Harnessing Noncovalent Interactions for a Directed Evolution of a Six-Component Molecular Crystal

2021 ◽  
Author(s):  
Sucharita Mandal ◽  
Arun K. Pal ◽  
Nilangshu Mandal ◽  
Titas Kumar Mukhopadhyay ◽  
Ayan Datta
Keyword(s):  
Directed Evolution ◽  
Molecular Crystal ◽  
Noncovalent Interactions

Advancing the use of Voronoi–Dirichlet polyhedra to describe interactions in organic molecular crystal structures by the example of galunisertib polymorphs

CrystEngComm ◽  
2021 ◽  
Author(s):  
Viktor N. Serezhkin ◽  
Anton V. Savchenkov
Keyword(s):  
Crystal Structures ◽  
Molecular Crystal ◽  
Noncovalent Interactions ◽  
Organic Molecular Crystal ◽  
Universal Approach ◽  
Structure Properties

The universal approach for studying structure/properties relationships shows that every polymorph of galunisertib is characterized with unique noncovalent interactions.

scholarly journals Catalytic iron-carbene intermediate revealed in a cytochromeccarbene transferase

2018 ◽  
Vol 115 (28) ◽  
pp. 7308-7313 ◽  
Author(s):  
Russell D. Lewis ◽  
Marc Garcia-Borràs ◽  
Matthew J. Chalkley ◽  
Andrew R. Buller ◽  
K. N. Houk ◽  
...  
Keyword(s):  
Directed Evolution ◽  
Computational Methods ◽  
Active Site ◽  
Noncovalent Interactions ◽  
Chemical Transformations ◽  
Rhodothermus Marinus ◽  
Geometrical Constraints ◽  
Carbene Transfer ◽  
Catalyzed Reactions ◽  
Enzyme Catalyzed Reactions

Recently, heme proteins have been discovered and engineered by directed evolution to catalyze chemical transformations that are biochemically unprecedented. Many of these nonnatural enzyme-catalyzed reactions are assumed to proceed through a catalytic iron porphyrin carbene (IPC) intermediate, although this intermediate has never been observed in a protein. Using crystallographic, spectroscopic, and computational methods, we have captured and studied a catalytic IPC intermediate in the active site of an enzyme derived from thermostableRhodothermus marinus(Rma) cytochromec. High-resolution crystal structures and computational methods reveal how directed evolution created an active site for carbene transfer in an electron transfer protein and how the laboratory-evolved enzyme achieves perfect carbene transfer stereoselectivity by holding the catalytic IPC in a single orientation. We also discovered that the IPC inRmacytochromechas a singlet ground electronic state and that the protein environment uses geometrical constraints and noncovalent interactions to influence different IPC electronic states. This information helps us to understand the impressive reactivity and selectivity of carbene transfer enzymes and offers insights that will guide and inspire future engineering efforts.

Noncovalent interactions in binary halides and oxides with a molecular crystal structure

2009 ◽  
Vol 54 (9) ◽  
pp. 1412-1418 ◽  
Author(s):  
V. N. Serezhkin ◽  
M. A. Prokaeva ◽  
D. V. Pushkin ◽  
L. B. Serezhkina
Keyword(s):  
Crystal Structure ◽  
Molecular Crystal ◽  
Noncovalent Interactions

The intermolecular anthracene-transfer in a regiospecific antipodal C60 difunctionalization

2020 ◽  
Author(s):  
Radu Talmazan ◽  
Klaus R. Liedl ◽  
Bernhard Kräutler ◽  
Maren Podewitz
Keyword(s):  
Noncovalent Interactions ◽  
Interaction Model ◽  
Alder Reaction ◽  
Diels Alder ◽  
Stacking Interactions ◽  
Pi Stacking ◽  
Diels Alder Reaction ◽  
Double Decker ◽  
Anthracene Molecule ◽  
New Strategies

We analyze the mechanism of the topochemically controlled difunctionalization of C60 and anthracene, where an anthracene molecule is transferred from one C60 monoadduct to another one under exclusive formation of equal amounts of C60 and the difficult to make antipodal C60 bisadduct. Our herein disclosed dispersion corrected DFT studies show the anthracene transfer to take place in a synchronous retro Diels-Alder/Diels-Alder reaction: an anthracene molecule dissociates from one fullerene under formation of an intermediate, while already undergoing stabilizing interactions with both neighboring fullerenes, facilitating the reaction kinetically. In the intermediate, a planar anthracene molecule is sandwiched between two neighboring fullerenes and forms equally strong "double-decker" type pi-pi stacking interactions with both of these fullerenes. Analysis with the distorsion interaction model shows that the anthracene unit of the intermediate is almost planar with minimal distorsions. This analysis sheds light on the existence of noncovalent interactions engaging both faces of a planar polyunsaturated ring and two convex fullerene surfaces in an unprecedented 'inverted sandwich' structure. Hence, it sheds light on new strategies to design functional fullerene based materials.<br>

The X40x10 Halogen Bonding Benchmark Revisited: Surprising Importance of (n-1)d Subvalence Correlation

2017 ◽  
Author(s):  
Manoj Kumar Kesharwani ◽  
Nitai Sylvetsky ◽  
Debashree Manna ◽  
Jan M.L. Martin
Keyword(s):  
Dissociation Energy ◽  
Noncovalent Interactions ◽  
Halogen Bonding ◽  
Coupled Cluster ◽  
Dissociation Energies ◽  
Iodine Species ◽  
Explicitly Correlated ◽  
High Level ◽  
Cluster Methods ◽  
Small Separation

<p>We have re-evaluated the X40x10 benchmark for halogen bonding using conventional and explicitly correlated coupled cluster methods. For the aromatic dimers at small separation, improved CCSD(T)–MP2 “high-level corrections” (HLCs) cause substantial reductions in the dissociation energy. For the bromine and iodine species, (n-1)d subvalence correlation increases dissociation energies, and turns out to be more important for noncovalent interactions than is generally realized. As in previous studies, we find that the most efficient way to obtain HLCs is to combine (T) from conventional CCSD(T) calculations with explicitly correlated CCSD-F12–MP2-F12 differences.</p>

Directed Evolution of P450 Fatty Acid Decarboxylases via High-Throughput Screening Towards Improved Catalytic Activity

2019 ◽  
Author(s):  
Huifang Xu ◽  
Weinan Liang ◽  
Linlin Ning ◽  
Yuanyuan Jiang ◽  
Wenxia Yang ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Fatty Acid ◽  
Directed Evolution ◽  
High Throughput ◽  
High Throughput Screening ◽  
Colorimetric Detection ◽  
Screening Method ◽  
Random Mutagenesis ◽  
Direct Production ◽  
Consumption Activity

P450 fatty acid decarboxylases (FADCs) have recently been attracting considerable attention owing to their one-step direct production of industrially important 1-alkenes from biologically abundant feedstock free fatty acids under mild conditions. However, attempts to improve the catalytic activity of FADCs have met with little success. Protein engineering has been limited to selected residues and small mutant libraries due to lack of an effective high-throughput screening (HTS) method. Here, we devise a catalase-deficient <i>Escherichia coli</i> host strain and report an HTS approach based on colorimetric detection of H<sub>2</sub>O<sub>2</sub>-consumption activity of FADCs. Directed evolution enabled by this method has led to effective identification for the first time of improved FADC variants for medium-chain 1-alkene production from both DNA shuffling and random mutagenesis libraries. Advantageously, this screening method can be extended to other enzymes that stoichiometrically utilize H<sub>2</sub>O<sub>2</sub> as co-substrate.

A Robust, Porous and Solution-Processable Molecular Crystal Containing Multiple Donor-Acceptor Units

2019 ◽  
Author(s):  
Shengxian Cheng ◽  
Xiaoxia Ma, ◽  
Yonghe He ◽  
Jun He ◽  
Matthias Zeller ◽  
...  
Keyword(s):  
Molecular Crystal ◽  
Bulk Sample ◽  
Intermolecular Forces ◽  
Close Packing ◽  
Molecular Solids ◽  
Molecular Scaffold ◽  
Excellent Thermal Stability ◽  
Crystalline Order ◽  
Donor Acceptor ◽  
Open Packing

We report a curious porous molecular crystal that is devoid of the common traits of related systems. Namely, the molecule does not rely on directional hydrogen bonds to enforce open packing; and it offers neither large concave faces (i.e., high internal free volume) to frustrate close packing, nor any inherently built-in cavity like in the class of organic cages. Instead, the permanent porosity (as unveiled by the X-ray crystal structure and CO<sub>2</sub> sorption studies) arises from the strong push-pull units built into a Sierpinski-like molecule that features four symmetrically backfolded (<b>SBF</b>) side arms. Each side arm consists of the 1,1,4,4-tetracyanobuta-1,3-diene acceptor (TCBD) coupled with the dimethylaminophenyl donor, which is conveniently installed by a cycloaddition-retroelectrocyclization (CA-RE) reaction. Unlike the poor/fragile crystalline order of many porous molecular solids, the molecule here readily crystallizes and the crystalline phase can be easily deposited into thin films from solutions. Moreover, both the bulk sample and thin film exhibit excellent thermal stability with the porous crystalline order maintained even at 200 °C. The intermolecular forces underlying this robust porous molecular crystal likely include the strong dipole interactions and the multiple C···N and C···O short contacts afforded by the strongly donating and accepting groups integrated within the rigid molecular scaffold.

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