Search results for: molecular orbital theory

Authors: Olaide O. Wahab, Lukman O. Olasunkanmi, Krishna K. Govender, Penny P. Govender

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The economic and environmental challenges associated with azo disperse dyes applications are due to poor aqueous solubility and low degradation tendency which stems from low chemical reactivity. Poor aqueous solubility property of this group of dyes necessitates the use of dispersing agents which increase operational costs and also release toxic chemical components into the environment, while their low degradation tendency is due to the high stability of the azo functional group (-N=N-) in their chemical structures. To address these problems, this study investigated theoretically the effects of some polar substituents on the aqueous solubility and reactivity properties of disperse yellow (DY) 119 dye with a view to theoretically develop new azo disperse dyes with improved solubility in water and higher degradation tendency in the environment using DMol³ computational code. All calculations were carried out using the Becke and Perdew version of Volsko-Wilk-Nusair (VWN-BP) level of density functional theory in conjunction with double numerical basis set containing polarization function (DNP). The aqueous solubility determination was achieved with conductor-like screening model for realistic solvation (COSMO-RS) in conjunction with known empirical solubility model, while the reactivity was predicted using frontier molecular orbital calculations. Most of the new derivatives studied showed evidence of higher aqueous solubility and degradation tendency compared to the parent dye. We conclude that these derivatives are promising alternative dyes for more economic and environmental benign dyeing practice and therefore recommend them for synthesis.

Keywords: aqueous solubility, azo disperse dye, degradation, disperse yellow 119, DMol³, reactivity

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Authors: Paramita Banerjee, K. R. S. Chandrakumar, G. P. Das

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Bulk MgH2 has drawn much attention for the purpose of hydrogen storage because of its high hydrogen storage capacity (~7.7 wt %) as well as low cost and abundant availability. However, its practical usage has been hindered because of its high hydrogen desorption enthalpy (~0.8 eV/H2 molecule), which results in an undesirable desorption temperature of 3000C at 1 bar H2 pressure. To surmount the limitations of bulk MgH2 for the purpose of hydrogen storage, a detailed first-principles density functional theory (DFT) based study on the structure and stability of neutral (Mgm) and positively charged (Mgm+) Mg nanoclusters of different sizes (m = 2, 4, 8 and 12), as well as their interaction with molecular hydrogen (H2), is reported here. It has been found that due to the absence of d-electrons within the Mg atoms, hydrogen remained in molecular form even after its interaction with neutral and charged Mg nanoclusters. Interestingly, the H2 molecules do not enter into the interstitial positions of the nanoclusters. Rather, they remain on the surface by ornamenting these nanoclusters and forming new structures with a gravimetric density higher than 15 wt %. Our observation is that the inclusion of Grimme’s DFT-D3 dispersion correction in this weakly interacting system has a significant effect on binding of the H2 molecules with these nanoclusters. The dispersion corrected interaction energy (IE) values (0.1-0.14 eV/H2 molecule) fall in the right energy window, that is ideal for hydrogen storage. These IE values are further verified by using high-level coupled-cluster calculations with non-iterative triples corrections i.e. CCSD(T), (which has been considered to be a highly accurate quantum chemical method) and thereby confirming the accuracy of our ‘dispersion correction’ incorporated DFT calculations. The significance of the polarization and dispersion energy in binding of the H2 molecules are confirmed by performing energy decomposition analysis (EDA). A total of 16, 24, 32 and 36 H2 molecules can be attached to the neutral and charged nanoclusters of size m = 2, 4, 8 and 12 respectively. Ab-initio molecular dynamics (AIMD) simulation shows that the outermost H2 molecules are desorbed at a rather low temperature viz. 150 K (-1230C) which is expected. However, complete dehydrogenation of these nanoclusters occur at around 1000C. Most importantly, the host nanoclusters remain stable up to ~500 K (2270C). All these results on the adsorption and desorption of molecular hydrogen with neutral and charged Mg nanocluster systems indicate towards the possibility of reducing the dehydrogenation temperature of bulk MgH2 by designing new Mg-based nano materials which will be able to adsorb molecular hydrogen via this weak Mg-H2 interaction, rather than the strong Mg-H bonding. Notwithstanding the fact that in practical applications, these interactions will be further complicated by the effect of substrates as well as interactions with other clusters, the present study has implications on our fundamental understanding to this problem.

Keywords: density functional theory, DFT, hydrogen storage, molecular dynamics, molecular hydrogen adsorption, nanoclusters, physisorption

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Authors: Saeed Vahedikamal, Ian Hepburn

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Microwave Kinetic Inductance Detectors (MKIDs) are considered as one of the most promising photon detectors of the future in many Astronomical applications such as exoplanet detections. The MKID advantages stem from their single photon sensitivity (ranging from UV to optical and near infrared), photon energy resolution and high temporal capability (~microseconds). There has been substantial progress in the development of these detectors and MKIDs with Megapixel arrays is now possible. The unique capability of recording an incident photon and its energy (or wavelength) while also registering its time of arrival to within a microsecond enables an array of MKIDs to produce a four-dimensional data block of x, y, z and t comprising x, y spatial, z axis per pixel spectral and t axis per pixel which is temporal. This offers the possibility that the spectrum and brightness variation for any detected piece of space debris as a function of time might offer a unique identifier or fingerprint. Such a fingerprint signal from any object identified in multiple detections by different observers has the potential to determine the orbital features of the object and be used for their tracking. Modelling performed so far shows that with a 20 cm telescope located at an Astronomical observatory (e.g. La Palma, Canary Islands) we could detect sub cm objects at GEO. By considering a Lambertian sphere with a 10 % reflectivity (albedo of the Moon) we anticipate the following for a GEO object: 10 cm object imaged in a 1 second image capture; 1.2 cm object for a 70 second image integration or 0.65 cm object for a 4 minute image integration. We present details of our modelling and the potential instrument for a dedicated GEO surveillance system.

Keywords: space debris, orbital debris, detection system, observation, microwave kinetic inductance detectors, MKID

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Authors: Arthur Baraov

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Nearly all rocket and spacecraft propulsion concepts in existence today can be linked one way or the other to one of the two ancient warfare devices: the gun and the sling. Chemical, thermoelectric, ion, nuclear thermal and electromagnetic rocket engines – all fall into the first group which, for obvious reasons, can be categorized as “hot” space propulsion concepts. Space elevator, orbital tower, rolling satellite, orbital skyhook, tether propulsion and gravitational assist – are examples of the second category which lends itself for the title “cold” space propulsion concepts. The “hot” space propulsion concepts skyrocketed – literally and figuratively – from the naïve ideas of Jules Verne to the manned missions to the Moon. On the other hand, with the notable exception of gravitational assist, hardly any of the “cold” space propulsion concepts made any progress in terms of practical application. Why is that? This article aims to show that the right answer to this question has the potential comparable by its implications and practical consequences to that of transition from Jules Verne’s stillborn and impractical conceptions of space flight to cogent and highly fertile ideas of Konstantin Tsiolkovsky and Yuri Kondratyuk.

Keywords: propulsion, rocket, rollet, spacecraft

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Authors: H. Hadjeris, R. B. Ghoul, Lekhlaf, M. Nebbal

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Introduction: Adenoid cystic carcinomas of the lacrimal gland or orbital cylindroma constitute the second cause of epithelial tumors of this gland. It is a malignant tumor usually developed at the expense of the salivary glands; its orbital location is exceptional. It is a rare clinical entity, formidable by its malignancy and local aggressiveness; the recurrence rate is high. Materials and methods: Clinical case: 63 years old woman who presents with irreducible no pulsatile painful left exophthalmos with inflammatory chemosis and a decrease in visual acuity with a moderate intracranial hypertension syndrome that has been evolving for 03 months. Antecedent; a biopsy of the tumor was made; the histological examination was in favor of an adenoid cystic carcinoma of the lacrimal gland. Lesion assessment: computed tomography and brain MRI: show an intra and extra-conical mass; with sinus (ethmoido-frontal) and cerebral (left frontal) extension strongly enhanced after injection of contrast product surrounded by edema around the lesion, associated with left frontal bone lysis extension assessment: unremarkable treatment: Patient operated by left frontotemporal approach, a total exenteration was performed with macroscopically complete excision of the frontal lesion and wide frontal craniectomy with craniofacial reconstruction, followed by complementary radiotherapy. Results: The patient was seen again after 3 months in consultation; she does not present any signs in favor of a recurrence. Conclusion: Adenoid cystic carcinomas of the lacrimal gland are rare malignant tumors; they are very infiltrating and invasive. The prognosis is strongly linked to the treatment time.

Keywords: adenoid cystic, lacrimal gland, orbital location, fronto-temporal approac

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Authors: K. Veluraja

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Glycan of glycolipids and glycoproteins is playing a significant role in living systems particularly in molecular recognition processes. Molecular recognition processes are attributed to their occurrence on the surface of the cell, sequential arrangement and type of sugar molecules present in the oligosaccharide structure and glyosidic linkage diversity (glycoinformatics) and conformational diversity (glycoconformatics). Molecular Dynamics Simulation study is a theoretical-cum-computational tool successfully utilized to establish glycoconformatics of glycan. The study on various oligosaccharides of glycan clearly indicates that oligosaccharides do exist in multiple conformational states and these conformational states arise due to the flexibility associated with a glycosidic torsional angle (φ,ψ) . As an example: a single disaccharide structure NeuNacα(2-3) Gal exists in three different conformational states due to the differences in the preferential value of glycosidic torsional angles (φ,ψ). Hence establishing three dimensional structural and conformational models for glycan (cartesian coordinates of every individual atoms of an oligosaccharide structure in a preferred conformation) is quite crucial to understand various molecular recognition processes such as glycan-toxin interaction and glycan-virus interaction. The gycoconformatics models obtained for various glycan through Molecular Dynamics Simulation stored in our 3DSDSCAR (3DSDSCAR.ORG) a public domain database and its utility value in understanding the molecular recognition processes and in drug design venture will be discussed.

Keywords: glycan, glycoconformatics, molecular dynamics simulation, oligosaccharide

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Authors: David Ompong, Jai Singh

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A better understanding of the open-circuit voltage (Voc) related losses in organic solar cells (OSCs) is desirable in order to assess the photovoltaic performance of these devices. We have derived Voc as a function of charge carrier mobilities (μe and μh) for organic and hybrid solar cells by optimizing the drift-diffusion current density. The optimum Voc thus obtained depends on the energy difference between the highest occupied molecular orbital (HOMO) level and the quasi-Fermi level of holes of the donor material. We have found that the Voc depends on the ratio of the electron (μe) and hole (μh) mobilities and when μh > μe the Voc increases. The most important loss term in the Voc arises from the energetics of the donor and acceptor materials, which will be discussed in detail in this paper.

Keywords: charge carrier mobility, open-circuit voltage, organic solar cells, quasi-fermi levels

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Authors: Jaan Lellep, Shahid Mubasshar

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A numerical solution is developed for simply supported nanoarches based on the non-local theory of elasticity. The nanoarch under consideration has a step-wise variable cross-section and is weakened by crack-like defects. It is assumed that the cracks are stationary and the mechanical behaviour of the nanoarch can be modeled by Eringen’s non-local theory of elasticity. The physical and thermal properties are sensitive with respect to changes of dimensions in the nano level. The classical theory of elasticity is unable to describe such changes in material properties. This is because, during the development of the classical theory of elasticity, the speculation of molecular objects was avoided. Therefore, the non-local theory of elasticity is applied to study the vibration of nanostructures and it has been accepted by many researchers. In the non-local theory of elasticity, it is assumed that the stress state of the body at a given point depends on the stress state of each point of the structure. However, within the classical theory of elasticity, the stress state of the body depends only on the given point. The system of main equations consists of equilibrium equations, geometrical relations and constitutive equations with boundary and intermediate conditions. The system of equations is solved by using the method of separation of variables. Consequently, the governing differential equations are converted into a system of algebraic equations whose solution exists if the determinant of the coefficients of the matrix vanishes. The influence of cracks and steps on the natural vibration of the nanoarches is prescribed with the aid of additional local compliance at the weakened cross-section. An algorithm to determine the eigenfrequencies of the nanoarches is developed with the help of computer software. The effects of various physical and geometrical parameters are recorded and drawn graphically.

Keywords: crack, nanoarches, natural frequency, step

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Authors: Irfan Nazir Wani, Pushpendra Kumar Shukla, Manoj Kumar

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Debris, also called waste or junk, present in orbit of Earth or orbital debris, offers a substantial challenge to space exploration. Satellite operations and other space-based activities. This research paper delves into the causes and effects of space debris accumulation, explores current mitigation techniques, and presents a hopeful outlook on the potential for future sustainable space activities. The paper emphasizes the necessity of addressing planetary fragments to ensure durable sustainability in universe exploration and utilization. It examines various strategies for mitigating space debris, including debris removal technologies, spacecraft design improvements, and international collaboration efforts. Additionally, the paper highlights the importance of space debris monitoring and tracking systems in preventing collisions and minimizing the growth of orbital debris. By comprehending the complexities of space debris and implementing effective mitigation measures, the space industry can work towards a future where sustainable space activities are achievable.

Keywords: space shuttle, debris, space junk, satellite, fragments, orbit

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Authors: Catherine Vasnetsov, Victor Vasnetsov

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Context: Thermo-responsive polymers are materials that undergo significant changes in their physical properties in response to temperature changes. These polymers have gained significant attention in research due to their potential applications in various industries and medicine. However, the molecular mechanisms underlying their behavior are not well understood, particularly in relation to cosolvency, which is crucial for practical applications. Research Aim: This study aimed to theoretically investigate the phenomenon of cosolvency in long-chain polymers using the Flory-Huggins statistical-mechanical framework. The main objective was to understand the interactions between the polymer, solvent, and cosolvent under different conditions. Methodology: The research employed a combination of Monte Carlo computer simulations and advanced machine-learning methods. The Flory-Huggins mean field theory was used as the basis for the simulations. Spinodal graphs and ternary plots were utilized to develop an initial computer model for predicting polymer behavior. Molecular dynamic simulations were conducted to mimic real-life polymer systems. Machine learning techniques were incorporated to enhance the accuracy and reliability of the simulations. Findings: The simulations revealed that the addition of very low or very high volumes of cosolvent molecules resulted in smaller radii of gyration for the polymer, indicating poor miscibility. However, intermediate volume fractions of cosolvent led to higher radii of gyration, suggesting improved miscibility. These findings provide a possible microscopic explanation for the cosolvency phenomenon in polymer systems. Theoretical Importance: This research contributes to a better understanding of the behavior of thermo-responsive polymers and the role of cosolvency. The findings provide insights into the molecular mechanisms underlying cosolvency and offer specific predictions for future experimental investigations. The study also presents a more rigorous analysis of the Flory-Huggins free energy theory in the context of polymer systems. Data Collection and Analysis Procedures: The data for this study was collected through Monte Carlo computer simulations and molecular dynamic simulations. The interactions between the polymer, solvent, and cosolvent were analyzed using the Flory-Huggins mean field theory. Machine learning techniques were employed to enhance the accuracy of the simulations. The collected data was then analyzed to determine the impact of cosolvent volume fractions on the radii of gyration of the polymer. Question Addressed: The research addressed the question of how cosolvency affects the behavior of long-chain polymers. Specifically, the study aimed to investigate the interactions between the polymer, solvent, and cosolvent under different volume fractions and understand the resulting changes in the radii of gyration. Conclusion: In conclusion, this study utilized theoretical modeling and computer simulations to investigate the phenomenon of cosolvency in long-chain polymers. The findings suggest that moderate cosolvent volume fractions can lead to improved miscibility, as indicated by higher radii of gyration. These insights contribute to a better understanding of the molecular mechanisms underlying cosolvency in polymer systems and provide predictions for future experimental studies. The research also enhances the theoretical analysis of the Flory-Huggins free energy theory.

Keywords: molecular modelling, flory-huggins, cosolvency, stimuli-responsive polymers

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Authors: Mohanad Moustafa, Julia Sieberer, Rhys Davies

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Background: Orbital compartment syndrome (OCS) is a sight-threatening Ophthalmologic emergency caused by rapidly increasing intraorbital pressure. It is usually caused by a retrobulbar hemorrhage as a result of trauma. If not treated in a timely manner, permanent vision loss can occur. Lateral canthotomy and cantholysis are minor procedures that can be performed bedside with equipment available in the emergency department. The aim of the procedure is to release the attachments between the suspensory ligaments of the eye and the bony orbital wall, leading to a decrease in intraorbital pressure and preventing irreversible loss of vision. As most Ophthalmologists across the UK provide non-resident on-call service, this may lead to a delay in the treatment of OCS and stresses the need for Emergency medical staff to be able to provide this sight-saving procedure independently. Aim: To survey current training, experience, and confidence levels among Emergency Medicine doctors in performing emergency lateral canthotomy and to establish whether these variables change the following teaching from experienced ophthalmologists. RESULTS: Most EM registrars had little to no experience in performing lateral canthotomy and cantholysis. The majority of them showed a significant increase in their confidence to perform the procedure following ophthalmic-led teaching. The survey also showed that the registrars felt such training should be added to/part of the EM curriculum. Conclusion: The involvement of Ophthalmologists in the teaching of EM doctors to recognise and treat OCS independently may prevent delays in treatment and reduce the risk of permanent sight loss. This project showed potential in improving patient care and will lead to a National Survey of EM doctors across the UK.

Keywords: lateral canthotomy, retrobulbar hemorrhage, Ophthalmology, orbital compartment syndrome, sight loss, blindness

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Authors: Sunatda Arayachukiat, Shogo Nobukawa, Masayuki Yamaguchi

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A new self-healing material was developed utilizing molecular entanglements for poly(vinyl butyral) (PVB) containing plasticizers. It was found that PVB shows autonomic self-healing behavior even below the glass transition temperature Tg because of marked molecular motion at surface. Moreover, the plasticizer addition enhances the chain mobility, leading to good healing behavior.

Keywords: Poly(vinyl butyral) (PVB), rheological properties, self-healing behaviour, molecular diffusion

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Authors: Giulia Sarego, Lorenzo Olivieri, Andrea Valmorbida, Carlo Bettanini, Giacomo Colombatti, Marco Pertile, Enrico C. Lorenzini

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International guidelines recommend removing any artificial body in Low Earth Orbit (LEO) within 25 years from mission completion. Among disposal strategies, electrodynamic tethers appear to be a promising option for LEO, thanks to the limited storage mass and the minimum interface requirements to the host spacecraft. In particular, recent technological advances make it feasible to deorbit large objects with tether lengths of a few kilometers or less. To further investigate such an innovative passive system, the European Union is currently funding the project E.T.PACK – Electrodynamic Tether Technology for Passive Consumable-less Deorbit Kit in the framework of the H2020 Future Emerging Technologies (FET) Open program. The project focuses on the design of an end of life disposal kit for LEO satellites. This kit aims to deploy a taped tether that can be activated at the spacecraft end of life to perform autonomous deorbit within the international guidelines. In this paper, the orbital performance of the E.T.PACK deorbiting kit is compared to other disposal methods. Besides, the orbital decay prediction is parametrized as a function of spacecraft mass and tether system performance. Different values of length, width, and thickness of the tether will be evaluated for various scenarios (i.e., different initial orbital parameters). The results will be compared to other end-of-life disposal methods with similar allocated resources. The analysis of the more innovative system’s performance with the tape coated with a thermionic material, which has a low work-function (LWT), for which no active component for the cathode is required, will also be briefly discussed. The results show that the electrodynamic tether option can be a competitive and performant solution for satellite disposal compared to other deorbit technologies.

Keywords: deorbiting performance, H2020, spacecraft disposal, space electrodynamic tethers

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Authors: Rajandeep Kaur, Rajeev Gupta

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Background: Chronic myeloid leukemia (CML) is the most common leukaemia in India. The annual incidence of chronic myeloid leukemia in India was originally reported to be 0.8 to 2.2 per 1,00,000 population. CML is a clonal disorder that is usually easily diagnosed because the leukemic cells of more than 95% of patients have a distinctive cytogenetic abnormality, the Philadelphia chromosome (Ph1). The approval of tyrosine kinase inhibitors (TKIs), which target BCR-ABL1 kinase activity, has significantly reduced the mortality rate associated with chronic myeloid leukemia (CML) and revolutionized treatment. Material and Methods: 80 diagnosed cases of CML were taken. Investigations were done. Bone marrow and molecular studies were also done and with EUTOS, patients were stratified into low and high-risk groups and then treatment with Imatinib was given to all patients and the molecular response was evaluated at 6 months and 12 months follow up with BCR-ABL by RT-PCR quantitative assay. Results: In the study population, out of 80 patients in the study population, 40 were females and 40 were males, with M: F is 1:1. Out of total 80 patients’ maximum patients (54) were in 31-60 years age group. Our study showed a most common symptom of presentation is abdominal discomfort followed by fever. Out of the total 80 patients, 25 (31.3%) patients had high EUTOS scores and 55 (68.8%) patients had low EUTOS scores. On 6 months follow up 36.3% of patients had Complete Molecular Response, 16.3% of patients had Major Molecular Response and 47.5% of patients had No Molecular Response but on 12 months follow up 71.3% of patients had Complete Molecular Response, 16.25% of patients had Major Molecular Response and 12.5% patients had No Molecular Response. Conclusion: In this study, we found a significant correlation between EUTOS score and Molecular response at 6 months and 12 months follow up after Imatinib therapy.

Keywords: chronic myeloid leukemia, European treatment and outcome study score, hematological response, molecular response, tyrosine kinase inhibitor

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Authors: Mahsa Fathollahzadeh

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The quick advancement of nanotechnology necessitates the creation of innovative theoretical approaches to elucidate complex experimental findings and forecast novel capabilities of nanodevices. Therefore, over the past ten years, a difficult task in quantum chemistry has been comprehending electron and spin transport in molecular devices. This thorough evaluation presents a comprehensive overview of current research and its status in the field of molecular electronics, emphasizing the theoretical applications to various device types and including a brief introduction to theoretical methods and their practical implementation plan. The subject matter includes a variety of molecular mechanisms like molecular cables, diodes, transistors, electrical and visual switches, nano detectors, magnetic valve gadgets, inverse electrical resistance gadgets, and electron tunneling exploration. The text discusses both the constraints of the method presented and the potential strategies to address them, with a total of 183 references.

Keywords: chemistry, nanotechnology, quantum, molecule, spin

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Authors: Mohammad Ahmadi

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Argumentative writing is a highly opinion-based form of discourse that necessitates the ability to address commonly held opinions (endoxa). To enhance the development of persuasive, argumentative essays, the incorporation of classical rhetorical theory, with a specific focus on topics related to the canon of Invention (inventio), can be advantageous. This research investigates the practical application of rhetorical theory in teaching students how to construct compelling argumentative essays. The fundamental premise of this study is the limited familiarity of rhetoric and composition students with rhetorical theory. Consequently, this paper presents an effective pedagogical approach to introduce rhetorical theory to students, beginning from a foundational level. It delineates the procedures and progression that educators should adopt to elucidate and facilitate students' comprehension of rhetorical theory while demonstrating its utilization in the writing of an argumentative essay.

Keywords: argumentative essay, rhetorical theory, pedagogy, invention

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Authors: Sanja O. Podunavac-Kuzmanović, Lidija R. Jevrić, Strahinja Z. Kovačević

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Benzimidazoles are a group of compounds with significant antibacterial, antifungal and anticancer activity. The studied compounds consist of the main benzimidazole structure with different combinations of substituens. This study is based on the two-dimensional and three-dimensional molecular modeling and calculation of molecular descriptors (physicochemical and lipophilicity descriptors) of structurally diverse benzimidazoles. Molecular modeling was carried out by using ChemBio3D Ultra version 14.0 software. The obtained 3D models were subjected to energy minimization using molecular mechanics force field method (MM2). The cutoff for structure optimization was set at a gradient of 0.1 kcal/Åmol. The obtained set of molecular descriptors was used in principal component analysis (PCA) of possible similarities and dissimilarities among the studied derivatives. After the molecular modeling, the quantitative structure-property relationship (QSPR) analysis was applied in order to get the mathematical models which can be used in prediction of pKb values of structurally similar benzimidazoles. The obtained models are based on statistically valid multiple linear regression (MLR) equations. The calculated cross-validation parameters indicate the high prediction ability of the established QSPR models. This study is financially supported by COST action CM1306 and the project No. 114-451-347/2015-02, financially supported by the Provincial Secretariat for Science and Technological Development of Vojvodina.

Keywords: benzimidazoles, chemometrics, molecular modeling, molecular descriptors, QSPR

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Authors: Jannes Quer, Amir Niknejad, Marcus Weber

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Computational Drug Design is often based on Molecular Dynamics simulations of molecular systems. Molecular Dynamics can be used to simulate, e.g., the binding and unbinding event of a small drug-like molecule with regard to the active site of an enzyme or a receptor. However, the time-scale of the overall binding event is many orders of magnitude longer than the time-scale of simulation. Thus, there is a need to speed-up molecular simulations. In order to speed up simulations, the molecular dynamics trajectories have to be ”steared” out of local minimizers of the potential energy surface – the so-called metastabilities – of the molecular system. Increasing the kinetic energy (temperature) is one possibility to accelerate simulated processes. However, with temperature the entropy of the molecular system increases, too. But this kind ”stearing” is not directed enough to stear the molecule out of the minimum toward the saddle point. In this article, we give a new mathematical idea, how a potential energy surface can be changed in such a way, that entropy is kept under control while the trajectories are still steared out of the metastabilities. In order to compute the unsteared transition behaviour based on a steared simulation, we propose to use extrapolation methods. In the end we mathematically show, that our method accelerates the simulations along the direction, in which the curvature of the potential energy surface changes the most, i.e., from local minimizers towards saddle points.

Keywords: extrapolation, Eyring-Kramers, metastability, multilevel sampling

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Authors: A. Azari, S. S. K. Seyyedi

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One of the unaddressed and open challenges in the nano-networking is the characteristics of noise. The previous analysis, however, has concentrated on end-to-end communication model with no separate modelings for propagation channel and noise. By considering a separate signal propagation and noise model, the design and implementation of an optimum receiver will be much easier. In this paper, we justify consideration of a separate additive Gaussian noise model of a nano-communication system based on the molecular communication channel for which are applicable for MSK and MOSK modulation schemes. The presented noise analysis is based on the Brownian motion process, and advection molecular statistics, where the received random signal has a probability density function whose mean is equal to the mean number of the received molecules. Finally, the justification of received signal magnitude being uncorrelated with additive non-stationary white noise is provided.

Keywords: molecular, noise, diffusion, channel

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Authors: M. Shoukath Ali, Rajendra Prasad Singh

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Game Theory approaches and their application in improving the performance of Wireless Sensor Networks (WSNs) are discussed in this paper. The mathematical modeling and analysis of WSNs may have low success rate due to the complexity of topology, modeling, link quality, etc. However, Game Theory is a field, which can efficiently use to analyze the WSNs. Game Theory is related to applied mathematics that describes and analyzes interactive decision situations. Game theory has the ability to model independent, individual decision makers whose actions affect the surrounding decision makers. The outcome of complex interactions among rational entities can be predicted by a set of analytical tools. However, the rationality demands a stringent observance to a strategy based on measured of perceived results. Researchers are adopting game theory approaches to model and analyze leading wireless communication networking issues, which includes QoS, power control, resource sharing, etc.

Keywords: wireless sensor network, game theory, cooperative game theory, non-cooperative game theory

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Authors: Paweł Stączek, Tomasz Plech, Aleksandra Strzelczyk, Katarzyna Dzitko, Monika Wujec, Edyta Kuśmierz, Piotr Paneth, Agata Paneth

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In this contribution, we will describe the inhibitory potency of nine thiosemicarbazide derivatives against bacterial type IIA topoisomerases, their antibacterial profile, and molecular modeling evaluation. We have found that one of the tested compounds, 4-benzoyl-1-(2-methyl-furan-3-ylcarbonyl) thiosemicarbazide, remarkably inhibits the activity of S. aureus DNA gyrase with the IC50 below 5 μM. Besides, this compound displays antibacterial activity on Staphylococcus spp. and E. faecalis at non-cytotoxic concentrations in mammalian cells, with minimal inhibitory concentrations (MICs) values at 25 μg/mL. Based on the enzymatic and molecular modeling studies we propose two factors, i.e. geometry of molecule and hydrophobic/hydrophilic balance as important molecular properties for developing thiosemicarbazide derivatives as potent Staphylococcus aureus DNA gyrase inhibitors.

Keywords: bioactivity, drug design, topoisomerase, molecular modeling

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Authors: B. Roopa Sri, Y Lakshmi Naidu

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Chemical Graph Theory (CGT) is the branch of mathematical chemistry in which molecules are modeled to study their physicochemical properties using molecular descriptors. Amongst these descriptors, topological indices play a vital role in predicting the properties by defining the graph topology of the molecule. Recently, the bond-additive topological index known as the Mostar index has been proposed. In this paper, we compute the Mostar-type indices of octane isomers and use the data obtained to perform QSPR analysis. Furthermore, we show the correlation between the Mostar type indices and the properties.

Keywords: chemical graph theory, mostar type indices, octane isomers, qspr analysis, topological index

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Authors: Amir Deljoo

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The endeavor to comprehend the existence have been the center of thought for human in form of different disciplines and now basically in physics as the theory of everything. Here, after a brief review of the basic frameworks of thought, and a history of thought since ancient up to present, a logical methodology is presented based on a core axiom after which a function, a proto-field and then a coordinates are explained. Afterwards a generalization to Standard Model is proposed as General Standard Model which is believed to be the base of the Unified Theory of Everything.

Keywords: general relativity, grand unified theory, quantum mechanics, standard model, theory of everything

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Authors: Hai Hoang, Thanh Xuan Nguyen Thi, Guillaume Galliero

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Coarse-Grained (CG) molecular simulations have shown to be an efficient way to estimate thermophysical (static and dynamic) properties of fluids. Several strategies have been developed and reported in the literature for defining CG molecular models. Among them, those based on a top-down strategy (i.e. CG molecular models related to macroscopic observables), despite being heuristic, have increasingly gained attention. This is probably due to its simplicity in implementation and its ability to provide reasonable results for not only simple but also complex systems. Regarding simple Force-Fields associated with these CG molecular models, it has been found that the four parameters Mie chain model is one of the best compromises to describe thermophysical static properties (e.g. phase diagram, saturation pressure). However, parameterization procedures of these Mie-chain GC molecular models given in literature are generally insufficient to simultaneously provide static and dynamic (e.g. viscosity) properties. To deal with such situations, we have extended the corresponding states by using a quantity associated with the liquid viscosity. Results obtained from molecular simulations have shown that our approach is able to yield good estimates for both static and dynamic thermophysical properties for various real non-associating fluids. In addition, we will show that on simple (e.g. phase diagram, saturation pressure) and complex (e.g. thermodynamic response functions, thermodynamic energy potentials) static properties, results of our scheme generally provides improved results compared to existing approaches.

Keywords: coarse-grained model, mie potential, molecular simulations, thermophysical properties, phase equilibria

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Authors: Amr Abdel Azim Ali, G. A. Elsheikh, Moutaz Hegazy

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This paper presents verification of a modeling and simulation for a Spacecraft (SC) attitude and orbit control system. Detailed formulation of coupled SC orbital and attitude equations of motion is performed in order to achieve accepted accuracy to meet the requirements of multitargets tracking and orbit correction complex modes. Correction of the target parameter based on the estimated state vector during shooting time to enhance pointing accuracy is considered. Time-optimal nonlinear feedback control technique was used in order to take full advantage of the maximum torques that the controller can deliver. This simulation provides options for visualizing SC trajectory and attitude in a 3D environment by including an interface with V-Realm Builder and VR Sink in Simulink/MATLAB. Verification data confirms the simulation results, ensuring that the model and the proposed control law can be used successfully for large and fast tracking and is robust enough to keep the pointing accuracy within the desired limits with considerable uncertainty in inertia and control torque.

Keywords: attitude and orbit control, time-optimal nonlinear feedback control, modeling and simulation, pointing accuracy, maximum torques

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Authors: Brian J. Graham, Ronald T. Raines

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The presence of a nearly vacant p orbital on boron endows boronic acids with unique abilities as a catalyst and ligand. An organocatalytic process has been developed for the conversion of biomass-derived sugars to 5-hydroxymethylfurfural, which is a platform chemical. Specifically, 2-carboxyphenylboronic acid (2-CPBA) has been shown to be an optimal catalyst for this process, promoting the desired transformation in the absence of metals. The attributes of 2-CPBA as a catalyst led to additional investigations of its structure and reactivity. 2-CPBA was found to exist as a cyclized benzoxaborolone adduct rather than a free carboxylic acid. This cyclization has profound consequences for the oxidative stability of the boronic acid. Stereoelectronic effects within the oxaborolone ring destabilize the oxidation transition state by reducing electron donation from the cyclic oxygen to the developing p orbital on boron. That leads to a 10,000-fold increase in oxidative stability while maintaining the normal reactivity of boronic acids toward diols (e.g., carbohydrates) and nucleophiles in proteins while also presenting numerous hydrogen-bond accepting and donating groups. Thus, benzoxaborolones are useful in catalysis, chemical biology, medicinal chemistry, and allied fields.

Keywords: bioisosteres, boronic acid, catalysis, oxidative stability, pharmacophore, stereoelectronic effects

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Authors: Mahdiyeh Gholaminezhad

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Context: The study focuses on the potential impact of Sorafenib on SOAT1 protein in liver cancer treatment, addressing the need for more effective therapeutic options. Research aim: To explore the effects of Sorafenib on the activity of SOAT1 protein in liver cancer cells. Methodology: Molecular docking was employed to analyze the interaction between Sorafenib and SOAT1 protein. Findings: The study revealed a significant effect of Sorafenib on the stability and activity of SOAT1 protein, suggesting its potential as a treatment for liver cancer. Theoretical importance: This research highlights the molecular mechanism underlying Sorafenib's anti-cancer properties, contributing to the understanding of its therapeutic effects. Data collection: Data on the molecular structure of Sorafenib and SOAT1 protein were obtained from computational simulations and databases. Analysis procedures: Molecular docking simulations were performed to predict the binding interactions between Sorafenib and SOAT1 protein. Question addressed: How does Sorafenib influence the activity of SOAT1 protein and what are the implications for liver cancer treatment? Conclusion: The study demonstrates the potential of Sorafenib as a targeted therapy for liver cancer by affecting the activity of SOAT1 protein. Reviewers' Comments: The study provides valuable insights into the molecular basis of Sorafenib's action on SOAT1 protein, suggesting its therapeutic potential. To enhance the methodology, the authors could consider validating the docking results with experimental data for further validation.

Keywords: liver cancer, sorafenib, SOAT1, molecular docking

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Authors: Martin Juckel

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Probably no other field of inorganic chemistry has undergone such a rapid development in the past two decades than the low oxidation state chemistry of main group elements. This rapid development has only been possible by the development of new bulky ligands. In case of our research group, super-bulky monodentate amido ligands and β-diketiminate ligands have been used to a great success. We first synthesized the unprecedented magnesium(I) dimer [ᴹᵉˢNacnacMg]₂ (ᴹᵉˢNacnac = [(ᴹᵉˢNCMe)₂CH]-; Mes = mesityl, which has since been used both as reducing agent and also for the synthesis of new metal-magnesium bonds. In case of the zinc bromide precursor [L*ZnBr] (L*=(N(Ar*)(SiPri₃); (Ar* = C₆H₂{C(H)Ph₂}₂Me-2,6,4, the reduction with [ᴹᵉˢNacnacMg]₂ led to such a metal-magnesium bond. This [L*ZnMg(ᴹᵉˢNacnac)] compound can be seen as an ‘inorganic Grignard reagent’, which can be used to transfer the metal fragment onto other functional groups or other metal centers; just like the conventional Grignard reagent. By simple addition of (TBoN)GeCl (TBoN = N(SiMe₃){B(DipNCH)₂) to the aforesaid compound, we were able to transfer the amido-zinc fragment to the Ge center of the germylene starting material and to synthesize the first example of a germanium(II)-zinc bond: [:Ge(TBoN)(ZnL*)]. While these reactions typically led to complex product mixture, [:Ge(TBoN)(ZnL*)] could be isolated as dark blue crystals in a good yield. This new compound shows interesting reactivity towards small molecules, especially dihydrogen gas. This is of special interest as dihydrogen is one of the more difficult small molecules to activate, due to its strong (BDE = 108 kcal/mol) and non-polar bond. In this context, the interaction between H₂ σ-bond with the tetrelylene p-Orbital (LUMO), with concomitant donation of the tetrelylene lone pair (HOMO) into the H₂ σ* orbital are responsible for the activation of dihydrogen gas. Accordingly, the narrower the HOMO-LUMO gap of tertelylene, the more reactivity towards H₂ it typically is. The aim of a narrow HOMO-LUMO gap was reached by transferring electropositive substituents respectively metal substituents with relatively low Pauling electronegativity (zinc: 1.65) onto the Ge center (here: the zinc-amido fragment). In consideration of the unprecedented reactivity of [:Ge(TBoN)(ZnL*)], a computational examination of its frontier orbital energies was undertaken. The energy separation between the HOMO, which has significant Ge lone pair character, and the LUMO, which has predominantly Ge p-orbital character, is narrow (40.8 kcal/mol; cf.∆S-T= 24.8 kcal/mol), and comparable to the HOMO-LUMO gaps calculated for other literature known complexes). The calculated very narrow HOMO-LUMO gap for the [:Ge(TBoN)(ZnL*)] complex is consistent with its high reactivity, and is remarkable considering that it incorporates a π-basic amide ligand, which are known to raise the LUMO of germylenes considerably.

Keywords: activation of dihydrogen gas, narrow HOMO-LUMO gap, first germanium(II)-zinc bond, inorganic Grignard reagent

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Authors: Archana Gupta, Rajesh Kumar

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The chemistry of chalcones has generated intensive scientific studies throughout the world. Especially, interest has been focused on the synthesis and biodynamic activities of chalcones. The blue light transmittance, excellent crystallizability and the two planar rings connected through a conjugated double bond show that chalcone derivatives are superior nonlinear organic compounds. 3-(2-Chloro-6-fluoro¬phen¬yl)-1-(2-thien¬yl) prop-2-en-1-one, 3-(2, 4- Dichlorophenyl) – 1 - (4-methylphenyl) – prop -2-en-1-one, (2E)-3-[4-(methylsulfanyl) phenyl]-1-(4-nitrophenyl) prop-2-en-1-one are some chalcone derivatives exhibiting non linear optical (NLO) properties. NLO materials have been extensively investigated in recent years as they are the key elements for photonic technologies of optical communication, optical interconnect oscillator, amplifier, frequency converter etc. Due to their high molecular hyperpolarizabilities, organic materials display a number of significant NLO properties. Experimental measurements and theoretical calculations on molecular hyperpolarizability β have become one of the key factors in the design of second order NLO materials. Theoretical determination of hyperpolarizability is quite useful both in understanding the relationship between the molecular structure and NLO properties. It also provides a guideline to experimentalists for the design and synthesis of organic NLO materials. Quantum-chemical calculations have made an important contribution to the understanding of the electronic polarization underlying the molecular NLO processes and the establishment of structure–property relationships. In the present investigation, the detailed vibrational analysis of some chalcone derivatives is taken up to understand the correlation of the charge transfer interaction and the NLO activity of the molecules based on density functional theory calculations. The vibrational modes contributing toward the NLO activity have been identified and analyzed. Rather large hyperpolarizability derived by theoretical calculations suggests the possible future use of these compounds for non-linear optical applications. The study suggests the importance of π - conjugated systems for non-linear optical properties and the possibility of charge transfer interactions. We hope that the results of the present study of chalcone derivatives are of assistance in development of new efficient materials for technological applications.

Keywords: hyperpolarizability, molecular structure, NLO material, quantum chemical calculations

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Authors: S. Chandrasekaran, S. Nandita, M. Shivathmika, Srikrishnan Shivakumar

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The objective of the research work is to analyze the computational chemical-composition of carbohydrates in the context of healthcare informatics. The computation involves the representation of complex chemical molecular structure of carbohydrate using graph theory and in a deployable Chemical Markup Language (CML). The parallel molecular structure of the chemical molecules with or without other adulterants for the sake of business profit can be analyzed in terms of robustness and derivatization measures. The rural healthcare program should create awareness in malnutrition to reduce ill-effect of decomposition and help the consumers to know the level of such energy storage mixtures in a quantitative way. The earlier works were based on the empirical and wet data which can vary from time to time but cannot be made to reuse the results of mining. The work is carried out on the quantitative computational chemistry on carbohydrates to provide a safe and secure right to food act and its regulations.

Keywords: carbohydrates, chemical-composition, chemical markup, robustness, food safety

Procedia PDF Downloads 374