4P086

Elongation dynamics と反応部位局所遷移状態探索(九大院・総理工 1，SCNU2，JST-CREST3）Xie Peng1，折本 裕一 1，Liu Kai1，Yan Yun-an1，
Gu Feng Long2, 3，青木 百合子 1, 3

Elongation dynamics and local transition state search on
reaction site
(KYUSHU Univ.1, SCNU2, JST-CREST3) Peng Xie1，Yuuichi Orimoto1，Kai Liu1，Yun-an
Yan1，Feng Long Gu2, 3，Yuriko Aoki1, 3[Introduction]
Many essential biological processes are often accompanied by electron-related events suchas chemical reactions. The mechanisms of these chemical reactions are significant for theunderstanding of biomolecular functions. Ab initio molecular dynamics (AIMD) method is a
powerful tool to describe chemical reactions involving bond breaking and forming in whichelectrons play an important role, but the number of atoms handled with quantum
mechanics is much smaller than the number of atoms in a biological system for thelimitation of computer technologies. Elongation method (ELG)1,2 can efficiently calculate theelectronic structure of large aperiodic polymers with high accuracy on ab-initio level, so weproposed a new method named Elongation molecular dynamics (ELG-MD) by combine theelongation method with dynamics method.
This ELG-MD method makes it possible toefficiently analyze the mechanisms ofchemical reactions for biomolecule. To
describe a chemical reaction, we may propose
several kinds of chemical mechanism. It is
important to make clear the transition statesalong the reaction pathway. To find andconfirm the saddle point, we need calculate
the Hessian matrix based on quantummechanical principles. For this purpose, wedeveloped ELG-Hessian algorithm which canefficiently calculate the local Hessian matrix
for the reaction site.
[Methodology]
In ELG-MD method, we use gear predictor
corrector (GPC) method to solve the equations Figure 1: The workflow of ELG-MDof motion for wavefunction and coordinate
dynamic variables within the ELG method. The procedure is as follows (Fig. 1): The whole
molecule will be divided into a number of units. The first step, we select the 1st unit (Aregion) and a suitable number of units (B region, to ensure A region has no interaction withM region) as the starting cluster to perform AIMD calculation for a certain number of steps.

The second step, A region will be frozen and a new unit (M region) will be attached at thetail site of B region. The local force on each atom of the active region (B+M region) will beobtained by ELG method, then the acceleration and new position of each atom will becalculated by GPC method. After a certain number steps of dynamics, we can repeat thesecond step till we obtain the whole system in equilibrium.
Hessian matrix calculation is considerable expensive for biological system when aquantum mechanical description is used, but the chemical reaction region is always on asmall part, the most regions do not interact with the reaction region. So in ELG-Hessian
calculation, we take the chemical reaction region as the last unit (N) of elongation. From thestarting cluster to the second last step, we only need to obtain local molecular orbitas for thefrozen region (A region). For the last step of ELG-Hessian,
we use full molecular orbitals to calculate the Hessian
matrix element for B+M region.

Hx y =∂2 Etotal∂x∂yx ∈ B + M,y ∈ B+M(1)[Results and Discussion]
Polyglycine with water was selected as a target system
to test the ELG-MD method. In each ELG step, weperformed 4000 steps dynamics calculation at HF/STO-3Glevel. The initial structure and the final structure areshown in Fig. 2 (a) and (b) respectively. Fig. 2(c) showed
the structure obtained by ELG-optimization at HF/STOFig. 2: (a) The initial structure of poly3G level. By comparing the Fig. 2 (b) and (c), we foundglycine with water. (b) The structure
obtained by ELG-MD. (c) The structure
that: the structure in Fig. 2 (b) has more helix caused byobtained by ELG-optimization.
hydrogen bond forming than Fig. 2 (c). That means theprevious structure is more close to the real structure of polyglycine.
Before performing ELG-MD calculation, we need use ELG-Hessian method to find thetransition state of the reaction site. To examine the accuracy and efficiency of ELG-Hessian,
we compared the vibration modes of linear polyglycine (20 units) at HF/STO-3G level withconventional (CNV) Hessian calculation.
Table 1 The last five intra-molecular vibration modes forThe comparisons are shown in Table 1.
linear polyglycine Frequency unit (wavenumber)
ELG 4054.98 4055.27 4055.62 4056.32 4057.51 We can see the error of frequency isCNV 4058.98 4060.24 4058.21 4058.85 4060.86 considerable small. The mostly timeconsuming part of Hessian calculation is CPHF part, we checked the CPU time for CPHF
calculation. We found that the CPU time for CPHF calculation can significantly drop, from615.5 second (CNV) to 389.8 second (ELG).
[Future plan]
ELG-Hessian and ELG-MD can work well now, as the next step, elongation transitionstates (ELG-TS) method will be programmed for efficient investigation on chemical reaction.
1. Imamura, A.; Aoki, Y.; Maekawa, K. Journal of Chemical Physics 1991, 95, 5419-5431.
2. Gu, F. L.; Aoki, Y.; Korchowiec, J.; Imamura, A.; Kirtman, B. Journal of ChemicalPhysics 2004, 121, 10385-10391.