Publications by authors named "Hoje Chun"

7 Publications

  • Page 1 of 1

First-Principles-Based Machine-Learning Molecular Dynamics for Crystalline Polymers with van der Waals Interactions.

J Phys Chem Lett 2021 Jul 24;12(25):6000-6006. Epub 2021 Jun 24.

Department of Chemical and Biomolecular Engineering, Yonsei University, Seoul 03722, Republic of Korea.

Machine-learning (ML) techniques have drawn an ever-increasing focus as they enable high-throughput screening and multiscale prediction of material properties. Especially, ML force fields (FFs) of quantum mechanical accuracy are expected to play a central role for the purpose. The construction of ML-FFs for polymers is, however, still in its infancy due to the formidable configurational space of its composing atoms. Here, we demonstrate the effective development of ML-FFs using kernel functions and a Gaussian process for an organic polymer, polytetrafluoroethylene (PTFE), with a data set acquired by first-principles calculations and molecular dynamics (AIMD) simulations. Even though the training data set is sampled only with short PTFE chains, structures of longer chains optimized by our ML-FF show an excellent consistency with density functional theory calculations. Furthermore, when integrated with molecular dynamics simulations, the ML-FF successfully describes various physical properties of a PTFE bundle, such as a density, melting temperature, coefficient of thermal expansion, and Young's modulus.
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http://dx.doi.org/10.1021/acs.jpclett.1c01140DOI Listing
July 2021

Optical bioelectronic nose of outstanding sensitivity and selectivity toward volatile organic compounds implemented with genetically engineered bacteriophage: Integrated study of multi-scale computational prediction and experimental validation.

Biosens Bioelectron 2021 Apr 13;177:112979. Epub 2021 Jan 13.

Department of Chemical and Biomolecular Engineering, Yonsei University, Seoul, 03722, Republic of Korea. Electronic address:

Genetic engineering of a bacteriophage is a promising way to develop a highly functional biosensor. Almost countless configurational degree of freedom in the manipulation, considerable uncertainty and cost involved with the approach, however, have been huddles for the objective. In this paper, we demonstrate rapidly responding optical biosensor with high selectivity toward gaseous explosives with genetically engineered phages. The sensors are equipped with peptide sequences in phages optimally interacting with the volatile organic compounds (VOCs) in visible light regime. To overcome the conventional issues, we use extensive utilization of empirical calculations to construct a large database of 8000 tripeptides and screen the best for electronic nose sensing performance toward nine VOCs belonging to three chemical classes. First-principles density functional theory (DFT) calculations unveil underlying correlations between the chemical affinity and optical property change on an electronic band structure level. The computational outcomes are validated by in vitro experimental design and testing of multiarray sensors using genetically modified phage implemented with five selected tripeptide sequences and wild-type phages. The classification success rates estimated from hierarchical cluster analysis are shown to be very consistent with the calculations. Our optical biosensor demonstrates a 1 ppb level of sensing resolution for explosive VOCs, which is a substantial improvement over conventional biosensor. The systematic interplay of big data-based computational prediction and in situ experimental validation can provide smart design principles for unconventionally outstanding biosensors.
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http://dx.doi.org/10.1016/j.bios.2021.112979DOI Listing
April 2021

Unique design of superior metal-organic framework for removal of toxic chemicals in humid environment via direct functionalization of the metal nodes.

J Hazard Mater 2020 11 18;398:122857. Epub 2020 May 18.

Research Center for Nanocatalysts, Korea Research Institute of Chemical Technology (KRICT), Jang-dong, Yuseong, Daejeon 34114, Republic of Korea; Department of Advanced Materials and Chemical Engineering, University of Science and Technology (UST), Gajeong-dong, Yuseong, Daejeon 34113, Republic of Korea. Electronic address:

Unique chemical and thermal stabilities of a zirconium-based metal-organic framework (MOF) and its functionalized analogues play a key role to efficiently remove chemical warfare agents (ex., cyanogen chloride, CNCl) and simulant (dimethyl methylphosphonate, DMMP) as well as industrial toxic gas, ammonia (NH). Herein, we for the first time demonstrate outstanding performance of MOF-808 for removal of toxic chemicals in humid environment via special design of functionalization of hydroxo species bridging Zr-nodes using a triethylenediamine (TEDA) to form ionic frameworks by gas phase acid-base reactions. In situ experimental analyses and first-principles density functional theory calculations unveil underlying mechanism on the selective deposition of TEDA on the Zr-bridging hydroxo sites (μ-OH) in Zr-MOFs. The crystal structure of TEDA-grafted MOF-808 was confirmed using synchrotron X-ray powder diffraction (SXRPD). Furthermore, operando FT-IR spectra elucidate why the TEDA-grafted MOF-808 shows by far superior sorption efficiency to other MOF varieties. This work provides design principles and applications how to optimize MOFs for the preparation for versatile adsorbents using diamine grafting chemistry, which is also potentially applicable to various catalysis.
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http://dx.doi.org/10.1016/j.jhazmat.2020.122857DOI Listing
November 2020

Critical differences in 3D atomic structure of individual ligand-protected nanocrystals in solution.

Science 2020 04;368(6486):60-67

Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul 08826, Republic of Korea.

Precise three-dimensional (3D) atomic structure determination of individual nanocrystals is a prerequisite for understanding and predicting their physical properties. Nanocrystals from the same synthesis batch display what are often presumed to be small but possibly important differences in size, lattice distortions, and defects, which can only be understood by structural characterization with high spatial 3D resolution. We solved the structures of individual colloidal platinum nanocrystals by developing atomic-resolution 3D liquid-cell electron microscopy to reveal critical intrinsic heterogeneity of ligand-protected platinum nanocrystals in solution, including structural degeneracies, lattice parameter deviations, internal defects, and strain. These differences in structure lead to substantial contributions to free energies, consequential enough that they must be considered in any discussion of fundamental nanocrystal properties or applications.
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http://dx.doi.org/10.1126/science.aax3233DOI Listing
April 2020

First-principles database driven computational neural network approach to the discovery of active ternary nanocatalysts for oxygen reduction reaction.

Phys Chem Chem Phys 2018 Oct;20(38):24539-24544

Department of Chemical and Biomolecular Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea.

An elegant machine-learning-based algorithm was applied to study the thermo-electrochemical properties of ternary nanocatalysts for oxygen reduction reaction (ORR). High-dimensional neural network potentials (NNPs) for the interactions among the components were parameterized from big dataset established by first-principles density functional theory calculations. The NNPs were then incorporated with Monte Carlo (MC) and molecular dynamics (MD) simulations to identify not only active, but also electrochemically stable nanocatalysts for ORR in acidic solution. The effects of surface strain caused by selective segregation of certain components on the catalytic performance were accurately characterized. The computationally efficient and precise approach proposes a promising ORR candidate: 2.6 nm icosahedron comprising 60% of Pt and 40% Ni/Cu. Our methodology can be applied for high-throughput screening and designing of key functional nanomaterials to drastically enhance the performance of various electrochemical systems.
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http://dx.doi.org/10.1039/c8cp03801eDOI Listing
October 2018

First principles computational study on hydrolysis of hazardous chemicals phosphorus trichloride and oxychloride (PCl and POCl) catalyzed by molecular water clusters.

J Hazard Mater 2018 Jan 24;341:457-463. Epub 2017 Aug 24.

Department of Chemical and Biomolecular Engineering, Yonsei University, Seoul 03722, Republic of Korea. Electronic address:

Using first principles calculations we unveil fundamental mechanism of hydrolysis reactions of two hazardous chemicals PCl and POCl with explicit molecular water clusters nearby. It is found that the water molecules play a key role as a catalyst significantly lowing activation barrier of the hydrolysis via transferring its protons to reaction intermediates. Interestingly, torsional angle of the molecular complex at transition state is identified as a vital descriptor on the reaction rate. Analysis of charge distribution over the complex further reinforces the finding with atomic level correlation between the torsional angle and variation of the orbital hybridization state of phosphorus (P) in the complex. Electronic charge separation (or polarization) enhances thermodynamic stability of the activated complex and reduces the activation energy through hydrogen bonding network with water molecules nearby. Calculated potential energy surfaces (PES) for the hydrolysis of PCl and POCl depict their two contrastingly different profiles of double- and triple-depth wells, respectively. It is ascribed to the unique double-bonding O=P in the POCl. Our results on the activation free energy show well agreements with previous experimental data within 7kcalmol deviation.
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http://dx.doi.org/10.1016/j.jhazmat.2017.08.054DOI Listing
January 2018

First principles computational study on the adsorption mechanism of organic methyl iodide gas on triethylenediamine impregnated activated carbon.

Phys Chem Chem Phys 2016 Nov;18(47):32050-32056

Department of Chemical and Biomolecular Engineering, Yonsei University, Seoul, 03722, Republic of Korea.

We study removal of gas-phase organic methyl iodide (CHI) from an ambient environment via adsorption onto triethylenediamine (TEDA) impregnated activated carbon (AC). First principles density functional theory (DFT) calculations and ab-initio molecular dynamics (AIMD) simulations were extensively utilized to understand the underlying mechanism for the chemical reaction of CHI on the surface. Our results suggest that the adsorption energy of CHI shows substantial heterogeneity depending on the adsorption site, porosity of the AC, and humidity. It is observed that the CHI dissociative chemisorption is largely influenced by the adsorption site and porosity. Most importantly, it is clearly shown through free energy diagrams that the impregnated TEDA not only reduces the dissociation activation barrier of CHI but also attracts HO molecules relieving the AC surface from poisoning by humidity, and also enhances the removal efficiency of CHI through the chemical dissociation reaction. Our computational study can help to open new routes to design highly efficient materials for removing environmentally and biologically hazardous materials, for example radioactive iodine gas emitted following accidents at a nuclear power plant.
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http://dx.doi.org/10.1039/c6cp06483cDOI Listing
November 2016
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