scholarly journals cis–trans-Amide isomerism of the 3,4-dehydroproline residue, the ‘unpuckered’ proline

2016 ◽  
Vol 12 ◽  
pp. 589-593 ◽  
Author(s):  
Vladimir Kubyshkin ◽  
Nediljko Budisa
Keyword(s):  
Amino Acid ◽  
Double Bond ◽  
Transition State ◽  
Physicochemical Properties ◽  
Crystal Structures ◽  
Experimental Work ◽  
Theoretical Calculations ◽  
Biological Systems ◽  
Amide Bond ◽  
Rotational Barriers

Proline (Pro) is an outstanding amino acid in various biochemical and physicochemical perspectives, especially when considering the cis–trans isomerism of the peptidyl-Pro amide bond. Elucidation of the roles of Pro in chemical or biological systems and engineering of its features can be addressed with various Pro analogues. Here we report an experimental work investigating the basic physicochemical properties of two Pro analogues which possess a 3,4-double bond: 3,4-dehydroproline and 4-trifluoromethyl-3,4-dehydroproline. Both indicate a flat pyrroline ring in their crystal structures, in agreement with previous theoretical calculations. In solution, the peptide mimics exhibit an almost unchanged equilibrium of the trans/cis ratios compared to that of Pro and 4-trifluoromethylproline derivatives. Finally we demonstrate that the 3,4-double bond in the investigated structures leads to an increase of the amide rotational barriers, presumably due to an interplay with the transition state.

Controlling the self-assembly of homochiral coordination architectures of CuII by substitution in amino acid based ligands: synthesis, crystal structures and physicochemical properties

2015 ◽  
Vol 44 (12) ◽  
pp. 5672-5687 ◽  
Author(s):  
Navnita Kumar ◽  
Sadhika Khullar ◽  
Sanjay K. Mandal
Keyword(s):  
Amino Acid ◽  
Physicochemical Properties ◽  
Crystal Structures ◽  
Self Assembly ◽  
The Self ◽  
Chiral Ligands

In this paper we report six chiral ligands based on l-tyrosine, l-serine and l-phenylalanine and their homochiral CuII complexes to study the effect of various substitutions in the ligands on the formation of diverse coordination architectures.

scholarly journals Crystal structures of two molecules with small chemical structure difference

2014 ◽  
Vol 70 (a1) ◽  
pp. C1686-C1686
Author(s):  
Agris Berzins ◽  
Andris Actins
Keyword(s):  
Double Bond ◽  
Crystal Structures ◽  
Intermolecular Interactions ◽  
Potential Energy Surfaces ◽  
Chemical Structure ◽  
Theoretical Calculations ◽  
Torsion Angles ◽  
Structural Formation ◽  
Energy Surfaces ◽  
Molecule Conformation

Droperidol and benperidol, neuroleptic pharmaceuticals, both are used as antipsychotics. The chemical structure of these two compounds differs only by one double bond in the middle of the molecule (see Scheme). It is known that both of these substances can form several polymorphs and solvates. Crystal structures of most of these phases are known [1, 2]. Despite the molecular structure similarities, there are no known droperidol polymorph or solvate isostructural to those of benperidol. Although there has been studies characterizing the crystal structures of chemically very similar compounds, general explanation to observed structural differences was not found (e.g. [3]). In this study we analyse the crystal structures of benperidol and droperidol by comparing the molecule conformation and packing in crystal structures of both of these compounds. Molecule conformation is compared and torsion angles which differ and therefore lead to different crystal structures are identified. Theoretical calculation of potential energy surfaces of these torsion angles are performed in Gaussian09. Intermolecular interactions and molecule packing in all crystal structures are compared by trying to understand the general differences between both molecules. Analysis of structures deposited in Cambridge Structural Database is performed to find conformations and intermolecular interactions characteristic for similar molecules by therefore trying to generalize structural formation possibilities for both pharmaceuticals and understand the reasons for crystallization of only observed structures. Theoretical calculations of benperidol and droperidol crystal structures where benperidol molecules are replaced by droperidol and vice versa are performed in CASTEP to compare the energy of experimentally observed crystal structure with that of theoretically possible structure isostructural to double-bond-different molecule.

An NBO-TS predictive approach for torquoselectivity of ring opening in 3-substituted cyclobutenes

2017 ◽  
Author(s):  
Arpita Yadav ◽  
Dasari L V K Prasad ◽  
Veejendra Yadav
Keyword(s):  
Transition State ◽  
Ring Opening ◽  
Natural Bond Orbital ◽  
Theoretical Calculations ◽  
Lone Pair ◽  
Product Distribution ◽  
Acceptor Substituent ◽  
Important Contributor ◽  
Predictive Approach ◽  
Donor Substituent

<p>The torquoselectivity, the inward or outward ring opening of 3-substituted cyclobutenes, is conventionally guided by the donor and/or acceptor ability of the substituent (S). It is typically predicted by estimating the respective ring opening transition state (TS) barriers. While there is no known dissent in regard to the outward rotation of electron-rich substituents from the approaches of TS calculations, the inward rotation was predicted for some electron-accepting substituents and outward for others. To address this divergence in predicting the torquoselectivity, we have used reliable orbital descriptors through natural bond orbital theoretical calculations and demonstrated that (a) interactions <i>n</i><i><sub>S</sub></i>→s*<sub>C3C4</sub> for a lone pair containing substituent, s<sub>S</sub>→s*<sub>C3C4</sub> for a s-donor substituent, s<sub>C3C4</sub>→p*<sub>S</sub> for a resonance-accepting substituent and s<sub>C3C4</sub>→s*<sub>S</sub> for a s-acceptor substituent constitute the true electronic controls of torquoselectivity, and (b) reversibility of the ring opening event is an additional important contributor to the observed product distribution.</p>

Amino Acids Sequence-based Analysis of Arginine Deiminase from Different Prokaryotic Organisms: An In Silico Approach

2020 ◽  
Vol 14 (3) ◽  
pp. 235-246
Author(s):  
Sara Abdollahi ◽  
Mohammad H. Morowvat ◽  
Amir Savardashtaki ◽  
Cambyz Irajie ◽  
Sohrab Najafipour ◽  
...  
Keyword(s):  
Amino Acid ◽  
Physicochemical Properties ◽  
Sequence Alignment ◽  
Multiple Sequence Alignment ◽  
In Silico ◽  
Bacterial Species ◽  
Arginine Deiminase ◽  
Antitumor Effects ◽  
Multiple Sequence ◽  
In Silico Studies

Background: Arginine deiminase is a bacterial enzyme, which degrades L-arginine. Some human cancers such as hepatocellular carcinoma (HCC) and melanoma are auxotrophic for arginine. Therefore, PEGylated arginine deiminase (ADI-PEG20) is a good anticancer candidate with antitumor effects. It causes local depletion of L-arginine and growth inhibition in arginineauxotrophic tumor cells. The FDA and EMA have granted orphan status to this drug. Some recently published patents have dealt with this enzyme or its PEGylated form. Objective: Due to increasing attention to it, we aimed to evaluate and compare 30 arginine deiminase proteins from different bacterial species through in silico analysis. Methods: The exploited analyses included the investigation of physicochemical properties, multiple sequence alignment (MSA), motif, superfamily, phylogenetic and 3D comparative analyses of arginine deiminase proteins thorough various bioinformatics tools. Results: The most abundant amino acid in the arginine deiminase proteins is leucine (10.13%) while the least amino acid ratio is cysteine (0.98%). Multiple sequence alignment showed 47 conserved patterns between 30 arginine deiminase amino acid sequences. The results of sequence homology among 30 different groups of arginine deiminase enzymes revealed that all the studied sequences located in amidinotransferase superfamily. Based on the phylogenetic analysis, two major clusters were identified. Considering the results of various in silico studies; we selected the five best candidates for further investigations. The 3D structures of the best five arginine deiminase proteins were generated by the I-TASSER server and PyMOL. The RAMPAGE analysis revealed that 81.4%-91.4%, of the selected sequences, were located in the favored region of arginine deiminase proteins. Conclusion: The results of this study shed light on the basic physicochemical properties of thirty major arginine deiminase sequences. The obtained data could be employed for further in vivo and clinical studies and also for developing the related therapeutic enzymes.

A Quaternary Nitronyl Nitroxide α-Amino Acid: Synthesis, Configurational and Conformational Assignments, and Physicochemical Properties

2014 ◽  
Vol 2014 (8) ◽  
pp. 1741-1752 ◽  
Author(s):  
Karen Wright ◽  
Edouard d'Aboville ◽  
Joseph Scola ◽  
Tommaso Margola ◽  
Antonio Toffoletti ◽  
...  
Keyword(s):  
Amino Acid ◽  
Physicochemical Properties ◽  
Acid Synthesis ◽  
Nitronyl Nitroxide ◽  
Amino Acid Synthesis

CAN SEMIEMPIRICAL QUANTUM MODELS CALCULATE THE BINDING ENERGY OF HYDROGEN BONDING FOR BIOLOGICAL SYSTEMS?

2009 ◽  
Vol 08 (04) ◽  
pp. 691-711 ◽  
Author(s):  
FENG FENG ◽  
HUAN WANG ◽  
WEI-HAI FANG ◽  
JIAN-GUO YU
Keyword(s):  
Hydrogen Bonding ◽  
Amino Acid ◽  
Amino Acid Residue ◽  
Density Functional ◽  
Biological Systems ◽  
Binding Energies ◽  
Semiempirical Model ◽  
Hydrogen Bonded Systems ◽  
High Level ◽  
Hydrogen Bonded

A modified semiempirical model named RM1BH, which is based on RM1 parameterizations, is proposed to simulate varied biological hydrogen-bonded systems. The RM1BH is formulated by adding Gaussian functions to the core–core repulsion items in original RM1 formula to reproduce the binding energies of hydrogen bonding of experimental and high-level computational results. In the parameterizations of our new model, 35 base-pair dimers, 18 amino acid residue dimers, 14 dimers between a base and an amino acid residue, and 20 other multimers were included. The results performed with RM1BH were compared with experimental values and the benchmark density-functional (B3LYP/6-31G**/BSSE) and Möller–Plesset perturbation (MP2/6-31G**/BSSE) calculations on various biological hydrogen-bonded systems. It was demonstrated that RM1BH model outperforms the PM3 and RM1 models in the calculations of the binding energies of biological hydrogen-bonded systems by very close agreement with the values of both high-level calculations and experiments. These results provide insight into the ideas, methods, and views of semiempirical modifications to investigate the weak interactions of biological systems.

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