Quantum Mechanical Investigation of the Oxidative Cleavage of the C-C Backbone Bonds in Polyethylene Model Molecules.
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ABSTRACT:
SUBMITTER: Jiang Q
PROVIDER: S-EPMC8398876 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Polyethylene mimics of semicrystalline polyphosphoesters (PPEs) with an adjustable amount of noncovalent cross-links were synthesized. Acyclic diene metathesis copolymerization of a phosphoric acid triester (M1) with a novel phosphoric acid diester monomer (M2) was achieved. PPEs with different co-monomer ratios and 0, 20, 40, and 100% of phosphodiester content were synthesized. The phosphodiester groups result in supramolecular interactions between the polymer chains, with the P-OH functionality as an H-bond donor and the P=O group as an H-bond acceptor. A library of unsaturated and saturated PPEs was prepared and analyzed in detail by NMR spectroscopy, size exclusion chromatography, differential scanning calorimetry, thermogravimetry, rheology, and stress-strain measurements. The introduction of the supramolecular cross-links into the aliphatic and hydrophobic PPEs showed a significant impact on the material properties: increased glass-transition and melting temperatures were observed and an increase in the storage modulus of the polymers was achieved. This specific combination of a flexible aliphatic backbone and a supramolecular H-bonding interaction between the chains was maximized in the homopolymer of the phosphodiester monomer, which featured additional properties, such as shape-memory properties, and polymer samples could be healed after cutting. The P-OH groups also showed a strong adhesion toward metal surfaces, which was used together with the shape-memory function in a model device that responds to a temperature stimulus with shape change. This systematic variation of phosphodiesters/phosphotriesters in polyethylene mimics further underlines the versatility of the phosphorus chemistry to build up complex macromolecular architectures.
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Project description:The activation and cleavage of C-C bonds remains a critical scientific issue in many organic reactions and is an unmet challenge due to their intrinsic inertness and ubiquity. Meanwhile, it is crucial for the valorization of lignin into high-value chemicals. Here, we proposed a novel strategy to enhance the Caromatic-Cα bond cleavage by pre-functionalization with amine sources, in which an active amine intermediate is first formed through Markovnikov hydroamination to reduce the dissociation energy of the Caromatic-Cα bond which is then cleaved to form target chemicals. More importantly, this strategy provides a method to achieve the maximum utilization of the aromatic nucleus and side chains in lignin or its platform molecules. Phenols and N,N-dimethylethylamine compounds with high yields were produced from herbaceous lignin or the p-coumaric acid monomer in the presence of industrially available dimethylamine (DMA).
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Project description:We use quantum mechanics/molecular mechanics simulations to study the cleavage of the ribonucleic acid (RNA) backbone catalyzed by ribonuclease H. This protein is a prototypical member of a large family of enzymes that use two-metal catalysis to process nucleic acids. By combining Hamiltonian replica exchange with a finite-temperature string method, we calculate the free energy surface underlying the RNA-cleavage reaction and characterize its mechanism. We find that the reaction proceeds in two steps. In a first step, catalyzed primarily by magnesium ion A and its ligands, a water molecule attacks the scissile phosphate. Consistent with thiol-substitution experiments, a water proton is transferred to the downstream phosphate group. The transient phosphorane formed as a result of this nucleophilic attack decays by breaking the bond between the phosphate and the ribose oxygen. In the resulting intermediate, the dissociated but unprotonated leaving group forms an alkoxide coordinated to magnesium ion B. In a second step, the reaction is completed by protonation of the leaving group, with a neutral Asp132 as a likely proton donor. The overall reaction barrier of ?15 kcal mol(-1), encountered in the first step, together with the cost of protonating Asp132, is consistent with the slow measured rate of ?1-100/min. The two-step mechanism is also consistent with the bell-shaped pH dependence of the reaction rate. The nonmonotonic relative motion of the magnesium ions along the reaction pathway agrees with X-ray crystal structures. Proton-transfer reactions and changes in the metal ion coordination emerge as central factors in the RNA-cleavage reaction.
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Project description:Quantum-mechanical methods are used for understanding molecular interactions throughout the natural sciences. Quantum diffusion Monte Carlo (DMC) and coupled cluster with single, double, and perturbative triple excitations [CCSD(T)] are state-of-the-art trusted wavefunction methods that have been shown to yield accurate interaction energies for small organic molecules. These methods provide valuable reference information for widely-used semi-empirical and machine learning potentials, especially where experimental information is scarce. However, agreement for systems beyond small molecules is a crucial remaining milestone for cementing the benchmark accuracy of these methods. We show that CCSD(T) and DMC interaction energies are not consistent for a set of polarizable supramolecules. Whilst there is agreement for some of the complexes, in a few key systems disagreements of up to 8 kcal mol-1 remain. These findings thus indicate that more caution is required when aiming at reproducible non-covalent interactions between extended molecules.
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Project description:Pauling and Corey proposed a pleated-sheet configuration, now called alpha-sheet, as one of the protein secondary structures in addition to alpha-helix and beta-sheet. Recently, it has been suggested that alpha-sheet is a common feature of amyloidogenic intermediates. We have investigated the stability of antiparallel beta-sheet and two conformations of alpha-sheet in solution phase using the density functional theoretical method. The peptides are modeled as two-strand acetyl-(Ala)(2)-N-methylamine. Using stages of geometry optimization and single point energy calculation at B3LYP/cc-pVTZ//B3LYP/6-31G* level and including zero-point energies, thermal, and entropic contribution, we have found that beta-sheet is the most stable conformation, while the alpha-sheet proposed by Pauling and Corey has 13.6 kcal/mol higher free energy than the beta-sheet. The alpha-sheet that resembles the structure observed in molecular dynamics simulations of amyloidogenic proteins at low pH becomes distorted after stages of geometry optimization in solution. Whether the alpha-sheets with longer chains would be increasingly favorable in water relative to the increase in internal energy of the chain needs further investigation. Different from the quantum mechanics results, AMBER parm94 force field gives small difference in solution phase energy between alpha-sheet and beta-sheet. The predicted amide I IR spectra of alpha-sheet shows the main band at higher frequency than beta-sheet.
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Project description:Linear triatomic molecules (CO2, N2O, and OCS) are scrutinized for their propensity to form perpendicular tetrel (CO2 and OCS) or pnictogen (N2O) bonds with Lewis bases (dimethyl ether and trimethyl amine) as compared with their tendency to form end-on chalcogen bonds. Comparison of the IR spectra of the complexes with the corresponding monomers in cryogenic solutions in liquid argon enables to determine the stoichiometry and the nature of the complexes. In the present cases, perpendicular tetrel and pnictogen 1:1 complexes are identified mainly on the basis of the lifting of the degenerate ν 2 bending mode with the appearance of both a blue and a red shift. Van 't Hoff plots of equilibrium constants as a function of temperature lead to complexation enthalpies that, when converted to complexation energies, form the first series of experimental complexation energies on sp1 tetrel bonds in the literature, directly comparable to quantum-chemically obtained values. Their order of magnitude corresponds with what can be expected on the basis of experimental work on halogen and chalcogen bonds and previous computational work on tetrel bonds. Both the order of magnitude and sequence are in fair agreement with both CCSD(T) and DFA calculations, certainly when taking into account the small differences in complexation energies of the different complexes (often not more than a few kJ mol-1) and the experimental error. It should, however, be noted that the OCS chalcogen complexes are not identified experimentally, most probably owing to entropic effects. For a given Lewis base, the stability sequence of the complexes is first successfully interpreted via a classical electrostatic quadrupole-dipole moment model, highlighting the importance of the magnitude and sign of the quadrupole moment of the Lewis acid. This approach is validated by a subsequent analysis of the molecular electrostatic potential, scrutinizing the σ and π holes, as well as the evolution in preference for chalcogen versus tetrel bonds when passing to "higher" chalcogens in agreement with the evolution of the quadrupole moment. The energy decomposition analysis gives further support to the importance/dominance of electrostatic effects, as it turns out to be the largest attractive term in all cases considered, followed by the orbital interaction and the dispersion term. The natural orbitals for chemical valence highlight the sequence of charge transfer in the orbital interaction term, which is dominated by an electron-donating effect of the N or O lone-pair(s) of the base to the central atom of the triatomics, with its value being lower than in the case of comparable halogen bonding situations. The effect is appreciably larger for TMA, in line with its much higher basicity than DME, explaining the comparable complexation energies for DME and TMA despite the much larger dipole moment for DME.
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