|
|
|
|
| LEADER |
01000naa a22002652 4500 |
| 001 |
NLM184497140 |
| 003 |
DE-627 |
| 005 |
20231223170739.0 |
| 007 |
cr uuu---uuuuu |
| 008 |
231223s2009 xx |||||o 00| ||eng c |
| 024 |
7 |
|
|a 10.1002/jcc.21156
|2 doi
|
| 028 |
5 |
2 |
|a pubmed24n0615.xml
|
| 035 |
|
|
|a (DE-627)NLM184497140
|
| 035 |
|
|
|a (NLM)19009605
|
| 040 |
|
|
|a DE-627
|b ger
|c DE-627
|e rakwb
|
| 041 |
|
|
|a eng
|
| 100 |
1 |
|
|a Kiyota, Yasuomi
|e verfasserin
|4 aut
|
| 245 |
1 |
2 |
|a A multicore QM/MM approach for the geometry optimization of chromophore aggregate in protein
|
| 264 |
|
1 |
|c 2009
|
| 336 |
|
|
|a Text
|b txt
|2 rdacontent
|
| 337 |
|
|
|a ƒaComputermedien
|b c
|2 rdamedia
|
| 338 |
|
|
|a ƒa Online-Ressource
|b cr
|2 rdacarrier
|
| 500 |
|
|
|a Date Completed 14.07.2009
|
| 500 |
|
|
|a Date Revised 07.04.2009
|
| 500 |
|
|
|a published: Print
|
| 500 |
|
|
|a Citation Status MEDLINE
|
| 520 |
|
|
|a 2008 Wiley Periodicals, Inc.
|
| 520 |
|
|
|a In this article, we present the multicore (mc) QM/MM method, a QM/MM method that can optimize the structure of chromophore aggregate in protein. A QM region is composed of the sum of the QM subregions that are small enough to apply practical electronic structure calculations. QM/MM energy gradient calculations are performed for each QM subregion. Several benchmark examinations were carried out to figure out availabilities and limitations. In the interregion distances of more than 3.5-4.0 A, the mcQM/MM energy gradient is very close to that obtained by the ordinary QM/MM method in which all the QM subregions were treated together as a single QM region. In van der Waals complex, the error exponentially drops with the distance, while the error decreases slowly in a hydrogen bonding complex. On the other hand, the optimized structures were reproduced with reasonable accuracy in both cases. The computational efficiency is the best advantage in the mcQM/MM approach, especially when the QM region is significantly large and the QM method used is computationally demanding. With this approach, we could optimize the structures of a bacterial photosynthetic reaction center protein in the ground and excited states, which consists of more than 14,000 atoms
|
| 650 |
|
4 |
|a Journal Article
|
| 650 |
|
4 |
|a Research Support, Non-U.S. Gov't
|
| 650 |
|
7 |
|a Proteins
|2 NLM
|
| 700 |
1 |
|
|a Hasegawa, Jun-ya
|e verfasserin
|4 aut
|
| 700 |
1 |
|
|a Fujimoto, Kazuhiro
|e verfasserin
|4 aut
|
| 700 |
1 |
|
|a Swerts, Ben
|e verfasserin
|4 aut
|
| 700 |
1 |
|
|a Nakatsuji, Hiroshi
|e verfasserin
|4 aut
|
| 773 |
0 |
8 |
|i Enthalten in
|t Journal of computational chemistry
|d 1984
|g 30(2009), 8 vom: 20. Juni, Seite 1351-9
|w (DE-627)NLM098138448
|x 1096-987X
|7 nnns
|
| 773 |
1 |
8 |
|g volume:30
|g year:2009
|g number:8
|g day:20
|g month:06
|g pages:1351-9
|
| 856 |
4 |
0 |
|u http://dx.doi.org/10.1002/jcc.21156
|3 Volltext
|
| 912 |
|
|
|a GBV_USEFLAG_A
|
| 912 |
|
|
|a SYSFLAG_A
|
| 912 |
|
|
|a GBV_NLM
|
| 912 |
|
|
|a GBV_ILN_350
|
| 951 |
|
|
|a AR
|
| 952 |
|
|
|d 30
|j 2009
|e 8
|b 20
|c 06
|h 1351-9
|