The character of molecular modeling

In asking what progress might occur in molecular modeling in the next 25 years it is worth asking what progress has been made in the last twenty-five. In doing so it is hard to be optimistic for the future of the field unless a greater commitment is made to basic science.     

Tuning the Photocatalytic Activity of CdS Nanocrystals through Intermolecular Interactions in Ionic‐Liquid Solvent Systems

Synthetic solvent systems for the fine‐tuned preparation of CdS nanocrystallites, active in visible‐light photocatalytic hydrogen production, were studied. To control crystallite size and spectral properties, the CdS crystals were synthesised by using different solvent systems, containing a series of tetrabutylammonium amino carboxylate ionic liquids as the crystal‐growth control agents. Six samples of CdS, all with similar physical and spectral properties, exhibited greatly varying photocatalytic activity, with the most active sample outperforming the least active one by almost 60 %. To rationalise this effect, the intermolecular interactions of the synthesis solvent system with the growing CdS nanocrystallites were characterised by using the Reichart betaine dye and the ${E{{{\rm N}\hfill \atop {\rm T}\hfill}}}$ polarity scale. A correlation was observed between the ${E{{{\rm N}\hfill \atop {\rm T}\hfill}}}$ values of the solvent system and the photocatalytic activity of the CdS nanocrystallite, suggesting that the hydrogen‐bond‐donating ability and/or dipolarity/polarisability interactions of the solvent system led to the preferential formation of active surfaces/surface sites on the CdS crystals.     

New H-bonding patterns in biphenyl-based synthetic lectins; pyrrolediamine bridges enhance glucose-selectivity

Synthetic lectins are molecules designed for the challenging task of biomimetic carbohydrate recognition in water. Previous work has explored a family of such systems based on bi/terphenyl units as hydrophobic surfaces and isophthalamide spacers to provide polar binding groups. Here we report a related receptor which employs a new spacer, 2,5-bis-(aminomethyl)-pyrrole, with an alternative (A-D-A) set of H-bonding valencies. The modified spacer leads to significant changes in binding selectivity, including a preference for glucose over all other tested substrates.     

peri-Dimethylamino substituent effects on proton transfer at carbon in α-naphthylacetate esters: a model for mandelate racemase

The rate constants for exchange of hydrogen for deuterium at the α-CH(2) positions of 8-(N,N-dimethylaminonaphthalen-1-yl)acetic acid tert-butyl ester 1 and naphthalen-1-ylacetic acid tert-butyl ester 2 have been determined in potassium deuteroxide solutions in 1 : 1 D(2)O : CD(3)CN, in order to quantify the effect of the neighbouring peri-dimethylamino substituent on α-deprotonation. Intramolecular general base catalysis by the (weakly basic) neighbouring group was not detected. Second-order rate constants, k(DO), for the deuterium exchange reactions of esters 1 and 2 have been determined as 1.35 × 10(-4) M(-1) s(-1) and 3.95 × 10(-3) M(-1) s(-1), respectively. The unexpected 29-fold decrease in the k(DO) value upon the introduction of a peri-dimethylamino group is attributed to an unfavourable steric and/or electronic substituent effect on intermolecular deprotonation by deuteroxide ion. From the experimental k(DO) values, carbon acid pK(a) values of 26.8 and 23.1 have been calculated for esters 1 and 2.     

Rate equation modelling of erbium luminescence dynamics in erbium-doped silicon-rich-silicon-oxide

Erbium doped silicon-rich silica offers broad band and very efficient excitation of erbium photoluminescence (PL) due to a sensitization effect attributed to silicon nanocrystals (Si-nc), which grow during thermal treatment. PL decay lifetime measurements of sensitised Er³⁺ ions are usually reported to be stretched or multi exponential, very different to those that are directly excited, which usually show a single exponential decay component.In this paper, we report on SiO₂ thin films doped with Si-nc's and erbium. Time resolved PL measurements reveal two distinct 1.54 μm Er decay components; a fast microsecond component, and a relatively long lifetime component (10 ms). We also study the structural properties of these samples through TEM measurements, and reveal the formation of Er clusters. We propose that these Er clusters are responsible for the fast μs decay component, and we develop rate equation models that reproduce the experimental transient observations, and can explain some of the reported transient behaviour in previously published literature.     

Novel Synthesis of 2‐Alkylquinolizinium‐1‐olates and Their 1,3‐Dipolar Cycloaddition Reactions with Acetylenes

Several 2‐alkylquinolizinium‐1‐olates 9 , i.e., heterobetaines, were prepared from ketone 11 , the latter being readily available either from pyridine‐2‐carbaldehyde via a Grignard reaction, followed by oxidation with MnO₂, or from 2‐picolinic acid (=pyridine‐2‐carboxylic acid) via the corresponding Weinreb amide and subsequent Grignard reaction. Mesoionic heterobetaines such as quinolizinium derivatives have the potential to undergo cycloaddition reactions with double and triple bonds, e.g., 1,3‐dipolar cycloadditions or Diels? Alder reactions. We here report on the scope and limitations of cycloaddition reactions of 2‐alkylquinolizinium‐1‐olates 9 with electron‐poor acetylene derivatives. As main products of the reaction, 5‐oxopyrrolo[2,1,5‐de]quinolizines (=‘[2.3.3]cyclazin‐5‐ones’) 19 were formed via a regioselective [2+3] cycloaddition, and cyclohexadienone derivatives, formed via a Diels? Alder reaction, were obtained as side products. The structures of 2‐benzylquinolizinium‐1‐olate ( 9a ) and two ‘[2.3.3]cyclazin‐5‐ones’ 19i and 19l were established by X‐ray crystallography.     

Unexpected Course of the Reaction of 2‐Unsubstituted 1H‐Imidazole 3‐Oxides with Ethyl Acrylate

The attempted ethenylation at C(2) of 2‐unsubstituted 1H‐imidazole N‐oxides with ethyl acrylate (=prop‐2‐enoate) in the presence of Pd(OAc)₂ does not occur. In contrast to the other aromatic N‐oxides, the [2+3] cycloaddition of imidazole N‐oxides predominates, and 3‐hydroxyacrylates, isomeric with the cycloadducts, are key products for the subsequent reaction. The final products were identified as dehydrated 2+1 adducts of 1H‐imidazole N‐oxide and ethyl acrylate. The role of the catalyst is limited to the dehydration of the intermediate 3‐hydroxypropanoates to give 1H‐imidazol‐2‐yl‐substituted acrylates.     

Total syntheses of angelicoin A, hericenone J, and hericenol A via migratory prenyl- and geranylation-aromatization sequences

A five-step synthesis of the natural product angelicoin A using a late stage highly regioselective palladium(0)-catalyzed decarboxylative prenyl migration and aromatization sequence as the key step is reported. The method was extended with geranyl migration in eight-step total syntheses of hericenone J and hericenol A from geraniol.     

Biodegradation of Polyhydroxyalkanoate Films in Natural Environments

Summary: Biodegradation of film specimens from polyhydroxyalkanoates (PHAs) of two types – poly-3-hydroxybutyrate (PHB) and poly-3-hydroxybutyrate-co-3-hydroxyvalerate (PHBV) – was analysed in different environments: tropical sea waters of the South China Sea (Nha Trang, Vietnam) and soils in the environs of Hanoi (Vietnam), Nha Trang (Vietnam) and Krasnoyarsk (Siberia, Russia). In seawater, the mass loss of the specimens of both types was almost equal. However, in tropical soils, PHB degraded quicker than PHBV. In the Siberian soil, the degradation rate of the PHBV was generally higher than that of PHBV. Analysis of molecular mass of PHA specimens showed its decreasing during biodegradation. In the tropical sea conditions, PHA degrading microorganisms were represented by bacteria of Enterobacter, Bacillus and Gracilibacillus genera. Among PHA degrading bacteria, Burkholderia, Alcaligenes, Bacillus, Mycobacterium and Streptomyces genera were identified in Vietnamese soils, and Variovorax, Stenotrophomonas, Acinetobacter, Pseudomonas, Bacillus and Xanthomonas genera in Siberian soils. Micromycetes of Gongronella, Paecilomyces, Penicillium and Trichoderma genera exhibited PHA degrading activity in Vietnamese soils, and Paecilomyces, Penicillium, Acremonium, Verticillium and Zygosporium genera – in Siberian soils.     

Euphohelioscopin A Is a PKC Activator Capable of Inducing Macrophage Differentiation

To identify small molecules that selectively control hematopoietic stem cell differentiation, we performed an unbiased screen using primary human CD34(+) cells. We identified a plant-derived natural product, euphohelioscopin A, capable of selectively differentiating CD34(+) cells down the granulocyte/monocytic lineage. Euphohelioscopin A also inhibits proliferation and induces differentiation of the myeloid leukemia cell lines THP-1 and HL-60. Mechanistic studies revealed that euphohelioscopin A is an activator of protein kinase C (PKC), and that the promonocytic effects of this natural product are mediated by PKC activation. In addition to shedding insights into normal hematopoiesis, this work may ultimately facilitate the application of stem cell therapies to a host of myeloid dysfunctions.