• Bulletin of the Korean Chemical Society
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• v.35 no.12
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• pp.3495-3501
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• 2014

A novel crystal, the mono-protonated metformin acetate (1), was obtained and characterized by elemental analysis, IR spectroscopy and X-ray crystallography. It was found that one of the imino group in the metformin cation was protonated along with the proton transfer from the secondary amino group to the other imino group. Its crystal structure was then compared with the previously reported diprotonated metformin oxalate (2). The difference between them is that the mono-protonated metformin cations can be linked by hydrogen bonding to form dimers while the diprotonated metformin cations cannot. Both of them are stabilized by intermolecular hydrogen bonds to assemble a 3-D supermolecular structure. The four potential tautomer of the mono-protonated metformin cation (tautomers 1a, 1b, 1c and 1d) were optimized and their single point energies were calculated by Density Functional Theory (DFT) B3LYP method based on the Polarized Continuum Model (PCM) in water, which shows that the most likely existed tautomer in human cells is the same in the crystal structure. Based on the optimized structure, their Wiberg bond orders, Natural Population Analysis (NPA) atomic charges, molecular electrostatic potential (MEP) maps were calculated to analyze their electronic structures, which were then compared with the corresponding values of the diprotonated metformin cation (cation 2) and the neutral metformin (compound 3). Finally, the possible tautomeric mechanism of the mono-protonated metformin cation was discussed based on the observed phenomena.

• Journal of Integrative Natural Science
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• v.3 no.4
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• pp.226-230
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• 2010

Calculation of partial charge is important in chemistry. However, because there are many methods developed, it is of considerable interest to know how to calculate and apply properly to address various chemical problems. For basis set, usually double zeta quality is acceptable, and double zeta polarization function would be enough for most cases. To describe electronic state more accurately, Many electron configurations would be necessary to describe highly strained or anionic species. The NPA population introduced new concept about amide bonds, i.e., the planar geometry of nitrogen atom may not come from resonance, but from the lowering of p-orbital energy by electronegative carbonyl carbon atom. The issues for hypervalent atomic charges was also addressed by various charge derivation scheme. When the charge schemes were applied to organolithium compounds, the ionic nature of boding was revealed. This comes from the fact that previous Mulliken partial atomic charges overemphasized the covalent character, wihout much justification. The other partial charge derivation schemes such as NPA(natural population analysis), IPP (Integrated Projected Population) showed that much more ionic picture. ESP potential derived charges are generally believed to be suitable to describe intermolecular interactions, therefore they are used for molecular dynamics simulations and CoMFA (comparative molecular field analysis). The charge derivation schemes using multipole polarization was mainly applied to reproduce experimental infrared spectroscopy. In some reports these schemes are also suitable for intermecular electrostatic interactions. Charges derived from electron density gradient have shown the some bonds are not straight, but actually bent. The proper choice of charge-calculation method along with suitable level of theory and basis set are briefly discussed.

• Genomics & Informatics
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• v.14 no.2
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• pp.53-61
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• 2016

Toxoplasma gondii is an intracellular Apicomplexan parasite and a causative agent of toxoplasmosis in human. It causes encephalitis, uveitis, chorioretinitis, and congenital infection. T. gondii invades the host cell by forming a moving junction (MJ) complex. This complex formation is initiated by intermolecular interactions between the two secretory parasitic proteins-namely, apical membrane antigen 1 (AMA1) and rhoptry neck protein 2 (RON2) and is critically essential for the host invasion process. By this study, we propose two potential leads, NSC95522 and NSC179676 that can efficiently target the AMA1 hydrophobic cleft, which is a hotspot for targeting MJ complex formation. The proposed leads are the result of an exhaustive conformational search-based virtual screen with multilevel precision scoring of the docking affinities. These two compounds surpassed all the precision levels of docking and also the stringent post docking and cumulative molecular dynamics evaluations. Moreover, the backbone flexibility of hotspot residues in the hydrophobic cleft, which has been previously reported to be essential for accommodative binding of RON2 to AMA1, was also highly perturbed by these compounds. Furthermore, binding free energy calculations of these two compounds also revealed a significant affinity to AMA1. Machine learning approaches also predicted these two compounds to possess more relevant activities. Hence, these two leads, NSC95522 and NSC179676, may prove to be potential inhibitors targeting AMA1-RON2 complex formation towards combating toxoplasmosis.

• The Korean Journal of Pain
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• v.34 no.3
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• pp.262-270
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• 2021

Background: Transient receptor potential vanilloid 1 (TRPV1) is a non-selective cation channel implicated in pain sensation in response to heat, protons, and capsaicin (CAPS). It is well established that TRPV1 is involved in mechanical allodynia. This study investigates the effect of Ononis spinosa (Fabaceae) in CAPS-induced mechanical allodynia and its mechanism of action. Methods: Mechanical allodynia was induced by the intraplantar (ipl) injection of 40 ㎍ CAPS into the left hind paw of male Wistar rats. Animals received an ipl injection of 100 ㎍ O. spinosa methanolic leaf extract or 2.5% diclofenac sodium 20 minutes before CAPS injection. Paw withdrawal threshold (PWT) was measured using von Frey filament 30, 90, and 150 minutes after CAPS injection. A molecular docking tool, AutoDock 4.2, was used to study the binding energies and intermolecular interactions between O. spinosa constituents and TRPV1 receptor. Results: The ipsilateral ipl injection of O. spinosa before CAPS injection increased PWT in rats at all time points. O. spinosa decreased mechanical allodynia by 5.35-fold compared to a 3.59-fold decrease produced by diclofenac sodium. The ipsilateral pretreatment with TRPV1 antagonist (300 ㎍ 4-[3-Chloro-2-pyridinyl]-N-[4-[1,1-dimethylethyl] phenyl]-1-piperazinecarboxamide [BCTC]) as well as the β2-adrenoreceptor antagonist (150 ㎍ butoxamine) attenuated the action of O. spinosa. Depending on molecular docking results, the activity of the extract could be attributed to the bindings of campesterol, stigmasterol, and ononin compounds to TRPV1. Conclusions: O. spinosa alleviated CAPS-induced mechanical allodynia through 2 mechanisms: the direct modulation of TRPV1 and the involvement of β2 adrenoreceptor signaling.

• Applied Chemistry for Engineering
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• v.32 no.3
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• pp.277-282
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• 2021

Two hydrophobic imidazolium based ionic liquids including 1-benzyl-3-butylimidazolium hexafluorophosphate [BzBIM]PF₆ and 1-pentyl-3-butylimidazolium hexafluorophosphate [PBIM]PF₆ having the same anion and different cation parts were synthesized. The structural composition of these ionic liquids were confirmed with Fourier-transform infrared spectroscopy (FT-IR) and proton nuclear magnetic resonance (¹H-NMR). Their physiochemical properties such as viscosity, ionic conductivity and thermal stability alongside electrochemical potential window range for both ionic liquid electrolytes were characterized and compared to each other. The overall results revealed that [BzBIM]PF₆ has higher thermal and electrochemical stabilities and viscosity than that of [PBIM]PF₆ probably due to the presence of benzyl ring in the imidazolium cation providing strong intermolecular π-π interactions.

• Bulletin of the Korean Chemical Society
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• v.26 no.4
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• pp.523-528
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• 2005

Diblock copolymers with different poly($\varepsilon$-caprolactone) (PCL) block lengths were synthesized by ringopening polymerization of $\varepsilon$-caprolactone in the presence of monomethoxy poly(ethylene glycol) (mPEG-OH, MW 2000) as initiator. The self-aggregation behaviors of the diblock copolymer nanoparticle, prepared by the diafiltration method, were investigated by using $^1H$ NMR, dynamic light scattering (DLS), and fluorescence spectroscopy. The PEG-PCL block copolymers formed the nano-sized self-aggregate in an aqueous environment by intrsa- and/or intermolecular association between hydrophobic PCL chains. The critical aggregation concentrations (cac) of the block copolymer self-aggregate became lower with increasing hydrophobic PCL block length. On the other hand, reverse trends of mean hydrodynamic diameters were measured by DLS owing to the increasing bulkiness of the hydrophobic chains and hydrophobic interaction between the PCL microdomains. The hydrodynamic diameters of the block copolymer nanoparticles, measured by DLS, were in the range of 65-270 nm. Furthermore, the size of the nanoparticles was scarcely affected by the concentration of the block copolymers in the range of 0.125-5 mg/mL owing to the negligible interparticular aggregation between the self-aggregated nanoparticles. Considered with the fairly low cac and nanoparticle stability, the PEG-PCL nanoparticles can be considered a potential candidate for biomedical applications such as drug carrier or imaging agent.

• Bulletin of the Korean Chemical Society
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• v.35 no.12
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• pp.3590-3594
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• 2014

Blue phosphorescent $(dfpypy)_2Ir(mppy)$, where dfpypy = 2',6'-difluoro-2,3'-bipyridine and mppy = 5-methyl-2-phenylpyridine, has been synthesized by newly developed effective method and its solid state structure and photoluminescent properties are investigated. The glass-transition and decomposition temperature of the compound appear at $160^{\circ}C$ and $360^{\circ}C$, respectively. In a crystal packing structure, there are two kinds of intermolecular interactions such as hydrogen bonding ($C-H{\cdots}F$) and edge-to-face $C-H{\cdots}{\pi}(py)$ interaction. This compound emits bright blue phosphorescence with ${\lambda}_{max}=472nm$ and quantum efficiencies of 0.23 and 0.32 in fluid and the solid state. The emission band of the compound is red-shifted by 40 nm relative to homoleptic congener, $Ir(dfpypy)_3$. The ancillary ligand in $(dfpypy)_2Ir(mppy)$ has been found to significantly destabilize HOMO energy, compared to $Ir(dfpypy)_3$, $(dfpypy)_2Ir(acac)$ and $(dfpypy)_2Ir(dpm)$, without significantly changing LUMO energy.

• Journal of the Korean Chemical Society
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• v.21 no.2
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• pp.75-82
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• 1977

The isotope effect of pure liquid on vapor pressure is examined, and the vapor pressure ratios of two different isotopes are calculated. Based on the Significant Structure Theory of Liquids, the effect of molecular weight and the effect of moments of inertia are dominant in ordinary/trans-$d_2$ ethylene isotopes; the effect of hindered rotational zero-point energy is dominant in trans-$d_2$/cis-$d_2$ ethylene isotopes; and the effect of intermolecular potential difference is found in $CH_3OH/CH_3OD$ isotopes. In the isotopes of $CH_4/CD_4,\;SiH_4/SiD_4\;and\;GeH_4/GeD_4$, the weight effect decrease in the order of $CH_4/CD_4 >SiH_4/SiD_4 >GeH_4/GeD_4$.

• Proceedings of the Korean Vacuum Society Conference
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• 2010.02a
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• pp.358-358
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• 2010

Ion beam bombardment at low energy forms nanosize patterns such as ripples, dots or wrinkles on the surface of polymers in ambient temperature and pressure. It has been known that the ion beam can alter the polymer surface that induces skins stiffer or the density higher by higher compressive stress or strain energies associated with chain scissions and crosslinks of the polymer. Atomic scale structure evolution in polymers is essential to understand a stress generation mechanism during the ion beam bombardment, which governs the nanoscale surface structure evolution. In this work, Molecular Dynamics (MD) simulations are employed to characterize the phenomenon occurred in bombardment between the ion beam and polymers that forms nanosize patterns. We investigate the structure evolution of Low Density Polyethylene (LDPE) at 300 K as the polymer is bombarded with Argon ions having various kinetic energies ranging from 100 eV to 1 KeV with 50 eV intervals having the fluence of $1.45\;{\times}\;1014 #/cm2$. These simulations use the Reactive Force Field (ReaxFF), which can mimic chemical covalent bonds and includes van der Waals potentials for describing the intermolecular interactions. The results show the details of the structural evolution of LDPE by the low energy Ar ion bombardment. Analyses through kinetic and potential energy, number of crosslinks and chain scissions, level of local densification and motions of atoms support that the residual strain energies on the surface is strongly associated with the number of crosslinks or scissored chains. Also, we could find an optimal Ar ion beam energy to make crosslinks well.

• Proceedings of the Korean Vacuum Society Conference
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• 2013.08a
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• pp.76.2-76.2
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• 2013

Advanced electronic application areas have strongly required new materials due to the continuous shrinking dimensions of their devices. Specially, the development and use of metal precursors for atomic layer deposition has been extensively focused on application to electronic devices. Thus the systematic design and synthesis of metal compounds with relevant chemical and physical properties, such as stability, volatility, and resistance to air and moisture are very important in the vacuum deposition fields. In many case, organic ligands for metal precursors are especially focused in the related research areas because the large scale synthesis of the metal complexes with excellent properties exclusively depends on the potential usefulness of the ligands. It is recommended for metal complexes to be in monomeric forms because mononuclear complexes generally show high vapor pressures comparing with their oligomeric structure such as dimer and trimer. Simple metal alkoxides complexes are involatile except several examples such as Ti(OiPr)4, Si(OEt)4, and Hf(OtBu)4. Thus the coordinated atom of alkoxide ligands should be crowded in its own environment with some substituents by prohibiting the coordinated atoms from bonding to another metal through oxygen-bridging configuration. Alkoxide ligands containing donor-functionalized group such as amino and alkoxy which can induce the increasing of the coordinative saturation of the metal complexes and the decreasing of the intermolecular interaction between or among the metal compounds. In this presentation, we will discuss the development of metal compounds which adopted donor-functionalized alkoxide ligands derived from their alcohols for electronic application. Some recent results on ALD using metal precursors such as tin, nickel, ruthenium, and tungsten developed in our group will be disclosed.