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  1. Article: Bridging the 12-6-4 Model and the Fluctuating Charge Model.

    Li, Pengfei

    Frontiers in chemistry

    2021  Volume 9, Page(s) 721960

    Abstract: Metal ions play important roles in various biological systems. Molecular dynamics (MD) using classical force field has become a popular research tool to study biological systems at the atomic level. However, meaningful MD simulations require reliable ... ...

    Abstract Metal ions play important roles in various biological systems. Molecular dynamics (MD) using classical force field has become a popular research tool to study biological systems at the atomic level. However, meaningful MD simulations require reliable models and parameters. Previously we showed that the 12-6 Lennard-Jones nonbonded model for ions could not reproduce the experimental hydration free energy (HFE) and ion-oxygen distance (IOD) values simultaneously when ion has a charge of +2 or higher. We discussed that this deficiency arises from the overlook of the ion-induced dipole interaction in the 12-6 model, and this term is proportional to 1/
    Language English
    Publishing date 2021-07-22
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2711776-5
    ISSN 2296-2646
    ISSN 2296-2646
    DOI 10.3389/fchem.2021.721960
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  2. Article ; Online: Glycan-specific molecularly imprinted polymers towards cancer diagnostics: merits, applications, and future perspectives.

    Li, Pengfei / Liu, Zhen

    Chemical Society reviews

    2024  Volume 53, Issue 4, Page(s) 1870–1891

    Abstract: Aberrant glycans are a hallmark of cancer states. Notably, emerging evidence has demonstrated that the diagnosis of cancers with tumour-specific glycan patterns holds great potential to address unmet medical needs, especially in improving diagnostic ... ...

    Abstract Aberrant glycans are a hallmark of cancer states. Notably, emerging evidence has demonstrated that the diagnosis of cancers with tumour-specific glycan patterns holds great potential to address unmet medical needs, especially in improving diagnostic sensitivity and selectivity. However, despite vast glycans having been identified as potent markers, glycan-based diagnostic methods remain largely limited in clinical practice. There are several reasons that prevent them from reaching the market, and the lack of anti-glycan antibodies is one of the most challenging hurdles. With the increasing need for accelerating the translational process, numerous efforts have been made to find antibody alternatives, such as lectins, boronic acids and aptamers. However, issues concerning affinity, selectivity, stability and versatility are yet to be fully addressed. Molecularly imprinted polymers (MIPs), synthetic antibody mimics with tailored cavities for target molecules, hold the potential to revolutionize this dismal progress. MIPs can bind a wide range of glycan markers, even those without specific antibodies. This capacity effectively broadens the clinical applicability of glycan-based diagnostics. Additionally, glycoform-resolved diagnosis can also be achieved through customization of MIPs, allowing for more precise diagnostic applications. In this review, we intent to introduce the current status of glycans as potential biomarkers and critically evaluate the challenges that hinder the development of
    MeSH term(s) Molecularly Imprinted Polymers ; Molecular Imprinting/methods ; Lectins/metabolism ; Biomarkers ; Antibodies ; Polysaccharides ; Neoplasms/diagnosis
    Chemical Substances Molecularly Imprinted Polymers ; Lectins ; Biomarkers ; Antibodies ; Polysaccharides
    Language English
    Publishing date 2024-02-19
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 1472875-8
    ISSN 1460-4744 ; 0306-0012
    ISSN (online) 1460-4744
    ISSN 0306-0012
    DOI 10.1039/d3cs00842h
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  3. Article ; Online: Development of a Fluctuating Charge Model for Zinc-Containing Metalloproteins.

    Landry, Luke / Li, Pengfei

    Journal of chemical information and modeling

    2024  Volume 64, Issue 3, Page(s) 812–824

    Abstract: Metalloproteins widely exist in biology and play important roles in various processes. To accurately simulate metalloprotein systems, modeling polarization and charge transfer effects is vital. The fluctuating charge (FQ) model can efficiently generate ... ...

    Abstract Metalloproteins widely exist in biology and play important roles in various processes. To accurately simulate metalloprotein systems, modeling polarization and charge transfer effects is vital. The fluctuating charge (FQ) model can efficiently generate atomic charges and simulate the charge transfer effect; it has been developed for a wide range of applications, but few models have been specifically tailored for metalloproteins. In this study, we present a fluctuating charge model specifically for zinc-containing metalloproteins based on the extended charge equilibration (EQeq) scheme. Our model was parametrized to reproduce CM5 charges instead of RESP/CHELPG charges because the former is less dependent on the conformation or basis set, does not suffer from unphysical charges for buried atoms, and is still being able to well reproduce the molecular dipoles. During our study, we found that adding the Pauling-bond-order-like term (referred to as the "+C term" in a previous study) between the zinc ion and ligating atoms significantly improves the model's performance. Although our model was trained for four-coordinated zinc sites only, our results indicated it can well describe the atomic charges in diverse zinc sites. Morever, our model was used to generate partial charges for the metal sites in three different zinc-containing metalloproteins (with four-, five-, and six-coordinated metal sites, respectively). These charges exhibited performance comparable to that of the RESP charges in molecular dynamics (MD) simulations. Additional tests indicated our model could also well reproduce the CM5 charges when geometric changes were involved. Those results indicate that our model can efficiently calculate the atomic charges for metal sites and well simulate the charge transfer effect, which marks an important step toward developing versatile polarizable force fields for metalloproteins.
    MeSH term(s) Zinc ; Metalloproteins/metabolism ; Metals ; Molecular Dynamics Simulation ; Molecular Conformation
    Chemical Substances Zinc (J41CSQ7QDS) ; Metalloproteins ; Metals
    Language English
    Publishing date 2024-01-10
    Publishing country United States
    Document type Journal Article
    ZDB-ID 190019-5
    ISSN 1549-960X ; 0095-2338
    ISSN (online) 1549-960X
    ISSN 0095-2338
    DOI 10.1021/acs.jcim.3c01815
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1230: Show issues Location:
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  4. Article ; Online: The "Hand as Foot" teaching method in the classification of thoracoabdominal aortic aneurysm and aortic dissection.

    Li, Pengfei / Zhang, Xuejuan

    Asian journal of surgery

    2024  

    Language English
    Publishing date 2024-02-20
    Publishing country Netherlands
    Document type Letter
    ZDB-ID 1068461-x
    ISSN 0219-3108 ; 1015-9584
    ISSN (online) 0219-3108
    ISSN 1015-9584
    DOI 10.1016/j.asjsur.2024.02.051
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    In stock of ZB MED Cologne/Königswinter

    Zs.B 2831: Show issues Location:
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  5. Article ; Online: Recovery of Zn and Cu from municipal solid waste incineration fly ash by integrating ammonium leaching and ammonia removal.

    Li, Pengfei / Shimaoka, Takayuki

    Waste management (New York, N.Y.)

    2024  Volume 178, Page(s) 115–125

    Abstract: This study introduces an environmentally friendly process for recovering zinc (Zn) and copper (Cu) from municipal solid waste incineration (MSWI) fly ash using ammonium chloride leaching and ammonia removal. The leaching rates for Zn and Cu were 54.39% ... ...

    Abstract This study introduces an environmentally friendly process for recovering zinc (Zn) and copper (Cu) from municipal solid waste incineration (MSWI) fly ash using ammonium chloride leaching and ammonia removal. The leaching rates for Zn and Cu were 54.39% and 86.23%, respectively, with total recovery rates reaching 52.21% and 85.28%, respectively. The recovered precipitate demonstrated significant Zn (33.62%) and Cu (14.19%) contents, making it ideal for metal smelting. The ammonium leaching process also showcased effective reduction and dechlorination effects on the fly ash. The treated fly ash had a reduced mass of only 30.63% of the original, and chlorine content decreased from 26.23% to 0.84%. The results of this study support the sustainable utilization of MSWI fly ash by facilitating valuable resource recovery and promoting its conversion into construction materials.
    MeSH term(s) Coal Ash ; Zinc ; Solid Waste/analysis ; Metals, Heavy/analysis ; Ammonia ; Ammonium Compounds ; Incineration/methods ; Carbon ; Particulate Matter ; Refuse Disposal
    Chemical Substances Coal Ash ; Zinc (J41CSQ7QDS) ; Solid Waste ; Metals, Heavy ; Ammonia (7664-41-7) ; Ammonium Compounds ; Carbon (7440-44-0) ; Particulate Matter
    Language English
    Publishing date 2024-02-23
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2001471-5
    ISSN 1879-2456 ; 0956-053X
    ISSN (online) 1879-2456
    ISSN 0956-053X
    DOI 10.1016/j.wasman.2024.02.036
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  6. Article ; Online: Pericyte Loss in Diseases.

    Li, Pengfei / Fan, Hongkuan

    Cells

    2023  Volume 12, Issue 15

    Abstract: Pericytes are specialized cells located in close proximity to endothelial cells within the microvasculature. They play a crucial role in regulating blood flow, stabilizing vessel walls, and maintaining the integrity of the blood-brain barrier. The loss ... ...

    Abstract Pericytes are specialized cells located in close proximity to endothelial cells within the microvasculature. They play a crucial role in regulating blood flow, stabilizing vessel walls, and maintaining the integrity of the blood-brain barrier. The loss of pericytes has been associated with the development and progression of various diseases, such as diabetes, Alzheimer's disease, sepsis, stroke, and traumatic brain injury. This review examines the detection of pericyte loss in different diseases, explores the methods employed to assess pericyte coverage, and elucidates the potential mechanisms contributing to pericyte loss in these pathological conditions. Additionally, current therapeutic strategies targeting pericytes are discussed, along with potential future interventions aimed at preserving pericyte function and promoting disease mitigation.
    MeSH term(s) Humans ; Pericytes/pathology ; Endothelial Cells ; Blood-Brain Barrier/pathology ; Stroke/pathology ; Brain Injuries, Traumatic/pathology
    Language English
    Publishing date 2023-07-26
    Publishing country Switzerland
    Document type Journal Article ; Review ; Research Support, N.I.H., Extramural
    ZDB-ID 2661518-6
    ISSN 2073-4409 ; 2073-4409
    ISSN (online) 2073-4409
    ISSN 2073-4409
    DOI 10.3390/cells12151931
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  7. Article ; Online: Organocatalytic Regio- and Enantioselective Allylic Alkylation of Indolin-2-imines with MBH Carbonates toward 3-Allylindoles.

    Chen, Lunfeng / Li, Pengfei

    The Journal of organic chemistry

    2023  Volume 88, Issue 12, Page(s) 7810–7814

    Abstract: An organocatalytic asymmetric C3-allylic alkylation of indolone-2-imines with MBH carbonates has been developed for the first time. As opposed to previous reports, an "interrupted" annulation was achieved, affording 3-allylindoles in generally high ... ...

    Abstract An organocatalytic asymmetric C3-allylic alkylation of indolone-2-imines with MBH carbonates has been developed for the first time. As opposed to previous reports, an "interrupted" annulation was achieved, affording 3-allylindoles in generally high yields with excellent stereoselectivities. The representative scale-up reaction and transformation of 3-allylindoles were examined. A possible mechanism was also proposed.
    MeSH term(s) Molecular Structure ; Stereoisomerism ; Imines ; Catalysis ; Carbonates ; Alkylation
    Chemical Substances Imines ; Carbonates
    Language English
    Publishing date 2023-01-26
    Publishing country United States
    Document type Journal Article
    ZDB-ID 123490-0
    ISSN 1520-6904 ; 0022-3263
    ISSN (online) 1520-6904
    ISSN 0022-3263
    DOI 10.1021/acs.joc.2c02310
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 4473: Show issues Location:
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  8. Article ; Online: Myofascial treatment technique combined with functional exercise in lower extremity sports injury rehabilitation.

    Xiao, Nan / Li, Pengfei

    Minerva medica

    2023  

    Language English
    Publishing date 2023-11-21
    Publishing country Italy
    Document type Journal Article
    ZDB-ID 123586-2
    ISSN 1827-1669 ; 0026-4806
    ISSN (online) 1827-1669
    ISSN 0026-4806
    DOI 10.23736/S0026-4806.23.08954-1
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    In stock of ZB MED Cologne/Königswinter

    Ua VI Zs.132: Show issues Location:
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  9. Article ; Online: Organocatalytic (1+4)-Annulations of MBH Adducts with Electron-Deficient Systems.

    Chen, Xuling / Li, Pengfei

    Chemical record (New York, N.Y.)

    2023  Volume 23, Issue 11, Page(s) e202300152

    Abstract: Benefited from the rapid development of MBH reaction, the reaction of MBH adducts have been established as the most synthetically useful transformations. However, compared with the well-established allylic alkylations and (3+2)-annulations, the (1+4)- ... ...

    Abstract Benefited from the rapid development of MBH reaction, the reaction of MBH adducts have been established as the most synthetically useful transformations. However, compared with the well-established allylic alkylations and (3+2)-annulations, the (1+4)-annulations of MBH adducts have not developed rapidly until recently. As a helpful complement to the (3+2)-annulations of MBH adducts, the (1+4)-annulations of MBH adducts opens a robust access to structurally diverse five-membered carbo- and heterocycles. This paper summarizes recent advances in organocatalytic (1+4)-annulations using MBH adducts as 1 C-synthons for the construction of functionalized five-membered carbo- and heterocycles.
    Language English
    Publishing date 2023-06-09
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 2044646-9
    ISSN 1528-0691 ; 1527-8999
    ISSN (online) 1528-0691
    ISSN 1527-8999
    DOI 10.1002/tcr.202300152
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  10. Article ; Online: Study on micromolecular mechanical properties of C-atom reinforced SBR polymer composites.

    Chen, Hongyue / Liu, Siyuan / Fan, Jingdao / Li, Pengfei

    Scientific reports

    2024  Volume 14, Issue 1, Page(s) 104

    Abstract: A three-layer microscopic model with Fe atoms as the top and bottom layer and SBR polymer composites as the middle layer and SBR polymer composite was established and studied. By adding C atoms as reinforcement, the stability and elastic modulus and ... ...

    Abstract A three-layer microscopic model with Fe atoms as the top and bottom layer and SBR polymer composites as the middle layer and SBR polymer composite was established and studied. By adding C atoms as reinforcement, the stability and elastic modulus and frictional coefficient changes of SBR polymer composites before and after adding C atoms were studied. In this study, the molecular dynamics method was used to change of elastic modulus was observed by stretching, compression and shear of the SBR polymer composite; The simulation shows that after adding C atom the elastic modulus of SBR polymer composite increased, the friction coefficient of polymer composite upper and lower decreases and the relative atomsic concentration, temperature, velocity, overall temperature average, kinetic energy, total energy and MSD in the thickness direction are reduced after adding C atoms. The stability of SBR polymer composites is enhanced, and the deformation under shear is weakened. In addition, it is found that the binding energy between SBR polymer composites and Fe atoms is reduced after adding C atoms.The stability of SBR polymer composites is improved during use. This work provides a method for studying the properties of rubber composites by studying the enhancement of the stability of SBR polymer composites from the microscopic point of view.
    Language English
    Publishing date 2024-01-02
    Publishing country England
    Document type Journal Article
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-023-49640-x
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