Molecular Topology and Computation

Journal Name	Impact Factor	CiteScore	Launched Year	First Decision (median)	APC
Chemistry chemistry	2.4	3.2	2019	17.2 Days	CHF 1800
International Journal of Molecular Sciences ijms	4.9	8.1	2000	16.8 Days	CHF 2900
Mathematics mathematics	2.3	4.0	2013	18.3 Days	CHF 2600
Symmetry symmetry	2.2	5.4	2009	17.3 Days	CHF 2400
Computation computation	1.9	3.5	2013	18.6 Days	CHF 1800

38 pages, 6005 KiB

Open AccessReview

Pure Hydrolysis of Polyamides: A Comparative Study

by Mathis Mortensen Brette, Allan Hjarbæk Holm, Aleksey D. Drozdov and Jesper de Claville Christiansen

Chemistry 2024, 6(1), 13-50; https://doi.org/10.3390/chemistry6010002 - 20 Dec 2023

Cited by 11 | Viewed by 5533

Polyamides (PAs) undergo local environmental degradation, leading to a decline in their mechanical properties over time. PAs can experience various forms of degradation, such as thermal degradation, oxidation, hydrothermal oxidation, UV oxidation, and hydrolysis. In order to better comprehend the degradation process of [...] Read more.

Polyamides (PAs) undergo local environmental degradation, leading to a decline in their mechanical properties over time. PAs can experience various forms of degradation, such as thermal degradation, oxidation, hydrothermal oxidation, UV oxidation, and hydrolysis. In order to better comprehend the degradation process of PAs, it is crucial to understand each of these degradation mechanisms individually. While this review focuses on hydrolysis, the data from degrading similar PAs under pure thermal oxidation and/or hydrothermal oxidation are also collected to grasp more perspective. This review analyzes the available characterization data and evaluates the changes in molecular weight, crystallinity, chemical structure, and mechanical properties of PAs that have aged in oxygen-free water at high temperatures. The molecular weight and mechanical strength decrease as the crystallinity ratio rises over aging time. This development is occurring at a slower rate than degradation in pure thermal oxidation. By combining the data for the changes in mechanical properties with the ones for molecular weight and crystallinity, the point of embrittlement can be not only predicted, but also modeled. This prediction is also shown to be dependent on the fibers, additives, types of PA, pH, and more. Full article

(This article belongs to the Topic Molecular Topology and Computation)

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17 pages, 3006 KiB

Open AccessArticle

Characterizations of Chemical Networks Entropies by K-Banhatii Topological Indices

by Muhammad Usman Ghani, Francis Joseph H. Campena, Shahbaz Ali, Sanaullah Dehraj, Murat Cancan, Fahad M. Alharbi and Ahmed M. Galal

Symmetry 2023, 15(1), 143; https://doi.org/10.3390/sym15010143 - 3 Jan 2023

Cited by 22 | Viewed by 2215

Abstract

Entropy is a thermodynamic function in physics that measures the randomness and disorder of molecules in a particular system or process based on the diversity of configurations that molecules might take. Distance-based entropy is used to address a wide range of problems in [...] Read more.

Entropy is a thermodynamic function in physics that measures the randomness and disorder of molecules in a particular system or process based on the diversity of configurations that molecules might take. Distance-based entropy is used to address a wide range of problems in the domains of mathematics, biology, chemical graph theory, organic and inorganic chemistry, and other disciplines. We explain the basic applications of distance-based entropy to chemical phenomena. These applications include signal processing, structural studies on crystals, molecular ensembles, and quantifying the chemical and electrical structures of molecules. In this study, we examine the characterisation of polyphenylenes and boron (

$B_{12}$ ) using a line of symmetry. Our ability to quickly ascertain the valences of each atom, and the total number of atom bonds is made possible by the symmetrical chemical structures of polyphenylenes and boron

$B_{12}$ . By constructing these structures with degree-based indices, namely the K Banhatti indices,

$R e Z G_{1}$ -index,

$R e Z G_{2}$ -index, and

$R e Z G_{3}$ -index, we are able to determine their respective entropies. Full article

(This article belongs to the Topic Molecular Topology and Computation)

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15 pages, 4434 KiB

Open AccessArticle

Structural Factors That Determine the Activity of the Xenobiotic Reductase B Enzyme from Pseudomonas putida on Nitroaromatic Compounds

by Manuel I. Osorio, Nicolás Bruna, Víctor García, Lisdelys González-Rodríguez, Matías S. Leal, Francisco Salgado, Matías Vargas-Reyes, Fernando González-Nilo, José M. Pérez-Donoso and Osvaldo Yáñez

Int. J. Mol. Sci. 2023, 24(1), 400; https://doi.org/10.3390/ijms24010400 - 26 Dec 2022

Cited by 2 | Viewed by 2782

Abstract

Xenobiotic reductase B (XenB) catalyzes the reduction of the aromatic ring or nitro groups of nitroaromatic compounds with methyl, amino or hydroxyl radicals. This reaction is of biotechnological interest for bioremediation, the reuse of industrial waste or the activation of prodrugs. However, the [...] Read more.

Xenobiotic reductase B (XenB) catalyzes the reduction of the aromatic ring or nitro groups of nitroaromatic compounds with methyl, amino or hydroxyl radicals. This reaction is of biotechnological interest for bioremediation, the reuse of industrial waste or the activation of prodrugs. However, the structural factors that explain the binding of XenB to different substrates are unknown. Molecular dynamics simulations and quantum mechanical calculations were performed to identify the residues involved in the formation and stabilization of the enzyme/substrate complex and to explain the use of different substrates by this enzyme. Our results show that Tyr65 and Tyr335 residues stabilize the ligands through hydrophobic interactions mediated by the aromatic rings of these aminoacids. The higher XenB activity determined with the substrates 1,3,5-trinitrobenzene and 2,4,6-trinitrotoluene is consistent with the lower energy of the highest occupied molecular orbital (LUMO) orbitals and a lower energy of the homo orbital (LUMO), which favors electrophile and nucleophilic activity, respectively. The electrostatic potential maps of these compounds suggest that the bonding requires a large hydrophobic region in the aromatic ring, which is promoted by substituents in ortho and para positions. These results are consistent with experimental data and could be used to propose point mutations that allow this enzyme to process new molecules of biotechnological interest. Full article

(This article belongs to the Topic Molecular Topology and Computation)

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16 pages, 5277 KiB

Open AccessArticle

Molecular Dynamics of CYFIP2 Protein and Its R87C Variant Related to Early Infantile Epileptic Encephalopathy

by Ísis V. Biembengut, Patrícia Shigunov, Natalia F. Frota, Marcos R. Lourenzoni and Tatiana A. C. B. de Souza

Int. J. Mol. Sci. 2022, 23(15), 8708; https://doi.org/10.3390/ijms23158708 - 5 Aug 2022

Cited by 3 | Viewed by 2637

Abstract

The CYFIP2 protein (cytoplasmic FMR1-interacting protein 2) is part of the WAVE regulatory complex (WRC). CYFIP2 was recently correlated to neurological disorders by the association of the R87C variant with early infantile epileptic encephalopathy (EIEE) patients. In this set of syndromes, the epileptic [...] Read more.

The CYFIP2 protein (cytoplasmic FMR1-interacting protein 2) is part of the WAVE regulatory complex (WRC). CYFIP2 was recently correlated to neurological disorders by the association of the R87C variant with early infantile epileptic encephalopathy (EIEE) patients. In this set of syndromes, the epileptic spasms and seizures since early childhood lead to impaired neurological development in children. Inside the WRC, the variant residue is at the CYFIP2 and WAVE1 protein interface. Thus, the hypothesis is that the R87C modification weakens this interaction, allowing the WRC complex’s constant activation. This work aimed to investigate the impacts of the mutation on the structure of the WRC complex through molecular dynamics simulation. For that, we constructed WRC models containing WAVE1-NCKAP1 proteins complexed with WT or R87C CYFIP2. Our simulations showed a flexibilization of the loop comprising residues 80–110 due to the loss of contacts between internal residues in the R87C CYFIP2 as well as the key role of residues R/C87, E624, and E689 in structural modification. These data could explain the mechanism by which the mutation impairs the stability and proper regulation of the WRC. Full article

(This article belongs to the Topic Molecular Topology and Computation)

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16 pages, 7748 KiB

Open AccessArticle

Effects of Tearing Conditions on the Crack Propagation in a Monolayer Graphene Sheet

by Jiao Shi, Weihua Yu, Chunwei Hu, Haiyan Duan, Jiaxing Ji, Yuanyuan Kang and Kun Cai

Int. J. Mol. Sci. 2022, 23(12), 6471; https://doi.org/10.3390/ijms23126471 - 9 Jun 2022

Cited by 2 | Viewed by 1886

Abstract

The path of crack propagation in a graphene sheet is significant for graphene patterning via the tearing approach. In this study, we evaluate the fracture properties of pre-cracked graphene during the tearing process, with consideration of the effects of the aspect ratio, loading [...] Read more.

The path of crack propagation in a graphene sheet is significant for graphene patterning via the tearing approach. In this study, we evaluate the fracture properties of pre-cracked graphene during the tearing process, with consideration of the effects of the aspect ratio, loading speed, loading direction, and ambient temperatures on the crack propagation in the monolayer sheet. Some remarkable conclusions are drawn based on the molecular dynamic simulation results, i.e., a higher loading speed may result in a complicated path of crack propagation, and the propagation of an armchair crack may be accompanied by sp carbon links at high temperatures. The reason for this is that the stronger thermal vibration reduces the load stress difference near the crack tip and, therefore, the crack tip can pass through the sp link. A crack propagates more easily along the zigzag direction than along the armchair direction. The out-of-plane tearing is more suitable than the in-plane tearing for graphene patterning. The path of crack propagation can be adjusted by changing the loading direction, e.g., a rectangular graphene ribbon can be produced by oblique tearing. This new understanding will benefit the application of graphene patterning via the tearing approach. Full article

(This article belongs to the Topic Molecular Topology and Computation)

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21 pages, 5991 KiB

Open AccessArticle

Biochemical, Structural Analysis, and Docking Studies of Spiropyrazoline Derivatives

by Angelika A. Adamus-Grabicka, Mateusz Daśko, Pawel Hikisz, Joachim Kusz, Magdalena Malecka and Elzbieta Budzisz

Int. J. Mol. Sci. 2022, 23(11), 6061; https://doi.org/10.3390/ijms23116061 - 27 May 2022

Cited by 4 | Viewed by 2506

Abstract

In this study, we evaluated the antiproliferative potential, DNA damage, crystal structures, and docking calculation of two spiropyrazoline derivatives. The main focus of the research was to evaluate the antiproliferative potential of synthesized compounds towards eight cancer cell lines. Compound I demonstrated promising [...] Read more.

In this study, we evaluated the antiproliferative potential, DNA damage, crystal structures, and docking calculation of two spiropyrazoline derivatives. The main focus of the research was to evaluate the antiproliferative potential of synthesized compounds towards eight cancer cell lines. Compound I demonstrated promising antiproliferative properties, especially toward the HL60 cell line, for which IC₅₀ was equal to 9.4 µM/L. The analysis of DNA damage by the comet assay showed that compound II caused DNA damage to tumor lineage cells to a greater extent than compound I. The level of damage to tumor cells of the HEC-1-A lineage was 23%. The determination of apoptotic and necrotic cell fractions by fluorescence microscopy indicated that cells treated with spiropyrazoline-based analogues were entering the early phase of programmed cell death. Compounds I and II depolarized the mitochondrial membranes of cancer cells. Furthermore, we performed simple docking calculations, which indicated that the obtained compounds are able to bind to the PARP1 active site, at least theoretically (the free energy of binding values for compound I and II were −9.7 and 8.7 kcal mol⁻¹, respectively). In silico studies of the influence of the studied compounds on PARP1 were confirmed in vitro with the use of eight cancer cell lines. The degradation of the PARP1 enzyme was observed, with compound I characterized by a higher protein degradation activity. Full article

(This article belongs to the Topic Molecular Topology and Computation)

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15 pages, 6690 KiB

Open AccessArticle

Computed Mass-Fragmentation Energy Profiles of Some Acetalized Monosaccharides for Identification in Mass Spectrometry

by Mihai-Cosmin Pascariu, Nicolae Dinca, Carolina Cojocariu, Eugen Sisu, Alina Serb, Romina Birza and Marius Georgescu

Symmetry 2022, 14(5), 1074; https://doi.org/10.3390/sym14051074 - 23 May 2022

Cited by 2 | Viewed by 2277

Abstract

Our study found that quantum calculations can differentiate fragmentation energies into isomeric structures with asymmetric carbon atoms, such as those of acetalized monosaccharides. It was justified by the good results that have been published in recent years on the discrimination of structural isomers [...] Read more.

Our study found that quantum calculations can differentiate fragmentation energies into isomeric structures with asymmetric carbon atoms, such as those of acetalized monosaccharides. It was justified by the good results that have been published in recent years on the discrimination of structural isomers and diastereomers by correlating the calculated mass energy fragmentation profiles with their mass spectra. Based on the quantitative structure–fragmentation relationship (QSFR), this technique compares the intensities of primary ions from the experimental spectrum using the mass energy profiles calculated for the candidate structures. Maximum fit is obtained for the true structure. For a preliminary assessment of the accuracy of the identification of some di-O-isopropylidene monosaccharide diastereomers, we used fragmentation enthalpies (Δ_fH) and Gibbs energies (Δ_fG) as the energetic descriptors of fragmentation. Four quantum chemical methods were used: RM1, PM7, DFT Δ_fH and DFT Δ_fG. The mass energy database shows that the differences between the profiles of the isomeric candidate structures could be large enough to be distinguished from each other. This database allows the optimization of energy descriptors and quantum computing methods that can ensure the correct identification of these isomers. Full article

(This article belongs to the Topic Molecular Topology and Computation)

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14 pages, 3078 KiB

Open AccessArticle

Sombor Index over the Tensor and Cartesian Products of Monogenic Semigroup Graphs

by Seda Oğuz Ünal

Symmetry 2022, 14(5), 1071; https://doi.org/10.3390/sym14051071 - 23 May 2022

Cited by 9 | Viewed by 2493

Abstract

Consider a simple graph G with vertex set

$V (G)$ and edge set

$E (G)$ . A graph invariant for G is a number related to the structure of G, which is invariant under the symmetry of G [...] Read more.

Consider a simple graph G with vertex set

$V (G)$ and edge set

$E (G)$ . A graph invariant for G is a number related to the structure of G, which is invariant under the symmetry of G. The Sombor index of G is a new graph invariant defined as

$S O (G) = \sum_{u v \in E (G)} \sqrt{{(d_{u})}^{2} + {(d_{v})}^{2}}$ . In this work, we connected the theory of the Sombor index with abstract algebra. We computed this topological index over the tensor and Cartesian products of a monogenic semigroup graph by presenting two different algorithms; the obtained results are illustrated by examples. Full article

(This article belongs to the Topic Molecular Topology and Computation)

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18 pages, 1902 KiB

Open AccessArticle

Integration of Neighbor Topologies Based on Meta-Paths and Node Attributes for Predicting Drug-Related Diseases

by Ping Xuan, Zixuan Lu, Tiangang Zhang, Yong Liu and Toshiya Nakaguchi

Int. J. Mol. Sci. 2022, 23(7), 3870; https://doi.org/10.3390/ijms23073870 - 31 Mar 2022

Cited by 3 | Viewed by 2126

Abstract

Identifying new disease indications for existing drugs can help facilitate drug development and reduce development cost. The previous drug–disease association prediction methods focused on data about drugs and diseases from multiple sources. However, they did not deeply integrate the neighbor topological information of [...] Read more.

Identifying new disease indications for existing drugs can help facilitate drug development and reduce development cost. The previous drug–disease association prediction methods focused on data about drugs and diseases from multiple sources. However, they did not deeply integrate the neighbor topological information of drug and disease nodes from various meta-path perspectives. We propose a prediction method called NAPred to encode and integrate meta-path-level neighbor topologies, multiple kinds of drug attributes, and drug-related and disease-related similarities and associations. The multiple kinds of similarities between drugs reflect the degrees of similarity between two drugs from different perspectives. Therefore, we constructed three drug–disease heterogeneous networks according to these drug similarities, respectively. A learning framework based on fully connected neural networks and a convolutional neural network with an attention mechanism is proposed to learn information of the neighbor nodes of a pair of drug and disease nodes. The multiple neighbor sets composed of different kinds of nodes were formed respectively based on meta-paths with different semantics and different scales. We established the attention mechanisms at the neighbor-scale level and at the neighbor topology level to learn enhanced neighbor feature representations and enhanced neighbor topological representations. A convolutional-autoencoder-based module is proposed to encode the attributes of the drug–disease pair in three heterogeneous networks. Extensive experimental results indicated that NAPred outperformed several state-of-the-art methods for drug–disease association prediction, and the improved recall rates demonstrated that NAPred was able to retrieve more actual drug–disease associations from the top-ranked candidates. Case studies on five drugs further demonstrated the ability of NAPred to identify potential drug-related disease candidates. Full article

(This article belongs to the Topic Molecular Topology and Computation)

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