20 results on '"Jaebeom Han"'
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2. Calculated Reduction Potentials of Electrolyte Species in Lithium–Sulfur Batteries
- Author
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Perla B. Balbuena, Yu Zheng, Jaebeom Han, and Ningxuan Guo
- Subjects
inorganic chemicals ,Battery (electricity) ,Materials science ,Inorganic chemistry ,macromolecular substances ,02 engineering and technology ,Electrolyte ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,0104 chemical sciences ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials ,Reduction (complexity) ,Solvent ,General Energy ,Molecule ,Voltage range ,Density functional theory ,Lithium sulfur ,Physical and Theoretical Chemistry ,0210 nano-technology - Abstract
Reduction potentials of electrolyte molecules in the lithium–sulfur (Li/S) battery and their variations in several solvent environments are studied using the density functional theory method with D...
- Published
- 2020
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3. Effect of the polarization effect on the charge-transfer process of triad organic photovoltaic material
- Author
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Margaret Cheung, Barry Dunietz, Eitan Geva, Xiang Sun, Buddhadev Maiti, Huseyin Aksu, and Jaebeom Han
- Published
- 2020
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4. First-principles calculations of oxidation potentials of electrolytes in lithium–sulfur batteries and their variations with changes in environment
- Author
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Perla B. Balbuena and Jaebeom Han
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Battery (electricity) ,chemistry.chemical_classification ,Passivation ,020209 energy ,Inorganic chemistry ,General Physics and Astronomy ,chemistry.chemical_element ,Salt (chemistry) ,02 engineering and technology ,Electrolyte ,021001 nanoscience & nanotechnology ,Sulfur ,Solvent ,chemistry ,0202 electrical engineering, electronic engineering, information engineering ,Physical and Theoretical Chemistry ,0210 nano-technology ,Carbon ,Chemical decomposition - Abstract
Oxidation potentials of electrolyte molecules in Li-sulfur (Li/S) batteries and their variations in various solvent environments are investigated using first-principles calculations in order to understand oxidative decomposition reactions of electrolytes for cathode passivation. Electrolyte solvents, Li salts, and various additives in Li/S batteries along with some Li-ion battery additives are studied. Oxidation potentials of isolated electrolyte molecules are found to be out of the operating range of typical Li/S batteries. The complexation of electrolyte molecules with Li+, salt anion, salt, S8, and pyrene alters oxidation potentials compared to those of the isolated systems. The salt anion lowers oxidation potentials of electrolyte molecules by at least 4.7% while the complexes with Li+ have higher oxidation potentials than the isolated molecules by at least 10.4%. S8 and pyrene, used as model compounds for sulfur and sulfur/carbon composite cathode materials, also affect oxidation potentials of electrolyte molecules, but their influence is negligible and the oxidation trends differ from those of the Li+ and salt anion. Although complexations change the oxidation potentials of electrolyte molecules, they are still higher than the operating voltage range of Li/S batteries, which indicates that oxidation of the studied electrolytes in Li/S batteries is not expected under ambient conditions.
- Published
- 2018
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5. Site-specific hydrogen bonding interaction between N-acetylproline amide and protic solvent molecules: Comparisons of IR and VCD measurements with MD simulations
- Author
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Kwang-Im Oh, Jaebeom Han, Kyung-Koo Lee, Seungsoo Hahn, Hogyu Han, and Minhaeng Cho
- Subjects
Amides -- Chemical properties ,Hydrogen bonding -- Research ,Conformational analysis ,Chemicals, plastics and rubber industries - Abstract
The amide 1 IR and VCD spectra of N-acetylproline amide (AP) were measured to study the effect of hydrogen bonding interactions on peptide solution structures. The results show that regardless of the hydrogen bond network-forming ability of a given protic solvent and the solvent polarity, the AP dipeptide mainly adopts the PII conformation in protic solvents.
- Published
- 2006
6. Determining the atomic charge of calcium ion requires the information of its coordination geometry in an EF-hand motif
- Author
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Margaret S. Cheung, Piotr Cieplak, Jaebeom Han, and Pengzhi Zhang
- Subjects
Quantitative Biology - Subcellular Processes ,Static Electricity ,Ab initio ,General Physics and Astronomy ,Ionic bonding ,Context (language use) ,Molecular Dynamics Simulation ,010402 general chemistry ,01 natural sciences ,Quantitative Biology::Cell Behavior ,Coordination complex ,Quantitative Biology::Subcellular Processes ,ARTICLES ,Calmodulin ,0103 physical sciences ,Animals ,Humans ,Molecule ,EF Hand Motifs ,Physical and Theoretical Chemistry ,Subcellular Processes (q-bio.SC) ,Coordination geometry ,Physics ,chemistry.chemical_classification ,Quantitative Biology::Biomolecules ,Binding Sites ,Quantitative Biology::Neurons and Cognition ,010304 chemical physics ,Force field (physics) ,Water ,Biomolecules (q-bio.BM) ,0104 chemical sciences ,Atomic radius ,Quantitative Biology - Biomolecules ,chemistry ,Chemical physics ,FOS: Biological sciences ,Quantum Theory ,Calcium ,Cattle ,Protein Binding - Abstract
It is challenging to parameterize the force field for calcium ions (Ca2+) in calcium-binding proteins because of their unique coordination chemistry that involves the surrounding atoms required for stability. In this work, we observed wide variation in Ca2+ binding loop conformations of the Ca2+-binding protein calmodulin (CaM), which adopts the most populated ternary structures determined from the MD simulations, followed by ab initio quantum mechanical (QM) calculations on all twelve amino acids in the loop that coordinate Ca2+ in aqueous solution. Ca2+ charges were derived by fitting to the electrostatic potential (ESP) in the context of a classical or polarizable force field (PFF). We discovered that the atomic radius of Ca2+ in conventional force fields is too large for the QM calculation to capture the variation in the coordination geometry of Ca2+ in its ionic form, leading to unphysical charges. Specifically, we found that the fitted atomic charges of Ca2+ in the context of PFF depend on the coordinating geometry of electronegative atoms from the amino acids in the loop. Although nearby water molecules do not influence the atomic charge of Ca2+, they are crucial for compensating for the coordination of Ca2+ due to the conformational flexibility in the EF-hand loop. Our method advances the development of force fields for metal ions and protein binding sites in dynamic environments., Comment: The following article has been accepted by Journal of Chemical Physics
- Published
- 2021
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7. Phenol-benzene complexation dynamics: Quantum chemistry calculation, molecular dynamics simulations, and two dimensional IR spectroscopy.
- Author
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Kijeong Kwac, Chewook Lee, Yousung Jung, Jaebeom Han, Kyungwon Kwak, Junrong Zheng, Fayer, M. D., and Minhaeng Cho
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PHENOL ,BENZENE ,QUANTUM chemistry ,MOLECULAR dynamics ,INFRARED spectroscopy ,QUANTUM theory - Abstract
Molecular dynamics (MD) simulations and quantum mechanical electronic structure calculations are used to investigate the nature and dynamics of the phenol-benzene complex in the mixed solvent, benzene/CCl
4 . Under thermal equilibrium conditions, the complexes are continuously dissociating and forming. The MD simulations are used to calculate the experimental observables related to the phenol hydroxyl stretching mode, i.e., the two dimensional infrared vibrational echo spectrum as a function of time, which directly displays the formation and dissociation of the complex through the growth of off-diagonal peaks, and the linear absorption spectrum, which displays two hydroxyl stretch peaks, one for the complex and one for the free phenol. The results of the simulations are compared to previously reported experimental data and are found to be in quite reasonable agreement. The electronic structure calculations show that the complex is T shaped. The classical potential used for the phenol-benzene interaction in the MD simulations is in good accord with the highest level of the electronic structure calculations. A variety of other features is extracted from the simulations including the relationship between the structure and the projection of the electric field on the hydroxyl group. The fluctuating electric field is used to determine the hydroxyl stretch frequency-frequency correlation function (FFCF). The simulations are also used to examine the number distribution of benzene and CCl4 molecules in the first solvent shell around the phenol. It is found that the distribution is not that of the solvent mole fraction of benzene. There are substantial probabilities of finding a phenol in either a pure benzene environment or a pure CCl4 environment. A conjecture is made that relates the FFCF to the local number of benzene molecules in phenol’s first solvent shell. [ABSTRACT FROM AUTHOR]- Published
- 2006
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8. Explicit polarization (X-Pol) potential using ab initio molecular orbital theory and density functional theory
- Author
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Lingchun Song, Jaebeom Han, Yen-lin Lin, Wangshen Xie, and Gao, Jiali
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Biomolecules -- Structure ,Biomolecules -- Chemical properties ,Biomolecules -- Electric properties ,Density functionals -- Usage ,Molecular orbitals -- Analysis ,Polarization (Electricity) -- Analysis ,Chemicals, plastics and rubber industries - Published
- 2009
9. Computational Study on Oxidation Potential Variations of Electrolytes with Complexation in Lithium-Sulfur (Li/S) Batteries
- Author
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Jaebeom Han and Perla B Balbuena
- Abstract
Lithium-sulfur (Li/S) batteries are attractive substitutes for current lithium-ion batteries (LIBs) because of the lower cost and higher theoretical capacity of the cathode materials compared to the current transition metal oxide cathode materials in LIBs. However, the polysulfide (PS) redox shuttle causes severe capacity fading of Li/S batteries during cycling, and a strong self-discharge behavior. Although there can be a lot of efforts to reduce or prevent the PS redox shuttle, the development of additives to cover the surface of the cathode is the most efficient way to resolve the PS redox shuttle in the Li/S battery. The passivation film generated by electrolyte additives can not only reduce the oxidation of electrolyte solvents on the surface of the sulfur cathode but also inhibit the dissolution of PS from the cathode into the electrolyte. Few studies have been carried out for this purpose in Li/S batteries even when there have been a variety of studies in LIBs for high-voltage cathode materials. In order to understand how surface films are generated, oxidation potentials and oxidative decomposed products should be studied first. In this study, the oxidation potentials of electrolyte solvents, Li salts, and additives are calculated using the density functional theory (DFT) with a continuum solvation model. Together with electrolyte solvents and Li salts in Li/S batteries, the mostly employed cathode passivation additives in Li-ion batteries and in Li/S batteries are investigated for additives. In addition, it is also investigated how oxidation potentials of these electrolyte systems are varied by complexations with Li+, anions of Li salts, and S8 and pyrene as model systems to mimic the sulfur-carbon electrode materials in Li/S batteries.
- Published
- 2018
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10. Explicit Polarization (X-Pol) Potential Using ab Initio Molecular Orbital Theory and Density Functional Theory
- Author
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Jiali Gao, Jaebeom Han, Lingchun Song, Yen-Lin Lin, and Wangshen Xie
- Subjects
Hydrogen bond ,Chemistry ,Orbital-free density functional theory ,Ab initio ,Water ,Hydrogen Bonding ,Molecular orbital theory ,Electronic structure ,Time-dependent density functional theory ,Molecular physics ,Article ,Physics::Atomic and Molecular Clusters ,Quantum Theory ,Density functional theory ,Physics::Chemical Physics ,Physical and Theoretical Chemistry ,Atomic physics ,Dimerization ,Fragment molecular orbital - Abstract
The explicit polarization (X-Pol) method has been examined using ab initio molecular orbital theory and density functional theory. The X-Pol potential was designed to provide a novel theoretical framework for developing next-generation force fields for biomolecular simulations. Importantly, the X-Pol potential is a general method, which can be employed with any level of electronic structure theory. The present study illustrates the implementation of the X-Pol method using ab initio Hartree-Fock theory and hybrid density functional theory. The computational results are illustrated by considering a set of bimolecular complexes of small organic molecules and ions with water. The computed interaction energies and hydrogen bond geometries are in good accord with CCSD(T) calculations and B3LYP/aug-cc-pVDZ optimizations.
- Published
- 2009
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11. Site-Specific Hydrogen-Bonding Interaction between N-Acetylproline Amide and Protic Solvent Molecules: Comparisons of IR and VCD Measurements with MD Simulations
- Author
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Kyung Koo Lee, Jaebeom Han, Seungsoo Hahn, Hogyu Han, Kwang-Im Oh, and Minhaeng Cho
- Subjects
education.field_of_study ,Hydrogen bond ,Stereochemistry ,Population ,chemistry.chemical_compound ,Molecular dynamics ,chemistry ,Computational chemistry ,Amide ,Molecule ,Peptide bond ,Physical and Theoretical Chemistry ,education ,Protic solvent ,Polyproline helix - Abstract
The effects of solute-solvent interactions on solution structures of small peptides have been paid a great deal of attention. To study the effect of hydrogen-bonding interactions on peptide solution structures, we measured the amide I IR and VCD spectra of N-acetylproline amide (AP) in various protic solvents, i.e., D2O, MeOD, EtOD, and PrOD, and directly compared them with theoretically simulated ones. The numbers of protic solvent molecules hydrogen-bonded to the two peptide bonds in the AP were quantitatively determined by carrying out the molecular dynamics (MD) simulations and then compared with the spectral analyses of the experimentally measured amide I bands. The two peptides in the AP have different propensities of forming H-bonds with protic solvent molecules, and the H-bond population distribution is found to be strongly site-specific and solvent-dependent. However, it is found that adoption of the polyproline II (PII) conformation by AP in protic solvents does not strongly depend on the hydrogen bond network-forming ability of protic solvents nor on the solvent polarity. We present a brief discussion on the validity as well as limitation of the currently available force field parameters used for the present MD simulation study.
- Published
- 2006
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12. Vertically Aligned Carbon Nanotubes Grown by Pyrolysis of Iron, Cobalt, and Nickel Phthalocyanines
- Author
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Seung Yeol Choi, Nam Seo Kim, Yun Tack Lee, Jaebeom Han, Jaebum Choo, G. H. Lee, Jeunghee Park, and Young S. Choi
- Subjects
Materials science ,chemistry.chemical_element ,Nanotechnology ,Carbon nanotube ,Atmospheric temperature range ,Nitrogen ,Arrhenius plot ,Surfaces, Coatings and Films ,Catalysis ,law.invention ,Nickel ,chemistry ,Chemical engineering ,law ,Materials Chemistry ,Physical and Theoretical Chemistry ,Silicon oxide ,Cobalt - Abstract
Carbon nanotubes (CNTs) were grown vertically aligned on silicon oxide substrates by pyrolyzing iron phthalocyanine (FePc), cobalt phthalocyanine (CoPc), and nickel phthalocyanine (NiPc) in the temperature range 700−1000 °C. As the temperature increases from 700 to 1000 °C, the growth rate of CNTs increases by a factor of approximately 45 and the average diameter increases from 30 to 80 nm. The CNTs grown using FePc exhibit about 2 times higher growth rate than those using CoPc and NiPc. The CNTs usually have a cylindrical structure, and a bamboo-like structure with a larger diameter at the higher temperature. The CNTs are doped with 2−6 at. % nitrogen atoms. The nitrogen content tends to decrease with the temperature increase. The CNTs grown using NiPc contain a higher nitrogen concentration compared to those grown using FePc and CoPc. The degree of crystalline perfection of the graphitic sheets increases with the temperature, but depends on the catalyst and the nitrogen content. The Arrhenius plot provi...
- Published
- 2003
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13. Temperature-dependent growth of carbon nanotubes by pyrolysis of ferrocene and acetylene in the range between 700 and 1000 °C
- Author
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Jeunghee Park, Jaebeom Han, Nam Seo Kim, Young S. Choi, Hwack Joo Lee, Hyun Ryu, and Yun Tack Lee
- Subjects
Carbon nanofiber ,General Physics and Astronomy ,chemistry.chemical_element ,Nanotechnology ,Activation energy ,Carbon nanotube ,Atmospheric temperature range ,Arrhenius plot ,law.invention ,Condensed Matter::Materials Science ,chemistry.chemical_compound ,chemistry ,Chemical engineering ,Acetylene ,law ,Physics::Chemical Physics ,Physical and Theoretical Chemistry ,Carbon ,Pyrolysis - Abstract
Aligned carbon nanotubes were grown by pyrolysis of ferrocene and acetylene in the temperature range 700–1000 °C. The average diameter is constantly 20 nm for all growth temperatures. As the temperature increases, the growth rate increases by 60 times. The length reaches up to 3 mm at 1000 °C. These long carbon nanotubes exhibit a cylindrical structure. The relative amount of crystalline graphitic sheets increases significantly with the growth temperature. The Arrhenius plot yields the activation energy 35±3 kcal/mol, which is close to the diffusion energy of carbon in bulk γ-Fe. We suggest that the bulk diffusion of carbons would play an important role in the growth of cylindrical structured carbon nanotubes.
- Published
- 2003
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14. Intermolecular potential for Ar-HBr (ν1 = 1) studied by high resolution near infrared spectroscopy
- Author
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John W. Bevan, Z. Wang, Robert R. Lucchese, Jaebeom Han, and A. L. McIntosh
- Subjects
Chemistry ,Near-infrared spectroscopy ,Quadrupole ,Intermolecular potential ,Analytical chemistry ,General Physics and Astronomy ,High resolution ,Physical and Theoretical Chemistry ,Hot band ,Isotopomers - Abstract
The fundamental ν1, combinations ν1 + 2ν20, ν1 + ν21, ν1 + ν3, ν1 + 2ν20 + ν3, hot band ν1 + 2ν20 − 2ν20, and difference band ν1 − 2ν20 have been rovibrationally for both 79Br and 81Br isotopomers in Ar-HBr. The bands involving 2ν20 directly sample the second minimum of the intermolecular potential surface of the complex, corresponding to the isomeric structure Ar-BrH. Nuclear quadrupole structure has also been partially resolved in the Q branch transitions of the ν1 + ν21 band. In addition, a strong Coriolis perturbation between the ν1 + ν21e and ν1 + ν3 states was investigated. A model potential surface for Ar-HBr (HBr ν1 = 1) was derived and compared with the H4 intermolecular potential for Ar-HBr (HBr ν1 = 0).
- Published
- 1997
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15. A rovibrational analysis of the ν1 and ν2 bands of OCDF by supersonic jet FTIR spectroscopy
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John W. Bevan, Jaebeom Han, A. L. McIntosh, and C. L. Hartz
- Subjects
Jet (fluid) ,Chemistry ,Analytical chemistry ,General Physics and Astronomy ,Infrared spectroscopy ,Rotational–vibrational spectroscopy ,symbols.namesake ,Fourier transform ,Dark state ,Excited state ,symbols ,Rotational spectroscopy ,Physical and Theoretical Chemistry ,Fourier transform infrared spectroscopy - Abstract
High resolution spectra of the ν1 (DF stretch) and ν2 (CO stretch) vibrations of the hydrogen bonded dimer OCDF were recorded using a supersonic jet Fourier transform infrared spectrometer. The following molecular constants were obtained (in cm−1): for ν1, ν0=2819.90104(18), B′=0.1031110(13), D′=3.113(22)×10−7; for ν2, ν0=2168.86239(16), B′=0.1010374(17), D′=3.355(45)×10−7. A Coriolis interaction between the ν1 excited state and a dark state was analyzed, which led to the estimation of the vibrational term value and rotational constant of the dark state.
- Published
- 1997
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16. Optimization of the explicit polarization (X-Pol) potential using a hybrid density functional
- Author
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Jaebeom Han, Donald G. Truhlar, and Jiali Gao
- Subjects
Physics ,Hydrogen bond ,Binding energy ,Electronic structure ,Molecular physics ,Article ,symbols.namesake ,Quantum mechanics ,symbols ,Molecular orbital ,Physical and Theoretical Chemistry ,Hamiltonian (quantum mechanics) ,Root-mean-square deviation ,Basis set ,Macromolecule - Abstract
The explicit polarization (X-Pol) method is a self-consistent fragment-based electronic structure theory in which molecular orbitals are block-localized within fragments of a cluster, macromolecule, or condensed-phase system. To account for short-range exchange repulsion and long-range dispersion interactions, we have incorporated a pairwise, empirical potential, in the form of Lennard-Jones terms, into the X-Pol effective Hamiltonian. In the present study, the X-Pol potential is constructed using the B3LYP hybrid density functional with the 6-31G(d) basis set to treat interacting fragments, and the Lennard-Jones parameters have been optimized on a dataset consisting of 105 bimolecular complexes. It is shown that the X-Pol potential can be optimized to provide a good description of hydrogen bonding interactions; the root mean square deviation of the computed binding energies from full (i.e., nonfragmental) CCSD(T)/aug-cc-pVDZ results is 0.8 kcal/mol, and the calculated hydrogen bond distances have an average deviation of about 0.1 A from those obtained by full B3LYP/aug-cc-pVDZ optimizations.
- Published
- 2012
17. Classical and quantum mechanical/molecular mechanical molecular dynamics simulations of alanine dipeptide in water: comparisons with IR and vibrational circular dichroism spectra
- Author
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Kwang-Im Oh, Kyung Koo Lee, Jaebeom Han, Minhaeng Cho, and Kijeong Kwac
- Subjects
Circular dichroism ,Dipeptide ,Spectrophotometry, Infrared ,Circular Dichroism ,Molecular Conformation ,General Physics and Astronomy ,Computational Biology ,Water ,Hydrogen Bonding ,Dipeptides ,Quantum chemistry ,Molecular physics ,Molecular dynamics ,chemistry.chemical_compound ,chemistry ,Polarizability ,Molecular vibration ,Vibrational circular dichroism ,Quantum Theory ,Computer Simulation ,Physical and Theoretical Chemistry ,Mulliken population analysis - Abstract
We have implemented the combined quantum mechanical (QM)/molecular mechanical (MM) molecular dynamics (MD) simulations of alanine dipeptide in water along with the polarizable and nonpolarizable classical MD simulations with different models of water. For the QM/MM MD simulation, the alanine dipeptide is treated with the AM1 or PM3 approximations and the fluctuating solute dipole moment is calculated by the Mulliken population analysis. For the classical MD simulations, the solute is treated with the polarizable or nonpolarizable AMBER and polarizable CHARMM force fields and water is treated with the TIP3P, TIP4P, or TIP5P model. It is found that the relative populations of right-handed alpha-helix and extended beta and P(II) conformations in the simulation trajectory strongly depend on the simulation method. For the QM/MM MD simulations, the PM3/MM shows that the P(II) conformation is dominant, whereas the AM1/MM predicts that the dominant conformation is alpha(R). Polarizable CHARMM force field gives almost exclusively P(II) conformation and other force fields predict that both alpha-helical and extended (beta and P(II)) conformations are populated with varying extents. Solvation environment around the dipeptide is investigated by examining the radial distribution functions and numbers and lifetimes of hydrogen bonds. Comparing the simulated IR and vibrational circular dichroism spectra with experimental results, we concluded that the dipeptide adopts the P(II) conformation and PM3/MM, AMBER03 with TIP4P water, and AMBER polarizable force fields are acceptable for structure determination of the dipeptide considered in this paper.
- Published
- 2008
18. Phenol-benzene complexation dynamics: quantum chemistry calculation, molecular dynamics simulations, and two dimensional IR spectroscopy
- Author
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Kijeong Kwac, Kyungwon Kwak, Yousung Jung, Minhaeng Cho, Chewook Lee, Jaebeom Han, Michael D. Fayer, and Junrong Zheng
- Subjects
Models, Molecular ,Absorption spectroscopy ,Spectrophotometry, Infrared ,Macromolecular Substances ,Molecular Conformation ,General Physics and Astronomy ,Infrared spectroscopy ,Electronic structure ,Quantum chemistry ,Molecular physics ,chemistry.chemical_compound ,Molecular dynamics ,Physics::Atomic and Molecular Clusters ,Vibrational energy relaxation ,Computer Simulation ,Physics::Chemical Physics ,Physical and Theoretical Chemistry ,Benzene ,Carbon Tetrachloride ,Phenol ,chemistry ,Models, Chemical ,Chemical physics ,Solvents ,Quantum Theory ,Density functional theory - Abstract
Molecular dynamics (MD) simulations and quantum mechanical electronic structure calculations are used to investigate the nature and dynamics of the phenol-benzene complex in the mixed solvent, benzene∕CCl4. Under thermal equilibrium conditions, the complexes are continuously dissociating and forming. The MD simulations are used to calculate the experimental observables related to the phenol hydroxyl stretching mode, i.e., the two dimensional infrared vibrational echo spectrum as a function of time, which directly displays the formation and dissociation of the complex through the growth of off-diagonal peaks, and the linear absorption spectrum, which displays two hydroxyl stretch peaks, one for the complex and one for the free phenol. The results of the simulations are compared to previously reported experimental data and are found to be in quite reasonable agreement. The electronic structure calculations show that the complex is T shaped. The classical potential used for the phenol-benzene interaction in the MD simulations is in good accord with the highest level of the electronic structure calculations. A variety of other features is extracted from the simulations including the relationship between the structure and the projection of the electric field on the hydroxyl group. The fluctuating electric field is used to determine the hydroxyl stretch frequency-frequency correlation function (FFCF). The simulations are also used to examine the number distribution of benzene and CCl4 molecules in the first solvent shell around the phenol. It is found that the distribution is not that of the solvent mole fraction of benzene. There are substantial probabilities of finding a phenol in either a pure benzene environment or a pure CCl4 environment. A conjecture is made that relates the FFCF to the local number of benzene molecules in phenol’s first solvent shell.
- Published
- 2007
19. Quantum mechanical force field for water with explicit electronic polarization
- Author
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Michael J. M. Mazack, Jiali Gao, Donald G. Truhlar, Jaebeom Han, and Peng Zhang
- Subjects
Physics ,Intermolecular force ,Water ,General Physics and Astronomy ,Electrons ,Electronic structure ,Liquids, Glasses, and Crystals ,Potential energy ,symbols.namesake ,Chemical physics ,Proton transport ,Intramolecular force ,symbols ,Water model ,Quantum Theory ,Quantum-mechanical explanation of intermolecular interactions ,Physical and Theoretical Chemistry ,Atomic physics ,Hamiltonian (quantum mechanics) - Abstract
A quantum mechanical force field (QMFF) for water is described. Unlike traditional approaches that use quantum mechanical results and experimental data to parameterize empirical potential energy functions, the present QMFF uses a quantum mechanical framework to represent intramolecular and intermolecular interactions in an entire condensed-phase system. In particular, the internal energy terms used in molecular mechanics are replaced by a quantum mechanical formalism that naturally includes electronic polarization due to intermolecular interactions and its effects on the force constants of the intramolecular force field. As a quantum mechanical force field, both intermolecular interactions and the Hamiltonian describing the individual molecular fragments can be parameterized to strive for accuracy and computational efficiency. In this work, we introduce a polarizable molecular orbital model Hamiltonian for water and for oxygen- and hydrogen-containing compounds, whereas the electrostatic potential responsible for intermolecular interactions in the liquid and in solution is modeled by a three-point charge representation that realistically reproduces the total molecular dipole moment and the local hybridization contributions. The present QMFF for water, which is called the XP3P (explicit polarization with three-point-charge potential) model, is suitable for modeling both gas-phase clusters and liquid water. The paper demonstrates the performance of the XP3P model for water and proton clusters and the properties of the pure liquid from about 900 × 10(6) self-consistent-field calculations on a periodic system consisting of 267 water molecules. The unusual dipole derivative behavior of water, which is incorrectly modeled in molecular mechanics, is naturally reproduced as a result of an electronic structural treatment of chemical bonding by XP3P. We anticipate that the XP3P model will be useful for studying proton transport in solution and solid phases as well as across biological ion channels through membranes.
- Published
- 2013
- Full Text
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20. Nitrile and thiocyanate IR probes: Molecular dynamics simulation studies
- Author
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Hochan Lee, Minhaeng Cho, Kwang-Im Oh, Joo Hyun Lee, Jaebeom Han, and Jun Ho Choi
- Subjects
Molecular dynamics ,chemistry.chemical_compound ,Partial charge ,Nitrile ,chemistry ,Hydrogen bond ,Ab initio quantum chemistry methods ,Ab initio ,General Physics and Astronomy ,Physical chemistry ,Infrared spectroscopy ,Physical and Theoretical Chemistry ,Triple bond - Abstract
Nitrile- and thiocyanate-derivatized amino acids have been found to be useful IR probes for investigating their local electrostatic environments in proteins. To shed light on the CN stretch frequency shift and spectral lineshape change induced by interactions with hydrogen-bonding solvent molecules, we carried out both classical and quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations for MeCN and MeSCN in water. These QM/MM and conventional force field MD simulation results were found to be inconsistent with the experimental results as well as with the high-level ab initio calculation results of MeCN-water and MeSCN-water potential energies. Thus, a new set of atomic partial charges of MeCN and MeSCN is obtained. By using the MD simulation trajectories and the electrostatic potential model recently developed, the CN and SCN stretching mode frequency trajectories were obtained and used to simulate the IR spectra. The C[Triple Bond]N frequency blueshifts of MeCN and MeSCN in water are estimated to be 9.0 and 1.9 cm(-1), respectively, in comparison with those of gas phase values. These values are found to be in reasonable agreement with the experimentally measured IR spectra of MeCN, MeSCN, beta-cyano-L-alanine, and cyanylated cysteine in water and other polar solvents.
- Published
- 2008
- Full Text
- View/download PDF
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