Free‐energy calculations of residue mutations in a tripeptide using various methods to overcome inefficient sampling

Previous free‐energy calculations have shown that the seemingly simple transformation of the tripeptide KXK to KGK in water holds some unobvious challenges concerning the convergence of the forward and backward thermodynamic integration processes (i.e., hysteresis). In the current study, the central residue X was either alanine, serine, glutamic acid, lysine, phenylalanine, or tyrosine. Interestingly, the transformation from alanine to glycine yielded the highest hysteresis in relation to the extent of the chemical change of the side chain. The reason for that could be attributed to poor sampling of φ₂/ψ₂ dihedral angles along the transformation. Altering the nature of alanine's C_β atom drastically improved the sampling and at the same time led to the identification of high energy barriers as cause for it. Consequently, simple strategies to overcome these barriers are to increase simulation time (computationally expensive) or to use enhanced sampling techniques such as Hamiltonian replica exchange molecular dynamics and one‐step perturbation. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.     

An improved synthesis of 2-(1,2,4-thiadiazol-5-yl)pyridine by interception of an intermediate involved in a competing cyclisation reaction

Reaction of thiopicolinamide with N,N′-dimethylformamide dimethyl acetal leads to the formation of 3-(dimethylamino)-1-methylthioimidazo[1,5-a]pyridine (3). However, the course of the reaction can be diverted to produce the title compound (1) in good yield by timely interception of the intermediate thioacylamidine (2).     

Coenzyme biosynthesis: enzyme mechanism, structure and inhibition

This review highlights five key reactions in vitamin biosynthesis and in particular focuses on their mechanisms and inhibition and insights from structural studies. Each of the enzymes has the potential to be a target for novel antimicrobial agents.     

Discovery of chemical reactions through multidimensional screening

Multidimensional reaction screening of ortho-alkynyl benzaldehydes with a variety of catalysts and reaction partners was conducted in an effort to identify new chemical reactions. Reactions affording unique products were selected for investigation of preliminary scope and limitations.     

Assessing the statistical validity of proteomics based biomarkers

A strategy is presented for the statistical validation of discrimination models in proteomics studies. Several existing tools are combined to form a solid statistical basis for biomarker discovery that should precede a biochemical validation of any biomarker. These tools consist of permutation tests, single and double cross-validation. The cross-validation steps can simply be combined with a new variable selection method, called rank products. The strategy is especially suited for the low-samples-to-variables-ratio (undersampling) case, as is often encountered in proteomics and metabolomics studies. As a classification method, principal component discriminant analysis is used; however, the methodology can be used with any classifier. A dataset containing serum samples from Gaucher patients and healthy controls serves as a test case. Double cross-validation shows that the sensitivity of the model is 89% and the specificity 90%. Potential putative biomarkers are identified using the novel variable selection method. Results from permutation tests support the choice of double cross-validation as the tool for determining error rates when the modelling procedure involves a tuneable parameter. This shows that even cross-validation does not guarantee unbiased results. The validation of discrimination models with a combination of permutation tests and double cross-validation helps to avoid erroneous results which may result from the undersampling.     

When is H2O not water?

We have combined a computational search strategy with first-principles density-functional-theory calculations to identify metastable phases of H(2)O under pressure. The most stable structures consist of water molecules, while the most energetic metastable phases consist of oxygen and hydrogen molecules. In between lie many other metastable phases, consisting of various combinations of a few small molecules. It may be possible to synthesize some of these metastable phases, and we use our results to understand the nature of the crystalline metastable phase of H(2)O recently synthesized by Mao et al. [Science 314, 636 (2006)].     

Zero electron kinetic energy spectroscopy of the para-fluorotoluene cation

Zero electron kinetic energy (ZEKE) spectroscopy is employed to gain information on the vibrational energy levels of the para-fluorotoluene (pFT) cation. Vibrationally resolved spectra are obtained following excitation through a range of intermediate vibrational energy levels in the S1 state. These spectra allow the observation of different cationic vibrational modes, whose assignment is achieved both from a knowledge of the S1 vibrational states and also by comparison with density functional calculations. In one notable case, clean ZEKE spectra were obtained from two overlapped S1 features. From the authors' data, the adiabatic ionization energy of pFT was derived as 70,946+/-4 cm(-1). The information on the cationic energy levels obtained will be useful in untangling the intramolecular vibrational redistribution dynamics of pFT in the S1 state.     

The total synthesis of neoamphimedine

Neoamphimedine, a pyridoacridine alkaloid from Xestospongia sp., is a potent antitumor agent both in vitro and in vivo. Neoamphimedine can efficiently induce topoisomerase II mediated catenation of plasmid DNA in vitro and is the only member of more than one hundred pyridoacridines thus far to have this mechanism of action. Herein we report the first total synthesis of neoamphimedine.     

Tandem Pd(II)-catalyzed vinyl ether exchange-Claisen rearrangement as a facile approach to gamma,delta-unsaturated aldehydes

A sequential allyl vinyl ether formation-Claisen rearrangement process catalyzed by a palladium(II)-phenanthroline complex is reported. The effects of allylic alcohol structure, type of vinylating agent, and palladium catalysts are discussed. This method provides a convenient approach to gamma,delta-unsaturated aldehydes under mild conditions that avoid the use of toxic Hg(II) catalysts. The new methodology has been successfully demonstrated on the kilogram scale.     

Artificial Neural Networks for Noise Removal in Data-Sparse Charged Particle Imaging Experiments

We present the first demonstration of artificial neural networks (ANNs) for the removal of Poissonian noise in charged particle imaging measurements with very low overall counts. The approach is successfully applied to both simulated and real experimental image data relating to the detection of photoions/photoelectrons in unimolecular photochemical dynamics studies. Specific examples consider the multiphoton ionization of pyrrole and (S)-camphor. Our results reveal an extremely high level of performance, with the ANNs transforming images that are unusable for any form of quantitative analysis into statistically reliable data with an impressive similarity to benchmark references. Given the widespread use of charged particle imaging methods within the chemical dynamics community, we anticipate that the use of ANNs has significant potential impact – particularly, for example, when working in the limit of very low absorption/photoionization cross-sections, or when attempting to reliably extract subtle image features originating from phenomena such as photofragment vector correlations or photoelectron circular dichroism.