Retrieval of crystallographically-derived molecular geometry information

The crystallographically determined bond length, valence angle, and torsion angle information in the Cambridge Structural Database (CSD) has many uses. However, accessing it by means of conventional substructure searching requires nontrivial user intervention. In consequence, these valuable data have been underutilized and have not been directly accessible to client applications. The situation has been remedied by development of a new program (Mogul) for automated retrieval of molecular geometry data from the CSD. The program uses a system of keys to encode the chemical environments of fragments (bonds, valence angles, and acyclic torsions) from CSD structures. Fragments with identical keys are deemed to be chemically identical and are grouped together, and the distribution of the appropriate geometrical parameter (bond length, valence angle, or torsion angle) is computed and stored. Use of a search tree indexed on key values, together with a novel similarity calculation, then enables the distribution matching any given query fragment (or the distributions most closely matching, if an adequate exact match is unavailable) to be found easily and with no user intervention. Validation experiments indicate that, with rare exceptions, search results afford precise and unbiased estimates of molecular geometrical preferences. Such estimates may be used, for example, to validate the geometries of libraries of modeled molecules or of newly determined crystal structures or to assist structure solution from low-resolution (e.g. powder diffraction) X-ray data.     

Potentiometric determination of weak bases by titration to a fixed pH value

The theoretical fundamentals of the pH-metric determination of weak bases by titration with solutions of strong acids to a fixed pH value were considered. A simple and rapid procedure for determining ε-aminocaproic acid in medicinal preparations was developed.     

Adding value to the Brazilian sisal: acid hydrolysis of its pulp seeking production of sugars and materials

The present work is inserted into the broad context of the upgrading of lignocellulosic fibers. Sisal was chosen in the present study because more than 50% of the world’s sisal is cultivated in Brazil, it has a short life cycle and its fiber has a high cellulose content. Specifically, in the present study, the subject addressed was the hydrolysis of the sisal pulp, using sulfuric acid as the catalyst. To assess the influence of parameters such as the concentration of the sulfuric acid and the temperature during this process, the pulp was hydrolyzed with various concentrations of sulfuric acid (30–50%) at 70 °C and with 30% acid (v/v) at various temperatures (60–100 °C). During hydrolysis, aliquots were withdrawn from the reaction media, and the solid (non-hydrolyzed pulp) was separated from the liquid (liquor) by filtering each aliquot. The sugar composition of the liquor was analyzed by HPLC, and the non-hydrolyzed pulps were characterized by viscometry (average molar mass), and X-ray diffraction (crystallinity). The results support the following conclusions: acid hydrolysis using 30% H₂SO₄ at 100 °C can produce sisal microcrystalline cellulose and the conditions that led to the largest glucose yield and lowest decomposition rate were 50% H₂SO₄ at 70 °C. In summary, the study of sisal pulp hydrolysis using concentrated acid showed that certain conditions are suitable for high recovery of xylose and good yield of glucose. Moreover, the unreacted cellulose can be targeted for different applications in bio-based materials. A kinetic study based on the glucose yield was performed for all reaction conditions using the kinetic model proposed by Saeman. The results showed that the model adjusted to all 30–35% H₂SO₄ reactions but not to greater concentrations of sulfuric acid. The present study is part of an ongoing research program, and the results reported here will be used as a comparison against the results obtained when using treated sisal pulp as the starting material.     

RAFT Polymerization: Adding to the Picture

SUMMARY: Factors affecting the choice of RAFT agent [RSC(Z) = S] for a given polymerization are discussed. For polymerization of methyl methacrylate (MMA), tertiary cyanoalkyl trithiocarbonates provide very good control over molecular weight and distribution and polymerizations show little retardation. The secondary trithiocarbonate RAFT agents with R = CHPh(CN) also gives good control but an inhibition period attributed to slow reinitiation is manifest. Radical induced reduction with hypophosphite salts provides a clean and convenient process for removal of thiocarbonylthio end groups of RAFT-synthesized polymers. Two methods providing simultaneous control over stereochemistry and molecular weight distribution of chains formed by radical polymerization are reported. Polymerization of MMA in the presence of scandium triflate provides a more isotactic PMMA. A similar RAFT polymerization with trithiocarbonate RAFT agents also provides control and avoids issues of RAFT agent instability seen with dithiobenzoate RAFT agents in the presence of Lewis acids. RAFT polymerization of tetramethylammonium methacrylate at 45 °C provides a more syndiotactic PMMA of controlled molecular weight and distribution (after methylation; mm:mr:rr 2:21:77 compared to 3:35:62 when formed by bulk polymerization of MMA).     

Synthesis of novel Mannich bases and hybrid Mannich bases related to isoindolin-1,3-dione

Treatment of isoindolin-1,3-dione ( 1 ) with formalin and the appropriate amine or diamine afforded new N-Mannich bases and bis-(Mannich bases) 2 to 6 . The use of the appropriate hydrazide or dihydrazide as the amine component in the Mannich reaction with 1 led to Mannich bases and bis-(Mannich bases) incorporating a hydrazide moiety. The synthetic potential of sec-Mannich bases as precursors in synthesis of hybrid Mannich bases incorporating 1 was described. The N-alkylation of 1 with ketonic Mannich bases was investigated.     

GARLEEK: Adding an extra flavor to ONIOM

The ONIOM method, developed in the group of Keiji Morokuma, is one of the most successful examples of quantum mechanics/molecular mechanics (QM/MM) treatments, and of multilayer methods in general. Its implementation in the Gaussian program package is in particular widely used. This implementation has access to the wide variety of QM methods available in Gaussian, but is limited to only three specific force fields. The current article presents the GARLEEK interface, which expands the availability of molecular mechanics methods to the wide variety of force fields available in MM packages. The focus is in the simple installation and use. Two examples of the performance of the interface with selected systems are provided. GARLEEK is MIT-licensed and freely available at https://github.com/insilichem/garleek . © 2018 Wiley Periodicals, Inc.     

Data,knowledge and method bases in chemical sciences. Part IV. Current status in databases

Computer readable databases have become an integral part of chemical research right from planning data acquisition to interpretation of the information generated. The databases available today are numerical, spectral and bibliographic. Data representation by different schemes--relational, hierarchical and objects--is demonstrated. Quality index (QI) throws light on the quality of data. The objective, prospects and impact of database activity on expert systems are discussed. The number and size of corporate databases available on international networks crossed manageable number leading to databases about their contents. Subsets of corporate or small databases have been developed by groups of chemists. The features and role of knowledge-based or intelligent databases are described.     

Conversion of polyalkylated cyclohexadienones to alkylphenols with bases

Conclusions The dealkylation of polyalkylcyclohexadienones forming polyalkylphenols is accomplished by the action of strong bases at 250–320°C.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 4, pp. 936–937, April, 1976.     

Complex bases. XIV. Use of sodamide containing complex bases as versatile,inexpensive reagents to generate carbanions

It is shown that Complex Bases NaNH₂-RONa are very efficient in carbanion preparations and allow alkylation of imines, aldehydes, 1,3-dithianes, dithioketals as well as methylsulfenylation of ketones.     

Transformations to diagonal bases in closed-loop quantum learning control experiments

This paper discusses transformations between bases used in closed-loop learning control experiments. The goal is to transform to a basis in which the number of control parameters is minimized and in which the parameters act independently. We demonstrate a simple procedure for testing whether a unitary linear transformation (i.e., a rotation amongst the control variables) is sufficient to reduce the search problem to a set of globally independent variables. This concept is demonstrated with closed-loop molecular fragmentation experiments utilizing shaped, ultrafast laser pulses.     

Synthesis of carboline bases

A study has been made of the condensation of serotonin with aldehydes to give the corresponding -carboline derivatives. In most cases the reaction was run under biological conditions (pH 5. 4, 36). The following aldehydes were reacted: acetaldehyde, butyraldehyde, isobutyraldehyde, benzaldehyde, n-octaldehyde, and formaldehyde. The corresponding -carboline derivatives are obtained from the first 5 of these. The reaction with formaldehyde leads to complete resinification.     

From self-assembly fundamental knowledge to nanomedicine developments

This review highlights the key role of NMR techniques in demonstrating the molecular aspects of the self-assembly of surfactant molecules that nowadays constitute the basic knowledge which modern nanoscience relies on. The aim is to provide a tutorial overview.     

Pyrrolizidine alkaloids necine bases: II. Conformational analysis of free bases

Molecular mechanics calculations were applied to the conformational analysis of two diasteroisomers, the pyrrolizidine alkaloids (PAs) retronecine and heliotridine. The application of reoptimized parameters for H bonding corrected the tendency of MM3(92) calculations to give unrealistic H(DOTTED BOND)O distances for intramolecular OH interactions occurring in both diasterisomers. Inversions in the H-bond direction of exo-retronecine and in the relative stability of heliotridine endo–exo conformers were also observed with the application of the new parameters. A set of probable conformers was obtained for each diasterisomer, based on conformational and Boltzmann population analysis. Only exo-puckered conformers were found in the retronecine set, whereas both exo- and endo-puckered conformers were obtained for heliotridine. Transition state conformations supplied arguments supporting the design of models for H-bond interconversion in the case of exo-retronecine and for the exo–endo interconversion of heliotridine. Reactivity behaviors and ¹H-NMR data of both diasterisomers were elucidated in light of the theoretical results. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1853–1861, 1998     

Synthesis of isatin-N-mannich bases

The synthesis of a series of isatin-N-Mannich bases derived from isatin, 5-methyl and 5-bromoisatins as the active hydrogen component and dimethylamine, diethylamine, morpholine, piperidine, N-ethylcyclohexylamine, 3-azabicyclo[3.2.2]nonane and 3-aza-bicyclo[3.2.1]octane as the secondary amine moiety is described. These compounds are to be screened for their pharmacological properties.