## Hydrocarbons Parser

_{x}H

_{y}hydrocarbon formulas. Compute number of sigma, pi, single, double, and triple bonds without using Molecular Orbital Theory. Calculate number of unsaturation degrees and functional isomers. Estimates elemental compositions, boiling points, and densities. Forward queries to third-party databases. Double check homework calculations.

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- Please enter one or more hydrocarbon formulas, one per line, in the textarea. End each line by pressing the
`Enter`

key so these are recognized as individual entries. The formulas you enter must correspond to neutral molecules (no fragments or charge particles) and be of the form C_{x}H_{y}where x and y are the numbers of carbon and hydrogen atoms, respectively. - The tool validates the formulas by storing these in an array and mapping its elements to a PHP regular expression pattern. Those that are duplicates or not of the form C
_{x}H_{y}are ignored. - As part of the validation process, the array is reindexed and its elements used to count chemical bonds, degrees of unsaturation (DoU), discriminate between functional isomers, and predict physical properties, without using Molecular Orbital Theory (MOT) or a database.
- This tool was developed to help users elucidate hydrocarbon formulas of neutral molecules that follow the octect rule. Supports elucidations of cyclic, polycyclic, and open chain hydrocarbons. The tool also lets users forward queries to other databases like RSC ChemSpider, NIST WebBook, Wikipedia, and Google by clicking on the corresponding links.

**Chemical Bonds**

Chemical bonds are counted using Das methodologies for counting bonds in hydrocarbons (Das, 2013; Das et. al., 2014a, 2014b, 2014c).- Das time-economic methodologies for counting bonds are fast processed.
- A modification of these calculations now allows the counting of bonds in prismanes and polycyclics.

**Boiling Points**

For the sake of transparency, normal boiling points are computed in degrees Kelvin, Celsius, and Fahrenheit. These are predicted with Al-Malah model (Al-Malah, 2013) by using the corresponding molecular weights and carbon atomic fractions in his model regression equation.- Al-Malah documented that his model returns boiling point results with relative errors less than 5% in 433 of 476 hydrocarbons studied.
- He also documented relative errors higher than 10% in the case of small hydrocarbons like CH
_{4}(methane), C_{2}H_{4}(ethylene), and C_{2}H_{2}(acetylene).- Al-Malah computed all relative errors in degrees Kelvin for a good reason: A relative error only makes sense when measured on a ratio scale, (i.e. a scale which has a true meaningful zero), otherwise it would be sensitive to the measurement units (Wikipedia, 2015a). The reason is that Celsius is an interval scale, whereas Kelvin is a ratio scale (with a true zero).
- The above is easy to prove. Because
^{o}C = K - 273.15, the relative error in the Celsius scale is Δ^{o}C/^{o}C = ΔK/(K - 273.15); i.e., without a true zero. If K = 273.15, then Δ^{o}C/^{o}C is undefined for ΔK ≠ 0 and indeterminate for ΔK = 0. This is why temperature relative errors should always be computed in degrees Kelvin.

**Densities**

Densities of alkanes are predicted with Kuwata, Zorn, and Martin governing equation (Kuwata, Zorn, Martin, 2012) for density estimations based on C, H, and O formula fractions, by setting oxygen fractions to zero.- Kuwata e.t. al documented that their governing equation returns density results with relative errors within the 12% mark in 28 of 31 compounds studied.
- Their equation seems to accurately predicts the densities of large open chain n-alkanes and light compounds. Our tool confirms this in the case of alkanes with 9 or more carbons. As they stated, the error introduced can be above the 12% mark for small alkanes and other types of organic compounds.

**Degrees of Unsaturation (DoU)**

We define the Degrees of Unsaturation (DoU) as the total number of π bonds + rings that are removed (need to be saturated) to obtain the corresponding saturated molecule.- We compute this number as DoU = (2*x + 2 - y)/2. If the result is a negative or non-integer number, the formula is considered invalid for a neutral hydrocarbon molecule.
- Originally known as the
*rings-plus-double-bonds equivalent*(RDBE) or*double-bond equivalent*(DBE) concept, DoU values can help users elucidate chemical formulas of neutral molecules and polycyclic hydrocarbons (Quach, 2015). - However, the DoU concept is of limited help for elucidating fragments, non-hydrocarbons formulas, or those that do not follow the octect rule. Moreover, for these cases we cannot
*a priori*exclude negative or non-integer DoUs (Kind & Fiehn, 2007) so formula elucidation can be challenging. Our tool was not designed to address these cases. - Contrary to pedagogical misconstructs, the DoU concept does not need to equate to the counting of double bonds or rings in a molecule (Kind & Fiehn, 2007), but of those that are removed via saturation, to obtain a saturated molecule. This is a subtle conceptual difference that can be easily demonstrated with prismanes (hydrocarbons with a prismatic structure). For instance cubane (C
_{8}H_{8}) has 6 rings, but its DoU is 5 because only 5 rings need to be saturated to obtain the corresponding saturated molecule (P2C2E, 2015). -
DoU values can, to some extend, help users elucidate formulas of polycyclic hydrocarbons (Quach, 2015). For instance for C
_{14}H_{10}, DoU = 10 and the tool returns a cycloalkene with 9 π bonds + 1 ring. Thus, the following candidate results with more than one ring can be proposed:- one with 8 π bonds + 2 rings (e.g., diphenylacetylene)
- one with 7 π bonds + 3 rings (e.g., anthracene, phenanthrene)
- one with 6 π bonds + 4 rings (e.g., 1,2-Dihydrocyclopenta[fg]acenaphthylene)
- and a few more.

**Validation**

The following classification criteria are applied to the results obtained from counting bonds.- Any hydrocarbon formula that produces a negative or non-integer bond count is classified as an invalid formula.
- Any hydrocarbon formula that returns a negative or non-integer DoU is invalid for a neutral hydrocarbon molecule. Such a formula is likely to correspond to a charged molecule or fragment that normally do not exist, except as a mental construct or in special environments such as those found in mass spectrometers.
- Any hydrocarbon formula that returns more double bonds than the number of carbons minus 1 in it (#double bonds > x - 1) is invalid.
- Any hydrocarbon formula with less than three carbons (x < 3) obviously is invalid for a cyclic hydrocarbon.
- Validation algorithms just check if a set of rules are fulfilled. The fact that a hydrocarbon formula conforms or not to our validation algorithm says nothing about the stability of said hydrocarbon or whether they exist or not or can be synthetized. To establish we need additional chemical information and the necessary experimental conditions which can be extreme. This is particularly true for small strained cycloalkynes and cycloalkenes (Wikipedia, 2015b, 2015c).
For instance, the tool predicts the existence of C

_{3}H_{2}with two pi/double bonds (1,2-cyclopropadiene), but what actually exists is c-C_{3}H_{2}(cyclopropenylidene; Wikipedia, 2015c) which has a double bond and an electron lone pair. The tool parses this specie as behaving with two delocalized pi/double bonds. Interestingly, a search in ChemSpider for 1,2-cyclopropadiene returns cyclopropenylidene as an accepted synonym. The tool also predicts the existence of the smallest possible cyclic alkynes (Wikipedia, 2015b): cyclopropyne (C_{3}H_{2}) and cyclobutyne (C_{4}H_{4}). - In general, the tool considers invalid those cases that do not follow the octect rule or are chemical fragments.

**Tool Limitations**- Although our tool can discriminate between functional isomers, it cannot do so with other types of isomers.
- Another limitation of our tool comes from the calculation of boiling points with Al-Malah model. At the time of writing, said model does not discriminate between isomers of same molecular weight and chemical formula.
- Our tool estimates boiling points from a regression formula limited to a small set of 476 hydrocarbons. To improve the calculations, more data points and additional work must be done along these lines.
- In addition, our tool estimates densities using Kuwata et al. working formula whose accuracy was reported based on a small set of 31 results. More work with larger data sets is required. At the time of writing, their formula does not discriminate between isomers of same molecular weight and chemical formula. For small alkanes, the relative error introduced can be above the 12% mark.

- Data miners, computational chemists, chemical engineers, chemists, and chemistry teachers and their students.

- Explain in terms of molecular orbital theory (MOT) why for neutral hydrocarbon molecules, formulas with x = y =
*even number*are valid, but those with x = y =*odd number*are not. Hint: Compute DoUs. - Cycloalkynes with less than 8 carbons are unstable. Why?
- Identify valid hydrocarbon formulas that conform to any of the following patterns.
- y = 2x + 2
- y = 2x
- y = 2x - 2
- y = 2x - 4
- y = 2x - 6
- y = 2x - 8

- Compute the DoU of a hydrocarbon with the molecular formula C
_{3}H_{4}and draw all possible functional isomers. - Compute the DoU of prismane (C
_{6}H_{6}), an isomer of benzene.

- We are sincerely in debt to Dr. Arijit Das from Ramthakur College, Agartala, West Tripura, India for encouraging feedback.

- Al-Malah, K. I. (2013). Prediction of Normal Boiling Points of Hydrocarbons Using Simple Molecular Properties. Journal of Advanced Chemical Engineering
Vol. 3 (2013), Article ID 235654, 9 pages; doi:10.4303/jace/235654. Ashdin Publishing.

Retrieved from http://www.omicsonline.com/open-access/prediction-of-normal-boiling-points-of-hydrocarbons-using-simple-molecular-properties-2090-4568-3-235654.pdf - Das, A. (2013). Simple Thinking Makes Chemistry Metabolic and Interesting - A Review Article. IOSR Journal of Applied Chemistry (IOSR-JAC)
e-ISSN: 2278-5736. Vol. 6, Issue 4 (Nov. - Dec. 2013), PP 08-15. IOSR Journals.

Retrieved from http://iosrjournals.org/iosr-jac/papers/vol6-issue4/B0640815.pdf

See also Dr. Das personal site http://www.arijitchemistryworld.com/. - Das, A., Pal, D., Paul, B., Sanjeev, R., and Jagannadham, V. (2014a). Rapid calculation of the number of π-bonds, σ-bonds, single and double bonds in aliphatic unsaturated open chain and cyclic olefinic hydrocarbons. Education in Chemical Science and Technology, Ind. Chem. Soc., Aug-2014, 2(1), 41- 46.

Referenced from http://chemwiki.ucdavis.edu/Organic_Chemistry/Fundamentals/Bonding_in_Organic_Compounds/Calculating_of_%CF%80-bonds%2C_%CF%83-bonds%2C_single_and_double_bonds_in_Straight_Chain_and_Cycloalkene_System -
Das, A., Pal, D., Paul, B., Sanjeev, R., and Jagannadham, V. (2014b). Innovative and Time Economic Pedagogical Views in Chemical Education - A Review Article. World Journal of Chemical Education, 2014, Vol. 2, No. 3, 29-38.

Retrieved from http://pubs.sciepub.com/wjce/2/3/1/ - Das, A., Pal, D., Paul, B., Sanjeev, R., and Jagannadham, V. (2014c). Rapid Calculation of the Number of π-bonds, σ-bonds, Single and Triple Bonds in Aliphatic Unsaturated Open Chain and Cycloalkynes. World Journal of Chemical Education, 2014, Vol. 2, No. 1, 1-3.

Retrieved from http://pubs.sciepub.com/wjce/2/1/1/ - Kuwata, M., Zorn, S. R., and Martin, S. T. (2012). Using Elemental Ratios to Predict the Density of Organic Material Composed of Carbon, Hydrogen, and Oxygen. Environ. Sci. Technol. 2012, 46, 787-794. ACS Publication. dx.doi.org/10.1021/es202525q

Retrieved from https://www.ncbi.nlm.nih.gov/pubmed/22145565 - Kind, T., Fiehn, O. (2007). BMC Bioinformatics. 2007; 8: 105. doi: 10.1186/1471-2105-8-105. Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry

Retrieved from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1851972/pdf/1471-2105-8-105.pdf - P2C2E Blog (2015). What is the ring count for the structure Cubane? Phylosophy to Chemistry to Elucidation Blog

Retrieved from http://acdlabs.typepad.com/elucidation/2008/03/what-is-the-rdb.html - Quach, K. (2015). Degree of Unsaturation.

Retrieved from http://chemwiki.ucdavis.edu/Organic_Chemistry/Hydrocarbons/Alkenes/Properties_of_Alkenes/Degree_of_Unsaturation - Wikipedia (2015a). Approximation Error.

Retrieved from https://en.wikipedia.org/wiki/Approximation_error - Wikipedia (2015b). Cycloalkyne.

Retrieved from https://en.wikipedia.org/wiki/Cycloalkyne - Wikipedia (2015c). Cyclopropenylidene.

Retrieved from https://en.wikipedia.org/wiki/Cyclopropenylidene

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