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Molecular Nano-Architectures 2.0: Chemistry and Physics

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Physical Chemistry and Chemical Physics".

Deadline for manuscript submissions: closed (31 December 2022) | Viewed by 14307

Special Issue Editor


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Guest Editor
1. Laboratory of Structural and Computational Physical-Chemistry for Nanosciences and QSAR, Biology-Chemistry Department, West University of Timisoara, Str. Pestalozzi 16, 300115 Timisoara, Romania
2. Laboratory of Renewable Energies-Photovoltaics, R&D National Institute for Electrochemistry and Condensed Matter–INCEMC–Timisoara, Str. Dr. Aurel Podeanu 144, 300569 Timișoara, Romania
Interests: quantum physical chemistry; nanochemistry; reactivity indices and principles; electronegativity; density functional theory; path integrals; enzyme kinetics; QSAR; epistemology and philosophy of science
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Special Issue Information

Dear Colleagues, 

Once, the XXI century was predicted to belong to Faith, then to Biology, then to Informatics and Communication. Yet, the living reality hardly orients the present and forthcoming humankind needs on sustainable/healthy chemicals, and on material sciences, nano-integrated systems, nano-everything, from atoms, molecules to proteins, cells and their interaction having at the horizon the nano-medicine. However, facing such reality the basic grounded principles of physics sand chemistry are put to work at nano-scale, while discovering the “larger bottom room” with each new achievement, either theoretically or by experimental methods: from defective topologies of graphene to spine exo-functionalization of fullerene (mimicking coronaviruses), to negative surfaces of nanotori and allied carbon extended structures, just to name a few already basic nano-systems; to the nano-implants, laser ablation, cryogenic, baric, ultrasound and hyphenated techniques – all put at work towards artificially (i.e. smart/intelligent) synthesis and functionalization of novel materials, either hetero by stacking or in matrix ablation – to enhance the quantum causes and novel adaptive effects – at the distance of a triggering of a molecular switch or a molecular shuttle (viz. the molecular machines and the molecular interlocked molecules, etc.), etc. Accordingly, I warmly invite you to contribute either on fundamental and/or applicative sides of these challenged and necessary developments in post-modern nano-chemistry and nano-materials’ sciences as based on ground and groundbreaking physical-chemistry and chemical-physics principles of atoms, molecules and of their multi-scaled spaces of bondings and reactivity.

Prof. Dr. Mihai V. Putz
Guest Editor

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Keywords

  • molecular physics
  • chemical bonding and reactivity
  • nanolandia: direct graphs and negative surfaces
  • graphene, fulerene, nanotori
  • molecular interlocked molecules
  • nanomaterials and methods
  • nanotechnology: smart/inteligent systems

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Published Papers (3 papers)

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Research

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21 pages, 6805 KiB  
Article
SARS-CoV-2 Spike Protein Interaction Space
by Claudiu N. Lungu and Mihai V. Putz
Int. J. Mol. Sci. 2023, 24(15), 12058; https://doi.org/10.3390/ijms241512058 - 27 Jul 2023
Viewed by 2514
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a +sense single-strand RNA virus. The virus has four major surface proteins: spike (S), envelope (E), membrane (M), and nucleocapsid (N), respectively. The constitutive proteins present a high grade of symmetry. Identifying a binding site [...] Read more.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a +sense single-strand RNA virus. The virus has four major surface proteins: spike (S), envelope (E), membrane (M), and nucleocapsid (N), respectively. The constitutive proteins present a high grade of symmetry. Identifying a binding site is difficult. The virion is approximately 50–200 nm in diameter. Angiotensin-converting enzyme 2 (ACE2) acts as the cell receptor for the virus. SARS-CoV-2 has an increased affinity to human ACE2 compared with the original SAR strain. Topological space, and its symmetry, is a critical component in molecular interactions. By exploring this space, a suitable ligand space can be characterized accordingly. A spike protein (S) computational model in a complex with ACE 2 was generated using silica methods. Topological spaces were probed using high computational throughput screening techniques to identify and characterize the topological space of both SARS and SARS-CoV-2 spike protein and its ligand space. In order to identify the symmetry clusters, computational analysis techniques, together with statistical analysis, were utilized. The computations are based on crystallographic protein data bank PDB-based models of constitutive proteins. Cartesian coordinates of component atoms and some cluster maps were generated and analyzed. Dihedral angles were used in order to compute a topological receptor space. This computational study uses a multimodal representation of spike protein interactions with some fragment proteins. The chemical space of the receptors (a dimensional volume) suggests the relevance of the receptor as a drug target. The spike protein S of SARS and SARS-CoV-2 is analyzed and compared. The results suggest a mirror symmetry of SARS and SARS-CoV-2 spike proteins. The results show thatSARS-CoV-2 space is variable and has a distinct topology. In conclusion, surface proteins grant virion variability and symmetry in interactions with a potential complementary target (protein, antibody, ligand). The mirror symmetry of dihedral angle clusters determines a high specificity of the receptor space. Full article
(This article belongs to the Special Issue Molecular Nano-Architectures 2.0: Chemistry and Physics)
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Review

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15 pages, 5442 KiB  
Review
Recent Advances in Nanoparticle-Mediated Co-Delivery System: A Promising Strategy in Medical and Agricultural Field
by Mingshan Li, Xiaowei Sun, Meizhen Yin, Jie Shen and Shuo Yan
Int. J. Mol. Sci. 2023, 24(6), 5121; https://doi.org/10.3390/ijms24065121 - 7 Mar 2023
Cited by 17 | Viewed by 3528
Abstract
Drug and gene delivery systems mediated by nanoparticles have been widely studied for life science in the past decade. The application of nano-delivery systems can dramatically improve the stability and delivery efficiency of carried ingredients, overcoming the defects of administration routes in cancer [...] Read more.
Drug and gene delivery systems mediated by nanoparticles have been widely studied for life science in the past decade. The application of nano-delivery systems can dramatically improve the stability and delivery efficiency of carried ingredients, overcoming the defects of administration routes in cancer therapy, and possibly maintaining the sustainability of agricultural systems. However, delivery of a drug or gene alone sometimes cannot achieve a satisfactory effect. The nanoparticle-mediated co-delivery system can load multiple drugs and genes simultaneously, and improve the effectiveness of each component, thus amplifying efficacy and exhibiting synergistic effects in cancer therapy and pest management. The co-delivery system has been widely reported in the medical field, and studies on its application in the agricultural field have recently begun to emerge. In this progress report, we summarize recent progress in the preparation and application of drug and gene co-delivery systems and discuss the remaining challenges and future perspectives in the design and fabrication. Full article
(This article belongs to the Special Issue Molecular Nano-Architectures 2.0: Chemistry and Physics)
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21 pages, 727 KiB  
Review
Current Molecular Combination Therapies Used for the Treatment of Breast Cancer
by Yiling Wang and Audrey Minden
Int. J. Mol. Sci. 2022, 23(19), 11046; https://doi.org/10.3390/ijms231911046 - 20 Sep 2022
Cited by 38 | Viewed by 7449
Abstract
Breast cancer is the second leading cause of death for women worldwide. While monotherapy (single agent) treatments have been used for many years, they are not always effective, and many patients relapse after initial treatment. Moreover, in some patients the response to therapy [...] Read more.
Breast cancer is the second leading cause of death for women worldwide. While monotherapy (single agent) treatments have been used for many years, they are not always effective, and many patients relapse after initial treatment. Moreover, in some patients the response to therapy becomes weaker, or resistance to monotherapy develops over time. This is especially problematic for metastatic breast cancer or triple-negative breast cancer. Recently, combination therapies (in which two or more drugs are used to target two or more pathways) have emerged as promising new treatment options. Combination therapies are often more effective than monotherapies and demonstrate lower levels of toxicity during long-term treatment. In this review, we provide a comprehensive overview of current combination therapies, including molecular-targeted therapy, hormone therapy, immunotherapy, and chemotherapy. We also describe the molecular basis of breast cancer and the various treatment options for different breast cancer subtypes. While combination therapies are promising, we also discuss some of the challenges. Despite these challenges, the use of innovative combination therapy holds great promise compared with traditional monotherapies. In addition, the use of multidisciplinary technologies (such as nanotechnology and computer technology) has the potential to optimize combination therapies even further. Full article
(This article belongs to the Special Issue Molecular Nano-Architectures 2.0: Chemistry and Physics)
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