Resolution and Determination of the Absolute Configuration of a Twisted Bis-Lactam Analogue of Tröger’s Base: A Comparative Spectroscopic and Computational Study

Quantum chemical package Jaguar: A survey of recent developments and unique features

This paper is dedicated to the quantum chemical package Jaguar, which is commercial software developed and distributed by Schrödinger, Inc. We discuss Jaguar's scientific features that are relevant to chemical research as well as describe those aspects of the program that are pertinent to the user interface, the organization of the computer code, and its maintenance and testing. Among the scientific topics that feature prominently in this paper are the quantum chemical methods grounded in the pseudospectral approach. A number of multistep workflows dependent on Jaguar are covered: prediction of protonation equilibria in aqueous solutions (particularly calculations of tautomeric stability and pKa), reactivity predictions based on automated transition state search, assembly of Boltzmann-averaged spectra such as vibrational and electronic circular dichroism, as well as nuclear magnetic resonance. Discussed also are quantum chemical calculations that are oriented toward materials science applications, in particular, prediction of properties of optoelectronic materials and organic semiconductors, and molecular catalyst design. The topic of treatment of conformations inevitably comes up in real world research projects and is considered as part of all the workflows mentioned above. In addition, we examine the role of machine learning methods in quantum chemical calculations performed by Jaguar, from auxiliary functions that return the approximate calculation runtime in a user interface, to prediction of actual molecular properties. The current work is second in a series of reviews of Jaguar, the first having been published more than ten years ago. Thus, this paper serves as a rare milestone on the path that is being traversed by Jaguar's development in more than thirty years of its existence.

A green bio-organic catalyst (taurine) promoted one-pot synthesis of (R/S)-2-thioxo-3,4-dihydropyrimidine(TDHPM)-5-carboxanilides: chiral investigations using circular dichroism and validation by computational approaches

Owing to the massive importance of dihydropyrimidine (DHPMs) scaffolds in the pharmaceutical industry and other areas, we developed an effective and sustainable one-pot reaction protocol for the synthesis of (R/S)-2-thioxo-DHPM-5-carboxanilides via the Biginelli-type cyclo-condensation reaction of aryl aldehydes, thiourea and various acetoacetanilide derivatives in ethanol at 100 °C. In this protocol, taurine was used as a green and reusable bio-organic catalyst. Twenty-three novel derivatives of (R/S)-TDHPM-5-carboxanilides and their structures were confirmed by various spectroscopy techniques. The aforementioned compounds were synthesized via the formation of one asymmetric centre, one new C-C bond, and two new C-N bonds in the final product. All the newly synthesized compounds were obtained in their racemic form with up to 99% yield. In addition, the separation of the racemic mixture of all the newly synthesized compounds was carried out by chiral HPLC (Prep LC), which provided up to 99.99% purity. The absolute configuration of all the enantiomerically pure isomers was determined using a circular dichroism study and validated by a computational approach. With up to 99% yield of 4d, this one-pot synthetic approach can also be useful for large-scale industrial production. One of the separated isomers (4R)-(+)-4S developed as a single crystal, and it was found that this crystal structure was orthorhombic.

Acyclic Twisted Amides

In this contribution, we provide a comprehensive overview of acyclic twisted amides, covering the literature since 1993 (the year of the first recognized report on acyclic twisted amides) through June 2020. The review focuses on classes of acyclic twisted amides and their key structural properties, such as amide bond twist and nitrogen pyramidalization, which are primarily responsible for disrupting nN to π*C═O conjugation. Through discussing acyclic twisted amides in comparison with the classic bridged lactams and conformationally restricted cyclic fused amides, the reader is provided with an overview of amidic distortion that results in novel conformational features of acyclic amides that can be exploited in various fields of chemistry ranging from organic synthesis and polymers to biochemistry and structural chemistry and the current position of acyclic twisted amides in modern chemistry.

Absolute Configurations of Synthetic Molecular Scaffolds from Vibrational CD Spectroscopy

Vibrational circular dichroism (VCD) spectroscopy is one of the most powerful techniques for the determination of absolute configurations (AC), as it does not require any specific UV/vis chromophores, no chemical derivatization, and no growth of suitable crystals. In the past decade, it has become increasingly recognized by chemists from various fields of synthetic chemistry such as total synthesis and drug discovery as well as from developers of asymmetric catalysts. This perspective article gives an overview about the most important experimental aspects of a VCD-based AC determination and explains the theoretical analysis. The comparison of experimental and computational spectra that leads to the final conclusion about the AC of the target molecules is described. In addition, the review summarizes unique VCD studies carried out in the period 2008-2018 that focus on the determination of unknown ACs of new compounds, which were obtained in its enantiopure form either through direct asymmetric synthesis or chiral chromatography.

Tröger's Base Twisted Amides: High Amide Bond Twist and N-/O-Protonation Aptitude

Tröger's base twisted amides have emerged as attractive scaffolds to readily achieve substantial nonplanarity of the amide bond in a bicyclic lactam framework. Herein, we report structures and proton affinities of a diverse set of Tröger's base twisted amides and compare them with related nonplanar bridged lactams. The data demonstrate that Tröger's base twisted amides embedded in a [3.3.1] scaffold are among the most twisted bridged lactams prepared to date. Intriguingly, while these amides also favor N-protonation, our data show that the best model for probing N-protonation aptitude in the series of nonplanar amides are less twisted benzofused 1-azabicyclo[3.3.1]nonan-2-one derivatives. This work (1) provides the understanding for future design of nonplanar bridged lactams to directly access N-protonated amide bonds, (2) validates the use of the additive Winkler-Dunitz distortion parameter, and (3) emphasizes the importance of peripheral modification to modulate properties of nonplanar amides.

Twisting the ethano-Tröger's base: the bisamide

The typically planar amide when incorporated into bicyclic systems can undergo a significant distortion from planarity resulting in physical properties and reactivity that deviate from classical amide behaviour. Herein, we report a succinct protocol that utilises potassium permanganate to selectively α-oxygenate the benzylic position of ethano-Tröger's base derivatives to yield a new class of twisted bisamides. Additionally, we report the first synthesis of an ethano-Tröger's base derivative bearing substituents in the positions ortho to the nitrogen atoms.

Diastereoselective Self-Assembly of a Neutral Dinuclear Double-Stranded Zinc(II) Helicate via Narcissistic Self-Sorting

A new bis(salicylimine) ligand based on the Tröger's base scaffold was synthesized in racemic and enantiomerically pure form. Upon coordination to zinc(II) ions this ligand undergoes highly diastereoselective self-assembly into neutral dinuclear double-stranded helicates as proven by XRD analysis and via comparison of experimental ECD spectra with those simulated with quantum-chemical methods. When the racemic ligand was used, self-assembly occurs under narcissistic self-sorting resulting in the formation of a racemic pair of helicates as revealed by NMR spectroscopy and XRD analysis.

Resolution of Thiele’s acid

Thiele’s acid has been resolved for the first time by diastereomeric salt formation with brucine. Determination of absolute stereochemistry was accomplished by X-ray crystallography of the corresponding diester. We anticipate that access to optically resolved Thiele’s acid will stimulate its use in a diverse range of applications requiring chiral molecular clefts.