scholarly journals A Computational Study of the Mechanism of Succinimide Formation in the Asn–His Sequence: Intramolecular Catalysis by the His Side Chain

Molecules ◽  
2016 ◽  
Vol 21 (3) ◽  
pp. 327 ◽  
Author(s):  
Ohgi Takahashi ◽  
Noriyoshi Manabe ◽  
Ryota Kirikoshi
Keyword(s):  
Computational Study ◽  
Side Chain ◽  
Intramolecular Catalysis

scholarly journals Steroid Hydroxylation by Basidiomycete Peroxygenases: a Combined Experimental and Computational Study

2015 ◽  
Vol 81 (12) ◽  
pp. 4130-4142 ◽  
Author(s):  
Esteban D. Babot ◽  
José C. del Río ◽  
Marina Cañellas ◽  
Ferran Sancho ◽  
Fátima Lucas ◽  
...  
Keyword(s):  
Computational Study ◽  
Biological Activities ◽  
Side Chain ◽  
Enzymatic Reactions ◽  
Fungal Enzymes ◽  
Content Type ◽  
Protein Energy ◽  
Esterified Sterols ◽  
Ligand Diffusion ◽  
Protein Energy Landscape

ABSTRACTThe goal of this study is the selective oxyfunctionalization of steroids under mild and environmentally friendly conditions using fungal enzymes. With this purpose, peroxygenases from three basidiomycete species were tested for the hydroxylation of a variety of steroidal compounds, using H2O2as the only cosubstrate. Two of them are wild-type enzymes fromAgrocybe aegeritaandMarasmius rotula, and the third one is a recombinant enzyme fromCoprinopsis cinerea. The enzymatic reactions on free and esterified sterols, steroid hydrocarbons, and ketones were monitored by gas chromatography, and the products were identified by mass spectrometry. Hydroxylation at the side chain over the steroidal rings was preferred, with the 25-hydroxyderivatives predominating. Interestingly, antiviral and other biological activities of 25-hydroxycholesterol have been reported recently (M. Blanc et al., Immunity 38:106–118, 2013,http://dx.doi.org/10.1016/j.immuni.2012.11.004). However, hydroxylation in the ring moiety and terminal hydroxylation at the side chain also was observed in some steroids, the former favored by the absence of oxygenated groups at C-3 and by the presence of conjugated double bonds in the rings. To understand the yield and selectivity differences between the different steroids, a computational study was performed using Protein Energy Landscape Exploration (PELE) software for dynamic ligand diffusion. These simulations showed that the active-site geometry and hydrophobicity favors the entrance of the steroid side chain, while the entrance of the ring is energetically penalized. Also, a direct correlation between the conversion rate and the side chain entrance ratio could be established that explains the various reaction yields observed.

scholarly journals Ab-Initio Computational Study : The Activation Energy Changes and Steric Effects In Peptide Synthesis Of Ac-AA-NH2 and Ac-AP-NH2

Molekul ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. 137
Author(s):  
Indah Pratiwi ◽  
Bambang Cahyono ◽  
Parsaoran Siahaan
Keyword(s):  
Activation Energy ◽  
Reaction Mechanism ◽  
Ab Initio ◽  
Peptide Synthesis ◽  
Reaction Mechanisms ◽  
Steric Effect ◽  
Computational Study ◽  
Computational Method ◽  
Side Chain ◽  
Concerted Reaction

Ab-Initio computational method can be used for simulating reaction mechanisms, such as concerted reaction mechanism on peptide synthesis. The concerted reaction is one of many possible pathways on how peptide can be synthesized. The purpose of this study are probing the concerted reaction mechanism and comparing the steric effect to the reaction, given by different side-chain of alanine (A) and proline (P). Two dipeptides formed from alanine and proline were computed at HF-SCF/6-31G** theory level: Ac-AA-NH2 and Ac-AP-NH2. The res.lts show the activation energy of Ac-AA-NH2  and Ac-AP-NH2 forming via concerted pathway are 167.541 kJ/mol and 161.044 kJ/mol, respectively. The steric difference in side-chain affects the dihedral angle of the structure, and also gives difference to the entropy value of reaction.

Tuning the Band-gap of Pt(II) Di-ynes and Poly-ynes by Incorporating Cl(CO)3Re(I) side-chain

2018 ◽  
Vol 1 (1) ◽  
pp. 45
Author(s):  
Idris Juma Al-Busaidi ◽  
Ashanul Haque ◽  
Muhammad S. Khan
Keyword(s):  
Band Gap ◽  
Density Functional ◽  
Computational Study ◽  
Side Chain ◽  
Highest Occupied Molecular Orbital ◽  
The Density Functional Theory ◽  
Device Applications ◽  
Group Variation ◽  
The Impact

Band-gap (Eg) of a material is an important criterion for application in opto-electronic (O-E) devices.1,2 Both low- and high Eg materials are useful and being synthesized by chemists via core structure modification, functional group variation and metal incorporation.3,4 We present herein computational study on the impact of incorporation of a Re(I) side-chain in 2,2’-bipyridine based Pt(II) di-ynes and poly-ynes. The density functional theory (DFT) calculation shows that the incorporation Cl(CO)3Re(I) as pendant functionality in 2,2’-bipyridine-based main-chain Pt(II) di- ynes and poly-ynes significantly reduce the Eg of the materials. Furthermore, to assess the role of positional isomerism, we compare the electronic structure and properties of 5,5’-and 6,6’- disubstituted 2,2’-bipyridine incorporated homo- and hetero-bimetallic diynes and poly-ynes . We find that the coordination of ReCO3 Cl moiety to Pt(II) di-yne introduces new Re(I)-localized highest occupied molecular orbital (HOMO) and the lowers the Eg by around 0.7 eV. Furthermore, our experimental results reveal that 5,5’-disubstituted 2,2’-bipyridine-based hetero-bimetallic di- ynes and polyynes are better materials for future O-E device applications.

scholarly journals Effect of Side Chain Length on Polycarboxylate Superplasticizer in Aqueous Solution: A Computational Study

Polymers ◽  
2019 ◽  
Vol 11 (2) ◽  
pp. 346 ◽  
Author(s):  
Po-Hsiang Chuang ◽  
Yu-Hui Tseng ◽  
Yunhui Fang ◽  
Miaomiao Gui ◽  
Xiuxing Ma ◽  
...  
Keyword(s):  
Aqueous Solution ◽  
Chain Length ◽  
Computational Study ◽  
Side Chain ◽  
Water Molecules ◽  
Side Chain Length ◽  
Dynamics Simulations ◽  
Chain Lengths ◽  
Polycarboxylate Ether ◽  
Diffusion Properties

Molecular dynamics simulations were carried out to study the conformations of polycarboxylate ether (PCE) superplasticizers with different side chain lengths in aqueous solution. For four types of PCE molecules—PCE1, PCE2, PCE3, and PCE4—the steric hindrance between the PCE molecules increased with increasing side chain length. The side chain length not only affects water mobility but also affects the distribution of water molecules in the system. Simulation results indicate that water molecules were trapped by the PCE molecules, reducing the diffusion properties. PCE molecules with long side chains have more water molecules probability around the main chain and fewer water molecules probability near the side chain. Microscopic-level knowledge of the interaction between superplasticizer and water molecules facilitates understanding of the performance of superplasticizers in cement systems.

Impact of morphology, side-chains, and crystallinity on charge-transport properties of π-extended double helicenes

2019 ◽  
Vol 21 (2) ◽  
pp. 901-914 ◽  
Author(s):  
Ilhan Yavuz ◽  
Janice B. Lin ◽  
K. N. Houk
Keyword(s):  
Charge Transport ◽  
Transport Properties ◽  
Crystal Packing ◽  
Computational Study ◽  
Side Chain ◽  
Side Chains

We report a computational study on the effect of side-chain substitution, heteroaromatic substitution and unique crystal packing on the charge transport and mobility of three double helicene molecules.

Peptide cation-radicals. A computational study of the competition between peptide N?C? bond cleavage and loss of the side chain in the [GlyPhe-NH2 + 2H]+? cation-radical

2003 ◽  
Vol 38 (10) ◽  
pp. 1093-1104 ◽  
Author(s):  
Franti?ek Ture?ek ◽  
Erik A. Syrstad ◽  
Jennifer L. Seymour ◽  
Xiaohong Chen ◽  
Chunxiang Yao
Keyword(s):  
Computational Study ◽  
Bond Cleavage ◽  
Cation Radical ◽  
Side Chain ◽  
Cation Radicals
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