X-Ray Crystal Structures of Amino Acids and Selected Derivatives

Cody, Vivian

doi:10.1007/978-94-009-4832-7_22

Cited by 6 publications

(3 citation statements)

References 116 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The conformational insensitivity of leucine is accompanied by a general transferability of equivalent atoms from one conformation to another as well as the transferability of bond distances, bond angles, and of the rest of the bond properties 2. Because dihedral angles are the most sensitive parameters to crystal packing effects, these angles determined experimentally can differ widely for one and the same molecule from one crystal system to another and depending on the presence and on the nature of solvent or counterion(s) that cocrystallizes 27. Therefore, a detailed discussion of trends in these angles is not warranted.…”

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Atoms‐in‐molecules study of the genetically encoded amino acids. II. Computational study of molecular geometries

Matta

Bader

2002

Proteins

View full text Add to dashboard Cite

The geometries of the 20 genetically encoded amino acids were optimized at the restricted Hartree-Fock level of theory using the 6-31+G* basis set. A detailed comparison showed the calculated geometries to be in excellent agreement with those determined by X-ray crystallography. The study demonstrated that the geometric parameters for the main-chain group and for the bonds and common functional groups of the side-chains exhibit a high degree of transferability among the members of this set of molecules. This geometric transferability is a necessary prerequisite for the corresponding transferability of their electron density distributions and hence of their bond and atomic properties. The transferability of the electron distributions will be demonstrated and exploited in the following paper of this series, which uses the topology of the electron density to define an atom within the quantum theory of atoms in molecules. Particular features of the geometries of the amino acids are discussed. It has been shown, for example, how the apparent anomaly of the Calpha-N bond length in a peptide being shorter than in the charged species Calpha-NH3+ is resolved when the charge separation is gauged by the differences in the charges of the Calpha and N atoms as opposed to the use of formal charges. A compilation of literature sources on experimental geometries covering each member of the 20 amino acids is presented. A set of rules for labeling the atoms and bonds, complementing the generally accepted IUPAC-IUB rules, is proposed to uniquely identify every atom and bond in the amino acids.

show abstract

Section: Resultsmentioning

confidence: 99%

“…A list of experimental geometries of the amino acids, determined in single‐crystal X‐ray and neutron diffraction experiments, are compiled in Appendix . As early as 1985, over 1000 crystallographic studies dealing with the geometry of the amino acids had already been published (see review in Ref 27…”

Section: Resultsmentioning

confidence: 99%

Atoms‐in‐molecules study of the genetically encoded amino acids. II. Computational study of molecular geometries

Matta

Bader

2002

Proteins

View full text Add to dashboard Cite

show abstract

“…The layer periodicity, crystal structure, and conformation of cysteine (Cody, 1985), and the ease with which cysteine oxidizes (Bigham and Shapley, 1991), suggest that the complex Cu-cysteine and/or Cu-cystine forms in the interlayer.…”

Section: Na- Ca- and Cu-rich Smectite-cysteine Complexesmentioning

confidence: 99%

Effects of Exchange Cations and Layer-Charge Location on Cysteine Retention by Smectites

Brigatti

Lugli

Montorsi

et al. 1999

Clays and clay miner.

View full text Add to dashboard Cite

Abstract--This study investigates the complexes formed between amino acids, which are the natural degradation products of organic matter, and smectites. Thus, the adsorption and desorption behavior of cysteine and Na-, Ca-, Cu-homoionic smectites with different layer-charge location, a montmorillonite, and a beidellite, were studied. The clay samples were treated with Na, Ca, and Cu 1 N solutions and then with a 0.2 M cysteine solution. To test smectite-cysteine stability at acidic pH, the solids obtained were repeatedly treated with distilled water acidified to pH = 5. All treated samples were characterized by thermal, X-ray diffraction, chemical, and infrared analyses. The results showed that: 1) Na-and Carich smectites adsorbed and retained small amounts of cysteine, and did not show interlayer cationcysteine complexes, whereas the amino acid was strongly retained in the interlayer by Cu-rich smectites; 2) d(001)-values for Na-and Ca-rich smectites showed little or no expansion, whereas for the Cu-rich smectites the intercalation of the organic molecule produced a swelling of the structure; 3) the interaction mechanism of homoionic smectites with cysteine in an aqueous medium occurs by weak interactions, (e.g., van der Waals interactions, hydrogen bonding, dipole-dipole interactions, and other electrostatic forces such as entropy-driven hydrophobic bonding), and/or by complexes involving interlayer cations and organic ligands. The formation of a stable chelate complex with the saturating ion permits cysteine to be adsorbed by Cu(II)-rich smectites and to be resistant to migration in soils and groundwaters.

show abstract

The three‐dimensional similarity between a dimeric antiparallel extended structure and a β‐turn folded form of enkephalin

et al. 1987

View full text Add to dashboard Cite

The three-dimensional similarity between two fundamental conformations, a dimeric antiparallel extended structure and a type I' p-turn folded form, of enkephalin was examined by computer graphic and empirical energy calculation methods. By the rotation of Tyr and Phe side chains, one half of the former structure could mimic the three-dimensional form of the latter without a large loss of conformational energy. This result provides a new idea for considering the conformation of enkephalin suitable for the multiple opioid receptors. The active conformation of enkephalin for ,u-and S-opioid receptors is discussed in the light of the present study.

show abstract

X-Ray Crystal Structures of Amino Acids and Selected Derivatives

Cited by 6 publications

References 116 publications

Atoms‐in‐molecules study of the genetically encoded amino acids. II. Computational study of molecular geometries

Atoms‐in‐molecules study of the genetically encoded amino acids. II. Computational study of molecular geometries

Effects of Exchange Cations and Layer-Charge Location on Cysteine Retention by Smectites

The three‐dimensional similarity between a dimeric antiparallel extended structure and a β‐turn folded form of enkephalin

Contact Info

Product

Resources

About