Analysis of transition state stabilization by non-covalent interactions in the Houk–List model of organocatalyzed intermolecular Aldol additions using functional-group symmetry-adapted perturbation theory

2016 ◽  
Vol 18 (15) ◽  
pp. 10297-10308 ◽  
Author(s):  
Brandon W. Bakr ◽  
C. David Sherrill
Keyword(s):  
Perturbation Theory ◽  
Transition State ◽  
Rational Design ◽  
Functional Group ◽  
Group Symmetry ◽  
Aldol Additions ◽  
Transition State Stabilization ◽  
Non Covalent Interactions ◽  
Covalent Interactions ◽  
List Model

Rational design of catalysts would be aided by a better understanding of how non-covalent interactions stabilize transition states.

scholarly journals Symmetry-Adapted Perturbation Theory Decomposition of the Reaction Force: Insights into Substituent Effects Involved in Hemiacetal Formation Mechanisms

2019 ◽  
Author(s):  
Wallace Derricotte
Keyword(s):  
Perturbation Theory ◽  
Functional Group ◽  
Reaction Force ◽  
Substituent Effects ◽  
Formation Mechanisms ◽  
Lower Activation ◽  
Non Covalent Interactions ◽  
Force Components ◽  
Covalent Interactions ◽  
Lower Activation Energy

<div>The decomposition of the reaction force based on symmetry-adapted perturbation theory (SAPT) has been proposed. This approach was used to investigate the subtituent effects along the reaction coordinate pathway for the hemiacetal formation mechanism between methanol and substituted aldehydes of the form CX<sub>3</sub>CHO (X = H, F, Cl, and Br), providing a quantitative evaluation of the reaction-driving and reaction-retarding force components. Our results highlight the importance of more favorable electrostatic and induction effects in the reactions involving halogenated aldehydes that leads to lower activation energy barriers. These substituent effects are further elucidated by applying the functional-group partition of symmetry-adapted</div><div>perturbation theory (F-SAPT). The results show that the reaction is largely driven by favorable direct non-covalent interactions between the CX<sub>3</sub> group on the aldehyde and the OH group on methanol.</div>

scholarly journals Symmetry-Adapted Perturbation Theory Decomposition of the Reaction Force: Insights into Substituent Effects Involved in Hemiacetal Formation Mechanisms

2019 ◽  
Author(s):  
Wallace Derricotte
Keyword(s):  
Perturbation Theory ◽  
Functional Group ◽  
Reaction Force ◽  
Substituent Effects ◽  
Formation Mechanisms ◽  
Lower Activation ◽  
Non Covalent Interactions ◽  
Force Components ◽  
Covalent Interactions ◽  
Lower Activation Energy

<div>The decomposition of the reaction force based on symmetry-adapted perturbation theory (SAPT) has been proposed. This approach was used to investigate the subtituent effects along the reaction coordinate pathway for the hemiacetal formation mechanism between methanol and substituted aldehydes of the form CX<sub>3</sub>CHO (X = H, F, Cl, and Br), providing a quantitative evaluation of the reaction-driving and reaction-retarding force components. Our results highlight the importance of more favorable electrostatic and induction effects in the reactions involving halogenated aldehydes that leads to lower activation energy barriers. These substituent effects are further elucidated by applying the functional-group partition of symmetry-adapted</div><div>perturbation theory (F-SAPT). The results show that the reaction is largely driven by favorable direct non-covalent interactions between the CX<sub>3</sub> group on the aldehyde and the OH group on methanol.</div>

scholarly journals Functional group interaction profiles: a general treatment of solvent effects on non-covalent interactions

2020 ◽  
Vol 11 (17) ◽  
pp. 4456-4466 ◽  
Author(s):  
Mark D. Driver ◽  
Mark J. Williamson ◽  
Joanne L. Cook ◽  
Christopher A. Hunter
Keyword(s):  
Free Energy ◽  
Solvent Effects ◽  
Functional Group ◽  
Group Interaction ◽  
General Treatment ◽  
Effect Of Solvent ◽  
Non Covalent Interactions ◽  
Covalent Interactions ◽  
Quantitative Tool

Functional group interaction profiles are a quantitative tool for predicting the effect of solvent on the free energy changes associated with non-covalent interactions.

scholarly journals Reorganization of Self-Assembled DNA-Based Polymers Using Orthogonally Addressable Building Blocks

2021 ◽  
Author(s):  
Serena Gentile ◽  
Erica Del Grosso ◽  
Leonard J. Prins ◽  
Francesco Ricci
Keyword(s):  
Self Assembly ◽  
Rational Design ◽  
Building Blocks ◽  
Binding Domain ◽  
Non Covalent Interactions ◽  
Sticky Ends ◽  
Self Assembled ◽  
Block Structures ◽  
Covalent Interactions

Taking advantage of the addressability and programmability of DNA/DNA non-covalent interactions we report here the rational design of orthogonal DNA-based addressable tiles that self-assemble into polymer-like structures that can be reconfigured and reorganized by external inputs. The different tiles share the same 5-nucleotide sticky ends responsible for self-assembly but are rationally designed to contain a specific regulator-binding domain that can be orthogonally targeted by different DNA regulator strands (activators and inhibitors). We show that by sequentially adding specific activators and inhibitors it is possible to re-organize in a dynamic and reversible way the formed polymer-like structures to display well-defined distributions: homopolymers made of a single tile, random polymers in which different tiles are distributed randomly and block structures in which the tiles are organized in segments.

On the applicability of functional-group symmetry-adapted perturbation theory and other partitioning models for chiral recognition – the case of popular drug molecules interacting with chiral phases

2019 ◽  
Vol 21 (40) ◽  
pp. 22491-22510
Author(s):  
Michał Chojecki ◽  
Dorota Rutkowska-Zbik ◽  
Tatiana Korona
Keyword(s):  
Perturbation Theory ◽  
Interaction Energy ◽  
Chiral Recognition ◽  
Functional Group ◽  
Chiral Discrimination ◽  
Group Symmetry ◽  
Intermolecular Interaction Energy ◽  
Drug Molecules ◽  
Chiral Phases ◽  
Interacting Quantum Atoms

The F-SAPT partitioning of the intermolecular interaction energy, supported with the Interacting-Quantum-Atoms analysis, is a powerful tool for studies of the origin of chiral discrimination within diastereoisomeric complexes of the RR and RS types.

Synthesis of unsymmetrical porphyrin triad containing three different porphyrin subunits assembled by covalent and non-covalent interactions

2008 ◽  
Vol 12 (09) ◽  
pp. 1030-1040 ◽  
Author(s):  
Sokkalingam Punidha ◽  
Smita Rai ◽  
Mangalampalli Ravikanth
Keyword(s):  
Building Block ◽  
Functional Group ◽  
Photophysical Properties ◽  
Time Resolved Fluorescence ◽  
Efficient Energy Transfer ◽  
Time Resolved ◽  
Fluorescence Studies ◽  
Efficient Energy ◽  
Non Covalent Interactions ◽  
Covalent Interactions

Cis-21,23-dithiaporphyrin building block containing one iodophenyl and one pyridyl functional group at meso positions was synthesized by condensing unsymmetrical thiophene diol and symmetrical 16-thiatripyrrin under refluxing propionic acid conditions. The 21,23-dithiaporphyrin building block was coupled with mono-functionalized 21-thiaporphyrin building block containing meso-phenylethyne functional group under mild Pd (0) coupling conditions. The steady-state and time-resolved fluorescence studies support an efficient energy transfer in the singlet excited state from N 3 S porphyrin subunit to N 2 S 2 porphyrin subunit in the dyad. The N 3 S - N 2 S 2 porphyrin dyad was then treated with RuTPP ( CO )( EtOH ) in toluene at refluxing temperature and purified by column chromatography to afford a porphyrin triad containing N 3 S , N 2 S 2 and RuN 4 porphyrin subunits assembled using both covalent and non-covalent interactions. The photophysical properties showed the fluorescence quenching of N 3 S and N 2 S 2 porphyrin subunits in triad due to heavy ruthenium ion which was coordinated to meso-pyridyl ' N ' of N 2 S 2 porphyrin subunit of porphyrin triad.

Redox potential tuning in bio-relevant heterocycles via (anti)aromaticity modulated H-bonding (AMHB)

2020 ◽  
Vol 98 (7) ◽  
pp. 337-346
Author(s):  
Tayeb Kakeshpour ◽  
Adam Van Wiemeersch ◽  
James E. Jackson
Keyword(s):  
Redox Potential ◽  
Rational Design ◽  
Bond Formation ◽  
Complex Structures ◽  
Redox Potentials ◽  
Biologically Relevant ◽  
Connectivity Patterns ◽  
Non Covalent Interactions ◽  
Redox Potential Tuning ◽  
Covalent Interactions

Hydrogen bonds are arguably the most important non-covalent interactions in chemistry and biology, and their strength and directionality have been elegantly exploited in the rational design of complex structures. We recently noted that the variable responses of cyclic π-systems upon H-bond formation reciprocally lead to modulations of the H-bonds’ strengths, a phenomenon that we dubbed (anti)aromaticity-modulated hydrogen bonding (AMHB) [J. Am. Chem. Soc. 2016, 138, 3427–3432]. Species that switch from aromatic to antiaromatic or vice versa upon changing π-electron counts should be oppositely stabilized by the AMHB effects, so their redox potentials should be significantly “tuned” by H-bond formation. Herein, using quantum chemical simulations, we explore the effects of these H-bond induced π-electron polarizations on the redox potentials of (anti)aromatic heterocycles. The systems chosen for this study have embedded amide groups and amidine moieties capable of forming two-point H-bonds in their cyclic π-systems. Thus, as the 4-electron and 6-electron π-systems in redox-capable monocycles (e.g., quinones) can be differentially stabilized, their redox potentials can be modulated by H-bond formation by as much as 6 kcal/mol (258 mV for one electron transfer). In fused rings, the connectivity patterns are as important as the π-electron counts. Extending these ideas to flavin, a biologically relevant case, we find that H-bonding patterns like those found in its crystals can vary its redox potential by up to 1.3 kcal/mol.

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