The first polymorph in the family of nucleobases: a second form of cytosine

A new polymorph of cytosine, C₄H₅N₃O, is reported half a century after the report of its first known crystal structure [Barker & Marsh (1964). Acta Cryst. 17 , 1581–1587]. Cytosine thus provides the first polymorphic example in the category of parent nucleobases. The new form, denoted (Ib), was observed unexpectedly during an attempt to cocrystallize cytosine with catechol. Form (Ib) crystallizes in the orthorhombic centrosymmetric space group Pccn with two molecules in the asymmetric unit. The previously known form, denoted (Ia), crystallizes in the orthorhombic noncentrosymmetric space group P2₁2₁2₁. The cytosine molecule is planar in both forms. Hydrogen‐bonding interactions are also similar for both forms. Infinite one‐dimensional ribbons composed of cytosine base‐pair dimers in R₂²(8) arrangements are observed in both (Ia) and (Ib). However, the way that the ribbons are packed differs in (Ia) and (Ib). This appears to guide the centrosymmetric versus noncentrosymmetric space‐group selection through the formation of an inversion‐related motif in polymorph (Ib) and a helical propagation in polymorph (Ia). A few selected polymorphic systems have been gathered from the Cambridge Structural Database to understand possible structural features responsible for achiral molecules adopting centro‐ and noncentrosymmetric space groups.     

Four oxoindole‐linked α‐alkoxy‐β‐amino acid derivatives

Four structures of oxoindolyl α‐hydroxy‐β‐amino acid derivatives, namely, methyl 2‐{3‐[(tert‐butoxycarbonyl)amino]‐1‐methyl‐2‐oxoindolin‐3‐yl}‐2‐methoxy‐2‐phenylacetate, C₂₄H₂₈N₂O₆, (I), methyl 2‐{3‐[(tert‐butoxycarbonyl)amino]‐1‐methyl‐2‐oxoindolin‐3‐yl}‐2‐ethoxy‐2‐phenylacetate, C₂₅H₃₀N₂O₆, (II), methyl 2‐{3‐[(tert‐butoxycarbonyl)amino]‐1‐methyl‐2‐oxoindolin‐3‐yl}‐2‐[(4‐methoxybenzyl)oxy]‐2‐phenylacetate, C₃₁H₃₄N₂O₇, (III), and methyl 2‐[(anthracen‐9‐yl)methoxy]‐2‐{3‐[(tert‐butoxycarbonyl)amino]‐1‐methyl‐2‐oxoindolin‐3‐yl}‐2‐phenylacetate, C₃₈H₃₆N₂O₆, (IV), have been determined. The diastereoselectivity of the chemical reaction involving α‐diazoesters and isatin imines in the presence of benzyl alcohol is confirmed through the relative configuration of the two stereogenic centres. In esters (I) and (III), the amide group adopts an anti conformation, whereas the conformation is syn in esters (II) and (IV). Nevertheless, the amide group forms intramolecular N—H...O hydrogen bonds with the ester and ether O atoms in all four structures. The ether‐linked substituents are in the extended conformation in all four structures. Ester (II) is dominated by intermolecular N—H...O hydrogen‐bond interactions. In contrast, the remaining three structures are sustained by C—H...O hydrogen‐bond interactions.     

Sol–gel development activities at IGCAR,Kalpakkam

Sol–gel based fuel fabrication processes have the potential to be the nuclear fuel fabrication processes in the future. Hence development of sol–gel technology for nuclear fuel fabrication is being the pursued in the Department of Atomic Energy in India. As a part of the efforts, a laboratory scale facility for fabrication of test fuel pins for irradiation in the Fast Breeder Reactor (FBTR), Kalpakkam has been set up at the Indira Gandhi Centre for Atomic Research, Kalpakkam, India. These fuel pins will be vibropacked with sol–gel derived microspheres or stacked with pellets obtained by compaction of sol–gel derived microspheres. The facility is aimed at demonstration of the remote operation of the fuel pin fabrication process through the sol–gel route. A capsule containing three test pins from this facility will be irradiated in FBTR. The design features of the facility and the test fuel pins are described in this paper.     

Defense role of the cocoon in the silk worm Bombyx mori L

Silk from the domesticated silk worm Bombyx mori procures foreign body response naturally, so it has been utilized as a biomaterial for decades. In India the prime focus of the sericulture industry is to improve silk production with high quality silk. Naturally, the silk worm builds its cocoon not only with silk proteins, but also with antimicrobial proteins to avoid infection since the cocoon is non-motile and non-feeding. The aim of the present study is to elucidate the antimicrobial proteins that persist in the cocoon of the silk worm Bombyx mori. At the pupal stage, the silk worm cocoon shell extract was prepared from the day of pupation (P0) to the day of natural rupture of the cocoon for the eclosion of moth (NR). Using the cocoon shell extract a microbial susceptibility test was performed by the disc diffusion method against the microbes Escherchia coli, Bacillus cereus, Staphylococcus aureus, Pseudomonas aeruginosa, and Klebsiella pneumoniae. The development of a zone of inhibition against the microbes confirmed the presence of antimicrobial/immunogenic activity of the cocoon shell extract. For further analysis, the cocoon shell extract was subjected to 7-15% sodium dodecyl sulfate/polyacrylamide gel electrophoresis (SDS-PAGE). The protein profile of the cocoon extract revealed the coomassie blue stained bands resolved from the 150-15 kDa molecular range. Interestingly, a polypeptide localized at around 29 kDa showed remarkable expressional changes during the development of pupa. To characterize the 29 kDa protein, it was eluted from the gel, digested with trypsin and analyzed by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). The trypsin-digested peptide peaks were analyzed through MASCOT and peptides were matched with the NCBI nr database. The peptides were very well matched with the 18 wheeler protein, which is reported to be responsible for innate immunity, belonging to the Toll family in insects and responsible for cellular mediated immunity.     

Electrochemical-coupling layer-by-layer (ECC-LbL) assembly

Electrochemical-coupling layer-by-layer (ECC-LbL) assembly is introduced as a novel fabrication methodology for preparing layered thin films. This method allows us to covalently immobilize functional units (e.g., porphyrin, fullerene, and fluorene) into thin films having desired thicknesses and designable sequences for both homo- and heteroassemblies while ensuring efficient layer-to-layer electronic interactions. Films were prepared using a conventional electrochemical setup by a simple and inexpensive process from which various layering sequences can be obtained, and the photovoltaic functions of a prototype p/n heterojunction device were demonstrated.     

Gating the mechanistic pathway to the elusive 4-membered ring azeteoporphyrin

Photolysis of metalated (Cu and Ni) and free base 2-diazo-3-oxochlorins within a frozen matrix (λ = 457.9 nm, toluene, 80 K) generates a single photointermediate with a hypsochromically shifted electronic absorption spectrum relative to the starting diazochlorins. The appearance of ketene (~2131 cm(-1)) and azete (~1670 cm(-1)) vibrations in infrared absorption and Raman spectra, respectively, identifies this intermediate as resulting from the Wolff rearrangement of the diazochlorins upon N(2) loss. Computational modeling of the vibrational spectra and TDDFT simulation of the electronic transitions of potential photointermediates corroborate this assignment. Isolation and analysis of photoproducts of these diazochlorins formed within n-butanol-doped frozen toluene matrices indicate near exclusive formation of azeteoporphyrins. In sharp contrast, room temperature laser photolysis of these materials yields a mixture of photoproducts deriving from the presence of both carbene and ketene intermediates. Computational modeling of the intramolecular reactivity of the proposed sp(2) carbene intermediate shows exclusive bond insertion to the adjacent phenyl group, and no evidence of Wolff rearrangement. Computational reaction profile analyses reveal that the barrierless Wolff rearrangement proceeds via an out-of-plane carbene electronic configuration that is generated directly during the loss of N(2). The formation of out-of-plane carbene, resulting in the exclusive formation of the observed ketene photointermediate at low temperatures, is consistent with orbital symmetry considerations and by the geometric constraints imposed by the frozen matrix. Combined, this leads to a model showing that azeteoporphyrin formation via the Wolff rearrangement is dependent upon the structural disposition of the adjacent framework, and the specific reaction intermediate formed is very sensitive to this feature.     

Exact and heuristic methods for cell suppression in multi-dimensional linked tables

The increasing demand for information, coupled with the increasing capability of computer systems, has compelled information providers to reassess their procedures for preventing disclosure of confidential information. This paper considers the problem of protecting an unpublished, sensitive table by suppressing cells in related, published tables. A conventional integer programming technique for two-dimensional tables is extended to find an optimal suppression set for the public tables. This can be used to protect the confidentiality of sensitive data in three- and higher-dimensional tables. More importantly, heuristics that are intimately related to the structure of the problem are also presented to mitigate the computational difficulty of the integer program. An example is drawn from healthcare management. Data tables are randomly generated to assess the computational time/space restrictions of the IP model, and to evaluate the heuristics.     

QM:QM embedding using electronic densities within an ONIOM framework: energies and analytic gradients

Accurate calculations of large systems remain a challenge in electronic structure theory. Hybrid energy techniques are a promising family of methods for treating such systems. Expanding on previous developments, we present a QM:QM electronic embedding model whereby the high-level region is polarized by the electron density of the low-level region within an ONIOM framework. A direct Coulomb embedding model as well a more computationally efficient model involving a density fitting expansion are considered. We also develop a generalized theory for the first derivatives of these classes of QM:QM electronic embedding schemes, which requires solution of a single set of self-consistent field response equations. Two initial test cases are presented and discussed.