X-ray studies on crystalline complexes involving amino acids and peptides. XL. Conformational variability, recurring and new features of aggregation, and effect of chirality in the malonic acid complexes of DL- and L-arginine

2002 ◽  
Vol 58 (6) ◽  
pp. 1051-1056 ◽  
Author(s):  
N. T. Saraswathi ◽  
M. Vijayan

The crystal structures of the complexes of malonic acid with DL- and L-arginine, which contain positively charged argininium ions and negatively charged semimalonate ions, further demonstrate the conformational flexibility of amino acids. A larger proportion of folded conformations than would be expected on the basis of steric consideration appears to occur in arginine, presumably because of the requirements of hydrogen bonding. The aggregation pattern in the DL-arginine complex bears varying degrees of resemblance to patterns observed in other similar structures. An antiparallel hydrogen-bonded dimeric arrangement of arginine, and to a lesser extent lysine, is a recurring motif. Similarities also exist among the structures in the interactions with this motif and its assembly into larger features of aggregation. However, the aggregation pattern observed in the L-arginine complex differs from any observed so far, which demonstrates that all the general patterns of amino-acid aggregation have not yet been elucidated. The two complexes represent cases where the reversal of the chirality of half the amino-acid molecules leads to a fundamentally different aggregation pattern.

2002 ◽  
Vol 58 (4) ◽  
pp. 734-739 ◽  
Author(s):  
N.T. Saraswathi ◽  
M. Vijayan

The malonic acid complexes of DL- and L-histidine are made up of zwitterionic positively charged histidinium ions and semimalonate (hydrogen malonate) ions. They crystallise in space groups P21/n and P21, respectively, with nearly the same unit-cell parameters. The molecules aggregate in the two complexes in a remarkably similar manner. The two sets of crystallographically independent molecules are related by a pseudo-glide plane. This pseudo-symmetry is almost exact except in the case of the α-carboxylate group and, to some extent, the α-C and the α-N atoms. Preservation of the aggregation pattern to such an extent on the reversal of chirality of half the amino-acid molecules is observed for the first time in amino-acid complexes. This is achieved at the cost of considerable conformational strain in one of the two histidinium ions in the L-histidine complex.


2001 ◽  
Vol 57 (6) ◽  
pp. 842-849 ◽  
Author(s):  
N. T. Saraswathi ◽  
M. Vijayan

The complexes of glutaric acid with L-arginine and L-histidine (two crystal forms) exhibit different stoichiometries and ionization states. The aggregation patterns in two of the crystals are remarkably similar to those observed earlier in similar structures, while the pattern in the remaining one has not been seen earlier. The variability in the ionization state and stoichiometry observed in amino acid–dicarboxylic acid complexes appears to represent subtle differences in the response of a molecule to the presence in its neighbourhood of another type of molecule. The glutaric acid molecules (or glutarate or semiglutarate ions) in their complexes and in other crystals favour a fully extended conformation, albeit with frequent departures from it. The change in the chirality of the component molecules in the complex could lead to drastic changes in the aggregation pattern; alternatively, the effects of the change are accommodated through small adjustments in essentially the same pattern.


CrystEngComm ◽  
2018 ◽  
Vol 20 (46) ◽  
pp. 7413-7416 ◽  
Author(s):  
Mger A. Navasardyan ◽  
Dmitry A. Grishanov ◽  
Tatiana A. Tripol'skaya ◽  
Lyudmila G. Kuz'mina ◽  
Petr V. Prikhodchenko ◽  
...  

Novel peroxosolvates of the non-proteinogenic amino acids sarcosine C3H7NO2·H2O2 (1) and phenylserine C9H11NO3·H2O2 (2) were prepared and their structures were determined by X-ray crystallography.


Molecules ◽  
2018 ◽  
Vol 23 (12) ◽  
pp. 3368 ◽  
Author(s):  
Giovanna Brancatelli ◽  
Enrico Dalcanale ◽  
Roberta Pinalli ◽  
Silvano Geremia

Crystallization of tetraphosphonate cavitand Tiiii[H, CH3, CH3] in the presence of positively charged amino acids, namely arginine, lysine, or histidine, afforded host-guest complex structures. The X-ray structure determination revealed that in all three structures, the fully protonated form of the amino acid is ditopically complexed by two tetraphosphonate cavitand molecules. Guanidinium, ammonium, and imidazolium cationic groups of the amino acid side chain are hosted in the cavity of a phosphonate receptor, and are held in place by specific hydrogen bonding interactions with the P=O groups of the cavitand molecule. In all three structures, the positively charged α-ammonium groups form H-bonds with the P=O groups, and with a water molecule hosted in the cavity of a second tetraphosphonate molecule. Furthermore, water-assisted dimerization was observed for the cavitand/histidine ditopic complex. In this 4:2 supramolecular complex, a bridged water molecule is held by two carboxylic acid groups of the dimerized amino acid. The structural information obtained on the geometrical constrains necessary for the possible encapsulation of the amino acids are important for the rational design of devices for analytical and medical applications.


2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Shogo Nakano ◽  
Kohei Kozuka ◽  
Yuki Minamino ◽  
Hiroka Karasuda ◽  
Fumihito Hasebe ◽  
...  

AbstractL-amino acid oxidases (LAAOs) can be applied to convert racemic amino acids to D-isomers, which are potential precursors of pharmaceuticals. However, this application is hampered by the lack of available stable and structure-determined LAAOs. In this study, we attempt to address this limitation by utilizing two ancestral LAAOs: AncLAAO-N4 and AncLAAO-N5. AncLAAO-N4 has the highest thermal and temporal stabilities among the designed LAAOs that can be used for deracemization and stereoinversion. AncLAAO-N5 can provide X-ray crystal structures, which are helpful to reveal substrate recognition and reaction mechanisms of LAAOs at the molecular level. Next, we attempted to improve activity of AncLAAO-N4 toward L-Val through a semi-rational protein engineering method. Three variants with enhanced activity toward L-Val were obtained. Taken together, we believe that the activity and substrate selectivity of AncLAAOs give them the potential to be key enzymes in various chemoenzymatic reactions.


2003 ◽  
Vol 59 (5) ◽  
pp. 641-646 ◽  
Author(s):  
N. T. Saraswathi ◽  
Siddhartha Roy ◽  
M. Vijayan

The complexes of L-arginine and DL-lysine with pimelic acid are made up of singly positively charged zwitterionic amino acid cations and doubly negatively charged pimelate ions in a 2:1 ratio. In both structures, the amino acid molecules form twofold symmetric or centrosymmetric pairs that are stabilized by hydrogen bonds involving α-amino and α-carboxylate groups. In the L-arginine complex, these pairs form columns along the shortest cell dimension, stabilized by intermolecular hydrogen bonds involving α-amino and α-carboxylate groups. The columns are connected by hydrogen bonds and water bridges to give rise to an amino acid layer. Adjacent layers are then connected by pimelate ions. Unlike molecular ions aggregate into alternating distinct layers in the DL-lysine complex. In the amino acid layer, hydrogen-bonded lysinium dimers related by a glide plane are connected by hydrogen bonds involving α-amino and α-carboxylate groups into head-to-tail sequences. Interestingly, the aggregation pattern observed in L-arginine hemipimelate monohydrate is very similar to those in DL-arginine formate dihydrate, DL-arginine acetate monohydrate and L-arginine hemiglutarate monohydrate. Similarly, the aggregation of amino acid molecules is very similar in DL-lysine hemipimelate 0.53-hydrate, DL-lysine formate and DL-lysine hydrochloride. The complexes thus demonstrate how, in related structures, the effects of a change in composition, and sometimes even those of reversal in chirality, can be accommodated by minor adjustments in essentially the same aggregation pattern. It also transpires that the conformation of the argininium ion is the same in the four argininium complexes; the same is true about the conformation of the lysinium ion in the three lysinium complexes. This result indicates a relation between, and mutual dependence of, conformation and aggregation.


2020 ◽  
Vol 7 (21) ◽  
pp. 4197-4221 ◽  
Author(s):  
Francisco Colmenero ◽  
Jakub Plášil ◽  
Jiří Sejkora

The structure, hydrogen bonding, X-ray diffraction pattern and mechanical properties of six important uranyl carbonate minerals, roubaultite, fontanite, sharpite, widenmannite, grimselite and čejkaite, are determined using first principles methods.


2014 ◽  
Vol 70 (a1) ◽  
pp. C534-C534
Author(s):  
Nasreddine Ghouari ◽  
Nourreedine Benali-Cherif

The theme of this work is part of the study of intermolecular interactions that hold the crystal structures of hybrid compounds based sulphuric acid, nitric acid, Melamine, Diethylamine, L-(+) - glutamic acid, DL-2-amino butyric acid. The aim of this work is to enlarge our laboratory researches [1-3] and methods in synthesis of new hybrid compounds consisting in organic cation(s) and mineral anion(s). We have obtained single crystals of a few samples after several trials and we plan to synthesize and characterize these crystals by X-ray diffraction, FTIR and Raman. The crystals structures allow us to study the 3D network hydrogen bonding, electron density and collect several other informations useful in FTIR and Raman studies of these hybrid compounds.


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