scholarly journals An experimental/computational study of steric hindrance effects on CO2 absorption mechanism using nonaqueous/aqueous AMP

Author(s):  
Qinlan Luo ◽  
Mengjie Chen ◽  
Rui Dong ◽  
Hongxia Gao ◽  
Zhiwu Liang

The reaction kinetics and molecular mechanisms of CO2 absorption using nonaqueous and aqueous amine solutions were analyzed by the stopped-flow technique and ab initio molecular dynamics (AIMD) simulations. Pseudo first-order rate constants (k0) of reactions between CO2 and amines were measured. A kinetic model was proposed to correlate the k0 to the amine concentration, and was proved to perform well for predicting the relationship between k0 and the amine concentration. The experimental results showed that AMP/MDEA only took part in the deprotonation of MEA-zwitterion in nonaqueous MEA+AMP/MEA+MDEA. In aqueous solutions, AMP can also react with CO2 through base-catalyzed hydration mechanism beside the zwitterion mechanism. The molecular mechanisms of CO2 absorption were also explored by AIMD simulations coupled with metadynamics sampling. The predicted free-energy barriers of key elementary reactions verified the kinetic model and demonstrated the different molecular mechanisms for the reaction between CO2 and AMP in nonaqueous and aqueous systems.

2019 ◽  
Author(s):  
Michael Fischer

<p>The silicoaluminophosphate zeotype ECR-40, which has the MEI topology, contains linkages of AlO<sub>4</sub> tetrahedra via a common oxygen atom, thereby violating the famous “Löwenstein’s rule”. Due to the proven existence of Al-O-Al linkages in this material, it constitutes an ideal model system to study the acidity and mobility of protons associated with such unusual linkages. In addition, their properties can be directly compared to those of protons associated with more common Si-O-Al linkages, which are also present in ECR-40. In this work, static density functional theory (DFT) calculations including a dispersion correction were employed to study the preferred proton sites as well as the Brønsted acidity of the framework protons, followed by DFT-based ab-initio molecular dynamics (AIMD) to investigate the proton mobility in guest-free and hydrated ECR-40. Initially, two different proton arrangements were compared, one containing both H[O6] protons associated with Al-O-Al linkages and H[O10] protons at Si-O-Al linkages, the other one containing only H[O10] protons. The former model was found to be thermodynamically favoured, as a removal of protons from the Al-O-Al linkages causes a local accumulation of negative charge. Calculations of the deprotonation energy showed a moderately higher Brønsted acidity of the H[O10] protons, at variance with previous empirical explanations, which attributed the exceptional performance of ECR-40 as acid catalyst to the presence of Al‑O‑Al linkages. The AIMD simulations (<i>T</i> = 298 K) delivered no appreciable proton mobility for guest-free ECR-40 and for low levels of hydration (one H<sub>2</sub>O per framework proton). Under saturation conditions, framework deprotonation occurred, leading to the formation of protonated water clusters in the pores. Pronounced differences between the two types of framework protons were observed: While the H[O10] protons were always removed from the Si-O-Al linkages, the Al-O-Al linkages remained mostly protonated, but deprotonation did occur to a minor extent. The observation of a degree of framework deprotonation of Al-O-Al linkages differs from the findings reported in a recent computational study of hydrated aluminosilicate zeolites with such linkages (Heard et al., <i>Chem. Sci.</i> <b>2019</b>, <i>10</i>, 5705), pointing to an influence of the overall framework composition. Further inspection of the AIMD results showed that a coordination of water molecules to framework Al atoms occurred in many cases, especially in the vicinity of the Al-O-Al linkages, sometimes resulting in a pronounced modification of the linkages through additional bridging oxygen atoms. Given the changes in the local structure, it can be expected that such modified linkages are especially prone to break upon dehydration. Thus, in addition to elucidating the deprotonation behaviour of protons associated with different types of linkages, the calculations also provide insights into possible reasons for the instability of Al-O-Al linkages, clarifying why Löwenstein’s rule is mostly obeyed in materials that are formed via a hydrothermal route.</p>


2019 ◽  
Vol 77 (9) ◽  
Author(s):  
Narges Dastmalchi ◽  
Seyed Mahdi Banan Khojasteh ◽  
Mirsaed Miri Nargesi ◽  
Reza Safaralizadeh

ABSTRACT Helicobacter pylori infection performs a key role in gastric tumorigenesis. Long non-coding RNAs (lncRNAs) have demonstrated a great potential to be regarded as effective malignancy biomarkers for various gastrointestinal diseases including gastric cancer (GC). The present review highlights the relationship between lncRNAs and H. pylori in GC. Several studies have examined not only the involvement of lncRNAs in H. pylori-associated GC progression but also their molecular mechanisms of action. Among the pertinent studies, some have addressed the effects of H. pylori infection on modulatory networks of lncRNAs, while others have evaluated the effects of changes in the expression level of lncRNAs in H. pylori-associated gastric diseases, especially GC. The relationship between lncRNAs and H. pylori was found to be modulated by various molecular pathways.


2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Jizhe Yu ◽  
Yushuang Qin ◽  
Naxin Zhou

Abstract Background The dysregulation of circular RNAs (circRNAs) has been identified in various human diseases, including osteoarthritis (OA). The purpose of this study was to identify the role and mechanism of circ_SLC39A8 in regulating the progression of OA. Methods The expression levels of circ_SLC39A8, miR-591, and its potential target gene, interleukin-1-receptor-associated kinase 3 (IRAK3), were identified by quantitative real-time polymerase chain reaction (qRT-PCR). Cell viability and apoptosis were determined by Cell Counting Kit-8 (CCK-8) assay and flow cytometry, respectively. The relationship between miR-591 and circ_SLC39A8 or IRAK3 was predicted by bioinformatics tools and verified by dual-luciferase reporter. Results Circ_SLC39A8 and IRAK3 were upregulated and miR-591 was downregulated in OA cartilage tissues. Knockdown of circ_SLC39A8 inhibited apoptosis and inflammation in OA chondrocytes, while these effects were reversed by downregulating miR-591. Promotion cell viability effects of miR-591 were partially reversed by IRAK3 overexpression. Conclusion Our findings indicated that knockdown of circ_SLC39A8 delayed the progression of OA via modulating the miR-591-IRAK3 axis, providing new insight into the molecular mechanisms of OA pathogenesis.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Keiichi Kataoka ◽  
Hironori Fujita ◽  
Mutsumi Isa ◽  
Shimpei Gotoh ◽  
Akira Arasaki ◽  
...  

AbstractMorphological variations in human teeth have long been recognized and, in particular, the spatial and temporal distribution of two patterns of dental features in Asia, i.e., Sinodonty and Sundadonty, have contributed to our understanding of the human migration history. However, the molecular mechanisms underlying such dental variations have not yet been completely elucidated. Recent studies have clarified that a nonsynonymous variant in the ectodysplasin A receptor gene (EDAR370V/A; rs3827760) contributes to crown traits related to Sinodonty. In this study, we examined the association between theEDARpolymorphism and tooth root traits by using computed tomography images and identified that the effects of theEDARvariant on the number and shape of roots differed depending on the tooth type. In addition, to better understand tooth root morphogenesis, a computational analysis for patterns of tooth roots was performed, assuming a reaction–diffusion system. The computational study suggested that the complicated effects of theEDARpolymorphism could be explained when it is considered that EDAR modifies the syntheses of multiple related molecules working in the reaction–diffusion dynamics. In this study, we shed light on the molecular mechanisms of tooth root morphogenesis, which are less understood in comparison to those of tooth crown morphogenesis.


Biomolecules ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 868
Author(s):  
Jiayang Zhang ◽  
Ruoyu Sun ◽  
Tingting Jiang ◽  
Guangrui Yang ◽  
Lihong Chen

Blood pressure (BP) follows a circadian rhythm, it increases on waking in the morning and decreases during sleeping at night. Disruption of the circadian BP rhythm has been reported to be associated with worsened cardiovascular and renal outcomes, however the underlying molecular mechanisms are still not clear. In this review, we briefly summarized the current understanding of the circadian BP regulation and provided therapeutic overview of the relationship between circadian BP rhythm and cardiovascular and renal health and disease.


2021 ◽  
Vol 22 (10) ◽  
pp. 5227
Author(s):  
Yu Sawada ◽  
Motonobu Nakamura

Daily lifestyle is a fundamental part of human life and its influence accumulates daily in the human body. We observe that a good daily lifestyle has a beneficial impact on our health; however, the actual effects of individual daily lifestyle factors on human skin diseases, especially skin cancers, have not been summarized. In this review, we focused on the influence of daily lifestyle on the development of skin cancer and described the detailed molecular mechanisms of the development or regulation of cutaneous malignancies. Several daily lifestyle factors, such as circadian rhythm disruption, smoking, alcohol, fatty acids, dietary fiber, obesity, and ultraviolet light, are known to be associated with the risk of cutaneous malignancies, malignant melanoma, squamous cell carcinoma, basal cell carcinoma, and Merkel cell carcinoma. Although the influence of some daily lifestyles on the risk of skin cancers is controversial, this review provides us a better understanding of the relationship between daily lifestyle factors and skin cancers.


2020 ◽  
Vol 2020 ◽  
pp. 1-8
Author(s):  
Chengquan Shen ◽  
Jing Liu ◽  
Jirong Wang ◽  
Xiaokun Yang ◽  
Haitao Niu ◽  
...  

PTPN6 (protein tyrosine phosphatase nonreceptor type 6), a tyrosine phosphatase, is known to be signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. Previous studies have demonstrated that PTPN6 expression is relatively elevated in several malignancies. However, the role of PTPN6 in bladder cancer (BC) remains unclear. The purpose of this study was to explore the prognostic value of PTPN6 in BC. RNA-seq data from The Cancer Genome Atlas (TCGA) was used to identify the expression level of PTPN6 in BC. The relationship between clinical pathologic features and PTPN6 were analyzed with the Wilcoxon signed-rank test. The prognostic and predictive value of PTPN6 was evaluated by survival analysis and nomogram. Gene Set Enrichment Analysis (GSEA) was conducted to explore the potential molecular mechanisms of PTPN6 in BC. Finally, Tumor Immune Estimation Resource (TIMER) was applied to investigate the relationship between PTPN6 and immune cell infiltration in the tumor microenvironment. Results indicated that PTPN6 was overexpressed in BC tissues compared with normal bladder tissues and was significantly correlated with grade, stage, T, and N. Survival analysis showed that low expression of PTPN6 was significantly related to the poor overall survival (OS) in BC patients. Coexpression analysis showed that PTPN6 and TNFRSF14 (Tumor necrosis factor receptor superfamily member 14) have a close correlation in BC. GSEA showed that multiple cancer-associated signaling pathways are differentially enriched in the PTPN6 high expression phenotype. Moreover, the expression level of PTPN6 was positively associated with the infiltration of B cells, CD4+T cells, dendritic cells, and neutrophils and negatively associated with CD8+ T cells and macrophages in BC. In conclusion, we identified that PTPN6 may be a novel prognostic biomarker in BC based on the TCGA database. Further clinical trials are needed to confirm our observations and mechanisms underlying the prognostic value of PTPN6 in BC also deserve further experimental exploration.


2021 ◽  
Vol 27 ◽  
Author(s):  
Li-Ping Yu ◽  
Ting-Ting Shi ◽  
Yan-Qin Li ◽  
Jian-Kang Mu ◽  
Ya-Qin Yang ◽  
...  

: Mitophagy plays an important role in maintaining mitochondrial quality and cell homeostasis through the degradation of damaged, aged, and dysfunctional mitochondria and misfolded proteins. Many human diseases, particularly neurodegenerative diseases, are related to disorders of mitochondrial phagocytosis. Exploring the regulatory mechanisms of mitophagy is of great significance for revealing the molecular mechanisms underlying the related diseases. Herein, we summarize the major mechanisms of mitophagy, the relationship of mitophagy with human diseases, and the role of traditional Chinese medicine (TCM) in mitophagy. These discussions enhance our knowledge of mitophagy and its potential therapeutic targets using TCM.


Author(s):  
Sascha Jähnigen ◽  
Daniel Sebastiani ◽  
Rodolphe Vuilleumier

We present a computational study of vibrational circular dichroism (VCD) in solutions of (S)-lactic acid, relying on ab initio molecular dynamics (AIMD) and full solvation with bulk water. We discuss...


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