scholarly journals MrPIXEL: automated execution of Pixel calculations via the Mercury interface

2020 ◽  
Vol 53 (4) ◽  
pp. 1154-1162 ◽  
Author(s):  
Matthew G. Reeves ◽  
Peter A. Wood ◽  
Simon Parsons
Keyword(s):  
Intermolecular Interaction ◽  
Chemical Properties ◽  
Lattice Energy ◽  
Intermolecular Interaction Energy ◽  
Structure Information ◽  
Empirical Procedure ◽  
Remote Server ◽  
Pauli Repulsion ◽  
Semi Empirical ◽  
Physical And Chemical

The interpretation of crystal structures in terms of intermolecular interaction energies enables phase stability and polymorphism to be rationalized in terms of quantitative thermodynamic models, while also providing insight into the origin of physical and chemical properties including solubility, compressibility and host–guest formation. The Pixel method is a semi-empirical procedure for the calculation of intermolecular interactions and lattice energies based only on crystal structure information. Molecules are represented as blocks of undistorted ab initio molecular electron and nuclear densities subdivided into small volume elements called pixels. Electrostatic, polarization, dispersion and Pauli repulsion terms are calculated between pairs of pixels and nuclei in different molecules, with the accumulated sum equating to the intermolecular interaction energy, which is broken down into physically meaningful component terms. The MrPIXEL procedure enables Pixel calculations to be carried out with minimal user intervention from the graphical interface of Mercury, which is part of the software distributed with the Cambridge Structural Database (CSD). Following initial setup of a crystallographic model, one module assigns atom types and writes necessary input files. A second module then submits the required electron-density calculation either locally or to a remote server, downloads the results, and submits the Pixel calculation itself. Full lattice energy calculations can be performed for structures with up to two molecules in the crystallographic asymmetric unit. For more complex cases, only molecule–molecule energies are calculated. The program makes use of the CSD Python API, which is also distributed with the CSD.

scholarly journals Physico-chemical analysis, systematic benchmarking, and toxicological aspects of the JWH aminoalkylindole class-derived synthetic JWH cannabinoids

2021 ◽  
Vol 44 (1) ◽  
pp. 34-45
Author(s):  
Catalina Mercedes Burlacu ◽  
Adrian Constantin Burlacu ◽  
Mirela Praisler
Keyword(s):  
Synthetic Cannabinoids ◽  
Chemical Properties ◽  
Pharmacokinetic Profile ◽  
Spectral Techniques ◽  
Software Packages ◽  
Physico Chemical ◽  
Semi Empirical ◽  
Analytical Tools ◽  
Physical And Chemical ◽  
Toxicity Indices

We are presenting the results obtained by computing different toxicity indices for some of the newest JWH synthetic cannabinoids, by using (Q)SAR models, ADME(T) predictions, simulations of NMR spectral techniques and other different computational dedicated software packages and forensic analytical tools. We have examined the main physical and chemical properties and evaluated the behavioral neurotoxicity and pharmacokinetic profile of 16 aminoalkylindole class-derived synthetic cannabinoids JWH as compared to the Delta-9-tetrahydrocannabinol (Δ9-THC), which was chosen as a standard compound. For this purpose, the geometries of the molecules have been optimized by using the AM1 semi-empirical quantum method. The conclusions of a comparative analysis of the toxicities of synthetic and natural cannabinoids are presented.

scholarly journals Crystal structures and Hirshfeld surface analyses of (E)-N′-benzylidene-2-oxo-2H-chromene-3-carbohydrazide and the disordered hemi-DMSO solvate of (E)-2-oxo-N′-(3,4,5-trimethoxybenzylidene)-2H-chromene-3-carbohydrazide: lattice energy and intermolecular interaction energy calculations for the former

2019 ◽  
Vol 75 (10) ◽  
pp. 1403-1410 ◽  
Author(s):  
Ligia R. Gomes ◽  
John Nicolson Low ◽  
James L. Wardell ◽  
Camiola Capelini ◽  
Vitoria R.F. Câmara ◽  
...  
Keyword(s):  
Interaction Energy ◽  
Crystal Structures ◽  
Intermolecular Interaction ◽  
Three Dimensional ◽  
Lattice Energy ◽  
Hirshfeld Surface ◽  
Hydrogen Atoms ◽  
Intermolecular Interaction Energy ◽  
Energy Calculations ◽  
Dimensional Array

The crystal structures of the disordered hemi-DMSO solvate of (E)-2-oxo-N′-(3,4,5-trimethoxybenzylidene)-2H-chromene-3-carbohydrazide, C20H18N2O6·0.5C2H6OS, and (E)-N′-benzylidene-2-oxo-2H-chromene-3-carbohydrazide, C17H12N2O3 (4: R = C6H5), are discussed. The non-hydrogen atoms in compound [4: R = (3,4,5-MeO)3C6H2)] exhibit a distinct curvature, while those in compound, (4: R = C6H5), are essential coplanar. In (4: R = C6H5), C—H...O and π–π intramolecular interactions combine to form a three-dimensional array. A three-dimensional array is also found for the hemi-DMSO solvate of [4: R = (3,4,5-MeO)3C6H2], in which the molecules of coumarin are linked by C—H...O and C—H...π interactions, and form tubes into which the DMSO molecules are cocooned. Hirshfeld surface analyses of both compounds are reported, as are the lattice energy and intermolecular interaction energy calculations of compound (4: R = C6H5).

INVESTIGATION ON INTERMOLECULAR INTERACTION IN SUPERSATURATION STATE OF CADMIUM SULPHATE MIXED ZINC tris-THIOUREA SULPHATE SOLUTIONS

2014 ◽  
Vol 02 (03n04) ◽  
pp. 1450002 ◽  
Author(s):  
G. G. MULEY ◽  
A. B. NAIK ◽  
A. B. GAMBHIRE
Keyword(s):  
Crystal Growth ◽  
Intermolecular Interaction ◽  
Growth Parameters ◽  
Chemical Properties ◽  
Adiabatic Compressibility ◽  
Growth Conditions ◽  
Ft Ir ◽  
Solid Form ◽  
Physical And Chemical ◽  
And Chemical Properties

Zinc tris-thiourea sulphate (ZTS) is a well known nonlinear optical (NLO) crystal widely used for various NLO applications. The NLO, physical and chemical properties can be modified by adding impurities and/or modifying crystal growth conditions. The impurities present in the growth solution and growth conditions can affect the crystal growth parameters at great extent. Thus, the study on the nature of intermolecular interaction with the dopant in the solution during crystal growth process becomes important. In the present investigation, the ultrasonic velocity was measured in the aqueous solutions of pure and cadmium sulphate mixed ZTS in the supersaturation state at 313.15 K. The thermodynamic parameters such as adiabatic compressibility, inter molecular free length, acoustic impedance and relative associations have been calculated from the ultrasonic data and densities of water and solutions at 313.15 K, and the nature of intermolecular interaction has been discussed. FT-IR spectra of all mixtures in the solid form at room temperature were recorded and the shifts in the absorption peaks corresponding to the functional groups of ZTS have been reported.

scholarly journals Theoretical Prediction of Possible Drug Treatment of COVID-19 using Coumarins Containing Chloroquine Moeity

2020 ◽  
Vol 32 (12) ◽  
pp. 3120-3126
Author(s):  
A.A. Ibrahim ◽  
O.M. Yahya ◽  
M.A. Ibrahim
Keyword(s):  
Theoretical Calculations ◽  
Chemical Properties ◽  
Basis Sets ◽  
Am1 Method ◽  
Hartree Fock ◽  
Physico Chemical ◽  
Coumarin Compound ◽  
Semi Empirical ◽  
Physical And Chemical ◽  
And Chemical Properties

Chloroquine was theoretically reacted with the coumarin compound. Two compounds viz. [N-(7-chloroquinolin-4-yl)-N-(5-(diethylamino)-pentan-2-yl)-4-methyl-2-oxo-2H-chromene-7- sulfonamide] (3) and [N-(7-chloroquinolin-4-yl)-N-(5-(diethylamino)pentan-2-yl)-4-methyl-2-oxo- 2H-chromene-6-sulfonamide] (4) were suggested. The results showed that compound 4 may influence the COVID-19 treatment. The physico-chemical parameters were determined through theoretical calculations by using Hartree-Fock at different basis sets (6-31G), (STO/3G) and the semi-empirical (AM1) method. The calculations demonstrated the scheme of reaction between coumarin and the chloroquine structure by using the predicted mechanisms. The physical and chemical properties of the predicted compounds were determined to select the optimal form as the candidate for COVID-19 treatment. Compound 4 was more stable than compound 3, with different proteins viz. 6YHU, 6YI3 and 6LU7. Three types of software, including Gaussian 03, Chem-Bio office and molecular operating environment (MOE) were employed.

Statistical criteria of stellar population types

1966 ◽  
Vol 24 ◽  
pp. 101-110
Author(s):  
W. Iwanowska
Keyword(s):  
Stellar Population ◽  
Chemical Properties ◽  
Spectrophotometric Study ◽  
Physical And Chemical Properties ◽  
Population Type ◽  
The Galaxy ◽  
Distribution Parameters ◽  
Physical And Chemical ◽  
Statistical Criteria ◽  
And Chemical Properties

In connection with the spectrophotometric study of population-type characteristics of various kinds of stars, a statistical analysis of kinematical and distribution parameters of the same stars is performed at the Toruń Observatory. This has a twofold purpose: first, to provide a practical guide in selecting stars for observing programmes, second, to contribute to the understanding of relations existing between the physical and chemical properties of stars and their kinematics and distribution in the Galaxy.

Biophysical Measurement of Molecular Weight of Foot-and-Mouth Disease RNA Fragments

1974 ◽  
Vol 32 ◽  
pp. 262-263
Author(s):  
Sydney S. Breese ◽  
Howard L. Bachrach
Keyword(s):  
Chemical Properties ◽  
Foot And Mouth Disease ◽  
Mouth Disease ◽  
Distilled Water ◽  
Bovine Plasma ◽  
Mouth Disease Virus ◽  
Foot And Mouth ◽  
Carbon Coated ◽  
Rna Fragments ◽  
Physical And Chemical

Continuing studies on the physical and chemical properties of foot-and-mouth disease virus (FMDV) have included electron microscopy of RNA strands released when highly purified virus (1) was dialyzed against demlneralized distilled water. The RNA strands were dried on formvar-carbon coated electron microscope screens pretreated with 0.1% bovine plasma albumin in distilled water. At this low salt concentration the RNA strands were extended and were stained with 1% phosphotungstic acid. Random dispersions of strands were recorded on electron micrographs, enlarged to 30,000 or 40,000 X and the lengths measured with a map-measuring wheel. Figure 1 is a typical micrograph and Fig. 2 shows the distributions of strand lengths for the three major types of FMDV (A119 of 6/9/72; C3-Rezende of 1/5/73; and O1-Brugge of 8/24/73.

Tailoring microstructures of materials through biomimetics

1993 ◽  
Vol 51 ◽  
pp. 500-501
Author(s):  
Mehmet Sarikaya ◽  
Ilhan A. Aksay
Keyword(s):  
Chemical Properties ◽  
Design And Synthesis ◽  
Structure Sensitive ◽  
Macro Scale ◽  
Methods Of Synthesis ◽  
Successive Level ◽  
Engineering Materials ◽  
Physical And Chemical ◽  
And Chemical Properties ◽  
Synthesis Of Materials

Biomimetics involves investigation of structure, function, and methods of synthesis of biological composite materials. The goal is to apply this information to the design and synthesis of materials for engineering applications.Properties of engineering materials are structure sensitive through the whole spectrum of dimensions from nanometer to macro scale. The goal in designing and processing of technological materials, therefore, is to control microstructural evolution at each of these dimensions so as to achieve predictable physical and chemical properties. Control at each successive level of dimension, however, is a major challenge as is the retention of integrity between successive levels. Engineering materials are rarely fabricated to achieve more than a few of the desired properties and the synthesis techniques usually involve high temperature or low pressure conditions that are energy inefficient and environmentally damaging.In contrast to human-made materials, organisms synthesize composites whose intricate structures are more controlled at each scale and hierarchical order.

Response of corn (Zea mays L.) to various organic-based fertilizers in marginal upland of Sta. Rita, Samar

2017 ◽  
pp. 31-43
Author(s):  
Berta Ratilla ◽  
Loreme Cagande ◽  
Othello Capuno
Keyword(s):  
Block Design ◽  
Management Strategies ◽  
Chemical Properties ◽  
Organic Fertilizers ◽  
Growth And Yield ◽  
Physical And Chemical Properties ◽  
Total N ◽  
Randomized Complete Block Design ◽  
Physical And Chemical ◽  
And Chemical Properties

Organic farming is one of the management strategies that improve productivity of marginal uplands. The study aimed to: (1) evaluate effects of various organic-based fertilizers on the growth and yield of corn; (2) determine the appropriate combination for optimum yield; and (3) assess changes on the soil physical and chemical properties. Experiment was laid out in Randomized Complete Block Design, with 3 replications and 7 treatments, namely; T0=(0-0-0); T1=1t ha-1 Evans + 45-30-30kg N, P2O5, K2O ha-1; T2=t ha-1 Wellgrow + 45-30-30kg N, P2O5, K2O ha-1; T3=15t ha-1 chicken dung; T4=10t ha-1 chicken dung + 45-30-30kg N, P2O5, K2O ha-1; T5=15t ha-1 Vermicast; and T6=10t ha-1 Vermicast + 45-30-30kg N, P2O5, K2O ha-1. Application of organic-based fertilizers with or without inorganic fertilizers promoted growth of corn than the control. But due to high infestation of corn silk beetle(Monolepta bifasciata Horns), its grain yield was greatly affected. In the second cropping, except for Evans, any of these fertilizers applied alone or combined with 45-30-30kg N, P2O5, K2O ha-1 appeared appropriate in increasing corn earyield. Soil physical and chemical properties changed with addition of organic fertilizers. While bulk density decreased irrespective of treatments, pH, total N, available P and exchangeable K generally increased more with chicken dung application.

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