Quantum Confinements of Particles in Nanostructure with a Complex Form Energy Profile

We report a mechanism of adenosine triphosphate (ATP) to cyclic adenosine monophosphate (cAMP) conversion by the mammalian type V adenylyl cyclase revealed in molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) simulations. We characterize a set of computationally derived enzyme-substrate (ES) structures showing an important role of coordination shells of magnesium ions in the solvent accessible active site. Several stable six-fold coordination shells of MgA2+ are observed in MD simulations of ES complexes. In the lowest energy ES conformation, the coordination shell of MgA2+ does not include the Oδ1 atom of the conserved Asp440 residue. Starting from this conformation, a one-step reaction mechanism is characterized which includes proton transfer from the ribose O3'H3' group in ATP to Asp440 via a shuttling water molecule and PA-O3A bond cleavage and O3'-PA bond formation. The energy profile of this route is consistent with the observed reaction kinetics. In a higher energy ES conformation, MgA2+ is bound to the Oδ1(Asp440) atom as suggested in the relevant crystal structure of the protein with a substrate analog. The computed energy profile initiated by this ES is characterized by higher energy expenses to complete the reaction. Consistently with experimental data, we show that the Asp440Ala mutant of the enzyme should exhibit a reduced but retained activity. All considered reaction pathways include proton wires from the O3'H3' group via shuttling water molecules.

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Survey for Transition of Normal Reaction

International Journal of Recent Advances in Science and Technology ◽

10.30750/ijarst.536 ◽

2018 ◽

Vol 5 (3) ◽

Author(s):

Hassan Akbari Rahimi

Keyword(s):

Transition State ◽

Reactive Intermediates ◽

The State ◽

Energy Profile ◽

Normal Reaction ◽

Unstable Molecules ◽

The Difference ◽

Bond Vibration ◽

Unstable Molecule ◽

Profile Diagram

Transition of reaction is a short-lived unstable molecule in a reaction which is formed in between the reaction when reactants change into products. Whereas, transition state is just the state before formation of new molecule (involves breaking of bonds of reactants and formation of new ones) Transition of reaction differs from a transition state in that the intermediate has a discrete lifetime (be it a few nanoseconds or many days), whereas a transition state lasts for just one bond vibration cycle. Intermediates may be unstable molecules (in which case they are called reactive intermediates) or highly stable molecules. The difference between them can be better described through the energy profile diagram.

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Youth to Parent Violence: A More Complex Form of Family Violence?

SSRN Electronic Journal ◽

10.2139/ssrn.2256070 ◽

2013 ◽

Author(s):

Sophie A. Evekink

Keyword(s):

Family Violence ◽

Complex Form

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A new algorithm for finding CRM-model coefficients

Tyumen State University Herald Physical and Mathematical Modeling Oil Gas Energy ◽

10.21684/2411-7978-2019-5-3-164-185 ◽

2019 ◽

Vol 5 (3) ◽

pp. 164-185 ◽

Cited By ~ 1

Author(s):

Alexander D. Bekman ◽

Sergey V. Stepanov ◽

Alexander A. Ruchkin ◽

Dmitry V. Zelenin

Keyword(s):

Approximate Solution ◽

Optimization Problem ◽

Optimal Solution ◽

Complex Form ◽

Approximate Solutions ◽

The Other ◽

Programming Algorithm ◽

Stochastic Algorithms ◽

Large Set ◽

Flow Rates

The quantitative evaluation of producer and injector well interference based on well operation data (profiles of flow rates/injectivities and bottomhole/reservoir pressures) with the help of CRM (Capacitance-Resistive Models) is an optimization problem with large set of variables and constraints. The analytical solution cannot be found because of the complex form of the objective function for this problem. Attempts to find the solution with stochastic algorithms take unacceptable time and the result may be far from the optimal solution. Besides, the use of universal (commercial) optimizers hides the details of step by step solution from the user, for example — the ambiguity of the solution as the result of data inaccuracy. The present article concerns two variants of CRM problem. The authors present a new algorithm of solving the problems with the help of “General Quadratic Programming Algorithm”. The main advantage of the new algorithm is the greater performance in comparison with the other known algorithms. Its other advantage is the possibility of an ambiguity analysis. This article studies the conditions which guarantee that the first variant of problem has a unique solution, which can be found with the presented algorithm. Another algorithm for finding the approximate solution for the second variant of the problem is also considered. The method of visualization of approximate solutions set is presented. The results of experiments comparing the new algorithm with some previously known are given.

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Misconceptions arising from a Sign Discrepancy in Thermodynamic Data for the Gibbs Free Energy Profile of Ribonuclease A

Protein and Peptide Letters ◽

10.2174/0929866023408625 ◽

2002 ◽

Vol 9 (4) ◽

pp. 305-313

Author(s):

Paul Chun

Keyword(s):

Free Energy ◽

Gibbs Free Energy ◽

Thermodynamic Data ◽

Ribonuclease A ◽

Energy Profile ◽

Free Energy Profile

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Injectable in-situ Forming Depot Of Doxycycline Hyclate/α-Cyclodextrin Complex using PLGA for Periodontitis Treatment: Preparation, Charac-terization, and In-Vitro Evaluation

Current Drug Delivery ◽

10.2174/1567201817999201103195104 ◽

2020 ◽

Vol 17 ◽

Author(s):

Elham Khodaverdi ◽

Farhad Eisvand ◽

Mohammad Sina Nezami ◽

Seyedeh Nesa Rezaeian Shiadeh ◽

Hossein Kamali ◽

...

Keyword(s):

Complex Form ◽

Docking Studies ◽

Morphological Properties ◽

Burst Release ◽

Cyclodextrin Complex ◽

Doxycycline Hyclate ◽

Scanning Calorimetry ◽

In Situ Forming

Background:: Doxycycline (DOX) is used in treating a bacterial infection, especially for periodontitis treatment. Objective: To reduce irritation of DOX for subgingival administration and increase the chemical stability and against enzy-matic, the complex of α-cyclodextrin with DOX was prepared and loaded into injectable in situ forming implant based on PLGA. Methods:: FTIR, molecular docking studies, X-ray diffraction, and differential scanning calorimetry was performed to char-acterize the DOX/α-cyclodextrin complex. Finally, the in-vitro drug release and modeling, morphological properties, and cellular cytotoxic effects were also evaluated. Results:: The stability of DOX was improved with complex than pure DOX. The main advantage of the complex is the al-most complete release (96.31 ± 2.56 %) of the drug within 14 days of the implant, whereas in the formulation containing the pure DOX and the physical mixture the DOX with α-cyclodextrin release is reached to 70.18 ± 3.61 % and 77.03 ± 3.56 %, respectively. This trend is due to elevate of DOX stability in the DOX/ α-cyclodextrin complex form within PLGA implant that confirmed by the results of stability. Conclusion:: Our results were indicative that the formulation containing DOX/α-cyclodextrin complex was biocompatible and sustained-release with minimum initial burst release.

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Energy Profile Summary for North River WWTP Cogeneration Upgrades

Proceedings of the Water Environment Federation ◽

10.2175/193864715819558145 ◽

2015 ◽

Vol 2015 (2) ◽

pp. 1-28

Author(s):

Tia Trate ◽

Stephen Tarallo ◽

Anthony Fiore ◽

James Lauria

Keyword(s):

Energy Profile

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Polymer Composites with 0.98 Transparencies and Small Optical Energy Band Gap Using a Promising Green Methodology: Structural and Optical Properties

Polymers ◽

10.3390/polym13101648 ◽

2021 ◽

Vol 13 (10) ◽

pp. 1648

Author(s):

Muaffaq M. Nofal ◽

Shujahadeen B. Aziz ◽

Jihad M. Hadi ◽

Wrya O. Karim ◽

Elham M. A. Dannoun ◽

...

Keyword(s):

Refractive Index ◽

Optical Properties ◽

Polymer Composites ◽

Amorphous Phase ◽

Absorption Edge ◽

Complex Form ◽

Bandgap Energy ◽

Optical Parameters ◽

Visible Spectroscopy ◽

Uv Visible

In this work, a green approach was implemented to prepare polymer composites using polyvinyl alcohol polymer and the extract of black tea leaves (polyphenols) in a complex form with Co2+ ions. A range of techniques was used to characterize the Co2+ complex and polymer composite, such as Ultraviolet–visible (UV-Visible) spectroscopy, Fourier transform infrared spectroscopy (FTIR), and X-ray diffraction (XRD). The optical parameters of absorption edge, refractive index (n), dielectric properties including real and imaginary parts (εr, and εi) were also investigated. The FRIR and XRD spectra were used to examine the compatibility between the PVA polymer and Co2+-polyphenol complex. The extent of interaction was evidenced from the shifts and change in the intensity of the peaks. The relatively wide amorphous phase in PVA polymer increased upon insertion of the Co2+-polyphenol complex. The amorphous character of the Co2+ complex was emphasized with the appearance of a hump in the XRD pattern. From UV-Visible spectroscopy, the optical properties, such as absorption edge, refractive index (n), (εr), (εi), and bandgap energy (Eg) of parent PVA and composite films were specified. The Eg of PVA was lowered from 5.8 to 1.82 eV upon addition of 45 mL of Co2+-polyphenol complex. The N/m* was calculated from the optical dielectric function. Ultimately, various types of electronic transitions within the polymer composites were specified using Tauc’s method. The direct bandgap (DBG) treatment of polymer composites with a developed amorphous phase is fundamental for commercialization in optoelectronic devices.

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Free energy profile analysis to identify factors activating the aggregation-induced emission of a cyanostilbene derivative

Physical Chemistry Chemical Physics ◽

10.1039/d0cp04246c ◽

2021 ◽

Author(s):

Norifumi Yamamoto

Keyword(s):

Free Energy ◽

Profile Analysis ◽

Energy Profile ◽

Contributing Factors ◽

Free Energy Profile ◽

Aggregation Induced Emission ◽

Energy Profiles ◽

Free Energy Profiles

The contributing factors that cause the aggregation-induced emission (AIE) are determined by identifying characteristic differences in the free energy profiles of the AIE processes of the AIE-active E-form of CN-MBE and the inactive Z-form.

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