Images of Cholesterol
Based on Quantum Chemical Computations
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Executive Summary
High-quality images and the structure datafile of cholesterol based on a decent quantum chemical calculation have been prepared on this webpage, which are useful not only for further scientific research and development but also for preparing professional reports, articles, presentations, webpages, books, etc. The cholesterol images of 3-dimensional (3D) molecular structures, molecular surfaces, molecular orbitals, and an optimized 3D structure datafile (SDF/MOL File) are readily accessible for purchase, which have been generated on the basis of data derived from quantum chemical computations under DFT (Density Functional Theory) - B3LYP functional with 6-31G* basis set. The images have been generated on an automatic basis using the image generation engines developed as a part of Mol-Instincts Web-Information Project.
Identification of Target Chemical Substance
Due to the complicated nature of chemical substances, the pure substance to be dealt with on this webpage (target chemical substance) needs to be confirmed whether it is truly the one you are anticipating. Identification should be based upon not only its name but also its structure and/or other identifiers.
The target chemical substance is typically called “cholesterol”. It contains a total of 74 atom(s) , consisting of 46 Hydrogen atom(s), 27 Carbon atom(s), and 1 Oxygen atom(s). As for the chemical bonds and functional groups, a total of 77 bond(s) comprising 31 non-H bond(s), 1 multiple bond(s), 5 rotatable bond(s), 1 double bond(s), 1 five-membered ring(s), 3 six-membered ring(s), 1 nine-membered ring(s), 2 ten-membered ring(s), 1 hydroxyl group(s), and 1 secondary alcohol(s) exist within the chemical structure.
The 2-dimensional (2D) structure, IUPAC name, formula, molecular weight, and other identifiers of cholesterol are given below:
| IUPAC Name | (1S,2R,5S,10S,11S,14R,15R)-2,15-dimethyl-14-[(2R)-6-methylheptan-2-yl]tetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadec-7-en-5-ol |
|---|---|
| Chemical Formula | C27H46O |
| Molecular Weight | 386.65354 g/mol |
| SMILES String | CC(C)CCCC(C)C3CCC4C2CC=C1CC(O)CCC1(C)C2CCC34C |
| InChI | InChI=1S/C27H46O/c1-18(2)7-6-8-19(3)23-11-12-24-22-10-9-20-17-21(28)13-15-26(20,4)25(22)14-16-27(23,24)5/h9,18-19,21-25,28H,6-8,10-17H2,1-5H3/t19-,21+,22+,23-,24+,25+,26+,27-/m1/s1 |
| InChIKey | HVYWMOMLDIMFJA-DPAQBDIFSA-N |
Note that the IUPAC name, chemical formula, molecular weight, and SMILES (Simplified Molecular-Input Line-Entry System) string are supplementary and are not “necessary & sufficient” conditions for the identification. The 2D structure, InChI (International Chemical Identifier) and InChIKey are however unique identifiers. As an additional supplementary information for the identification, the cholesterol is also called in various chemical industries as given in this URL link.
Quantum Chemical Calculations
A robust quantum chemical calculation was performed to obtain physically meaningful structure data and images. A large number of test runs have been performed to determine an optimal combination of calculation methods (e.g., Hartree-Fock, Density Functional Theory; DFT, etc.) and basis sets (e.g., STO-3G, 6-31G*, etc.). Based on the prediction accuracy analysis of entropy, dipole moment, frequency, heat capacity, magnetic susceptibility, polarizability, radius of gyration, van der Waals area, and van der Waals volume, it was concluded that the DFT-B3LYP functional with 6-31G* basis set is an optimal combination, which provides a decent accuracy as well as a reasonable computation time.
The initial 3D structure of cholesterol was generated automatically by making use of the structure generation engine of Mol-Instincts, a chemical database powered by 41 patented technologies based on quantum chemical computations, statistical thermodynamics, QSPR (Quantitative Structure-Property Relationship), and an artificial neural network-based AI (Artificial Intelligence). Geometry optimization and frequency calculation followed by the RI-MP2 energy correction have been performed for cholesterol using the DFT-B3LYP functional with 6-31G* basis set. The optimized structure of cholesterol was verified to be at a true minimum with no imaginary frequencies.
Prior to performing the geometry optimization, the starting structure of the target chemical substance was determined with a great care to obtain a reliable optimized geometry without imaginary frequencies originated from local minima. The initial 3D structure generated by the structure generation engine was processed by a detailed conformer analysis when single bond(s) exist(s) in the target chemical substance. Depending on the number of the single bonds in the target substance, up to tens of thousands of conformers have been generated automatically. Subsequently, a simple potential energy calculation based on the MMFF94s force field was carried out for each conformer. The conformer with the lowest potential energy was then used as the starting structure of the geometry optimization.
Optimized 3D Structure Images of Cholesterol
Using the geometry optimization results, high-quality images of 3D molecular structures have been prepared for cholesterol in 3 different models, namely, stick, ball & stick, and space-filling, which provide not only the basic structure information but also a physically meaningful configuration (e.g., bond lengths, bond angles, etc.) at the lowest energy level. The animated gif of the ball & stick model is also provided for a better visualization, which may be useful for further professional presentation and/or web publication.
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- Title
- Stick Model Image of Optimized Cholesterol Structure
- Description
- Stick model image of 3D molecular structure of cholesterol created based on the quantum chemical geometry optimization results under DFT-B3LYP functional with 6-31G* basis set.
- Product Type
- Portable Network Graphics (PNG) 2,000 x 2,000 pixels
- Price
- $ USD per user per publication
-
- Title
- Ball & Stick Model Image of Optimized Cholesterol Structure
- Description
- Ball & stick model image of 3D molecular structure of cholesterol created based on the quantum chemical geometry optimization results under DFT-B3LYP functional with 6-31G* basis set.
- Product Type
- Portable Network Graphics (PNG) 2,000 x 2,000 pixels
- Price
- $ USD per user per publication
-
- Title
- Space-filling Model Image of Optimized Cholesterol Structure
- Description
- Space-filling model image of 3D molecular structure of cholesterol created based on the quantum chemical geometry optimization results under DFT-B3LYP functional with 6-31G* basis set.
- Product Type
- Portable Network Graphics (PNG) 2,000 x 2,000 pixels
- Price
- $ USD per user per publication
-
- Title
- Ball & Stick Model Animated Gif of Optimized Cholesterol Structure
- Description
- Ball & stick model animated gif of 3D molecular structure of cholesterol created based on the quantum chemical geometry optimization results under DFT-B3LYP functional with 6-31G* basis set.
- Product Type
- Animated Graphics Interchange Format (GIF) 800 x 800 pixels
- Price
- $ USD per user per publication
3D Molecular Surface Images of Cholesterol
High-quality images of van der Waals and solvent-accessible surface have been prepared based on the optimized structure of cholesterol. The animated gif of van der Waals surface is provided as well for a better observation and for presentation and/or web publication.
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- Title
- van der Waals Surface Image of Optimized Cholesterol Structure
- Description
- van der Waals surface image of cholesterol based on the optimized 3D structure determined by quantum chemical geometry optimization under DFT-B3LYP functional with 6-31G* basis set.
- Product Type
- Portable Network Graphics (PNG) 2,000 x 2,000 pixels
- Price
- $ USD per user per publication
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- Title
- Solvent-accessible Surface Image of Optimized Cholesterol Structure
- Description
- Solvent-accessible surface image of cholesterol based on the optimized 3D structure determined by quantum chemical geometry optimization under DFT-B3LYP functional with 6-31G* basis set.
- Product Type
- Portable Network Graphics (PNG) 2,000 x 2,000 pixels
- Price
- $ USD per user per publication
-
- Title
- van der Waals Surface Animated Gif of Optimized Cholesterol Structure
- Description
- van der Waals surface animated gif of cholesterol based on the optimized 3D structure determined by quantum chemical geometry optimization under DFT-B3LYP functional with 6-31G* basis set.
- Product Type
- Animated Graphics Interchange Format (GIF) 800 x 800 pixels
- Price
- $ USD per user per publication
3D Molecular Orbital Images of Cholesterol
Using the geometry optimization results, high-quality images of 3D molecular structures have been prepared for cholesterol in 3 different models, namely, stick, ball & stick, and space-filling, which provide not only the basic structure information but also a physically meaningful configuration (e.g., bond lengths, bond angles, etc.) at the lowest energy level. The animated gif of the ball & stick model is also provided for a better visualization, which may be useful for further professional presentation and/or web publication.
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- Title
- HOMO Image of Optimized Cholesterol Structure
- Description
- HOMO (Highest Occupied Molecular Orbital) image of cholesterol based on the 3D structure determined by quantum chemical geometry optimization under DFT-B3LYP functional with 6-31G* basis set.
- Product Type
- Portable Network Graphics (PNG) 2,000 x 2,000 pixels
- Price
- $ USD per user per publication
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- Title
- LUMO Image of Optimized Cholesterol Structure
- Description
- LUMO (Lowest Unoccupied Molecular Orbital) image of cholesterol based on the 3D structure determined by quantum chemical geometry optimization under DFT-B3LYP functional with 6-31G* basis set.
- Product Type
- Portable Network Graphics (PNG) 2,000 x 2,000 pixels
- Price
- $ USD per user per publication
-
- Title
- HOMO Animated Gif of Optimized Cholesterol Structure
- Description
- HOMO (Highest Occupied Molecular Orbital) animated gif of cholesterol based on the 3D structure determined by quantum chemical geometry optimization under DFT-B3LYP functional with 6-31G* basis set.
- Product Type
- Animated Graphics Interchange Format (GIF) 800 x 800 pixels
- Price
- $ USD per user per publication
-
- Title
- LUMO Animated Gif of Optimized Cholesterol Structure
- Description
- LUMO (Lowest Unoccupied Molecular Orbital) animated gif of cholesterol based on the 3D structure determined by quantum chemical geometry optimization under DFT-B3LYP functional with 6-31G* basis set.
- Product Type
- Animated Graphics Interchange Format (GIF) 800 x 800 pixels
- Price
- $ USD per user per publication
Optimized 3D Structure Datafile (SDF/MOL File) of Cholesterol
For those who want to create their own images using custom software, the structure datafile (SDF/MOL file) of cholesterol has been prepared and made available for purchase below. This structure datafile may readily be imported to most of the chemistry-related software packages, performing custom visualization as well as further scientific analysis. Given that many computational software and visualization programs require the structural information of the target molecule, the SDF/MOL file below would come in handy to fulfill your immediate needs.
As the structure data included in the SDF/MOL file below represent an optimized structure of cholesterol obtained from the quantum chemical geometry optimization under DFT-B3LYP functional with 6-31G* basis set, it would be an excellent starting geometry for further intensive quantum calculations while significantly lowering the overall computation time.
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- Title
- Structure Datafile (SDF/MOL File) of Optimized Cholesterol
- Description
- SDF/MOL File of cholesterol determined by quantum chemical geometry optimization under DFT-B3LYP functional with 6-31G* basis set.
- Product Type
- Text
- Price
- Nonprofit $ USD For-Profit $ USD
Search Other Chemical Substances
Click the link on the right to search for the images and structure datafiles of other chemical substances.
More Information of Cholesterol
Further scientific and engineering information on Cholesterol are accessible from Mol-Instincts. The URL links of the available physicochemical, thermodynamic, and transport properties are listed below:
- Absolute Entropy of Ideal Gas
- Acentric Factor
- Critical Compressibility Factor
- Critical Pressure
- Critical Temperature
- Critical Volume
- Dipole Moment
- Enthalpy of Formation
- Enthalpy of Fusion
- Gibbs Energy of Formation
- Liquid Molar Volume
- Enthalpy of Combustion
- Normal Boiling Point
- Radius of Gyration
- Refractive Index
- Solubility Parameter
- Standard State Absolute Entropy
- Standard State Enthalpy of Formation
- Standard State Gibbs Energy of Formation
- Van Der Waals Area
- Van Der Waals Reduced Volume
- Magnetic Susceptibility
- Ionization Potential
- Electron affinity
- Flash Point
- Parachor
- Lower Flammability Limit Temperature
- Lower Flammability Limit Volume Percent
- Upper Flammability Limit Temperature
- Upper Flammability Limit Volume Percent
- Liquid Density
- Heat of Vaporization at 298.15K
- Heat of Vaporization at Normal Boiling Point
The above properties are provided as constant values, while the properties listed below are provided as a function of temperature:
The following links provide the spectra information of Cholesterol for the activities in analytical chemistry:
For the properties related to the pharmaceutical area, visit the following URL links:
- LogP (Octanol-Water Partition Coefficient)
- LogS (Water Solubility)
- Number of Acceptor Atoms for H-bonds
- Number of Donor Atoms for H-bonds
- Ghose-Crippen Molar Refractivity
- Ghose-Crippen Octanol-Water Partition Coefficient (logP)
- Moriguchi Octanol-Water Partition Coefficient (logP)
- Lipinski Alert Index
- Drug-likeness
- Activity Score for GPCR Ligands
- Activity Score for Ion Channel Modulators
- Activity Score for Kinase Inhibitors
Visit the link below for the 3D visualization, a detailed observation of the structure by zooming and rotating the molecule, measuring bond distances & angles, vibrational frequency analysis with animation, and a detailed molecular orbital generation and analysis in addition to the HOMO and LUMO for the optimized geometry of the Cholesterol
- Interactive Optimized Structure of Chemical Compound
- Measurement of Bond Length, Bond Angle, and Dihedral Angle
- Normal Mode Frequency Analysis By Visualization & Animation
- Molecular Orbital (Including HOMO & LUMO) Visualization
The raw data of summarized quantum chemical calculation results, i.e., the summarized results of the geometry optimization and frequency calculation followed by the RI-MP2 energy correction for Cholesterol using the DFT-B3LYP functional with 6-31G* basis set are available at the following link:
The raw data of over 2,000 molecular descriptor values for Cholesterol are available at the link below:
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About Mol-Instincts Web-Information Project
For our Mol-Instincts and/or ChemRTP users to be more efficient in accessing the required data and information, we are publishing the webpages providing various properties of pure chemical substances that may be readily found by Google search. All the data and information in these webpages are originated from Mol-Instincts or ChemRTP. The amount of data and information to be published is up to 10 billion sets.
Mol-Instincts is a fundamental chemical database powered by 41 patented technologies based on quantum chemical, statistical thermodynamics, QSPR (Quantitative Structure-Property Relationship), and artificial neural network-based AI (Artificial Intelligence).
ChemRTP is a real-time predictor of the various properties of pure chemical substances based on QSPR (Quantitative Structure-Property Relationship), and artificial neural network-based AI (Artificial Intelligence).
Mol-Instincts and ChemRTP have been cited a number of times in high-impact scientific journals including but not limited to NATURE, ELSEVIER, Springer, American Chemical Society (ACS), Royal Society of Chemistry (RSC), Wiley, etc.
The image generation engine has been developed as a part of Mol-Instincts and ChemRTP platform to process dozens of millions of chemical substances at a time on an automatic basis. This process is executed on a parallel computational platform equipped with thousands of CPU cores. The engine is now applied to generate the images available on the web, targeting billions of pure substance images to be created in a few years.