ThermodynamicConstants

Full name Emily.eQuilibrator.Core.Constants.ThermodynamicConstants Assembly Emily.eQuilibrator Members 66

Thermodynamic constants used in Gibbs free energy calculations. Contains fundamental physical constants and default physiological conditions.

01 Syntax

Emily.eQuilibrator.Core.Constants.ThermodynamicConstants

02 Methods

Name	Overloads	Summary
DebyeHueckel	1	计算 Debye-Hückel 修正因子。等价于 Python debye_hueckel(ionic_strength_in_M, T_in_K)。该函数基于扩展 Debye-Hückel 方程计算活度系数修正因子，用于校正离子强度对标准 Gibbs 自由能的影响。修正因子的单位为 kJ/mol。
DebyeHueckelDerivative	1	计算 Debye-Hückel 修正因子对离子强度的导数。等价于 Python _debye_hueckel_derivative(ionic_strength, T_in_K)。
LegendreTransform	1	计算 Legendre 变换值。等价于 Python _legendre_transform(pH, pMg, ionic_strength_M, T_in_K, charge, num_protons, num_magnesiums)。 Legendre 变换用于将标准 Gibbs 自由能转换为指定 pH、pMg 和离子强度条件下的变换 Gi…
LnConcentrationRatio	1	Calculates the natural logarithm of the concentration ratio.
PHToHydrogenConcentration	1	Converts pH to hydrogen ion concentration
PMgToMagnesiumConcentration	1	Converts pMg to magnesium ion concentration
RT	1	Calculates RT at a given temperature
Ln10RT	1	Calculates 2.303 * RT at a given temperature (for pH calculations)

03 Fields

Name	Overloads	Summary
default_T	2	默认温度 298.15 K
default_T_in_K	2	默认温度（开尔文）
default_I	2	默认离子强度 0.25 M
default_I_in_M	2	默认离子强度（摩尔/升）
default_pH	2	默认 pH 值 7.0
default_pMg	2	默认 pMg 值 14.0
default_pMg_Quantity	2	默认 pMg（Quantity 形式）
R	2	气体常数 R = 8.314462618 J/(molK) = 8.314462618e-3 kJ/(molK)
default_R_in_kJ_per_mol_per_K	2	气体常数（kJ/(mol*K)）
FARADAY	2	法拉第常数 96485.33212 C/mol
LOG10	2	LOG10 = ln(10) = 2.302585...
standard_dg_formation_mg	2	Mg2+ 的标准生成 Gibbs 自由能 (kJ/mol)
standard_dh_formation_mg	2	Mg2+ 的标准生成焓 (kJ/mol)
PROTON_INCHI	2	质子的 InChI 标识符。
PROTON_INCHI_KEY	2	质子的 InChI Key。
WATER_INCHI	2	水的 InChI 标识符。
WATER_INCHI_KEY	2	水的 InChI Key。
FaradayConstant	2	Faraday constant in kJ/(V·mol) F = 96485.33212 C/mol = 96.48533212 kJ/(V·mol)
DefaultPH	2	Default pH value for physiological conditions
DefaultPMg	2	Default pMg (negative log of Mg2+ concentration) for physiological conditions
DefaultIonicStrength	2	Default ionic strength in molar (M) for physiological conditions
DefaultTemperature	2	Default temperature in Kelvin for physiological conditions
StandardConcentration	2	Standard concentration in molar (M)
PhysiologicalConcentration	2	Physiological concentration in molar (M) Typically 1 mM = 0.001 M
DefaultConcentrationLowerBound	2	Default lower bound for concentration in molar (M)
DefaultConcentrationUpperBound	2	Default upper bound for concentration in molar (M)
DefaultElectricalPotential	2	Default electrical potential in volts
DefaultRmseInf	2	Default RMSE infinity value in kJ/mol Used for reactions with very high uncertainty
DefaultPhase	2	Default phase for compounds

04 Members

method DebyeHueckel #

DebyeHueckel(Double, Double)

计算 Debye-Hückel 修正因子。等价于 Python debye_hueckel(ionic_strength_in_M, T_in_K)。

该函数基于扩展 Debye-Hückel 方程计算活度系数修正因子，用于校正离子强度对标准 Gibbs 自由能的影响。修正因子的单位为 kJ/mol。

Parameters

Name	Type	Description
`ionic_strength_in_M`	`Double`	离子强度（摩尔/升）
`T_in_K`	`Double`	温度（开尔文）

Returns

Debye-Hückel 修正因子 (kJ/mol)

method DebyeHueckelDerivative #

DebyeHueckelDerivative(Double, Double)

计算 Debye-Hückel 修正因子对离子强度的导数。等价于 Python _debye_hueckel_derivative(ionic_strength, T_in_K)。

Parameters

Name	Type	Description
`ionic_strength`	`Double`	离子强度（摩尔/升）
`T_in_K`	`Double`	温度（开尔文）

Returns

Debye-Hückel 修正因子对离子强度的导数 (kJ/mol)

method LegendreTransform #

LegendreTransform(Double, Double, Double, Double, Double, Double, Double)

计算 Legendre 变换值。等价于 Python _legendre_transform(pH, pMg, ionic_strength_M, T_in_K, charge, num_protons, num_magnesiums)。

Legendre 变换用于将标准 Gibbs 自由能转换为指定 pH、pMg 和离子强度条件下的变换 Gibbs 自由能。这是 Alberty 热力学框架的核心计算。

Parameters

Name	Type	Description
`pH`	`Double`	pH 值（-log10[H+])
`pMg`	`Double`	pMg 值（-log10[Mg2+])
`ionic_strength_M`	`Double`	离子强度（摩尔/升）
`T_in_K`	`Double`	温度（开尔文）
`charge`	`Double`	微粒子的电荷数
`num_protons`	`Double`	质子数
`num_magnesiums`	`Double`	镁离子数

Returns

Legendre 变换值（单位为 RT）

method LnConcentrationRatio #

LnConcentrationRatio(Double, Double)

Calculates the natural logarithm of the concentration ratio. ln(Q) where Q is the reaction quotient

Parameters

Name	Type	Description
`concentration`	`Double`	Concentration in molar
`standardConcentration`	`Double`	Standard concentration (default 1 M)

Returns

Natural logarithm of the concentration ratio

method PHToHydrogenConcentration #

PHToHydrogenConcentration(Double)

Converts pH to hydrogen ion concentration

Parameters

Name	Type	Description
`pH`	`Double`	pH value

Returns

Hydrogen ion concentration in molar

method PMgToMagnesiumConcentration #

PMgToMagnesiumConcentration(Double)

Converts pMg to magnesium ion concentration

Parameters

Name	Type	Description
`pMg`	`Double`	pMg value

Returns

Magnesium ion concentration in molar

method RT #

RT(Double)

Calculates RT at a given temperature

Parameters

Name	Type	Description
`temperatureK`	`Double`	Temperature in Kelvin

Returns

RT in kJ/mol

method Ln10RT #

Ln10RT(Double)

Calculates 2.303 * RT at a given temperature (for pH calculations)

Parameters

Name	Type	Description
`temperatureK`	`Double`	Temperature in Kelvin

Returns

2.303 * RT in kJ/mol

field default_T #

default_T

默认温度 298.15 K

field default_T_in_K #

default_T_in_K

默认温度（开尔文）

field default_I #

default_I

默认离子强度 0.25 M

field default_I_in_M #

default_I_in_M

默认离子强度（摩尔/升）

field default_pH #

default_pH

默认 pH 值 7.0

field default_pMg #

default_pMg

默认 pMg 值 14.0

field default_pMg_Quantity #

default_pMg_Quantity

默认 pMg（Quantity 形式）

field R #

气体常数 R = 8.314462618 J/(molK) = 8.314462618e-3 kJ/(molK)

field default_R_in_kJ_per_mol_per_K #

default_R_in_kJ_per_mol_per_K

气体常数（kJ/(mol*K)）

field FARADAY #

FARADAY

法拉第常数 96485.33212 C/mol

field LOG10 #

LOG10

LOG10 = ln(10) = 2.302585... 等价于 Python LOG10 = np.log(10)。注意：这是自然对数 ln(10)，不是 log10(e)。

field standard_dg_formation_mg #

standard_dg_formation_mg

Mg2+ 的标准生成 Gibbs 自由能 (kJ/mol)

field standard_dh_formation_mg #

standard_dh_formation_mg

Mg2+ 的标准生成焓 (kJ/mol)

field PROTON_INCHI #

PROTON_INCHI

质子的 InChI 标识符。

field PROTON_INCHI_KEY #

PROTON_INCHI_KEY

质子的 InChI Key。

field WATER_INCHI #

WATER_INCHI

水的 InChI 标识符。

field WATER_INCHI_KEY #

WATER_INCHI_KEY

水的 InChI Key。

field FaradayConstant #

FaradayConstant

Faraday constant in kJ/(V·mol) F = 96485.33212 C/mol = 96.48533212 kJ/(V·mol)

field DefaultPH #

DefaultPH

Default pH value for physiological conditions

field DefaultPMg #

DefaultPMg

Default pMg (negative log of Mg2+ concentration) for physiological conditions

field DefaultIonicStrength #

DefaultIonicStrength

Default ionic strength in molar (M) for physiological conditions

field DefaultTemperature #

DefaultTemperature

Default temperature in Kelvin for physiological conditions

field StandardConcentration #

StandardConcentration

Standard concentration in molar (M)

field PhysiologicalConcentration #

PhysiologicalConcentration

Physiological concentration in molar (M) Typically 1 mM = 0.001 M

field DefaultConcentrationLowerBound #

DefaultConcentrationLowerBound

Default lower bound for concentration in molar (M)

field DefaultConcentrationUpperBound #

DefaultConcentrationUpperBound

Default upper bound for concentration in molar (M)

field DefaultElectricalPotential #

DefaultElectricalPotential

Default electrical potential in volts

field DefaultRmseInf #

DefaultRmseInf

Default RMSE infinity value in kJ/mol Used for reactions with very high uncertainty

field DefaultPhase #

DefaultPhase

Default phase for compounds

field default_T overload 2 #

default_T

field default_T_in_K overload 2 #

default_T_in_K

field default_I overload 2 #

default_I

field default_I_in_M overload 2 #

default_I_in_M

field default_pH overload 2 #

default_pH

field default_pMg overload 2 #

default_pMg

field default_pMg_Quantity overload 2 #

default_pMg_Quantity

field R overload 2 #

field default_R_in_kJ_per_mol_per_K overload 2 #

default_R_in_kJ_per_mol_per_K

field FARADAY overload 2 #

FARADAY

field LOG10 overload 2 #

LOG10

field standard_dg_formation_mg overload 2 #

standard_dg_formation_mg

field standard_dh_formation_mg overload 2 #

standard_dh_formation_mg

field PROTON_INCHI overload 2 #

PROTON_INCHI

field PROTON_INCHI_KEY overload 2 #

PROTON_INCHI_KEY

field WATER_INCHI overload 2 #

WATER_INCHI

field WATER_INCHI_KEY overload 2 #

WATER_INCHI_KEY

field FaradayConstant overload 2 #

FaradayConstant

field DefaultPH overload 2 #

DefaultPH

field DefaultPMg overload 2 #

DefaultPMg

field DefaultIonicStrength overload 2 #

DefaultIonicStrength

field DefaultTemperature overload 2 #

DefaultTemperature

field StandardConcentration overload 2 #

StandardConcentration

field PhysiologicalConcentration overload 2 #

PhysiologicalConcentration

field DefaultConcentrationLowerBound overload 2 #

DefaultConcentrationLowerBound

field DefaultConcentrationUpperBound overload 2 #

DefaultConcentrationUpperBound

field DefaultElectricalPotential overload 2 #

DefaultElectricalPotential

field DefaultRmseInf overload 2 #

DefaultRmseInf

field DefaultPhase overload 2 #

DefaultPhase