scholarly journals Expedient synthesis of E-hydrazone esters and 1H-indazole scaffolds through heterogeneous single-atom platinum catalysis

2019 ◽  
Vol 5 (12) ◽  
pp. eaay1537 ◽  
Author(s):  
Cuibo Liu ◽  
Zhongxin Chen ◽  
Huan Yan ◽  
Shibo Xi ◽  
Kah Meng Yam ◽  
...  
Keyword(s):  
Density Functional ◽  
Stereoselective Synthesis ◽  
Density Functional Theory Calculations ◽  
Building Blocks ◽  
Hydrogenation Reaction ◽  
Biologically Active ◽  
Single Atom ◽  
One Pot ◽  
Platinum Catalysis ◽  
Scalable Synthesis

Unprotected E-hydrazone esters are prized building blocks for the preparation of 1H-indazoles and countless other N-containing biologically active molecules. Despite previous advances, efficient and stereoselective synthesis of these compounds remains nontrivial. Here, we show that Pt single atoms anchored on defect-rich CeO2 nanorods (Pt1/CeO2), in conjunction with the alcoholysis of ammonia borane, promotes exceptionally E-selective hydrogenation of α-diazoesters to afford a wide assortment of N-H hydrazone esters with an overall turnover frequency of up to 566 hours−1 upon reaction completion. The α-diazoester substrates could be generated in situ from readily available carboxylic esters in one-pot hydrogenation reaction. Utility is demonstrated through concise, scalable synthesis of 1H-indazole–derived pharmaceuticals and their 15N-labeled analogs. The present protocol highlights a key mechanistic nuance wherein simultaneous coordination of a Pt site with the diazo N═N and ester carbonyl motifs plays a central role in controlling stereoselectivity, which is supported by density functional theory calculations.

scholarly journals Diversity-oriented synthesis of glycomimetics

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Michael Meanwell ◽  
Gaelen Fehr ◽  
Weiwu Ren ◽  
Bharanishashank Adluri ◽  
Victoria Rose ◽  
...  
Keyword(s):  
Electrostatic Interactions ◽  
Density Functional ◽  
Kinetic Resolution ◽  
Density Functional Theory Calculations ◽  
Building Blocks ◽  
One Pot ◽  
Functional Theory ◽  
Diversity Oriented Synthesis ◽  
Naturally Occurring ◽  
Therapeutic Leads

AbstractGlycomimetics are structural mimics of naturally occurring carbohydrates and represent important therapeutic leads in several disease treatments. However, the structural and stereochemical complexity inherent to glycomimetics often challenges medicinal chemistry efforts and is incompatible with diversity-oriented synthesis approaches. Here, we describe a one-pot proline-catalyzed aldehyde α-functionalization/aldol reaction that produces an array of stereochemically well-defined glycomimetic building blocks containing fluoro, chloro, bromo, trifluoromethylthio and azodicarboxylate functional groups. Using density functional theory calculations, we demonstrate both steric and electrostatic interactions play key diastereodiscriminating roles in the dynamic kinetic resolution. The utility of this simple process for generating large and diverse libraries of glycomimetics is demonstrated in the rapid production of iminosugars, nucleoside analogues, carbasugars and carbohydrates from common intermediates.

scholarly journals Microhydration of ionized building blocks of DNA/RNA: infrared spectra of pyrimidine$$^{+}$$-$$(\hbox {H}_{2}\hbox {O})_{\text {1-3}}$$ clusters

2021 ◽  
Vol 75 (3) ◽  
Author(s):  
Kuntal Chatterjee ◽  
Otto Dopfer
Keyword(s):  
Density Functional ◽  
Size Range ◽  
Density Functional Theory Calculations ◽  
Building Blocks ◽  
Ion Solvation ◽  
Structure Stability ◽  
Consistent Picture ◽  
Three Body ◽  
And Function ◽  
Stable Structures

Abstract Hydration of biomolecules is an important physiological process that governs their structure, stability, and function. Herein, we probe the microhydration structure of cationic pyrimidine (Pym), a common building block of DNA/RNA bases, by infrared photodissociation spectroscopy (IRPD) of mass-selected microhydrated clusters, $$\hbox {Pym}^{+}$$ Pym + -$$\hbox {W}_{n}$$ W n (W=$$\hbox {H}_{2}\hbox {O}$$ H 2 O ), in the size range $$n=1$$ n = 1 –3. The IRPD spectra recorded in the OH and CH stretch range are sensitive to the evolution of the hydration network. Analysis with density functional theory calculations at the dispersion-corrected B3LYP-D3/aug-cc-pVTZ level provides a consistent picture of the most stable structures and their energetic and vibrational properties. The global minima of $$\hbox {Pym}^{+}$$ Pym + -$$\hbox {W}_{n}$$ W n predicted by the calculations are characterized by H-bonded structures, in which the H-bonded $$\hbox {W}_{n}$$ W n solvent cluster is attached to the most acidic C4–H proton of $$\hbox {Pym}^{+}$$ Pym + via a single CH...O ionic H-bond. These isomers are identified as predominant carrier of the IRPD spectra, although less stable local minima provide minor contributions. In general, the formation of the H-bonded solvent network (exterior ion solvation) is energetically preferred to less stable structures with interior ion solvation because of cooperative nonadditive three-body polarization effects. Progressive hydration activates the C4–H bond, along with increasing charge transfer from $$\hbox {Pym}^{+}$$ Pym + to $$\hbox {W}_{n}$$ W n , although no proton transfer is observed in the size range $$n\leqslant $$ n ⩽ 3. The solvation with protic, dipolar, and hydrophilic W ligands is qualitative different from solvation with aprotic, quadrupolar, and hydrophobic $$\hbox {N}_{2}$$ N 2 ligands, which strongly prefer interior ion solvation by $$\uppi $$ π stacking interactions. Comparison of $$\hbox {Pym}^{+}$$ Pym + -W with Pym-W and $$\hbox {H}^{+}$$ H + Pym-W reveals the drastic effect of ionization and protonation on the Pym...W interaction. Graphic Abstract

Two-dimensional metal-organic frameworks Mo3(C2O)12 as promising single-atom catalysts for selective nitrogen-to-ammonia

2022 ◽  
Author(s):  
Zhen Feng ◽  
Zelin Yang ◽  
Xiaowen Meng ◽  
Fachuang Li ◽  
Zhanyong Guo ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Metal Organic Frameworks ◽  
Density Functional Theory Calculations ◽  
Reduction Reaction ◽  
Single Atom ◽  
Two Dimensional ◽  
Functional Theory ◽  
New Family ◽  
Metal Organic

The development of single-atom catalysts (SACs) for electrocatalytic nitrogen reduction reaction (NRR) remains a great challenge. Using density functional theory calculations, we design a new family of two-dimensional metal-organic frameworks...

scholarly journals Spectroscopic identification of fragment ions of DNA/RNA building blocks: the case of pyrimidine

2020 ◽  
Vol 22 (30) ◽  
pp. 17275-17290
Author(s):  
Kuntal Chatterjee ◽  
Otto Dopfer
Keyword(s):  
Density Functional Theory ◽  
Infrared Spectroscopy ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Building Blocks ◽  
Functional Theory ◽  
Fragment Ions ◽  
Sequential Loss ◽  
Spectroscopic Identification

The structure of the predominant fragments of the fundamental pyrimidine cation arising from sequential loss of HCN are identified by infrared spectroscopy of tagged ions and dispersion-corrected density functional theory calculations.

scholarly journals Microhydration of protonated biomolecular building blocks: protonated pyrimidine

2020 ◽  
Vol 22 (23) ◽  
pp. 13092-13107
Author(s):  
Kuntal Chatterjee ◽  
Otto Dopfer
Keyword(s):  
Density Functional Theory ◽  
Infrared Spectroscopy ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Building Blocks ◽  
Protonation Site ◽  
Functional Theory

The protonation site and evolution of the hydration network in microsolvated protonated pyrimidine clusters, H+Pym–(H2O)n with n = 1–4, has been explored by infrared spectroscopy and density functional theory calculations.

Ruthenium single-atom catalysis for electrocatalytic nitrogen reduction unveiled by grand canonical density functional theory

2020 ◽  
Vol 8 (39) ◽  
pp. 20402-20407
Author(s):  
Yujin Ji ◽  
Yifan Li ◽  
Huilong Dong ◽  
Lifeng Ding ◽  
Youyong Li
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Catalytic Site ◽  
Single Atom ◽  
Functional Theory ◽  
Nitrogen Reduction ◽  
Grand Canonical

Grand canonical density functional theory calculations reveal that the Ru–N4 motif is the superior catalytic site for eNRR rather than the Ru–N3 motif.

scholarly journals Physicochemical Insight into Coordination Systems Obtained from Copper(II) Bromoacetate and 1,10-Phenanthroline

Molecules ◽  
2020 ◽  
Vol 25 (22) ◽  
pp. 5324
Author(s):  
Ewelina Krejner ◽  
Tomasz Sierański ◽  
Marcin Świątkowski ◽  
Marta Bogdan ◽  
Rafał Kruszyński
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Building Blocks ◽  
Radiation Absorption ◽  
Ir Absorption ◽  
Bromoacetic Acid ◽  
Functional Theory ◽  
Hirshfeld Analysis ◽  
Coordination Systems

Two different coordination compounds of copper were synthesized from the same building blocks (1,10-phenanthroline, bromoacetate anions, and copper cations). The synthesis parameters were carefully designed and evaluated to allow the change of the resulting compounds molecular structure, i.e., formation of mononuclear (bromoacetato-O,O’)(bromoacetato-O)aqua(1,10-phenanthroline-N,N’)copper(II) and dinuclear (μ-bromido-1:2κ2)bis(μ-bromoacetato-1κO,2κO’)bis(1,10-phenanthroline-N,N’)dicopper(II) bromoacetate bromoacetic acid solvate. The crystal, molecular and supramolecular structures of the studied compounds were determined and evaluated in Hirshfeld analysis. The UV-Vis-IR absorption and thermal properties were studied and discussed. For the explicit determination of the influence of compounds structure on radiation absorption in UV-Vis range, density functional theory and time-dependent density functional theory calculations were performed.

scholarly journals Development and Testing of an All-Atom Force Field for Diketopyrrolopyrrole Polymers with Conjugated Substituents

2020 ◽  
Author(s):  
Vivek Sundaram ◽  
Alexey V. Lyulin ◽  
Björn Baumeier
Keyword(s):  
Force Field ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Building Blocks ◽  
Variable Number ◽  
Polymer Chains ◽  
Relaxation Processes ◽  
Polymer Backbone ◽  
Dynamics Simulations ◽  
The Individual

We develop an all-atom force field for a series of diketopyrrolopyrrole polymers with two aromatic pyridine substituents and variable number of pi-conjugated thiophene units in the backbone, used as donor material in organic photovoltaic devices. Available intra-fragment parameterizations of the individual fragment building blocks are combined with inter-fragment bonded and non-bonded parameters explicitly derived from density-functional theory calculations. To validate the force field we perform classical molecular dynamics simulations of single polymer chains with 1, 2, and 3 thiophenes in good and bad solvents, and of melts. We observe the expected dependence of the chain conformation on the solvent quality, with the chain collapsing in water, and swelling in chloroform. The glass transition temperature for the polymer melts is found to be in the range of 340K to 370K. Analysis of the mobility of the conjugated segments in the polymer backbone reveals two relaxation processes: a fast one with a characteristic time at room temperature on the order of 10ps associated with nearly harmonic vibrations and a slow one on the order of 100 associated with temperature activated cis-trans transitions.

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