Topological Analysis of the Experimental Electron Densities of Amino Acids. 1.<scp>d,l</scp>-Aspartic Acid at 20 K

Flaig, Ralf; Koritsánszky, T.; Zöbel, Dieter; Luger, Peter

doi:10.1021/ja972620e

Cited by 107 publications

(104 citation statements)

References 35 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…The topology of such densities can also be analysed using the theory of atoms in molecules (AIM) (Bader, 1990). A variety of such studies has been published, ranging from the relatively simple NH 3 molecule (Boese et al, 1997) to more complex organic molecules (Flaig et al, 1998;Souhassou & Blessing, 1999;Koritsa Â nszky et al, 1999Koritsa Â nszky et al, , 2000, and transition-metal complexes (Smith et al, 1997;Iversen et al, 1997;Macchi et al, 1998a,b;Bianchi et al, 2000;Bytheway et al, 2001) as well as the bulk crystalline phase of SiO 2 (Rosso et al, 1999) and Cu 2 O (Lippmann & Schneider, 2000). Analysis of charge densities using the theory of AIM is appealing since it provides de®nitions of atoms and bonds that depend only on the charge density, not upon the method by which it was obtained.…”

Section: Introductionmentioning

confidence: 99%

Can a multipole analysis faithfully reproduce topological descriptors of a total charge density?

Bytheway¹,

Chandler²,

Figgis³

2002

Acta Cryst Sect A

View full text Add to dashboard Cite

Total charge densities &(r) of solid NH 3 have been derived using an ab initio crystalline molecular-orbital approach and also from multipole re®nement of the structure factors obtained from the same charge density. Comparison of the topological features of these charge densities, as de®ned by the quantum theory of atoms in molecules, has been used to probe the ability of the multipole analysis to reproduce exactly known total charge-density distributions. For the most part, multipole re®nement satisfactorily returns the features of the original density, although the ®t to theoretical data is not as good as that to the experimental data. The one topological parameter that is poorly reproduced is the Laplacian r 2 &r b at NH bond critical points.

show abstract

Section: Introductionmentioning

confidence: 99%

Can a multipole analysis faithfully reproduce topological descriptors of a total charge density?

Bytheway¹,

Chandler²,

Figgis³

2002

Acta Cryst Sect A

View full text Add to dashboard Cite

show abstract

“…Later, a measurement at 20 K (Flaig et al 1998) and a refinement of data gathered with neutron diffraction data (Sequeira et al 1989) were also reported.…”

Section: Aspartic Acidmentioning

confidence: 99%

Amino Acid Structures

Fleck

Petrosyan

2014

Salts of Amino Acids

View full text Add to dashboard Cite

Although this book deals with salts of amino acids, this chapter discusses the structures of pristine amino acids, since these molecular structures are also found in salts, and factors as solubility and conditions of crystal growth are important for the synthesis of amino acid salts as well as the pure form. In this context, the impact of minimal changes in conditions (such as impurities) on the growth of amino acid crystals is noted. The structural variation is very high, as not only amino acids differ from each other, but many amino acids exist in more than one form. This refers to the fact that enantiopure crystals can be grown as well as racemates (so-called DL-amino acids). Moreover, often more than one hydration state is found: Anhydrous forms are common, but many amino acids form hydrated crystals. For some amino acids (e.g., glycine, proline, methionine), more than one polymorph of the same hydration state is found. Some of these polymorphs form at ambient condition, often due to minuscule changes in conditions. For others, variation in temperature and pressure has been found to be the cause of the formation of different polymorphs. High-pressure data are available for some amino acids (e.g., alanine, serine, cysteine). Most amino acids are found to form a so-called head-to-tail motif, where acid and amino groups connect to form infinite chains. In some of the larger, nonpolar amino acids, a bilayer pattern is found, where polar groups of opposing molecules face each other, forming a layer, with the hydrophobic side chain facing outward (this motif is found in phenylalanine, methionine, leucine, or isoleucine). Not all amino acids crystallize readily, as is proved by the crystal structure of L-arginine, which could be determined only very recently, and that of lysine, which could not be solved at all to date. In addition to the standard 20, some nonstandard amino acids are discussed. Finally, notes on remarkable physical effects (such as piezoelectric data) or possible applications (as for instance the interactions of amino acids with carbon nanotubes) are presented.

show abstract

“…To evaluate the atomic volumes and charges the program TOPXD [4] was used.In order to examine the transferabillity of smaller fragments the topology of submolecular parts of the three molecules were compared with each other and with those of the Matta study.[1] Matta C.F., J. Phys. Chem., 2001 Nucleosides play a key role in life.…”

mentioning

confidence: 99%

“…From our investigation, we have discovered an E2 RXS feature, for which the azimuth dependence can be reconciled with an ordered octupole moment in phase IV. The results give, to our knowledge, the first direct evidence for a new order parameter in the Ce 0.7 La 0.3 B 6 ground.[ To answer the title question we computed for a variety of small molecules hydrogen ADPs as described in [4], implemented in the XD [5] suite. In that procedure the internal displacements for all atoms are calculated by an ab initio methods, and then subtracted from the experimental data that also contain the external modes.…”

mentioning

confidence: 99%

See 1 more Smart Citation

Anisotropic displacement parameters (ADPs) of hydrogen atoms. Can invariom modeling contribute?

Dittrich¹,

Whitten²,

Spackman³

2005

Acta Cryst Sect A

View full text Add to dashboard Cite

density gradient vector field according to the "atoms in molecule"-theory of Bader [3]. To evaluate the atomic volumes and charges the program TOPXD [4] was used.In order to examine the transferabillity of smaller fragments the topology of submolecular parts of the three molecules were compared with each other and with those of the Matta study.[1] Matta C.F., J. Phys. Chem., 2001 Nucleosides play a key role in life. Therefore they are interesting compounds for X-Ray charge density studies, because this would help to understand their biological function in more detail. The invariom aproach [1] uses small theoretically calculated model compounds to derrive the multipole populations without the need of high resolution data, because they are kept unrefined.Thymidin, which is one of the DNA nucleosides, was measured at 20K with Mo-K radiation up to a resolution of sin / =1.1Å -1 . After the spherical refinement of the structure a multipole refinement was executed and also the recently developed invariom transfer was applied. A topological analysis was done in both approaches.The results of the invariom transfer, the multipole refinement and the theoretical calculations were compared to have a better guess about the quality of the new approach.[1] Dittrich B., Korisánszky T., Luger P., Angew. Chem. Int. Ed., 2004Ed., , 38, 1397 Keywords: charge density studies, nucleosides, high resolution P.14.01.7 Acta Cryst. (2005). A61, C420 Experimental Electron Density and Topological Analysis of Dand DL-Camphoric Anhydride Kumaradhas Poomani, Tibor Koritsanszkyb, Periyar University, Department of Physics, 636011 Salem, Tamil Nadu, Parameter indeterminacies often encountered during pseudoatom modeling of non-centrosymmetric structures unavoidably bias the results of experimental charge density studies [1,2]. A comparative analysis of high-resolution X-ray data of both crystal forms of Camphoric Anhydride C 10 H 14 O 3 was performed to learn about model restrictions applicable to reduce correlations between least-squares parameter estimates and the transferability of experimental pseudoatoms. The title compound is an ideal candidate for such a study, since the two enantiomers have very similar crystal packing and thus density differences due to different intermolecular forces are expected to be negligible. All intensity data were collected at 100K using SMART 1K CCD area detector with Mo K radiation up to a resolution corresponding to (sin / ) max = 1.1Å -1 . The multipole refinement and the analysis of the static densities were performed using the XD program suite. The results obtained by different constrained models will be presented in terms of local and integrated topological properties of the densities.[1] Spackman M.A., Byrom P.G., Acta Cryst., 1997, B53, 553. [2] El Haouzi A., Hansen N.K., Le Hènaff, C., Portas L., Acta Cryst., 1996, A52, 291. [3] Koritsanszky T., Richter T., Macchi P., Volkov A., Gatti C., Howard S., Mallinson P.R., Farrugia L., Su Z., Hansen N. The 8 ground state of CeB 6 , which may support, dipole, ...

show abstract

Topological Analysis of the Experimental Electron Densities of Amino Acids. 1.d,l-Aspartic Acid at 20 K

Cited by 107 publications

References 35 publications

Can a multipole analysis faithfully reproduce topological descriptors of a total charge density?

Can a multipole analysis faithfully reproduce topological descriptors of a total charge density?

Amino Acid Structures

Anisotropic displacement parameters (ADPs) of hydrogen atoms. Can invariom modeling contribute?

Contact Info

Product

Resources

About