القائمة
Organic chemistry fundamentals including functional groups, reaction mechanisms, stereochemistry, synthesis planning, and molecular structure for chemistry applications.
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| name | Organic Chemistry |
| description | Organic chemistry fundamentals including functional groups, reaction mechanisms, stereochemistry, synthesis planning, and molecular structure for chemistry applications. |
| license | MIT |
| compatibility | python>=3.8 |
| audience | chemists, biochemists, pharmaceutical-scientists, researchers |
| category | chemistry |
I provide comprehensive organic chemistry tools including functional group analysis, reaction mechanism prediction, stereochemistry, molecular orbital theory, synthesis planning, and spectroscopic interpretation for chemistry applications.
import re
FUNCTIONAL_GROUPS = {
'alcohol': r'C\([A-Z][a-z]?\)?\([A-Z][a-z]?\)?O[H]',
'carbonyl': r'C(=O)',
'amine': r'N[H2]|[NHR]|[NR2]',
'ether': r'C-O-C',
'alkene': r'C=C',
'alkyne': r'C≡C',
'aromatic': r'c1ccccc1|c1ccccc1',
'carboxylic_acid': r'C(=O)O[H]',
'ester': r'C(=O)O[C]',
'amide': r'C(=O)N'
}
def detect_functional_groups(smiles):
detected = {}
for group, pattern in FUNCTIONAL_GROUPS.items():
if re.search(pattern, smiles):
detected[group] = True
return detected
smiles = "CC(=O)O"
print(f"Functional groups in {smiles}: {detect_functional_groups(smiles)}")
import numpy as np
PKA_DATA = {
'carboxylic_acid': 4.76,
'alcohol': 15.9,
'phenol': 10.0,
'amine': 9.25,
'amide': 15.0,
'water': 14.0
}
def estimate_pKa(functional_group, substituents=None):
base_pKa = PKA_DATA.get(functional_group, 14.0)
if substituents and 'electron_withdrawing' in substituents:
base_pKa -= substituents['electron_withdrawing'] * 0.5
if substituents and 'electron_donating' in substituents:
base_pKa += substituents['electron_donating'] * 0.5
return base_pKa
print(f"Acetic acid pKa: {estimate_pKa('carboxylic_acid')}")
print(f"Chloroacetic acid pKa: {estimate_pKa('carboxylic_acid', {'electron_withdrawing': 2})}")
from itertools import permutations
def count_stereoisomers(n_chiral_centers, meso_possible=False):
total = 2**n_chiral_centers
if meso_possible and n_chiral_centers > 1:
meso_count = n_chiral_centers // 2
return total - meso_count
return total
def r_s_configuration(priorities, hydrogen_position):
clockwise = [1, 2, 3]
counter_clockwise = [1, 3, 2]
if hydrogen_position in ['back', 'dashed']:
return 'R' if priorities == clockwise else 'S'
return 'S' if priorities == clockwise else 'R'
n_centers = 3
print(f"Max stereoisomers for {n_centers} chiral centers: {count_stereoisomers(n_centers)}")
REACTION_TYPES = {
'SN1': {'mechanism': 'unimolecular_nucleophilic_substitution',
'rate_limiting': 'carbocation_formation',
'stereochemistry': 'racemization'},
'SN2': {'mechanism': 'bimolecular_nucleophilic_substitution',
'rate_limiting': 'single_step',
'stereochemistry': 'inversion'},
'E1': {'mechanism': 'unimolecular_elimination',
'rate_limiting': 'carbocation_formation',
'stereochemistry': 'Zaitsev'},
'E2': {'mechanism': 'bimolecular_elimination',
'rate_limiting': 'single_step',
'stereochemistry': 'anti_periplanar'}
}
def classify_reaction(substrate, nucleophile, solvent, temperature):
if 'tertiary' in substrate and 'weak' in nucleophile:
return 'E1'
elif 'primary' in substrate and 'strong' in nucleophile:
return 'SN2'
return 'unknown'
print(f"Reaction type: {classify_reaction('tertiary', 'weak', 'polar_protic', 298)}")
from collections import Counter
ELEMENT_WEIGHTS = {
'H': 1.008, 'C': 12.011, 'N': 14.007, 'O': 15.999,
'F': 18.998, 'Cl': 35.45, 'Br': 79.904, 'S': 32.06
}
def parse_smiles_to_formula(smiles):
elements = re.findall(r'[A-Z][a-z]?', smiles)
counts = Counter(elements)
formula = ''
for element in ['C', 'H', 'N', 'O', 'F', 'Cl', 'Br', 'S', 'P']:
if element in counts:
count = counts[element]
formula += element
if count > 1:
formula += str(count)
del counts[element]
for element in sorted(counts.keys()):
formula += element
if counts[element] > 1:
formula += str(counts[element])
return formula
def calculate_molecular_weight(formula):
weight = 0
pattern = r'([A-Z][a-z]?)(\d*)'
matches = re.findall(pattern, formula)
for element, count in matches:
count = int(count) if count else 1
weight += ELEMENT_WEIGHTS.get(element, 0) * count
return weight
print(f"C6H12O6 formula: {parse_smiles_to_formula('C(C1C(C(C(C(O1)O)O)O)O)O')}")
# IUPAC naming helper
def iupac_stem(alkane_length):
stems = {1:'meth', 2:'eth', 3:'prop', 4:'but', 5:'pent',
6:'hex', 7:'hept', 8:'oct', 9:'non', 10:'dec'}
return stems.get(alkane_length, f'{alkane_length}')
# Degree of unsaturation
def degree_of_unsaturation(c, h, halogens=0, nitrogens=0):
return (2*c + 2 - h - halogens + nitrogens) / 2