• Bulletin of the Korean Chemical Society
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• 제32권5호
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• pp.1685-1691
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• 2011

The molecular structures of thiacalix[4]biscrown-5 (1) and p-tert-butylthiacalix[4]biscrown-5 (2) and their alkali-metal-ion complexes were optimized using the DFT BLYP/6-31G(d) and mPW1PW91/6-31G(d,p) (hybrid HF-DF) calculations. The total electronic energies, the normal vibrational modes, and the Gibbs free energies of the mono- and di-topic complexes of each host with the sodium and potassium ions were analyzed. The $K^+$-complexes exhibited relatively stronger binding efficiencies than $Na^+$-complexes for both the monoand di-topic complexes of 1 and 2 comparing the efficiencies of the sodium and potassium complexes with an anisole and phenol. The mPW1PW91/6-31G(d,p) calculated distances between the oxygen atoms and the alkali metal ions were reported in the alkali-metal-ion complexes ($1{\cdot}Na^+$, $1{\cdot}2Na^+$, $1{\cdot}K^+$, $1{\cdot}2K^+$, $2{\cdot}Na^+$, $2{\cdot}Na^+$, $2{\cdot}K^+$, $2{\cdot}2K^+$). The BLYP/6-31G(d) calculated IR spectra of the host 1 and its mono-topic alkali-metal-ion complexes are compared.

• 대한화학회지
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• 제33권6호
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• pp.623-632
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• 1989

$Mn^{2+}$-치환 제올라이트 A는 가열 탈수되어도 그 구조가 열적을 안정하였다. $Mn_{4,5}Na_3-A$의 수화상태 및 탈수상태에 있어서의 골조원자, 이온 및 물분자들의 위치와 결합에너지를 몇가지 퍼텐셜 함수들을 써서 계산하여 구하였다. 탈수상태의 $Mn_{4,5}Na_3-A$에 있어서 골조원자들의 결합에너지는 열적으로 안정한 것으로 알려져 있는 탈수상태의 $Ca^{2+}$-치환 제올라이트 A($Ca_6$-A) 및 $Co^{2+}$- 치환제올라이트 A($Co_4Na_4-A$)의 그것과 비슷하였다. $Mn^{2+}$-치환 제올라이트 A 골조 내에는 결합에너지의 결합형식이 서로 다른 세 가지 그룹의 물분자들 즉 인접 물분자 또는 골조 산소원자와 수소결합을 하고 있는 물; W(I), $Na^+$이온에 배위되면서 인접 물 분자와 수소결합을 하는 물; W(II) 및 $Mn^{2+}$에 배위면서 수소결합을 하는 W(III)그룹의 물분자들이 존재하였으며 그들의 결합에너지 및 탈수반응의 활성화에너지의 크기 순서는 W(III) > W(II) > W(I)이였다.

• Advances in nano research
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• 제7권3호
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• pp.209-221
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• 2019

Graphene, with impressive electronic properties, have high potential in the microelectronic field. However, graphene itself is a zero bandgap material which is not suitable for digital logic gates and its application. Thus, much focus is on graphene nanoribbons (GNRs) that are narrow strips of graphene. During GNRs fabrication process, the occurrence of defects that ultimately change electronic properties of graphene is difficult to avoid. The modelling of GNRs with defects is crucial to study the non-idealities effects. In this work, nearest-neighbor tight-binding (TB) model for GNRs is presented with three main simplifying assumptions. They are utilization of basis function, Hamiltonian operator discretization and plane wave approximation. Two major edges of GNRs, armchair-edged GNRs (AGNRs) and zigzag-edged GNRs (ZGNRs) are explored. With single vacancy (SV) defects, the components within the Hamiltonian operator are transformed due to the disappearance of tight-binding energies around the missing carbon atoms in GNRs. The size of the lattices namely width and length are varied and studied. Non-equilibrium Green's function (NEGF) formalism is employed to obtain the electronics structure namely band structure and density of states (DOS) and all simulation is implemented in MATLAB. The band structure and DOS plot are then compared between pristine and defected GNRs under varying length and width of GNRs. It is revealed that there are clear distinctions between band structure, numerical DOS and Green's function DOS of pristine and defective GNRs.

• Genomics & Informatics
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• 제19권3호
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• pp.29.1-29.10
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• 2021

In our previous studies, we have demonstrated the association of certain variants of the thyroid-stimulating hormone receptor (TSHR), thyroid peroxidase (TPO), and thyroglobulin (TG) genes with congenital hypothyroidism. Herein, we explored the mechanistic basis for this association using different in silico tools. The mRNA 3'-untranslated region (3'-UTR) plays key roles in gene expression at the post-transcriptional level. In TSHR variants (rs2268477, rs7144481, and rs17630128), the binding affinity of microRNAs (miRs) (hsa-miR-154-5p, hsa-miR-376a-2-5p, hsa-miR-3935, hsa-miR-4280, and hsa-miR-6858-3p) to the 3'-UTR is disrupted, affecting post-transcriptional gene regulation. TPO and TG are the two key proteins necessary for the biosynthesis of thyroid hormones in the presence of iodide and H₂O₂. Reduced stability of these proteins leads to aberrant biosynthesis of thyroid hormones. Compared to the wild-type TPO protein, the p.S398T variant was found to exhibit less stability and significant rearrangements of intra-atomic bonds affecting the stoichiometry and substrate binding (binding energies, ΔG of wild-type vs. mutant: -15 vs. -13.8 kcal/mol; and dissociation constant, K_d of wild-type vs. mutant: 7.2E^-12 vs. 7.0E^-11 M). The missense mutations p.G653D and p.R1999W on the TG protein showed altered ΔG(0.24 kcal/mol and 0.79 kcal/mol, respectively). In conclusion, an in silico analysis of TSHR genetic variants in the 3'-UTR showed that they alter the binding affinities of different miRs. The TPO protein structure and mutant protein complex (p.S398T) are less stable, with potentially deleterious effects. A structural and energy analysis showed that TG mutations (p.G653D and p.R1999W) reduce the stability of the TG protein and affect its structure-functional relationship.

• Journal of Veterinary Science
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• 제22권1호
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• pp.12.1-12.11
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• 2021

Background: Bats have been considered natural reservoirs for several pathogenic human coronaviruses (CoVs) in the last two decades. Recently, a bat CoV was detected in the Republic of Korea; its entire genome was sequenced and reported to be genetically similar to that of the severe acute respiratory syndrome CoV (SARS-CoV). Objectives: The objective of this study was to compare the genetic sequences of SARS-CoV, SARS-CoV-2, and the two Korean bat CoV strains 16BO133 and B15-21, to estimate the likelihood of an interaction between the Korean bat CoVs and the human angiotensin-converting enzyme 2 (ACE2) receptor. Methods: The phylogenetic analysis was conducted with the maximum-likelihood (ML) method using MEGA 7 software. The Korean bat CoVs receptor binding domain (RBD) of the spike protein was analyzed by comparative homology modeling using the SWISS-MODEL server. The binding energies of the complexes were calculated using PRODIGY and MM/GBGA. Results: Phylogenetic analyses of the entire RNA-dependent RNA polymerase, spike regions, and the complete genome revealed that the Korean CoVs, along with SARS-CoV and SARS-CoV-2, belong to the subgenus Sarbecovirus, within BetaCoVs. However, the two Korean CoVs were distinct from SARS-CoV-2. Specifically, the spike gene of the Korean CoVs, which is involved in host infection, differed from that of SARS-CoV-2, showing only 66.8%-67.0% nucleotide homology and presented deletions within the RBD, particularly within regions critical for cross-species transmission and that mediate interaction with ACE2. Binding free energy calculation revealed that the binding affinity of Korean bat CoV RBD to hACE2 was drastically lower than that of SARS-CoV and SARS-CoV-2. Conclusions: These results suggest that Korean bat CoVs are unlikely to bind to the human ACE2 receptor.

• Korean Chemical Engineering Research
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• 제55권5호
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• pp.704-710
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• 2017

가스 하이드레이트 형성원리를 이용한 해수담수화는 이미 상용화된 역삼투 방식에 비하여 아직 실증화 단계이지만 그 공정이 비교적 단순하고 특히 냉매를 객체가스로 사용할 경우 아주 낮은 공정 온도가 필요하지 않아 에너지 소비량(thermal budget)이 향상될 가능성이 있기 때문에 여전히 많은 관심을 받고 있다. 따라서 본 연구에서는 수소불화탄소(HFC, hydrofluorocarbon) 및 수소염화불화탄소(HCFC, hydrochlorofluorocarbon) 계열의 냉매들을 객체가스로 한 가스 하이드레이트 형성 거동을 에너지적인 관점에서 해석하고자 하였고 이를 위해 밀도 범함수(DFT, density functional method) 이론을 기반으로 한 분자모델링을 도입하였다. 객체가스(guest gas)로 R-134a, R-227ea, R-236fa, R-141b를 선정하였으며 계산을 위하여 물 분자로 이루어진 $5^{12}$, $5^{12}6^2$, $5^{12}6^4$의 세가지 구조의 동공들(cavities)을 구성하였다. 동공, 객체가스, 그리고 객체가스가 삽입된 동공의 구조를 분자모델링을 이용하여 각각 최적화하였고 계산된 각 구조의 에너지로부터 동공과 객체가스의 결합에너지(binding energy)를 계산하였다. 마지막으로 결합에너지를 비교함으로써 어느 냉매가 가장 유리한 조건에서 가스하이드레이트를 형성할 지를 판단하였다. 결과적으로 R-236fa가 가장 자발적(spontaneous)으로 가스 하이드레이트를 형성할 것으로 예상되었고 사람에 대한 낮은 독성과 물에 대한 작은 용해도 측면에서도 가장 적절한 선택으로 평가되었다.

• Bulletin of the Korean Chemical Society
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• 제31권2호
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• pp.453-456
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• 2010

The structural and energetic preferences of thiacalix[4]biscrown-5 with and without alkali metal ions ($Na^+$, $K^+$, $Rb^+$, and $Cs^+$) have been theoretically investigated for the first time using molecular dynamic (MD) simulations and density functional theory (MPWB1K/6-31G(d)//B3LYP/6-31G(d)) methods. The formation of the metal ion complex by the host is mainly driven by the electrostatic attraction between crown-5 oxygens and a cation together with the minor contribution of the cation-$\pi$ interaction between two facing phenyl rings around the cation. The computed binding energies and the atomic charge distribution analysis for the metal binding complexes indicate the selectivity toward a potassium ion. The theoretical results herein explain the experimentally observed extractability order by this host towards various alkali metal ions. The physical nature and the driving forces for cation recognition by this host are discussed in detail.

• 대한화학회지
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• 제23권6호
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• pp.374-384
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• 1979

Zeolite NaA의 ${\alpha}$ cage에 있어서의 수화에너지와 그 위치를 결정하였다. Na(1)과 Na(2)사이의 site selectivity를 에너지 계산으로부터 결정하였는데 Na(1)이 Na(2)보다 선택성이 있는 것을 알 수 있었다. ${\alpha}$-Cage에 수화된 물들은 일그러진 정 12면체를 형성함을 알 수 있었다. Water(1), Water(2), Water(3)의 평균수화에너지는 각각 -29.847, -25.344, -15.888kcal/mole이다. 이 에너지 계산으로부터 얻어진 수화된 물들의 산소원자의 위치는 X선값과 잘 일치함을 보여준다. 또 수화된 정도에 따른 수화에너지의 그래프를 얻었다. 이 결과는 실험으로부터 얻어진 differential heat of sorption curve와 잘 일치함을 보여준다. ${\alpha}$ Cage 속에서의 유전상수는 3.5가 적합함을 알 수 있었다.

• 정보저장시스템학회:학술대회논문집
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• 정보저장시스템학회 2005년도 추계학술대회 논문집
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• pp.124-127
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• 2005

Rewritable optical memory devices such as an CD-RW and DVD+RW are data storage media, which take advantage of the different optical properties in the amorphous and crystalline states of phase change materials. The switching property, structural transformation, transformation kinetics and chemical bindings of $Ge_xSb_{100-x}$($6{\le}x{\le}$34) were studied to investigate the feasibility of applying $Ge_xSb_{100-x}$ alloys in optical memory. The $Ge_xSb_{100-x}$ thin film was deposited by RF magnetron co-sputtering system and phase change characteristics were investigated by X-ray diffraction (XRD), static tester, inductively coupled plasma atomic emission spectrometer (ICP-AES) and atomic force microscopy (AEM). Optimum fiim composition of $Ge_xSb_{100-x}$ was studied and its minimum time fur laser induced crystallization and optical contrast fur phase transition was performed. These results might be correlated with the binding energies between Ge and Sb, and indicate that $Ge_xSb_{100-x}$ have an potential far optical memory applications.

• Bulletin of the Korean Chemical Society
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• 제33권6호
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• pp.1998-2004
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• 2012

We carried out DFT calculations for monohydrated sulfuric and phosphoric acids. We are interested in clusters which differ in orientation of hydrogen atoms only. Such molecular complexes are close in energy, since they lie in the vicinity of the global minimum energy structure on the flat potential energy surface. For monohydrated sulfuric acid we identified four different isomers. The monohydrated phosphoric acid forms five different conformers. These systems are difficult to study from the theoretical point of view, since binding energy differences in several cases are very small. For each structure, we calculated harmonic vibrational frequencies to be sure that if the optimized structures are at the local or global minima on the potential energy surface. The analysis of calculated -OH vibrational frequencies is useful in interpretation of infrared photodissociation spectroscopy experiments. We employed four different DFT functionals in our calculations. For each structure, we calculated binding energies, thermodynamic properties, and harmonic vibrational frequencies. Our analysis clearly shows that DFT approach is suitable for studying monohydrated inorganic acids with different hydrogen atom orientations. We carried out MP2 calculations with aug-cc-pVDZ basis set for both monohydrated acids. MP2 results serve as a benchmark for DFT calculations.