1. business and industrial
2. chemicals industry
3. dyes and pigments

Franck-Condon simulation with damped harmonic oscillators: solvent
effects for molecular electronic spectroscopy of azacarbazole and carbazole
Chen-Wen Wang (王辰文) and Chaoyuan Zhu* (朱超原)
Department of Applied Chemistry, National Chiao Tung University,
Address: 1001, Ta-Hsueh Rd. Hsinchu 30010, Taiwan
e-mail: [email protected]
We have developed Franck-Condon simulation with damped harmonic oscillators to deal
with solvent effects in molecular absorption and fluorescence spectra [1]. This method is
applied to study AC(1-azacarbazole) and CZ(carbazole) molecules in hexane and ACN
solutions [2]. Both AC and CZ are the crucial biomolecules that play an important role in the
human body and thus it is great interesting to understand solvent effect of spectra. In order to
simulate the absorption and fluorescence spectra in solutions observed in experiment, we first
utilize ab initio quantum chemistry method at the level of density functional theory (DFT) and
time-dependent DFT method, namely (TD)B3LYP, (TD)B3LYP35, (TD)B3LYP50 and
(TD)B3LYP100, to optimize structures of ground- and excited-state of AC and CZ molecules.
Then, we utilize the Franck-Condon simulation to study absorption and fluorescence spectra
in the two solutions mentioned above. We report our simulation results in this poster.
References
[1] C.-W. Wang, L. Yang, C. Zhu, J.-G. Yu, and S. H. Lin, J. Chem. Phys. 141, 084106 (2014).
[2] E. García-Fernández, C. Carmona, M. A. Munoz, J. Hidalgo, M. Balon, Spectrochimica
Acta Part A 84 130 (2011).
Gate Control of Single-Molecule Machines
Liang-Yan Hsu,∗,† Chun-Yin Chen,‡ Elise Y. Li,∗,‡ and Herschel Rabitz∗,†
†
Department of Chemistry, Princeton University, Princeton, New Jersey 08544,
United States, and ‡Department of Chemistry, National Taiwan Normal
University, Taipei 11677, Taiwan
[email protected]
Artificial molecular machines are a growing field in nanoscience and nanotechnology.
[1,2] This study proposes a new class of artificial molecular machines, the secondgeneration singlemolecule electric revolving doors (2G S-MERDs), a direct extension of
our previous work [3]. We investigate destructive quantum interference with tunneling
and conductance dependence upon molecular conformation in the 2G S-MERDs by using
the Green’s function method together with density functional theory. The simulations
show that the 2G S-MERDs have a large on-off conductance ratio (> 104), and that their
open and closed door states can be operated by an experimentally feasible external
electric field (1 V/nm). Conductance - gate electric field characteristics are also
introduced to illustrate the operation of the 2G S-MERDs.
References
[1] Koumura, N.; Zijlstra, R. W. J.; Delden, R. A. v.; Harada, N.; Feringa,
B. L. Light-Driven Monodirectional Molecular Rotor. Nature 1999,
401, 152–155.
[2] Delden, R. A. v.; Wiel, M. K. J. t.; Pollard, M. M.; Vicario, J.;
Koumura, N.; Feringa, B. L.Unidirectional Molecular Motor on a Gold
Surface. Nature 2005, 437, 1337–1340
[3] Hsu, L.-Y.; Li, E. Y.; Rabitz, H. Single-Molecule Electric Revolving
Door. Nano Lett. 2013,13, 5020–5025.
Semi-Quantitative Assessment of Intersystem Crossing Rate: An
Extension of El-Sayed Rule to the Emissive Transition Metal
Complexes
Elise Yu-Tzu Li1* (李祐慈),Tzung-Ying Jiang1(姜宗螢),Tsao-Pei Chou1(周晁霈), Yun
Chi2(季昀),Pi-Tai Chou3(周必泰)
1
Department of Chemistry, National Taiwan Normal University, Taipei 116, Taiwan
Department of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan
3
Department of Chemistry and Center for Emerging Material and Advanced Devices,
2
National Taiwan University, Taipei 106, Taiwan
The main goal of this study is to provide systematic elucidation of the parameters that influence S
 T intersystem crossing (ISC). Particular attention is paid to: (i) the computation of Sn  Tm spinorbit coupling strength based on a non-adiabatic approach, (ii) crucial factors that facilitate ISC, such
as the atomic number, ligand structure, and particularly types of electronic transition, (iii) formulating
a discussion on the standpoints of the fundamental photophysical theory. Combining the theoretical and
empirical approaches, we propose the following empirical rules as general guidelines for assessing the
ISC in a qualitative manner: (1) In general, the higher MLCT characteristic involved in the singlet and
triplet excited states, the stronger the SOC integral. However, the strength of SOC also depends strongly
on the detailed electronic structure of the states involved. (2) When the S1 and T1 originate from almost
identical electronic transitions, the major ISC channel usually occurs via S1 to higher Tm (m > 1) state,
which has both a proper orbital transition and a smaller energy gap with S1. (3) When the structure of
the ligands involves extended conjugated systems and that the lowest excited states have a more
dominating ππ* character, the ISC originating from higher singlet excited states can be large enough to
violate the Kasha’s rule. (4) The overall SOC strength (and ISC rate) relies on a delicate balance
between the one-electron SOC constant and the nature electronic structure of the involved states. In
other words, the “heavy atom effect” might not be so heavily weighted after all; through a careful design,
lighter elements may also exhibit similar emission efficiency with that of heavier elements.
References
[1] Cheng, Y. M.; Li, E. Y.; Lee, G. H.; Chou, P. T.; Lin, S. Y.; Shu, C. F.; Hwang, K. C.; Chen, Y. L.;
Song, Y. H.; Chi, Y. Inorg. Chem. 2007, 46, 10276–10286.
[2]Hsu, C. W.; Lin, C. C.; Chung, M. W.; Chi, Y.; Lee, G. H.; Chou, P. T.; Chang, C. H.; Chen, P. Y.
J. Am. Chem. Soc. 2011, 133, 12085
[3] El-Sayed, M. J. Chem. Phys. 1963, 38, 2834.
[4] Elise Yu-Tzu Li, Tzung-Ying Jiang, Yun Chi and Pi-Tai Chou. Phys. Chem. Chem. Phys., 2014,
DOI: 10.1039/c4cp03540b
Probing π→π* photoisomerization mechanism for cis-azobenzene by
on-the-fly trajectory-based nonadiabatic molecular dynamics simulation
Le Yu(于樂) and Chaoyuan Zhu*(朱超原)
Department of Applied Chemistry, National Chiao Tung University,
Address: 1001, Ta-Hsueh Rd. Hsinchu 30010, Taiwan
e-mail: [email protected]
We developed nonadiabatic trajectory surface hopping algorithm without calculating
nonadiabatic coupling vector and applied this new method to the azobenzene S1 state
photoisomerization dynamics for both cis-to-trans and trans-to-cis reactions [1]. Actually, the
photoisomerization dynamics observed in experiment is involved in several lowing lying
excited states. We probe this complicated π→π* photoisomerization reaction mechanisms
from cis-azobenzene. We found there are seven conical intersections among the four
low-lying singlet states and a long conical seam between S2 and S3 states. The
five-state-averaged CASSCF method was utilized in the trajectory simulation to probe the
cis-azobenzene photodynamic mechanisms. In both S2 and S3 states, we found significantly
distinguishable fast and slow reaction processes; the fast channels usually needs several
hundred fs to achieve the final product, and in the slow channels, there exists the excited state
trans-azobenzene intermediate which has been confirmed in the recent transient absorption
spectroscopy experiment [2]. For trajectories started from S2 state, all the mechanisms
dominated by the torsion of CNNC and NNCC moiety, while for trajectories started from S3
state, the mixed torsion of CNNC and inversion of NNC motions were confirmed by the
present nonadiabatic molecular dynamics simulation.
References
[1] L. Yu, C. Xu, , Y. Lei, C. Zhu, and Z. Wen, Phys. Chem. Chem. Phys., (in press, 2014).
[2] M. Quick, A. L. Dobryakov, M. Gerecke, C. Richter, F. Berndt, I. N. Ioffe, A. A.
Granovsky, R. Mahrwald, N. P. Ernsting, and S. A. Kovalenko, J. Phys. Chem. B, 118, 8756
(2014).
Nonadiabatic trajectory surface hopping for photochemical reaction of
o-nitrophenol in the low-lying singlet and triplet excited states
Chao Xu(徐超), Le Yu(于樂), Chaoyuan Zhu*(朱超原) and Jian-Guo Yu
Department of Applied Chemistry, National Chiao Tung University,
Address: 1001, Ta-Hsueh Rd. Hsinchu 30010, Taiwan
e-mail: [email protected]
We developed nonadiabatic trajectory surface hopping algorithm without calculating
nonadiabatic coupling vector for nonadiabatic processes involving in singlet excited states[1],
and plus calculating spin-orbital coupling we extend this method to deal with intersystem
crossing for nonadiabatic processes involving in both singlet and triplet excited states. We
study and analyze the most efficient photophysical and photochemical decay and
isomerization pathways for the o-nitrophenol molecule [2]. By using ab initio quantum
chemistry method at level of SA-CASSCF(10, 10)/6-31G (d, p) and MRCI+Q/cc-pVDZ, we
optimize the S0, T1, T2 and S1 equilibrium structures, and the several transition states linking
nitro with aci-nitro isomers in the T1 and S0 states. From those static points of potential energy
surfaces of low-lying singlet and triplet excited states, we could qualitatively understand
photochemical reaction mechanism of o-nitrophenol. However, for quantitatively
understanding, we perform nonadiabatic dynamics simulation involving on-the-fly calculation
of global potential energy surfaces on coupled low-lying singlet and triplet excited states. We
will report simulation results in this poster and hopefully provide detailed mechanistic insight
by depicting the most relevant channels for the decay and the reaction funnels.
References
[1] L. Yu, C. Xu, , Y. Lei, C. Zhu, and Z. Wen, Phys. Chem. Chem. Phys., (in press, 2014).
[2] I. Bejan, Y. A. E., I. Barnes et al., Phys. Chem. Chem. Phys. 8, 2028 (2006).
Shape resonances of H2S, H2Se, and H2Te
Yin-Cheng Chen and Hsiu-Yao Cheng
Department of Chemistry, Tunghai University, 1727, Taiwan Boulevard Sec. 4,
Taichung 40704, Taiwan, Republic of China.
e-mail: [email protected]; [email protected]
The stabilized Koopmans’ theorem in long-range corrected density
functional theory is used to investigate the shape resonances of H 2X
molecules (X: S, Se, and Te). In this approach, stabilization is
accomplished by varying the exponents of appropriate diffuse functions.
The resonance energies are then identified by investigating the
relationship between the resultant eigenvalues and scale parameter. The
characteristics of resonance orbitals are also examined. For the lowest
unfilled orbitals of H2X molecules, results indicate that they are
essentially *(H-X) in character. Moreover, several shape resonances
with strong X “d” characters have been identified. These results will help
us understand the bonding and chemical properties of these hydrides.
References:
1. Dezarnaud, C.; Tronc, M.; Modelli, A. Chem. Phys. 1991, 156,
129-140.
2. Varella, M. T. D. N.; Bettega, M. H.; Lima, M. A.; Ferreira, L. G. J.
Chem. Phys. 1999, 111, 6396-6406.
3. Cheng, H.-Y.; Chen, C.-W. J. Phys. Chem. A 2012, 116, 12364-12372.
Familial Mutations of Alzheimer Amyloid-Peptide Alter the Configurations of Central
Hydrophobic Core within Membrane: A Replica Exchange Molecular Dynamics Study
Jian-Bin Lee and Hui-Hsu Gavin Tsai*
Department of Chemistry, National Central University, Jhong-Li City, Tao-Yuan County 32001, Taiwan
Correspondence e-mail address: [email protected]
Extracellular deposits of amyloid (A) aggregates in the brain is the hallmark of
Alzheimer’s disease (AD). Ais cleaved from the amyloid precursor protein (APP) by- and
-secretases. A number of mutations in the APP have been shown to associate with several
familial AD. The significant pathogenic mutations occur in the region of E22 and D23 in the
A sequence. For instance, E22Q (Dutch) and D23N (Iowa) mutants exhibits higher
neurotoxicity and aggregation rate than wildtype A(1–40). To our best knowledge, there is
not systematic study of these mutants by MD simulation in a water-membrane environment.
Here, we employ replica–exchange molecular dynamics to investigate the configuration of the
A E22Q-A, D23N-A and E22Q/D23N-A mutants in
water-membrane environments. Based on our results, we observe that the network of residue
contacts between N-terminal (residues 1-16) and central hydrophobic core (CHC) fragment
(residues 17-21) is decreased on familial mutants. In addition, we observe that the
configuration transition of CHC fragment in familial mutants is easier than wildtype
A(1–40). It is indicated more independent N-terminal fragment and highly exposure of the
hydrophobic CHC fragment of familial mutants in water-membrane environment. Therefore,
the loose structure and frequently configurational transition of CHC fragments of familial Aβ
within the membrane is an important role for initial amyloid peptide aggregation. In this study,
the CHC fragment’s properties could explain a part of rapid amyloid aggregation of familial
mutant peptides and provide the insight to rational drug design to prevent amyloid associated
diseases.
Scanning Alanine Mutagenesis Study of the Stability of Alzheimer’s Amyloid
Fibril-like Oligomer by Molecular Dynamics Simulations
Wen-Yuan Chu and Hui-Hsu Gavin Tsai*
Department of Chemistry, National Central University, Jhong-Li City, Tao-Yuan County 32001, Taiwan
Correspondence e-mail address: [email protected]
Alzheimer’s disease (AD) is characterized by the extracellular deposit of senile plaques in the
brain. Senile plaques are mainly composed of the aggregated amyloid beta (Aβ) protein.
called amyloid. Amyloid fibrils are semi-ordered nanostructures as the result of self assembly
of proteins when they are misfolded under critical conditions. Due to the complexity of Aβ
amyloids, the underlying biophysical mechanisms of formation and toxicity are still unclear.
Therefore, it is crucial to determine the key residues in stabilizing Aβ amyloid fibrils.
In this study, we employed all atom molecular dynamics simulations to investigate the
relative stability of Aβ-fibril like oligomer and its mutants by point mutagenesis. To
investigate the intra-peptide interactions, we simulated the structures of Aβ-fibril like
oligomer with one of its residue is systemically mutated to Ala by MD simulations. The
secondary structure, inter-peptide backbone hydrogen-bonds, solvent-accessible surface area
(SASA) of the central hydrophobic core, and RMSD from the solid-state NMR determined
structure were analyzed.
Our results show the following tendency. For the mutagenesis of the residues within the
hydrophobic core, the simulated RMSD is increased when (a). charged and/or polar residues
were mutated to hydrophobic Ala such as D23A, K28A, and N27A and (b). larger
hydrophobic residues were mutated to smaller hydrophobic Ala such as F19A and V40A. The
former one is due to the imbalance of electrostatic interaction and the later one is due to the
loss of shape complementarity. Interestingly, the point mutations on the pointing-out residues
on 1-sheet do not cause significant structural instability, while the point mutations on the
pointing-out residues on 2-sheet generally lead to structural instability. These results provide
clues to design drugs preventing the formation of Aβ-fibrils.
Fig1.
Representation the F19A is loss of shape complementarity.
Fig2.
Representation the charged were mutated to hydrophobic Ala. D23A is absence of
the Asp23-Lys28 salt bridge.
Electron Transfer of Squaraine-Derived Dyes Adsorbed on TiO2
Clusters in Dye-Sensitized Solar Cells: A Density Functional
Theory Investigation
Chun-Jui Tan, Wen-Hsin Tseng and Hui-Hsu Gavin Tsai*
Department of Chemistry, National Central University, Jhong-Li City, Tao-Yuan County 32001,
Taiwan
E-mail: [email protected]
Squaraine (SQ) dyes are well-known for their intense absorption in the red/near-IR
spectral regions to ultilize the solar radiation. SQ-derived dyes are supposed to have
effective potential applied in dye-sensitized solar cells (DSCs). In this research, we
employed density functional theory (DFT) and time-dependent DFT to investigate the
structural, optical, and electron transfer properties of seven recently reported SQ-derived
dyes adsorbed on (TiO2)38 cluster with anatase (101) surface corresponding to DSCs.
Particular efforts were given to calculate the proportions of the electron densities in the
dye–(TiO2)38 systems transferred to TiO2 moieties upon photo-excitation, allowing us to
investigate their electron injection mechanisms. JD10 and YR6 have two intense absorption
bands with significant proportions of electron density delocalized into TiO 2 upon excitation
and have driving forces for excited-state electron injection, followed direct electron injection
mechanism. These results are compatible with their higher experimentally observed shortcircuit currents (Jsc) than those of the SQ dyes. In contrast, SQ12, SQ2, and SQ4 followed
the indirect electron injection mechanism because of their negligible proportion of electron
density injected into TiO2; in addition, SQ2 and SQ4 do not provide driving force for
electron injection. The Jsc values of SQ12, SQ2, and SQ4 dyes observed in experiment were
lower than that of other studied SQ dyes. The calculated probabilities of electron density
being delocalized into TiO2 and driving force for excited-state electron injection from these
studied SQ dyes are correlated with experimentally observed Jsc values. This study provides
insight into the electron injection mechanisms of SQ-derived dyes adsorbed on TiO2 upon
photo-excitation. Furthermore, our calculations and findings give clues for designing new
SQ-derived sensitizers for DSC applications.
A DFT Study of the Photo-Absorption and Photo-Emission
Properties of two Novel D−A−π−A organic dyes
Jia-Cheng Hu,a Sheng Hsiung Chang,b Kuo-Yuan Chiu,b
Chun-Guey Wu,a,b and Hui-Hsu Gavin Tsaia*
a. Department of Chemistry, National Central University, Jhong-Li City, Tao-Yuan County
32001, Taiwan
b. Research Center for New Generation Photovoltaics, National Central University
E-mail: [email protected]
The working principle of DSCs is light-harvesting processes similar to those of the
photosynthetic system in nature. One of the most successful and popular framework of
organic dyes is a dipolar D-π-A structure based the push-pull architecture. D-π-A dyes
generally have efficient intramolecular charge transfer (ICT) properties. Based on this strategy,
two novel donor−acceptor−π−acceptor (D−A−π−A) organic dyes (CKY-33 and CKY-34)
incorporating internal electron-withdrawing units of diketopyrrolopyrrole (DPP) have been
newly synthesized and tested for DSC applications. CKY-33 and CKY-34 have similar
framework, instead, CKY-33 has a phenyl ring for its π-spacer and CKY-34 a thiophene ring
for its π-spacer. CKY-34 has a more red-shifted and intense absorption than that of CKY-33.
In principle, CKY-34 has a better spectral match with sunlight radiation than that of CKY-33.
However, CKY-34 has a slightly lower Jsc value and lower photo-to-cuurent efficiency than
those of CKY-33. Broadband exciton dynamics of these two dye dissolved in THF solution
shows the lifetime of “cold” exciton of CKY-33 dye is longer than that of CKY-34 dye.
To understand the different lifetimes as well as different Jsc values of CKY-33 and
CKY-34 dyes we performed the DFT and TD-DFT calculations to investigate the absorption
and emission properties of these two dyes in THF and adosrbed on a (TiO2)38 cluster having
an anatase (101) surface, as a model for corresponding DSCs. Our calculations show the
CKY-34 has a stronger emission oscillator strength than that of CKY-33 indicating that the
“cold” excition of CKY-34 will have a shorter lifetime. Our calculations are consistent with
experimental observations.
Oxidation of CO on a Carbon-based Material Composed of Nickel
Hydroxide on Reduced Graphene Oxide, (Ni4(OH)3/rGO) － a FirstPrinciples Calculation
Chen-Hao Yeh(葉丞豪) and Jia-Jen Ho(何嘉仁)*
Department of Chemistry, National Taiwan Normal University,
No. 88, Section 4, Tingchow Road, Taipei, Taiwan
E-mail : [email protected]
Nickel or nickel hydroxide clusters on reduced graphene oxide (rGO) are novel
nanomaterials in the application of electrochemical catalysts. In this work, we calculated
the energy of Ni4 adsorbed on saturated hydroxyl GO, which forms a Ni4(OH)3 cluster on
the hydroxyl rGO (Ni4(OH)3/rGO) and releases 4.47 eV (5.22 eV with DFT-D3
correction). We subsequently studied the oxidation of CO on the Ni4(OH)3/rGO system
via three mechanisms – LH, ER and carbonated mechanisms. Our results show that the
activation energy for oxidation of the first CO molecule according to the ER mechanism
is 0.14 eV (0.12 eV with DFT-D3 correction), much smaller than that with LH (Ea = 0.65
eV, 0.61 eV with DFT-D3 correction) and with carbonated (Ea = 1.28 eV, 1.20 eV with
DFT-D3 correction) mechanisms. The barrier to oxidation of the second CO molecule to
CO2 with the ER mechanism increases to 0.43 eV (0.37 eV with DFT-D3 correction), but
still less than that via LH (Ea = 1.09 eV, 1.07 eV with DFT-D3 correction), indicating
that CO could be effectively oxidized through the ER mechanism on the Ni4(OH)3/rGO
catalyst.
[1] Y. Matsumoto, H. Tateishi, M. Koinuma, Y. Kamei, C. Ogata, K. Gezuhara, K. Hatakeyama, S. Hayami, T.
Taniguchi, A. Funatsu, J. Electroanal. Chem., 2013, 704, 233-241.
[2] S. Rastgar, S. Shahrokhian, Talanta, 2014, 119, 156-163.
CO Oxidation on Tungsten Carbide Surface: A Density
Functional Study
Yu-Jhe Tong, Hsin-Tsung Chen
[email protected], [email protected]
Chung Yuan Christian University, 200, Chung Pei Rd, Chung Li, Taiwan 32023,
R.O.C
Keywords: Tungsten carbide, gas adsorption, carbon oxide, Metal carbide, ab initio,
density functional theory
Abstract:
Tungsten carbide (WC) has been popular discuss while its properties such like
Platinum. WC is cheaper than Platinum and we can use it to replace Pt. It is a
potential material that we can use for gas adsorption. Nowadays, the carbon oxide is
a critical pollution in our life. We use the density functional theory calculation to
find out the reaction of WC surface and carbon oxide.
CO + O2 → CO2 + O
CO + H2O → CO2 + H2
Following to the reaction, we discuss and find out the mechanism of carbon oxide
react with other gas on WC surface. We also discuss different surface, location and
direct to find the best chemical mechanism. And expect the reaction will be useful in
the future.
References:
1. R.B. Levy, M. Boudart, Platinum-like behavior of tungsten carbide in surface
catalysis, Science 181 (1973) 547–549.
2. Zheng, W., Chen, L. , Ma, C, Density functional study of H2O adsorption and
dissociation on WC(0001), Computational and Theoretical Chemistry 1039 (2014)
75-80
Nitrogen-doped carbon nanotubes as a metal-free
catalyst for CO oxidation
I Hsiang, Lin (林逸庠), Hsin-Tsung, Chen (陳欣聰)*
Department of Chemistry, Chung Yuan Christian, University, Chung-Li, 32023,
Taiwan
[email protected], [email protected]*
The oxidation of carbon monoxide (CO) on catalyst has attracted considerable
research interest in recent years because it can remove CO from fuel cells or lower
CO pollution. The effective catalyst for CO oxidation must comprise metal. We
usually use noble metal catalyst for CO oxidation, but the noble metals ( Pd, Au, and
Pt) are rare and expensive. So we must to find the new catalysts replacing the noble
metals. In our research, We have study CO oxidation by O2 on nitrogen doped carbon
nanotube (NCNT) with different diameter ((n,n)-NCNT (n= 3,4,5))by the density
functional theory (DFT) calculations. We also find the reaction mechanism of CO
oxidation and use NEB to map the potential energy surfaces. In our result, we show
that the oxidation of CO energy barrier can reduce effectively. The result has
demonstrated that NCNT is a good, low-cost, and metal-free catalyst for CO
oxidation.
CO2 Capture in Aluminum Metal-Organic Frameworks:
A Theoretical Study
Yu-Huan Lu (盧禹寰), Hsin-Tsung Chen* (陳欣聰)
Department of Chemistry, Chung Yuan Christian University, Chungli 32023, Taiwan
[email protected], [email protected]
Keywords: DFT-D, MOF, Aluminum, TDC, FDCA
Using density functional theory with van der Waals corrected functional, we study
and explain trends in the binding between CO2 and two novel metal-organic
frameworks (MOFs) with two kinds of ligands: 2,5-thiophenedicarboxylic acid
(TDC), 2,5-furandicarboxylic acid (FDCA). The present work shows the TDC
ligands exhibit six coordination modes, structure analysis reveals that
2,5-thiophenedicarboxylic acid play a versatile role toward different metal ions to
form three-dimensional inorganic-organic hybrid frameworks.
We use one of these modes (Figure 1) to calculate how CO2 molecule binding with
TDC/FDCA-MOFs. A CO2 can form weak hydrogen bonding with electron deficient
hydrogen of thiophene and furan rings. The present sulfone groups increases
hydrogen bonding in CO2-TDC/FDCA complex. This study elucidates the
Lewis-base interaction and hydrogen bonding may be important stabilizing
interactions that merit consideration in the design of future CO2-philes.
Figure 1
Adsorption and Reaction of O2 and C2H4 on Cu38 Clusters:
A Computational Study
Chen-Chi, Lee (李偵綺), Hsin-Tsung, Chen (陳欣聰)*
Department of Chemistry, Chung Yuan Christian University, Chung-Li, 32023,
Taiwan
[email protected], [email protected]*
Keywords: DFT, Cu38, O2, C2H4, Coadsorption
The heterogeneously catalyzed epoxidation of alkenes is experimentally
challenging, so we try to use theoretically method to find the better route. We had
studied the adsorption of O2 and C2H4 molecules on Au38 by using density
functional theory (DFT) calculations already, in this case, we try to confer the
coadsorption on Cu38. Some adsorption sites were discussed in this study and
characterized as top, bridge, hollow, and hcp sites. Cooperative adsorption O2 and
C2H4 on Cu38 clusters were investigated. To predict the competing reaction
pathways for epoxide formation versus acetaldehyde formation on Cu38 and search
out a lower transition state (TS), we use NEB method to map the potential energy
surfaces (PES). Results suggest that epoxidation proceeds via a surface
oxametallacycle intermediate (OMME structure), such as a ring structure, Cu-CC-O-Cu, it is the key of this reaction.
Figure 1. Located isomers of coadsorbed O2&C2H4 on the Au38 nanoparticle . The bond
lengths are given in angstroms.
References
[1] Andrey, L.; Tetsuya T. J. Phys. Chem. Lett., 2009, 113, 12930-12934.
[2] W. Gao; X. F. Chen; J. C. Li; Q. Jiang. J. Phys. Chem. C, 2010, 114, 11481153.
[3] H. T. Chen; J. G. Chang; S. P. Ju; H. L. Chen. J. Phys. Chem. Lett., 2010, 1,
739-742.
A Study of the Reaction Mechanism of Wittig Rearrangements by Ab Initio
Computations
Pei-Kang Tsou and Chin-Hui Yu*
Department of Chemistry, National Tsing-Hua University, HsinChu 300 Taiwan
E-mail : [email protected]
The high regio- and stereo-selectivity of Wittig rearrangements makes them a versatile
tool in organic synthesis. The [2,3]-Wittig rearrangement is a concerted reaction with a high
degree of stereocontrol. On the other hand, the concerted [1,2]-Wittig rearrangement is a
orbital-symmetry forbidden process and is assumed to go through a stepwise pathway. An
ionic and a radical pair are proposed as possible intermediates along the stepwise path.
Simple model compounds are used to analyze important reaction structures along the
concerted and the stepwise reaction paths using the multireference CASSCF/CASPT2 and
density function theory methods. The oxygen-lithium chelation fixes the key intermediate
geometry, and controlls regio- and stereo-selectivity in the following [1,2] and [2,3]
rearrangements along the stepwise pathway. The interaction between the solvent molecules
and the Li+ are calculated to examine the salvation effect via DFT method.
A theoretical study on the phosphorescence spectra of
sulfur dioxide
Kuan-Cheng Lin (林冠臣), Jia-Lin Chang(張嘉麟)*
Department of Science Application and Dissemination, National Taichung University
of Education, Taichung 403, Taiwan (KCL email: [email protected];
JLC email: [email protected])
Abstract
The equilibrium geometries and vibrational frequencies of the singlet ground
state and three triplet excited states of sulfur dioxide were computed by using the
density-functional theory and the coupled-cluster theory with various basis sets. The
phosphorescence spectra of SO2 were simulated by using the approach developed by
our group, in which the harmonic-oscillator model with the Duschinscky effect was
taken into account.1 The adiabatic excitation energies were obtained by extrapolating
the CCSD(T) energies to the complete basis set (CBS) limit. The simulated
phosphorescence spectra are in agreement with the experiments and provide insights
into the vibrational structures. The calculated excitation energies are in excellent
agreement with the experimental values.
References
1. J.-L. Chang, C.-H. Huang, S.-C. Chen, T.-H. Yin, Y.-T. Chen, J. Comput. Chem. 34,
757 (2013).
FePt Nanodendrites with High-Index Facets as Active Electrocatalysts
for Oxygen Reduction Reaction – DFT Simulation Studies
Hung-Lung Chou,1,* Di-Yan Wang,2,3 Ching-Che Cheng,2 Yu-Han Wu,2 Chin-Ming Tsai,2 HengYi Lin,2 Yuh-Lin Wang,2 Bing-Joe Hwang,4,5 and Chia-Chun Chen,2,3
1
Graduate Institute of Applied Science and Technology, National Taiwan University of Science
and Technology, Taipei, 10617, Taiwan
2
Department of Chemistry, National Taiwan Normal University, Taipei 106, Taiwan.
3
Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan
Nanoelectrochemistry Laboratory, Department of Chemical Engineering, National Taiwan
University of Science & Technology, Taipei 106, Taiwan
5
National Synchrotron Radiation Research Center (NSRRC), Hsinchu 300, Taiwan.
Corresponding Information: [email protected]
4
Abstract
In this study, three different types of alloyed FePt nanstructures, nanodendrites, nanospheres and
nanocubes, were prepared and their catalytic activities for oxygen reduction reaction (ORR) were
studied. The ORR catalytic activity of the nanostructures were increased in the order of E-TEK
Pt/C < FePt nanospheres < FePt nanocubes < FePt nanodendrites. In particular, a cation
exchanging reaction was developed for the preparation of FePt nanodendrites, consisting of a
dense array of branches on a core. The FePt nanostructures were analyzed by high-resolution
transmission electron microscopy (HRTEM), high angle annular dark field (HAADF), scanning
transmission electron microscopy (STEM) and electron energy loss spectrum (EELS) mapping.
The HRTEM images revealed that the large surface area of FePt nanodendrites with a high
density of atomic steps was enclosed by high-index {311} facet. The density functional theory
simulation was performed to understand the origins of the enhanced electrochemical activity of
FePt nanodendrites. The enhancement could be attributed to the exposure of high-index {311}
facet of the nanodendrite with high surface energy in comparison to that low-index {111} and
{200} facets of FePt nanospheres and nanocubes, respectively. Our experimental and theoretical
studies have opened a route toward the syntheses of new nonprecious alloyed nanostructures to
replace Pt as active fuel cell catalysts.
Keywords: FePt, Nanodendrites, High-index Facet, Density Functional Theory, Oxygen
Reduction Reaction
Acknowledgement:
We thank the NCHC for providing massive computing time. Financial support from the National
Science Council under Contracts number MOST 103-2221-E-011-041 is gratefully acknowledged.
Investigation of Kinase-Ligand Binding Affinity Using
Thermodynamic Integration MD Simulation, Docking
Computation, and Kinase Assay
Hsing-Chou Lee (李興洲), Wen-Chi Hsu (許文綺), An-Lun Liu (劉安倫), ChiaJen Hsu (許嘉仁), Chia-Ming Chang(張家銘)Ying-Chieh Sun (孫英傑)
Department of Chemistry, National Taiwan Normal University
[email protected]; [email protected] (A.L. Liu)
Thermodynamic integration molecular dynamics simulation was used to investigate
how TI-MD simulation preforms in reproducing relative protein-ligand binding free
energy of a pair of analogous GSK3 kinase inhibitors of available experimental data,
and to predict the affinity for other analogs. The computation for the pair gave a G of
1.0 kcal/mol, which was in reasonably good agreement with the experimental value of 0.1 kcal/mol. The error bar was estimated at 0.5 kcal/mol. Subsequently, we employed
the same protocol to proceed with simulations to find analogous inhibitors with a stronger
affinity. Four analogs with a substitution at one site inside the binding pocket were the
first to be tried, but no significant enhancement in affinity was found. Subsequent
simulations for another 7 analogs was focused on substitutions at the benzene ring of
another site, which gave two analogs with G values of -0.6 and -0.8 kcal/mol,
respectively. Both analogs had a -OH group at the meta position and another -OH group
at the ortho position at the other side of the benzene ring. To explore further, another 4
analogs with this characteristic were investigated. Three analogs with G values of -2.2,
-1.7 and -1.2 kcal/mol, respectively, were found. Hydrogen bond analysis suggested that
the additional hydrogen bonds of the added –OH groups with Gln185 and/or Asn64 were
the main contributors to an enhanced affinity. Effect of displacement of crystal water
molecules at binding site will be discussed. The prediction for better inhibitors should
interest experimentalists of enzyme and/or cell assays.
Figure 1: Binding of the reference compound with GSK3 kinase [1]
In addition, progress in using new module in Amber package, pmemd, experimental
measurement for finding new GSK3 kinase inhibitors, and a study of p38 kinase-ligand
complexes will be reported and discussed. [2]
References
[1] Lee, H.C.; Hsu, W.C.; Liu, A.L.; Hsu, C.J.; Sun, Y.C., J. Mol. Graphics & Model.
2014, 51, 37-49.
[2] Hsu, W.C.; Liu, A.L.; Hsu, C.J.; Sun, Y.C. (in preparation).
Dynamic Solvation Shell and Solubility of C60 in Organic Solvents
Chun I Wang (王俊壹)1, Chi C. Hua (華繼中)1*, and Show A. Chen (陳壽安)2
1
Department of Chemical Engineering, National Chung Cheng University, Chia-Yi, Taiwan
2
Department of Chemical Engineering, National Tsing Hua University, Hsin-Chu, Taiwan
*E-mail: [email protected]
ABSTRACT
The notion of (static) solvation shells has recently proved fruitful in revealing key
molecular factors that dictate the solubility and aggregation properties of fullerene species
in polar or ionic solvent media. Using molecular dynamics schemes, we have scrutinized
both the static and the dynamic features of the solvation shells of single C 60 particle for
five non-polar organic solvents (i.e., chloroform, toluene, and chlorobenzene, 1,2dichlorobenzene, 1,4-dichlorobenzene) and a range of system temperatures (i.e., T = 250330 K). The central findings have been that, while the static structures of the solvation
shell remain, in general, insensitive to the effects of changing solvent type or system
temperature, the dynamic behavior of solvent molecules within the shell exhibits
prominent dependence on both factors. Detailed analyses led us to propose the notion of
dynamically stable solvation shell, effectiveness of which can be characterized by a new
physical parameter defined as the ratio of two fundamental time constants representing,
respectively, the solvent relaxation (or residence) time within the first solvation shell and
the characteristic time required for the fullerene particle to diffuse a distance comparable
to the shell thickness. We show that, for the six (one from the literature) different solvent
media and the range of system temperatures examined herein, this parameter bears a
value around unity and, in particular, correlates intimately with known trends of solubility
for C60 solutions. We also provide evidence revealing that, in addition to fullerene-solvent
interactions, solvent-solvent interactions play an important role, too, in shaping the
dynamic solvation shell, as implied by recent experimental trends.
A Computational Study of the Hydrogen Adduct of 4-, 6-,
7-membered N-Heterocyclic Carbene
Chin-Hung Lai
School of Medical Applied Chemistry, Chung Shan Medical University, 402,
Taichung, Taiwan; Department of Medical Education, Chung Shan Medical
University Hospital, 402, Taichung, Taiwan.
Phone: 886-4-24730022-12224
EMAIL ADDRESS: [email protected]
Keywords: N-heterocyclic carbene; N,N’-diamidocarbene; Hydrogen adduct;
Hydrogen storage material; ring size
In our previous study,1 we found that the hydrogen adduct of a N-heterocyclic
carbene is a more efficient hydrogen storage material than a N,N’-diamidocarbene
is. Furthermore, the efficiency of the hydrogen adduct of a N,N-diamidocarbene to
act as a hydrogen storage material is influenced by its ring size. In this study, the
influence of the ring size of a N-heterocyclic carbene on the efficiency to behave as
a hydrogen storage material is investigated.
Reference:
1. Lai, C.-H. J. Mol. Model. 2013, 19, 5523-5532.
The Capabilities of an Abnormal N-heterocyclic Carbene to
Form Hetero- and Homodimer
Chin-Hung Lai
School of Medical Applied Chemistry, Chung Shan Medical University, 402,
Taichung, Taiwan; Department of Medical Education, Chung Shan Medical
University Hospital, 402, Taichung, Taiwan.
Phone: 886-4-24730022-12224
EMAIL ADDRESS: [email protected]
Keywords: Heterodimer; Homodimer; DFT; abnormal N-heterocyclic carbene;
dimerization.
In this study, we investigate the capability of imidazol-4-ylidene (aNHC) to undergo
homodimerization or heterodimerization with its isomer imidazol-2-ylidene (NHC)
by the M06-2X functional. Unlike its NHC isomer, the stability of aNHCs does not
depend on low-barrier dimerization and they have a lower tendency toward
dimerization. We tentatively ascribe this to the fact that the aromatic stabilization
energy of imidazol-4-ylidene is larger than that of imidazol-2-ylidene.
Adsorption of a Pt13 Cluster on Graphene Oxides at Varied Ratios of
Oxygen to Carbon and Its Catalytic Reactions for CO Removal
Investigated with Quantum-chemical Calculations
Shiuan-Yau Wu (吳亘曜) and Jia-Jen Ho (何嘉仁)*
Department of Chemistry, National Taiwan Normal University,
No. 88, Section 4, Tingchow Road, Taipei, Taiwan
* Corresponding author E-mail: [email protected]
We applied periodic density-functional theory to investigate the
interaction of a Pt13 cluster on graphene-oxide (GO) sheets at varied ratios of
oxygen to carbon, and on a pristine graphene sheet. Relative to a pristine
graphene sheet, the existence of oxygen atoms in an appropriate proportion in the
formation of graphene oxide enhanced the adsorption capability of a Pt13 cluster.
The O/C ratio of GO sheets had the following influences on the Pt13 cluster
adsorption behavior: (i) for O/C ratio ＜ 0.125, the Pt13 cluster abstracted the
neighboring oxygen atom from a GO sheet to form Pt 13O, or aggregated with an
adjacent cluster to form a larger cluster; (ii) for O/C ratio≧ 0.125, the Pt 13 cluster
was stabilized and dispersed on the GO sheet. We calculated also the adsorption
behavior of carbon monoxide on a Pt13/GO sheet; a strong interaction between the
Pt13 cluster and the GO sheet modulated the electronic structure of the Pt13 cluster,
thus decreasing the CO adsorption energy, which in turn decreased the combined
barriers, CO + O and CO + OH, in the water-gas shift reaction (WGSR), and
improved the CO tolerance of the Pt catalyst.
Name: Chun-Chih Chang
Email: [email protected]
This abstract is for a:

Poster
Abstract
Catalytic Activity Enhancement of CO2 Dissociation on
Unzipped Graphene Oxide Supported Rhodium
Nanoclusters – A DFT Study
Chun-Chih Chang* and Jia-Jen Ho
Department of Chemistry, National Taiwan Normal University,
No. 88, Section 4, Tingchow Road, Taipei, Taiwan
*presenting author, email: [email protected]
The catalytic activity of rhodium nanoclusters on unzipped graphene oxide
(Rhn/UGO) has been investigated to compare with that of Rh nanoclusters and
that of Rh surfaces. The binding energies of Rh atoms on UGO were less than the
cohesive energy (- 5.75eV) of Rh bulk, indicating that the Rh atoms adsorbed on
UGO tend to collect to clusters. In our work, we systematically calculated the
CO2 adsorption energies dependent on the size and shape of the Rh n nanoclusters
(n = 1, 4, 5, 8, 13) on unzipped graphene oxide and found that the IcosahedralRh13/UGO had the largest one, -1.18eV with the C–O bond elongated from 1.18
to 1.29 Å . Furthermore,the dissociation barrier of CO2 on Icosahedral-Rh13/UGO
is very small (Ea = 0.41eV), indicating that the Icosahedral-Rh13/UGO might be
act as good catalyst to activate the scission of the C-O bond.
References
1.
L. C. Balba ´s,; A. Vega,; F. Aguilera-Granja J. Phys. Chem. A 2009, 113, 13483–13491.
2.
G. W. Rogers,; J. Z. Liu J. Am. Chem. Soc. 2012, 134, 1250−1255.
3.
T. Futschek,; M. Marsman, J. Hafner J. Phys.: Condens. Matter 2005, 17, 5927–5963.
題目: 利用線性響應理論預測分子內部訊息傳遞與異構調控效應
Title: intramolecular communications and allosteric regulations revealed by linear response theories
黃邦杰，楊立威
Bang-Chieh Huang and Lee-Wei Yang
清華大學生物資訊與結構生物研究所
Institute of bioinformatics and structural biology, National Tsing Hua University, Hsinchu, Taiwan
Abstract
Accumulated experimental and theoretical evidences have shown that protein functions as
a physiochemically connected network. Allostery, understood in this new context, is a manifestation of
residue communicating over remote sites via this network and hence a recently rising interest in
identifying communication pathways mediating allosteric controls. In this study, we demonstrate that a
new formulation of linear response theory (LRT) can describe a two-stage conformational relaxation- 1.
ligand-induced conformational changes at a few tens to a hundred of picoseconds and 2. an early
molecular ‘twitch’ that is faster than conformational relaxation by an order of magnitude. Predictions
based on LRT agree with observations from site-specific UV resonance Raman, time-resolved X-ray and
sound speed in a condensed medium. With the computational ease of the current implementation, we can
easily perturb the protein network by thousands of times where time-resolved atomic trajectories can be
tracked following each perturbation. Frequently used ‘communication centers’ are identified and it is
found by experiments that mutations of these centers, many remote from the catalytic site, would greatly
impact the hydride transfer rate in DHFR. Mutations on those that do not serve as communication centers
impact the catalysis minimally. We also show the signal propagation is directional, highly anisotropic and
need not be reciprocal. We favorably consider the method’s applicable future in probing functionally
sensitive distant mutants by the physical approach herein proposed.
Reference:
Yang, L. W., A. Kitao, B. C. Huang, and N. Go. 2014. Ligand-induced protein responses and mechanical signal
propagation described by linear response theories. Biophys J 107:1415-1425.
A Theoretical Study on the Reaction of Thiyl Radicals with
Nitrogen Dioxide : Biological Mechanisms
Shih-Sheng Wu (吳詩盛), Ching-Han Hu (胡景瀚)*
Department of Chemistry, National Changhua University of Education, Changhua
50058, Taiwan, Republic of China
Keywords: cis-trans isomerization; Nitrogen dioxide; Thiyl radicals
Many studies have demonstrated that fatty acid peroxidation and isomerization
can occur via radicals, such as thiyl radicals (RS․) and nitrogen dioxide (NO2․).1,2
These radicals can be obtained exogenously, such as cigarette smoke; or can be
generated endogenously by one-electron oxidation from hydrogen sulfide, cysteine
or glutathione.3 However, the reaction about RS․ in vivo is still unclear. In this
study, we used density functional theory and coupled cluster theory to investigate
the mechanism. Process of forming RS․ from hydrogen abstraction mechanism of
endogenous thiols with free radicals were investigated, and the environmental
effects were included using the polarizable continuum model. We found a feasible
․
․
mechanism for the formation of NO and sulfinyl radical (RSO ) by the reaction
of RS․ with NO2․. The NO2․ addition mechanism through the O-terminus is more
favorable than through the N-terminus. Sulfinyl nitrite (RS(O)NO) is probably
formed by rearrangement of sulfenyl nitrite (RSONO), and the release of NO․ and
RSO․ then take place after which the N—S bond is cleaved.
Hu, C.-H.; Tzeng, Y.-Z. J. Phys. Chem. A 2014, 118, 4554−4564.
2. Balazy, M.; Chemtob, S. Pharmacol Ther 2008, 119, 275−290.
3. Tweeddale, H. J.; Kondo, M.; Gebicki, J. M. Arch Biochem Biophys 2007, 459,
151−158.
1.
Novel Dipolar 5,5,10,10-tetraphenyl-5,10-dihydroindeno[2,1-a]- indene Derivatives
for SM-OPV: A Combined Theoretical and Experimental Study
新穎的小分子有機光伏材料: 雙偶極衍生物
(5,5,10,10-tetraphenyl-5,10-dihydroindeno[2,1-a]-indene)理論計算和實驗探討
Chin-Kuen Tai(戴欽坤), Chun-An Hsieh(謝淳安), Kai-Lun Hsiao(蕭凱倫), Ken-Hao
Chang(張根豪), Bo-ChengWang(王伯昌),Yi Wei(魏屹)
Department of Chemistry, Tamkang University, Tamsui 251, Taiwan
淡江大學 化學系
In order to investigate the photo-physical, electrochemical, and optoelectronic
properties of dipolar 5,5,10,10-tetraphenyl-5,10-dihydroindeno[2,1-a]-indene (TDI)
derivatives, a facile synthesis has been developed to integrate arylamine (electron
donor fragment, D) and aryl-2-methylenemalononitrile (electron acceptor fragment, A)
into the TDI bridge. According to calculation results using the DFT/B3LYP/6-31G(d)
method, the HOMO and LUMO energies of TDI derivatives are relevant to the extent
of corresponding electron donating and accepting abilities, and influence the
open-circuit voltage (Voc) and driving force (ΔE) in organic photovoltaics (OPV).
The projected density of state (pDOS) analysis shows that the electron density
distribution from the D fragment to TDI bridge in the HOMO is attributing to the
electron-donating ability, whereas the electrons are mainly localized on A fragment in
the LUMO. Calculations of the reorganization energy by the DFT/B3LYP/6-31G(d)
method suggest these D-TDI-A derivatives are hole-transporting type materials. On
the other hand, the calculated absorption spectra for these molecules in CH2Cl2 are
simulated by using the TD-DFT/BHandHLYP/6-31G(d) method within the
Polarizable Continuum Model (PCM) and provide the maximum absorption
wavelength (λmax), which can be assigned to the HOMO to LUMO transition.
HOMO is found to be the π orbital which is delocalized between the D fragment and
the π-linker and LUMO is the π* orbital which is concentrated on the A fragment.
The optical properties of D-TDI-A derivatives can be influenced by the D fragment
and π-conjugated length. Calculated results of D-TDI-A derivatives also exhibited a
large light harvesting efficiency related to the maximum absorption wavelength
(RLHE)) and, according to these results, the D-TDI-A derivatives containing the Ab
and Ad fragments would be useful electron donor materials for further development
of new small molecular organic photovoltaic solar cell (SM-OPV) devices.
Methane and Ethane Oxidative Dehydrogenation Mechanism on MoO3 and
Transition Metal Doped MoO3 Surfaces
Chen-Cheng Liao, Yao-Shun Zhan, Yu-Te Chan, Ming-Kang Tsai*
Department of Chemistry, National Taiwan Normal University, Taipei 10677, Taiwan
Massive production of shale gas becomes technologically accessible due to the development of
horizontal drilling and hydraulic fracturing in the recent years, especially in United States. The global energy
supply is therefore significantly reshaped in respect to the cost of liquefying shale gas for intercontinental
transport. With the fact that the primary composition of shale gas is methane or ethane, converting these
alkane into other derivatives play a crucial role to the current energy market. The recent experiment carried
out by Al-Hazmi et al. showed the use of Mo-V-Mn-W catalyst for ethane oxidative dehydrogenation (ODH)
to produce ethylene in short contact time.1 With varying the tungsten loading, different selectivity of ethylene
production ratios were observed. Therefore, the present study used the first-principles calculations to
compare the potential ethane dehydrogenation reaction mechanism on MoO3 surface and other V, W doped
MoO3 surfaces. The minimum energy pathway of producing ethylene as well as other potential chemical
product is discussed. The electronic structure effect introduced by V and W dopants are analyzed.
ad2_phy_ad
Reference
-251.0143602
1. "Enhanced catalytic activities for the oxidative dehydrogenation of ethane by the addition of W into
MoVMn mixed oxides at low temperature" T. Odedairo, Y.-S. Zhan, L. Atanda, Y. Choi, and M.H.
Al-Hazmi, SABIC Technology Center, Riyadh, Saudi Arabia (private communication).
Spectroscopic Study of the OH Stretching Motions in
H(CH3OH)13X02; X=Ar and N2
Hsiao-Han Chuanga, Jer-Lai Kuob, Kaito Takahashib, Asuka Fujiic
a
Department of Chemistry, National Taiwan University, Taipei, Taiwan.
Nano Science and Technology Program, Taiwan International Graduate Program.
b
c
Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, Taiwan.
Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Japan
[email protected]
Tagging messengers (usually stable atoms or molecules) on ionic clusters can resolve the
low-resolution infrared spectra through the vibrational pre-dissociation mechanism, and usually these
messengers deliver the information of large ionic cluster well [1]. Nevertheless, in the small clusters,
they perturb the system by themselves and would not act as a “messenger” anymore. Infrared
Pre-Dissociation (IR-PD) spectra of the mass-selected ionic cluster H(CH3OH)13X02 (X=Ar and N2)
were observed, and both Ar and N2 interfered the OH stretching motion between 2800 to 3800 cm1.
The observed sharp peaks were analyzed with theoretical simulations via different vibrational
calculations. In this work, expressions were derived in reduced dimension on vibrational discrete
variable representation (DVR) [2], which had high accuracy potential energy surface along several
selected normal mode coordinates, and had no coupling terms between kinetic operators. After
concerned the anharmonicity, simulation of covalent bonds were in agreement with experimental
results upon B3LYP/6-31+G(d,p) level, but overestimated the interaction between messengers and
ionic protonated methanol clusters, see the figure below.
Reference
[1] Okumura, M.; Yeh, L.I.; Myers, J.D.; Lee, Y.T. J. Phys. Chem., 1990, 94, 34163427.
[2] Light, J.C. Adv. Chem. Phys., 2000, 114, 263284.
編號 :
Theoretical Study on the Polynuclear Manganese-Binding Proteins
Pei-Chuan Chu (朱沛全)1, Jen-Shiang K. Yu(尤禎祥)1,2
1 Institute of Bioinformatics and System Biology, National Chiao Tung University, Hsinchu,300, Taiwan
2 Department of Biological Science and Technology, National Chiao Tung University, Hsinchu,300, Taiwan
Keywords: metal-binding protein, metallothionein
Metal-binding is a characteristic feature in some of the protein families. These proteins
play important roles in biological functions including catalysis, activation of substrates as
well as transportation and storage of metal ions1,2. Polynuclear manganese-binding proteins
such as arginase and metallothionein demonstrate their coordinated effects as active sites or
structural centers. The arginase is the final enzyme of the urea cycle, whereas the
manganese-containing metallothionein may serve for in vivo detoxification. The
coordination motif relates to the electronic structure and affects biological functions as well
as the folding of metalloproteins. In this study, the electronic structure of the binding center
of metallothionein is theoretically investigated using density function theories. The results
show that the manganese metals form an imperfect hexagonal geometry planar to the sulfur
atoms of surrounding residues. The manganese atoms exhibit antiferromagnetism according
to the calculated spin density: one α electron locates at one of the manganese sites, while the
β spin populates on the other manganese site in the optimized structural model of the β
domain in the metallothionein crystal isolated from Rattus rattus.
References
1. L.M. Kennedy, B.R. Gibney, Curr. Opin. Struct. Biol. 2001, 11, 485.
2. C. Liu, H. Xu, J. Inorg. Biochem. 2002, 88, 77.
Theoretical Study of Benzoylleucine Diethyl Amides Dimer
Benzoylleucine Diethyl Amides 二聚體之理論計算
Pei-Chen Lo(羅珮溱) and Yao-Yuan Chuang(莊曜遠) *
Department of Applied Chemistry, National University of Kaohsiung,
Kaohsiung 81148, Taiwan
本研究利用之前合成一系列具不同取代基的 Benzoylleucine
Diethyl Amides (BDA)的晶體進行晶體分析與量子化學計算，我們利
用 Hirshfeld Surface 分析，可以得知大部分具有 π-π 相互作用 BDA 二
聚體為相同掌性，此與之前文獻所得結果相同，但我們以非人工方式
篩選出具有 π-π 相互作用的分子晶體。相較於之前研究，我們可利用
指紋圖定量分析多種類型原子作用力於分子間的堆疊貢獻度。為了仔
細分析二聚體分子間作用力與比較不同取代基對 π-π 相互作用的影響，
我們利用具不同分散力(Dispersion Force)模型的密度泛函理論計算具
π-π 相互作用的 BDA 二聚體，也利用 SAPT 將 BDA 二聚體相互作用
力分解成各種具有物理意義的組成能量作探討。我們希望藉由分析已
知分子晶體結構的相互作用力，了解分子晶體堆疊的方式與不同分子
間作用力的協同作用，以達到利用理論計算從事分子識別研究的目的，
進而設計出可分離掌性化合物之管柱固定相晶體。
第一原理分子動態模擬 STM-tip 誘導 CO 去吸附反應及非彈性電子穿隧光譜研究
Ab-initio molecular dynamics simulations of STM-tip induced desorption process of
CO/Ag(110) : inelastic electron tunneling spectroscopy and anharmonic coupling
Shao-Yu Lu(呂紹宇) and Jyh-Shing Lin(林志興)
Department of Chemistry, Tamkang University, New Taipei City, Tamsui, 251, Taiwan
(淡江大學化學系)
E-mail : [email protected]
The effects of STM-tip on adsorption dynamics are important issues to understand the detailed
mechanisms in tunneling-current-induced reaction process. DFT-based molecular dynamic
simulations in combination with a Fourier transform of auto-correlation function[1-2] of the
derivative of local density of states (FT-ACF-δLDOS) are performed for simulating the
inelastic electron tunneling spectroscopy (IETS) of CO(ads) adsorbed on the Ag(110) surface. It
is found that the tunneling conductance generated based on the trajectories of LDOS is
significantly increased as a Ag5 cluster STM-tip is introduced and their vibrational amplitudes
of low-frequency modes are enhanced in IETS. In addition, the IETS shows the doublet
feature in the regions of frustrated rotation and C-O stretching, respectively, due to the change
of geometry of CO(ads). Furthermore, an anharmonic coupling between the low-frequency and
high-frequency modes is investigated by using a short-time Fourier transform (STFT)[3] and
single frequency pass filtter (SPFP)[4] approach. Finally, the key issue regarding to the
activation of the low-frequency modes by a Ag5 cluster STM-tip to cause the desorption
process of CO(ads) is addressed.
Figure 1. The spectrogram obtained by STFT analysis of IETS spectrum for the
Ag5(planar-tip)-CO(ads) adsorbed on the Ag(110) surface and corresponding structural changed
during 6ps MD simulation. The two kind of frustrated rotation motions are shown in inserted
Figure by SFPF analysis.
[1] Jyh Shing Lin, Shao-Yu Lu, Po-Jung Tseng and Wen-Chi Chou, J Comp. Chem., 33, 1274-1283 (2012).
[2] Shao-Yu Lu and Jyh-Shing Lin, J. Chem. Phys., 140, 024706 (2014).
[3] Yung-Ting Li and Jyh-Shing Lin, J Comp. Chem, 36, 2697-2706 (2013).
[4] Jen-Ping Su, Yung-Ting Lee, Shao-Yu Lu and Jyh Shing Lin, J Comp. Chem, 34, 2806-2815 (2013).
The Theoretical Studies of interstitial Boron in SiGe alloy
Ze-hui Yan, Yu-Wei Huang, Shyi-Long Lee*
國立中正大學暨生物化學系 621 嘉義線民雄鄉大學路一段 168 號
For years, the boron diffusion in Si and SiGe alloy have been extensively studied
because it play an important issues in Si-based semiconductor device. As the size of
devices components decreasing, the ultrashallow pn junction in the complementary
metal-oxide semiconductor (CMOS) is required in manufactory. The critical issues
in the formation of shallow junctions is the anomalous diffusion of dopant during
rapid thermal annealing (RTA) after ion implantation. The phenomenon is called
transient enhanced diffusion (TED). It is known that the B diffusion is dominated by
the self-interstitial (Sii) defect1 and the Boron TED is suppressed by Ge. The origin
of the retarded Boron diffusion is not clearly resolved, hence the formation of B-Sii
complexes in Si and SiGe alloys was investigated here.
In this work, the effects of Ge atoms on interstitial Boron in SiGe alloys were
investigated by using the density functional theory. The formation of B-Sii
complexes at neutral, positive and negative charged state in different configuration
SiGe alloys were studied here. Our computational results shows that the formation
energies of B-Sii complexes were slightly affected by replacing one Ge atom, even
we change the distance between Boron and Ge. The differences of the B-Sii
formation energies between pure Si and SiGe are all less than 0.1eV, while the
positive 110-split are unstable. As the number of Ge atoms increases, the formation
energies increases more significantly, when replacing four Ge atoms in the first
nearest neighboring positon of Boron, the largest different value up to 0.34eV,
causing the suppression of Boron transient enhanced diffusion.
References:
1. A. Ural, P. B. Griffin, and J. D. Plummer, J. Appl. Phys. 1999, 85
2. Windl, W. Bunea, M. Stumpf, R. Dunham, S. Masquelier, M. Physical Review Letters 1999, 83
3. Bang, JunhyeokKang, JoongooLee, Woo-jinChang, K.Kim, Hanchul. Physical Review B 2007, 76
Theoretical Study on the Reaction of C2 with C6H2
Yi-Lun Sun and Shih-Huang Lee
National Synchrotron Radiation Research Center, Hsinchu, Taiwan
Email: [email protected]
A product with a gross formula of C8H (m/z = 97 u) was observed in the experiment of
the reaction of C2 with C6H2 using a crossed molecular-beam apparatus and synchrotron
vacuum-ultraviolet ionization. In order to interpret the experimental observations, we
investigated the reaction mechanisms of C2 with C6H2 by the theoretical calculations. We used
B3LYP and CCSD(T) methods with aug-cc-pVDZ and aug-cc-pVTZ basis sets to calculate
structures and energies of reactants, intermediates, transition states, and products located on
the potential energy surface. The product C8H can be produced via H elimination from the
intermediate C8H2. The energy of triplet state C2 is higher than the singlet state C2 by 3.8
kcal/mol. Thus, the reactions of both singlet and triplet state C2 were considered in this
research. The calculated results show that there were four entrance channels in the singlet
state surface without barriers and the product C8H was lower than the reactant by 4.4 kcal/mol.
However, we found one entrance channel with a 3.3 kcal/mol barrier and three entrance
channels without any barrier in the triplet state surface. The product C8H was lower than the
reactant C2(T) + C8H2 by 8.2 kcal/mol.
The Catalytic Cycle of Water in CO Oxidation on
Ag(111): the Role of HO 2
Wen-Shyan Sheu* and Ming-Wen Chang
Department of Chemistry, Fu-Jen Catholic University, Xinzhuang, New Taipei City
24205, Taiwan, R. O. C.
*Corresponding author. Tel.: +886 2 29053724; Fax: +886 2 29023209.
E-mail: [email protected] (W.-S. Sheu).
ABSTRACT
The reaction mechanism for the oxidation of CO on Ag(111) in the presence of
trace amounts of water is investigated via density-functional-theory calculations. A
four-step cycle for the reaction is proposed: (1) H2O + O2 → HO + HO2; (2) HO2 +
CO → OH + CO2; (3) CO + OH  cis-OCOH; (4) cis-OCOH + OH  CO2 + H2O.
In the mechanism, water is found to directly participate in the reaction as a catalyst, in
addition to the previously proposed role of stabilizing the adsorbed oxygen molecules
on Ag(111). Moreover, HO2 is an important reaction intermediate, which is produced
via a hydrogen transfer from water to an oxygen molecule. Because the overall
reaction barrier is as low as 0.20 eV, the mechanism is expected to be operative at low
temperatures.
摘要
Probing water micro-solvation in proteins by water catalysed
proton-transfer tautomerism
利用經由水催化之質子轉移互變異構現象探討蛋白質中微水合作用
Jiun-Yi Shen (沈俊義)1, Wei-Chih Chao (趙偉志)1, Chun Liu (劉駿)1, Hsiao-An Pan
(潘校安)1, Hsiao-Ching Yang (楊小青)2, Chi-Lin Chen (陳其霖)1,2, Yi-Kang Lan (蘭
宜康)2, Li-Ju Lin (林麗如)3, Jinn-Shyan Wang (王進賢)3, Jyh-Feng Lu (盧志峰)3,
Steven Chun-Wei Chou (周君偉)1, Kuo-Chun Tang (唐國鈞)1, Pi-Tai Chou (周必泰)1
1
Department of Chemistry and Center for Emerging Material and Advanced Devices,
National Taiwan University, Taipei, Taiwan
台灣大學化學系及物質元件中心
2
Department of Chemistry, Fu-Jen Catholic University, New Taipei City, Taiwan
輔仁大學化學系
3
School of Medicine, Fu-Jen Catholic University, New Taipei City, Taiwan
輔仁大學醫學系
Scientists have made tremendous efforts to gain understanding of the water molecules
in proteins via indirect measurements such as molecular dynamic simulation and/or
probing the polarity of the local environment. Here we present a tryptophan analogue
that exhibits remarkable water catalysed proton-transfer properties. The resulting
multiple emissions provide unique fingerprints that can be exploited for direct sensing
of a site-specific water environment in a protein without disrupting its native structure.
Replacing tryptophan with the newly developed tryptophan analogue we sense
different water environments surrounding the five tryptophans in human thromboxane
A 2 synthase. This development may lead to future research to probe how water
molecules affect the folding, structures and activities of proteins.
Unique Excited-State Conformational/Electronic Responses of Saddle-Shaped N,N'Disubstituted-dihydrophenazines: Wide-Tuning Emission from Red to Deep Blue
獨特地激發態構象/電子响應之馬鞍形 N,N'-二取代二氫吩嗪：
宽调谐发射从红到深蓝色
Zhiyun Zhang 張志雲, Yu-Sin Wu 吳毓心, Chi-Lin Chen 陳其霖, and Pi-Tai Chou 周必泰*
Department of Chemistry, National Taiwan University, Taipei, 10617 Taiwan, R.O.C.
國立台灣大學化學系
Understanding excited-state process of luminophore is a long-standing challenge relevant to many phenomena,
such as large Stokes-shifted and/or multi- emissions, and environment-sensitive emissions. In this work, a tailored
strategy is utilized to modify
5,l0-dimethylphenazine (DMP) to donor-acceptor type N,N-disubstituteddihydrodibenzo[a,c]phenazines (DMAC (N,N-dimethyl), DPAC (N,N-diphenyl) and FlPAC (N-phenyl-Nfluorenyl)), exhibiting significant and varied nonplanar distortions (i.e., saddle-shaped) as a result of steric hindrance.
All compounds exhibit anomalously large Stokes-shifted emission (up to ~12000 cm-1) in solvents with slightly
polarity dependence, and DPAC and FlPAC also show another very weak and largely separated normal emission with
obvious solvatochromic effect. Furthermore, most of compounds but DMP exhibit prominent normal Stokes shifted
emission in rigid environments, and both DPAC and FlPAC can display a wide-tuning multi-emissions from red to
deep blue via white by proper control of the surrounding media. These results indicate that the symmetry rule, the key
factor responsible for the large red-shifted emission in DMP (Ber. Bunsen. Phys. Chem. 1974, 78, 1348), is not
enough or even does not apply to others. Instead, large excited-state conformational/electronic changes play a crucial
role to the unusual photophysical behaviors of N,N-disubstituted-dihydrodibenzo[a,c]phenazines. Further support is
rendered by the relaxation dynamics and simulation of the potential energy surfaces along the structural relaxation,
and time-resolved techniques are used to demonstrate the precursor-successor type of kinetic relationship. N,Ndisubstituted-dihydrodibenzo[a,c]phenazines, in their excited states, undergo a sequential three-state emission process:
upon photoexcitation, an intramolecular charge transfer reaction (1CTunrelaxed) happens instantly from donor to acceptor
units, and subsequently stabilized by the solvent polarity and accompanied/followed by suitably structural changes to
a new electronic density distribution (1CTrelaxed), and finally goes for a more planar configuration (1P) with large
skeletal motion and charge redistribution to extend the -delocalization for lowering the energy in the excited state.
Molecular Dynamics Simulations of Water Coupled Antifreeze Protein
Motions in Probing the Water-Ice Recognition Mechanism
分子動力模擬抗凍蛋白水耦合運動探測冰水辨識機理研究
Chi Wei (曲薇), Hsiao-Ching Yang (楊小青)*
Department of Chemistry, Fu Jen Catholic University, Hsinchuang, Taipei, Taiwan
(天主教輔仁大學化學系) E-mail:[email protected]
Antifreeze proteins (AFPs) protect the various organism from freezing injury with
protecting the growth of ice crystals, which if uncontrolled may fatal to organism cells.
AFPs have been found in fishes, plants, Insects and bacterium. The significant
characterization of AFPs is the ability for binding to ice crystal or the inhibition the ice
growth, which play an important role in many application and biology. Although many
reports had demonstrated the power of AFPs, how the water environment influence the
recognition mechanism of AFPs interaction with ice is rare. We develop the smart-jump
sampling approach and molecular dynamics simulation to investigate how water
interacts with AFPs in different temperature control environments. We are trying to
clarify the water coupled AFPs dynamics behavior–characterization of the ice-like
structures, exploring the surface induced recognition mechanism. Our results so far
reveal the water-protein interface environments for MpAFP (Marinomonas
primoryensis), that could be divide into two major factors. One is the grooved
recognition effect induced the ice-like structures in the ice binding site interface and the
other is the hydrophobic effect of the polypeptide backbone of the AFPs for the control
of the ice-like structure size (Fig.1).
Figure 1. (a) AFP Anchord clathrate grooved effect with water binding strutre. (b) Characterization of the
water binding antifreeze protein to ice-like structures.
References
[1] Garnham, C. P.; Campbell, R. L.; Davies, P. L. Anchored clathrate waters bind antifreeze proteins to
ice. PNAS 2011 , 108, 7363-7367.
[2] Jorov, A.; Zhorov, B.; and Yang, D. S. C. Theoretical study of interaction of winter flounder antifreeze
protein with ice. Protein Science 2004, 11, 1524-1537 .
[3] Lorv, J. S. H.; Rose, D. R.; and Glick, B. R. Bacterial Ice Crystal Controlling Proteins. Scientifica
Review 2014.
Probing Water Environment of Trp59 in Ribonuclease T1:
of the Structure−Water Network Relationship
Insight
透過偵測核糖核酸酶中色氨酸周圍的微水環境變化來探討蛋白質結
構與微水結構之交互關聯性
Shih-Hui Weng(翁詩惠), Cheng-Han Yang (楊承翰) ,Yi-Ching Kuo(郭宜靜),Hsiao-Ching Yang (楊
小青)*
Department of Chemistry, Fu Jen Catholic University, Hsinchuang, Taipei, Taiwan 24205 (新北市新莊
區,輔仁大學化學系)Tel: 02-2905-2534 ; E-mail: [email protected]
In this study, we used the tryptophan analogue, (2,7-aza)Trp, which exhibits water catalyzed proton
transfer isomerization among N(1)-H, N(7)-H, and N(2)-H isomers, to probe the water environment of
tryptophan-59 (Trp59) near the connecting loop region of ribonuclease Tl (RNase T1) by replacing the
tryptophan with (2,7-aza)Trp. The resulting (2,7-aza)Trp59 triple emission bands and their associated
relaxation dynamics, together with relevant data of 7-azatryptophan and molecular dynamics (MD)
simulation, lead us to propose two Trp59 containing conformers in RNase T1, namely, the loop-close
and loop-open forms. Water is rich in the loop-open form around the proximity of (2,7-aza)Trp59,
which catalyzes (2,7-aza)Trp59 proton transfer in the excited state, giving both N(1)-H and N(7)-H
isomer emissions. Existence of N(2)-H isomer in the loop-open form, supported by the MD simulation,
is mainly due to the specific hydrogen bonding between N(2)-H proton and water molecule that bridges
N(2)-H and the amide oxygen of Pro60, forming a strong network. The loop-close form is relatively
tight in space, which squeezes water molecules out of the interface of α-helix and β2 strand, joined by
the connecting loop region; accordingly, the water-scant environment leads to the sole existence of the
N(1)-H isomer emission. MD simulation also points out that the Trp-water pairs appear to
preferentially participate in a hydrogen bond network incorporating polar amino acid moieties on the
protein surface and bulk waters, providing the structural dynamic features of the connecting loop
region in RNaseT1.
Keywords: ribonuclease Tl, (2,7-aza)Trp, MD simulation, hydrogen bond network
Reference :
[1] Wei-Chih Chao, Jyh-Feng Lu, Jinn-Shyan Wang, Hsiao-Ching Yang, et.al Chou, Biochemistry, 2013,
52, 1113−1121
[2] Wei-Chih Chao, Hsiao-Ching Yang,* Jinn-Shyan Wang, Jyh-Feng Lu, Pi-Tai Chou,* Nature
Commun., 2013, 4, 2611.
Probing the Channel Regulation Step to Prostaglandin Isomerization
Mechanism by Cytochrome P450 Thromboxane Synthase
探討前列腺素在細胞色素 P450 血栓素合成酶通道調的異構化反應機制
Tai-An Pan(潘泰安) and Hsiao-Ching Yang* (楊小青)
Department of Chemistry, Fu Jen Catholic University, Hsinchuang, Taipei, Taiwan
(天主教輔仁大學化學系) E-mail:[email protected]
Thromboxane synthase (TXAS) belongs to the cytochrome P450 (CYP450) family
proteins. TXAS catalytic the isomerization prostaglandin H2 to thromboxane
A2(TXA2). We try to confirm that the substrate binding and catalytic activity is
associated with the substrate recognition sites (SRSs). The present evidence indicates
that there are six water micro-solvation SRS regions, SRS-1 to SRS-6 in sequence
assay, in assembly of the protein channel connecting to the buried heme site (Fig. 1a).
To explore the minimum energy path (MEP) along the channel regulation
coordination and study the substrate dynamics of passage through the dividing surface
separating reactants from products. We developed a smart-jump sampling and
performed molecular dynamics simulations to investigate the water coupled channel
regulation behavior and the relevant amino acids cluster guiding the stereo-selectivity
Energy (kcal/mol)
of eicosanoid PGH2. Our results reveal the nonbonding interactions, Van der Waals,
electrostatics and H-bonding along the MEP (Fig. 1b) and “flip-jump” motion of
PGH2 has been demonstrated to be involved in channel regulation of multistate
kinetics mechanism.
0
Interaction
VdW
Electrostatic
H-bonds
-20
-40
-60
-80
-2 0 2 4 6 8 10 12 14 16 18 20
RMSD
Figure 1. (a) TXAS channel with buried heme site. (b) Analysis of eicosanoid PGH2
binding energy along the MEP.
References
1. Wei-Chih Chao; Jyh-Feng Lu; Jinn-Shyan Wang; Hsiao-Ching Yang; Hsiao-Hui Chen; Yi-Kang Lan;
Ya-Chien Yu; Pi-Tai Chou, and Lee-Ho Wang. , J. Am. Chem. Soc., 2011, 133 (46), pp 18870–18879
2. Wei-Chih Chao; Jyh-Feng Lu; Jinn-Shyan Wang; Hsiao-Ching Yang; Tai-An Pan; Steven Chun-Wei;
Chou Lee-Ho Wang; Pi-Tai Chou. , Biochemistry,2013, 52 (6), pp 1113–1121
3. Jiun-Yi Shen; Wei-Chih Chao; Chun Liu; Hsiao-An Pan; Hsiao-Ching Yang; Chi-Lin Chen;
Yi-Kang Lan; Li-Ju Lin; Jinn-Shyan Wang. , Nat. Commun, 2013, 4,2611
Vibrational Levels of the C3Ar van der Waals complex
Yi-Ren Chen, K. S. Tham, Yi-Jen Wang, and Yen-Chu Hsu
Institute of Atomic and Molecular Sciences
Academia Sinica
P. O. Box 23-166, Taipei 10617, Taiwan, R. O. C.
The ground electronic state of the C3 molecule has an extremely low bending
vibrational frequency in comparison to other triatomic molecules. As a result the
vibrational level structure of C3Ar is expected to be very complicated, with no
fewer than four large-amplitude motions. To help assign the wavelength resolved
emission spectra of C3Ar1 and to understand the dynamics of its electronic states,
we have carried out MCTDH (Multi-channel time dependent Hartree) calculations2
of its lowest vibrational levels. The kinetic operators were derived from Yang and
Kühn.3 The ab initio 4D potential energies of C3Ar at the level of CCSD(T)/ccpVQZ were calculated for the following ranges:  C-C-C=112-248, vdW bond
length=3.4-6.0 Å , and vdW bond angles= 0-180 (azimuth) and 0-90 (colatitude);
the C-C bond length was fixed at 1.2981Å , Assuming that only the four low
frequency modes of the complex are perturbed by the Ar atom, the 6D potential
energy function was obtained by adding the 2D C-C stretching energies of free C3
to the calculated 4D potential energies of the Ar complex.
The calculated wavefunction of the zero point level of the complex suggests
that the C3 moiety of the complex is bent, rather than linear, as is free C3. The two
lowest energy excited vibrational levels are the out-of-plane and in-plane vdW
bending fundamentals. The wavefunctions of the first few levels show evidence of
strong coupling among the four low frequency modes. Calculations of the higher
vibrational levels are in progress.
References,
1. G. Zhang, B.-G. Lin, S.-M. Wen, and Y.-C. Hsu, J. Chem. Phys. 120,
3189 (2004).
2. H.-D. Meyer and G. A. Worth, Theor. Chem. Acc. 109, 251(2003).
3. Y. Yang and O. Kühn, Mol. Phys. 106, 2445(2008).
Mimicking the Organometallic Complexes for Small Molecule Activation: A
Computational Exploration Using Nitrogen doped Carbon Nanotube
Yu-Te Chan, Hsiang-Chun Yeh, Yu-Jou Huang, Ming-Kang Tsai*
Department of Chemistry, National Taiwan Normal University, Taipei 10677, Taiwan.
N doped carbon material have been study as a ORR catalysts where pyridinic-N and graphitic-N are
believed to exist in these material.1,2 In the present study, we explored the structure and chemical adsorption
properties of 3d and 4d transition metal incorporated into carbon nanotube and graphene (TM-xN-CNT, x =
3, 4)5,6 using density functional theory and showed that the d band splitting is related to ligand field
introduced by the curvature of N doped carbon nanotube. The split of the d band of the mounted TM also
affects the electronic structure of TM-xN-CNT via the displacement of Fermi level, subsequently transform
he pristine CNT into metallic or semiconductor. We would also discuss the adsorption properties for the
small molecule activation in terms of CNT curvature for the potential catalytic applications.
Unit cell size
Higher curvature
Higher density
Reference
1. Oh, H.-S.; Oh, J.-G.; Roh, B.; Hwang, I.; Kim, H. Electrochem.Commun. 2011, 13, 879.
2. Kiuchi, H.; Niwa, H.; Kobayashi, M.; Harada, Y.; Oshima, M.;Chokai, M.; Nabae, Y.; Kuroki, S.;
Kakimoto, M.-a.; Ikeda, T.; Terakura, K.; Miyata, S. Electrochim. Acta 2012, 82, 291.
3. Medard, C.; Lefevre, M.; Dodelet, J.; Jaouen, F.; Lindbergh, G.Electrochim. Acta 2006, 51, 3202–3213.
4. Charreteur, F.; Jaouen, F.; Ruggeri, S.; Dodelet, J.-P. Electrochim.Acta 2008, 53, 2925–2938.
DENSITY FUNCTIONAL THEORY STUDY OF THE MECHANISMS OF
CLAISEN REARRANGEMENT OF ARYL PROPARGYL ETHER IN THE
PRESENCE OF CESIUM FLUORIDE.
MENGISTU GEMECH (1), V. SRINIVASADESIKAN (2), SHYI-LONG LEE (1)*
(1): Department of Chemistry and Biochemistry, National Chung Cheng University, Taiwan.
(2): Department of Chemistry, National Chio Tung University, Taiwan.
ABSTRACT
Ishii1 and co-workers reported that the Claisen rearrangement of an aryl propargyl ether in the presence
of CsF led to exclusive formation of 2-methylarylfuran in excellent yield. The accepted mechanism2 for
formation of arylfuran and arylpyran from aryl propargyl ether under the condition of Claisen
rearrangement involves a concerted pericyclic [3,3]-sigmatropic rearrangement. A computational study
of the mechanisms of the Claisen rearrangement of aryl propargyl ether in the presence of CsF has been
performed by using DFT calculations. Our calculations indicated that the [3,3]- sigmatropic
rearrangement is the rate limiting step for the formation of arylfuran with G value of 37.1 kcal/mol in
N,N-diethylaniline solvent phase. Furthermore, the calculation results reveal that the enolization of
-allenyl ketone suffered from a higher energetic barrier and indeed unlikely to allow the
rearrangement reaction to proceed towards arylpyran cyclization. However, the abstraction of the
-hydrogen atom in the -allenyl ketone has a very low activation barrier and is the favored pathway
for the Claisen rearrangement of aryl propargyl ether in the presence of CsF. The effect of substituents,
both on phenyl ring and propargyl moiety, on the kinetics of the title reaction was also investigated.
Figure 1. Accepted mechanism for formation of arylfuran and arylpyran from aryl propargyl ether
under the condition of Claisen rearrangement.
References
[1] Ishii H., Ishikawa T., Takeda S., Ueki S. and Suzuki M, Chem. Pharm. Bulletin, 40, 5, (1992),
1148-1153.
[2] Zsindely J. and Schmid H. Helv. Chim. Acta. 51, (1968), 1510.; Hansen H.-J. and Schmid H. Chem.
Brit. 5, (1969), 111.
Theoretical Investigations on Electronic Spectra of
Protonated Pyrene
Chih-Hao Chin and Yu-Jong Wu
National Synchrotron Radiation Research Center,
101 Hsin-Ann Road, Hsinchu Science Park, Hsinchu, Taiwan
Keywords:(protonated pyrene, absorption spectrum, Franck-Condon, electronic
structure)
The electronic absorption spectrum of protonated pyrene has been recorded in the
visible spectral region, evidencing that absorptions appear largely red shifted in
comparison to that of pyrene. A set of quantum chemistry calculations, the harmonic
potential surfaces of the ground state (S0) and the first (S1) excited state of
protonated pyrene were investigated, and the electronic structures of the two states
were calculated and characterized using the time-dependent density functional
theory method in the adiabatic representation. The displaced harmonic oscillator
approximation is used to simulate the absorption spectrum of the S1 state along with
the Franck–Condon approximation [1]. The assignment of main vibronic transitions
was made for S1 state. A tentative plausible assignment has been proposed, which
takes into account a weak coupling between these electronic states. Our result shows
that the vibronic structures were dominated by the totally symmetric modes with
predicted intervals of 539 and 734 cm-1 and this agrees with the experimental
observations in solid neon matrices [2]. The present S1 state calculated in the
adiabatic representation effectively includes contribution from the adiabatic vibronic
coupling through the conical intersection.
References:
1. Chin, C.-H.; Mebel, A. M.; Kim, G.-S.; Hayashi, M.; Liang, K. K.; Lin, S. H. Theoretical
investigations of spectroscopy and excited state dynamics of adenine. Chem. Phys. Lett. 2007,
445, 361-369.
2. Garkusha, I.; Fulara, J.; Sarre, P. J.; Marier, J. P. Electronic absorption spectra of protonated
pyrene and coronene in neon matrixes. J. Phys. Chem. A 2011, 115, 10972-10978.
Table of content
報名代號：
分組編號：(主辦單位填寫)
Theoretical Study on the Prebiotic Strecker Synthesis of
Alanine Catalyzed by Water, Ammonia and the Chiral
Molecules
Chia-Yu Peng (彭家瑜),
Hsiao-Han Chuang (莊曉涵), Wei-Ping Hu (胡維平)*
Department of Chemistry and Biochemistry, National Chung Cheng University,
Chia-Yi, Taiwan
Keywords: alanine, prebiotic, chirality
The mechanisms and reaction paths of the prebiotic strecker synthesis of
alanine catalyzed by water, ammonia and the chiral molecules have been
studied by micro-solvation and PCM model. The calculated results at
MP2/6-31+G** level showed the high energy barriers of 31 and 46
kcal/mol in the uncatalyzed reaction for first and second steps,
respectively, it also showed that the reaction catalyzed by water and
ammonia could significantly reduce the barriers by 20 -30 kcal/mol.
When the reaction catalyzed by the chiral molecule CH 3 CHCl(OH);
interestingly, not only the barrier could be reduced by 20 -30 kcal/mol,
but the different optically active products (D - and L-Alanine) gave the
difference between both barriers of 0.6 kcal/mol. This result suggest the
chiral catalyst in prebiotic condition might be one of the possible reasons
for the majority of the L-amino acids in nature.
References:
Strecker, A. Liebigs Ann. 1954, 91, 349.
2. Shaw, A. M. Astrochemistry; Wiley, 2006.
3. Shibasaki, M.; Kanai, M.; Mita, K. Org. React. 2008, 70, 1.
1.
報名代號：
分組編號：(主辦單位填寫)
Theoretical Study on the isoelectronic OSO and SOO isomers
OSO 與 SOO 等電子化合物的理論預測
Ching-Chan Lin(林經展), Wei-Ping Hu*(胡維平)
Department of Chemistry and Biochemistry, National Chung Cheng University,
Chia-Yi , Taiwan
Keywords: isoelectronic ;sulfur compounds;
本篇使用 MP2、DFT 與 CCSD(T) 等方法計算與 O3 等電子化合物 SOO
與 OSO，並以 CASPT2、MRCISD+Q 等方法對 SOO 與 OSO 計算其結構及
能量，並探討 SOO 與 OSO 等電子化合物是否存在 cyclic form，並且比較 open
form 和 cyclic form 兩種結構的相對能量。計算結果顯示，以
B3LYP/aug-cc-pVTZ 計算出的結構在 MRCISD+Q 方法下，從 open-OSO 到
open-SOO 的反應能障 138.9 kcal/mol ；open-OSO 到 cyclic-OSO 的反應能障
115.6 kcal/mol 。將 OSO 結構固定在 CS 點群條件，計算 OSO 與 SOO 激發
態能量，得知 open-OSO 到 open-SOO 的 TS 激發態在 Cs 1A' 、1A'' 位能曲面
產生交會，而 open-OSO 到 cyclic-OSO 的 TS 激發態能量，在 Cs 1A' 、1A'' 位
能曲面則沒有交會。從 open-OSO 分解成 SO+O 與 S+O2 ，能量分別為 149.6
kcal/mol 與 145.2 kcal/mol 。於是我們推測 open-OSO 與 open-SOO 可能穩定存
在，cyclic-OSO 則較不穩定存在。
References:
Jien-Lian Chen and W.-P. Hu, J.Am. Chem. Soc, 2011 133, 16045
報名代號：LM0704-006
分組編號：(主辦單位填寫)
The MC-DFT Approach Including the MC-MP4 Energies
using "Calendar" Variations for the Dunning-Type Basis
Sets
Chia-Yu Peng,Wei-Hong Lin, Wei-Ping Hu*
Department of Chemistry and Biochemistry, National Chung Cheng University,
ChiaYi , Taiwan
Keywords: MC-DFT, SCS-MP2
本篇研究中，我們開發了一種新的 DFT 方法並測試其計算效能。此方法
結合本實驗室先前所開發的 multicoefficient density functional theory (MC-DFT)
及 spin-component-scaled second-order Møller-Plesset perturbation (SCS-MP2) 理
論，並額外增加 E3、E4 能量校正。本方法中我們使用 Dunning-type basis set 以
及經 Truhlar 團隊簡化高角動量 diffuse functions 之 "calendar" 系列 basis sets，
希望能夠提高計算效率。研究結果顯示表現最好的 functional DSD-BLYP 搭配
cc-pVDZ、aug-cc-pVDZ、may- cc-pVTZ 三個基底線性組合，然後將 SCS-MP2
搭配 cc-pVDZ、aug-cc-pVDZ、cc-pVTZ 三個基底線性組合進行計算，其 mean
unsigned errors (MUE)為 0.77 kcal/mol，但卻只需約 DSD-BLYP/aug-cc-pVTZ
(MUE =1.36 kcal/mol) 44% 的計算時間，若再進一步加入 E3、E4 能量校正，
我們發現 DSD-BLYP 部分改為搭配 cc-pVDZ、aug-cc-pVDZ、cc-pVTZ 效率較
高，其誤差為 0.73 kcal/mol 並只需花費 DSD-BLYP/aug-cc-pVTZ 47% 的計算時
間。
References:
1. Chen, J.-L.; Hong, J.-T.; Wu, K.-J.; Hu, W.-P. Chem. Phys. Lett. 2009, 468, 307.
2. Papajak, E.; Zheng, J.; Leverentz , H. R.;Truhlar,D. G. J. Chem. Theory Comput
2011, 7. 3027.
報名代號：LM0704-008
分組編號：(主辦單位填寫)
Theoretical Study on Metal-Containing Noble-Gas Anions
含金屬之惰性氣體陰離子的理論探討
JUN-Yl FU, Ching-Chan Lin,Wei-Ping Hu*
Department of Chemistry and Biochemistry, National Chung Cheng University,
Chia-Yi , Taiwan
Keywords: noble-gas; mental;
本研究以理論預測 MO-NgO 類型的陰離子(M=Li, Na, K, Cu, Ag, Au, Al
等金屬) ，並探討(1) MO-+ Ng + O(S) (2) MO +Ng + O- (3) Ng+ XO2-三種可能
的分解路徑。目前研究發現 MO group 的電子親和力 (EA)對路徑(2) MO +Ng
+ O- 的反應能影響甚大，是決定陰離子穩定度的關鍵，一般來說 MO group 的
電子親和力越大越利形成穩定的鈍氣陰離子。在 MP2/aug-cc-pVTZ 方法下，以
MO-NgO 為例，可看到隨著 EA 值從 24.2 kcal/mol(M = K) 增加至 78.2 kcal/mol
(M = Al)，路徑(2) 的反應能量從-25.2 kcal/mol 增加到 27.9 kcal/mol。此外，
本研究也發現 AlO-ArO
在路徑(3)的反應能障為 20.1 kcal/mol，在低溫下應該
可以穩定存在。也預測含硼之 BO-NgO 與 OB-NgO 類型的陰離子，試著探討不
同惰性氣體原子對此類陰離子的穩定性，在 MP2/aug-cc-pVTZ 方法下，以
ONgOB-為例，可看到惰性氣體從 He 至 Kr，其陰離子能量從放熱 24.9 kcal/mol
到吸熱 16.4kcal/mol，可以預測 ONgOB-類型的陰離子會隨著惰性氣體的原子序
變大而趨於穩定。
References:
1. Tsung-Hui Li; C.-H. Mou; H.-R. Chen; W.-P. Hu, J.Am.Chem. Soc. 2005, 127,
9241.
報名代號：
分組編號：(主辦單位填寫)
Tunneling Effects in Bimolecular Nucleophilic Substitution
(SN2) Reactions
Wan-Chen Tsai (蔡婉甄), Chong-En Wang (王崇恩), Wei-Ping Hu* (胡維平)
Department of Chemistry and Biochemistry, National Chung Cheng University
Chia-Yi 62102, Taiwan
Keywords: SN2, VTST/MT, KIE
離子-分子親核取代反應 (SN2) 在有機化學中是很常見的反應，而 SN2 反應
其離子和分子間的作用力會隨著反應在氣態、氣態微水合和水溶液中環境的不
同而有不同的性質，且在動力學上的特性也會有些許的差異。本研究利用雙層
VTST/MT (dual-level dynamics approach with variational transition state theory
including multidimensional tunneling) 計算三個 SN2 反應: (1) 氣態 CN+CH3F，
(2) 氣態微水合 OH(H2O)+CH3F，(3) 水溶液 OH+CH3F 的反應速率常數與
動力學同位素效應，此三個反應代表不同程度的水合情況。計算結果顯示，此
三個反應能障分別為 11.7、5.1 及 16.2 kcal/mol，而在室溫下穿隧效應對反應速
率就有不可忽略的貢獻，而在低溫下穿隧效應則有更明顯的貢獻。此外，當以
13C
及 14C 取代 alkyl halide 中心原子時，反應在低溫下有呈現明顯的動力學
同位素效應 (kinetic isotope effects, KIEs)，以 OH+CH3F 在水溶液中的反應為
例，其 KIE(CD3) 在 35 K 時為 0.608，而 KIE(13C) 和 KIE(14C) 在 35 K 時分
別可高達 7 以及 40，可得知此三個 SN2 反應的穿隧效應主要是由 alkyl halide
的中心碳原子參與，而不是一般認為質量較小的 primary hydrogens。
References:
1. Garver, J. M.; Fang, Y.-R.; Eyet, N.; Villano, S. M.; Bierbaum, V. M.; Westaway,
K. C. J. Am. Chem. Soc. 2010, 132, 3808.
2. Liu, Y.-P.; Lu, D.-H.; Gonzalez-lafont, A.; Truhlar, D. G.; Garrett, B. C. J. Am.
Chem. Soc. 1993, 115, 2408
報名代號：LM0704-009
非環鹵烷與環鹵烷類之 SN2 和 E2 的動力學分析
0574
Wan-Sam Lu, Wei-Ping Hu*
Department of Chemistry and Biochemistry, National Chung Cheng University,
Chia-Yi , Taiwan
Keywords: KIEs , SN2，E2
有機化學中，雙分子親核基取代(SN2)和消去(E2)反應性質的研究一直是受
到高度重視的課題， SN2 和 E2 的反應物相同，兩反應卻可能互相競爭，而在
分析上，由於產物陰離子相同，實驗上很難分辨主要的反應途徑，但從 deuterium
kinetic isotope effects (KIE)常可做正確的判斷，但過去研究都著重在直鏈或有支
鏈的鹵烷類的反應，對於環烷類則少有探討。本研究我們將比較環鹵烷與非環
鹵烷的 SN2 及 E2 的各種反應性質。
此研究探討的反應為 RBr+ SH- (R=CH3CH2、(CH3)2CH、(CH3)3C、C5H9、
C6H11)，我們使用 MP2/aug-cc-pVDZ 方法計算這一系列反應 RBr+ SH(R=CH3CH2、(CH3)2CH、(CH3)3C、C5H9)的 SN2 和 E2 路徑下的反應能量和反
應能障，並利用高階理論 CCSD(T)搭配 aug-cc-pVTZ 來計算單點，再將高階理
論所得的反應能障以過渡態理論(TST)來計算反應速率以及動力學同位素效
應。所使用的計算軟體是 Gaussian 09。
References:
1.
2.
DePuy, C. H.; Gronert, S.; Mullin, A.; Bierbaum, V. M., Gas-phase SN2 and E2
reactions of alkyl halides. Journal of the American Chemical Society 1990, 112
(24), 8650-8655.
Al - Ar: T.H. Dunning, Jr., K. A. Peterson and A. K. Wilson, J. Chem. Phys.
114, 9244 (2001).
報名代號：LM0704-005
分組編號：(主辦單位填寫)
Theoretical Prediction of Near-edge X-ray Absorption Fine
Structure of Peptides
Cheng-Cheng Tsai (蔡承成) Wei-Ping Hu* (胡維平)
Department of Chemistry and Biochemistry, National Chung Cheng University
Chia-Yi 62102, Taiwan
Keywords: NEXAFS, TDDFT, PEPTIDE
近年來由於 X-ray 光譜技術的發展，研究 Near edge X-ray absorption fine
structure (NEXAFS)是探討分子內化學環境的一種途徑，NEXAFS 光譜會因為
細微的化學環境不同而有所差異，二者之間的對應關係目前並沒有做很多系統
性的研究，近年來實驗上有意發展此種對應關係成為一種偵測技術，理論上的
模擬方法也因為如此而蓬勃發展。本研究藉由 TDDFT 理論來計算 peptide
(Glycine-Tyrosine)的 carbon K-edge NEXAFS 光譜，並且與過去文獻上的實驗光
譜相比較。本研究中分子結構最佳化方法是 B3LYP/6-311+G(d,p)，NXAFS 光
譜計算方法是 TD-LB94/6-31+G(d,p)。計算結果顯示，在較低能量區域 明顯的
吸收都是對應到苯環結構上碳的 1s → π*的 core excitation，較高能量區域則是
激發 carboxyl group 的碳到 π*以及一些碳的 1s → Rydberg orbitals，且對於化
學環境不同的原子，激發其 1s 電子所需的 core excitation energy 也會有不小的
差異。分子軌域分析的結果也顯示，如果被激發的 1s 電子所在原子旁邊接電負
度較大的原子，則 core excitation energy 會有變高的趨勢，造成能量不同的吸收
峰主要是因為 (1) 被激發電子從不同的 core orbital 出發 (2) 被激發到不同的
virtual orbital 造成的。光譜上高能量的區域在實驗上可能是對應到電子已經游
離的狀態，與 TDDFT 計算還處在個中性分子 bound state 的假設明顯不同，因
此目前高能量區域的光譜仍不易由理論模擬。整體來說目前 TDDFT 方法預測
Near edge X-ray absorption fine structure 結果在較低能量區域是可行的，可以看
出原子的化學環境與光譜的對應關係。
Besley, N. A.; Asmuruf, F. A. Phys. Chem. Chem. Phys. 2010, 12, 12024.
2. Hirata, S.; Head-Gordon, M. Chem. Phys. Lett. 1999, 314, 291.
3. Boese, J.; Osanna, A.; Jacobsen, C.; Kirz, J. J. Electron. Spectros. Relat. Phenom.
1.
1997, 85, 9.
Theoretical Study on the Thiocyanide Formation of
3-mercaptopyruvate Metal and Related Molecular Design
Tung-Lin Wua, Jen-Shiang K. Yua,b,*
a
Department of Biological Science and Technology, National Chiao Tung University
b
Institute of Bioinformatics and Systems Biology, National Chiao Tung University
In this study, computational design of efficient detoxification metal drugs to rescue for
the cyanide poisoning by molecular simulation is attempted. Two molecules of 3mercaptopyruvate (3-MP) are expected to chelate one metallic divalent cationic center
(MMCu and Zn) to form stable four-coordinate complexes. Geometry optimization of
the model complex (1), bis[2-(2-thienyl)-glyoxylato-O,O'] copper(II), is performed using
various density functionals including BP86, B3LYP, TPSS, and PBE. The structure of (1) may
be further reduced into (2) and optimized at identical levels. The geometries of the ligand
coordinations remain almost identical compared to the structure of 3-MP calculated at high
level CCSD theory. The energy profile and the mechanism for the detoxification of the bis[3MP]Cu(II) is proposed (Figure 1): in TS, the thiol group (SH) tends to shift to cyanide and
produce the thiocyanic acid. Subsequently, the thiocyanic acid approaches the oxygen atom of
the carboxyl group and transfers the proton to oxygen, forming thiocyanide, which is less
toxic and can be metabolized easily in urea. Energy profile of the dithiolation reaction is also
constructed.
Figure 1.
Energy profile of the detoxification carried at B3LYP and BP86, The relative energy is based on the
difference to RC state.
[1] Arnaud, C.; Faure, R.; Loiseleur, H. Acta Cryst. (1986). C42, 814-816
Theoretical Study on Relative Stability, Thermal Behaviors and Vibrational
Spectra of OH–(H2O)n, n = 4 – 7
Ren-Jie Lin(林仁傑)a, Quoc Chinh Nguyenb, Kaito Takahashi(高橋開人)a, Jer-Lai Kuo(郭哲來)a*
a
Institute of Atomic and Molecular Science, Academia Sinica, 106 Taipei, Taiwan, ROC.
b
School of Physical and Mathematical Science, Nanyang Technological University, 637371, Singapore
We have demonstrated the relative stability, thermal behaviors and vibrational spectra of deprotonated water
cluster OH–(H2O)n, n = 4 – 7 at B3LYP/6-311+G(d,p) level. There are 20, 65, 168 and 695 isomers of OH–
(H2O)n, n = 4 – 7, respectively. The isomers of deprotonated water clusters are classified into 5 categories
which are multi-ring (MR), double-ring (DR), single-ring (SR), treelike (T) and linear (L). For n = 4 – 7, the
categories of most stable isomers with zero-point energy are SR, DR, MR, MR, respectively. The thermal
behaviors of OH–(H2O)n, n = 4 – 7 are investigated by calculating the canonical heat capacity in classical
harmonic superposition approximation (C-HSA) and quantum harmonic superposition approximation
(Q-HSA) regimes. For studying the structural transitions, the canonical probability or population of each
topology is calculated as a function of temperature. The vibration spectrum is calculated as the sum of the
spectrum of each individual isomer weighted by its corresponding canonical probability. From the results,
the free OH-stretching vibration band is shown that a broad peak around 3600 cm-1 of vibrational spectra of
OH–(H2O)n, n = 4 – 7.