5-Nitroindole oligonucleotides with alkynyl side chains: universal base pairing, triple bond hydration and properties of pyrene “click” adducts

2014 ◽  
Vol 12 (42) ◽  
pp. 8519-8532 ◽  
Author(s):  
Sachin A. Ingale ◽  
Peter Leonard ◽  
Haozhe Yang ◽  
Frank Seela
Keyword(s):  
Triple Bond ◽  
Side Chains ◽  
Base Pairing

Influence of Flexible Side-Chains on the Breathing Phase Transition of Pillared Layer MOFs: A Force Field Investigation

2020 ◽  
Author(s):  
Julian Keupp ◽  
Johannes P. Dürholt ◽  
Rochus Schmid
Keyword(s):  
First Principles ◽  
Good Accuracy ◽  
Field Investigation ◽  
Square Lattice ◽  
Side Chain ◽  
Second Step ◽  
Side Chains ◽  
Dynamics Simulations ◽  
Complex Phenomena ◽  
Closed Pore

The prototypical pillared layer MOFs, formed by a square lattice of paddle-<br>wheel units and connected by dinitrogen pillars, can undergo a breathing phase<br>transition by a “wine-rack” type motion of the square lattice. We studied this not<br>yet fully understood behavior using an accurate first principles parameterized force<br>field (MOF-FF) for larger nanocrystallites on the example of Zn 2 (bdc) 2 (dabco) [bdc:<br>benzenedicarboxylate, dabco: (1,4-diazabicyclo[2.2.2]octane)] and found clear indi-<br>cations for an interface between a closed and an open pore phase traveling through<br>the system during the phase transformation [Adv. Theory Simul. 2019, 2, 11]. In<br>conventional simulations in small supercells this mechanism is prevented by periodic<br>boundary conditions (PBC), enforcing a synchronous transformation of the entire<br>crystal. Here, we extend this investigation to pillared layer MOFs with flexible<br>side-chains, attached to the linker. Such functionalized (fu-)MOFs are experimen-<br>tally known to have different properties with the side-chains acting as fixed guest<br>molecules. First, in order to extend the parameterization for such flexible groups,<br>1a new parametrization strategy for MOF-FF had to be developed, using a multi-<br>structure force based fit method. The resulting parametrization for a library of<br>fu-MOFs is then validated with respect to a set of reference systems and shows very<br>good accuracy. In the second step, a series of fu-MOFs with increasing side-chain<br>length is studied with respect to the influence of the side-chains on the breathing<br>behavior. For small supercells in PBC a systematic trend of the closed pore volume<br>with the chain length is observed. However, for a nanocrystallite model a distinct<br>interface between a closed and an open pore phase is visible only for the short chain<br>length, whereas for longer chains the interface broadens and a nearly concerted trans-<br>formation is observed. Only by molecular dynamics simulations using accurate force<br>fields such complex phenomena can be studied on a molecular level.

On the Linear Geometry of Lanthanide Hydroxide (Ln—OH, Ln=La-Lu)

2019 ◽  
Author(s):  
Hassan Harb ◽  
Lee Thompson ◽  
Hrant Hratchian
Keyword(s):  
Triple Bond ◽  
Density Functional ◽  
Valence Electron ◽  
Density Functional Theory Calculations ◽  
Electron Configuration ◽  
Functional Theory ◽  
Key Species ◽  
Pi Orbitals ◽  
Lanthanide Hydroxide ◽  
Linear Geometry

Lanthanide hydroxides are key species in a variety of catalytic processes and in the preparation of corresponding oxides. This work explores the fundamental structure and bonding of the simplest lanthanide hydroxide, LnOH (Ln=La-Lu), using density functional theory calculations. Interestingly, the calculations predict that all structures of this series will be linear. Furthermore, these results indicate a valence electron configuration featuring an occupied sigma orbital and two occupied pi orbitals for all LnOH compounds, suggesting that the lanthanide-hydroxide bond is best characterized as a covalent triple bond.

On the Linear Geometry of Lanthanide Hydroxide (Ln—OH, Ln=La-Lu)

2019 ◽  
Author(s):  
Hassan Harb ◽  
Lee Thompson ◽  
Hrant Hratchian
Keyword(s):  
Triple Bond ◽  
Density Functional ◽  
Valence Electron ◽  
Density Functional Theory Calculations ◽  
Electron Configuration ◽  
Functional Theory ◽  
Key Species ◽  
Pi Orbitals ◽  
Lanthanide Hydroxide ◽  
Linear Geometry

Lanthanide hydroxides are key species in a variety of catalytic processes and in the preparation of corresponding oxides. This work explores the fundamental structure and bonding of the simplest lanthanide hydroxide, LnOH (Ln=La-Lu), using density functional theory calculations. Interestingly, the calculations predict that all structures of this series will be linear. Furthermore, these results indicate a valence electron configuration featuring an occupied sigma orbital and two occupied pi orbitals for all LnOH compounds, suggesting that the lanthanide-hydroxide bond is best characterized as a covalent triple bond.

Pathway Complexity in the Stacking of Imine-linked Macrocycles Related to Two-Dimensional Covalent Organic Frameworks

2019 ◽  
Author(s):  
Shiwei Wang ◽  
Anton Chavez ◽  
Simil Thomas ◽  
Hong Li ◽  
Nathan C. Flanders ◽  
...  
Keyword(s):  
Temperature Dependence ◽  
Structural Similarity ◽  
Discrete Models ◽  
Side Chains ◽  
Two Dimensional ◽  
Assembly Process ◽  
Covalent Organic Frameworks ◽  
Electron Systems ◽  
Monomer Structure ◽  
Kinetic Traps

This work reports on the assembly of imine-linked macrocycles that serve as models of two-dimensional covalent organic frameworks (2D COFs). Interlayer interactions play an important role in the formation of 2D COFs, yet the effect of monomer structure on COF formation, crystallinity, and susceptibility to exfoliation are not well understood. For example, monomers with both electron-rich and electron-poor π-electron systems have been proposed to strengthen interlayer inter-actions and improve crystallinity. Here we probe these effects by studying the stacking behavior of imine-linked macrocycles that represent discrete models of 2D COFs. <div><br></div><div>Specifically, macrocycles based on terephthaldehyde (PDA) or 2,5-dimethoxyterephthaldehyde (DMPDA) stack upon cooling molecularly dissolved solutions. Both macrocycles assemble cooperatively with similar ΔHe values of -97 kJ/mol and -101 kJ/mol, respectively, although the DMPDA macrocycle assembly process showed a more straightforward temperature dependence. Circular dichroism spectroscopy performed on macrocycles bearing chiral side chains revealed a helix reversion process for the PDA macrocycles that was not observed for the DMPDA macrocycles. <br></div><div><br></div><div>Given the structural similarity of these monomers, these findings demonstrate that the stacking processes associated with nanotubes derived from these macrocycles, as well as for the corresponding COFs, are complex and susceptible to kinetic traps, casting doubt on the relevance of thermodynamic arguments for improving materials quality. <br></div>

Predicting the Strength of Stacking Interactions Between Heterocycles and Aromatic Amino Acid Side Chains

2019 ◽  
Author(s):  
Andrea N. Bootsma ◽  
Analise C. Doney ◽  
Steven Wheeler
Keyword(s):  
Amino Acid ◽  
Binding Sites ◽  
Aromatic Amino Acid ◽  
Aromatic Amino Acids ◽  
Biologically Active ◽  
Side Chains ◽  
Stacking Interactions ◽  
Inhibitor Binding ◽  
Protein Binding Sites ◽  
Amino Acid Side Chains

<p>Despite the ubiquity of stacking interactions between heterocycles and aromatic amino acids in biological systems, our ability to predict their strength, even qualitatively, is limited. Based on rigorous <i>ab initio</i> data, we have devised a simple predictive model of the strength of stacking interactions between heterocycles commonly found in biologically active molecules and the amino acid side chains Phe, Tyr, and Trp. This model provides rapid predictions of the stacking ability of a given heterocycle based on readily-computed heterocycle descriptors. We show that the values of these descriptors, and therefore the strength of stacking interactions with aromatic amino acid side chains, follow simple predictable trends and can be modulated by changing the number and distribution of heteroatoms within the heterocycle. This provides a simple conceptual model for understanding stacking interactions in protein binding sites and optimizing inhibitor binding in drug design.</p>

A Strategy for Thioamide Incorporation During Fmoc Solid-Phase Peptide Synthesis with Robust Stereochemical Integrity

2019 ◽  
Author(s):  
luis camacho III ◽  
Bryan J. Lampkin ◽  
Brett VanVeller
Keyword(s):  
Amino Acid ◽  
Functional Groups ◽  
Peptide Synthesis ◽  
Solid Phase ◽  
Solid Phase Peptide Synthesis ◽  
Side Chains ◽  
Amino Acid Side Chains ◽  
Peptide Elongation

We describe a method to protect the sensitive stereochemistry of the thioamide—in analogy to the protection of the functional groups of amino acid side chains—in order to preserve the thioamide moiety during peptide elongation.<br>

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