Optimization of a genetic algorithm for searching molecular conformer space

We present two sets of tunings that are broadly applicable to conformer searches of isolated molecules using a genetic algorithm (GA). In order to find the most efficient tunings for the GA, a second GA--a meta-genetic algorithm--was used to tune the first genetic algorithm to reliably find the already known a priori correct answer with minimum computational resources. It is shown that these tunings are appropriate for a variety of molecules with different characteristics, and most importantly that the tunings are independent of the underlying model chemistry but that the tunings for rigid and relaxed surfaces differ slightly. It is shown that for the problem of molecular conformational search, the most efficient GA actually reduces to an evolutionary algorithm.     

An enantioselective formal synthesis of berkelic acid

An enantioselective formal synthesis of berkelic acid is described. The key step involves a late-stage silyl enol ether addition to a benzannulated oxonium ion with subsequent spiroketalization leading to construction of the tetracyclic core. Thermodynamically controlled equilibration under acidic conditions affords the desired spiroketal configuration as a single diastereoisomer.     

Checking key integrity efficiently for high-speed quantum key distribution using combinatorial group testing

With the increasing key generation rate in practical quantum key distribution, checking key integrity efficiently becomes an important problem. Since the original method that utilizes one hash value for a key string has to discard all the key bits even if just one error bit exists, it may eventually limit the practical rate of key generation. In this paper, we propose a new scheme based on combinatorial group testing to identify the rare error bits so as to avoid dropping all the key bits. Experimental results show that the scheme can precisely locate the error bits if the number of error bits is within the maximum guaranteed number set by the scheme while the overhead is insignificant (for a 10⁶-bit key, additional bits: 0.1% of the key; hashing time: 16 ms; checking time: 22 ms) and it can still keep the majority of the correct bits (95%) even if the number of error bits is 10 times of the maximum. The results also indicate that the minimum key size for the CGT-based scheme to gain an advantage over the original method is about 2 × 10⁴ bits.     

Reassessment of N2 activation by low-valent Ti-amide complexes: a remarkable side-on bridged bis-N2 adduct is actually an arene adduct

The complex {(TMEDA)₂Li}{[Ti(N(TMS)₂)₂]₂(μ-η²:η²-N₂)₂} (5-Li) is the only transition metal N₂ complex ever reported with two side-on N₂ adducts. In this report, the similarity of 5-Li to a new inverse sandwich toluene adduct {(PhMe)K}{[Ti(N(TMS)₂)₂]₂(μ-PhMe)} (6-K) necessitated a re-examination of the structure of 5-Li. Through a reassessment of the original disordered crystal data of 5-Li and new independent syntheses brought about through revisitation of the original reaction conditions, 5-Li has been re-assigned as an inverse sandwich toluene adduct, {(TMEDA)₂Li}{[Ti(N(TMS)₂)₂]₂(μ-PhMe)} (6-Li). The original crystal data could be fitted almost equally well to structural solutions as either 5-Li or 6-Li, and this study highlights the importance of a holistic examination of modeled data and the need for secondary/complementary analytical methods in paramagnetic inorganic syntheses, especially when presenting unique and unexpected results. In addition, further examination of reduction reactions of Ti[N(TMS)₂]₃ and [(TMS)₂N]₂TiCl(THF) in the presence of KC₈ revealed rich solvent- and counterion-dependent chemistry, including several degrees of N₂ activation (bridging nitride complexes, terminal bridging N₂ complexes) as well as ligand C–H activation.

The complex {(TMEDA)₂Li}{[Ti(N(TMS)₂)₂]₂(μ-η²:η²-N₂)₂} (5-Li) was the only transition metal N₂ complex ever reported with two side-on N₂ adducts. Reanalysis of 5-Li has revealed that it is an inverse-sandwich toluene adduct, not an N₂ adduct.     

Biopolymers as a Flexible Resource for Nanochemistry

Biomass is an abundant source of chemically diverse macromolecules, including polysaccharides, polypeptides, and polyaromatics. Many of these biological polymers (biopolymers) are highly evolved for specific functions through optimized chain length, functionalization, and monomer sequence. As biopolymers are a chemical resource, much current effort is focused on the breakdown of these molecules into fuels or platform chemicals. However there is growing interest in using biopolymers directly to create functional materials. This Minireview uses recent examples to show how biopolymers are providing new directions in the synthesis of nanostructured materials.     

Differential effects of cholesterol, ergosterol and lanosterol on a dipalmitoyl phosphatidylcholine membrane: a molecular dynamics simulation study

Lipid raft/domain formation may arise as a result of the effects of specific sterols on the physical properties of membranes. Here, using molecular dynamics simulation, we examine the effects of three closely-related sterols, ergosterol, cholesterol, and lanosterol, at a biologically relevant concentration (40 mol %) on the structural properties of a model dipalmitoyl phosphatidylcholine (DPPC) membrane at 309 and 323 K. All three sterols are found to order the DPPC acyl tails and condense the membrane relative to the DPPC liquid-phase membrane, but each one does this to a significantly different degree. The smooth alpha-face of ergosterol, together with the presence of tail unsaturation in this sterol, leads to closer interaction of ergosterol with the lipids and closer packing of the lipids with each other, so ergosterol has a higher condensing effect on the membrane, as reflected by the area per lipid. Moreover, ergosterol induces a higher proportion of trans lipid conformers, a thicker membrane, and higher lipid order parameters and is aligned more closely with the membrane normal. Ergosterol also positions itself closer to the bilayer/water interface. In contrast, the rough alpha-face of lanosterol leads to a less close interaction of the steroid ring system with the phospholipid acyl chains, and so lanosterol orders, straightens, and packs the lipid acyl chains less well and is less closely aligned with the membrane normal. Furthermore, lanosterol lies closer to the relatively disordered membrane center than do the other sterols. The behavior of cholesterol in all the above respects is intermediate between that of lanosterol and ergosterol. The findings here may explain why ergosterol is the most efficient of the three sterols at promoting the liquid-ordered phase and lipid domain formation and may also furnish part of the explanation as to why cholesterol is evolutionarily preferred over lanosterol in higher-vertebrate plasma membranes.