scholarly journals Rational Design of Mononuclear Iron Porphyrins for Facile and Selective 4e–/4H+ O2 Reduction: Activation of O–O Bond by 2nd Sphere Hydrogen Bonding

2018 ◽  
Vol 140 (30) ◽  
pp. 9444-9457 ◽  
Author(s):  
Sarmistha Bhunia ◽  
Atanu Rana ◽  
Pronay Roy ◽  
Daniel J. Martin ◽  
Michael L. Pegis ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Rational Design ◽  
Iron Porphyrins ◽  
Mononuclear Iron ◽  
O2 Reduction

Hierarchy of π-Stacking Determines the Conformational Preference of Bis-Squaraines

2020 ◽  
Author(s):  
Abhishek Singh ◽  
Reman K. Singh ◽  
G Naresh Patwari
Keyword(s):  
Hydrogen Bonding ◽  
Rational Design ◽  
Biological Molecules ◽  
Conformational Space ◽  
X Ray Crystallography ◽  
Simple Strategy ◽  
Induced Folding ◽  
Π Stacking ◽  
Varying Length ◽  
Dynamics Simulations

The rational design of conformationally controlled foldable modules can lead to a deeper insight into the conformational space of complex biological molecules where non-covalent interactions such as hydrogen bonding and π-stacking are known to play a pivotal role. Squaramides are known to have excellent hydrogen bonding capabilities and hence, are ideal molecules for designing foldable modules that can mimic the secondary structures of bio-molecules. The π-stacking induced folding of bis-squaraines tethered using aliphatic primary and secondary-diamine linkers of varying length is explored with a simple strategy of invoking small perturbations involving the length linkers and degree of substitution. Solution phase NMR investigations in combination with molecular dynamics simulations suggest that bis-squaraines predominantly exist as extended conformations. Structures elucidated by X-ray crystallography confirmed a variety of folded and extended secondary conformations including hairpin turns and 𝛽-sheets which are determined by the hierarchy of π-stacking relative to N–H···O hydrogen bonds.

Hierarchy of π-Stacking Determines the Conformational Preference of Bis-Squaraines

2020 ◽  
Author(s):  
Abhishek Singh ◽  
Reman K. Singh ◽  
G Naresh Patwari
Keyword(s):  
Hydrogen Bonding ◽  
Rational Design ◽  
Biological Molecules ◽  
Conformational Space ◽  
X Ray Crystallography ◽  
Simple Strategy ◽  
Induced Folding ◽  
Π Stacking ◽  
Varying Length ◽  
Dynamics Simulations

The rational design of conformationally controlled foldable modules can lead to a deeper insight into the conformational space of complex biological molecules where non-covalent interactions such as hydrogen bonding and π-stacking are known to play a pivotal role. Squaramides are known to have excellent hydrogen bonding capabilities and hence, are ideal molecules for designing foldable modules that can mimic the secondary structures of bio-molecules. The π-stacking induced folding of bis-squaraines tethered using aliphatic primary and secondary-diamine linkers of varying length is explored with a simple strategy of invoking small perturbations involving the length linkers and degree of substitution. Solution phase NMR investigations in combination with molecular dynamics simulations suggest that bis-squaraines predominantly exist as extended conformations. Structures elucidated by X-ray crystallography confirmed a variety of folded and extended secondary conformations including hairpin turns and 𝛽-sheets which are determined by the hierarchy of π-stacking relative to N–H···O hydrogen bonds.

scholarly journals Stabilization of the Low-Spin State in a Mononuclear Iron(II) Complex and High-Temperature Cooperative Spin Crossover Mediated by Hydrogen Bonding

2015 ◽  
Vol 22 (1) ◽  
pp. 331-339 ◽  
Author(s):  
Sipeng Zheng ◽  
Niels R. M. Reintjens ◽  
Maxime A. Siegler ◽  
Olivier Roubeau ◽  
Elisabeth Bouwman ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
High Temperature ◽  
Spin State ◽  
Spin Crossover ◽  
Mononuclear Iron

scholarly journals Improving the Substrate Affinity and Catalytic Efficiency of β-Glucosidase Bgl3A from Talaromyces leycettanus JCM12802 by Rational Design

Biomolecules ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 1882
Author(s):  
Wei Xia ◽  
Yingguo Bai ◽  
Pengjun Shi
Keyword(s):  
Hydrogen Bonding ◽  
Rational Design ◽  
Substrate Binding ◽  
Enzymatic Saccharification ◽  
Catalytic Efficiency ◽  
Binding Pocket ◽  
Glycoside Hydrolases ◽  
Cellulosic Biomass ◽  
Substrate Affinity ◽  
Hydrogen Bonding Networks

Improving the substrate affinity and catalytic efficiency of β-glucosidase is necessary for better performance in the enzymatic saccharification of cellulosic biomass because of its ability to prevent cellobiose inhibition on cellulases. Bgl3A from Talaromyces leycettanus JCM12802, identified in our previous work, was considered a suitable candidate enzyme for efficient cellulose saccharification with higher catalytic efficiency on the natural substrate cellobiose compared with other β-glucosidase but showed insufficient substrate affinity. In this work, hydrophobic stacking interaction and hydrogen-bonding networks in the active center of Bgl3A were analyzed and rationally designed to strengthen substrate binding. Three vital residues, Met36, Phe66, and Glu168, which were supposed to influence substrate binding by stabilizing adjacent binding site, were chosen for mutagenesis. The results indicated that strengthening the hydrophobic interaction between stacking aromatic residue and the substrate, and stabilizing the hydrogen-bonding networks in the binding pocket could contribute to the stabilized substrate combination. Four dominant mutants, M36E, M36N, F66Y, and E168Q with significantly lower Km values and 1.4–2.3-fold catalytic efficiencies, were obtained. These findings may provide a valuable reference for the design of other β-glucosidases and even glycoside hydrolases.

Sulfur as hydrogen-bond acceptor in cocrystals of 2-thio-modified thymine

2018 ◽  
Vol 74 (1) ◽  
pp. 21-30 ◽  
Author(s):  
Wilhelm Maximilian Hützler ◽  
Michael Bolte
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Crystal Engineering ◽  
Rational Design ◽  
Three Dimensional ◽  
Good Reliability ◽  
Hydrogen Bond Acceptor ◽  
Hydrogen Bonding Interactions ◽  
Hydrogen Bonding Site ◽  
Hydrogen Bonded

Doubly and triply hydrogen-bonded supramolecular synthons are of particular interest for the rational design of crystal and cocrystal structures in crystal engineering since they show a high robustness due to their high stability and good reliability. The compound 5-methyl-2-thiouracil (2-thiothymine) contains an ADA hydrogen-bonding site (A = acceptor and D = donor) if the S atom is considered as an acceptor. We report herein the results of cocrystallization experiments with the coformers 2,4-diaminopyrimidine, 2,4-diamino-6-phenyl-1,3,5-triazine, 6-amino-3H-isocytosine and melamine, which contain complementary DAD hydrogen-bonding sites and, therefore, should be capable of forming a mixed ADA–DAD N—H...S/N—H...N/N—H...O synthon (denoted synthon 3s N·S;N·N;N·O), consisting of three different hydrogen bonds with 5-methyl-2-thiouracil. The experiments yielded one cocrystal and five solvated cocrystals, namely 5-methyl-2-thiouracil–2,4-diaminopyrimidine (1/2), C5H6N2OS·2C4H6N4, (I), 5-methyl-2-thiouracil–2,4-diaminopyrimidine–N,N-dimethylformamide (2/2/1), 2C5H6N2OS·2C4H6N4·C3H7NO, (II), 5-methyl-2-thiouracil–2,4-diamino-6-phenyl-1,3,5-triazine–N,N-dimethylformamide (2/2/1), 2C5H6N2OS·2C9H9N5·C3H7NO, (III), 5-methyl-2-thiouracil–6-amino-3H-isocytosine–N,N-dimethylformamide (2/2/1), (IV), 2C5H6N2OS·2C4H6N4O·C3H7NO, (IV), 5-methyl-2-thiouracil–6-amino-3H-isocytosine–N,N-dimethylacetamide (2/2/1), 2C5H6N2OS·2C4H6N4O·C4H9NO, (V), and 5-methyl-2-thiouracil–melamine (3/2), 3C5H6N2OS·2C3H6N6, (VI). Synthon 3s N·S;N·N;N·O was formed in three structures in which two-dimensional hydrogen-bonded networks are observed, while doubly hydrogen-bonded interactions were formed instead in the remaining three cocrystals whereby three-dimensional networks are preferred. As desired, the S atoms are involved in hydrogen-bonding interactions in all six structures, thus illustrating the ability of sulfur to act as a hydrogen-bond acceptor and, therefore, its value for application in crystal engineering.

scholarly journals Atropisomeric Hydrogen Bonding Control for CO 2 Binding and Enhancement of Electrocatalytic Reduction at Iron Porphyrins

2020 ◽  
Vol 132 (50) ◽  
pp. 22637-22641
Author(s):  
Philipp Gotico ◽  
Loïc Roupnel ◽  
Regis Guillot ◽  
Marie Sircoglou ◽  
Winfried Leibl ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Electrocatalytic Reduction ◽  
Iron Porphyrins

Structural Factors Determining the Absorption Spectrum of Channelrhodopsins: A Case Study of the Chimera C1C2

2020 ◽  
Author(s):  
Suliman Adam ◽  
Christian Wiebeler ◽  
Igor Schapiro
Keyword(s):  
Hydrogen Bonding ◽  
Absorption Spectrum ◽  
Schiff Base ◽  
Absorption Maximum ◽  
Rational Design ◽  
Blue Shift ◽  
Spectral Shift ◽  
Structural Basis ◽  
Neural Cells ◽  
Structural Factors

Channelrhodopsins are photosensitive proteins that trigger flagella motion in single cell algae and have been successfully utilized in optogenetic applications. In optogenetics light is used to activate neural cells in living organisms, which can be achieved by exploiting the ion channel signaling of channelrhodopsins. Tailoring channelrhodopsins for such applications includes the tuning of the absorption maximum. In order to establish rational design and to obtain a desired spectral shift, a basic understanding of the absorption spectrum is required. We have studied the chimera C1C2 as a representative of this protein family and the first member with an available crystal structure. For this purpose, we sampled the conformations of C1C2 using QM/MM molecular dynamics, and subjected the resulting snapshots of the trajectory to excitation energy calculations using ADC(2) and simplified TD-DFT. In contrast to previous reports, we found that different hydrogen-bonding networks—involving the retinal protonated Schiff base, the putative counterions E162 and D292 as well as water molecules—had only a small impact on the absorption spectrum. However, in case of deprotonated E162 increasing the distance to the Schiff base hydrogen-bonding partner led to a systematic blue shift. The β-ionone ring rotation was identified as another important contributor. Yet the most important factor was found to be the bond length alternation and bond order alternation that were linearly correlated to the absorption maximum by up to 62 % and 82 %, respectively. We ascribe this novel insight into the structural basis of the absorption spectrum to our enhanced protein setup that includes membrane embedding as well as long and extensive sampling.

Molecular Catalysis of O2 Reduction by Iron Porphyrins in Water: Heterogeneous versus Homogeneous Pathways

2015 ◽  
Vol 137 (42) ◽  
pp. 13535-13544 ◽  
Author(s):  
Cyrille Costentin ◽  
Hachem Dridi ◽  
Jean-Michel Savéant
Keyword(s):  
Iron Porphyrins ◽  
O2 Reduction ◽  
Molecular Catalysis

scholarly journals Atropisomeric Hydrogen Bonding Control for CO 2 Binding and Enhancement of Electrocatalytic Reduction at Iron Porphyrins

2020 ◽  
Vol 59 (50) ◽  
pp. 22451-22455
Author(s):  
Philipp Gotico ◽  
Loïc Roupnel ◽  
Regis Guillot ◽  
Marie Sircoglou ◽  
Winfried Leibl ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Electrocatalytic Reduction ◽  
Iron Porphyrins

Rational Design of Metal-free Doped Carbon Nanohorn Catalysts for Efficient Electrosynthesis of H2O2 from O2 Reduction

2021 ◽  
Author(s):  
Pongkarn Chakthranont ◽  
Sakvarit Nitrathorn ◽  
Sutarat Thongratkaew ◽  
Pongtanawat Khemthong ◽  
Hideki Nakajima ◽  
...  
Keyword(s):  
Rational Design ◽  
Metal Free ◽  
O2 Reduction
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