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101.
To raise the accuracy of the force field for nucleic acids, several parameters were elaborated, focusing on the rotation around chi torsion axis. The reliability of molecular dynamics (MD) simulation was significantly increased by improving the torsion parameters at C8--N9--C1'--X (X = H1', C2', O4') in A, G and those at C6--N1--C1'--X in C, T, and U. In this work, we constructed small models representing the chemical structure of A, G, C, T, and U, and estimated energy profile for chi-axis rotation by executing numerous quantum mechanical (QM) calculations. The parameters were derived by discrete Fourier transformation of the calculated QM data. A comparison in energy profile between molecular mechanical (MM) calculation and QM one shows that our presently derived parameters well reproduce the energy surface of QM calculation for all the above torsion terms. Furthermore, our parameters show a good performance in MD simulations of some nucleic acids. Hence, the present refinement of parameters will enable us to perform more accurate simulations for various types of nucleic acids. 相似文献
102.
103.
Sonomi Arata Dr. Yuna Kim Prof. Norihisa Hoshino Dr. Keishiro Tahara Dr. Kiyonori Takahashi Dr. Tomofumi Kadoya Tomonori Inoue Prof. Takayoshi Nakamura Prof. Tomoyuki Akutagawa Prof. Jun-ichi Yamada Prof. Kazuya Kubo 《欧洲无机化学杂志》2023,26(12):e202300017
Unsymmetrical gold(III)-dithiolene complexes are potential candidates for molecular materials that exhibit thermal structural phase transitions. In this study, unsymmetrical ppy-gold(III) (ppy−=C-deprotonated-2-phenylpyridine(−)) complexes [AuC5] and [AuC6] coordinated by dithiolene ligands containing tetrathiafulvalene (TTF) skeletons with pentylthio (2-{bis(pentylthio)-1,3-dithiol-2-ylidene}-1,3-dithiol-4,5-dithiolate(2−)) and hexylthio groups (2-{bis(hexylthio)-1,3-dithiol-2-ylidene}-1,3-dithiol-4,5-dithiolate(2−)) were synthesized. Both complexes exhibited a large absorption band at approximately 508 nm, owing to intramolecular ligand-to-ligand charge transfer. One-dimensional columnar structures with head-to-tail molecular arrangements around the metal ions were constructed in the crystals. The flexible alkylthio groups were intercalated into crystalline spaces between dithiolene ligands in the columns. [AuC5] exhibits a simple phase transition at 198 °C between crystalline and isotropic phases irreversibly. The crystalline phase of [AuC6] observed at 25 °C melted at 148 °C. Another crystalline phase grew above 148 °C with a very slow crystallization rate from the liquid phase and was completely transformed into an isotropic phase at 200 °C. 相似文献
104.
Yujiro Hayashi 《Chemical record (New York, N.Y.)》2023,23(7):e202200159
The aldol reaction is one of the most important carbon-carbon bond-forming reactions in organic chemistry. Asymmetric direct cross-aldol reaction of two different aldehydes has been regarded as a difficult reaction because of the side reactions such as self-aldol reaction and over reaction. We found that trifluoromethyl-substituted diarylprolinol, α,α-bis[3,5-bis(trifluoromethyl)phenyl]-2-pyrrolidinemethanol ( 1 ), is an effective organocatalyst that promotes several cross-aldol reactions of aldehydes with excellent diastereo- and enantioselectivities. Acetaldehyde can be employed as a suitable nucleophilic aldehyde. Successful electrophilic aldehydes are ethyl glyoxylate, chloroacetaldehyde, dichloroacetaldehyde, chloral, α-alkyl-α-oxo aldehyde, trifluoroacetaldehyde, glyoxal, alkenyl aldehyde, alkynyl aldehyde, and formaldehyde. Some of the aldehydes are commercially available as a polymer solution, an aqueous solution, or in the hydrated form. They can be used directly in the asymmetric aldol reaction as a commercially available form, which is a synthetic advantage. Given that the obtained aldol products possess several functional groups along with a formyl moiety, they are synthetically useful chiral building blocks. 相似文献
105.
Sterically Demanding Oxidative Amidation of α‐Substituted Malononitriles with Amines Using O2 下载免费PDF全文
Jing Li Dr. Martin J. Lear Prof. Dr. Yujiro Hayashi 《Angewandte Chemie (International ed. in English)》2016,55(31):9060-9064
An efficient amidation method between readily available 1,1‐dicyanoalkanes and either chiral or nonchiral amines was realized simply with molecular oxygen and a carbonate base. This oxidative protocol can be applied to both sterically and electronically challenging substrates in a highly chemoselective, practical, and rapid manner. The use of cyclopropyl and thioether substrates support the radical formation of α‐peroxy malononitrile species, which can cyclize to dioxiranes that can monooxygenate malononitrile α‐carbanions to afford activated acyl cyanides capable of reacting with amine nucleophiles. 相似文献
106.
We study the global Cauchy problem for the mass critical nonlinear Schrödinger equations. We prove the global existence of analytic solutions in both space and time variables for sufficiently small and exponentially decaying Cauchy data. The method of proof depends on the Leibniz rule for the generator of pseudo-conformal transforms at the L 2 critical level. 相似文献
107.
Yuki H Tanaka Y Hata M Ishikawa H Neya S Hoshino T 《Journal of computational chemistry》2007,28(6):1091-1099
No explicit pi-pi interaction term has been incorporated in the conventional molecular dynamics (MD) simulation programs in spite of its significant role in the folding of biomolecules and the clustering of organic chemicals. In this article, we propose a technique to emphasize the effect of pi-pi interactions using a function of energy and implement it into an MD simulation program. Several trial calculations show that the pi-pi incorporated program gives improved results consistent with experimental data on atom geometry and has no unfavorable interference with the conventional computational framework. This indicates an importance of the explicit consideration of pi-pi interactions in MD simulation. 相似文献
108.
Hayashi Y Aratake S Itoh T Okano T Sumiya T Shoji M 《Chemical communications (Cambridge, England)》2007,(9):957-959
Dry and wet prolines were found to catalyze the direct aldol reactions of aldehyde-aldehyde and aldehyde-ketone, respectively, to afford aldols with excellent diastereo- and enantioselectivities, and an organic solvent-free reaction was realized in some cases. 相似文献
109.
Aratake S Itoh T Okano T Usui T Shoji M Hayashi Y 《Chemical communications (Cambridge, England)》2007,(24):2524-2526
A small organic molecule, Pro-NH(2), catalyzing the enantioselective aldol reaction "in water" not merely "in the presence of water" with good enantioselectivity has been discovered for the first time. 相似文献
110.
Shinoda K Hasegawa T Sato H Shinozaki M Kuramoto H Takamiya Y Sato T Nikaidou N Watanabe T Hoshino T 《Chemical communications (Cambridge, England)》2007,(40):4140-4142
A biosynthetic intermediate of violacein produced by the mixed enzymes of VioABDE was elucidated to be 5-(5-hydroxy-1H-indol-3-yl)-3-(1H-indol-3-yl)-1H-pyrrole-2-carboxylic acid, named protoviolaceinic acid, indicating that VioC, responsible for the final biosynthetic step, works to oxygenate at the 2-position of the right side indole ring, and that the oxygenation reaction to form the central pyrrolidone core proceeds in a non-enzymatic fashion. 相似文献