Journal of Atomic and Molecular Sciences
type: channel
description: The Journal of Atomic and Molecular Sciences (JAMS) presents new and original research results in broard areas of atomic and molecular sciences. The regular articles and feature articles are also acceptable. Substantial survey papers on topics of exceptional interest will also be published occasionally. The journal is published quarterly.
publisher: Global Science Press
language: en
publication name: Journal of Atomic and Molecular Sciences
issn: 2075-1303
items: Author Index to Volume 2
items: Phase Control of the Temporal Envelope of an Ultrashort Pulse Propagating in an Strongly Driven Atomic Medium
items: Bound State Solutions of the $s$-Wave Klein-Gordon Equation with Position Dependent Mass for Exponential Potential
items: First-Principles Study of Electronic and Magnetic Properties and Tetragonal Distortion of the Heusler Alloy $Mn_2NiAl$
items: Nonclassical Properties and Generation of Superposition State of Excited Coherent States of Motion of Trapped Ion
items: First-Principles Study on the Electronic and Magnetic Properties of C- and N-Doped ZnS Nanowires
items: Preparation and Second-Order Nonlinearity of Organic/Inorganic Hybrid Materials Doped with Organic Chromophore
items: Three-Body Dispersion Coefficients for Excited Hydrogen Atoms
items: Adsorption of Anionic Dyes from Aqueous Solution on Zeolite from Fly Ash-Iron Oxide Magnetic Nanocomposite
items: Relativistic Paramagnetism of a Weakly Interacting Fermi Gas
items: Elastic Scattering of Positron by Gold Atom
items: The Properties of Glycophorin a Transmembrane Helices in Erythrocyte Asymmetric Membrane: A Molecular Dynamics Study
items: Calculation of the Van der Waals Potential of Argon Dimer Using a Modified Tang-Toennies Model
items: B-NiCo$_2$O$_4$/NF as an Efficient Electrocatalyst for HER
items: Integrated Co-Ni-Se Network on Ni Foam as an Efficient Electrocatalyst for Alkaline Hydrogen Evolution
items: Sulfide Doped Cobalt Oxide Nanosphere as a Highly Efficient Electrocatalyst for Oxygen Evolution Reaction
items: New Insight into the Hydrogen Bond Effects in One of PRODAN Derivatives (1a) on Excited State in Methanol Solvent
items: A Novel Imprinted Electrochemical Sensor for Dopamine Determination Based on Electron Conductivity Enhanced by Ferrocenyl Chalcone Derivative Film
items: Configurational Prediction of CYP2A6 Substrate Would Guide the Screening of Potential Substrate
items: Can the Fluorescence Quantum Yield Be Enhanced by Introducing the Benzene Ring to the Blue Fluorescent Protein Chromophore?
items: Outperformance of CAM-B3LYP than M062X Density Functional in Mixed Transition of Local Excitation and Charge Transfer
items: The Solvent Effects on the Energy Gap Between the $n\pi^*$ State and $\pi\pi^*$ State and Fluorescence of Benzoyleneurea
items: Theoretical Calculations for Spectroscopic Constants and Anharmonic Force Field of ${\rm N}_2{\rm CO}$
items: An Potential Energy Surface for the $O+O_2$ Reaction Using Neural Network Approach
items: Angular Distributions of Molecular Photofragments by Intense Ultrashort Laser Pulses
items: Modulating N-H-Based Excited-State Intramolecular Proton Transfer by Different Electron-Donating/Withdrawing Substituents in 2-(2’-Aminophenyl)Benzothiazole Compounds
items: Theoretical Investigation on the Antioxidant Activity of p-Cresol and Its Derivatives: Effects of Propenyl Group and Solvents
items: Theoretical Insights into the Excited State Hydrogen Bond and ESIPT Reaction for 2-Amino-3-(2’-Benzoxazolyl)Quinoline and 2-Amino-3-(2’-Benzothiazolyl)-Quinoline
items: Theoretical Elaboration about Excited State Behaviors and Fluoride Anion Sensor Mechanism for 2-{[2-(2-Hydroxy-Phenyl)-1H-Benzoimidazo-5-yl]-Phenyl-Methylene} Malononitrile
items: Excited State Process of a Novel NIR-BODI Molecule in Toluene and Acetonitrile Solvents: A Theoretical Study

Author Index to Volume 2
type: item
subject: Articles
  topic: section
subject:
  topic: subjects
rights: Copyright (c) 2025 COPYRIGHT: © Global Science Press
date: 2011-02-01
publication date: 2011-02-01
starting page: 385
ending page: 386

Phase Control of the Temporal Envelope of an Ultrashort Pulse Propagating in an Strongly Driven Atomic Medium
type: item
description: We consider a double two-level system in which each single two-level system is driven by a strong linearly polarized pulse. The system is probed by a weak pulse orthogonally polarized. We study the distortion experienced by the probe temporal envelope when the relative phase between the pump and the probe is varied. We show that pulse behavior oscillates between two regimes that corresponds to transparency and amplification respectively. Interpretation of this effect is given within adiabatic representation.
subject: Articles
  topic: section
subject: coherent control
  topic: keywords
subject: propagation effects
  topic: keywords
subject: light shifts.
  topic: keywords
subject:
  topic: subjects
creator: M. A. Bouchene
creator: J. C. Delagnes
rights: Copyright (c) 2025 COPYRIGHT: © Global Science Press
date: 2011-02-01
publication date: 2011-02-01
starting page: 377
ending page: 384
doi: 10.4208/jams.071611.073011a

Bound State Solutions of the $s$-Wave Klein-Gordon Equation with Position Dependent Mass for Exponential Potential
type: item
description: Bound state solutions of the s-wave Klein-Gordon equation with spatially dependent exponential-type mass for exponential-type scalar and vector potential are studied by using the Nikiforov-Uvarov method. The wave functions of the system are taken on the form of the Laguerre polynomials and the energy spectra of the system are discussed. In limit of constant mass, the wave functions and energy eigenvalues are in good agreement with the results previously.
subject: Articles
  topic: section
subject: Klein-Gordon equation
  topic: keywords
subject: Bound state solution
  topic: keywords
subject: position dependent mass
  topic: keywords
subject: exponential potential.
  topic: keywords
subject:
  topic: subjects
creator: Tong-Qing Dai
rights: Copyright (c) 2025 COPYRIGHT: © Global Science Press
date: 2011-02-01
publication date: 2011-02-01
starting page: 360
ending page: 367
doi: 10.4208/jams.012511.030511a

First-Principles Study of Electronic and Magnetic Properties and Tetragonal Distortion of the Heusler Alloy $Mn_2NiAl$
type: item
description: The crystal structure, tetragonal distortion, magnetism, electronic structure and pressure response of $Mn_2NiAl$ are calculated by first-principles method based on the density functional theory. The calculations show, the equilibrium structure of $Mn_2NiAl$ in the cubic austenitic phase is the MnMnNiAl structure with Mn atoms occupy $A$ and $B$ sites and two Mn atoms occupy inequivalent positions. In the process of transform from a cubic to a tetragonal structure, $Mn_2NiAl$ alloys exhibit a stable martensitic phase near $c/a = 1.24.$ In both the austenite and martensite phases, Mn atoms are the main contributors to the magnetism in $Mn_2NiAl,$ $Mn_2NiAl$ alloys show ferrimagnetism due to antiparallel but unbalanced magnetic moments of Mn(A) atom and Mn(B) atom. The direct $d-d$ exchange interactions between Mn(A) atom and Mn(B) atom are weak because of small overlap of $d$-projected DOS of Mn(A) atom and Mn(B) atom nearby the Fermi level, but the intra-atomic interactions in Mn atoms are strong, this is the reason why the $Mn_2NiAl$ alloys show ferrimagnetism. The findings strongly suggests that $Mn_2NiAl$ alloys would behave like a magnetic shape memory alloy.
subject: Articles
  topic: section
subject: first-principles
  topic: keywords
subject: tetragonal distortion
  topic: keywords
subject: martensite phase transformation
  topic: keywords
subject: ferrimagnetism.
  topic: keywords
subject:
  topic: subjects
creator: Li-Jin Luo
creator: Chong-Gui Zhong
creator: Jing-Huai Fang
creator: Peng-Xia Zhou
creator: Yong-Lin Zhao
creator: Xue-Fan Jiang
rights: Copyright (c) 2025 COPYRIGHT: © Global Science Press
date: 2011-02-01
publication date: 2011-02-01
starting page: 368
ending page: 376
doi: 10.4208/jams.021911.041411a

Nonclassical Properties and Generation of Superposition State of Excited Coherent States of Motion of Trapped Ion
type: item
description: We have studied the intensity squeezing of superposition state of excited coherent states and proposed a new method to prepare superposition state of excited coherent states of vibrational motion of trapped ion. This method is based on the interaction of a single trapped ion with two traveling wave light fields with different frequencies. An obvious merit of this method is that it works without application of the perturbation theory.
subject: Articles
  topic: section
subject: trapped ion
  topic: keywords
subject: excited coherent states
  topic: keywords
subject: intensity squeezing.
  topic: keywords
subject:
  topic: subjects
creator: Zhong-Jie Wang
creator: Chao-Yang Fan
rights: Copyright (c) 2025 COPYRIGHT: © Global Science Press
date: 2011-02-01
publication date: 2011-02-01
starting page: 352
ending page: 359
doi: 10.4208/jams.010811.022311a

First-Principles Study on the Electronic and Magnetic Properties of C- and N-Doped ZnS Nanowires
type: item
description: We comparatively study the electronic and magnetic properties of unpassivated (NP) and H-passivated (HP) ZnS nanowire (NWs) doped with one C (or N) atom in terms of the first-principle calculation. The result shows that C (or N) atom preferring to the surface position for both of the NP and HP NWs. All of the C-doped ZnS NWs show semiconductor character. The magnetic moments are mainly contributed by the C-2p orbital. The magnetic moments of the C, Zn, and S atoms in the super cell have the same direction, indicating FM coupling between them. While for N-doped ZnS NWs, it is interesting that an N atom substituting an S atom in the middle position of NP ZnS NWs change the host from semiconductor to metal. These results show that the doping atom, doping position, and surface condition can significantly change the properties of semiconducting ZnS NWs.
subject: Articles
  topic: section
subject: nanowires
  topic: keywords
subject: magnetic properties
  topic: keywords
subject: density functional theory.
  topic: keywords
subject:
  topic: subjects
creator: Jian-Ming Xie
rights: Copyright (c) 2025 COPYRIGHT: © Global Science Press
date: 2011-02-01
publication date: 2011-02-01
starting page: 342
ending page: 351
doi: 10.4208/jams.123010.122710a

Preparation and Second-Order Nonlinearity of Organic/Inorganic Hybrid Materials Doped with Organic Chromophore
type: item
description: A kind of hybrid material was made through sol-gel process with the PMMA, TEOS, and 4-[N]-ethyl-N-(2-hydroxyethyl) amino-4'-nitro-azobenzene (DR1). And the films of sol were prepared by using the spin-coated method. Through all optical poling, it could be found that there exists an optimum thickness for film. In addition, the higher of sample temperature was, the smaller intensity of SHG was. The experiment showed that the $SiO_2$ network was existent, and hybrid materials significantly improved orientation stability.
subject: Articles
  topic: section
subject: thin film
  topic: keywords
subject: all-optical poling
  topic: keywords
subject: SHG
  topic: keywords
subject: temperature.
  topic: keywords
subject:
  topic: subjects
creator: Yun-Long Liu
creator: Wen-Jun Wang
creator: Xue-Xi Gao
creator: Bing-Yuan Zhang
creator: Hui Li
rights: Copyright (c) 2025 COPYRIGHT: © Global Science Press
date: 2011-02-01
publication date: 2011-02-01
starting page: 334
ending page: 341
doi: 10.4208/jams.123010.021411a

Three-Body Dispersion Coefficients for Excited Hydrogen Atoms
type: item
description: The three-body van der Waals dispersion coefficients $Z(l_1l_2l_2)$ (up to $l_i = 5$) for the $H(1s)-H(1s)-H(1s)$ and $H(2s)-H(2s)-H(2s)$ systems are calculated by virtue of the dynamic polarizabilities at imaginary photon frequencies. The expression for the $2^l$-pole dynamic polarizabilities of atomic hydrogen is derived by application of the integration properties of the one-dimensional radial Coulomb Green's function. The results for the $H(1s)-H(1s)-H(1s)$ system are consistent with previous calculation in the literature, while the results for the $H(2s)-H(2s)-H(2s)$ systems are reported for the first time, and they are the main contribution of this work.
subject: Articles
  topic: section
subject: hydrogen
  topic: keywords
subject: excited state
  topic: keywords
subject: three-body dispersion coefficient.
  topic: keywords
subject:
  topic: subjects
creator: Shi-Zhong Huang
creator: Qiu-Feng Sun
rights: Copyright (c) 2025 COPYRIGHT: © Global Science Press
date: 2011-02-01
publication date: 2011-02-01
starting page: 325
ending page: 333
doi: 10.4208/jams.121210.012111a

Adsorption of Anionic Dyes from Aqueous Solution on Zeolite from Fly Ash-Iron Oxide Magnetic Nanocomposite
type: item
description: Magnetic zeolite/iron oxide nanocomposite was prepared by mixing zeolite synthesized from coal fly ashes with magnetite nanoparticles in suspension and was used for the removal of Reactive Orange 16 (RO16) and Indigo Carmine (IC) from aqueous solutions. The effect of various experimental parameters such as contact time, pH, adsorbent dose and temperature were investigated. The experimental data were analyzed using the pseudo-first-order and pseudo-second-order adsorption kinetic models. The experimental data fit the second-order kinetic model. The Langmuir and Freundlich isotherm models were tested for their applicability. Results indicated that according to the Langmuir isotherm, the maximum sorption capacities are 1.1 and 0.58 $mg$$\cdot$$g^{-1}$ for RO16 and IC, respectively. Thermodynamic parameters showed that adsorption of dyes were endothermic and spontaneous in nature.
subject: Articles
  topic: section
subject: magnetically modified zeolite
  topic: keywords
subject: coal fly ash
  topic: keywords
subject: nanocomposite
  topic: keywords
subject: adsorption
  topic: keywords
subject: dye removal.
  topic: keywords
subject:
  topic: subjects
creator: D. A. Fungaro
creator: M. Yamaura
creator: T. E. M. Carvalho
rights: Copyright (c) 2025 COPYRIGHT: © Global Science Press
date: 2011-02-01
publication date: 2011-02-01
starting page: 305
ending page: 316
doi: 10.4208/jams.032211.041211a

Relativistic Paramagnetism of a Weakly Interacting Fermi Gas
type: item
description: By considering strict relativistic energy of single particle and using the methods of quantum statistics, the relativistic paramagnetism of a weakly interacting Fermi gas in a weak magnetic filed is studied, and the relativistic most probable paramagnetic susceptibility as well as the average magnetic susceptibility of the system are solved. On the basis, the influences of relativistic effect on the most probable paramagnetic susceptibility of the system are discussed, and the relativistic critical value of particle number is given. It is shown that, comparing with nonrelativistic situation, when $T\gg T_F,$ the relativistic most probable magnetic susceptibility and the relativistic critical value of particle number have not changed. When $T\ll T_F$, the relativistic effects make the system display paramagnetism easily and susceptibility increase, but the relativistic effects also amplified the impact of the interaction on the magnetic susceptibility.
subject: Articles
  topic: section
subject: Fermi gas
  topic: keywords
subject: the relativistic effect
  topic: keywords
subject: paramagnetism.
  topic: keywords
subject:
  topic: subjects
creator: Fu-Dian Men
creator: Xiao-Gang He
creator: Hui Liu
creator: Bin Dong
rights: Copyright (c) 2025 COPYRIGHT: © Global Science Press
date: 2011-02-01
publication date: 2011-02-01
starting page: 317
ending page: 324
doi: 10.4208/jams.121610.012211a

Elastic Scattering of Positron by Gold Atom
type: item
description: We present relativistic calculations of the differential, integrated elastic, momentum transfer total cross sections and spin polarization parameters for positrons scattered from Gold atom using a simple optical model potential to represent interaction between positron and target atoms in the energy range 2.0-500eV. In the present calculation we employ a parameter-free model potential for the correlation polarization and absorption potential as devised for positron-atom scattering. The theoretical results are obtained from relativistic approach based on solving the Dirac equation using Hartree-Fock and Dirac-Fock wave functions.
subject: Articles
  topic: section
subject: relativistic calculation
  topic: keywords
subject: positron scattering.
  topic: keywords
subject:
  topic: subjects
creator: Kapil K. Sharma
creator: Neerja Singh
creator: R. P. Vats
rights: Copyright (c) 2025 COPYRIGHT: © Global Science Press
date: 2011-02-01
publication date: 2011-02-01
starting page: 294
ending page: 304
doi: 10.4208/jams.022611.031311a

The Properties of Glycophorin a Transmembrane Helices in Erythrocyte Asymmetric Membrane: A Molecular Dynamics Study
type: item
description: We have performed an 80ns molecular dynamics (MD) simulation of human red blood erythrocyte asymmetric membrane model. The NAMD code and CHARMM27 force field were used. We have estimated some features of embedded Glycophorin A (GpA) protein and have discussed some important problems concerning the interaction between the protein and surrounding media. It is stated that the lipid environment and protein immediate neighboring lead to the changes in helix-helix association, as well as to the protein orientation. The interaction nature between protein and neighboring phospholipid chains are dominant forces governing to helix-helix association.
subject: Articles
  topic: section
subject: Glycophorin A (GpA) protein
  topic: keywords
subject: erythrocyte membrane
  topic: keywords
subject: molecular dynamics simulation
  topic: keywords
subject: helix-helix association.
  topic: keywords
subject:
  topic: subjects
creator: Paruyr K. Hakobyan
creator: Armen H. Poghosyan
creator: Aram A. Shahinyan
rights: Copyright (c) 2025 COPYRIGHT: © Global Science Press
date: 2011-02-01
publication date: 2011-02-01
starting page: 281
ending page: 288
doi: 10.4208/jams.012711.021511a

Calculation of the Van der Waals Potential of Argon Dimer Using a Modified Tang-Toennies Model
type: item
description: The Tang-Toennies (TT) potential model was modified based on the physical nature of the interatomic interaction to describe the $Ar-Ar$ potential very accurately in the short range of the repulsive region. Using the modified TT potential model, the ground state van der Waals potential energy curve of $Ar_2$ was calculated. Compare to the experimental result, the current potential shows that the modified potential model not only gives the precise result in the long-range part, but also gives quite accurate result in the short-range repulsive part.
subject: Articles
  topic: section
subject: modified TT potential model
  topic: keywords
subject: argon dimer
  topic: keywords
subject: van der Waals potential.
  topic: keywords
subject:
  topic: subjects
creator: J. F. Peng
creator: P. Li
creator: J. Ren
creator: L. W. Qiao
creator: K. T. Tang
rights: Copyright (c) 2025 COPYRIGHT: © Global Science Press
date: 2011-02-01
publication date: 2011-02-01
starting page: 289
ending page: 293
doi: 10.4208/jams.011511.022111a

B-NiCo$_2$O$_4$/NF as an Efficient Electrocatalyst for HER
type: item
description: The development of efficient catalysts for the hydrogen evolution reaction (HER) is of extreme importance for future renewable energy systems. In this work, we report on the synthesis of a novel hybrid electrode that boracic nanospheres grown on the top of some ${\rm NiCo}_2{\rm O}_4$ nanowires with nickel foam as the baseboard$({\rm B-NiCo}_2{\rm O}_4{\rm /NF}).$ Due to this unique structural features, the electrocatalyst has a good activity for HER, which needs overpotential of 150 mV to afford the current density of 10 mA ${\rm cm}^{-2},$ the catalytic activity is maintained for at least 18 h. This work provides a promising methodology for the designing and fabricating highly efficient boracic catalysts for HER.
subject: Articles
  topic: section
subject: Electrocatalyst
  topic: keywords
subject: HER
  topic: keywords
subject: boronation.
  topic: keywords
subject:
  topic: subjects
creator: Mengjie Zhang, Rongxing He & Ming Li
rights: Copyright (c) 2025 COPYRIGHT: © Global Science Press
date: 2019-04-09
publication date: 2019-04-09
starting page: 7
ending page: 9
doi: 10.4208/jams.022519.032219a

Integrated Co-Ni-Se Network on Ni Foam as an Efficient Electrocatalyst for Alkaline Hydrogen Evolution
type: item
description: Hydrogen evolution reaction (HER) is long considered as a promising chemical reaction that can produce the clean fuel hydrogen to resolve the energy crisis and environmental pollution. Herein, we report the in situ growth of Co-Ni-Se network on a 3D porous Ni foam support (Co-Ni-Se/NF) as an efficient electrocatalyst for HER. The obtained Co-Ni-Se/NF electrode exhibits high HER activity that only needs a low overpotential of 106 mV at 10 mA cm$^{-2}.$
subject: Articles
  topic: section
subject: Hydrogen evolution reaction
  topic: keywords
subject: Ni foam
  topic: keywords
subject: electrocatalyst.
  topic: keywords
subject:
  topic: subjects
creator: Shu Liu, Hanfei Zhang, Yi Wu, Rongxing He & Ming Li
rights: Copyright (c) 2025 COPYRIGHT: © Global Science Press
date: 2019-04-09
publication date: 2019-04-09
starting page: 4
ending page: 6
doi: 10.4208/jams.021519.031019a

Sulfide Doped Cobalt Oxide Nanosphere as a Highly Efficient Electrocatalyst for Oxygen Evolution Reaction
type: item
description: Electrochemical water splitting has been known as a promising and environmental approach to produce hydrogen by avoiding relying on fossil fuels. Unfortunately, the efficient and large-scale $H_2$ production is still hindered by the sluggish kinetics of the oxygen evolution reaction (OER) at the anode side of a water electrolyzer. Herein, we report a novel amorphous sulfide doped cobalt oxide (amorphous Co-S-O) nanosphere as an efficient electrocatalyst for OER. The Co-S-O electrode exhibits high HER activity and good stability.
subject: Articles
  topic: section
subject: OER
  topic: keywords
subject: Electrocatalyst
  topic: keywords
subject: Sulfide Cobalt
  topic: keywords
subject: Nanosphere.
  topic: keywords
subject:
  topic: subjects
creator: Qifei Guo, Yu Han & Rongxing He
rights: Copyright (c) 2025 COPYRIGHT: © Global Science Press
date: 2019-04-09
publication date: 2019-04-09
starting page: 1
ending page: 3
doi: 10.4208/jams.010819.022419a

New Insight into the Hydrogen Bond Effects in One of PRODAN Derivatives (1a) on Excited State in Methanol Solvent
type: item
description: PRODAN derivatives would be a potential probe molecules. The hydrogen bond effects in PRODAN derivatives on excited state in methanol solvent have some significance to explain their dynamic experiments. In this paper, we have presented a theoretical investigation into the influence of hydrogen bonding on the structural and spectral properties of PRODAN derivative (1a) and methanol complexes using time dependent density functional theory. The focused work is the structures and vibrational spectra of PRODAN derivative (1a) hydrogen bonding compounds in methanol solvent. It was observed that the distances of hydrogen bonding between derivative and methanol molecule in complexes shortened in the $S_1$ state. The results suggested that the behavior and effect of hydrogen bonds increased in the excited proceed. In addition, the IR vibrational spectra of PRODAN-1a-MeOH complex occurred shift in the $S_1$ state. As a consequence, the hydrogen bonding of PRODAN derivative (1a) could play a role in the geometries and electronic spectra in excited state.
subject: Articles
  topic: section
subject: Hydrogen bond
  topic: keywords
subject: TDDFT
  topic: keywords
subject: Excited state
  topic: keywords
subject: Infrared spectra.
  topic: keywords
subject:
  topic: subjects
creator: Yang Liu, Dan Zhao, Jiawei Gao & Zhen Zhao
rights: Copyright (c) 2025 COPYRIGHT: © Global Science Press
date: 2019-04-09
publication date: 2019-04-09
starting page: 53
ending page: 57
doi: 10.4208/jams.120518.123018a

A Novel Imprinted Electrochemical Sensor for Dopamine Determination Based on Electron Conductivity Enhanced by Ferrocenyl Chalcone Derivative Film
type: item
description: A novel biochemical sensor based on molecular imprinted technology was built through electropolymerization. One of the keystones of the technology is the discovery and application of new conductive polymer. Herein, a new conductive ferrocenyl chalcone derivative: [1-Oxo-3-(3-thienyl)-2-propen-1-yl] ferrocene (OTPylFc) was synthesized and characterized by nuclear magnetic resonance (NMR) and finally adopted in the technology. The OTPylFc and pyrrole mixture was eletropolymerized in this work and showed satisfying result in improving current peaks. The linear relationship was 1.729× 10$^{-6}$ M to 6.916 × 10$^{-4}$ M. It is believed that the structure and their conductive analogs formed co-polymers would have a promising prospect in future research.
subject: Articles
  topic: section
subject: OTPylFc
  topic: keywords
subject: Molecular Imprinted Technology
  topic: keywords
subject: DPV
  topic: keywords
subject: Electrochemical Sensor.
  topic: keywords
subject:
  topic: subjects
creator: Liming Chen, Defang Liu & Caixia Wang
rights: Copyright (c) 2025 COPYRIGHT: © Global Science Press
date: 2019-04-09
publication date: 2019-04-09
starting page: 58
ending page: 61
doi: 10.4208/jams.100818.112418a

Configurational Prediction of CYP2A6 Substrate Would Guide the Screening of Potential Substrate
type: item
description: Cytochrome P450 2A6 (CYP2A6) substrate database constitute a potential class of disease related molecules as well as therapeutic molecules, primarily expressed in liver and lungs. The prediction of CYP2A6-related metabolism is of great interest. In this study, a docking protocol was presented which made use of poses of known substrate to help guide the configurational search and to rank predicted poses of test substrates. As a result, a 68% success rate was obtained. Predicting ideal configurations of compound would make significant impact on screening potential substrate, as the predicted bound conformations of 3 Tanshinone IIa (CYP2A6 substrate) analogues revealed differences among them and the inappropriate characteristic to be selected as substrates which was confirmed experimently.
subject: Articles
  topic: section
subject:
  topic: subjects
creator: Huizi Man & Yan Jia
rights: Copyright (c) 2025 COPYRIGHT: © Global Science Press
date: 2019-04-09
publication date: 2019-04-09
starting page: 46
ending page: 52
doi: 10.4208/jams.111518.122818a

Can the Fluorescence Quantum Yield Be Enhanced by Introducing the Benzene Ring to the Blue Fluorescent Protein Chromophore?
type: item
description: The green fluorescent protein (GFP) has been widely used in biochemical and biological fields for its strong fluorescence emitting property. The effective fluorescence emitting property lies in its chromophore P-HBI. Compared with GFP, the low fluorescence quantum yield (0.2 vs. 0.8 of GFP) of the wild blue fluorescent protein (BFP) restrict its extensive applications. In order to enhance the fluorescent quantum yield of BFP, numerous attempts have been executed to modify the molecular configuration such as introducing the intramolecular hydrogen bond (IHB) or benzene ring to the parent structure. In the present work, we employed the high-level quantum chemistry calculation method CASSCF to investigate the excited state deactivation mechanism of 4-BFP, which is a newly synthesized BFP chromophore derivative by introducing a benzene ring to the five-membered heterocycle attempting to increase the fluorescence quantum yield. By combination of the optimization of stable electronic structures, scanning of potential energy surfaces and construction of energy profile, we found that the fluorescent quantum yield could not be enhanced for the 4-BFP molecule. One minimum energy conical intersection was located between the S1 and S0 states, which could act as the gateway for the 4-BFP to funnel to the ground state by the internal conversion process. The current work could provide fundamental guide for further molecular structure modification or improvement to enhance the fluorescent quantum yield of BFP analogues.
subject: Articles
  topic: section
subject: Fluorescence
  topic: keywords
subject: Excited state
  topic: keywords
subject: Decay process
  topic: keywords
subject: Photoisomerization.
  topic: keywords
subject:
  topic: subjects
creator: Bing Liu, Qi Wei, Ruihu Tao, Pengjie Gao, Panwang Zhou, Chaozhuo Liu & Li Zhao
rights: Copyright (c) 2025 COPYRIGHT: © Global Science Press
date: 2019-01-30
publication date: 2019-01-30
starting page: 42
ending page: 45
doi: 10.4208/jams.102518.113018a

Outperformance of CAM-B3LYP than M062X Density Functional in Mixed Transition of Local Excitation and Charge Transfer
type: item
description: A balance between the local excitation (LE) and charge-transfer (CT) transitions is an important issue of a density functional. In this work, we compare the performance between the global hybrid functional M062X and long-range separated functional CAM-B3LYP when they calculate the absorption energies of visible light photoswitches hemithioindigo (HTI) Z1, Z2, Z4, Z5 and Z7. The electronic excitations of HTI Z1 and Z2 are mixtures of LE and CT transitions. CAM-B3LYP succeeds to predict the same absorption energy sequence of the five compounds as the experimental results while M062X predicts a wrong sequence of HTI Z1 and Z2. Another global hybrid functional M06 is also employed for a comparison. Finally, we suggest CAM-B3LYP rather than M062X when dealing with mixed electronic transtions.
subject: Articles
  topic: section
subject: Photoswitches
  topic: keywords
subject: Hemithioindigo
  topic: keywords
subject: Vertical Excitation Energy
  topic: keywords
subject: Density Functional.
  topic: keywords
subject:
  topic: subjects
creator: Jian Luo
creator: Yan Liu
rights: Copyright (c) 2025 COPYRIGHT: © Global Science Press
date: 2019-01-30
publication date: 2019-01-30
starting page: 39
ending page: 41
doi: 10.4208/jams.100718.111518a

The Solvent Effects on the Energy Gap Between the $n\pi^*$ State and $\pi\pi^*$ State and Fluorescence of Benzoyleneurea
type: item
description: Benzoyleneurea (BenzU), a fluorescent nucleobase analog, exhibits strong solvent dependent fluorescence intensity. With the increasing of the concentration of polar and protic solvents, BenzU exhibits enhanced fluorescence. To understand the photophysical properties of BenzU, the energy gaps (ΔE) between dark $n\pi^*$ state and bright $\pi\pi^*$ state of BenzU are calculated in several solvents. The solvent dielectric constant and hydrogen bond between BenzU and protic solvent both have effects on ΔE. And the fluorescence quantum yields of BenzU are linear response to ΔE. Furthermore, we find that the more hydrogen bonds are formed between BenzU and protic solvent, the higher ΔE and fluorescence intensity are obtained.
subject: Articles
  topic: section
subject: Fluorescence quantum yields
  topic: keywords
subject: Hydrogen bonds
  topic: keywords
subject: Solvent effects.
  topic: keywords
subject:
  topic: subjects
creator: Songqiu Yang & Jianyong Liu
rights: Copyright (c) 2025 COPYRIGHT: © Global Science Press
date: 2019-01-30
publication date: 2019-01-30
starting page: 33
ending page: 38
doi: 10.4208/jams.100818.112418a

Theoretical Calculations for Spectroscopic Constants and Anharmonic Force Field of ${\rm N}_2{\rm CO}$
type: item
description: The anharmonic force fields and spectroscopic constants of electronic ground state ($\widetilde{X}^1$A') of diazirinone $({\rm N}_2{\rm CO})$ has been investigated employing the DFT (B3LYP, B3PW91, and B3P86) and MP2 methods with the cc-pVnZ (n = D, T, Q) basis sets. The calculated equilibrium geometries, ground state rotational constants, fundamental vibrational frequencies, and equilibrium quartic centrifugal distortion constants of ${\rm N}_2{\rm CO}$ are in comparison with experimental or theoretical data. The B3LYP results well reproduce the equilibrium geometries and spectroscopic constants. The anharmonic constants, vibration–rotation interaction constants, equilibrium sextic centrifugal distortion constants, Coriolis coupling constants, cubic and quartic force constants of ${\rm N}_2{\rm CO}$ are theoretically predicted. The results show that DFT methods can afford more reliable theoretical values than MP2 method.
subject: Articles
  topic: section
subject: Spectroscopic constant
  topic: keywords
subject: anharmonic force field
  topic: keywords
subject: ab initio calculation
  topic: keywords
subject: diazirinone
  topic: keywords
subject:
  topic: subjects
creator: Qiushuang Xu, Meishan Wang, Yanliang Zhao, Yanli Liu, Xuejun Wang & Chuanlu Yang
rights: Copyright (c) 2025 COPYRIGHT: © Global Science Press
date: 2019-01-30
publication date: 2019-01-30
starting page: 21
ending page: 24
doi: 10.4208/jams.081818.093018a

An Potential Energy Surface for the $O+O_2$ Reaction Using Neural Network Approach
type: item
description: A new potential energy surface (PES) of the $O_3$ system was reported, based on the PESs reported by Dawes et al. and Schinke et al. The PES of $O_3$ reported by Dawes et al. was fitted using least square method based upon accurate high level ab initio points, and has been applied to many dynamics calculations. However, it is computationally slow and need lots of time to obtain the energy points from the PES. At the same time, the threshold of the ab initio points is low as 2.6 eV, relative to the minimum of the PES, which limits its application. On the contrary, the PES reported by Schinke et al. numerically is fast and extends to high energy. In this work, we first calculated the energy points from these two PESs. Then we fitted these energy points using PIP-NN approach. In this way, a revised version of the PES of $O_3$ was constructed and we used it to perform quantum reactive scattering dynamics calculation.
subject: Articles
  topic: section
subject: Weak Interaction
  topic: keywords
subject: Hydrogen Bond
  topic: keywords
subject: ESIPT
  topic: keywords
subject: Charge Redistribution.
  topic: keywords
subject:
  topic: subjects
creator: Wentao Li & Zhigang Sun
rights: Copyright (c) 2025 COPYRIGHT: © Global Science Press
date: 2019-01-30
publication date: 2019-01-30
starting page: 25
ending page: 27
doi: 10.4208/jams.101518.112818a

Angular Distributions of Molecular Photofragments by Intense Ultrashort Laser Pulses
type: item
description: We theoretically study the photofragmentation reaction of the hydrogen molecular ion $H^+_2$ by a single intense ultrashort laser pulse. Simulation results obtained from numerical solutions of time-dependent Schrödinger equations show that quantum interference patterns are constructed in the photofragment spectra and the induced angular distributions of photofragments are sensitive to the wavelength of the laser pulse. These phenomena are successfully explained by using the concept of the light-induced conical intersection.
subject: Articles
  topic: section
subject:
  topic: subjects
creator: Kai-Jun Yuan & Chuan-Cun Shu
rights: Copyright (c) 2025 COPYRIGHT: © Global Science Press
date: 2019-01-30
publication date: 2019-01-30
starting page: 28
ending page: 32
doi: 10.4208/jams.081918.101518a

Modulating N-H-Based Excited-State Intramolecular Proton Transfer by Different Electron-Donating/Withdrawing Substituents in 2-(2’-Aminophenyl)Benzothiazole Compounds
type: item
description: At the B3LYP/6-311+G(d, p)/IEFPCM (in dichloromethane) theory level, the N-H-based excited-state intramolecular proton transfer (N-H-based ESIPT) process of 2-(2’-aminophenyl)benzothiazole (PBT-NH2) and its three derivatives 2-(2’-methylaminophenyl) benzothiazole(PBT-NHMe), 2-(2’-acetylaminophenyl)benzothiazole (PBT-NHAc) and 2-(2’-tosylaminophenyl) benzothiazole (PBT-NHTs) have been explored by the time-dependent density functional theory (TD-DFT) method. Our calculated hydrogen bond lengths and angles sufficiently confirm that the intramolecular hydrogen bonds $N_1-H$•••$N_2$ formed at the $S_0$ states of the four compounds should be significantly strengthened in the $S_1$ state, which are further supported by the results obtained based on the analyses of infrared spectra shifts. The scanned potential energy curves reveal that the energy barriers of the first singlet excited state of the four titled compounds along the ESIPT reactions are predicted at 8.74, 8.98, 6.72 and 1.69 kcal/mol, respectively, suggesting that the inclusion of a strong electron-withdrawing tosyl (Ts) group can remarkably facilitate the occurrence of the ESIPT reaction, while the involvement of an electron-donating methyl group has slight opposite effect on the ESIPT process of the amino-type hydrogen-bonding system.
subject: Articles
  topic: section
subject: N-H-based excited-state intramolecular proton transfer
  topic: keywords
subject: electron-donating/withdrawing substituents
  topic: keywords
subject: potential energy curves
  topic: keywords
subject: TDDFT method.
  topic: keywords
subject:
  topic: subjects
creator: Dapeng Yang, Guang Yang, Min Jia, Xiaoyan Song, Qiaoli Zhang & Tianjie Zhang
rights: Copyright (c) 2025 COPYRIGHT: © Global Science Press
date: 2018-10-04
publication date: 2018-10-04
starting page: 17
ending page: 20
doi: 10.4208/jams.030618.051518a

Theoretical Investigation on the Antioxidant Activity of p-Cresol and Its Derivatives: Effects of Propenyl Group and Solvents
type: item
description: The effect of propenyl group on the antioxidant activity of p-cresol and its derivatives were investigated in gas and solvent phases by using density functional theory (DFT) method. Three accepted antioxidant mechanisms, including hydrogen atom transfer (HAT), single-electron transfer followed by proton transfer (SET-PT) and sequential proton loss electron transfer (SPLET), were considered to explore which mechanism p-cresol and its derivatives preferred to in different environments. The bond dissociation enthalpy (BDE), ionization potential (IP), proton dissociation enthalpy (PDE), proton affinity (PA) and electron transfer enthalpy (ETE), closely related to the above three antioxidant mechanisms, were calculated systematically. The obtained results indicate that the antioxidant process of studied compounds prefers to the SET-PT and SPLET mechanism in gas phase and polar solvents, respectively. Meaningfully, the introduction of the propenyl group into the molecular structure can reduce the PA values and then improve the antioxidant activity of the studied compounds, which can provide theoretical guidance for the synthesis of novel antioxidants in the experiment.
subject: Articles
  topic: section
subject: Proton transfer
  topic: keywords
subject: Substituent group
  topic: keywords
subject: Solvent effects
  topic: keywords
subject: Density functional theory.
  topic: keywords
subject:
  topic: subjects
creator: Chaofan Sun, Huifang Zhao, Xiaochun Liu, Hang Yin & Ying Shi
rights: Copyright (c) 2025 COPYRIGHT: © Global Science Press
date: 2018-10-04
publication date: 2018-10-04
starting page: 13
ending page: 16
doi: 10.4208/jams.050818.072418a

Theoretical Insights into the Excited State Hydrogen Bond and ESIPT Reaction for 2-Amino-3-(2’-Benzoxazolyl)Quinoline and 2-Amino-3-(2’-Benzothiazolyl)-Quinoline
type: item
description: Two N-H type excited state intramolecular proton transfer (ESIPT) systems (i.e., 2-amino-3-(2’-benzoxazolyl)quinoline (ABO) and 2-amino-3-(2’-benzothiazolyl)-quinoline (ABT)) have been investigated. Adopting DFT and TDDFT methods coupling with B3LYP functional and TZVP basis set, our simulations about ABO and ABT molecules have successfully reappeared experimental results, based on which the rationality of our calculations is confirmed. Using Atoms in Molecules (AIM) analytical method, we firstly explore the interactions about chemical bond and verify the formation of hydrogen bond N-H•••N for ABO and ABT in the $S_0$ state. Investigating the primary geometrical parameters involved in N-H•••N, we find it should be strengthened in the $S_1$ state. Upon photoexcitation, charge transfer phenomenon is found via frontier molecular orbitals (MOs), and charge redistribution provides the tendency of ESIPT reaction for ABO and ABT. According to our constructed potential energy curves of both $S_0$ and $S_1$ states for ABO and ABT using two kinds of methods (i.e., the elongation of N-H single bond and the weakening of H•••N hydrogen bond), we clarify the ESIPT mechanisms and explain the recovery of four-level reaction cycle. Our searching transition state (TS) structures and simulated intrinsic reaction coordinate (IRC) path further confirm the ESIPT reaction.
subject: Articles
  topic: section
subject: Weak Interaction
  topic: keywords
subject: Hydrogen Bond
  topic: keywords
subject: ESIPT
  topic: keywords
subject: Charge Redistribution.
  topic: keywords
subject:
  topic: subjects
creator: Qiaoli Zhang, Guang Yang, Xiaoyan Song, Jinfeng Zhao & Dapeng Yang
rights: Copyright (c) 2025 COPYRIGHT: © Global Science Press
date: 2018-10-04
publication date: 2018-10-04
starting page: 7
ending page: 12
doi: 10.4208/jams.042518.081318a

Theoretical Elaboration about Excited State Behaviors and Fluoride Anion Sensor Mechanism for 2-{[2-(2-Hydroxy-Phenyl)-1H-Benzoimidazo-5-yl]-Phenyl-Methylene} Malononitrile
type: item
description: In view of the enormous potential of fluorescence chemosensors in recent years, more and more people focus on their developments. In the present work, we theoretically investigate a novel fluorescence sensor 2-{[2-(2-Hydroxy-phenyl)-1H-benzoimidazo-5-yl]-phenyl-methylene}-malononitrile (HBPMM) [J. Lumin. 2016, 173, 165] about its excited state intramolecular proton transfer (ESIPT) and probe response mechanism. Based on density functional theory (DFT) and time-dependent density functional theory (TDDFT) methods, we focus on the $S_0$-state and $S_1$-state hydrogen bonds dynamical behaviors and confirm that the strengthening intramolecular hydrogen bond in the $S_1$ state may promote the ESIPT reaction. In view of the photoexcitation, we find that the charge redistribution around hydroxyl moiety plays important roles in providing driving force for ESIPT. And the constructed potential energy curves further verify the ESIPT process of HBPMM should be ultrafast. That is the reason why the normal HBPMM fluorescence cannot be detected in previous experiment. Further, with the addition of fluoride anions, the exothermal deprotonation process occurs spontaneously along with the intermolecular hydrogen bond O-H•••F. It reveals the uniqueness of detecting fluoride anion using HBPMM molecule. As a whole, the fluoride anion inhibits the initial ESIPT process of HBPMM, which results in different fluorescence behaviors. This work presents the clear ESIPT process and fluoride anion sensing mechanism for the novel HBPMM chemosensor.
subject: Articles
  topic: section
subject: Intramolecular hydrogen bond
  topic: keywords
subject: Fluoride anion
  topic: keywords
subject: Charge transfer
  topic: keywords
subject: ESIPT
  topic: keywords
subject: MOs.
  topic: keywords
subject:
  topic: subjects
creator: Jia Li, Xiaodong Li, Shibo Cheng, Peng Song & Jinfeng Zhao
rights: Copyright (c) 2025 COPYRIGHT: © Global Science Press
date: 2018-10-04
publication date: 2018-10-04
starting page: 1
ending page: 6
doi: 10.4208/jams.011818.042318a

Excited State Process of a Novel NIR-BODI Molecule in Toluene and Acetonitrile Solvents: A Theoretical Study
type: item
description: In this work, using DFT and TDDFT methods, we investigated the excited-state intramolecular proton transfer (ESIPT) mechanism of a novel NIR-BODI system [Org Biomol Chem 15:4072, 2017.] in both toluene and acetonitrile $({\rm CH}_3{\rm CN})$ solvents theoretically. Comparing the prime structural variations of NIR-BODI involved in the intramolecular hydrogen bond, we can conclude that O-H∙∙∙N should be strengthened in the $S_1$ state, which may facilitate the ESIPT process. Concomitantly, infrared vibrational spectra analysis further verify the stability of hydrogen bond. In good agreement with previous experimental results, NIR-BODI reveals two kinds of excited-state structures (NIR-BODI-enol* and NIR-BODI-keto*). Analysis about charge redistribution reveals the tendency of ESIPT process. Our scanned potential energy curves according to variational O-H coordinate demonstrates that the proton transfer process should be more likely to occur in the $S_1$ state due to the inappreciable potential energy barriers. In addition, due to the minute differences of potential energy curves contrasting toluene (the NIR-BODI-keto could be not located) and ${\rm CH}_3{\rm CN}$ (the NIR-BODI-keto can be located) solvents in $S_0$ state, we deem that solvent effect could play roles NIR-BODI system. Given the $S_1$-state potential energy barriers, we confirm that the ESIPT process is easier in ${\rm CH}_3{\rm CN}$ solvent.
subject: Articles
  topic: section
subject:
  topic: subjects
creator: Jia Li, Meixia Zhang, Can Du, Peng Song & Xiaodong Li
rights: Copyright (c) 2025 COPYRIGHT: © Global Science Press
date: 2018-07-10
publication date: 2018-07-10
starting page: 162
ending page: 168
doi: 10.4208/jams.102617.120817a