Journal articles: 'Industrial Chemistry - Computational Study - Molecules and Processes'

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Oyewola, David Opeoluwa, Emmanuel Gbenga Dada, Onyeka Emebo, and Olugbenga Oluseun Oluwagbemi. "Using Deep 1D Convolutional Grated Recurrent Unit Neural Network to Optimize Quantum Molecular Properties and Predict Intramolecular Coupling Constants of Molecules of Potential Health Medications and Other Generic Molecules." Applied Sciences 12, no. 14 (July 18, 2022): 7228. http://dx.doi.org/10.3390/app12147228.

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A molecule is the smallest particle in a chemical element or compound that possesses the element or compound’s chemical characteristics. There are numerous challenges associated with the development of molecular simulations of fluid characteristics for industrial purposes. Fluid characteristics for industrial purposes find applications in the development of various liquid household products, such as liquid detergents, drinks, beverages, and liquid health medications, amongst others. Predicting the molecular properties of liquid pharmaceuticals or therapies to address health concerns is one of the greatest difficulties in drug development. Computational tools for precise prediction can help speed up and lower the cost of identifying new medications. A one-dimensional deep convolutional gated recurrent neural network (1D-CNN-GRU) was used in this study to offer a novel forecasting model for molecular property prediction of liquids or fluids. The signal data from molecular properties were pre-processed and normalized. A 1D convolutional neural network (1D-CNN) was then built to extract the characteristics of the normalized molecular property of the sequence data. Furthermore, gated recurrent unit (GRU) layers processed the extracted features to extract temporal features. The output features were then passed through several fully-connected layers for final prediction. For both training and validation, we used molecular properties obtained from the Kaggle database. The proposed method achieved a better prediction accuracy, with values of 0.0230, 0.1517, and 0.0693, respectively, in terms of the mean squared error (MSE), root mean square error (RMSE), and mean absolute error (MAE).

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Lanero, Francesco, Bianca Maria Bresolin, Anna Scettri, Marco Nogarole, Elisabetta Schievano, Stefano Mammi, Giacomo Saielli, et al. "Activation of Vegetable Oils by Reaction with Maleic Anhydride as a Renewable Source in Chemical Processes: New Experimental and Computational NMR Evidence." Molecules 27, no. 23 (November 23, 2022): 8142. http://dx.doi.org/10.3390/molecules27238142.

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Vegetable oils are bio−based and sustainable starting materials that can be used to develop chemicals for industrial processes. In this study, the functionalization of three vegetable oils (grape, hemp, and linseed) with maleic anhydride was carried out either by conventional heating or microwave activation to obtain products that, after further reactions, can enhance the water dispersion of oils for industrial applications. To identify the most abundant derivatives formed, trans-3-octene, methyl oleate, and ethyl linoleate were reacted as reference systems. A detailed NMR study, supported by computational evidence, allowed for the identification of the species formed in the reaction of trans-3-octene with maleic anhydride. The signals in the 1H NMR spectra of the alkenyl succinic anhydride (ASA) moieties bound to the organic chains were clearly identified. The reactions achieved by conventional heating were carried out for 5 h at 200 °C, resulting in similar or lower amounts of ASA units/g of oil with respect to the reactions performed by microwave activation, which, however, induced a higher viscosity of the samples.

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Ang, Dale L., Mubasher Zahir Hoque, Md Abir Hossain, Gea Guerriero, Roberto Berni, Jean-Francois Hausman, Saleem A. Bokhari, Wallace J. Bridge, and Khawar Sohail Siddiqui. "Computational Analysis of Thermal Adaptation in Extremophilic Chitinases: The Achilles’ Heel in Protein Structure and Industrial Utilization." Molecules 26, no. 3 (January 29, 2021): 707. http://dx.doi.org/10.3390/molecules26030707.

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Understanding protein stability is critical for the application of enzymes in biotechnological processes. The structural basis for the stability of thermally adapted chitinases has not yet been examined. In this study, the amino acid sequences and X-ray structures of psychrophilic, mesophilic, and hyperthermophilic chitinases were analyzed using computational and molecular dynamics (MD) simulation methods. From the findings, the key features associated with higher stability in mesophilic and thermophilic chitinases were fewer and/or shorter loops, oligomerization, and less flexible surface regions. No consistent trends were observed between stability and amino acid composition, structural features, or electrostatic interactions. Instead, unique elements affecting stability were identified in different chitinases. Notably, hyperthermostable chitinase had a much shorter surface loop compared to psychrophilic and mesophilic homologs, implying that the extended floppy surface region in cold-adapted and mesophilic chitinases may have acted as a “weak link” from where unfolding was initiated. MD simulations confirmed that the prevalence and flexibility of the loops adjacent to the active site were greater in low-temperature-adapted chitinases and may have led to the occlusion of the active site at higher temperatures compared to their thermostable homologs. Following this, loop “hot spots” for stabilizing and destabilizing mutations were also identified. This information is not only useful for the elucidation of the structure–stability relationship, but will be crucial for designing and engineering chitinases to have enhanced thermoactivity and to withstand harsh industrial processing conditions

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Cruz, Guillermo, Javier Acosta, Jose Miguel Mancheño, Jon Del Arco, and Jesús Fernández-Lucas. "Rational Design of a Thermostable 2′-Deoxyribosyltransferase for Nelarabine Production by Prediction of Disulfide Bond Engineering Sites." International Journal of Molecular Sciences 23, no. 19 (October 5, 2022): 11806. http://dx.doi.org/10.3390/ijms231911806.

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One of the major drawbacks of the industrial implementation of enzymatic processes is the low operational stability of the enzymes under tough industrial conditions. In this respect, the use of thermostable enzymes in the industry is gaining ground during the last decades. Herein, we report a structure-guided approach for the development of novel and thermostable 2′-deoxyribosyltransferases (NDTs) based on the computational design of disulfide bonds on hot spot positions. To this end, a small library of NDT variants from Lactobacillus delbrueckii (LdNDT) with introduced cysteine pairs was created. Among them, LdNDTS104C (100% retained activity) was chosen as the most thermostable variant, displaying a six- and two-fold enhanced long-term stability when stored at 55 °C (t1/255 °C ≈ 24 h) and 60 °C (t1/260 °C ≈ 4 h), respectively. Moreover, the biochemical characterization revealed that LdNDTS104C showed >60% relative activity across a broad range of temperature (30–90 °C) and pH (5–7). Finally, to study the potential application of LdNDTS104C as an industrial catalyst, the enzymatic synthesis of nelarabine was successfully carried out under different substrate conditions (1:1 and 3:1) at different reaction times. Under these experimental conditions, the production of nelarabine was increased up to 2.8-fold (72% conversion) compared with wild-type LdNDT.

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Pilon, Alan Cesar, Marcelo Del Grande, Maíra R. S. Silvério, Ricardo R. Silva, Lorena C. Albernaz, Paulo Cézar Vieira, João Luis Callegari Lopes, Laila S. Espindola, and Norberto Peporine Lopes. "Combination of GC-MS Molecular Networking and Larvicidal Effect against Aedes aegypti for the Discovery of Bioactive Substances in Commercial Essential Oils." Molecules 27, no. 5 (February 28, 2022): 1588. http://dx.doi.org/10.3390/molecules27051588.

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Dengue is a neglected disease, present mainly in tropical countries, with more than 5.2 million cases reported in 2019. Vector control remains the most effective protective measure against dengue and other arboviruses. Synthetic insecticides based on organophosphates, pyrethroids, carbamates, neonicotinoids and oxadiazines are unattractive due to their high degree of toxicity to humans, animals and the environment. Conversely, natural-product-based larvicides/insecticides, such as essential oils, present high efficiency, low environmental toxicity and can be easily scaled up for industrial processes. However, essential oils are highly complex and require modern analytical and computational approaches to streamline the identification of bioactive substances. This study combined the GC-MS spectral similarity network approach with larvicidal assays as a new strategy for the discovery of potential bioactive substances in complex biological samples, enabling the systematic and simultaneous annotation of substances in 20 essential oils through LC50 larvicidal assays. This strategy allowed rapid intuitive discovery of distribution patterns between families and metabolic classes in clusters, and the prediction of larvicidal properties of acyclic monoterpene derivatives, including citral, neral, citronellal and citronellol, and their acetate forms (LC50 < 50 µg/mL).

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Toghan, Arafat, Ahmed Fawzy, Areej Al Bahir, Nada Alqarni, Moustafa M. S. Sanad, Mohamed Khairy, Abbas I. Alakhras, and Ahmed A. Farag. "Computational Foretelling and Experimental Implementation of the Performance of Polyacrylic Acid and Polyacrylamide Polymers as Eco-Friendly Corrosion Inhibitors for Copper in Nitric Acid." Polymers 14, no. 22 (November 8, 2022): 4802. http://dx.doi.org/10.3390/polym14224802.

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Copper is primarily used in many industrial processes, but like many other metals, it suffers from corrosion damage. Polymers are not only one of the effective corrosion inhibitors but also are environmentally friendly agents in doing so. Hence, in this paper, the efficacy of two polyelectrolyte polymers, namely poly(acrylic acid) (PAA) and polyacrylamide (PAM), as corrosion inhibitors for copper in molar nitric acid medium was explored. Chemical, electrochemical, and microscopic tools were employed in this investigation. The weight-loss study revealed that the computed inhibition efficiencies (% IEs) of both PAA and PAM increased with their concentrations but diminished with increasing HNO3 concentration and temperature. The results revealed that, at similar concentrations, the values of % IEs of PAM are slightly higher than those recorded for PAA, where these values at 298 K reached 88% and 84% in the presence of a 250 mg/L of PAM and PAA, respectively. The prominent IE% values for the tested polymers are due to their strong adsorption on the Cu surface and follow the Langmuir adsorption isoform. Thermodynamic and kinetic parameters were also calculated and discussed. The kinetics of corrosion inhibition by PAA and PAM showed a negative first-order process. The results showed also that the used polymers played as mixed-kind inhibitors with anodic priority. The mechanisms of copper corrosion in nitric acid medium and its inhibition by the tested polymers were discussed. DFT calculations and molecular dynamic (MD) modelling were used to investigate the effect of PAA and PAM molecular configuration on their anti-corrosion behavior. The results indicated that the experimental and computational study are highly consistent.

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Villalba-Diez, Javier, and Xiaochen Zheng. "Quantum Strategic Organizational Design: Alignment in Industry 4.0 Complex-Networked Cyber-Physical Lean Management Systems." Sensors 20, no. 20 (October 16, 2020): 5856. http://dx.doi.org/10.3390/s20205856.

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The strategic design of organizations in an environment where complexity is constantly increasing, as in the cyber-physical systems typical of Industry 4.0, is a process full of uncertainties. Leaders are forced to make decisions that affect other organizational units without being sure that their decisions are the right ones. Previously to this work, genetic algorithms were able to calculate the state of alignment of industrial processes that were measured through certain key performance indicators (KPIs) to ensure that the leaders of the Industry 4.0 make decisions that are aligned with the strategic objectives of the organization. However, the computational cost of these algorithms increases exponentially with the number of KPIs. That is why this work makes use of the principles of quantum computing to present the strategic design of organizations from a novel point of view: Quantum Strategic Organizational Design (QSOD). The effectiveness of the application of these principles is shown with a real case study, in which the computing time is reduced from hundreds of hours to seconds. This has very powerful practical applications for industry leaders, since, with this new approach, they can potentially allow a better understanding of the complex processes underlying the strategic design of organizations and, above all, make decisions in real-time.

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Hu, Youxi, Chao Liu, Ming Zhang, Yu Jia, and Yuchun Xu. "A Novel Simulated Annealing-Based Hyper-Heuristic Algorithm for Stochastic Parallel Disassembly Line Balancing in Smart Remanufacturing." Sensors 23, no. 3 (February 2, 2023): 1652. http://dx.doi.org/10.3390/s23031652.

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Remanufacturing prolongs the life cycle and increases the residual value of various end-of-life (EoL) products. As an inevitable process in remanufacturing, disassembly plays an essential role in retrieving the high-value and useable components of EoL products. To disassemble massive quantities and multi-types of EoL products, disassembly lines are introduced to improve the cost-effectiveness and efficiency of the disassembly processes. In this context, disassembly line balancing problem (DLBP) becomes a critical challenge that determines the overall performance of disassembly lines. Currently, the DLBP is mostly studied in straight disassembly lines using single-objective optimization methods, which cannot represent the actual disassembly environment. Therefore, in this paper, we extend the mathematical model of the basic DLBP to stochastic parallel complete disassembly line balancing problem (DLBP-SP). A novel simulated annealing-based hyper-heuristic algorithm (HH) is proposed for multi-objective optimization of the DLBP-SP, considering the number of workstations, working load index, and profits. The feasibility, superiority, stability, and robustness of the proposed HH algorithm are validated through computational experiments, including a set of comparison experiments and a case study of gearboxes disassembly. To the best of our knowledge, this research is the first to introduce gearboxes as a case study in DLBP which enriches the research on disassembly of industrial equipment.

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Andrade, Ana, Kennedy Lopes, Bernardo Lima, and André Maitelli. "Development of a Methodology Using Artificial Neural Network in the Detection and Diagnosis of Faults for Pneumatic Control Valves." Sensors 21, no. 3 (January 27, 2021): 853. http://dx.doi.org/10.3390/s21030853.

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To satisfy the market, competition in the industrial sector aims for productivity and safety in industrial plant control systems. The appearance of a fault can compromise the system’s proper functioning process. Therefore, Fault Detection and Diagnosis (FDD) methods contribute to avoiding any undesired events, as there are techniques and methods that study the detection, isolation, identification and, consequently, fault diagnosis. In this work, a new methodology that uses faults emulation to obtain parameters similar to the Development and Application of Methods for Diagnosis of Actuators in Industrial Control Systems (DAMADICS) benchmark model will be developed. This methodology uses previous information from tests on sensors with and without faults to detect and classify the situation of the plant and, in the presence of faults, perform the diagnosis through a process of elimination in a hierarchical manner. In this way, the definition of residue signature is used as well as the creation of a decision tree. The whole process is carried out incorporating FDD techniques, through the Non-Linear Auto-Regressive Neural Network Model With Exogenous Inputs (NARX), in the diagnosis of the behavioral prediction of the signals to generate the residual values. Then, it is applied to the construction of the decision tree based on the most significant residue of a certain signal, enabling the process of acquisition and formation of the signature matrix. With the procedures in this article, it is possible to demonstrate a practical and systematic method of how to emulate faults for control valves and the possibility of carrying out an analysis of the data to acquire signatures of the fault behavior. Finally, simulations resulting from the most sensitized variables for the production of residuals that is generated by neural networks are presented, which are used to obtain signatures and isolate the flaws. The process proves to be efficient in computational time and makes it easy to present a fault diagnosis strategy that can be reproduced in other processes.

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Marinov, Marin B., Nikolay Nikolov, Slav Dimitrov, Todor Todorov, Yana Stoyanova, and Georgi T. Nikolov. "Linear Interval Approximation for Smart Sensors and IoT Devices." Sensors 22, no. 3 (January 26, 2022): 949. http://dx.doi.org/10.3390/s22030949.

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In this work, we introduce and use an innovative approach for adaptive piecewise linear interval approximation of sensor characteristics, which are differentiable functions. The aim is to obtain a discreet type of inverse sensor characteristic, with a predefined maximum approximation error, with minimization of the number of points defining the characteristic, which in turn is related to the possibilities for using microcontrollers with limited energy and memory resources. In this context, the results from the study indicate that to overcome the problems arising from the resource constraints of smart devices, appropriate “lightweight” algorithms are needed that allow efficient connectivity and intelligent management of the measurement processes. The method has two benefits: first, low-cost microcontrollers could be used for hardware implementation of the industrial sensor devices; second, the optimal subdivision of the measurement range reduces the space in the memory of the microcontroller necessary for storage of the parameters of the linearized characteristic. Although the discussed computational examples are aimed at building adaptive approximations for temperature sensors, the algorithm can easily be extended to many other sensor types and can improve the performance of resource-constrained devices. For prescribed maximum approximation error, the inverse sensor characteristic is found directly in the linearized form. Further advantages of the proposed approach are: (i) the maximum error under linearization of the inverse sensor characteristic at all intervals, except in the general case of the last one, is the same; (ii) the approach allows non-uniform distribution of maximum approximation error, i.e., different maximum approximation errors could be assigned to particular intervals; (iii) the approach allows the application to the general type of differentiable sensor characteristics with piecewise concave/convex properties.

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Yang, Bo, Ni Yang, Dan Zhao, Fengyang Chen, Xingping Yuan, Yanqing Hou, and Gang Xie. "Numerical Simulation of a Simplified Reaction Model for the Growth of Graphene via Chemical Vapor Deposition in Vertical Rotating Disk Reactor." Coatings 13, no. 7 (June 30, 2023): 1184. http://dx.doi.org/10.3390/coatings13071184.

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The process of graphene growth by CVD involves a series of complex gas-phase surface chemical reactions, which generally go through three processes, including gas phase decomposition, surface chemical reaction, and gas phase diffusion. The complexity of the CVD process for growing graphene is that it involves not only chemical reactions but also mass, momentum, and energy transfer. To solve these problems, the method of numerical simulation combined with the reactor structure optimization model provides a good tool for industrial production and theoretical research to explore the influencing factors of the CVD growth of graphene. The objective of this study was to establish a simplified reaction model for the growth of graphene by chemical vapor deposition(CVD) in a vertical rotating disk reactor (VRD). From a macroscopic modeling perspective, computational fluid dynamics (CFD) was used to investigate the conditions for the growth of graphene by chemical vapor deposition in a high-speed rotating vertical disk reactor on a copper substrate surface at atmospheric pressure (101,325 Pa). The effects of gas temperature, air inlet velocity, base rotation speed, and material ratio on the surface deposition rate of graphene in a VRD reactor were studied, and the technological conditions for the preparation of graphene via the CVD method in a VRD reactor based on a special structure were explored. Compared with existing models, the numerical results showed the following: the ideal growth conditions of graphene prepared using a CVD method in a VRD reactor involve a growth temperature of 1310 K, an intake speed of 470 mL/min, a base speed of 300 rpm, and an H2 flow rate of 75 sccm; thus, more uniform graphene with a better surface density and higher quality can be obtained. The effect of the carbon surface deposition rate on the growth behavior of graphene was studied using molecular dynamics (MD) from a microscopic perspective. The simulation showed that the graphene surface deposition rate could control the nucleation density of graphene. The combination of macro- and microsimulation methods was used to provide a theoretical reference for the production of graphene.

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Chesnut, D. B. "Localization function study of excitation processes in a set of small isoelectronic molecules." Journal of Computational Chemistry 22, no. 14 (2001): 1702–11. http://dx.doi.org/10.1002/jcc.1125.

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Budziak, Iwona, Marta Arczewska, and Daniel M. Kamiński. "Structure and Physical Properties of Cardamonin: A Spectroscopic and Computational Approach." Molecules 25, no. 18 (September 6, 2020): 4070. http://dx.doi.org/10.3390/molecules25184070.

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This is the first study of the crystal structure of cardamonin (CA) confirmed using single-crystal XRD analysis. In the crystal lattice of CA, two symmetry independent molecules are linked by hydrogen bonds within the layers and by the π···π stacking interactions in the columns which lead to the occurrence of two types of conformations among the CA molecules in the crystal structure. To better understand the stability of these arrangements in both crystals and the gaseous phase, seven different CA dimers were theoretically calculated. The molecular structures were optimized using density functional theory (DFT) at the B3LYP/6–311G+(d,p) level and the spectroscopic results were compared. It was found that the calculated configurations of dimer I and III were almost identical to the ones found in the CA crystal lattice. The calculated UV-Vis spectra for the CA monomer and dimer I were perfectly consistent with the experimental spectroscopic data. Furthermore, enhanced emissions induced by aggregated CA molecules were registered in the aqueous solution with the increase of water fractions. The obtained results will help to further understand the relation between a variety of conformations and the biological properties of CA, and the results are also promising in terms of the applicability of CA as a bioimaging probe to monitor biological processes.

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Moreno, Miquel, José M. Lluch, and Ricard Gelabert. "On the Computational Design of Azobenzene-Based Multi-State Photoswitches." International Journal of Molecular Sciences 23, no. 15 (August 4, 2022): 8690. http://dx.doi.org/10.3390/ijms23158690.

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In order to theoretically design multi-state photoswitches with specific properties, an exhaustive computational study is first carried out for an azobenzene dimer that has been recently synthesized and experimentally studied. This study allows for a full comprehension of the factors that govern the photoactivated isomerization processes of these molecules so to provide a conceptual/computational protocol that can be applied to generic multi-state photoswitches. From this knowledge a new dimer with a similar chemical design is designed and also fully characterized. Our theoretical calculations predict that the new dimer proposed is one step further in the quest for a double photoswitch, where the four metastable isomers could be selectively interconverted through the use of different irradiation sequences.

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Abe, Shigeaki, Yoshinori Nagoya, Fumio Watari, and Hiroto Tachikawa. "Evaporation processes of water molecules from graphene edge: DFT and MD study." Computational Materials Science 50, no. 9 (July 2011): 2640–43. http://dx.doi.org/10.1016/j.commatsci.2011.04.009.

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Williams, David, and Serena Viti. "Modelling interstellar physics and chemistry: implications for surface and solid-state processes." Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 371, no. 1994 (July 13, 2013): 20110587. http://dx.doi.org/10.1098/rsta.2011.0587.

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We discuss several types of regions in the interstellar medium of the Milky Way and other galaxies in which the chemistry appears to be influenced or dominated by surface and solid-state processes occurring on or in interstellar dust grains. For some of these processes, for example, the formation of H 2 molecules, detailed experimental and theoretical approaches have provided excellent fundamental data for incorporation into astrochemical models. In other cases, there is an astrochemical requirement for much more laboratory and computational study, and we highlight these needs in our description. Nevertheless, in spite of the limitations of the data, it is possible to infer from astrochemical modelling that surface and solid-state processes play a crucial role in astronomical chemistry from early epochs of the Universe up to the present day.

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Lungu, Claudiu N., Violeta Mangalagiu, Ionel I. Mangalagiu, and Mihaela C. Mehedinti. "Benzoquinoline Chemical Space: A Helpful Approach in Antibacterial and Anticancer Drug Design." Molecules 28, no. 3 (January 20, 2023): 1069. http://dx.doi.org/10.3390/molecules28031069.

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Benzoquinolines are used in many drug design projects as starting molecules subject to derivatization. This computational study aims to characterize e benzoquinone drug space to ease future drug design processes based on these molecules. The drug space is composed of all benzoquinones, which are active on topoisomerase II and ATP synthase. Topological, chemical, and bioactivity spaces are explored using computational methodologies based on virtual screening and scaffold hopping and molecular docking, respectively. Topological space is a geometrical space in which the elements composing it can be defined as a set of neighbors (which satisfy a particular axiom). In such space, a chemical space can be defined as the property space spanned by all possible molecules and chemical compounds adhering to a given set of construction principles and boundary conditions. In this chemical space, the potentially pharmacologically active molecules form the bioactivity space. Results show a poly-morphological chemical space that suggests distinct characteristics. The chemical space is correlated with properties such as steric energy, the number of hydrogen bonds, the presence of halogen atoms, and membrane permeability-related properties. Lastly, novel chemical compounds (such as oxadiazole methybenzamide and floro methylcyclohexane diene) with drug-like potential, active on TOPO II and ATP synthase have been identified.

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Cheng, Yu, Si Da Ling, Yuhao Geng, Yundong Wang, and Jianhong Xu. "Microfluidic synthesis of quantum dots and their applications in bio-sensing and bio-imaging." Nanoscale Advances 3, no. 8 (2021): 2180–95. http://dx.doi.org/10.1039/d0na00933d.

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Biosensing and bioimaging of organisms or molecules allows for the study of physiological processes or the diagnosis of diseases. QDs are promising optical detectors and microfluidic technology is one promising path for their industrial production.

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Gimenez-Dejoz, Joan, Katsuhiko Tsunoda, Yasuo Fukushima, and Keiji Numata. "Computational study of the interaction between natural rubber α-terminal groups and l-quebrachitol, one of the major components of natural rubber." Polymer Journal 54, no. 2 (October 29, 2021): 229–33. http://dx.doi.org/10.1038/s41428-021-00569-w.

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AbstractNatural rubber is a biomaterial with unique physical and chemical features that are indispensable for many industrial applications. It is widely accepted that the α-terminal groups of its biopolymer molecules play a critical role in its exceptional characteristics. Herein, we used molecular dynamics to model recently structurally defined α-terminal groups and their interaction with l-quebrachitol, which is the second most common compound found in natural rubber particles.

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Wan, Jing, Yang Li, Jared Benson, Richards Miller, Mikhail Zhernenkov, Guillaume Freychet, and Randall L. Headrick. "Dynamic processes in transient phases during self-assembly of organic semiconductor thin films." Molecular Systems Design & Engineering 7, no. 1 (2022): 34–43. http://dx.doi.org/10.1039/d1me00078k.

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Crystallization of organic semiconductor small molecules from solution proceeds in multiple steps. This study describes how asymmetric molecules lead to long-lived transient phases and their impact on carrier mobility for electronic devices.

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Abplanalp, Matthew J., Samer Gozem, Anna I. Krylov, Christopher N. Shingledecker, Eric Herbst, and Ralf I. Kaiser. "A study of interstellar aldehydes and enols as tracers of a cosmic ray-driven nonequilibrium synthesis of complex organic molecules." Proceedings of the National Academy of Sciences 113, no. 28 (July 5, 2016): 7727–32. http://dx.doi.org/10.1073/pnas.1604426113.

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Complex organic molecules such as sugars and amides are ubiquitous in star- and planet-forming regions, but their formation mechanisms have remained largely elusive until now. Here we show in a combined experimental, computational, and astrochemical modeling study that interstellar aldehydes and enols like acetaldehyde (CH3CHO) and vinyl alcohol (C2H3OH) act as key tracers of a cosmic-ray-driven nonequilibrium chemistry leading to complex organics even deep within low-temperature interstellar ices at 10 K. Our findings challenge conventional wisdom and define a hitherto poorly characterized reaction class forming complex organic molecules inside interstellar ices before their sublimation in star-forming regions such as SgrB2(N). These processes are of vital importance in initiating a chain of chemical reactions leading eventually to the molecular precursors of biorelevant molecules as planets form in their interstellar nurseries.

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Chen, Ke-Wei, Yun-Dong Wu, and Tian-Yu Sun. "Critical Computational Evidence Regarding the Long-Standing Controversy over the Main Electrophilic Species in Hypochlorous Acid Solution." Molecules 27, no. 6 (March 11, 2022): 1843. http://dx.doi.org/10.3390/molecules27061843.

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Although hypochlorous acid (HOCl) solution has become a popular electrophilic reagent for industrial uses, the question of which molecule (HOCl or Cl2) undergoes electrophilic addition with olefins remains a controversial issue in some literature and textbooks, and this problem has been largely underexplored in theoretical studies. In this work, we computationally studied the electrophilic addition mechanism of olefins using three experimentally predicted effective electrophilic chlorinating agents, i.e., HOCl, Cl2, and Cl2O molecules. Our results demonstrate that Cl2 and Cl2O are the main electrophilic agents in HOCl solution, whereas the HOCl molecule cannot be the electrophile since the energy barrier when directly adding HOCl molecule to olefins is too high to overcome and the “anti-Markovnikov” regioselectivity for tri-substituted olefin is not consistent with experiments. Notably, the HOCl molecule prefers to form oxonium ion intermediate with a double bond, rather than the generally believed chlorium ion intermediate. This work could benefit mechanistic studies of critical biological and chemical processes with HOCl solution and may be used to update textbooks.

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Roman, Claudia, Miguel Angel Delgado, Liliana Lazar, and Moises Garcia-Morales. "Computational design applied to equilibrium-staged and rate-based absorption processes." Revista de Chimie 71, no. 7 (August 4, 2020): 88–96. http://dx.doi.org/10.37358/rc.20.7.8228.

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Simulators are of great interest in Chemical Engineering because they facilitate process optimization and help evaluate different solutions through the so-called �what-if� approach. They include the most advanced thermodynamical models and complete libraries for the calculation of physicochemical properties and estimation of phase equilibria data which are successfully integrated in the process design. Moreover, simulators allow addressing both stationary and batch operations. For this reason, their use in the design of Industrial Chemistry processes has gained much acceptance in the last decades. Even so, simulations should be accompanied by another computational tool which allows the professionals to implement specific algorithms which relate inputs and outputs, so as to get the most out of the computing power. We herein exemplify how Aspen Plus and Mathcad Prime software packages were successfully integrated in a case study on the removal of carbon disulphide by contact with a paraffinic oil in an absorption tower. This absorption operation was studied in both trayed and packed columns. Regarding the first contact type, i.e. trays, Mathcad�s powerful programming tool and graphical interface enabled to corroborate and to better understand the effect of temperature on the number of theoretical stages previously observed with Aspen Plus.

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Shafranyosh, M., and D. Kish. "Processes of formation of positive ions at the electron - thymine molecule interactions." Bulletin of Taras Shevchenko National University of Kyiv. Series: Physics and Mathematics, no. 2 (2019): 104–7. http://dx.doi.org/10.17721/1812-5409.2019/2.14.

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The work is aimed to solve the key problems of modern biophysics related to the study of fundamental mechanisms of interaction of ionizing radiation on living cells and stability of biological systems to its influence. The obtained data and their generalizations create a basis for understanding the interaction mechanisms and stability of biological systems to its influence. Investigation is aimed on the obtaining the new priority data about the characteristics of the life important biological molecules, establishing the mechanisms and features of dissociative capture, excitation and ionization under the slow electrons; the study of the influence of intermolecular interactions on these processes and solution of some applications concerning the definition of physical stability of biomolecules in different states of aggregation. The AM1 method that was used in research is a semi-empirical method for the quantum calculation of molecular electronic structure in computational chemistry. It is based on the neglect of differential diatomic overlap integral approximation and investigates the processes of formation of positive ions, which are formed during the interaction of thymine molecules with slow electrons. Fragmentation model of thymine molecules under electron ipmpact is proposed. Six most likely bond breaks in the cyclic structure of thymine molecular ion are identified. The obtained results are in good agreement with experimental data.

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Comito, Marziale, Riccardo Monguzzi, Silvia Tagliapietra, Giovanni Palmisano, and Giancarlo Cravotto. "Towards Antibiotic Synthesis in Continuous-Flow Processes." Molecules 28, no. 3 (February 2, 2023): 1421. http://dx.doi.org/10.3390/molecules28031421.

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Continuous-flow chemistry has become a mainstream process and a notable trend among emerging technologies for drug synthesis. It is routinely used in academic and industrial laboratories to generate a wide variety of molecules and building blocks. The advantages it provides, in terms of safety, speed, cost efficiency and small-equipment footprint compared to analog batch processes, have been known for some time. What has become even more important in recent years is its compliance with the quality objectives that are required by drug-development protocols that integrate inline analysis and purification tools. There can be no doubt that worldwide government agencies have strongly encouraged the study and implementation of this innovative, sustainable and environmentally friendly technology. In this brief review, we list and evaluate the development and applications of continuous-flow processes for antibiotic synthesis. This work spans the period of 2012–2022 and highlights the main cases in which either active ingredients or their intermediates were produced under continuous flow. We hope that this manuscript will provide an overview of the field and a starting point for a deeper understanding of the impact of flow chemistry on the broad panorama of antibiotic synthesis.

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Lichołai, Sabina, Dorota Studzińska, Hanna Plutecka, Tomasz Gubała, and Marek Sanak. "Comprehensive Analysis of Circular RNAs in Endothelial Cells." International Journal of Molecular Sciences 24, no. 12 (June 12, 2023): 10025. http://dx.doi.org/10.3390/ijms241210025.

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Non-coding RNAs constitute a heterogeneous group of molecules that lack the ability to encode proteins but retain the potential ability to influence cellular processes through a regulatory mechanism. Of these proteins, microRNAs, long non-coding RNAs, and more recently, circular RNAs have been the most extensively described. However, it is not entirely clear how these molecules interact with each other. For circular RNAs, the basics of their biogenesis and properties are also lacking. Therefore, in this study we performed a comprehensive analysis of circular RNAs in relation to endothelial cells. We identified the pool of circular RNAs present in the endothelium and showed their spectrum and expression across the genome. Using different computational strategies, we proposed approaches to search for potentially functional molecules. In addition, using data from an in vitro model that mimics conditions in the endothelium of an aortic aneurysm, we demonstrated altered expression levels of circRNAs mediated by microRNAs.

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Wang, Hangyao, Heather A. G. Stern, Debashis Chakraborty, Hua Bai, Vincent DiFilippo, Jitendra S. Goela, Michael A. Pickering, and Julian D. Gale. "Computational Study of Surface Deposition and Gas Phase Powder Formation during Spinel Chemical Vapor Deposition Processes." Industrial & Engineering Chemistry Research 52, no. 44 (April 24, 2013): 15270–80. http://dx.doi.org/10.1021/ie400502u.

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Wang, Linzhu, Junqi Li, Shufeng Yang, Chaoyi Chen, Huixin Jin, Xiang Li, Changling Zhuang, and Jiantao Ju. "Industrial experiment study on inclusion evolution in 95CrMo Steel." Metallurgical Research & Technology 116, no. 5 (2019): 518. http://dx.doi.org/10.1051/metal/2019015.

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In order to clarify the evolution mechanism of inclusions in 95CrMo, the industrial experiments were conducted. The composition, morphology and size of inclusions during refining and solidifying processes were analyzed by SEM-EDS detection and thermodynamic calculations. The inclusion evolution during refining process in molten 95CrMo steel can be concluded as: Al2O3 → Al2O3-MgO-CaO/CaS → Al2O3-MgO-SiO2-CaO-CaS, which is affected by slag-metal reaction and corrosion of refractory. The change of inclusion size during refining was analyzed based on their collision and floatation behavior. The composition of inclusions in billets indicate that there were mainly five types of inclusions, including spinel with sharp angle, spherical oxide inclusion composed of Al2O3, MgO, SiO2 and CaO, oxide-sulfide inclusion with single phase, inclusion with duplex phase, and MnS inclusion. The type of inclusions affects their size. The thermodynamic results indicate that most complex oxides formed in molten steel and no spinel generated during cooling process. CaS formed in the molten steel after tundish metallurgy and there were still some CaS precipitated in solid steel. MnS precipitated after steel solidification. The calculated results based on FACTSAGE 7.1 are in agreement with experimental results on the whole.

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Bartolomé, Alejandra, Gema Rodríguez-Moro, Juan-Luis Fuentes, Mariana Lopes, Juana Frontela, Jesús Lázaro, María Cuaresma, José-Luis Gómez-Ariza, Tamara García-Barrera, and Carlos Vílchez. "Biodegradation of a Complex Phenolic Industrial Stream by Bacterial Strains Isolated from Industrial Wastewaters." Processes 9, no. 11 (November 3, 2021): 1964. http://dx.doi.org/10.3390/pr9111964.

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Molecular and metabolomic tools were used to design and understand the biodegradation of phenolic compounds in real industrial streams. Bacterial species were isolated from an industrial wastewater treatment plant of a phenol production factory and identified using molecular techniques. Next, the biodegradation potential of the most promising strains was analyzed in the presence of a phenolic industrial by-product containing phenol, alfa-methylstyrene, acetophenone, 2-cumylphenol, and 4-cumylphenol. A bacterial consortium comprising Pseudomonas and Alcaligenes species was assessed for its ability to degrade phenolic compounds from the phenolic industrial stream (PS). The consortium adapted itself to the increasing levels of phenolic compounds, roughly up to 1750 ppm of PS; thus, becoming resistant to them. In addition, the consortium exhibited the ability to grow in the presence of PS in repeated batch mode processes. Results from untargeted metabolomic analysis of the culture medium in the presence of PS suggested that bacteria transformed the toxic phenolic compounds into less harmful molecules as a survival mechanism. Overall, the study demonstrates the usefulness of massive sequencing and metabolomic tools in constructing bacterial consortia that can efficiently biodegrade complex PS. Furthermore, it improves our understanding of their biodegradation capabilities.

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Barone, Vincenzo, and Cristina Puzzarini. "Looking for the bricks of the life in the interstellar medium: The fascinating world of astrochemistry." EPJ Web of Conferences 246 (2020): 00021. http://dx.doi.org/10.1051/epjconf/202024600021.

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The discovery in the interstellar medium of molecules showing a certain degree of complexity, and in particular those with a prebiotic character, has attracted great interest. A complex chemistry takes place in space, but the processes that lead to the production of molecular species are a matter of intense discussion, the knowledge still being at a rather primitive stage. Debate on the origins of interstellar molecules has been further stimulated by the identification of biomolecular building blocks, such as nucleobases and amino acids, in meteorites and comets. Since many of the molecules found in space play a role in the chemistry of life, the issue of their molecular genesis and evolution might be related to the profound question of the origin of life itself. Understanding the underlying chemical processes, including the production, reactions and destruction of compounds, requires the concomitant study of spectroscopy, gas-phase reactivity, and heterogeneous processes on dust-grains. The aim of this contribution is to provide a general view of a complex and multifaceted challenge, while focusing on the role played by molecular spectroscopy and quantum-chemical computations. In particular, the derivation of the molecular spectroscopic features and the investigation of gas-phase formation routes of prebiotic species in the interstellar medium are addressed from a computational point of view.

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MEI, YE, and JOHN Z. H. ZHANG. "NUMERICAL STABILITIES IN FITTING ATOMIC CHARGES TO ELECTRIC FIELD AND ELECTROSTATIC POTENTIAL." Journal of Theoretical and Computational Chemistry 08, no. 05 (October 2009): 925–42. http://dx.doi.org/10.1142/s0219633609005295.

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It is known that electrostatic potential (ESP) derived atomic charges for molecular systems suffer from rank deficiency in least-square fitting. In this paper, we studied numerical properties of atomic charges by fitting to ESP and electric field (EF) for a series of molecular systems, ranging from small molecules to peptides. Our study shows that although atomic charges of certain atoms in a molecule may differ a lot resulting from different fitting schemes, the effect on some observed physical properties of the molecules, such as solvation free energy and radial distributions of the solvent, are negligible. For all the molecules studied in this paper, it is shown that by incorporating EF terms in the least-square fitting, the rank of the least-squares matrix is increased, and the full rank is achieved when only EF terms are included. The current study demonstrates that by using EF, instead of the widely used ESP, in least-square fitting of atomic charges, one can obtain numerically more stable and better defined atomic charges in molecules. Such derived atomic charges may have more desirable properties and better numerical stabilities in studying detailed molecular processes such as in molecular dynamics simulation of macromolecules.

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Ončák, Milan, Rebecca Meißner, Eugene Arthur-Baidoo, Stephan Denifl, Thomas F. M. Luxford, Andriy Pysanenko, Michal Fárník, Jiří Pinkas, and Jaroslav Kočišek. "Ring Formation and Hydration Effects in Electron Attachment to Misonidazole." International Journal of Molecular Sciences 20, no. 18 (September 6, 2019): 4383. http://dx.doi.org/10.3390/ijms20184383.

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We study the reactivity of misonidazole with low-energy electrons in a water environment combining experiment and theoretical modelling. The environment is modelled by sequential hydration of misonidazole clusters in vacuum. The well-defined experimental conditions enable computational modeling of the observed reactions. While the NO 2 − dissociative electron attachment channel is suppressed, as also observed previously for other molecules, the OH − channel remains open. Such behavior is enabled by the high hydration energy of OH − and ring formation in the neutral radical co-fragment. These observations help to understand the mechanism of bio-reductive drug action. Electron-induced formation of covalent bonds is then important not only for biological processes but may find applications also in technology.

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Stefaniu, Amalia, and Lucia Camelia Pirvu. "In Silico Study Approach on a Series of 50 Polyphenolic Compounds in Plants; A Comparison on the Bioavailability and Bioactivity Data." Molecules 27, no. 4 (February 19, 2022): 1413. http://dx.doi.org/10.3390/molecules27041413.

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Fifty (50) phytocompounds from several subclasses of polyphenols, chosen based on their abundance in the plant world, were analyzed through density functional methods, using computational tools to evaluate their oral availability and particular bioactivity on several cell modulators; key descriptors and molecular features related to the electron density and electrostatic potential for the lowest energy conformers of the investigated molecules were computed. An analysis of the bioactivity scores towards six cell modulators (GPCR ligand, ion channel modulator, kinase inhibitor, nuclear receptor ligand, protease inhibitor and enzyme inhibitor) was also achieved, in the context of investigating their potential side effects on the human digestive processes. Summarizing, computational results confirmed in vivo and in vitro data regarding the high bioavailability of soy isoflavones and better bioavailability of free aglycones in comparison with their esterified and glycosylated forms. However, by a computational approach analyzing Lipinski’s rule, apigenin and apigenin-7-O-rhamnoside, naringenin, hesperetin, genistein, daidzin, biochanin A and formonetin in the flavonoid series and all hydroxycinnamic acids and all hydroxybenzoic acids excepting ellagic acid were proved to have the best bioavailability data; rhamnoside derivatives, the predominant glycosides in green plants, which were reported to have the lowest bioavailability values by in vivo studies, were revealed to have the best bioavailability data among the studied flavonoids in the computational approach. Results of in silico screening on the phenolic derivatives series also revealed their real inhibitory potency on the six parameters studied, showing a remarkable similitude between the flavonoid series, while flavonoids were more powerful natural cell modulators than the phenyl carboxylic acids tested. Thus, it can be concluded that there is a need for supplementation with digestive enzymes, mainly in the case of individuals with low digestive efficiency, to obtain the best health benefits of polyphenols in humans.

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Ahmed, Aftab, Sajid-ur Rehman, Syeda Abida Ejaz, Aamer Saeed, Rabail Ujan, Pervaiz Ali Channar, Khalida Mahar, et al. "Exploring 2-Tetradecanoylimino-3-aryl-4-methyl-1,3-thiazolines Derivatives as Alkaline Phosphatase Inhibitors: Biochemical Evaluation and Computational Analysis." Molecules 27, no. 19 (October 10, 2022): 6766. http://dx.doi.org/10.3390/molecules27196766.

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The current study focused on the laboratory approach in conjunction with computational methods for the synthesis and bioactivity assessment of unique 2-tetradecanoylimino-3-aryl-4-methyl-1,3-thiazolines (2a–2k). Processes included cyclizing 1-aroyl-3-arylthioureas with propan-2-one in the presence of trimethylamine and bromine. By using spectroscopic techniques and elemental analyses, structures were elucidated. To assess the electronic properties, density functional theory (DFT) calculations were made, while binding interactions of synthesized derivatives were studied by the molecular docking tool. Promising results were found during the evaluation of bioactivity of synthesized compounds against alkaline phosphatase. The drug likeliness score, an indicator used for any chemical entity posing as a drug, was within acceptable limits. The data suggested that most of the derivatives were potent inhibitors of alkaline phosphatase, which in turn may act as lead molecules to synthesize derivatives having desired pharmacological profiles for the treatment of specific diseases associated with abnormal levels of ALPs.

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LI, XIN, and ZHONG-ZHI YANG. "AN AB INITIO STUDY OF PROTON-TRANSFER REACTION IN Be2+(H2O)n AND THE SPATIAL CHANGING FEATURE IN THE FORMATION PROCESS OF HYDROXIDE." Journal of Theoretical and Computational Chemistry 05, no. 01 (March 2006): 75–85. http://dx.doi.org/10.1142/s0219633606002064.

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The proton-transfer reaction in Be 2+( H 2 O )n is investigated by an ab initio calculation. With an increasing number of water molecules, there are different formation processes of hydroxide, and the reaction barrier is dependent on the cluster size n. By MELD ab initio program and own-coding programs, we have calculated the potential acting on an electron within a molecule, and have investigated the changing of spatial appearance for the formation process of hydroxide, by the molecular intrinsic characteristic contour defined in terms of the classical turning point of electron movement.

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Schmidt, Martin, Stefan Zahn, Florian Gehlhaar, Andrea Prager, Jan Griebel, Axel Kahnt, Wolfgang Knolle, Robert Konieczny, Roger Gläser, and Agnes Schulze. "Radiation-Induced Graft Immobilization (RIGI): Covalent Binding of Non-Vinyl Compounds on Polymer Membranes." Polymers 13, no. 11 (June 2, 2021): 1849. http://dx.doi.org/10.3390/polym13111849.

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Radiation-induced graft immobilization (RIGI) is a novel method for the covalent binding of substances on polymeric materials without the use of additional chemicals. In contrast to the well-known radiation-induced graft polymerization (RIGP), RIGI can use non-vinyl compounds such as small and large functional molecules, hydrophilic polymers, or even enzymes. In a one-step electron-beam-based process, immobilization can be performed in a clean, fast, and continuous operation mode, as required for industrial applications. This study proposes a reaction mechanism using polyvinylidene fluoride (PVDF) and two small model molecules, glycine and taurine, in aqueous solution. Covalent coupling of single molecules is achieved by radical recombination and alkene addition reactions, with water radiolysis playing a crucial role in the formation of reactive solute species. Hydroxyl radicals contribute mainly to the immobilization, while solvated electrons and hydrogen radicals play a minor role. Release of fluoride is mainly induced by direct ionization of the polymer and supported by water. Hydrophobic chains attached to cations appear to enhance the covalent attachment of solutes to the polymer surface. Computational work is complemented by experimental studies, including X-ray photoelectron spectroscopy (XPS) and fluoride high-performance ion chromatography (HPIC).

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Trebuna, Peter, Miriam Pekarcikova, Richard Duda, and Tomas Svantner. "Virtual Reality in Discrete Event Simulation for Production–Assembly Processes." Applied Sciences 13, no. 9 (April 27, 2023): 5469. http://dx.doi.org/10.3390/app13095469.

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The connection of simulation models with virtual reality (VR) technology is of great importance in implementing Industry 4.0 in industrial practice. The article deals with the use of virtual reality in discrete event simulation (DES) using the Tecnomatix Plant Simulation software to visualize, analyze and optimize the modelled production–assembly process. The importance of virtual reality is evident in the academic sphere in connection with interactive teaching and its use for industrial practice. The article presents a case study focused on creating a virtual environment and optimizing the production–assembly process in the TX Plant Simulation software environment. During the mentioned study, the analysis of production–assembly flows, the processing of input data into the simulation model, the creation of 3D elements for the needs of virtualization—which are not part of the TX Plant Simulation software library—and the visualization that simulates the real environment based on computational algorithms were carried out. Virtualization was solved using the Oculus Rift S Headset. The output is a generally applicable procedure for modelling and testing a virtual model with its verification on a case study.

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Salamonowicz, Zdzislaw, Andrzej Krauze, Malgorzata Majder-Lopatka, Anna Dmochowska, Aleksandra Piechota-Polanczyk, and Andrzej Polanczyk. "Numerical Reconstruction of Hazardous Zones after the Release of Flammable Gases during Industrial Processes." Processes 9, no. 2 (February 6, 2021): 307. http://dx.doi.org/10.3390/pr9020307.

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The storage of large numbers of batteries and accumulators is associated with an increased risk of their ignition, which results in the release of significant amounts of hydrogen into the environment. The aim of the study was to reconstruct hazardous zones after hydrogen and liquefied propane–butane (reference gas) release for different industrial processes with the use of numerical methods. Two numerical tools (Fire Dynamics Simulator and Ansys software) were applied for the three-dimensional reconstruction of flammable gas release. Propane–butane was produced from aerosol packages, and hydrogen was produced during battery charging. Emission was analyzed in an industrial building, and both emissions were independent processes. The obtained results indicated that the hazardous zones correspond to the lower explosive level concentrations for both analyzed gasses. Moreover, the high-resolution computational fluid dynamic (CFD) model for flammable gas emissions provided noninvasive and direct quantitative evidence that may influence the safety procedures prepared by regulatory agencies in refining the safety limits in the cost-effective and time-saving manners.

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Kumar, Rupesh, Maged Mostafa Mahmoud, Hanaa M. Tashkandi, Shafiul Haque, Steve Harakeh, Kalaiarasan Ponnusamy, and Shazia Haider. "Combinatorial Network of Transcriptional and miRNA Regulation in Colorectal Cancer." International Journal of Molecular Sciences 24, no. 6 (March 10, 2023): 5356. http://dx.doi.org/10.3390/ijms24065356.

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Colorectal cancer is one of the leading causes of cancer-associated mortality across the worldwide. One of the major challenges in colorectal cancer is the understanding of the regulatory mechanisms of biological molecules. In this study, we aimed to identify novel key molecules in colorectal cancer by using a computational systems biology approach. We constructed the colorectal protein–protein interaction network which followed hierarchical scale-free nature. We identified TP53, CTNBB1, AKT1, EGFR, HRAS, JUN, RHOA, and EGF as bottleneck-hubs. The HRAS showed the largest interacting strength with functional subnetworks, having strong correlation with protein phosphorylation, kinase activity, signal transduction, and apoptotic processes. Furthermore, we constructed the bottleneck-hubs’ regulatory networks with their transcriptional (transcription factor) and post-transcriptional (miRNAs) regulators, which exhibited the important key regulators. We observed miR-429, miR-622, and miR-133b and transcription factors (EZH2, HDAC1, HDAC4, AR, NFKB1, and KLF4) regulates four bottleneck-hubs (TP53, JUN, AKT1 and EGFR) at the motif level. In future, biochemical investigation of the observed key regulators could provide further understanding about their role in the pathophysiology of colorectal cancer.

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Kim, Hongdeok, Byeonghwa Goh, Sol Lee, Kyujo Lee, and Joonmyung Choi. "Computational Study on Interfacial Interactions between Polymethyl Methacrylate-Based Bone Cement and Hydroxyapatite in Nanoscale." Applied Sciences 11, no. 7 (March 25, 2021): 2937. http://dx.doi.org/10.3390/app11072937.

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Polymethyl methacrylate (PMMA)-based bone cement (BC) is a key material in joint replacement surgery that transfers external forces from the implant to the bone while allowing their robust binding. To quantitatively evaluate the effect of polymerization on the thermomechanical properties of the BC and on the interaction characteristics with the bone ceramic hydroxyapatite (HAp), molecular dynamics simulations were performed. The mechanical stiffness of the BC material under external loading increased gradually with the crosslinking reaction occurrence, indicating increasing load transfer between the constituent molecules. In addition, as the individual Methyl Methacrylate (MMA) segments were interconnected in the system, the freedom of the molecular network was largely suppressed, resulting in more thermally stable structures. Furthermore, the pull-out tests using HAp/BC bilayer models under different constraints (BC at 40% and 85%) revealed the cohesive characteristics of the BC with the bone scaffold in molecular detail. The stiffness and the fracture energy increased by 32% and 98%, respectively, with the crosslink density increasing.

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Bukowski, Brandon C., Frerich J. Keil, Peter I. Ravikovitch, German Sastre, Randall Q. Snurr, and Marc-Olivier Coppens. "Connecting theory and simulation with experiment for the study of diffusion in nanoporous solids." Adsorption 27, no. 5 (April 22, 2021): 683–760. http://dx.doi.org/10.1007/s10450-021-00314-y.

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AbstractNanoporous solids are ubiquitous in chemical, energy, and environmental processes, where controlled transport of molecules through the pores plays a crucial role. They are used as sorbents, chromatographic or membrane materials for separations, and as catalysts and catalyst supports. Defined as materials where confinement effects lead to substantial deviations from bulk diffusion, nanoporous materials include crystalline microporous zeotypes and metal–organic frameworks (MOFs), and a number of semi-crystalline and amorphous mesoporous solids, as well as hierarchically structured materials, containing both nanopores and wider meso- or macropores to facilitate transport over macroscopic distances. The ranges of pore sizes, shapes, and topologies spanned by these materials represent a considerable challenge for predicting molecular diffusivities, but fundamental understanding also provides an opportunity to guide the design of new nanoporous materials to increase the performance of transport limited processes. Remarkable progress in synthesis increasingly allows these designs to be put into practice. Molecular simulation techniques have been used in conjunction with experimental measurements to examine in detail the fundamental diffusion processes within nanoporous solids, to provide insight into the free energy landscape navigated by adsorbates, and to better understand nano-confinement effects. Pore network models, discrete particle models and synthesis-mimicking atomistic models allow to tackle diffusion in mesoporous and hierarchically structured porous materials, where multiscale approaches benefit from ever cheaper parallel computing and higher resolution imaging. Here, we discuss synergistic combinations of simulation and experiment to showcase theoretical progress and computational techniques that have been successful in predicting guest diffusion and providing insights. We also outline where new fundamental developments and experimental techniques are needed to enable more accurate predictions for complex systems.

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Altin, Ozan, Dagbjørn Skipnes, Torstein Skåra, and Ferruh Erdogdu. "A computational study for the effects of sample movement and cavity geometry in industrial scale continuous microwave systems during heating and thawing processes." Innovative Food Science & Emerging Technologies 77 (May 2022): 102953. http://dx.doi.org/10.1016/j.ifset.2022.102953.

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Caseiro, Catarina, Joana Nunes Ribeiro Dias, Carlos Mendes Godinho de Andrade Fontes, and Pedro Bule. "From Cancer Therapy to Winemaking: The Molecular Structure and Applications of β-Glucans and β-1, 3-Glucanases." International Journal of Molecular Sciences 23, no. 6 (March 15, 2022): 3156. http://dx.doi.org/10.3390/ijms23063156.

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β-glucans are a diverse group of polysaccharides composed of β-1,3 or β-(1,3-1,4) linked glucose monomers. They are mainly synthesized by fungi, plants, seaweed and bacteria, where they carry out structural, protective and energy storage roles. Because of their unique physicochemical properties, they have important applications in several industrial, biomedical and biotechnological processes. β-glucans are also major bioactive molecules with marked immunomodulatory and metabolic properties. As such, they have been the focus of many studies attesting to their ability to, among other roles, fight cancer, reduce the risk of cardiovascular diseases and control diabetes. The physicochemical and functional profiles of β-glucans are deeply influenced by their molecular structure. This structure governs β-glucan interaction with multiple β-glucan binding proteins, triggering myriad biological responses. It is then imperative to understand the structural properties of β-glucans to fully reveal their biological roles and potential applications. The deconstruction of β-glucans is a result of β-glucanase activity. In addition to being invaluable tools for the study of β-glucans, these enzymes have applications in numerous biotechnological and industrial processes, both alone and in conjunction with their natural substrates. Here, we review potential applications for β-glucans and β-glucanases, and explore how their functionalities are dictated by their structure.

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RAMALHO, TEODORICO C., ELAINE F. F. DA CUNHA, and RICARDO BICCA DE ALENCASTRO. "THEORETICAL STUDY OF ADIABATIC AND VERTICAL ELECTRON AFFINITY OF RADIOSENSITIZERS IN SOLUTION PART 2: ANALOGUES OF TIRAPAZAMINE." Journal of Theoretical and Computational Chemistry 03, no. 01 (March 2004): 1–13. http://dx.doi.org/10.1142/s0219633604000866.

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Tirapazamine is a radiosensitizer, whose biological activity is associated to its electron affinity (EA). The electron affinity can be divided in two main processes: Vertical and Adiabatic. In this work, we calculated the EAs of nitroimidazoles (Fig. 2) using HF and DFT methods and evaluated solvent effects (water and carbon tetrachloride) on EAs. For water, we combined the Polarized Continuum Model (PCM) and free energy perturbation (Finite Difference Thermodynamic Integration, FDTI) methods. For carbon tetrachloride, we used the FDTI method. The values of adiabatic EA obtained are in agreement with experimental data (deviations of 13.25 meV). The vertical EA were calculated according to Cederbaum's Outer Valence Green Function (OVGF) method. This study, which relays on theoretical aspects of free energy calculations on charged molecules in solution, could be helpful in the rational design of new and more selective bioreductive anticancer drugs.

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Lo Giudice, Valentina, Immacolata Faraone, Maria Roberta Bruno, Maria Ponticelli, Fabiana Labanca, Donatella Bisaccia, Carmine Massarelli, Luigi Milella, and Luigi Todaro. "Olive Trees By-Products as Sources of Bioactive and Other Industrially Useful Compounds: A Systematic Review." Molecules 26, no. 16 (August 22, 2021): 5081. http://dx.doi.org/10.3390/molecules26165081.

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The need to produce an ever-increasing quantity of material products and food resulting from the planet globalization process has contributed to the spread of modern agriculture based on a linear production resulting in the generation of tons of waste. This huge amount of waste is generally accumulated in landfills, causing different environmental problems. Hence, researchers moved on to study the processes used to recover agro-industrial by-products within a circular and sustainable bio-economy concept. A systematic quest on Scopus and PubMed databases was performed to identify the data available to date on recycling agro-industrial by-products of Olea europaea L. This systematic review summarizes the knowledge regarding the use of olive trees by-products for producing animal feed, biocomposites, bioethanol, cellulose pulp, activated carbon, and as a fuel source for energy production. Furthermore, the data regarding the potential biological activity of extracts from olive roots, wood, bark, and pruning were analyzed. Olive trees by-products are, indeed, rich in molecules with antioxidant, antimicrobial, cardioprotective, and anticancer activity, representing a promising candidate for treat several human diseases.

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Levine, Benjamin G., Michael P. Esch, B. Scott Fales, Dylan T. Hardwick, Wei-Tao Peng, and Yinan Shu. "Conical Intersections at the Nanoscale: Molecular Ideas for Materials." Annual Review of Physical Chemistry 70, no. 1 (June 14, 2019): 21–43. http://dx.doi.org/10.1146/annurev-physchem-042018-052425.

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The ability to predict and describe nonradiative processes in molecules via the identification and characterization of conical intersections is one of the greatest recent successes of theoretical chemistry. Only recently, however, has this concept been extended to materials science, where nonradiative recombination limits the efficiencies of materials for various optoelectronic applications. In this review, we present recent advances in the theoretical study of conical intersections in semiconductor nanomaterials. After briefly introducing conical intersections, we argue that specific defects in materials can induce conical intersections between the ground and first excited electronic states, thus introducing pathways for nonradiative recombination. We present recent developments in theoretical methods, computational tools, and chemical intuition for the prediction of such defect-induced conical intersections. Through examples in various nanomaterials, we illustrate the significance of conical intersections for nanoscience. We also discuss challenges facing research in this area and opportunities for progress.

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Burlini, Ilaria, and Gianni Sacchetti. "Secondary Bioactive Metabolites from Plant-Derived Food Byproducts through Ecopharmacognostic Approaches: A Bound Phenolic Case Study." Plants 9, no. 9 (August 19, 2020): 1060. http://dx.doi.org/10.3390/plants9091060.

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The climate emergency and the risks to biodiversity that the planet is facing nowadays, have made the management of food resources increasingly complex but potentially interesting. According to FAO, one-third of the edible parts of food produced throughout the whole food supply chain gets lost or wasted globally every year. At the same time, demographic growth makes it necessary to change course toward sustainable economic development in order to satisfy market demands. The European Union supported the idea of a Circular Economy from 2015 and arranged annual Action Plans toward a greener, climate-neutral economy. Following the biorefinery concept, food waste becomes byproducts that can be recovered and exploited as high added-value materials for industrial applications. The use of sustainable extraction processes to manage food byproducts is a task that research has to support through the development of low environmental impact strategies. This review, therefore, aims to take stock of the possibilities of extracting molecules from food waste biomass following ecopharmacognostic approaches inspired by green chemistry guidelines. In particular, the use of innovative hybrid techniques to maximize yields and minimize the environmental impact of processes is reviewed, with a focus on bound phenolic extractions.

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48

Meacci, Luca, Gustavo C. Buscaglia, Fernando Mut, Roberto F. Ausas, and Mario Primicerio. "A new two-component approach in modeling red blood cells." Communications in Applied and Industrial Mathematics 11, no. 1 (January 1, 2020): 55–71. http://dx.doi.org/10.1515/caim-2020-0004.

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Abstract:

Abstract This work consists in the presentation of a computational modelling approach to study normal and pathological behavior of red blood cells in slow transient processes that can not be accompanied by pure particle methods (which require very small time steps). The basic model, inspired by the best models currently available, considers the cytoskeleton as a discrete non-linear elastic structure. The novelty of the proposed work is to couple this skeleton with continuum models instead of the more common discrete models (molecular dynamics, particle methods) of the lipid bilayer. The interaction of the solid cytoskeleton with the bilayer, which is a two-dimensional fluid, will be done through adhesion forces adapting e cient solid-solid adhesion algorithms. The continuous treatment of the fluid parts is well justified by scale arguments and leads to much more stable and precise numerical problems when, as is the case, the size of the molecules (0.3 nm) is much smaller than the overall size (≃ 8000 nm). In this paper we display some numerical simulations that show how our approach can describe the interaction of an RBC with an exogenous body as well as the relaxation of the shape of an RBC toward its equilibrium configuration in absence of external forces.

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49

Meacci, Luca, Gustavo C. Buscaglia, Fernando Mut, Roberto F. Ausas, and Mario Primicerio. "A new two-component approach in modeling red blood cells." Communications in Applied and Industrial Mathematics 11, no. 1 (January 1, 2020): 55–71. http://dx.doi.org/10.2478/caim-2020-0004.

Full text

Abstract:

Abstract This work consists in the presentation of a computational modelling approach to study normal and pathological behavior of red blood cells in slow transient processes that can not be accompanied by pure particle methods (which require very small time steps). The basic model, inspired by the best models currently available, considers the cytoskeleton as a discrete non-linear elastic structure. The novelty of the proposed work is to couple this skeleton with continuum models instead of the more common discrete models (molecular dynamics, particle methods) of the lipid bilayer. The interaction of the solid cytoskeleton with the bilayer, which is a two-dimensional fluid, will be done through adhesion forces adapting e cient solid-solid adhesion algorithms. The continuous treatment of the fluid parts is well justified by scale arguments and leads to much more stable and precise numerical problems when, as is the case, the size of the molecules (0.3 nm) is much smaller than the overall size (≃ 8000 nm). In this paper we display some numerical simulations that show how our approach can describe the interaction of an RBC with an exogenous body as well as the relaxation of the shape of an RBC toward its equilibrium configuration in absence of external forces.

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50

Matica, Mariana, Diana Roman, Vasile Ostafe, and Adriana Isvoran. "Deeper inside the use of chitooligosaccharides in wound healing process: A computational approach." Journal of the Serbian Chemical Society, no. 00 (2022): 81. http://dx.doi.org/10.2298/jsc220702081m.

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Abstract:

Chitooligosaccharides (COs) containing up to 10 monomeric units of Nacetyl D-glucosamine and/or D-glucosamine are water-soluble molecules revealing numerous biological activities and low toxicological profiles. Within this study, a computational approach has been used to predict the involvement of the COs having distinct chemical properties (molecular weight, deacetylation degree and acetylation pattern) in all the four wound healing phases: hemostasis, inflamemation, proliferation and tissue remodeling. There are predictions, for the investigated COs, regarding their molecular targets and the biological activities that are reliant to the wound healing process. Furthermore, a molecular docking approach was used to assess the interactions of the investigated COs with the myeloid differentiation factor 2 (MD-2), a protein involved in the inflammatory processes. The investigation confirms the functional roles of the investigated COs in wound healing. The molecular targets predicted for the COs containing totally and partially acetylated units are galectins and selectins and those predicted for COs containing totally deacetylated units are fibroblast growing factors, the COs containing 3 units revealing the higher number of molecular targets. All these proteins are involved in mediating immune response, inducing cell division, growth and cell adhesion during the process of wound healing. All the COs containing from 2 to 8 monomeric units are able to interact with the MD-2 protein, the interactions being stronger for the COs containing 6 and 8 monomeric units. The interaction energies increase with the increasing molecular weight and with decreasing deacetylation degree and are reliant on acetylation patterns. Among the investigated COs, the totally acetylated COs containing 6 and 8 N-acetyl glucosamine units can be better inhibitors of the LPS binding to MD-2 protein. Consequently, mixtures of COs with distinct properties should be considered suitable candidates as adjuvants in developing scaffolds for the wound healing process.

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Journal articles on the topic 'Industrial Chemistry - Computational Study - Molecules and Processes'

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