• 한국진공학회:학술대회논문집
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• 한국진공학회 2014년도 제46회 동계 정기학술대회 초록집
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• pp.191.1-191.1
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• 2014

Crystallization has become the most popular technique for the separation of enantiomers since the Pasteur's discovery. To investigate mechanism of crystallization of chiral molecules, it is necessary to study self-assembled structures on two-dimensional surface. Here, we have studied two-dimensional self-assembled structures of an unnatural amino acid, (S)-${\beta}$-methyl naphthalen-1-${\gamma}$-aminobutyric acid (${\gamma}^2$-1-naphthylalanine) on Au(111) surface at 150 K using scanning tunneling microscopy (STM). At initial stage, we found two chiral honeycomb structures which are counter-clockwise and clockwise configurations in one domain. The molecules are arranged around molecular vacancies, dark hole. By further increasing the amounts of adsorbed ${\gamma}^2$-1-naphthylalanine, a well-ordered square packed structure was observed. In addition, we found the other structure that molecules were trapped in the pore of the hexagonal molecular assembly.

• 한국진공학회:학술대회논문집
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• 한국진공학회 2009년도 제38회 동계학술대회 초록집
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• pp.354-354
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• 2010

Supramolecualr ordering has been actively studied due to it's possible applications to the fabrication processes of nano-electronic devices. Van der Waals interaction and hydrogen bonding are frequently studied mechanisms for various molecular structures based on non-uniform charge distributions. Halogen atoms in molecules can have electrostatic interactions with similar strength. Big halogen atoms have strong non-uniform charge distributions. To study molecular orderings formed by hydrogen and halogen interactions, we chose a molecular system containing oxygen, hydrogen, and bromine atoms, a bromo-quinone. A two-dimensional molecular network was studied on Au(111) using a low-temperature scanning tunneling microscope. Bromo-quinone molecules form self-assembled square grids having windmill structures. Their molecular orderings, chiral structures, and defects are explained in terms of hydrogen and halogen interactions.

• Animal Bioscience
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• 제36권2호
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• pp.256-263
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• 2023

Objective: Feed molecular structures can affect its availability to gastrointestinal enzymes which impact its digestibility and absorption. The molecular spectroscopy-attenuated total reflectance Fourier transform infrared vibrational spectroscopy (ATR-FTIR) is an advanced technique that measures the absorbance of chemical functional groups on the infrared region so that we can identify and quantify molecules and functional groups in a feed. The program aimed to reveal the association of intrinsic molecular structure with nutrient supply to animals from canola feedstocks and co-products from bio-oil processing. The objective of this study was to characterize special intrinsic carbohydrate and protein-related molecular structure spectral profiles of feedstock and co-products (meal and pellets) from bio-oil processing from two source origins: Canada (CA) and China (CH). Methods: The samples of feedstock and co-products were obtained from five different companies in each country arranged by the Canola Council of Canada (CCC). The molecular structure spectral features were analyzed using advanced vibrational molecular spectroscopy-ATR-FTIR. The spectral features that accessed included: i) protein-related spectral features (Amide I, Amide II, α-helix, β-sheet, and their spectral intensity ratios), ii) carbohydrate-related spectral features (TC1, TC2, TC3, TC4, CEC, STC1, STC2, STC3, STC4, TC, and their spectral intensity ratios). Results: The results showed that significant differences were observed on all vibrationally spectral features related to total carbohydrates, structural carbohydrates, and cellulosic compounds (p<0.05), except spectral features of TC2 and STC1 (p>0.05) of co-products, where CH meals presented higher peaks of these structures than CA. Similarly, it was for the carbohydrate-related molecular structure of canola seeds where the difference between CA and CH occurred except for STC3 height, CEC and STC areas (p>0.05). The protein-related molecular structures were similar for the canola seeds from both countries. However, CH meals presented higher peaks of amide I, α-helix, and β-sheet heights, α-helix:β-sheet ratio, total amide and amide I areas (p<0.05). Conclusion: The principal component analysis was able to explain over 90% of the variabilities in the carbohydrate and protein structures although it was not able to separate the samples from the two countries, indicating feedstock and coproducts interrelationship between CH and CA.

• 한국진공학회:학술대회논문집
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• 한국진공학회 2011년도 제41회 하계 정기 학술대회 초록집
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• pp.107-107
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• 2011

Supramolecular structures of anthraquinone molecules on a metallic surface are studied using scanning tunneling microscope (STM) under ultrahigh-vacuum conditions. When we deposited anthraquinone molecules on Au(111) substrate, the molecules formed three different phases (Chevron type, tetragon type and disordered type) on the surface. Based on our STM measurements, we proposed models for the observed molecular structures. Chevrons are consisted of several molecular chains, which make well-ordered two-dimensional islands by some weak interrow interactions and we could observe tetragon structures which make array of (111) metallic surface. each molecular rows in the chevrons are stabilized by two parallel O-H hydrogen bonds and disordered structures are observed 1-dimensional phase with hydrogen bond. First-principles calculations based on density functional theory are performed to reproduce the proposed models. Distances and energy gains for each intermolecular bond are estimated. In this presentation, we explain possible origins of these molecular structures in terms of hydrogen bonds, Van der Waals interactions and molecule-substrate interactions.

• Food Science and Biotechnology
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• 제16권5호
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• pp.663-674
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• 2007

Starches from different botanical sources differ in the ratio of amylose to amylopectin contents, molecular structures of amylose and amylopectin, granule morphology, and minor-component contents. These structural features result in different gelatinization, pasting, retrogradation properties, and enzyme digestibility of starch granules. In this review, compositions and molecular structures of starches and their effects on the physicochemical properties are summarized and discussed.

• 천문학회지
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• 제29권spc1호
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• pp.161-163
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• 1996

We have studied the response of molecular clouds in the Galactic disk to a rotating bar by conducting Smoothed Particle Hydrodynamics (SPH) simulations for the Galaxy in order to understand the dynamical structures of the Galactic Center (GC) molecular clouds, and their implications. In our study it was found that the structures of GC molecular clouds could be induced by the combined effects of rotating bar potential, the hydrodynamic collisions and gravitational miss collisions between the clouds.

• 한국진공학회:학술대회논문집
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• 한국진공학회 2009년도 제38회 동계학술대회 초록집
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• pp.11-11
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• 2010

Supramolecualr ordering has been actively studied due to it's possible applications to the fabrication processes of nano-electronic devices. Van der Waals interaction and hydrogen bonding are frequently studied mechanisms for various molecular structures based on non-uniform charge distributions. Halogen atoms in molecules can have electrostatic interactions with similar strength. Big halogen atoms have strong non-uniform charge distributions. To study molecular orderings formed by hydrogen and halogen interactions, we chose a molecular system containing oxygen, hydrogen, and bromine atoms, a bromo-quinone. A two-dimensional molecular network was studied on Au(111) using a low-temperature scanning tunneling microscope. Bromo-quinonemolecules form self-assembled square grids having windmill structures. Their molecular orderings, chiral structures, and defects are explained in terms of hydrogen and halogen interactions.

• Bulletin of the Korean Chemical Society
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• 제31권9호
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• pp.2581-2587
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• 2010

Nitration of tyrosine and tryptophan residues is common in cells under nitrative stress. However, physiological consequences of protein nitration are not well characterized on a molecular level due to limited availability of the 3D structures of nitrated proteins. Molecular dynamics (MD) simulation can be an alternative tool to probe the structural perturbations induced by nitration. In this study we developed molecular mechanics parameters for 3-nitrotyrosine (NIY) and 6-nitrotryptophan (NIW) that are compatible with the AMBER-99 force field. Partial atomic charges were derived by using a multi-conformational restrained electrostatic potential (RESP) methodology that included the geometry optimized structures of both $\alpha$- and $\beta$-conformers of a capped tripeptide ACE-NIY-NME or ACE-NIW-NME. Force constants for bonds and angles were adopted from the generalized AMBER force field. Torsional force constants for the proper dihedral C-C-N-O and improper dihedral C-O-N-O of the nitro group in NIY were determined by fitting the torsional energy profiles obtained from quantum mechanical (QM) geometry optimization with those from molecular mechanical (MM) energy minimization. Force field parameters obtained for NIY were transferable to NIW so that they reproduced the QM torsional energy profiles of ACE-NIW-NME accurately. Moreover, the QM optimized structures of the tripeptides containing NIY and NIW were almost identical to the corresponding structures obtained from MM energy minimization, attesting the validity of the current parameter set. Molecular dynamics simulations of thioredoxin nitrated at the single tyrosine and tryptophan yielded well-behaved trajectories suggesting that the parameters are suitable for molecular dynamics simulations of a nitrated protein.

• Korean Chemical Engineering Research
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• 제58권2호
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• pp.230-234
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• 2020

딥러닝 기법을 활용하여 분자 구조로부터 물성을 예측하는 시스템은 화학, 생물학, 재료 연구에 적용하기 위해 개발되었다. 분자 구조와 물성 정보가 축적된 데이터베이스를 기반으로, 구조와 물성간의 관계식을 찾는 딥러닝 모형을 구축한 후 최종적으로는 새로운 분자 구조에 대한 물성 예측값을 제공할 수 있다. 또한 선정된 분자 구조의 실제 물성값에 대한 실험을 병행하여 지속적인 검증 및 모형 업데이트를 수행하게 된다. 이를 통해 다량의 분자구조로부터 물성이 우수한 분자 구조를 빠른 시간 안에 스크리닝할 수 있으며, 연구의 효율성 및 성공률을 높일 수 있다. 본 논문에서는 딥러닝을 활용한 물성 예측 시스템의 전반적인 구성과 LG화학에서 실제 신규 구조 발굴에 적용된 사례를 중심으로 소개하고자 한다.

• 한국진공학회:학술대회논문집
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• 한국진공학회 2013년도 제44회 동계 정기학술대회 초록집
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• pp.270-270
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• 2013

We have investigated the self-assembled structures of glutaric acid (HOOC-(CH2)3-COOH) on the Cu(110) surface as a function of coverage using Scanning Tunneling Microscopy (STM). At low coverage, glutaric acid molecules diffuse freely on Cu(110) surface at room temperature, thus they can't form ordered structures at this coverage. However, when we scanned the same area several times, novel structures have been created during scanning due to the field-induced self-assembly. Also, the induced structures are quite stable during continuous scanning process. At 0.25 ML, glutaric acid adsorbs as a bi-glutarate (-OOC(CH2)3-COO-) after annealing to 450 K producing a racemic conglomerate of coexisting mirror domains. Although the molecule is achiral, it forms chiral domains on the surface from adsorption-induced asymmetrization. At 0.5 ML coverage, zigzag structure is observed, and still gltutaric acid adsorbs as a bidentate configuration. This bi-glutarate structure is stable until 650. Finally, at 1ML, glutaric acid adsorbs as a mono-glutarate at room temperature forming close packed structures.