The Pauli Repulsion-Lowering Concept in Catalysis

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One-Step Assembly of Functionalized Morpholinones and 1,4-Oxazepane-3-ones via [3 + 3]- And [3 + 4]-Annulation of Aza-Oxyallyl Cation and Amphoteric Compounds

A new [3 + 3]- and [3 + 4]-annulation strategy involving azaoxyallyl cation and [1,m]-amphoteric compounds (m = 3,4) is presented. This concise method enables easy assembly of functionalized saturated N-heterocycles, comprised of six-and seven-membered rings and is of high significance in the context of drug discovery approaches. This reaction also represents a new trapping modality of the azaoxyallyl cation with amphoteric agents of different chain lengths that consist of a heteroatom nucleophilic site and a π-electrophilic site

B-{DNA} Structure and Stability: The Role of Nucleotide Composition and Order

We have quantum chemically analyzed the influence of nucleotide composition and sequence (that is, order) on the stability of double-stranded B-DNA triplets in aqueous solution. To this end, we have investigated the structure and bonding of all 32 possible DNA duplexes with Watson-Crick base pairing, using dispersion-corrected DFT at the BLYP-D3(BJ)/TZ2P level and COSMO for simulating aqueous solvation. We find enhanced stabilities for duplexes possessing a higher GC base pair content. Our activation strain analyses unexpectedly identify the loss of stacking interactions within individual strands as a destabilizing factor in the duplex formation, in addition to the better-known effects of partial desolvation. Furthermore, we show that the sequence-dependent differences in the interaction energy for duplexes of the same overall base pair composition result from the so-called "diagonal interactions" or "cross terms". Whether cross terms are stabilizing or destabilizing depends on the nature of the electrostatic interaction between polar functional groups in the pertinent nucleobases

Understanding chemical reactivity using the activation strain model

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On the Origin of Regioselectivity in Palladium-Catalyzed Oxidation of Glucosides

The palladium-catalyzed oxidation of glucopyranosides has been investigated using relativistic density functional theory (DFT) at ZORA-BLYP−D3(BJ)/TZ2P. The complete Gibbs free energy profiles for the oxidation of secondary hydroxy groups at C2, C3, and C4 were computed for methyl β-glucoside and methyl carba-β-glucoside. Both computations and oxidation experiments on carba-glucosides demonstrate the crucial role of the ring oxygen in the C3 regioselectivity observed during the oxidation of glucosides. Analysis of the model systems for oxidized methyl β-glucoside shows that the C3 oxidation product is intrinsically favored in the presence of the ring oxygen. Subsequent energy decomposition analysis (EDA) and Hirschfeld charge analysis reveal the role of the ring oxygen: it positively polarizes C1/C5 by inductive effects and disfavors any subsequent buildup of positive charge at neighboring carbon atoms, rendering C3 the most favored site for the β-hydride elimination

Development of New Synthetic Methods, Mechanistic Elucidation of Novel Organic Reactions Using Quantum Calculations, and Harnessing the Power of Continuous Flow Technologies

The development of synthetic methodologies can be aided and improved upon by a critical understanding of the mechanistic pathways at play during a chemical reaction. Computational modeling has proven very valuable in this endeavor. My graduate research has focused on three areas in particular: (1) development of synthetic methodologies, (2) quantum chemical modeling, and (3) utilization of emerging technologies. These topics are highly relevant in the literature today and serve as a foundation to aid researchers in generations to come

Raman spectroscopy as a tool for monitoring mesoscale continuous-flow organic synthesis: Equipment interface and assessment in four medicinally-relevant reactions

An apparatus is reported for real-time Raman monitoring of reactions performed using continuous-flow processing. Its capability is assessed by studying four reactions, all involving formation of products bearing α,β-unsaturated carbonyl moieties; synthesis of 3-acetylcoumarin, Knoevenagel and Claisen–Schmidt condensations, and a Biginelli reaction. In each case it is possible to monitor the reactions and also in one case, by means of a calibration curve, determine product conversion from Raman spectral data as corroborated by data obtained using NMR spectroscopy

Real-time Monitoring of Reactions Performed Using Continuous-flow Processing: The Preparation of 3-Acetylcoumarin as an Example

By using inline monitoring, it is possible to optimize reactions performed using continuous-flow processing in a simple and rapid way. It is also possible to ensure consistent product quality over time using this technique. We here show how to interface a commercially available flow unit with a Raman spectrometer. The Raman flow cell is placed after the back-pressure regulator, meaning that it can be operated at atmospheric pressure. In addition, the fact that the product stream passes through a length of tubing before entering the flow cell means that the material is at RT. It is important that the spectra are acquired under isothermal conditions since Raman signal intensity is temperature dependent. Having assembled the apparatus, we then show how to monitor a chemical reaction, the piperidine-catalyzed synthesis of 3-acetylcoumarin from salicylaldehyde and ethyl acetoacetate being used as an example. The reaction can be performed over a range of flow rates and temperatures, the in-situ monitoring tool being used to optimize conditions simply and easily

Origin of Catalysis and Regioselectivity of Lewis Acid-Catalyzed Diels-Alder Reactions with Tropone

We have studied the uncatalyzed and Lewis acid (LA)-catalyzed cycloaddition reaction between tropone and 1,1-dimethoxyethene using dispersion-corrected relativistic density functional theory (DFT). The LA catalysts BF3, B(C6H5)3, and B(C6F5)3 efficiently accelerate both the competing [4+2] and [8+2] cycloaddition reactions by lowering the activation barrier up to 12 kcal mol–1 compared to the uncatalyzed reaction. Our study reveals that the LA catalyst promotes both cycloaddition reaction pathways by LUMO-lowering catalysis and demonstrates that Pauli-lowering catalysis is not always the operative catalytic mechanism in cycloaddition reactions. Judicious choice of the LA catalyst can effectively impart regiocontrol of the cycloaddition: B(C6H5)3 furnishes the [8+2] adduct while B(C6F5)3 yields the [4+2] adduct. We discovered that the regioselectivity shift finds its origin in the ability of the LA to absorb distortion by adopting a trigonal pyramidal geometry around the boron atom