Three-Dimensional Chemical Structure Search Using the Conformational Code for Organic Molecules (CCOM) Program

Chirality ◽  
2016 ◽  
Vol 28 (5) ◽  
pp. 370-375 ◽  
Author(s):  
Hiroshi Izumi ◽  
Laurence A. Nafie ◽  
Rina K. Dukor
Keyword(s):  
Chemical Structure ◽  
Organic Molecules ◽  
Three Dimensional ◽  
Structure Search

3D simulations of warm and hot Jupiter atmospheres: the role of 3D mixing in shaping CH4-to-CO conversion pathways

2021 ◽  
Author(s):  
Maria Zamyatina ◽  
Eric Hebrard ◽  
Nathan Mayne ◽  
Benjamin Drummond
Keyword(s):  
Chemical Structure ◽  
Three Dimensional ◽  
Chemical Species ◽  
Radiation Chemistry ◽  
3D Simulations ◽  
Horizontal Advection ◽  
Co Conversion ◽  
Area Of Influence ◽  
Different Parts

<p>We present results from a set of cloud-free simulations of exoplanet atmospheres using a coupled three-dimensional (3D) hydrodynamics-radiation-chemistry model. We report in particular our investigation of the thermodynamic and chemical structure of the atmospheres of HAT-P-11b and WASP-17b and their comparison with the results for the atmospheres of HD 189733b and HD 209458b presented in Drummond et al. (2020). We found that the abundances of chemical species from simulations with interactive chemistry depart from their respective abundances computed at local chemical equilibrium, especially at higher latitudes. To understand this departure, we analysed the CH<sub>4</sub>-to-CO conversion pathways within the Venot et al. (2019) reduced chemical network used in our model using a chemical network analysis. We found that at steady state nine CH<sub>4</sub>-to-CO conversion pathways manifest in our 3D simulations with interactive chemistry, with different pathways dominating different parts of the atmosphere and their area of influence being determined by the vertical and horizontal advection and shifting between planets.</p>

scholarly journals Identification of new superwarfarin-type rodenticides by structural similarity. The docking of ligands on the vitamin K epoxide reductase enzyme’s active site

2015 ◽  
Vol 7 (1) ◽  
pp. 108-122
Author(s):  
László Ferencz ◽  
Daniela Lucia Muntean
Keyword(s):  
Vitamin K ◽  
Chemical Structure ◽  
Enzyme Inhibitors ◽  
Structural Similarity ◽  
Vitamin K Epoxide Reductase ◽  
Pubchem Compound ◽  
Structure Search ◽  
Epoxide Reductase ◽  
Compound Database ◽  
Similarity Thresholds

Abstract The rodenticide brodifacoum is highly toxic to mammals and birds, and extremely toxic to fish. It is a highly cumulative poison due to its high lipophilicity and extremely slow elimination. For this reason, it may be interesting to find similar compounds in order to enlarge the spectrum of vitamin K epoxide reductase enzyme inhibitors used today in pest control. We used the Similar Compounds search type of the Chemical Structure Search of the PubChem Compound Database to locate records that are similar to the chemical structure of brodifacoum, using pre-specified similarity thresholds. Using the threshold ≥ than 95% for the similar structures criteria, we found 14 compounds (from over 30 million entries) that meet this criteria. Two of these compounds have a better binding affinity to vitamin K epoxide reductase enzyme than brodifacoum, but the binding energy of the other 12 substances is also high, having identical or lower lipophilicity; consequently, they will eliminate faster, possibly lacking a part of the adverse effects.

Ordered Assembling of Size and Shape Selected Nanocrystals

1998 ◽  
Vol 4 (S2) ◽  
pp. 728-729
Author(s):  
Z.L. Wang
Keyword(s):  
Organic Molecules ◽  
Three Dimensional ◽  
Building Blocks ◽  
Organic Coating ◽  
Self Organization ◽  
Functional Specificity ◽  
Orientation Order ◽  
Self Assembled ◽  
Superlattice Structures ◽  
Physical And Chemical

Nanoparticles and the physical and chemical functional specificity and selectivity they possess, suggest them as ideal building blocks for two- and three-dimensional cluster self-assembled superlattice structures, in which the particles behave as well-defined molecular matter and they are arranged with long-range translation and even orientation order [1]. Self-assembled arrays involve self-organization into monolayers, thin films, and superlattices of size-selected nanoclusters encapsulated in protective compact organic coating. The macroscopic properties of the nanocrystal superlattice (NCS) are determined not only by the properties of each individual particle but by the coupling/interaction between nanocrystals interconnected and isolated by a monolayer of thin organic molecules.Periodic packing of nanocrystals is different from the 3-D packing of atoms. First, to an excellent approximation atoms are spherical, while nanoparticles can be faceted polyhedra, thus, the 3-D packing of particles can be critically affected by their shapes and sizes.

The Effect of Acidity Coefficient on Crystallization Behavior of Blast Furnace Slag Fibers

2018 ◽  
Vol 37 (1) ◽  
pp. 33-37
Author(s):  
Tie-Lei Tian ◽  
Yu-Zhu Zhang ◽  
Hong-wei Xing ◽  
Jie Li ◽  
Zun-Qian Zhang
Keyword(s):  
Thermal Stability ◽  
Crystallization Kinetics ◽  
Blast Furnace Slag ◽  
Chemical Structure ◽  
Crystallization Behavior ◽  
Three Dimensional ◽  
Mineral Wool ◽  
Mineral Wool Fiber ◽  
Kinetics Of ◽  
Furnace Slag

AbstractThe chemical structure of mineral wool fiber was investigated by using Fourier Transform Infrared Spectroscopy (FTIR). Next, the glass transition temperature and the crystallization temperature of the fibers were studied. Finally, the crystallization kinetics of fiber was studied. The results show that the chemical bond structure of fibers gets more random with the increase of acidity coefficient. The crystallization phases of the fibers are mainly melilites, and also a few anorthites and diopsides. The growth mechanism of the crystals is three dimensional. The fibers with acidity coefficient of 1.2 exhibit the best thermal stability and is hard to crystallize as it has the maximum aviation energy of crystallization kinetics.

A Mechanism for Supercooling in Organic Liquids

1995 ◽  
Vol 398 ◽  
Author(s):  
Paul E. Thoma
Keyword(s):  
Melting Temperature ◽  
Chemical Structure ◽  
Three Dimensional ◽  
Freezing Temperature ◽  
Organic Liquids ◽  
Molecular Characteristics ◽  
A Charge

ABSTRACTIn this investigation, a mechanism for supercooling in organic liquids is formulated. By comparing the melting temperature and spontaneous freezing temperature of the chemicals evaluated with their molecular characteristics, the factors promoting supercooling are developed. The results obtained indicate that the following molecular characteristics promote supercooling in organic liquids:sharing of electrons between the atoms of a molecule;A three-dimensional chemical structure;A permanent, three-dimensional, and partially charged pocket within the chemical structure;A partially charged projection having a charge opposite that of the pocket and located on the side of the molecule opposite that of the pocket.

scholarly journals G-RMSD: Root Mean Square Deviation Based Method for Three-dimensional Molecular Similarity Determination

2020 ◽  
Author(s):  
Tomonori Fukutani, ◽  
kohei Miyazawa ◽  
Satoru Iwata ◽  
Hiroko Satoh
Keyword(s):  
Root Mean Square ◽  
Root Mean Square Deviation ◽  
Three Dimensional ◽  
Valence Bond ◽  
Optimization Method ◽  
Molecular Structures ◽  
Mean Square ◽  
Mean Square Deviation ◽  
Atomic Structures ◽  
Structure Search

<div>We present the Generalized Root Mean Square Deviation (G-RMSD) method. G-RMSD is an optimization method to calculate the minimal RMSD value of two atomic structures by optimal superimposition. The method is not restricted to systems with an equal number of atoms or a unique atom matching and can handle any type of chemical structure, including transition states and non-valence bond structures. It requires only Cartesian coordinates for the structures, but can also include further information, i.e. atom and bond types. Applications of G-RMSD to the classification of alpha-D-glucose conformers and 3D partial structure search using a dataset containing equilibrium (EQ), dissociation channel (DC), and transition state (TS) structures are demonstrated. We find that G-RMSD allows for a successful classification and mapping for a wide variety of molecular structures.</div><div><br></div>

scholarly journals G-RMSD: Root Mean Square Deviation Based Method for Three-dimensional Molecular Similarity Determination

2020 ◽  
Author(s):  
Tomonori Fukutani, ◽  
kohei Miyazawa ◽  
Satoru Iwata ◽  
Hiroko Satoh
Keyword(s):  
Root Mean Square ◽  
Root Mean Square Deviation ◽  
Three Dimensional ◽  
Valence Bond ◽  
Optimization Method ◽  
Molecular Structures ◽  
Mean Square ◽  
Mean Square Deviation ◽  
Atomic Structures ◽  
Structure Search

<div>We present the Generalized Root Mean Square Deviation (G-RMSD) method. G-RMSD is an optimization method to calculate the minimal RMSD value of two atomic structures by optimal superimposition. The method is not restricted to systems with an equal number of atoms or a unique atom matching and can handle any type of chemical structure, including transition states and non-valence bond structures. It requires only Cartesian coordinates for the structures, but can also include further information, i.e. atom and bond types. Applications of G-RMSD to the classification of alpha-D-glucose conformers and 3D partial structure search using a dataset containing equilibrium (EQ), dissociation channel (DC), and transition state (TS) structures are demonstrated. We find that G-RMSD allows for a successful classification and mapping for a wide variety of molecular structures.</div><div><br></div>

Up-Conversion Nanoparticles/PMMA Composites for Light-Emitting Applications

NANO ◽  
2020 ◽  
Vol 15 (02) ◽  
pp. 2050023
Author(s):  
Yongling Zhang ◽  
Peng Lv ◽  
Xiang Liu ◽  
Haoyuan Chi ◽  
Guoqing Xi ◽  
...  
Keyword(s):  
Chemical Structure ◽  
Fluorescence Spectra ◽  
In Situ Polymerization ◽  
Three Dimensional ◽  
Luminescence Spectra ◽  
3D Display ◽  
Light Emitting ◽  
Bulk Polymers ◽  
Doping Ratio

In this paper, we prepared KMnF3:Yb[Formula: see text], Er[Formula: see text] nanoparticles (NPs)/polymethyl methacrylate (PMMA) composites, NaYF4:Yb[Formula: see text], Tm[Formula: see text]NPs/PMMA composites and NaYF4Yb[Formula: see text], Er[Formula: see text]NPs/PMMA composites by in situ polymerization, and these NPs/PMMA composites can emit red, blue and green up-conversion fluorescence excited by 980[Formula: see text]nm, respectively. The mixed white NPs/PMMA composites were obtained by adjusting the doping ratio of the above three NPs. These NPs/PMMA composites are transparent. We tested the up-conversion fluorescence spectra of all the NPs and NPs/PMMA composites, under 980[Formula: see text]nm excitation. The up-conversion luminescence spectra of the NPs and NPs/PMMA composites are consistent, which further indicates that the in situ polymerization has not changed the chemical structure of the NPs. Then, we prepared transparent bulk polymers by curing these NPs/PMMA composites. Under 980[Formula: see text]nm laser excitation, these NPs/PMMA bulk polymers can emit red, blue, green and white up-conversion emissions, respectively. The results indicate that the NPs/PMMA composites can be applied to three-dimensional (3D) display.

scholarly journals Amide Bond Activation of Biological Molecules

Molecules ◽  
2018 ◽  
Vol 23 (10) ◽  
pp. 2615 ◽  
Author(s):  
Sriram Mahesh ◽  
Kuei-Chien Tang ◽  
Monika Raj
Keyword(s):  
Organic Molecules ◽  
Unique Feature ◽  
Bond Activation ◽  
Three Dimensional ◽  
Review Article ◽  
Biological Molecules ◽  
Amide Bond ◽  
Amide Bonds ◽  
Dna And Rna ◽  
Peptide Acids

Amide bonds are the most prevalent structures found in organic molecules and various biomolecules such as peptides, proteins, DNA, and RNA. The unique feature of amide bonds is their ability to form resonating structures, thus, they are highly stable and adopt particular three-dimensional structures, which, in turn, are responsible for their functions. The main focus of this review article is to report the methodologies for the activation of the unactivated amide bonds present in biomolecules, which includes the enzymatic approach, metal complexes, and non-metal based methods. This article also discusses some of the applications of amide bond activation approaches in the sequencing of proteins and the synthesis of peptide acids, esters, amides, and thioesters.

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