chains, a connecting poly(ethylene oxide) block, and the presence of secondary structure elements along the polypeptide backbone. It is synthesized from the abundant plasma protein serum albumin and the polypeptide backbone is fully biodegradable. This approach represents a convenient and efficient strategy for preparing giant polypeptide‐based block copolymers of defined structure via a semi‐synthetic strategy. Such high‐molecular‐weight, biodegradable copolymers are attractive for various biomedical applications     

New difference sets in nonabelian groups of order 100

In two groups of order 100 new difference sets are constructed. The existence of a difference set in one of them has not been known. The correspondence between a (100, 45, 20) symmetric design having regular automorphism group and a difference set with the same parameters has been used for the construction. © 2001 John Wiley & Sons, Inc. J Combin Designs 9: 424–434, 2001     

Radiation‐grafted ion‐exchange membranes: Influence of the initial matrix on the synthesis and structure

A series of commercial fluoropolymer films was irradiated with an electron beam, grafted with styrene, and sulfonated. The influence of the initial fluoropolymer on the grafting yields and the properties of the grafted and sulfonated membranes were investigated. The same synthesis procedure can be followed for most fluoropolymers and samples with a similar degree of grafting, and a homogenous polystyrene distribution can be prepared by varying the absorbed dose. The main difference among different fluoropolymer‐based membranes is the water uptake from liquid water that has a roughly linear dependence on the crystallinity of the sample. The more amorphous the initial material, the greater the water uptake. Mechanical properties of the membranes at 50% relative humidity differ less than those of the starting materials and are comparable to those of Nafion® 105. © 2001 John Wiley & Sons, Inc. J Polym Sci Part A: Polym Chem 39: 3008–3017, 2001     

Two isomorphous benzene­sulfon­amide crystal structures determined by intermolecular C—H⃛O,C—H⃛π and C—H⃛Cl interactions

The title compounds, N‐[5‐(4‐chloro­phenyl)­furan‐2‐yl­methyl]‐4‐methyl‐N‐(prop‐2‐ynyl)­benzene­sulfon­amide, (Ia), and N‐[5‐(2‐chloro­phenyl)­furan‐2‐yl­methyl]‐4‐methyl‐N‐(prop‐2‐ynyl)­benzene­sulfon­amide, (Ib), both C₂₁H₁₈ClNO₃S, have isomorphous crystal structures. The crystal packing is mainly determined by intermolecular C—H?O and C—H?π interactions. These interactions are very similar in (Ia) and (Ib). Additional intermolecular C—H?Cl interactions appear less important and are different in (Ia) and (Ib). The different positions of the Cl atoms result in small variations of the crystal packing of the two compounds.     

A Polyclonal Selex Aptamer Library Directly Allows Specific Labelling of the Human Gut Bacterium Blautia producta without Isolating Individual Aptamers

Recent studies have demonstrated that changes in the abundance of the intestinal bacterium Blautia producta, a potential probiotic, are closely associated with the development of various diseases such as obesity, diabetes, some neurodegenerative diseases, and certain cancers. However, there is still a lack of an effective method to detect the abundance of B. producta in the gut rapidly. Especially, DNA aptamers are now widely used as biometric components for medical testing due to their unique characteristics, including high chemical stability, low production cost, ease of chemical modification, low immunogenicity, and fast reproducibility. We successfully obtained a high-affinity nucleic acid aptamer library (B.p-R14) after 14 SELEX rounds, which efficiently discriminates B. producta in different analysis techniques including fluorometric suspension assays or fluorescence microscopy from other major gut bacteria in complex mixtures and even in human stool samples. These preliminary findings will be the basis towards aptamer-based biosensing applications for the fast and reliable monitoring of B. producta in the human gut microbiome.     

Computational Insights into β-Carboline Inhibition of Monoamine Oxidase A

Monoamine oxidases (MAOs) are an important group of enzymes involved in the degradation of neurotransmitters and their imbalanced mode of action may lead to the development of various neuropsychiatric or neurodegenerative disorders. In this work, we report the results of an in-depth computational study in which we performed a static and a dynamic analysis of a series of substituted β-carboline natural products, found mainly in roasted coffee and tobacco smoke, that bind to the active site of the MAO-A isoform. By applying molecular docking in conjunction with structure-based pharmacophores and molecular dynamics simulations coupled with dynamic pharmacophores, we extensively investigated the geometric aspects of MAO-A binding. To gain insight into the energetics of binding, we used the linear interaction energy (LIE) method and determined the key anchors that allow productive β-carboline binding to MAO-A. The results presented herein could be applied in the rational structure-based design and optimization of β-carbolines towards preclinical candidates that would target the MAO-A enzyme and would be applicable especially in the treatment of mental disorders such as depression.     

Reactions of GeCl2 with the Thiolate LiSC(SiMe3)3: From thf Activation to Insertion of GeCl2 Molecules into C−S Bonds

The reaction system GeCl₂ ⋅ dioxane/LiSTsi (Tsi=C(SiMe₃)₃) opens a fruitful area in germanium chemistry, depending on the stoichiometry and solvent used during the reaction. For example, the reaction of GeCl₂ ⋅ dioxane in toluene with two equivalents of the thiolate gives the expected germylene Ge(STsi)₂ in excellent yield. This germylene readily reacts with hydrogen and acetylene, however, in a non-selective way. By using an excess amount of the thiolate and toluene as the solvent, the germanide [Ge(STsi)₃][Li(thf)] is obtained. Performing the same reaction in thf leads to a C−H activation of thf to give (H₇C₄O)Ge[STsi](μ²-S)₂Ge[STsi]₂, in which the thf molecule is still intact. Using a sub-stoichiometric amount of the thiolate leads to the heteroleptic compound [ClGe(STsi)]₂ and to the insertion product (thf)Ge[S-GeCl₂-Tsi]₂, in which additional GeCl₂ molecules insert into the C−S bonds of Ge(STsi)₂. The synthesis and the experimentally determined structures of all compounds are presented together with first reactivity studies of Ge(STsi)₂.     

Similarities and Differences between Crystal and Enzyme Environmental Effects on the Electron Density of Drug Molecules

The crystal interaction density is generally assumed to be a suitable measure of the polarization of a low-molecular weight ligand inside an enzyme, but this approximation has seldomly been tested and has never been quantified before. In this study, we compare the crystal interaction density and the interaction electrostatic potential for a model compound of loxistatin acid (E64c) with those inside cathepsin B, in solution, and in vacuum. We apply QM/MM calculations and experimental quantum crystallography to show that the crystal interaction density is indeed very similar to the enzyme interaction density. Less than 0.1 e are shifted between these two environments in total. However, this difference has non-negligible consequences for derived properties.