Non-overlapping Common Substrings Allowing Mutations

This paper studies several combinatorial problems arising from finding the conserved genes of two genomes (i.e., the entire DNA of two species). The input is a collection of n maximal common substrings of the two genomes. The problem is to find, based on different criteria, a subset of such common substrings with maximum total length. The most basic criterion requires that the common substrings selected have the same ordering in the two genomes and they do not overlap among themselves in either genome. To capture mutations (transpositions and reversals) between the genomes, we do not insist the substrings selected to have the same ordering. Conceptually, we allow one ordering to go through some mutations to become the other ordering. If arbitrary mutations are allowed, the problem of finding a maximum-length, non-overlapping subset of substrings is found to be NP-hard. However, arbitrary mutations probably overmodel the problem and are likely to find more noise than conserved genes. We consider two criteria that attempt to model sparse and non-overlapping mutations. We show that both can be solved in polynomial time using dynamic programming.      

Efficient catalytic oxidation of alkanes by Lewis acid/[Os(VI)(N)Cl4]- using peroxides as terminal oxidants. Evidence for a metal-based active intermediate

The oxidation of alkanes by various peroxides ((t)BuOOH, H2O2, PhCH2C(CH3)2OOH) is efficiently catalyzed by [Os(VI)(N)Cl4](-)/Lewis acid (FeCl3 or Sc(OTf)3) in CH2Cl2/CH3CO2H to give alcohols and ketones. Oxidations occur rapidly at ambient conditions, and excellent yields and turnover numbers of over 7500 and 1000 can be achieved in the oxidation of cyclohexane with (t)BuOOH and H2O2, respectively. In particular, this catalytic system can utilize PhCH2C(CH3)2OOH (MPPH) efficiently as the terminal oxidant; good yields of cyclohexanol and cyclohexanone (>70%) and MPPOH (>90%) are obtained in the oxidation of cyclohexane. This suggests that the mechanism does not involve alkoxy radicals derived from homolytic cleavage of MPPH but is consistent with heterolytic cleavage of MPPH to produce a metal-based active intermediate. The following evidence also shows that no free alkyl radicals are produced in the catalytic oxidation of alkanes: (1) The product yields and distributions are only slightly affected by the presence of O2. (2) Addition of BrCCl3 does not affect the yields of cyclohexanol and cyclohexanone in the oxidation of cyclohexane. (3) A complete retention of stereochemistry occurs in the hydroxylation of cis- and trans-1,2-dimethylcyclohexane. The proposed mechanism involves initial O-atom transfer from ROOH to [Os(VI)(N)Cl4](-)/Lewis acid to generate [Os(VIII)(N)(O)Cl4](-)/Lewis acid, which then oxidizes alkanes via H-atom abstraction.     

Synthesis, characterization, and DFT/TD-DFT calculations of highly phosphorescent blue light-emitting anionic iridium complexes

Highly phosphorescent blue-light-emitting anionic iridium complexes (C4H9)4N[Ir(2-phenylpyridine)2(CN)2] (1), (C4H9)4N[Ir(2-phenyl-4-dimethylaminopyridine)2(CN)2] (2), (C4H9)4N[Ir(2-(2,4-difluorophenyl)-pyridine)2(CN)2] (3), (C4H9)4N[Ir(2-(2,4-difluorophenyl)-4-dimethylaminopyridine)2(CN)2] (4), and (C4H9)4N[Ir(2-(3,5-difluorophenyl)-4-dimethylaminopyridine)2(CN)2] (5) were synthesized and characterized using NMR, UV-vis absorption, and emission spectroscopy and electrochemical methods. In these complexes color and quantum yield tuning aspects are demonstrated by modulating the ligands with substituting donor and acceptor groups on both the pyridine and phenyl moieties of 2-phenylpyridine. Complexes 1-5 display intense photoluminescence maxima in the blue region of the visible spectrum and exhibit very high phosphorescence quantum yields, in the range of 50-80%, with excited-state lifetimes of 1-4 micros in acetonitrile solution at 298 K. DFT and time dependent-DFT calculations were performed on the ground and excited states of the investigated complexes to provide insight into the structural, electronic, and optical properties of these systems.     

Front Cover: Synthesis,Characterization, and Cytotoxicity of a Reactive Platinum(IV) Monotrifluoromethyl Complex (Eur. J. Inorg. Chem. 3/2023)

Platinum-based complexes are among the most widely utilized cancer therapeutics. Current Pt(II) drugs face some challenges including toxicity and drug resistance. To solve these issues, great efforts have been devoted to developing nonclassical platinum complexes, such as Pt(IV) prodrugs, that act via mechanisms distinct from those of the approved drugs. Compared with active Pt(II) counterparts, Pt(IV) complexes are relatively inert. Although direct interactions between Pt(IV) complexes and nucleotides have been reported, the reaction is slow due to the kinetic inertness of Pt(IV) complexes. Herein, we design and synthesize a Pt(IV) monotrifluoromethyl complex, in which the chloride ligand that is trans to trifluoromethyl ligand is reactive. The Pt(IV) monotrifluoromethyl complex is very stable in water but displays high reactivity towards various substrates including buffer components and 5’-dGMP. The study of reaction mechanism reveals that this Pt(IV) complex reacts with phosphate via S_N2 nucleophilic substitution pathway, which is different from Pt(II) drugs. The Pt(IV) monotrifluoromethyl complex is cytotoxic in human ovarian cancer cells. Our work reports an example of a reactive organometallic Pt(IV) complex that can directly interact with nucleophiles and implies its potential as an anticancer agent.     

The effect of sound level on perception of reproduced soundscapes

The aim of this work was to investigate the perception of soundscape reproduced by an ambisonic reproduction system on a horizontal plane, how the experience of space affected the perception of soundscape reproduction, and how the sound level adjustment on soundscape reproduction affected the perception of soundscape compared with actual conditions. There were three experiments conducted: a soundwalk in situ in Manchester (United Kingdom) city centre, listening tests in Salford (United Kingdom), and listening tests in Bandung (Indonesia). The listening tests used material recorded from four locations on the soundwalk route in Manchester. The Salford listening tests were performed at the in-situ measured sound level, and the participants were asked to adjust the sound level to the level that represents actual locations. The listening test in Bandung was conducted to understand the effect of participants who never come to the actual location to the perception of soundscape and the sound level adjustment. The listening tests in Bandung were conducted at the in situ sound level, at 9.5 dB below the in situ sound level (based on the preference sound level from the experiment in Salford), and the participants were also requested to adjust the sound level to the level that represents the actual space (to examine the consistency with the experiment in Salford). In each case, soundscape perception was measured on 19 semantic differential scales. Analysis of the semantic differential results showed that the ambisonic reproduction produced a similar subjective experience to the in situ soundwalk when the reproduction sound level was 9.5 dB lower than the actual sound level in situ. Reproduction at the actual sound level in situ produced a different dimensional space. The study shows that the sound level adjustment of soundscape reproduction in laboratory experiment produces more ecologically valid results compared to the reproduction at the actual sound level in situ.     

Positive curvature effects and interparticle capillary condensation during nitrogen adsorption in particulate porous materials

The adsorption of nitrogen in a collection of spheres that touch or merge in a sintering-like manner is modeled using a Derjaguin-Broeckhof-de Boer approach. The proposed model accounts for both positive curvature effects and for capillary condensation at the contact between two spheres. A methodology is proposed to fit the P/P(0)>0.4 adsorption region with the coordination number of the spheres as the only adjustable parameter. The use of the model is illustrated on a series of silica aerogels. The suitability of various standard isotherms needed for the modeling is also discussed.     

Surface functionalization of polymer latex particles. II. Catalytic oxidation of poly(methylstyrene) latexes in the presence of cetyltrimethylammonium bromide

Surface-functionalized cationic poly(methylstyrene) (PMS) latex particles containing aldehyde and carboxylic acid groups were successfully achieved via an emulsion polymerization of 3(4)-methylstyrene in the presence of cetyltrimethylammonium bromide, followed by an in-situ oxidation catalyzed by copper chloride and tert-butyl hydroperoxide (t-BuOOH). Factors such as the type of metal catalyst, oxidant, and their concentration strongly affected the rate of oxidation. Step addition of t-BuOOH resulted in both a higher degree of oxidation and a more uniform distribution of particle size of the functionalized PMS as compared to the batch addition method. The effect of organic solvent was found to be insignificant, and the oxidation could still proceed in its absence. The particle sizes increased significantly during the oxidation but could be controlled by using crosslinked PMS latexes. Finally, the versatility of this oxidation process was demonstrated by oxidation of the polymer with a solid loading as high as 28%. © 1997 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 35 : 3585–3593, 1997     

Simultaneous measurement of proline and related compounds in oak leaves by high-performance ligand-exchange chromatography and electrospray ionization mass spectrometry for environmental stress studies

A mass spectrometer was coupled to high-performance ligand-exchange liquid chromatography (HPLEC) for simultaneous analysis of stress associated solutes such as proline, hydroxyproline, methylproline, glycine betaine and trigonelline extracted from leaves of drought stressed oaks and an internal standard namely N-acetylproline. Methanol/chloroform/water extracts were analyzed using an Aminex HPX-87C column and specifically quantified by the positive ion mode of an electrospray ionisation-mass spectrometry (ESI-MS) in single ion monitoring (SIM) mode. The recovery of N-acetyl proline added to oak leaf extracts ranged from 85.2 to 122.1% for an intra-day study. Standard calibration curves showed good linearity in the measured range from 0.3125 to 10 μmol L⁻¹ with the lowest correlation coefficient of 0.99961 for trigonelline. The advantages of this alternative procedure, compared to previously published methods using fluorescence or amperometric detections, are the simultaneous and direct detection of osmoprotectants in a single chromatographic run, a minimal sample preparation, a good specificity and reduced limits of quantification, ranging from 0.1 to 0.6 μmol L⁻¹. Fifty-six days of water deficit exposure resulted in increased foliar free proline levels (2.4-fold, P < 0.001, 155 μmol g⁻¹ FW) and glycine betaine contents (2.5-fold, P < 0.05, 175 μmol g⁻¹ FW) of drought stressed oak compared to control.     

An improvement on Marotto’s theorem and its applications to chaotification of switching systems

The controversy surrounding the correctness of Marotto’s theorem continues over the last two decades, with many researchers claiming to have found an error in the proof. In this paper, we show that Marotto’s theorem is indeed correct for analyzing the existence of chaos in the sense of Li-Yorke even after relaxing certain assumptions in the proof. In addition, we extend the theory to derive the conditions for the existence of chaos in the sense of Devaney. We show that these results can be applied to study the chaotification of linear switching systems.