Yong Ye

Hubei University, Wu-han-shih, Hubei, China

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Publications (21)36.94 Total impact

  • [Show abstract] [Hide abstract]
    ABSTRACT: The oxidation of adenine in phosphate buffer solution is investigated using square-wave voltammetry and in situ UV spectroelectrochemistry. The geometry of adenine and the derivatives optimized at DFTB3LYP-6-31G (d, p)-PCM level is in agreement with the crystal structure, and the imitated UV spectra of adenine and the product at electrode are consistent with the in situ UV spectra. The relationship between the electrochemical property and the molecular structure is also discussed. The experimental and theoretical results show that the adenine oxidation origins from the neutral adenine.
    Computers in biology and medicine 07/2010; 40(7):671-9. · 1.27 Impact Factor
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    ABSTRACT: A novel (3,4-disfluoro)phenylquione (2F-PQ) was synthesized through the reaction of 3,4-Difluoroaniline and 1,4-benzoquinone. Its structure was verified by (1)H NMR, FTIR and Raman spectra. The ground-state geometries were optimized by using density functional theory (DFT) at B3LYP/6-311G+(d,p), B3PW91/6-311G+(d,p) and MPB3PW91/6-311G+(d,p) level without symmetry constrains, respectively. The predicted FTIR and Raman spectra scaled by factor are well consistent with experimental spectra.
    Spectrochimica Acta Part A Molecular and Biomolecular Spectroscopy 08/2009; 73(1):96-100. · 1.98 Impact Factor
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    ABSTRACT: 2-(4-Fluorobenzylideneamino) propanoic acid was synthesized through the reaction of 4-fluorobenzaldehyde and alpha-alanine in refluxing EtOH. Its structure was verified by (1)H NMR, FTIR and Raman spectroscopy. The ground-state geometries were optimized at B3LYP/6-31G*, B3LYP/6-31+G** and B3LYP/6-31G** level without symmetry constrains. The vibrational wavenumbers of 4-FA were calculated at same level. The scaled theoretical spectra using B3LYP methods are in a good agreement with the experimental ones. The title compound was tested for anticancer activity of the Hela cell line (using an MTT viability assay) with an IC(50) 166.6 microg/mL.
    Spectrochimica Acta Part A Molecular and Biomolecular Spectroscopy 08/2008; 72(1):26-31. · 1.98 Impact Factor
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    ABSTRACT: 2-(4-Fluorobenzylideneamino)-3-(4-hydroxyphenyl) propanoic acid (4-FT) was synthesized through the reaction of 4-fluorobenzaldehyde and l-tyrosine in refluxing EtOH. The structure of 4-FT was verified by measuring 1H NMR, FTIR and Raman. The ground-state geometries were optimized at B3LYP/6-31G**, B3LYP/6-31G*, HF/6-31G** and HF/6-31G* levels without symmetry constrains. The vibrational wavenumbers of 4-FT were calculated at same levels. The scaled spectra using B3LYP methods, which are in a good agreement with the measured spectra, are superior to those calculated using HF methods.
    Spectrochimica Acta Part A Molecular and Biomolecular Spectroscopy 03/2008; 69(2):682-7. · 1.98 Impact Factor
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    ABSTRACT: Five triphenyl phosphonium salts including N-phenylacetamidyl triphenyl phosphonium chloride (1), N-phenylpropanamidyl triphenyl phosphonium chloride (2), ethyl 2-methylacetatyl triphenyl phosphonium chloride (3), ethyl butyryl triphenyl phosphonium chloride (4) and hexadecyl triphenyl phosphonium bromide (5) were synthesized and then were characterized by FT-Raman spectroscopy. Surface-enhanced Raman spectroscopy (SERS) in conjunction with electronic absorption spectroscopy was employed to study their interaction with DNA. The decreasing of Raman intensity at 1000, 1029, 1103 and 1588cm−1 from compound 5 indicated that this compound has affinity for DNA. This was probably because compound 5 inserted into DNA and a new conjugated system was formed. The results of electronic absorption spectra were coincident with those of SERS. On the other hand, compound 5 showed a significant higher inhibitory rate on human cervix cancer cells. The targets of the compounds in the anti-cancer process were discussed. The mechanism of the anti-cancer process of compound 5 might be related to its interaction with DNA.
    Vibrational Spectroscopy - VIB SPECTROSC. 01/2008; 47(2):119-123.
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    ABSTRACT: 2-(4-Fluorobenzylideneamino)-3-mercaptopropanoic acid (4-FC) was synthesized through the reaction of 4-fluorobenzaldehyde and l-cysteine in refluxing EtOH. Its structure was verified by (1)H NMR, FT-IR and Raman. The ground-state geometries were optimized at B3LYP/6-31G**, B3LYP/6-31G*, HF/6-31G** and HF/6-31G* levels without symmetry constrains, respectively. The vibrational wavenumbers of 4-FC were calculated at same level. The scaled theoretical spectra using B3LYP methods, which are in a good agreement with the experimental ones, are superior to those using HF methods.
    Spectrochimica Acta Part A Molecular and Biomolecular Spectroscopy 10/2007; 68(1):85-93. · 1.98 Impact Factor
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    ABSTRACT: Quantitative structure-retention relationship (QSRR) models have been used successfully to predict and explain retention behavior of pigments in reversed-phase high-performance liquid chromatography (HPLC). The semi-empirical quantum chemical method (PM3) in Gaussian98 was employed to calculate a set of molecular descriptors of pigments. Using multiple linear regression (MLR), we obtained empirical functions with high correlation coefficient between retention times and quantum-chemical descriptors. This analysis indicated that the proposed QSRR models were satisfactory.
    Computers in Biology and Medicine 04/2007; 37(3):315-9. · 1.16 Impact Factor
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    ABSTRACT: Bis(pyrrol-2-ylmethyleneamine) ligands and their mononuclear monomeric and dinuclear dimeric self-assembly complexes with Cu(II) were investigated by means of IR and Raman spectroscopies and density functional theory. The ground-state geometries were calculated by using the BeckeLeeYangParr composite exchange-correlation functional (B3LYP) and a combined basis set (LanL2DZ for Cu; 6–31G(d) for C, H, N), and they were compared with the single-crystal X-ray diffraction (XRD) structures. The DFT-calculated CuN bond lengths are generally higher by 0.001–0.040 Å than those determined through XRD. The vibrational spectra were also calculated at the same level of theory for the optimized geometries. The calculated wavenumbers were scaled by a uniform scaling factor and compared with the experimental fundamentals. The predicted spectra are in good agreement with the experimental ones with the deviations generally less than 30 cm−1. In comparison with the spectra of the ligands, the coordination effect shifts the υ(CN) wavenumber by about 50 cm−1 toward a lower value. Because of the weak intermolecular CH···Cu hydrogen bond, the CuN stretching mode is shifted toward a lower wavenumber. Copyright © 2006 John Wiley & Sons, Ltd.
    Journal of Raman Spectroscopy 12/2006; 38(5):483 - 495. · 2.68 Impact Factor
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    ABSTRACT: FT-IR, FT-Raman and electronic absorption spectroscopies were utilized in conjunction with density functional theory (DFT) calculations to investigate the ground and excited states of self-assembled dinuclear dimeric helicates (ZnL)2 and (NiL)2 [L = bis(2,4-dimethyldipyrrin-3-yl)methane]. These studies afford a detailed description of the ground-state geometric and electronic structures of (ZnL)2 and (NiL)2 and provide a comparison with similar geometrical metal-porphyrins. The results demonstrate that enlarging the basis set used in the DFT calculations results in an obvious alteration of the calculated bond lengths but negligible alteration of the calculated bond angles. The predicted spectra are in good agreement with the experimental ones with the deviations generally less than 30 cm(-1). In comparison with vibrational spectra of metal-porphyrins, the breathing vibration of the pyrrole ring is shifted by over 100 cm(-1) toward higher wavenumber due to local conjugation of molecular geometry. Time-dependent density functional theory (TD-DFT) provides a good description of the excitation energy. Because of the break in symmetry, the absorption band (corresponding to the Q-band of porphyrin) of (ZnL)2 and (NiL)2 is no longer weak. Local conjugation makes the absorption wavelength of (NiL)2 and (ZnL)2 shift to the blue compared with those of NiP and ZnP.
    The Journal of Physical Chemistry B 12/2006; 110(43):21958-65. · 3.61 Impact Factor
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    ABSTRACT: Quantitative structure-retention relationship (QSRR) models for the chromatographic (GC) retention times of alcohols on Superox 20M-diglycerol polarity stationary phase have been developed. Semi-empirical quantum chemical method (AM1) in MOPAC and Hartree-Fock (HF) method in Gaussian 98 implemented were employed to calculate a set of molecular descriptors of alcohols and ethyl acetate. Using multiple linear regression (MLR), we obtained the empirical functions with high correlation coefficient between retention times and quantum-chemical descriptors. The retention mechanism of alcohols of separation operating in the gas chromatogram was discussed. The results indicated that the QSRR models proposed were satisfactory.
    Bioorganic & Medicinal Chemistry 06/2005; 13(9):3169-73. · 2.90 Impact Factor
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    ABSTRACT: The FT-Raman and UV-visible spectra of (12S)-1,4,7,10-tetraazadicyclo[10,3,0]-pentadecane-3,11-dione and its derivatives were obtained and discussed. The harmonic vibrational wavenumbers and the corresponding Raman scattering activities in their electronic ground-states were calculated at the DFT-B3LYP/6-31G(d) level of theory. The calculated wavenumbers were then scaled and compared with the experimental values. The 7-(2,4-dinitrophenyl)-(12S)-1,4,7,10-tetrazadicyclo[10,3,0]-pentadecane-3,11-dione derivative has mainly an amide (II) character, while the others have an amide (I) character. Moreover, the different substituents do not cause a significant shift of the vibrational mode of the macrocyclic plane. The electronic vertical excitation energy and the oscillator strength were determined with the help of TDDFT calculations and by employing pure (BLYP) and hybrid (B3LYP, B3P86, and mPW1PW91) functionals together with the 6-31G(d) basis set. The BLYP functional reproduces the UV-vis absorption spectra better than the B3LYP, B3P86, or mPW1PW91 hybrid functionals. A dimolecular model, which considers hydrogen-bonded structures, proved that strong inter- and intramolecular hydrogen bonds are present in these compounds. Due to the transannular effect, the UV-vis absorption spectrum of macrocyclic dioxotetraamines is completely different from that of single amide compounds.
    The Journal of Physical Chemistry A 04/2005; 109(12):2878-86. · 2.77 Impact Factor
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    ABSTRACT: The high SNR (Signal-to-Noise) spectra from 20 cases of gastric carcinoma and normal mucosa were obtained by confocal Raman microspectroscopy. Consistent spectral features were observed at different sites of one tissue slice for both typical tissues. Raman spectra of normal gastric mucosa shows two peaks which are assigned to amide I vibration of proteins in 1640-1670(cm(-1)) spectral region. However, in gastric carcinoma, only one peak of amino I vibrational mode of proteins can be observed. The obviously different spectral characters of the two types of tissues are in accordance to clinicopathologic diagnosis. The result shows Raman spectroscopy might be a potential method in the diagnosis of gastric carcinoma.
    Sheng wu yi xue gong cheng xue za zhi = Journal of biomedical engineering = Shengwu yixue gongchengxue zazhi 01/2005; 21(6):910-2.
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    ABSTRACT: Pterygia, caused by fibrovascular growth of conjunctiva, are a common ophthalmic disease. However, the molecular composition of pterygium tissue has not been completely understood, and therefore the aim of this study is to investigate the spectroscopic differences between normal human bulbar conjunctiva and human pterygium tissue using a confocal Raman system. The high signal-to-noise ratio spectra from pterygium and conjunctiva tissue were obtained by this technique without any sample preparation and the time of detection required less than 3 min. Comparing Raman spectra of two types of tissue, there are obvious changes, including intensity decrease at approximately 1585 cm(-1) and intensity increase at approximately 1748, 1156, and 1521 cm(-1) with the lesion of conjunctiva. Additionally, the amide I vibrational mode of proteins in conjunctiva is significantly different than that in pterygium. The use of pathology, immunology, and the peroxidation of the lipids in conjunction with the Raman results indicate that the presence of additional elastic fibers, mast cells, and lymphocytes in pterygium, as compared with normal bulbar conjunctiva, have fewer unsaturated fat acids. The present study demonstrates that Raman spectroscopy can be potentially applied to diagnose pterygia clinically.
    Journal of Biomedical Optics 01/2005; 10(2):024036. · 2.88 Impact Factor
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    ABSTRACT: The low-lying excited states of 21 compounds of polycyclic cinnoline, monoaza-hydrocarbon and their corresponding polycyclic aromatic hydrocarbon (PAH) analogues have been investigated in the framework of time-dependent density functional theory (TDDFT). The gradient corrected BLYP, hybrid B3LYP and B3P86 functionals together with 6-31G (d) basis set have been used. The hybrid-type B3LYP and B3P86 systematically overestimate the excitation energies for states with dominating ionic character (corresponding to group III band), with a mean absolute deviation (MAD) of 0.33eV (B3LYP) and 0.34eV (B3P86), respectively. However, they can accurately predict the excitation energies for states with covalent character (corresponding to group II and I bands). The MAD for group II (B3LYP: 0.05eV; B3P86: 0.05eV) and I bands (B3LYP: 0.12eV; B3P86: 0.12eV) are significantly smaller. The BLYP outperforms B3LYP and B3P86 for group III band (MAD: 0.09eV), but has a worse performance for group II (MAD: 0.15eV) and I (MAD: 0.13eV) bands. Comparison of the lowest-lying excited states for polycyclic cinnolines with those of the corresponding PAH analogues, the first excited states of polycyclic cinnolines mainly result from n→π0* transitions. Therefore, in non-polar solvents, the spectra of some polycyclic cinnolines exhibit an additional absorption band at longer wavelengths.
    Journal of Molecular Structure-theochem - J MOL STRUC-THEOCHEM. 01/2005; 732(1):21-32.
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    ABSTRACT: The ground-state geometries, electronic structures and vibrational wavenumbers of S-1,3-benzothiazolyl-4-bromobenzenecarbothioate and S-(5,7-dimethyl-3H-4lambda-5-[1,2,4]triazolo[1,5-a]pyridinyl)4-chlorobenzenecarbothioate were studied by DFT-B3LYP, BLYP and ab initio RHF method with different basis sets. The comparison was performed for optimized geometries, thermodynamic parameters and electronic structures at different levels of theory. Because of the larger repulsion effect in triazole ring, the vibrational wavenumbers of skeleton vibration of triazole ring are significantly lower than that of thiazole ring.
    Spectrochimica Acta Part A Molecular and Biomolecular Spectroscopy 09/2004; 60(10):2343-54. · 1.98 Impact Factor
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    ABSTRACT: The ground-state geometries and electronic structures of 2-nitrotetraphenylporphyrin (H2-2-NO2-TPP) and zinc 2-nitrotetraphenylporphyrin (Zn-2-NO2-TPP) with Cs and C1 symmetry have been determined from density functional theory, using the Becke−Lee−Yang−Parr composite exchange-correlation functional (B3-LYP) and ab initio RHF method and 6-31G(d) basis set. The optimized geometries are then compared with the crystallographic data of related compounds. The energy and electronic structures of different conformers are analyzed and compared with each other. The conformers with C1 symmetry are found to be more stable than that of Cs symmetry. The relative order of the highest occupied a2u and a1u orbitals determined by B3LYP (a2u > a1u) is reversed by RHF (a1u > a2u). The vibrational wavenumber, IR, and Raman intensities are also calculated at B3LYP/6-31G(d) optimized geometries. The calculated wavenumbers are scaled by a uniform scaling factor and compared with the experimental one. Most of the scaled modes are found to be in good agreement with the observed fundamentals. A single β-NO2 substitution slightly changes the geometries, the vibrational wavenumbers, and the frontier orbitals energy level.
    Journal of Physical Chemistry A - J PHYS CHEM A. 06/2004; 108(28).
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    ABSTRACT: A tentative user-friendly auto-classifying system is developed to classify Raman spectra of gastric carcinoma tissues. By combining two efficient fuzzy clustering methods: artificial neural network (ANN) and fuzzy C-means (FCM), the software system integrates high robustness of ANN and strong quantity estimation ability of FCM, and provides more credible classifying results for the Raman spectroscopy auto-diagnosis of gastric carcinoma. Also the system can be applied to classifying of other spectroscopy by some necessary alteration of feature vector.
    Machine Learning and Cybernetics, 2003 International Conference on; 12/2003
  • Journal of Raman Spectroscopy 11/2003; 34(11):892-901. · 2.68 Impact Factor
  • Journal of Raman Spectroscopy 12/2001; 32(12):1018-1020. · 2.68 Impact Factor
  • Journal of Raman Spectroscopy 01/2001; 32(12):1059-1063. · 2.68 Impact Factor

Publication Stats

43 Citations
36.94 Total Impact Points

Institutions

  • 2007–2010
    • Hubei University
      • Key Laboratory of Synthesis and Application of Organic Functional Molecules of the Education Ministry
      Wu-han-shih, Hubei, China
  • 1999–2007
    • Wuhan University
      • • College of Chemistry and Molecular Sciences
      • • Department of Analysis-Measurement Science
      Wu-han-shih, Hubei, China