Help

This website is designed to assist the user in rapidly locating the relevant or desired content. The primary interface is a single search box located immediately underneath the depiction of a PAH molecule. When a user begins typing a PAH name, chemical formula, or CAS number into the search box, a list of matching compounds will appear immediately below. Note that the user must type at least three characters before possible matches appear. Selecting one of the names from the list by clicking or tapping on the name will cause the information on the selected molecule to be displayed in the space immediately below the search box.

The space in which results are displayed is organized into collapsible sections: Identifiers, Structure, Links, Spectra, Estimated Properties, and Thermochemistry. The data that appears in each section is described below. By default, on the Identifiers section will be open the user selects a compound. Other sections may be opened by clicking or tapping the title bar of the section (or the name or "+" icon in the title bar).

Identifiers

A selection of identifying information including

• Primary Name - A name for the molecule shown. Generally a systematic or common name, and one that may be the most commonly used to refer to the molecule.
• Other Names - Additional names for the molecule. These may be systematic, common, or some other valid chemical name.
• Molecular Formula - An expression of the composition of the molecule, gibing the types of atoms present in the molecule and the number of each type of atom present. The molecular formula is given in the Hill notation in which the carbon atoms are indicated first, followed by the hydrogen atoms, and all other chemical elements in alphabetical order.
• Molar Mass - The mass of 1 mol of the indicated molecule in units of g/mol.
• CAS Registry Number - A unique numerical identifier assigned to the molecule by the Chemical Abstracts Service.

appears in this section.

Structure

This section contains two tabs that may be used to view a 2d or 3d depiction of the molecule.

2d Tab

In the 2d tab, a "stick structure" is displayed along with structural identifiers such as the SMILES notation, the International Chemical Identifier (InChI), and the InChIKey (a compact form of the InChI notation).

3d Tab

In the 3d tab, a rotatable 3d structure of the molecule is shown. The user may rotate the molecule by clicking and dragging within the molecule display area. This functionality is powered by JSmol which provides a great deal of additional functionality that is documented on their website. The structures that are displayed have been optimized at the B3LYP/cc-pVDZ level of theory.

Links

Links are provided that permit download of

• 2d Structure (MDL MOL format) - MOL MOL representation of the 2-dimensional structure of the molecule. This format is suitable for import into many chemical structure drawing programs.
• 2d Structure Image (PNG format) - Graphical depiction of the 2-dimensional structure of the molecule in portable network graphics (PNG) format.
• 3d Structure (XYZ) - Cartesian coordinates of the molecule in Xmol format, suitable for many molecular viewers. Units of the coordinates are Angstroms (Å).

Links to several other sources of information on the compound of interest are provided. Note that in some cases these may not lead to a match.

• NIST Chemistry WebBook - the WebBook may contain experimental data on the selected compound or other information not provided on this web site.
• PubChem (U.S. National Library of Medicine, National Center for Biotechnology Information, National Institutes of Health) - contains an extensive collection including substance information, compound structures, and BioActivity data.
• ChemSpider (Royal Society of Chemistry) - a large collection containing literature references, physical property, spectra, and chemical supplier data.

Spectra

In this section, three types of spectra are presented

• IR spectra - data (vibrational frequencies and intensities) derived from quantum chemistry calculations.
• UV/Vis spectra - data (wavelength (nm) and oscillator strength) taken from time-dependent density functional theory (TD-DFT) calculations.
• NICS - the nucleus independent chemical shift is tabulated at a number of points including atomic centers, centers of aromatic rings, and close to the C atoms in the molecule. The data are taken from a gauge-independent atomic orbital orbital (GIAO) method DFT calculation.

The IR and UV/Vis spectra are displayed as "stick spectra" (red lines). The effect of spectral broadening is simulated by centering a Gaussian function on each "stick." The sum of these Gaussians is displayed in blue. The width of the Gaussian function is determined by the slider below the plot, and the value is displayed in a box at the left. The slider may be adjusted by clicking/tapping and dragging the slider to the desired broadening value. The broadened plot will adjust in real time as the slider is adjusted. Unchecking the "Plot stick spectrum" box will remove the disply of the stick spectrum from the plot. Similarly, unchecking the "Plot broadened spectrum" box will remove display of the broadened spectrum from the plot. Boxes may be checked/uncheck by clicking or tapping. The plot parameters may be reset to the default values by clicking or tapping the "Reset Plot" button at the bottom of the Spectra section. It is possible to zoom in on the plot area by selecting a range of frequencies/wavelengths. This is done by clicking and dragging in the plot area. This functionality may not work on mobile devices or devices with a touch interface.

NICS data are displayed using JMol, just like the 3d structure. In fact, a 3d depiction of the molecules with a number of additional small pink spheres is displayed. Clicking/tapping on or hovering over (mouse only) an atom or sphere will display the value of the magnetic shielding (ppm) at that point in space.

Estimated Properties

Four parameters which give information on the size of the molecule

• Length - Length (Å) of a minimal three-dimensional box that fully contains the molecule.
• Width - Width (Å) of a minimal three-dimensional box that fully contains the molecule.
• Breadth - Breadth (Å) of a minimal three-dimensional box that fully contains the molecule.
• L/W Ratio - Ratio of the length to the width.

are shown. This information is useful for predicting chromatographic retention times, and its use is more fully described in SP922 and elsewhere.

A number of properties derived from the quantum chemistry calculation (DFT) are displayed

• Total energy (E_h) - the total energy from the quantum chemistry calculation. calculation
• HOMO-LUMO gap (E_h) - the difference in energy between the lowest unoccupied molecular orbital (LUMO) and the highest occupied molecular orbital (HOMO). Note that DFT methods are known to underestimate the HOMO-LUMO gap.
• Ionization potential (E_h) - this is taken to be the negative of the energy of the highest occupied molecular orbital. Though this is frequently a reasonable approximation, it can yield poor results in some cases.
• Rotational constants (GHz) - the rotational contants are derived from the optimized molecular geometry using the isotope-averaged atomic masses.
• Dipole moment (Debye) - the dipole moment is calculated form the optimized molecular structure and the isotope-average atomic masses.
• Polarizability (cm³) - the polarizabilities α_xx, α_xy, α_yy, α_xz, α_yz, α_zz are computed at the optimized molecular geometry.

The output from a transport property code (ZENO) is given. The user may download the output or scroll through it. Similarly, output from the US EPA EPI Suite is given.

Thermochemistry

In this section, a thermodynamic table in the style of the NIST-JANAF tables is given in the temperature range 0 - 5000 K. The enthalpy of formation data are computed from the results of an energy-extrapolated B3LYP/cc-pVDZ optimization and frequency calculation, and the remainder of the values are computed using statistical thermodynamics functions. All results are computed within the ideal gas, rigid rotor, harmonic oscillator approximation. For the enthalpy of formation data, an empirical correction based on a chemical group scheme is applied. For a complete description of how these data were derived, see "First Principles Prediction of Enthalpies of Formation for Polycyclic Aromatic Hydrocarbons and Derivatives," Thomas C. Allison and Donald R. Burgess Jr., manuscript in preparation. Additional information may be found in NIST Special Publication 1186: Thermodynamic Properties of Polycyclic Aromatic Hydrocarbons.

Menu

A menu appears in the upper left of the web site with links to information about the database (About), this help (Help), links to other web sites at NIST that may be of interest (Links), and credits for development of this web site (Credits). A set of indices (by name, formula, and CAS number) may be accessed from this menu as well.

Other controls

The "X" button at the right of the search box will erase the contents of the search box when clicked.