scholarly journals Understand the Specific Regio- and Enantioselectivity of Fluostatin Conjugation in the Post-Biosynthesis

Biomolecules ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 815
Author(s):  
Yuanqi Wang ◽  
Changsheng Zhang ◽  
Yi-Lei Zhao ◽  
Rosalinda Zhao ◽  
Kendall N. Houk
Keyword(s):  
Molecular Orbital ◽  
Density Functional ◽  
Critical Role ◽  
Strain Analysis ◽  
Coupling Reaction ◽  
Density Functional Theory Calculations ◽  
Stacking Interactions ◽  
Coupling Reactions ◽  
Reaction Bonding ◽  
Π Stacking

Fluostatins, benzofluorene-containing aromatic polyketides in the atypical angucycline family, conjugate into dimeric and even trimeric compounds in the post-biosynthesis. The formation of the C–C bond involves a non-enzymatic stereospecific coupling reaction. In this work, the unusual regio- and enantioselectivities were rationalized by density functional theory calculations with the M06-2X (SMD, water)/6–311 + G(d,p)//6–31G(d) method. These DFT calculations reproduce the lowest energy C1-(R)-C10′-(S) coupling pathway observed in a nonenzymatic reaction. Bonding of the reactive carbon atoms (C1 and C10′) of the two reactant molecules maximizes the HOMO–LUMO interactions and Fukui function involving the highest occupied molecular orbital (HOMO) of nucleophile p-QM and lowest unoccupied molecular orbital (LUMO) of electrophile FST2− anion. In particular, the significant π–π stacking interactions of the low-energy pre-reaction state are retained in the lowest energy pathway for C–C coupling. The distortion/interaction–activation strain analysis indicates that the transition state (TScp-I) of the lowest energy pathway involves the highest stabilizing interactions and small distortion among all possible C–C coupling reactions. One of the two chiral centers generated in this step is lost upon aromatization of the phenol ring in the final difluostatin products. Thus, the π–π stacking interactions between the fluostatin 6-5-6 aromatic ring system play a critical role in the stereoselectivity of the nonenzymatic fluostatin conjugation.

scholarly journals Unexpected Sandwiched-Layer Structure of the Cocrystal Formed by Hexamethylbenzene with 1,3-Diiodotetrafluorobenzene: A Combined Theoretical and Crystallographic Study

Crystals ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 379 ◽  
Author(s):  
Yu Zhang ◽  
Jian-Ge Wang ◽  
Weizhou Wang
Keyword(s):  
Gas Phase ◽  
Density Functional ◽  
Layer Structure ◽  
Noncovalent Interactions ◽  
Density Functional Theory Calculations ◽  
Stacking Interactions ◽  
Halogen Bonds ◽  
Functional Theory ◽  
Π Stacking ◽  
Cocrystal Structure

The cocrystal formed by hexamethylbenzene (HMB) with 1,3-diiodotetrafluorobenzene (1,3-DITFB) was first synthesized and found to have an unexpected sandwiched-layer structure with alternating HMB layers and 1,3-DITFB layers. To better understand the formation of this special structure, all the noncovalent interactions between these molecules in the gas phase and the cocrystal structure have been investigated in detail by using the dispersion-corrected density functional theory calculations. In the cocrystal structure, the theoretically predicted π···π stacking interactions between HMB and the 1,3-DITFB molecules in the gas phase can be clearly seen, whereas there are no π···π stacking interactions between HMB molecules or between 1,3-DITFB molecules. The attractive interactions between HMB molecules in the corrugated HMB layers originate mainly in the dispersion forces. The 1,3-DITFB molecules form a 2D sheet structure via relatively weak C–I···F halogen bonds. The theoretically predicted much stronger C–I···π halogen bonds between HMB and 1,3-DITFB molecules in the gas phase are not found in the cocrystal structure. We concluded that it is the special geometry of 1,3-DITFB that leads to the formation of the sandwiched-layer structure of the cocrystal.

scholarly journals A novel selective fluorescent chemosensor for Fe3+ ions based on phthalonitrile dimer: synthesis, analysis, and theoretical studies

2020 ◽  
Vol 44 (5) ◽  
pp. 1254-1264
Author(s):  
Shaya AL-RAQA ◽  
İpek ÖMEROĞLU ◽  
Doğan ERBAHAR ◽  
Mahmut DURMUŞ
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Interaction Mechanism ◽  
Coupling Reaction ◽  
Cross Coupling ◽  
Density Functional Theory Calculations ◽  
Theoretical Studies ◽  
Functional Theory ◽  
Cross Coupling Reaction ◽  
Ft Ir

Phenyl-4,4-di(3,6-dibutoxyphthalonitrile) (3) was synthesized by the reaction of 1,4-phenylenebisboronic acid (1) and 4-bromo-3,6-dibutoxyphthalonitrile (2), using Suzuki cross-coupling reaction. The newly synthesized compound (3) was characterized by FT-IR, MALDI-MS, ESI-MS, 1H-NMR, 13C-NMR, and 13C-DEPT-135-NMR. The fluorescence property of phenyl-4,4-di(3,6- dibutoxyphthalonitrile) (3) towards various metal ions was investigated by fluorescence spectroscopy, and it was observed thatthe compound (3) displayed a significantly ‘turn-off’ response to Fe3+, which was referred to 1:2 complex formation between ligand (3) and Fe3+. The compound was also studied via density functional theory calculations revealing the interaction mechanism of the molecule with Fe3+ ions.

scholarly journals Copper-catalyzed aerobic oxidative coupling: From ketone and diamine to pyrazine

2015 ◽  
Vol 1 (9) ◽  
pp. e1500656 ◽  
Author(s):  
Kun Wu ◽  
Zhiliang Huang ◽  
Xiaotian Qi ◽  
Yingzi Li ◽  
Guanghui Zhang ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Oxidative Coupling ◽  
Density Functional ◽  
Coupling Reaction ◽  
Density Functional Theory Calculations ◽  
Radical Species ◽  
Functional Theory ◽  
X Ray ◽  
Oxidative Coupling Reaction ◽  
X Ray Absorption

Copper-catalyzed aerobic oxidative C–H/N–H coupling between simple ketones and diamines was developed toward the synthesis of a variety of pyrazines. Various substituted ketones were compatible for this transformation. Preliminary mechanistic investigations indicated that radical species were involved. X-ray absorption fine structure experiments elucidated that the Cu(II) species 5 coordinated by two N atoms at a distance of 2.04 Å and two O atoms at a shorter distance of 1.98 Å was a reactive one for this aerobic oxidative coupling reaction. Density functional theory calculations suggested that the intramolecular coupling of cationic radicals was favorable in this transformation.

scholarly journals Synthesis, Characterization, Catalytic Activity, and DFT Calculations of Zn(II) Hydrazone Complexes

Molecules ◽  
2020 ◽  
Vol 25 (18) ◽  
pp. 4043 ◽  
Author(s):  
Temiloluwa T. Adejumo ◽  
Nikolaos V. Tzouras ◽  
Leandros P. Zorba ◽  
Dušanka Radanović ◽  
Andrej Pevec ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Gas Phase ◽  
Molecular Orbital ◽  
Density Functional ◽  
Chemical Potential ◽  
Chemical Reactivity ◽  
Geometry Optimization ◽  
Coupling Reaction ◽  
Functional Theory ◽  
Reactivity Descriptors

Two new Zn(II) complexes with tridentate hydrazone-based ligands (condensation products of 2-acetylthiazole) were synthesized and characterized by infrared (IR) and nuclear magnetic resonance (NMR) spectroscopy and single crystal X-ray diffraction methods. The complexes 1, 2 and recently synthesized [ZnL3(NCS)2] (L3 = (E)-N,N,N-trimethyl-2-oxo-2-(2-(1-(pyridin-2-yl)ethylidene)hydrazinyl)ethan-1-aminium) complex 3 were tested as potential catalysts for the ketone-amine-alkyne (KA2) coupling reaction. The gas-phase geometry optimization of newly synthesized and characterized Zn(II) complexes has been computed at the density functional theory (DFT)/B3LYP/6–31G level of theory, while the highest occupied molecular orbital and lowest unoccupied molecular orbital (HOMO and LUMO) energies were calculated within the time-dependent density functional theory (TD-DFT) at B3LYP/6-31G and B3LYP/6-311G(d,p) levels of theory. From the energies of frontier molecular orbitals (HOMO–LUMO), the reactivity descriptors, such as chemical potential (μ), hardness (η), softness (S), electronegativity (χ) and electrophilicity index (ω) have been calculated. The energetic behavior of the investigated compounds (1 and 2) has been examined in gas phase and solvent media using the polarizable continuum model. For comparison reasons, the same calculations have been performed for recently synthesized [ZnL3(NCS)2] complex 3. DFT results show that compound 1 has the smaller frontier orbital gap so, it is more polarizable and is associated with a higher chemical reactivity, low kinetic stability and is termed as soft molecule.

Quantum processes in 8-Oxo-Guanine-Ru(bipyridine)32+ photosynthetic systems of artificial minimal cells

Open Physics ◽  
2011 ◽  
Vol 9 (3) ◽  
Author(s):  
Arvydas Tamulis ◽  
Mantas Grigalavicius ◽  
Sarunas Krisciukaitis ◽  
Giedrius Medzevicius
Keyword(s):  
Fatty Acid ◽  
Molecular Orbital ◽  
Electron Correlation ◽  
Self Assembly ◽  
Density Functional ◽  
Energy Levels ◽  
Critical Role ◽  
Quantum Processes ◽  
Photoexcited Electron ◽  
Minimal Cells

AbstractDensity functional theory methods were used to investigate various self-assembled photoactive bioorganic systems of interest for artificial minimal cells. The cell systems studied are based on nucleotides or their compounds and consisted of up to 123 atoms (not including the associated water or methanol solvent shells) and are up to 2.5 nm in diameter. The electron correlation interactions responsible for the weak hydrogen and Van derWaals chemical bonds increase due to the addition of a polar solvent (water or methanol). The precursor fatty acid molecules of the system also play a critical role in the quantum mechanical interaction based self-assembly of the photosynthetic center and the functioning of the photosynthetic processes of the artificial minimal cells. The distances between the separated sensitizer, fatty acid precursor, and methanol molecules are comparable to Van derWaals and hydrogen bonding radii. As a result the associated electron correlation interactions compress the overall system, resulting in an even smaller gap between the highest occupied molecular orbital (HOMO), and lowest unoccupied molecular orbital (LUMO) electron energy levels and photoexcited electron tunnelling occurs from the sensitizer (either Ru(bpy)32+ or [Ru(bpy)2(4-Bu-4’-Me-2,2’-bpy)]2++ derivatives) to the precursor fatty acid molecules (notation used: Me = methyl; Bu = butyl; bpy = bipyridine). The shift of the absorption spectrum to the red for the artificial protocell photosynthetic centers might be considered as the measure of the complexity of these systems.

AB INITIO AND DFT THEORETICAL INVESTIGATIONS ON NOVEL PORPHYRIN–FULLERENE SUPRAMOLECULAR DYADS FOR PHOTOVOLTAIC DEVICES

2008 ◽  
Vol 07 (05) ◽  
pp. 1055-1069 ◽  
Author(s):  
TAPAS MANNA ◽  
SUMANTA BHATTACHARYA
Keyword(s):  
Ab Initio ◽  
Molecular Orbital ◽  
Density Functional ◽  
Conformational Stability ◽  
Density Functional Theory Calculations ◽  
Orbital State ◽  
Highest Occupied Molecular Orbital ◽  
Theoretical Investigations ◽  
Lowest Unoccupied Molecular Orbital ◽  
Porphyrin Moiety

The conformational stability and electronic structures of novel H 2-(1) and Zn-tetraphenylporphyrin–[60]fullerene (2) dyads, in which the [60]fullerene is directly linked to the tetrapyrrolic rings by ethynylenephenylene subunits, have been studied by ab initio and density functional theory calculations. From the investigation on frontier molecular orbitals, it was found that the lowest unoccupied molecular orbital state of these supramolecules is localized on the fullerene and that the highest occupied molecular orbital state is localized on the porphyrin moiety. Molecular electrostatic potential maps clearly demonstrate the electron transfer phenomena from the porphyrin moiety to the fullerene in dyads 1 and 2.

scholarly journals The Role of Structural Flexibility in Plasmon-Driven Coupling Reactions: Kinetic Limitations in the Dimerization of Nitro-Benzenes

2021 ◽  
Author(s):  
Wouter Koopman ◽  
Evgenii Titov ◽  
Radwan Mohamed Sarhan ◽  
Tina Gaebel ◽  
Robin Schürmann ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Photoelectron Spectroscopy ◽  
Density Functional ◽  
Bond Activation ◽  
Density Functional Theory Calculations ◽  
Surface Enhanced Raman Spectroscopy ◽  
Bimolecular Reaction ◽  
Structural Flexibility ◽  
Coupling Reactions ◽  
Time Resolved

<div>The plasmon-driven dimerization of 4-nitrothiophenol (4NTP) to 4-4’-dimercaptoazobenzene (DMAB) has become a testbed for understanding bimolecular photoreactions enhanced by nanoscale metals, in particular, regarding the relevance of electron transfer and heat transfer from the metal to the molecule. By adding a methylene group between the thiol bond and the nitrophenyl, we add structural flexibility to the reactant molecule. Time-resolved surface-enhanced Raman-spectroscopy proves that this (4-nitrobenzyl)mercaptan (4NBM) molecule has a larger dimerization rate and dimerization yield than 4NTP and higher selectivity towards dimerization. X-ray photoelectron spectroscopy and density functional theory calculations show that the electron transfer would prefer activation of 4NTP over 4NBM. We conclude that the rate limiting step of this plasmonic reaction is the dimerization step, which is dramatically enhanced by the additional flexibility of the reactant. This study may serve as an example for using nanoscale metals to simultaneously provide charge carriers for bond activation and localized heat for driving bimolecular reaction steps. The molecular structure of reactants can be tuned to control the reaction kinetics.<br></div>

Sign in / Sign up

Export Citation Format

Share Document