Ab initio mechanistic study of the protection of alcohols and amines with anhydrides

Unexpected Nucleophile Masking in Acyl Transfer to Sterically Crowded and Conformationally Restricted Galactosides

Design and synthesis of orthogonally protected monosaccharide building blocks are crucial for the preparation of well-defined oligosaccharides in a stereo- and regiocontrolled manner. Selective introduction of protecting groups to partially protected monosaccharides is nontrivial due to the often unpredictable electronic, steric, and conformational effects of the substituents. Abolished reactivity toward a commonly used Lewis base-catalyzed acylation of O-2 was observed in conformationally restricted 4,6-O-benzylidene-3-O-Nap galactoside. Investigation of analogous systems, crystallographic characterization, and quantum chemical calculations highlighted the overlooked conformational and steric considerations, the combination of which produces a unique passivity of the 2-OH nucleophile. Evaluating the role of electrophile counterion and auxiliary base in the acylation of the sterically crowded and conformationally restricted galactoside system revealed an alternative Brønsted base-driven reaction pathway via nucleophilic activation. Insights gained from this model system were utilized to access the target galactoside intermediate within the envisioned synthetic route. The acylation strategy described herein can be implemented in future syntheses of key monomeric building blocks with unique protecting group hierarchies.

Base- and Catalyst-Induced Orthogonal Site Selectivities in Acylation of Amphiphilic Diols

Seeking to selectively functionalize natural and synthetic amphiphiles, we explored acylation of model amphiphilic diols. The use of a nucleophilic catalyst enabled a remarkable shift of the site selectivity from the polar site, preferred in background noncatalyzed or base-promoted reactions, to the apolar site. This tendency was significantly enhanced for organocatalysts comprising an imidazole active site surrounded by long/branched tails. An explanation of these orthogonal modes of selectivity is supported by competitive experiments with monoalcohol substrates.

Concerted hydrolysis mechanism of HIV-1 natural substrate against subtypes B and C-SA PR: insight through molecular dynamics and hybrid QM/MM studies

It is well known that understanding the catalytic mechanism of HIV-1 PR is the rationale on which its inhibitors were developed; therefore, a better understanding of the mechanism of natural substrate hydrolysis is important. Herein, the reaction mechanism of HIV-1 natural substrates with subtypes B and common mutant in South Africa (subtype C-SA) protease were studied through transition state modelling, using a general acid-general base (GA-GB) one-step concerted process. The activation free energies of enzyme-substrate complexes were compared based on their rate of hydrolysis using a two-layered ONIOM (B3LYP/6-31++G(d,p):AMBER) method. We expanded our computational model to obtain a better understanding of the mechanism of hydrolysis as well as how the enzyme recognises or chooses the cleavage site of the scissile bonds. Using this model, a potential substrate-based inhibitor could be developed with better potency. The calculated activation energies of natural substrates in our previous study correlated well with experimental data. A similar trend was observed for the Gag and Gag-Pol natural substrates in the present work for both enzyme complexes except for the PR-RT substrate. Natural bond orbital (NBO) analysis was also applied to determine the extent of charge transfer within the QM part of both enzymes considered and the PR-RT natural substrate. The result of this study shows that the method can be utilized as a dependable computational technique to rationalize lead compounds against specific targets.

The Driving Force for the Acylation of β-Lactam Antibiotics by L,D-Transpeptidase 2: Quantum Mechanics/Molecular Mechanics (QM/MM) Study

β-lactam antibiotics, which are used to treat infectious diseases, are currently the most widely used class of antibiotics. This study focused on the chemical reactivity of five- and six-membered ring systems attached to the β-lactam ring. The ring strain energy (RSE), force constant (FC) of amide (C-N), acylation transition states and second-order perturbation stabilization energies of 13 basic structural units of β-lactam derivatives were computed using the M06-2X and G3/B3LYP multistep method. In the ring strain calculations, an isodesmic reaction scheme was used to obtain the total energies. RSE is relatively greater in the five-(1a-2c) compared to the six-membered ring systems except for 4b, which gives a RSE that is comparable to five-membered ring lactams. These variations were also observed in the calculated inter-atomic amide bond distances (C-N), which is why the six-membered ring lactams C-N bond are more rigid than those with five-membered ring lactams. The calculated ΔG^# values from the acylation reaction of the lactams (involving the S-H group of the cysteine active residue from L,D transpeptidase 2) revealed a faster rate of C-N cleavage in the five-membered ring lactams especially in the 1-2 derivatives (17.58 kcal mol^-1 ). This observation is also reflected in the calculated amide bond force constant (1.26 mDyn/A) indicating a weaker bond strength, suggesting that electronic factors (electron delocalization) play more of a role on reactivity of the β-lactam ring, than ring strain.

Crystal structure, spectroscopic studies and theoretical studies of thiobarbituric acid derivatives: understanding the hydrogen-bonding patterns

In addition to their wide-ranging applications in the pharmaceutical industry, thiobarbituric acid (TBA) derivatives are also known to possess applications in engineering and materials science. 20 TBA derivatives, with diversity at the N and C-5 positions through acylation, Schiff base formation, Knoevenagel condensation, thioamide and enamine formation, were studied. The absolute configurations for six derivatives, namely 5-acetyl-1,3-diethyl-2-thioxodihydropyrimidine-4,6(1H,5H)-dione, C₁₀H₁₄N₂O₃S, A01, 1,3-diethyl-5-propionyl-2-thioxodihydropyrimidine-4,6(1H,5H)-dione, C₁₁H₁₆N₂O₃S, A02, tert-butyl [1-(1,3-diethyl-4,6-dioxo-2-thioxohexahydropyrimidin-5-yl)-3-methyl-1-oxobutan-2-yl]carbamate, C₁₈H₂₉N₃O₅S, A06, 1,3-diethyl-4,6-dioxo-2-thioxo-N-(p-tolyl)hexahydropyrimidine-5-carbothioamide, C₁₆H₁₉N₃O₂S₂, A13, 5-(1-aminoethylidene)-1,3-diethyl-2-thioxodihydropyrimidine-4,6(1H,5H)-dione, C₁₀H₁₅N₃O₂S, A17, and 5-(1-aminopropylidene)-1,3-diethyl-2-thioxodihydropyrimidine-4,6(1H,5H)-dione, C₁₁H₁₇N₃O₂S, A18, were confirmed by single-crystal X-ray crystallography, which indicates the formation of intramolecular hydrogen bonding in all six cases and intermolecular hydrogen bonding for A17. In A13, the presence of two intramolecular hydrogen bonds was observed. The stabilization of the enol form over the keto form was confirmed by computation. In order to convert the keto form to the enol form, an energy barrier of 55.05 kcal mol^-1 needs to be overcome, as confirmed by transition-state calculations.

The catalytic role of water in the binding site of l,d-transpeptidase 2 within acylation mechanism: A QM/MM (ONIOM) modelling

Mycobacterium tuberculosis is the causative agent of Tuberculosis. Formation of 3 → 3 crosslinks in the peptidoglycan layer of M. tuberculosis is catalyzed by l,d-transpeptidases. These enzymes can confer resistance against classical β-lactams that inhibit enzymes that generate 4 → 3 peptidoglycan crosslinks. The focus of this study is to investigate the catalytic role of water molecules in the acylation mechanism of the β-lactam ring within two models; 4- and 6-membered ring systems using two-layered our Own N-layer integrated Molecular Mechanics ONIOM (B3LYP/6-311++G(2d,2p): AMBER) model. The obtained thermochemical parameters revealed that the 6-membered ring model best describes the inhibition mechanism of acylation which indicates the role of water in the preference of 6-membered ring reaction pathway. This finding is in accordance with experimental data for the rate-limiting step of cysteine protease with the same class of inhibitor and binding affinity for both inhibitors. As expected, the ΔG^# results also reveal that the 6-membered ring reaction pathway is the most favourable. The electrostatic potential (ESP) and the natural bond orbital analysis (NBO) showed stronger interactions in 6-membered ring transition state (TS-6) mechanism involving water in the active site of the enzyme. This study could be helpful in the development of novel antibiotics against l,d-transpeptidase.

Mechanistic investigation of the uncatalyzed esterification reaction of acetic acid and acid halides with methanol: a DFT study

Implementation of catalysts to drive reactions from reactants to products remains a burden to synthetic and organic chemists. In spite of investigations into the kinetics and mechanism of catalyzed esterification reactions, less effort has been made to explore the possibility of an uncatalyzed esterification process. Therefore, a comprehensive mechanistic perspective for the uncatalyzed mechanism at the molecular level is presented. Herein, we describe the non-catalyzed esterification reaction of acetic acid and its halide derivatives (XAc, where X= OH, F, Cl, Br, I) with methanol (MeOH) through a concerted process. The reaction in vacuum and methanol was performed using the density functional theory (DFT) method at M06-2X level with def2-TZVP basis set after a careful literature survey and computations. Esterification through cyclic 4- or 6-membered transition state structures in one- or two-step concerted mechanisms were investigated. The present study outlines the possible cyclic geometry conformations that may occur during experiments at simple ratio of reactants. The free energy of activation for acetic acid and acetyl chloride are 36 kcal mol(-1) and 21 kcal mol(-1), respectively. These are in good agreement with available experimental results from the literature. The selected quantum chemical descriptors proved to be useful tools in chemical reactivity prediction for the reaction mechanism. This quantum mechanics study can serve as a necessary step towards revisiting uncatalyzed reaction mechanisms in some classical organic reactions.

Pentacycloundecane lactam vs lactone norstatine type protease HIV inhibitors: binding energy calculations and DFT study

Background

Novel pentacycloundecane (PCU)-lactone-CO-EAIS peptide inhibitors were designed, synthesized, and evaluated against wild-type C-South African (C-SA) HIV-1 protease. Three compounds are reported herein, two of which displayed IC₅₀ values of less than 1.00 μM. A comparative MM-PB(GB)SA binding free energy of solvation values of PCU-lactam and lactone models and their enantiomers as well as the PCU-lactam-NH-EAIS and lactone-CO-EAIS peptide inhibitors and their corresponding diastereomers complexed with South African HIV protease (C-SA) was performed. This will enable us to rationalize the considerable difference between inhibitory concentration (IC₅₀) of PCU-lactam-NH-EAIS and PCU-lactone-CO-EAIS peptides.

Results

The PCU-lactam model exhibited more negative calculated binding free energies of solvation than the PCU-lactone model. The same trend was observed for the PCU-peptide inhibitors, which correspond to the experimental activities for the PCU-lactam-NH-EAIS peptide (IC₅₀ = 0.076 μM) and the PCU-lactone-CO-EAIS peptide inhibitors (IC₅₀ = 0.850 μM). Furthermore, a density functional theory (DFT) study on the natural atomic charges of the nitrogen and oxygen atoms of the three PCU-lactam, PCU-lactim and PCU-lactone models were performed using natural bond orbital (NBO) analysis. Electrostatic potential maps were also used to visualize the electron density around electron-rich regions. The asymmetry parameter (η) and quadrupole coupling constant (χ) values of the nitrogen and oxygen nuclei of the model compounds were calculated at the same level of theory. Electronic molecular properties including polarizability and electric dipole moments were also calculated and compared. The Gibbs theoretical free solvation energies of solvation (∆G_solv) were also considered.

Conclusions

A general trend is observed that the lactam species appears to have a larger negative charge distribution around the heteroatoms, larger quadrupole constant, dipole moment and better solvation energy, in comparison to the PCU-lactone model. It can be argued that these characteristics will ensure better eletronic interaction between the lactam and the receptor, corresponding to the observed HIV protease activities in terms of experimental IC₅₀ data.

Electronic supplementary material

The online version of this article (doi:10.1186/s12929-015-0115-5) contains supplementary material, which is available to authorized users.

The effect of N-methylation of amino acids (Ac-X-OMe) on solubility and conformation: a DFT study

N-Methylation of amino acid derivatives (Ac-X-OMe, X = Gly, Val, Leu, Ile, Phe, Met, Cys, Ser, Asp and His) leads to an increase in aqueous solubility, lipophilicity and lowering of the cis/trans amide conformational energy barrier (E_A).