dirac coneの出現条件関連

J. von Neumann and E.P. Wigner,  Phys. Z. 30 467 (1929)
 E Teller, J. Phys.Chem.41 (1937) 109
M.V. Berry and M. Wilkinson , Proc. R. Soc. Lond. A 392 (1984) 15

delta-SCF, Δ-SCF

通常のDFTの解に対して、occupied stateに穴を開けてSCFを実行する。

CP2K、XAS core level

Inner-shell spectroscopy by the Gaussian and augmented plane wave method

Marcella Iannuzzi and Jürg Hutter 

Phys. Chem. Chem. Phys., 2007, 9, 1599-1610
DOI: 10.1039/B615522G 

A method for inner-shell spectroscopy simulations based on all-electron GAPW is presented. Accuracy and efficiency are discussed for molecular and condensed matter systems.

対義語

http://www.mrsano.jp/CL051.htm
http://www17.ocn.ne.jp/~inotec/kanji/kanji2/kanji2-taigi.html

B3LYP*

J. Chem. Phys. 117, 4729 (2002); doi:10.1063/1.1493179 (9 pages)

Assertion and validation of the performance of theB3LYP^⋆ functional for the first transition metal row and the G2 test set

Oliver Salomon, Markus Reiher, and Bernd Artur Hess


Feのhigh,low spinのenergy差を補正するためにexact exchangeを足す項c3を0.20->0.15にしたB3LYP。
exact exchange成分が多いとexchange splittingの大きさに悪影響と書いてある。
簡単な分子のenergy比較はしてあるが、もっとも大事な遷移金属のspin stateに関するenergyの比較がなされていない。遷移金属に関してはpi-cationのmagnetic momentとbond length。

Maximally localized Wannier functions for GW quasiparticles

PHYSICAL REVIEW B 79, 045109 2009
Hamman, Vanderbilt

fast water

translation, rotationが速い水

Ni-Fe, molecular channel

Martin J Fieldの話から
H2 <-> 2H+ + e-
Ni-Fe hydrogenase
Molecular channel
proton channels or pathways

Gas access to the active site of Ni-Fe hydrogenases probed by X-ray crystallography and molecular dynamics
Yael Montet, et al., Nature Structural & Molecular Biology 4, 523 - 526 (1997)

論文が取れない。

pdynamo, fdynamo, Martin J. Field

http://www.pdynamo.org/mainpages/

論文もそこにlinkされている。

PSII, Mn4Ca clustdr, X-ray damage

Cyanobacterial photosystem II at 2.9-A resolution and the role of quinones, lipids, channels and chloride

Albert Guskov, et al., Nature Structural & Molecular Biology 16, 334 - 342 (2009) 

X-ray damage to the Mn4Ca complex in single crystals of photosystem II: A case study for metalloprotein crystallography,

Junko Yano, et al., PNAS August 23, 2005 vol. 102 no. 34 12047-12052

Origin and temperature dependence of radiation damage in biological samples at cryogenic temperatures

Alke Meents, et al., PNAS 2010 107 (3) 1094-1099

FT-IR,
Y.  Shimada et al. Biochemistry 48, 6095, 2009.
M. A. Strickler, Philos. Trans. R. Soc. London, Ser. B, 363, 1179, 2009.

The MoD-QM/MM methodology for structural refinement of photosystem II and other biological macromolecules

Eduardo M. Sproviero, Michael B. Newcomer, Jose A. Gascon, Enrique R. Batista and Gary W. Brudvig, et , photosynth res. 201, 455 (2009).

Structure of the oxygen-evolving complex of photosystem II: information on the S2 state through quantum chemical calculation of its magnetic properties

Dimitrios A. Pantazis, Maylis Orio, Taras Petrenko, Samir Zein, Wolfgang Lubitz, Johannes Messinger and Frank Neese 

Phys. Chem. Chem. Phys., 2009, 11, 6788-6798 

P450 review

Theoretical Perspective on the Structure and Mechanism of Cytochrome P450 Enzymes

Sason Shaik, et al., Chem. Rev., 2005, 105 (6), pp 2279?2328

Density Functional Studies on Isomerization of Prostaglandin?H2 to Prostacyclin Catalyzed by Cytochrome P450

Tetsuya K. Yanai,  Seiji Mori Prof. Dr., 

Chemistry-A European Journal

Volume 15, Issue 17, pages 4464?4473, April 20, 2009

B3LYPはhigh spin stateを安定化しすぎるのでB3LYP*というのがあるらしい。

neutron, proton

Preliminary neutron and X-ray crystallographic studies of equine cyanomethemoglobin

1. A. Y. Kovalevsky

1. 
   

   Acta Crystallographica Section F

   Volume 66, Issue 4, pages 474-477, April 2010

1.6, 1.7A, protonを見た。