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A. The effects of conjugation and hyperconjugation can be seen in molecules to show how electronic orbitals interact to stabilize them.
The interaction of σ- and π-orbitals is defined as hyperconjugation. whereas conjugation refers to the interaction of π-orbitals.
Hyperconjugation is the most common of the stereoelectronic effects and it can be further classified as negative, neutral, and positive hyperconjugation.
#B.
import studio_0_utils
import autode as ade # Let's start by importing autodE
ade.methods.get_hmethod()
L_tryptophan = ade.Molecule(smiles='C1=CC=C2C(=C1)C(=CN2)C[C@@H](C(=O)O)N', name = 'L_tryptophan')
L_tryptophan.optimise(method=ade.methods.XTB())
print(L_tryptophan.energy)
studio_0_utils.MolTo3DView("L_tryptophan_opt_xtb.xyz")
Execution error
ModuleNotFoundError: No module named 'studio_0_utils'
L_tryptophan.single_point(method=ade.methods.ORCA())
print(L_tryptophan.energy)
Execution error
CalculationException: Failed to calculate a single point energy for L_tryptophan_0_1_CCCCCCCCNCCCOONHHHHHHHHHHHH_none
ade.Config.n_cores = 1
HF_3c_nbo_orca = ade.methods.ORCA()
HF_3c_nbo_orca.keywords.sp = ade.SinglePointKeywords(['HF-3c', 'NBO'])
L_tryptophan.single_point(method=HF_3c_nbo_orca)
HF_3c_opt_nbo_orca = ade.methods.ORCA()
HF_3c_opt_nbo_orca.keywords.sp = ade.OptKeywords(['HF-3c', 'NBO'])
L_tryptophan.optimise(method=HF_3c_opt_nbo_orca)
2. A. The interactions between filled π- or p-orbitals and adjacent antibondingσ ∗-orbitals are referred to as negative hyperconjugation.
e.g., Methyl amine
Lengthening of C–H bond.
Positive hyperconjugation favors when a very strong p- or π-acceptor, or a very strong σ-donor is present in a molecule.
e.g., Methylborane
The resonance description of such interaction is consistent with the elongation of the interacting C–H bond.
The decrease of the HCB angle.
In neutral huperconjugation all antiperiplanar C–H bonds interact with each other both as a donor and an acceptor.
e.g,, Ethane
By symmetry, these interactions are identical in magnitude.
from utils import *
from py3Dmol_utils import MolTo3DView
from utils import CIRconvert
from nbo_parser import nbo_parser
hyperconjugation_types_examples_mols_id = [0, 1, 2]
hyperconjugation_types_examples_mols_names = ['ethane', 'methyl_amine', 'methyl_borane']
hyperconjugation_types_examples_mols_smiles = ['CC', 'CN', 'CB']
HF_3c_opt_nbo_orca = ade.methods.ORCA()
HF_3c_opt_nbo_orca.keywords.opt = ade.OptKeywords(['HF-3c', 'NBO'])
PBE0_sp_nbo_orca = ade.methods.ORCA()
PBE0_sp_nbo_orca.keywords.sp = ade.SinglePointKeywords(['PBE0', 'NBO', 'def2-SV(P)', 'def2/J', 'D3BJ', 'RIJCOSX'])
def run_xtb_HF_3c_opt_PBE0_sp_nbo_orca(amino_acid, name, smiles):
amino_acid = ade.Molecule(name = name, smiles = smiles)
amino_acid.optimise(method=ade.methods.XTB())
amino_acid.optimise(method=HF_3c_opt_nbo_orca)
amino_acid.single_point(method=PBE0_sp_nbo_orca)
print(amino_acid.energy)
for i in hyperconjugation_types_examples_mols_id:
run_xtb_HF_3c_opt_PBE0_sp_nbo_orca(hyperconjugation_types_examples_mols_names[i],
hyperconjugation_types_examples_mols_names[i], hyperconjugation_types_examples_mols_smiles[i])
Execution error
CalculationException: Failed to calculate a single point energy for ethane_0_1_CCHHHHHH_none
nbo_parser('ethane_sp_orca.out')['perturbation_energy']
Execution error
HeaderNotFoundError: Header Summary of Natural Population Analysis: could not be found in the lines.
nbo_parser('methyl_amine_sp_orca.out')['perturbation_energy']
Execution error
FileNotFoundError: [Errno 2] No such file or directory: 'methyl_amine_sp_orca.out'
nbo_parser('methyl_borane_sp_orca.out')['perturbation_energy']
Execution error
FileNotFoundError: [Errno 2] No such file or directory: 'methyl_borane_sp_orca.out'
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3.A Negative conjugation: The interactions between empty π- or p-orbitals or lone pair orbital and adjacent antibondingσ ∗-orbitals.
Positive conjugation: when a very strong p- or π-acceptor is present in a molecule.
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