• Bulletin of the Korean Chemical Society
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• v.34 no.4
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• pp.1055-1060
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• 2013

The adsorption structures of threonine on the Ge(100) surface were investigated using core-level photoemission spectroscopy (CLPES) in conjunction with density functional theory (DFT) calculations. CLPES measurements were performed to identify the experimentally preferred adsorption structure. The preferred structure indicated the relative reactivities of the carboxyl and hydroxymethyl groups as electron donors to the Ge(100) surface during adsorption. The core-level C 1s, N 1s, and O 1s CLPES spectra indicated that the carboxyl oxygen competed more strongly with the hydroxymethyl oxygen during the adsorption reaction. Three among six possible adsorption structures were identified as energetically favorable using DFT calculation methods that considered the inter- and intra-bonding configurations upon adsorption onto the Ge(100) surface. These structures were O-H dissociated N dative inter bonding, O-H dissociated N dative intra bonding, O-H dissociation bonding. One of the adsorption structures: O-H dissociated N dative inter bonding was predicted to be stable in light of the transition state energies. We thus confirmed that the most favorable adsorption structure is the O-H dissociated N dative-inter bonding structure using CLPES and DFT calculation.

• Proceedings of the Korean Vacuum Society Conference
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• 2010.02a
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• pp.367-367
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• 2010

The adsorption configurations of S-proline on Ge(100) were studied using scanning tunneling microscopy (STM), density functional theory (DFT) calculations, and high-resolution core-level photoemission spectroscopy (HRCLPES). We identified three adsorption structures of S-proline on Ge(100) through analysis of the STM images, DFT calculations, and HRCLPES results: (i) an 'intrarow O - H dissociated and N dative bonded structure', (ii) an 'O - H dissociation structure', and (iii) an 'N dative bonded structure'. Moreover, because adsorption through the N atom of S-proline produces a new chiral center due to symmetry reduction by N dative bonding, the adsorption configurations have either (R,S) or (S,S) chirality, yielding an (R,S)-'intrarow O - H dissociated and N dative bonded structure' and an (R,S)-'N dative bonded structure', with a preference for reaction at the Re face. This work presents a novel method for generating stereoselective attachment using S-proline molecules adsorbed onto a Ge(100) surface.

• Journal of the Korean Vacuum Society
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• v.15 no.1
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• pp.50-56
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• 2006

We investigated the adsorption of benzene and pyridine on $Si(5\;5\;12)-2\times1$ at 80 K by using variable-low temperature scanning tunneling microscopy (STM) and density functional theory (DFT) calculations. The benzene molecule most strongly binds to two adatoms on the D3 and D2 units in a tilted butterfly configuration, which consists of $di-\sigma$ bonds between C atoms and Si adatoms and two C=C double bonds in the benzene molecule Pyridine molecules interact with adatom(s) on the D2 and D3 units through both Si-N dative bonding and $di-\sigma$ bonds. The dative bonding through the lone pair electrons of N atom produces a vertical configuration (pyridine-like), which is more stable than $di-\sigma$ bonds $Di-\sigma$ bonds can be formed either through Si-N1 and Si-C4 or Si-C2 and Si-C5.

• Proceedings of the Korean Vacuum Society Conference
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• 2012.08a
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• pp.212-212
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• 2012

The Coverage dependent attachment of multifunctional groups included in threonine molecules adsorbed to Ge (100)$-2{\times}1$ surface was investigated using core-level photoemission spectroscopy (CLPES) and density functional theory (DFT) calculations. The core-level spectra at a low coverage indicated that the both carboxyl and amine groups participated in the bonding with the Ge (100) surface by "O-H dissociated and N-dative bonded structure". However, at high coverage level, additional adsorption geometry of "O-H dissociation bonded structure" appeared possibly to minimize the steric hindrance between adsorbed molecules. Moreover, the C 1s, N 1s, and O 1s core level spectra confirmed that the carboxyl oxygen is more competitive against the hydroxymethyl oxygen in the adsorption reaction. The adsorption energies calculated using DFT methods suggested that four of six adsorption structures were plausible. These structures were the "O-H dissociated-N dative bonded structure", the "O-H dissociation bonded structure", the "Om-H dissociated-N dative bonded structure", and the "Om-H dissociation bonded structure" (where Om indicates the hydroxymethyl oxygen). These structures are equally likely, according to the adsorption energies alone. Conclusively, we investigate in threonine on Ge (100) surface system that the "O-H dissociated-N dative bonded structure" and the "O-H dissociation bonded structure" are preferred at low coverage and high coverage.

• Proceedings of the Korean Vacuum Society Conference
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• 2011.08a
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• pp.216-216
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• 2011

We will investigate the bonding configurations of phenylalanine and tyrosine adsorbed on the Ge(100) surface using CLPES and DFT calculations. First, the C 1s, N 1s, and O 1s spectra obtained at 300 K revealed that both the amine and carboxyl groups of phenylalanine and tyrosine concurrently participated in adsorption on the Ge(100) surface without bond breaking using CLPES, depending on the extent of coverage. In the second place, we confirmed that the "O-H dissociated-N dative bonded structure" is the most stable structure implying kinetically favorable structure, and the "O-H dissociation bonded structure" is another stable structure manifesting thermodynamically advantageous structure using DFT calculations. This tendency turns up both phenylalanine and tyrosine, similarly. Furthermore, through the CLPES data and DFT calculation data, we discovered that the "O-H dissociated-N dative bonded structure" and the "O-H dissociation bonded structure" are preferred at 0.30 ML and 0.60 ML, respectively. Moreover, we found that the phenyl ring of phenylalanine is located in axial position to Ge(100) surface, but the phenyl ring of tyrosine is located in parallel to Ge(100) surface using DFT calculations.

• Proceedings of the Korean Vacuum Society Conference
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• 2011.08a
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• pp.215-215
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• 2011

The bonding configuration and adsorption stability of alanine and leucine adsorbed on Ge(100)-2${\times}$1 surface were investigated and compared using core-level photoemission spectroscopy (CLPES) and density functional theory (DFT) calculations. The bonding configuration, stability, and adsorption energies were evaluated for two different coverage levels. In both cases, the C 1s, N 1s, and O 1s core-level spectra at a low coverage (0.30 ML) indicated that the carboxyl and amine groups participated in bonding with the Ge(100) surface in an "O-H dissociated-N dative bonded structure". At high coverage levels (0.60 ML), both this structure and an "O-H dissociation bonded structure" were present. As a result, we found that alanine adsorbs more easily (lower adsorption energy) than leucine on Ge(100) surfaces due to less steric hindrance of side chain.

• Proceedings of the Korean Vacuum Society Conference
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• 2004.02a
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• pp.61-61
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• 2004

• Proceedings of the Korean Vacuum Society Conference
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• 2013.08a
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• pp.137-137
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• 2013

The most stable adsorption structures and their corresponding energies of 4-pyridone, 4-hydroxypyridine, 2-pyridone and 2-hydroxypyridine have been investigated by Density Functional Theory (DFT) calculation method and high-resolution photoemission spectroscopy (HRPES). We confirmed that between the two reaction centers of 4- and 2-pyridone, only O atom of carbonyl functional group can act as a Lewis base and thus, O dative bonding structure is the most stable. On the other hand, we clarified that both the two reaction centers (the cyclic N atom and the O atom of hydroxyl functional group) of 4- and 2-hydroxypyridine (tautomers of 4- and 2-pyridone) can successfully function as a Lewis base. Through the interpretation of the N 1s and O 1s core level spectra obtained using HRPES, we could confirm the electronic structures and bonding configurations of these molecules with a coverage dependence on the Ge(100) surface.

• Journal of the Korean Chemical Society
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• v.38 no.3
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• pp.241-245
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• 1994

The oxidative addition reaction has been employed to synthesize heteropolynuclear compounds containing Si-M bonding interaction between the silicon atom of silatrane, pentacoordinate silicon derivative with transannular Si-N dative bond, and the main group element. The reaction of $SnBr_2 with 1-bromosilatrane(1a) in acetonitrile gives the mixture of yellow(2a) and white(2b) solids which were isolated and charaterized by ^1H-NMR, ^{29}Si-NMR, ^{119}Sn-NMR and Mass spectroscopy. The yellow compound was characterized as 1-tribromotinsilatrane which had Si-Sn bonding interaction. The reaction of SnBr2 with 1-bromo-3,7,10-trimethylsilatrane(1b) in methanol gives the Sn(Ⅳ) complex, N[CH_2CH(CH_3)O]_3SiSnBr_3(CH_3OH)_2(3),$ which was characterized by various means.