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The yield of a chemical reaction is obtained by solving its rate equation. This study introduces an approach for differentiating yields by utilizing the parameters of the rate equation, which is expressed as a first-order linear differential equation. The yield derivative for a specific pair of reactants and products is derived by mathematically expressing the rate constant matrix contraction method, which is a simple kinetic analysis method. The parameters of the rate equation are the Gibbs energies of the intermediates and transition states in the reaction path network used to formulate the rate equation. Thus, our approach for differentiating the yield allows a numerical evaluation of the contribution of energy variation to the yield for each intermediate and transition state in the reaction path network. In other words, a comparison of these values automatically extracts the factors affecting the yield from a complicated reaction path network consisting of numerous reaction paths and intermediates. This study verifies the behavior of the proposed approach through numerical experiments on the reaction path networks of a model system and the Rh-catalyzed hydroformylation reaction. Moreover, the possibility of using this approach for designing ligands in organometallic catalysts is discussed.

Complex chromosomal rearrangements (CCRs) are often observed in clinical samples from patients with cancer and congenital diseases but are difficult to induce experimentally. Here, we report the first success in establishing animal models for CCRs. Mutation in Recql5, a crucial member of the DNA helicase RecQ family involved in DNA replication, transcription, and repair, enabled CRISPR/Cas9-mediated CCRs, establishing a mouse model containing triple fusion genes and megabase-sized inversions. Some of these structural features of individual chromosomal rearrangements use template switching and microhomology-mediated break-induced replication mechanisms and are reminiscent of the newly described phenomenon “chromoanasynthesis.” These data show that Recql5mutant mice could be a powerful tool to analyze the pathogenesis of CCRs (particularly chromoanasynthesis) whose underlying mechanisms are poorly understood. The Recql5mutants generated in this study are to be deposited at key animal research facilities, thereby making them accessible for future research on CCRs.Researchers have created animal models to study complex chromosomal rearrangements linked to cancer and congenital diseases by altering the Recql5gene in mice. This breakthrough, using CRISPR/Cas9 technology, allows for detailed examination of genetic disruptions often seen in these conditions. The genetically modified mice offer a new resource for understanding and researching complex genetic issues.

Generalized root mean square deviation (G-RMSD) is an optimization method for three-dimensional molecular similarity determination. It calculates the minimum value of RMSD among all the possible one-to-one matchings between the atoms and positions of the molecules. The first paper on G-RMSD introduced two approaches called alternating optimization (AO) and tangent space relaxation (TSR) methods, which give local optimum solutions. We propose here a new method of G-RMSD using a branch-and-bound method (BnB) on isometric transformations, called IsometryOpt, which is mathematically proven to give an exact G-RMSD index, i.e. this method can reach the global optimum solution. The performance of IsometryOpt was compared to AO and TSR, as well as the MatchFastOpt method. IsometryOpt shows better performance than MatchFastOpt for molecules with the same number of atoms. AO and TSR fail to reach exact values in some cases. We also have developed two improved methods to search for all possible matches of a substructure in one or more molecules. One is called IsometrySearch, which uses BnB on isometric transformations. The other is a variant version of MatchFPT, called MatchFPT-delta. Computer experiments indicate that MatchFPT-delta performs better than MatchFPT and IsometrySearch.Generalized root mean square deviation (G-RMSD) is an optimization method for three-dimensional molecular similarity determination. It calculates the minimum RMSD values without fixing both, atom mapping and superimposition. We propose a new method of G-RMSD using a branch-and-bound method which is mathematically proven to give an exact solution of the G-RMSD index.

We present the Generalized Root Mean Square Deviation (G-RMSD) method. G-RMSD is an optimization method to calculate the minimal RMSD value of two atomic structures by optimal superimposition. G-RMSD is not restricted to systems with an equal number of atoms to compare or a unique atom mapping between two molecules. The method can handle any type of chemical structure, including transition states and structures which cannot be explained only with valence bond (VB) theory (non-VB structures). It requires only Cartesian coordinates for the structures. Further information, i.e. atom- and bond types can also be included. Applications of G-RMSD to the classification of α-d-glucose conformers and 3D partial structure search using a dataset containing equilibrium (EQ), dissociation channel (DC), and transition state (TS) structures are demonstrated. We find that G-RMSD allows for a successful classification and mapping for a wide variety of molecular structures.G-RMSD, an optimization method to calculate the minimal RMSD (Root Mean Square Deviation) value of two atomic structures by optimal superimposition, solves a problem of comparing 3D-molecules of different size without a unique atom mapping. It was successfully applied to searching a quantum mechanical based reaction pathway database containing not only equilibrium structures, but also transition state and non-valence structures.

Novel photosensitized trifluoromethylthiazole-5-carboxylic acid dyes having different numbers of thiophene π-conjugation spacers (MCL15, MCL17, and MCL19) and a benzodithiophene spacer with long alkyl side chains (MCL40) are synthesized. The resulting extension of the π-conjugation system leads to redshift in the absorption wavelength. The long alkyl side chains of benzodithiophene cause a dispersed aggregation effect; therefore, the co-adsorbent becomes unnecessary for dye-sensitized solar cell (DSSC) fabrication. The DSSCs fabricated using these dyes exhibit increased conversion efficiency compared with those without a thiophene unit (MCL05).Novel photosensitized trifluoromethylthiazole-5-carboxylic acid dyes having different numbers of thiophene π-conjugation spacers (MCL15, MCL17, and MCL19) and a benzodithiophene spacer with long alkyl side chains (MCL40) were synthesized. The long alkyl side chains of benzodithiophene caused a dispersed aggregation effect. It was found that all dyes exhibited a high IPCE of 85% or more with a wide wavelength range.

The membrane trafficking events that regulate unicellular tube formation and maintenance are not well understood. Here, using an RNAi screen, we identified the small GTPase ARF1 homolog ARF-1.2 as a regulator of excretory tube formation in Caenorhabditis elegans. RNAi-mediated knockdown and knockout of the arf-1.2gene resulted in the formation of large intracellular vacuoles at the growth sites (varicosities) of the excretory canals. arf-1.2mutant animals were sensitive to hyperosmotic conditions. arf-1.2RNAi affected the localization of the anion transporter SULP-8, which is expressed in the basal plasma membrane of the excretory canals, but did not affect the expression of SULP-4, which is expressed in the apical membrane. The phenotype of arf-1.2mutants was suppressed by mutation of the small Rho GTPase CDC-42, a regulator of apical/basal traffic balance. These results suggest that ARF-1.2 plays an essential role in basal membrane traffic to regulate the formation of the unicellular excretory tube.

Balancer chromosomes are critical tools for genetic research. In C. elegans, reciprocal translocations that lead to aneuploidy have been widely used to maintain lethal and sterile mutations in stable stocks. Here, we generated a set of aneuploidy-free and structurally defined crossover suppressors that contain two overlapping inversions using the CRISPR/Cas9 system. The toolkit includes 13 crossover suppressors and covers approximately 63% of all C. eleganscoding genes. Together with the classical intrachromosomal crossover suppressors, the system now covers 89% of the coding genes. We also labeled the created balancers with fluorescent and phenotypic markers. We show that the crossover suppressors are better for embryonic analysis compared with translocational balancers. Additionally, we demonstrate an efficient method to generate lethal alleles by targeting essential genes on a chromosome balanced with a crossover suppressor. The toolkit will allow more efficient experiments in which lethal and sterile mutants can be analyzed.

This paper describes our approach that is built upon the potential energy surface (PES)-based conformational analysis. This approach automatically deduces a conformational transition network, called a conformational reaction route map(r-map), by using the Scaled Hypersphere Search of the Anharmonic Downward Distortion Followingmethod (SHS-ADDF). The PES-based conformational search has been achieved by using large ADDF, which makes it possible to trace only low transition state (TS) barriers while restraining bond lengths and structures with high free energy. It automatically performs sampling the minima and TS structures by simply taking into account the mathematical feature of PES without requiring any a priori specification of variable internal coordinates. An obtained r-map is composed of equilibrium (EQ) conformers connected by reaction routes via TS conformers, where all of the reaction routes are already confirmed during the process of the deduction using the intrinsic reaction coordinate (IRC) method. The postcalculation analysis of the deduced r-map is interactively carried out using the RMapViewer software we have developed. This paper presents computational details of the PES-based conformational analysis and its application to d-glucose. The calculations have been performed for an isolated glucose molecule in the gas phase at the RHF/6-31G level. The obtained conformational r-map for α-d-glucose is composed of 201 EQ and 435 TS conformers and that for β-d-glucose is composed of 202 EQ and 371 TS conformers. For the postcalculation analysis of the conformational r-maps by using the RMapViewer software program we have found multiple minimum energy paths (MEPs) between global minima of 1C4and 4C1chair conformations. The analysis using RMapViewer allows us to confirm the thermodynamic and kinetic predominance of 4C1conformations; that is, the potential energy of the global minimum of 4C1is lower than that of 1C4(thermodynamic predominance) and that the highest energy of those of all the TS structures along a route from 4C1to 1C4is lower than that of 1C4to 4C1(kinetic predominance).

A new 1:1 alternating copolymerization of a five-membered, six-membered, and seven-membered cyclic germylene having a Me3Si-N group with N-phenyl-p-quinoneimine has successfully been demonstrated. The germylenes behaved as a reductant monomer whereas N-phenyl-p-quinoneimine as an oxidant monomer to give copolymers (oxidation-reduction copolymerization). In contrast to the previous observation that the copolymerization of cyclic germylenes with p-benzoquinone led to the formation of 2:1 periodic copolymers, the present copolymerization using a p-quinoneimine derivative produces all 1:1 alternating copolymers.

The germylenes bis[bis(trimethylsilyl)amido]germanium (1a) and bis[t-butyl-trimethylsilyl]amido]germanium (1b) were reacted with N-phenyl-p-quinoneimine (2) to give copolymers (3aand 3b) with alternating tetravalent germanium and p-aminophenol units. The copolymerization took place smoothly at 0°C without added catalyst or initiator. 1acted as a reductant monomer, and 2acted as an oxidant monomer (oxidation-reduction alternating copolymerization). Product copolymers were obtained in very high yields and had high molecular weights. The copolymers were soluble in toluene, benzene, n-hexane and chloroform, whereas they were insoluble in acetonitrile and acetone. Additionally, they were stable toward hydrolytic degradation. Electron spin resonance (ESR) spectroscopic studies of the reaction suggested a structure of a stable germyl radical and a plausible mechanism of biradical copolymerization.

23,4,5,6Tetrafluoro2hydroxyphenylimidazo1,2apyridine 1 emits long wavelength light around 540 nm both in polar and in nonpolar solvents. Zn2perchlorate in acetonitrile causes the intermediate wavelength emission around 430 nm, which is ascribed to the species where the imidazole nitrogen atom and the phenolate oxygen atom bridge Zn2. In the presence of Hg2and Al3perchlorates, short wavelength emission around 370 nm is strongly increased and this fluorescent enhancement is attributable not to the coordination of Hg2and Al3to 1but to the formation of the salt of perchloric acid of 1.

Tutte associates a V by V skew-symmetric matrix T, having indeterminate entries, with a graph G=(V,E). This matrix, called the Tutte matrix, has rank exactly twice the size of a maximum cardinality matching of G. Thus, to find the size of a maximum matching it suffices to compute the rank of T. We consider the more general problem of computing the rank of T + K where K is a real V by V skew-symmetric matrix. This modest generalization of the matching problem contains the linear matroid matching problem and, more generally, the linear delta-matroid parity problem. We present a tight upper bound on the rank of T + K by decomposing T + K into a sum of matrices whose ranks are easy to compute.

This paper presents a new algorithm for computing the maximum degree δk (A) of a minor of order k in a matrix pencil A(s) . The problem is of practical significance in the field of numerical analysis and systems control. The algorithm adopts a general framework of ``combinatorial relaxation'' due to Murota. It first solves the weighted bipartite matching problem to obtain an estimate $\hat{\delta}_k(A)$ on δk (A) , and then checks if the estimate is correct, exploiting the optimal dual solution. In case of incorrectness, it modifies the matrix pencil A(s) to improve the estimate $\hat{\delta}_k(A)$ without changing δk(A) . The present algorithm performs this matrix modification by an equivalence transformation with constant matrices, whereas the previous one uses biproper rational function matrices. Thus the present approach saves memory space and reduces the running time bound by a factor of rank A.

This paper presents two fast cycle canceling algorithms for the submodular ?ow problem. The ?rst uses an assignment problem whose optimal solution identi?es most negative node-disjoint cycles in an auxiliary network. Canceling these cycles lexicographically makes it possible to obtain an optimal submodular ?ow in O( n 4 h log( nC)) time, which almost matches the current fastest weakly polynomial time for submodular flow (where n is the number of nodes, h is the time for computing an exchange capacity, and C is the maximum absolute value of arc costs). The second algorithm generalizes Goldberg’s cycle canceling algorithm for min cost flow to submodular flow to also get a running time of O( n 4 h log( nC)).. We show how to modify these algorithms to make them strongly polynomial, with running times of O( n 6 h log n), which matches the fastest strongly polynomial time bound for submodular flow. We also show how to extend both algorithms to solve submodular flow with separable convex objectives.

2‐(3,4,5,6‐Tetrafluoro‐2‐hydroxyphenyl)benzoxazole (2) emits the long wavelength fluorescence around 500 nm in nonpolar solvent viathe intramolecular proton transfer process in the excited state of 2(enol‐form) and also emits the intermediate wavelength fluorescence around 440 nm in polar solvent, which is assumed to originate from the excited state of 2(anion). The ease of formation of 2(anion), compared to 2‐(2‐hydroxyphenyl)benzoxazole (1), is explained by the strongly inductive fluorine atoms. In a solvent with the intermediate polarity, 2emits both fluorescences and their relative intensity is dependent on the concentration of 2, which is supposed to be caused by the high sensitivity of the intermediate wavelength emission to the concentration quenching.

Novel photosensitized dyes having trifluoromethylacrylic acid as an acceptor-anchor moiety (MCL26–29) are synthesized. These dyes seem to suppress the back-donation currents from the conduction band of TiO2semiconductor to the electrolyte. Their fabricated dye-sensitized solar cells (DSCs) show high IPCE performances (MCL27; over 80% between 400–520 nm, max 90% at 465 nm). In particular, the high IPCE properties are compared with more than 80 article examples.

5,15-cis-Bis(2-trifluoroacetamidophenyl)porphyrin 2c and its pentafluorobenzamidophenyl analogue 2e have significant recognising ability for p-benzoquinone 3a, which is explained by the large negative enthalpy change of the 2c–3a complex and by the small entropy change of the 2e–3a complex, respectively. Porphyrin 2e recognises electron-rich p-benzoquinone more effectively than electron-deficient p-benzoquinone, which is ascribed to the enthalpy change of the complexation induced by the hydrogen bonding of amide protons of 2e with oxygen atoms of the substituted p-benzoquinone.

AbstractMetal Complexes of 5-[3′-(12-crown-4)methyloxy-carbonylphenyl]-15-phenylporphyrin (H2-MCEPP) are synthesized as the hosts which have two receptor sites, the crown ether moiety being for cations and the porphyrin-metal site for the counter anions. Cation or anion recognition is highly dependent on the porphyrin-metal; that is, the zinc complex (Zn-MCEPP) recognizes anions preferentially and, on the contrary, the magnesium complex (Mg-MCEPP) recognizes cations more effectively.

This paper discusses the principal structure of submodular systems due to S. Fujishige. It is shown that the principal structure is the coarsest decomposition that is finer than any decomposition induced by the principal partition with respect to a minimal nonnegative superbase. The concept of “Hitchcock-type independent flow” is introduced so that previously known results on the principal structures for bipartite matchings, layered mixed matrices and independent matchings can be understood as applications of the present result.

Abstract: This paper presents a scaling scheme for submodular functions. A small but strictly submodular function is added before scaling so that the resulting functions should be submodular. This scaling scheme leads to a weakly polynomial algorithm to solve minimum cost integral submodular flow problems with separable convex cost functions, provided that an oracle for exchange capacities is available.

2,3,6,7-Tetrahydro-1,4,5,8-tetrathiaanthracene (HTA), 9-amino-HTA, 9-acetyl-HTA, 9,10-dimethyl-HTA, and 1,4,5,8-tetrathiaanthracene have been synthesized. Electrochemical properties and preparation of the charge transfer complexes of HTAs with several acceptors are also reported.

Lithiation of 3,5-dimethyl- and 5-trifluoromethyl-1-phenylpyrazoles with butyllithium is found to be directed to an orthoposition. The orthodirection is ascribed to coordination of lithium with pyrazole 2-nitrogen or 5-trifluoromethyl group, respectively.

3,4-Dihydroisoquinoline N-oxide (1) cycloadded with methyl 4,4,4-trifluoro-2-butenoate at 20 °C to give a mixture of the cycloadduct with a 1,10b-cis-configuration, methyl (1R*, 2R*, 10bR*)-2-trifluoromethyl-1,5,6,10b-tetrahydro-2 H-isoxazolo[3,2-a]isoquinoline-1-carboxylate, and its stereoisomer with a 1,10b-trans-configuration in a ratio of 3 : 1. Nitrone 1cycloadded with methyl 2-butenoate to afford the cycloadduct with a 1,10b-cis-configuration exclusively. The stereoselectivity in the cycloadditions was reproduced by calculations of the transition structures by the PM3 method.

The cation radicals of 2,3,6,7-tetrahydro-1,4,5,8-tetrathiaanthracene (HTA) and 2,3,6,7-tetrathia-1,4,5,8-tetrathiaphenanthrene (HTP) have been characterized by ESR spectroscopy. The remarkable alternating linewidth effects were observed in the spectra of HTA+•and HTP+•both in concd H2SO4and in AlCl3/CH3NO2.

Additions of various carbanion nucleophiles to 3,3,3-trifluoro-1-nitropropene (1) proceeded regiospecifically at the C-2 position of 1to give the corresponding adducts. The nitro group of the adducts, derived from the reactions with acetylacetone and ethyl acetoacetate, was reduced to the corresponding amines, which were cyclized in situ to the 3-(trifluoromethyl)pyrrole derivatives.

Novel photosensitized dyes containing 4-trifluoromethylthiazole-5-carboxylic acid as an acceptor are synthesized. Stilbene-type dyes with this acceptor show high performance as dye-sensitized solar cells. The trifluoromethyl group is assumed to act as a suppressor of electron back-donation from the TiO2conduction band to the electrolyte and as an accelerator of charge separation in the photoexcited state.

The peak potentials Ep of 3substituted pyrido1′,2′:1,2imidazo4,5bpyrazine and pyrido1′,2′:1,2imidazo4,5bquinoxaline derivatives are sufficiently correlated with Hammett substituent constant ∼mand with the PM3 calculated LUMO energy levels, and the linear relationship between electron potentials of 9substituted pyridoimidazoquinoxalines and the LUMO energy levels is also found out.

Benzoyl-substituted hemithioindigo 1has a novel type of photochromic behavior based on the formation of the photoinduced [2+4] cycloadduct; that is, irradiation of 1produces the cycloadduct 2with all trans-configurations between the adjacent carbonyl moieties; this is completely dissociated back to 1on heating.

Calculations at ab initiolevels of theory of the nucleophilic aromatic substitution of pentafluoronitrobenzene with amines demonstrate an addition–elimination mechanism (SNAr), with the rate-determining step at the second transition state involving C–F bond breaking, and support the ortho-selectivity of the reactions based on the stability of the second transition states.

Calculations at ab initio levels of theory of the nucleophilic aromatic substitution of pentafluoronitrobenzene with amines demonstrate an addition–elimination mechanism (SNAr), with the rate-determining step at the second transition state involving C–F bond breaking, and support the ortho-selectivity of the reactions based on the stability of the second transition states.

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A recent paper of mine [1] contains an error, which is not critical to the main result but still may confuse the readers. I would like to apologize this sincerely and show how to flix it.