Thierry Kogej

Bio: Thierry Kogej is an academic researcher from AstraZeneca. The author has contributed to research in topics: Two-photon absorption & Virtual screening. The author has an hindex of 21, co-authored 46 publications receiving 4176 citations. Previous affiliations of Thierry Kogej include University of Mons & UCB.

Design of Organic Molecules with Large Two-Photon Absorption Cross Sections

Abstract: A strategy for the design of molecules with large two-photon absorption cross sections, δ, was developed, on the basis of the concept that symmetric charge transfer, from the ends of a conjugated system to the middle, or vice versa, upon excitation is correlated to enhanced values of δ. Synthesized bis(styryl)benzene derivatives with donor-π-donor, donor-acceptor-donor, and acceptor-donor-acceptor structural motifs exhibit exceptionally large values of δ, up to about 400 times that of trans-stilbene. Quantum chemical calculations performed on these molecules indicate that substantial symmetric charge redistribution occurs upon excitation and provide δ values in good agreement with experimental values. The combination of large δ and high fluorescence quantum yield or triplet yield exhibited by molecules developed here offers potential for unprecedented brightness in two-photon fluorescent imaging or enhanced photosensitivity in two-photon sensitization, respectively.

Generating Focused Molecule Libraries for Drug Discovery with Recurrent Neural Networks

Abstract: In de novo drug design, computational strategies are used to generate novel molecules with good affinity to the desired biological target. In this work, we show that recurrent neural networks can be trained as generative models for molecular structures, similar to statistical language models in natural language processing. We demonstrate that the properties of the generated molecules correlate very well with the properties of the molecules used to train the model. In order to enrich libraries with molecules active toward a given biological target, we propose to fine-tune the model with small sets of molecules, which are known to be active against that target. Against Staphylococcus aureus, the model reproduced 14% of 6051 hold-out test molecules that medicinal chemists designed, whereas against Plasmodium falciparum (Malaria), it reproduced 28% of 1240 test molecules. When coupled with a scoring function, our model can perform the complete de novo drug design cycle to generate large sets of novel molecule...

Tuning the two-photon absorption response of quadrupolar organic molecules

Abstract: We apply correlated quantum-chemical techniques to study the origin of the large two-photon absorption (TPA) cross sections, δ, in stilbene derivatives in which electron-donating and electron-withdrawing substituents provide a quadrupolar charge-transfer arrangement. An additional field created by a set of point charges is used to systematically modify the ground-state polarization to determine its consequences for the TPA response. The effect on the molecular structure can be quantified by the evolution of the π-bond-order alternation (π-BOA) of the conjugated backbone. For moderate ground-state polarizations, a marked increase of the TPA response occurs; for large polarizations, δ peaks and then drops dramatically. Insight into the origin of this evolution is gained by comparing the values of δ obtained via the converged sum-over-states approach to the results of a simple three-state model.

Open Babel: An open chemical toolbox

Abstract: A frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language) and de facto standards have arisen (for example, SMILES format), the need to interconvert formats is a continuing problem due to the multitude of different application areas for chemistry data, differences in the data stored by different formats (0D versus 3D, for example), and competition between software along with a lack of vendor-neutral formats. We discuss, for the first time, Open Babel, an open-source chemical toolbox that speaks the many languages of chemical data. Open Babel version 2.3 interconverts over 110 formats. The need to represent such a wide variety of chemical and molecular data requires a library that implements a wide range of cheminformatics algorithms, from partial charge assignment and aromaticity detection, to bond order perception and canonicalization. We detail the implementation of Open Babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion. Open Babel presents a solution to the proliferation of multiple chemical file formats. In addition, it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching. For developers, it can be used as a programming library to handle chemical data in areas such as organic chemistry, drug design, materials science, and computational chemistry. It is freely available under an open-source license from http://openbabel.org .

Aggregation-Induced Emission: Together We Shine, United We Soar!

Abstract: Ju Mei,†,‡,∥ Nelson L. C. Leung,†,‡,∥ Ryan T. K. Kwok,†,‡ Jacky W. Y. Lam,†,‡ and Ben Zhong Tang*,†,‡,§ †HKUST-Shenzhen Research Institute, Hi-Tech Park, Nanshan, Shenzhen 518057, China ‡Department of Chemistry, HKUST Jockey Club Institute for Advanced Study, Institute of Molecular Functional Materials, Division of Biomedical Engineering, State Key Laboratory of Molecular Neuroscience, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China Guangdong Innovative Research Team, SCUT-HKUST Joint Research Laboratory, State Key Laboratory of Luminescent Materials and Devices, South China University of Technology, Guangzhou 510640, China

Luminescent Metal–Organic Frameworks

Abstract: Metal–organic frameworks (MOFs) display a wide range of luminescent behaviors resulting from the multifaceted nature of their structure. In this critical review we discuss the origins of MOF luminosity, which include the linker, the coordinated metal ions, antenna effects, excimer and exciplex formation, and guest molecules. The literature describing these effects is comprehensively surveyed, including a categorization of each report according to the type of luminescence observed. Finally, we discuss potential applications of luminescent MOFs. This review will be of interest to researchers and synthetic chemists attempting to design luminescent MOFs, and those engaged in the extension of MOFs to applications such as chemical, biological, and radiation detection, medical imaging, and electro-optical devices (141 references).

Nonlinear magic: multiphoton microscopy in the biosciences

Abstract: Multiphoton microscopy (MPM) has found a niche in the world of biological imaging as the best noninvasive means of fluorescence microscopy in tissue explants and living animals. Coupled with transgenic mouse models of disease and 'smart' genetically encoded fluorescent indicators, its use is now increasing exponentially. Properly applied, it is capable of measuring calcium transients 500 microm deep in a mouse brain, or quantifying blood flow by imaging shadows of blood cells as they race through capillaries. With the multitude of possibilities afforded by variations of nonlinear optics and localized photochemistry, it is possible to image collagen fibrils directly within tissue through nonlinear scattering, or release caged compounds in sub-femtoliter volumes.