L-2-Aminobutyric acid: two fully ordered polymorphs with Z′ = 4

2010 ◽  
Vol 66 (2) ◽  
pp. 253-259 ◽  
Author(s):  
Carl Henrik Görbitz
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Amino Acid ◽  
Diffraction Data ◽  
Aminobutyric Acid ◽  
Side Chain ◽  
Hydrogen Bond Network ◽  
Asymmetric Unit ◽  
Space Groups ◽  
Bond Network

The crystal structure of L-2-aminobutyric acid, an L-alanine analogue with an ethyl rather than a methyl side chain, has proved elusive owing to problems growing diffraction quality crystals. Good diffraction data have now been obtained for two polymorphs, in space groups P21 and I2, revealing surprisingly complex, yet fully ordered crystalline arrangements with Z′ = 4. The closely related structures are divided into hydrophilic and hydrophobic layers, the latter being the thinnest ever found for an amino acid (other than α-glycine). The hydrophobic layers furthermore contain conspicuous pseudo-centers-of-symmetry, leading to overall centrosymmetric intensity statistics. Uniquely, the four molecules in the asymmetric unit can be divided into two pairs that each forms an independent hydrogen-bond network.

scholarly journals Characterizing Hydropathy of Amino Acid Side Chain in a Protein Environment by Investigating the Structural Changes of Water Molecules Network

2021 ◽  
Vol 8 ◽  
Author(s):  
Lorenzo Di Rienzo ◽  
Mattia Miotto ◽  
Leonardo Bò ◽  
Giancarlo Ruocco ◽  
Domenico Raimondo ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Amino Acid ◽  
Computational Method ◽  
Side Chain ◽  
Water Molecules ◽  
Amino Acid Side Chain ◽  
Hydrogen Bond Network ◽  
Bond Network ◽  
Protein Environment

Assessing the hydropathy properties of molecules, like proteins and chemical compounds, has a crucial role in many fields of computational biology, such as drug design, biomolecular interaction, and folding prediction. Over the past decades, many descriptors were devised to evaluate the hydrophobicity of side chains. In this field, recently we likewise have developed a computational method, based on molecular dynamics data, for the investigation of the hydrophilicity and hydrophobicity features of the 20 natural amino acids, analyzing the changes occurring in the hydrogen bond network of water molecules surrounding each given compound. The local environment of each residue is complex and depends on the chemical nature of the side chain and the location in the protein. Here, we characterize the solvation properties of each amino acid side chain in the protein environment by considering its spatial reorganization in the protein local structure, so that the computational evaluation of differences in terms of hydropathy profiles in different structural and dynamical conditions can be brought to bear. A set of atomistic molecular dynamics simulations have been used to characterize the dynamic hydrogen bond network at the interface between protein and solvent, from which we map out the local hydrophobicity and hydrophilicity of amino acid residues.

Supramolecular assembling using synthons with NH—CO(S)—CS—NH and NH—CO—CO—NH functionalities: crystal structures of (S,S)-N,N′-monothiooxalyldileucine methyl ester and its dithio analogue

2004 ◽  
Vol 60 (1) ◽  
pp. 90-96 ◽  
Author(s):  
Biserka Kojić-Prodić ◽  
Berislav Perić ◽  
Zoran Štefanić ◽  
Anton Meden ◽  
Janja Makarević ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Methyl Ester ◽  
Crystal Structures ◽  
Hydrogen Bond Network ◽  
Asymmetric Unit ◽  
Orthorhombic Space Group ◽  
Space Group ◽  
Bond Network ◽  
Bonding Systems

To compare the structural properties of oxalamide and thiooxalamide groups in the formation of hydrogen bonds suitable for supramolecular assemblies a series of retropeptides was studied. Some of them, having oxalamide bridges, are gelators of organic solvents and water. However, retropeptides with oxygen replaced by the sp 2 sulfur have not exhibited such properties. The crystal structures of the two title compounds are homostructural, i.e. they have similar packing arrangements. The monothio compound crystallizes in the orthorhombic space group P212121 with two molecules in the asymmetric unit arranged in a hydrogen-bond network with an approximate 41 axis along the crystallographic b axis. However, the dithio and dioxo analogues crystallize in the tetragonal space group P41 with similar packing patterns and hydrogen-bonding systems arranged in agreement with a crystallographic 41 axis. Thus, these two analogues are isostructural having closely related hydrogen-bonding patterns in spite of the different size and polarity of oxygen and sulfur which serve as the proton acceptors.

(NH4)[B3PO6(OH)3]·0.5H2O

2007 ◽  
Vol 63 (11) ◽  
pp. i185-i185 ◽  
Author(s):  
Wei Liu ◽  
Jingtai Zhao
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Water Molecules ◽  
Hydrogen Bond Network ◽  
Ammonium Ions ◽  
One Dimensional ◽  
Bond Network ◽  
Solvothermal Conditions

The title compound, ammonium catena-[monoboro-monodihydrogendiborate-monohydrogenphosphate] hemihydrate, was obtained under solvothermal conditions using glycol as the solvent. The crystal structure is constructed of one-dimensional infinite borophosphate chains, which are interconnected by ammonium ions and water molecules via a complex hydrogen-bond network to form a three-dimensional structure. The water molecules of crystallization are disordered over inversion centres, and their H atoms were not located.

Hydrogen-bond network and pH sensitivity in transthyretin: Neutron crystal structure of human transthyretin

2012 ◽  
Vol 177 (2) ◽  
pp. 283-290 ◽  
Author(s):  
Takeshi Yokoyama ◽  
Mineyuki Mizuguchi ◽  
Yuko Nabeshima ◽  
Katsuhiro Kusaka ◽  
Taro Yamada ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Ph Sensitivity ◽  
Hydrogen Bond Network ◽  
Bond Network

scholarly journals (Acetonitrile-κN)aqua[N,N′-bis(pyridin-2-ylmethyl)ethane-1,2-diamine-κ4N,N′,N′′,N′′′]zinc(II) perchlorate

2017 ◽  
Vol 73 (10) ◽  
pp. 1568-1571
Author(s):  
Ugochukwu Okeke ◽  
Yilma Gultneh ◽  
Ray J. Butcher
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Three Dimensional ◽  
Structural Features ◽  
Hydrogen Bond Network ◽  
Asymmetric Unit ◽  
Bond Network ◽  
Bifurcated Hydrogen Bond ◽  
Coordinated Water ◽  
Ionic Hydrogen Bonding

The structure of the title compound, [Zn(C14H18N4)(C2H3N)(H2O)](ClO4)2, contains a six-coordinate cation consisting of the tetradentate bispicen ligand, coordinated water, and coordinated acetonitrile, with the latter two ligands adopting acisconfiguration. There are two formula units in the asymmetric unit. Both cations show almost identical structural features with the bispicen ligand adopting the more commoncis-β conformation. One of the four perchlorate anions is disordered over two positions, with occupancies of 0.9090 (15) and 0.0910 (15). There is extensive inter-ionic hydrogen bonding between the perchlorate anions and O—H and N—H groups in the cations, including a bifurcated hydrogen bond between an N—H group and two O atoms of one perchlorate anion. As a result of this extended hydrogen-bond network, the ions are linked into a complex three-dimensional array.

Hydration and Proton Transfer in 3M™ PEM Ionomers: An Ab Initio Study

2012 ◽  
Vol 1384 ◽  
Author(s):  
Jeffrey K. Clark ◽  
Stephen J. Paddison
Keyword(s):  
Hydrogen Bond ◽  
Proton Transfer ◽  
The State ◽  
Side Chain ◽  
Water Molecules ◽  
Side Chains ◽  
Hydrogen Bond Network ◽  
Group Separation ◽  
Proton Dissociation ◽  
Bond Network

ABSTRACTElectronic structure calculations were performed to study the effects local hydration, neighboring side chain connectivity, and protogenic group separation have in facilitating proton dissociation and transfer in fragments of 3M ionomers under conditions of low hydration. Two different types of ionomers, each consisting of a poly(tetrafluoroethylene) (PTFE) backbone, were considered: (1) perfluorosulfonic acid (PFSA) ionomeric fragments containing two pendant side chains (–O(CF2)4SO3H) of distinct separation along the PTFE backbone to model different equivalent weight ionomers and (2) single side chain fragments of three bis(sulfonyl imide)- based fragments with multiple and distinct acid groups per side chain having structural and chemical differences mediating protogenic group separation (side chains: –O(CF2)4SO2(NH)- SO2C6H4SO3H) with the sulfonic acid group located in either the meta or the ortho position on the phenyl ring and –O(CF2)4SO2(NH)SO2(CF2)3SO3H). Fully optimized structures of these fragments with and without the addition of water molecules at the B3LYP/6-311G** level revealed that both side chain connectivity and protogenic group separation, along with local hydration, are key contributors to proton dissociation and the energetics of proton transfer in these materials. Specifically, cooperative interaction between protogenic groups through hydrogen bonding and electron withdrawing –CF2– groups are critical for first proton dissociation and the state of the dissociated proton at low levels of hydration. However, the close proximity of protogenic groups in the ortho bis acid precluded second proton dissociation at low hydration as the relatively fixed protogenic group separation promoted interactions between water molecules, while the labile side chains in the PFSA ionomers allowed for greater freedom in the hydrogen bond network formed. Potential energy profiles for proton transfer were determined at the B3LYP/6-31G** level. The energetic penalty associated with proton transfer was found to be strongly dependent on the surrounding hydrogen bond network and the state of the dissociated proton(s), as well as, the separation between protogenic groups.

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