Ingenuity in performing replica permutation: How to order the state labels for improving sampling efficiency

In the replica-permutation method, an advanced version of the replica-exchange method, all combinations of replicas and parameters are considered for parameter permutation, and a list of all the combinations is prepared. Here, we report that the temperature transition probability depends on how the list is created, especially in replica permutation with solute tempering (RPST). We found that the transition probabilities decrease at large replica indices when the combinations are sequentially assigned to the state labels as in the originally proposed list. To solve this problem, we propose to modify the list by randomly assigning the combinations to the state labels. We performed molecular dynamics simulations of amyloid-β(16–22) peptides using RPST with the “randomly assigned” list (RPST-RA) and RPST with the “sequentially assigned” list (RPST-SA). The results show the decreases in the transition probabilities in RPST-SA are eliminated, and the sampling efficiency is improved in RPST-RA.     

Non-glutamate type pyrrolo[2,3-d]pyrimidine antifolates. III. Synthesis and biological properties of N(omega)-masked ornithine analogs

The glutamic acid moiety of N-[4-[3-(2,4-diamino-7H-pyrrolo[2,3-d]pyrimidin-5-yl)propyl]benzoyl]-L-g lutamic acid (1b, TNP-351) and the related compound (1a), was replaced with various N(omega)-acyl-, sulfonyl-, carbamoyl- and aryl-2,omega-diaminoalkanoic acids, and the inhibitory effects of the resulting products (9, 11, 14, 18, 21, 23, 25, 30, 36) on dihydrofolate reductase (DHFR), the growth of murine fibrosarcoma Meth A cells, and methotrexate-resistant human CCRF-CEM cells, were examined. Compounds (9a-f) acylated with a hemiphthaloyl group were efficiently synthesized by coupling pyrrolo[2,3-d]pyrimidine carboxylic acids (7a,b) and N(omega)-phthaloyl 2,omega-diaminoalkanoic acid methyl esters (6a-c) and subsequent hydrolysis. The other N(omega)-acyl- and sulfonyl-ornithine analogs (21, 23, 25) were synthesized by acylation of free amino intermediates (19a,b) derived from tert-butoxycarbonyl-ornithine analogs (17a,b). A free ornithine analog (18) did not strongly inhibit Meth A cell growth, whereas all N(omega)-acyl-, sulfonyl-, carbamoyl- and aryl-ornithine analogs (9, 11, 21, 23, 25, 30, 36) exhibited much more potent inhibitory activities against both DHFR and Meth A cell growth. In particular, compounds 9c, 21k and 36a also showed remarkable growth-inhibitory activities against methotrexate-resistant CCRF-CEM cells. These results demonstrate that the potent inhibitory activities of N(omega)-masked ornithine analogs against the growth of Meth A cells and methotrexate-resistant CCRF-CEM cells, results from effective uptake via reduced folate carrier and their potent DHFR inhibition.     

The synthesis of isoquinoline alkaloid and its related compounds using alanine derivatives as chiral auxiliaries

Chiral 1-substituted isoquinoline derivatives, which were obtained by the reaction using alanine derivatives as chiral auxiliaries, were transformed to (S)-2,3,9,10,11-pentamethoxyhomoprotoberberine (7) and a synthetic intermediate for O-methylkreysigine (9) in good yields and high stereoselectivity. The corresponding chiral allyl derivative of isoquinoline was transformed to a pyrrolidinoisoquinoline (16) in a highly enantioselective manner.     

Structure and dioxygen-reactivity of copper(I) complexes supported by bis(6-methylpyridin-2-ylmethyl)amine tridentate ligands

The structure and dioxygen-reactivity of copper(I) complexes R supported by N,N-bis(6-methylpyridin-2-ylmethyl)amine tridentate ligands L2R[R (N-alkyl substituent)=-CH2Ph (Bn), -CH2CH2Ph (Phe) and -CH2CHPh2(PhePh)] have been examined and compared with those of copper(I) complex (Phe) of N,N-bis[2-(pyridin-2-yl)ethyl]amine tridentate ligand L1(Phe) and copper(I) complex (Phe) of N,N-bis(pyridin-2-ylmethyl)amine tridentate ligand L3(Phe). Copper(I) complexes (Phe) and (PhePh) exhibited a distorted trigonal pyramidal structure involving a d-pi interaction with an eta1-binding mode between the metal ion and one of the ortho-carbon atoms of the phenyl group of the N-alkyl substituent [-CH2CH2Ph (Phe) and -CH2CHPh2(PhePh)]. The strength of the d-pi interaction in (Phe) and (PhePh) was weaker than that of the d-pi interaction with an eta2-binding mode in (Phe) but stronger than that of the eta1 d-pi interaction in (Phe). Existence of a weak d-pi interaction in (Bn) in solution was also explored, but its binding mode was not clear. Redox potentials of the copper(I) complexes (E1/2) were also affected by the supporting ligand; the order of E1/2 was Phe>R>Phe. Thus, the order of electron-donor ability of the ligand is L1Phe相似文献   

Structure and O2-reactivity of copper(I) complexes supported by pyridylalkylamine ligands

The structure and O2-reactivity of a series of copper(I) complexes supported by the pyridylalkylamine ligands are summarized, and the ligand effects such as the chelate ring size effect (five- vs. six-membered ring), the denticity effect (tetradentate vs. tridentate vs. didentate), the steric effect of 6-methylpyridine and the steric and/or electronic effects of N-alkyl substituents are discussed in detail.     

Efficient biocatalysis for the production of enantiopure (S)-epoxides using a styrene monooxygenase (SMO) and Leifsonia alcohol dehydrogenase (LSADH) system

Herein we report the production of enantiopure epoxides through biocatalysis using recombinant Escherichia coli cells expressing Rhodococcus sp. ST-10 styrene monooxygenase (SMO) and Leifsonia sp. S749 alcohol dehydrogenase (LSADH) genes are described. Rhodococcus sp. ST-10 SMO catalyzed the epoxidation of various alkenes, including styrene derivatives, vinyl pyridines, and linear alkenes, to give (S)-epoxides. NADH was regenerated by the reduction of NAD⁺ by LSADH with 2-propanol. The E. coli biocatalyst was used in an aqueous/organic biphasic reaction system and the reaction conditions were optimized. Under the optimized conditions, 170 mM of (S)-styrene oxide was obtained from styrene in the organic phase with excellent enantiomeric excess (99.8%). This biocatalytic process was used to synthesize various (S)-epoxides.     

Cholesteric induction power of β-galactose derivatives

Galactose derivatives were explored as chiral dopants, effective for inducing chiral nematic liquid crystal (LC) phases. Galactose bearing O-isopropylidene substituents at the C3 and C4 and butoxybiphenyl substituents at the C2 and C6 positions exhibits a high helical twisting power (HTP) value of ?74.4 μm^?1. Such a high HTP value for the galactose derivative is attributed to (1) linkage of the C3 and C4 carbons with the O-isopropylidene substituent, which places the C2 and C6 substitutes in a skew arrangement at a large angle and (2) enhancement of the affinity with the host nematic LCs by incorporating aromatic substituents at the C2 and C6 positions that are similar to those in the host.     

Color centers in irradiated MgF2

Abstract

Color centers in rutile-structured MgF₂ single crystals irradiated at 20K/360K by reactor neutrons are investigated spectroscopically at LNT. Four different types of the F-F vacancy bond in MgF₂ are possibly identified to the observed absorption bands as due to the F₂ centers; instead of previous assignments, the 300nm band to the F₂(D_2h), the 325nm band to the F₂(C₁), the 355nm band to the F₂(C_2v), and the 400nm band to the F₂(C_2h) centers.     

Osmium(III) and Osmium(V) Complexes Bearing a Macrocyclic Ligand: A Simple and Efficient Catalytic System for cis‐Dihydroxylation of Alkenes with Hydrogen Peroxide

A simple protocol that uses [Os^III(OH)(H₂O)(L ‐N₄Me₂)](PF₆)₂ ( 1 ; L ‐N₄Me₂=N,N′‐dimethyl‐2,11‐diaza[3.3](2,6)pyridinophane) as a catalyst and H₂O₂ as a terminal oxidant for efficient cis‐1,2‐dihydroxylation of alkenes is presented. Unfunctionalized (or aliphatic) alkenes and alkenes/styrenes containing electron‐withdrawing groups are selectively oxidized to the corresponding vicinal diols in good to excellent yields (46–99 %). In the catalytic reactions, the stoichiometry of alkene:H₂O₂ is 1:1, and thus the oxidant efficiency is very high. For the dihydroxylation of cyclohexene, the catalytic amount of 1 can be reduced to 0.01 mol % to achieve a very high turnover number of 5500. The active oxidant is identified as the Os^V(O)(OH) species ( 2 ), which is formed via the hydroperoxide adduct, an Os^III(OOH) species. The active oxidant 2 is successfully isolated and crystallographically characterized.     

2-Chloroanthraquinone-catalyzed aerobic photo-oxidative synthesis of diacylamines from benzylamides

In this Letter, we report the aerobic photo-oxidative synthesis of diacylamines from benzylamides in the presence of molecular oxygen and catalytic amounts of 2-chloroanthraquinones under visible light irradiation from a fluorescent lamp.