mySQL Benson Tables

A Benson rule basically consists of two elements

• A structure consisting of a center atom and the atoms to which it is connected.

• The thermodynamic information represented as Standard enthapy, standard entropy and several Cp temperature dependent Cp values.

JThermodyanics represents this information in three separate tables:

• GroupElement: Center atom connectivity

• GroupStandardEnthalpy: Standard Enthalpy Value

• Standard Entropy Value

• The Cp values

These tables are connected with a given Benson rule through the 'ElementName' field. The complete Benson rule consists of all entries in these three tables with the given 'ElementName'

GroupElement: Center Atom Connectivity mySQL Table

The center atom connectivity of a single Benson rule is represented by several entries within the GroupElement table. All these entries has the same 'ElementName' of the given Benson rule. Each entry in the GroupElement table describes one connection to the center atom. The entry consists the following elements:

• CenterAtom: The atom or meta atom structure representing the center atom

• ConnectingAtom: One of the connecting atom or meta-atoms to the center atom.

• Count: The number of connections of this type.

• ElementName: The Benson rule name

• ConnectElementName: The name of this particular connection

For example, the set of connecting atoms for a primary carbon as the center atom is represented with two elements:

+------------+----------------+-------+-------------+--------------------+

| CenterAtom | ConnectingAtom | Count | ElementName | ConnectElementName |

+------------+----------------+-------+-------------+--------------------+

| c | c | 1 | c-(h)/3-(c) | c-(h)/3-(c)-1 |

| c | h | 3 | c-(h)/3-(c) | c-(h)/3-(c)-0 |

+------------+----------------+-------+-------------+--------------------+

The ElementName is c-(h)/3-(c) and the first is the connection to the (single) carbon in the rest of the chain. There is one of these, hence Count is 1. The second connection is the carbon-hydrogen connections. There are three of these (for the three primary hydrogens of the methyl), hence Count is 3.

GroupStandardEnthalpy: The standard enthalpy value

The standard enthalpy of a particular Benson rule is represented by the following elements in the GroupStandardEnthalpy mySQL table:

• ElementName: The name of the Benson rule

• StandardEnthalpy: The standard enthalpy value.

• Reference: This is a string reference to the value. This could be used to manage updates or deleting

• Time: The time the entry was created.

For example, the GroupStandardEnthalpy table for the primary carbon with the ElementName of c-(h)/3-(c) is:

+-------------+------------------+-----------+---------------------+

| ElementName | StandardEnthalpy | Reference | Time |

+-------------+------------------+-----------+---------------------+

| c-(h)/3-(c) | -10.098 | Standard | 2011-03-18 15:04:46 |

+-------------+------------------+-----------+---------------------+

The StandardEnthalpy value is given -10.098 Kilocalories/mole (following the convention of Thermochemical Kinetics: Methods for the Estimation of Thermochemical Data and Rate Parameters.

GroupStandardEntropy: The standard entropy value

The standard enthalpy of a particular Benson rule is represented by the following elements in the GroupStandardEntropy mySQL table:

• ElementName: The name of the Benson rule

• StandardEntropy: The standard enthalpy value.

• Reference: This is a string reference to the value. This could be used to manage updates or deleting

• Time: The time the entry was created.

For example, the GroupStandardEntropy table for the primary carbon with the ElementName of c-(h)/3-(c) is:

+-------------+------------------+-----------+---------------------+

| ElementName | StandardEntropy | Reference | Time |

+-------------+------------------+-----------+---------------------+

| c-(h)/3-(c) | 30.423 | Standard | 2011-03-18 15:04:46 |

+-------------+------------------+-----------+---------------------+

The StandardEnthalpy value is given 30.423 calories/(K mole) (following the convention of Thermochemical Kinetics: Methods for the Estimation of Thermochemical Data and Rate Parameters.

Finding a given connectivity

Finding a particular Benson rule entails collecting the set of elements that have each individual connection and the same ElementName. For the example of c-(h)/3-(c) there are two connections to the center atom c:

• three hydrogens (h)

• one carbon (c)

The mySQL query accomplishes this using a JOIN of the two connections and AND to set up the set of conditions for CenterAtom and ConnectingAtom:

SELECT DISTINCT p1.ElementName From GroupElement as p1

INNER JOIN GroupElement as p2

INNER JOIN GroupElement as p3

WHERE p1.ElementName = p2.ElementName AND

p2.ElementName = p3.ElementName AND

p1.CenterAtom = "c" AND

p1.ConnectingAtom = "h" AND

p1.Count = 3 AND

p2.ConnectingAtom = "c" AND

p2.Count = 1;

Within the JThermodynamic system, this query is built up. The result of this query is the ElementName that satisfies these conditions:

+-------------+

| ElementName |

+-------------+

| c-(h)/3-(c) |

+-------------+

We can check by seeing which elements have the corresponding ElementName:

select * from GroupElement where ElementName='c-(h)/3-(c)';

+------------+----------------+-------+-------------+--------------------+

| CenterAtom | ConnectingAtom | Count | ElementName | ConnectElementName |

+------------+----------------+-------+-------------+--------------------+

| c | c | 1 | c-(h)/3-(c) | c-(h)/3-(c)-1 |

| c | h | 3 | c-(h)/3-(c) | c-(h)/3-(c)-0 |

+------------+----------------+-------+-------------+--------------------+

The thermodynamic information is collected by queries to the GroupStandardEntropy, GroupStandardEnthalpy and the HeatCapacityElement.

Enthalpy:

select * from GroupStandardEnthalpy where ElementName='c-(h)/3-(c)';

+-------------+------------------+-----------+---------------------+

| ElementName | StandardEnthalpy | Reference | Time |

+-------------+------------------+-----------+---------------------+

| c-(h)/3-(c) | -10.098 | Standard | 2011-03-18 15:04:46 |

+-------------+------------------+-----------+---------------------+

Entropy:

select * from GroupStandardEntropy where ElementName='c-(h)/3-(c)';

+-------------+-----------+---------------------+-----------------+

| ElementName | Reference | Time | StandardEntropy |

+-------------+-----------+---------------------+-----------------+

| c-(h)/3-(c) | Standard | 2011-03-18 15:04:46 | 30.423 |

+-------------+-----------+---------------------+-----------------+

Heat Capacity:

select * from HeatCapacityElement where ElementName='c-(h)/3-(c)';

+-------------+--------------+-----------+---------------------+-------------+

| Temperature | HeatCapacity | Reference | Time | ElementName |

+-------------+--------------+-----------+---------------------+-------------+

| 1500 | 17.58 | Standard | 2011-03-18 15:04:46 | c-(h)/3-(c) |

| 1000 | 14.77 | Standard | 2011-03-18 15:04:46 | c-(h)/3-(c) |

| 800 | 13.02 | Standard | 2011-03-18 15:04:46 | c-(h)/3-(c) |

| 600 | 10.79 | Standard | 2011-03-18 15:04:46 | c-(h)/3-(c) |

| 500 | 9.4 | Standard | 2011-03-18 15:04:46 | c-(h)/3-(c) |

| 400 | 7.84 | Standard | 2011-03-18 15:04:46 | c-(h)/3-(c) |

| 300 | 6.15 | Standard | 2011-03-18 15:04:46 | c-(h)/3-(c) |

+-------------+--------------+-----------+---------------------+-------------+

The heat capacity has several elements, one for each of the temperatures.

GroupElement: Connectivity Table

The complete GroupElement connectivity table looks like this (read in from the standard thermodynamic values read as described here):

select * from GroupElement;

GroupStandardEnthalpy

select * from GroupStandardEnthalpy where ElementName='c-(h)/3-(c)';

+-------------+------------------+-----------+---------------------+

| ElementName | StandardEnthalpy | Reference | Time |

+-------------+------------------+-----------+---------------------+

| c-(h)/3-(c) | -10.098 | Standard | 2011-03-18 15:04:46 |

+-------------+------------------+-----------+---------------------+

select * from GroupStandardEnthalpy;

GroupStandardEntropy

select * from GroupStandardEntropy where ElementName='c-(h)/3-(c)';

+-------------+-----------+---------------------+-----------------+

| ElementName | Reference | Time | StandardEntropy |

+-------------+-----------+---------------------+-----------------+

| c-(h)/3-(c) | Standard | 2011-03-18 15:04:46 | 30.423 |

+-------------+-----------+---------------------+-----------------+

1 row in set (0.00 sec)

select * from GroupStandardEntropy;