Elucidation of collagen amino acid interactions with metals (B, Ni) encapsulated graphene/PEDOT material: Insight from DFT calculations and MD simulation

Timothy, Rawlings A.; Louis, Hitler; Adindu, Eze A.; Gber, Terkumbur E.; Agwamba, Ernest C.; Offiong, Offiong E.; Pembere, Anthony M.S.

doi:10.1016/j.molliq.2023.122950

Cited by 22 publications

(3 citation statements)

References 83 publications

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“…The DOS plot illustrates molecular orbital contribution of the interaction. It also explains the energy difference between the HOMO and LUMO of the complex after study which agrees with FMO analysis [60–62] . Figure 4 shows the DOS plots for the studied systems after interactions using the Multiwfn 3.7and plotted with Origin 2018.…”

Section: Resultssupporting

confidence: 77%

“…It also explains the energy difference between the HOMO and LUMO of the complex after study which agrees with FMO analysis. [60][61][62] Figure 4 shows the DOS plots for the studied systems after interactions using the Multiwfn 3.7and plotted with Origin 2018. From Figure 4, the highest peak on each of the plots corresponds to total density of state (TDOS) and the second intense and other peaks reflects partial density of state (PDOS) of the fragments of the systems.…”

Section: Density Of State Analysismentioning

confidence: 99%

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Theoretical Investigation of Single‐Atoms Encapsulated by Fullerenes (C59X: X=As, Ga, Ge) as Biosensors For Uric Acid (UA)

Timothy,

Okon,

Gber

et al. 2023

ChemistrySelect

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This work focuses on comparative investigation of three different doped surfaces on a nano‐cage C59As, C59Ga and C59Ge to understand their sensitivity and ability to adsorbed uric acid (UA). This is done using the density functional theory (DFT) computation, employing ωB97XD/def2SVP level of theory. After interaction of the surfaces with UA, FMO results reveal that UA@C59As is more reactive with Eg=5.1911 eV and UA@C59Ga is more stable with Eg=5.3304 eV, while UA@C59Ge is relatively reactive and relatively stable with Eg=5.2145 eV. Geometric optimization analysis reveals that UA@C59Ge shows the best interaction with the least adsorption distance (1.9437 Å) and UA@C59Ga shows a relatively good interaction with adsorption distance (1.9674 Å) while UA@C59As reveal the poorest interaction with adsorption distance of (3.6370 Å). The calculated thermodynamic parameters deduced that UA@C59Ga is more stable compared to UA@C59As and UA@C59Ge complexes, due to the fact that the calculated values of ℇ°+ℇZPE, ℇ°+Gcorr, ℇ°+Hcorr and ℇ°+Etot are less negative in compound UA@C59Ga. Negative Eads values of UA@C59As (−0.5968 eV), UA@C59Ga (−1.8798 eV) and UA@C59Ge (−1.1656 eV) were observed from adsorption studies and its sensor mechanism implying an enhanced chemical adsorption was manifested and this indicates the presence of a covalent interaction. Similarly, the result of interaction energy (Eint) reveal UA@C59Ge to have an Eint of 22.3978 eV greater than UA@C59Ga (21.5832 eV) and far greater than UA@C59As (2.4593 eV) there by confirming UA@C59Ga and UA@C59Ge to be strongly interacted. However, all analysis in this work has shown that C59Ge is the best promising biomarker candidate for adsorbing UA, although C59Ga has also demonstrated a good UA adsorption candidate.

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Section: Resultssupporting

confidence: 77%

Section: Density Of State Analysismentioning

confidence: 99%

Theoretical Investigation of Single‐Atoms Encapsulated by Fullerenes (C59X: X=As, Ga, Ge) as Biosensors For Uric Acid (UA)

Timothy,

Okon,

Gber

et al. 2023

ChemistrySelect

Self Cite

View full text Add to dashboard Cite

show abstract

“…1B). Density functional theory (DFT) is the most effective method to study the electronic structure of their excited states [27] . During the triplet state calculation, it needs to be emphasized that among these design PS, multi-spin states are considered for Fe-porphyrin and Fe-porphyrin-PDI [28] .…”

Section: Introductionmentioning

confidence: 99%

Porphyrin photosensitizer molecules as effective medicine candidates for photodynamic therapy: electronic structure information aided design

Yin,

Li,

Liu

et al. 2024

Preprint

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Traditional photosensitizers (PS) in photodynamic therapy (PDT) have limited tissue penetrability of light and lacked selectivity for tumor cells, which reduces the efficiency of PDT. Our aim is to effectively screen porphyrin-based PS medication through computational simulations of large-scale design and screening of PDT candidates via a precise description of the state of the light-stimulated PS molecule. Perylene-diimide (PDI) shows an absorption band in the near-infrared region (NIR) and a great photostability. Meanwhile, the insertion of metal can enhance tumor targeting. Therefore, on the basis of the original porphyrin PS segments, a series of metalloporphyrin combined with PDI and additional allosteric Zn-porphyrin-PDI systems were designed and investigated. Geometrical structures, frontier molecular orbitals, ultraviolet-visible (UV-Vis) absorption spectra, adiabatic electron affinities (AEA), especially the triplet excited states and spin-orbit coupling matrix elements (SOCME) of these expanded D-A porphyrin were studied in detail using the density functional theory (DFT) and time-dependent density functional theory (TDDFT) methods. PS candidates, conforming type I or II mechanism for PDT, have been researched carefully by molecular docking which targeted Factor-related apoptosis (Fas)/ Fas ligand (Fasl) mediated signaling pathway. It was found that Porphyrin-PDI, Fe2-porphyrin-PDI, Zn-porphyrin-PDI, Mg-porphyrin-PDI, Zn-porphyrin combined with PDI through single bond (Compound 1), and two acetylenic bonds (Compound 2) in this work would be proposed as potential PS candidates for PDT process. This study was expected to provide PS candidates for the development of novel medicine in PDT.

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Progress in the Computer‐Aided Analysis in Multiple Aspects of Nanocatalysis Research

Fan,

Shen,

Lou

et al. 2024

Adv Healthcare Materials

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Making the utmost of the differences and advantages of multiple disciplines, interdisciplinary integration breaks the science boundaries and accelerates the progress in mutual quests. As an organic connection of material science, enzymology, and biomedicine, nanozyme‐related research is further supported by computer technology, which injects in new vitality, and contributes to in‐depth understanding, unprecedented insights, and broadened application possibilities. Utilizing computer‐aided first‐principles method, high‐speed and high‐throughput mathematic, physic, and chemic models are introduced to perform atomic‐level kinetic analysis for nanocatalytic reaction process, and theoretically illustrate the underlying nanozymetic mechanism and structure‐function relationship. On this basis, nanozymes with desirable properties can be designed and demand‐oriented synthesized without repeated trial‐and‐error experiments. Besides that, computational analysis and device also play an indispensable role in nanozyme‐based detecting methods to realize automatic readouts with improved accuracy and reproducibility. Here, this work focuses on the crossing of nanocatalysis research and computational technology, to inspire the research in computer‐aided analysis in nanozyme field to a greater extent.

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Elucidation of collagen amino acid interactions with metals (B, Ni) encapsulated graphene/PEDOT material: Insight from DFT calculations and MD simulation

Cited by 22 publications

References 83 publications

Theoretical Investigation of Single‐Atoms Encapsulated by Fullerenes (C59X: X=As, Ga, Ge) as Biosensors For Uric Acid (UA)

Theoretical Investigation of Single‐Atoms Encapsulated by Fullerenes (C59X: X=As, Ga, Ge) as Biosensors For Uric Acid (UA)

Porphyrin photosensitizer molecules as effective medicine candidates for photodynamic therapy: electronic structure information aided design

Progress in the Computer‐Aided Analysis in Multiple Aspects of Nanocatalysis Research

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