A first-principles exploration of the conformational space of sodiated di-saccharides assisted by semi-empirical methods and neural network potentials.

Previous exploration of the conformational space of sodiated mono-saccharides using a random search algorithm leads to ∼10 structurally distinct conformers covering an energy range of ∼150 kJ mol. Thus, it is reasonable to expect that the number of distinct conformers for a given disaccharide would be on the order of 10. Efficient identification of distinct conformers at the first-principles level has been demonstrated with the assistance of neural network potential (NNP) with an accuracy of ∼1 kJ mol compared to DFT.

A first-principles exploration of the conformational space of sodiated pyranose assisted by neural network potentials.

Sampling the conformational space of monosaccharides using the first-principles methods is important and as a database of local minima provides a solid base for interpreting experimental measurements such as infrared photo-dissociation (IRPD) spectroscopy or collision-induced dissociation (CID). IRPD emphasizes low-energy conformers and CID can distinguish conformers with distinct reaction pathways. A typical computational approach is to engage empirical or semi-empirical methods to sample the conformational space first, and only selected minima are reoptimized at first-principles levels.

A self-adapting first-principles exploration on the dissociation mechanism in sodiated aldohexose pyranoses assisted with neural network potentials.

Understanding the mechanism of collision-induced dissociation (CID) in mono-saccharides with density functional theory (DFT) is challenging because of many possible reaction paths that originate from their high structural diversity. To search for the transition state (TS) from the huge number of conformers, we propose a three-step search scheme with the assistance of neural network potential (NNP). The search starts from a cross-checking of sugars, to a global search of all possible channels, and in the end, an exhaustive exploration around the low-lying channels.

Capturing the potential energy landscape of large size molecular clusters from atomic interactions up to a 4-body system using deep learning.

Exploring the structure and properties of molecular clusters with accuracy using the methods is a resource intensive task due to the increasing cost of the methods and the number of distinct conformers as the size increases. The energy landscape of methanol clusters has been previously explored using computationally efficient empirical models to collect a database of structurally distinct minima, followed by re-optimization using methods. In this work, we propose a new method that utilizes the database of stable conformers and borrow the fragmentation concept of many-body-expansion (MBE) methods in methods to train a deep-learning machine learning (ML) model using SchNet.

Enantiodivergent Steglich rearrangement of -carboxylazlactones catalyzed by a chirality switchable helicene containing a 4-aminopyridine unit.

A pseudo-enantiomeric pair of optically switchable helicenes containing a catalytic 4--methylaminopyridine (MAP) bottom unit and a -symmetric, (10,11)-dimethoxymethyl-dibenzosuberane top template was synthesized. They underwent complementary photoswitching at 290 nm (/', <1/>99) and 340 nm (/', 91/9) and unidirectional thermo-rotation at 130 °C (/', >99/<1). They were utilized to catalyze enantiodivergent Steglich rearrangement of - to -carboxylazlactones, with formation of either enantiomer with up to 91% ee () and 94% ee (), respectively.

Stereochemical Course of Wittig Rearrangements of Dihydropyran Allyl Propargyl Ethers.

[2,3]-Wittig rearrangements of sugar-derived dihydropyran allyl propargyl ethers located at the 2- or 4-position have been studied as useful means for extending the carbon chains of the 4- or 2-position with chirality transfer. The stereochemical course of these reactions depends on the following factors: (1) deprotonation of pro-R or pro-S-H, (2) equilibration of the lithiated stereogenic carbanion, (3) conformational inversion during the rearrangement, and (4) concerted [2,3]- or [1,2]-Wittig rearrangement. In some cases, a stepwise mechanism that involves the allyl-C-O bond cleavage is shared as the first step by both the [2,3]- and [1,2]-Wittig rearrangements.

A computational study of organic polyradicals stabilized by chromium atoms.

Density functional theory has been used to investigate the properties of organic high spin molecules. The M05/cc-pVDZ calculations predict a septet ground state for the 2,3,6,7,10,11-hexahydro-1,4,5,8,9,12-hexaoxocoronene-2,3,6,7,10,11-hexayl radical (coronene-6O). The computations show further that the formation of intermolecular carbon-carbon bonds yields a singlet ground state for the dimer rather than a possible tridectet state as expected from the monomer's multiplicity.