Experimental Charge Density of α-Glycine at 23 K

Destro, Riccardo; Roversi, Pietro; Barzaghi, Mario; Marsh, Richard E.

doi:10.1021/jp993505o

Cited by 120 publications

(150 citation statements)

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“…The structures derived from neutron diffraction data are acetylene at a temperature of 110 K, 36 urea at 123 K, 32 and benzene at 123 K, 37 and the structure of 2-methyl-4-nitroaniline ͑MNA͒ is taken from the data measured at 100 K, the details of which will be reported in a forthcoming publication. 38 The 90 K structure of formamide 39 and the 23 K structure of glycine 40 have been taken from the charge density analysis of accurate x-ray diffraction data, and the structure of hydrogen cyanide at 180 K was taken from the unpublished x-ray diffraction data, as described by Platts and Howard. 12 The ab initio calculations were then repeated using the MOLSPLIT option in CRYSTAL98, yielding the electron distribution due to a superposition of noninteracting molecules ͑hereafter referred to as "molecules"͒.…”

Section: Examples and Conclusionmentioning

confidence: 99%

Dipole and quadrupole moments of molecules in crystals: A novel approach based on integration over Hirshfeld surfaces

Whitten

Radford

McKinnon

et al. 2006

The Journal of Chemical Physics

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Interaction-induced dipoles of hydrogen molecules colliding with helium atoms: A new ab initio dipole surface for high-temperature applications J. Chem. Phys. 136, 044320 (2012) Elegant expressions are derived for the computation of dipole and quadrupole moments of molecules using the electrostatic potential and electric field evaluated on an oriented molecular surface. These expressions are implemented for Hirshfeld surfaces, applied to various molecular crystals, and compared with the results from the quantum theory of atoms in molecules. The effect of intermolecular interactions is also explored by examining the differences between electrostatic moments derived from a periodic Hartree-Fock electron density and an electron density resulting from a superposition of noninteracting molecules. The enhancement of the dipole moment for hydrogen bonded molecular crystals is typically 30%-40% and shown to be largely independent of the partitioning scheme. Dipole moments calculated from Hirshfeld surfaces systematically underestimate those from zero-flux surfaces, a result attributed to the translation of the Hirshfeld surface relative to the zero-flux surfaces for these molecules. For acetylene and benzene, the differences between a crystal calculation and the sum of noninteracting molecules are small, and both partitioning schemes yield quadrupole and second moment results in close agreement.

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Section: Examples and Conclusionmentioning

confidence: 99%

Dipole and quadrupole moments of molecules in crystals: A novel approach based on integration over Hirshfeld surfaces

Whitten

Radford

McKinnon

et al. 2006

The Journal of Chemical Physics

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“…The current analysis is based on six pairs (dimers) of zwitterionic glycine molecules such as occur in crystals of R-glycine 25 (Figure 1). …”

Section: Test Systems and Calculationsmentioning

confidence: 99%

Dependence of the Intermolecular Electrostatic Interaction Energy on the Level of Theory and the Basis Set

Volkov

King

Coppens

2005

J. Chem. Theory Comput.

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Abstract:As electrostatic forces play a prominent role in the process of folding and binding of biological macromolecules, an examination of the method dependence of the electrostatic interaction energy is of great importance. An extensive analysis of the basis set and method dependence of electrostatic interaction energies (E es ) in molecular systems using six test dimers of R-glycine is presented. A number of Hartree-Fock, Kohn-Sham, Møller-Plesset, configuration interaction (CI), quadratic CI, and coupled cluster calculations were performed using several double-, triple-, and quadruple--quality Gaussian-and Slater-type (Kohn-Sham calculations only) basis sets. The main factor affecting E es was found to be the inclusion of diffuse functions in the basis set expansions. Møller-Plesset (even at second order), quadratic CI, and coupled cluster calculations produce the most consistent results. Hartree-Fock and CI methods usually overestimate the E es , while the Kohn-Sham approach tends to underestimate the magnitude of the electrostatic interaction. The combination of the transferable-pseudoatom databank and the exact potential and multipole moment method reproduces Kohn-Sham B3LYP/6-31G** results on which it is based, confirming the excellent transferability of the pseudoatom densities within the systems studied. However, because Kohn-Sham calculations with double--quality basis sets show considerable deviations from advanced correlated methods, further development of the databank using electron densities from such methods is highly desirable.

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“…Topological properties of static electron densities are usually interpreted according to the quantum theory of atoms in molecules (QTAIM; Bader, 1994). This method has been extensively applied to crystals of amino acids and small peptides, especially tripeptides (Jelsch et al, 1998;Destro et al, 2000;Flaig et al, 2002;Rö del, 2003;Scheins et al, 2004;Dittrich et al, 2005;Mebs et al, 2006;Checiń ska et al, 2006;Kalinowski et al, 2007;Johnas et al, 2009). As opposed to static electron densities, dynamic electron densities employ both the atomic coordinates and the atomic displacements resulting from a structure refinement against diffraction data.…”

Section: Introductionmentioning

confidence: 99%

The active site of hen egg-white lysozyme: flexibility and chemical bonding

Held¹,

Smaalen²

2014

Acta Crystallogr D Biol Crystallogr

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Chemical bonding at the active site of hen egg-white lysozyme (HEWL) is analyzed on the basis of Bader's quantum theory of atoms in molecules [QTAIM;Bader (1994), Atoms in Molecules: A Quantum Theory. Oxford University Press] applied to electron-density maps derived from a multipole model. The observation is made that the atomic displacement parameters (ADPs) of HEWL at a temperature of 100 K are larger than ADPs in crystals of small biological molecules at 298 K. This feature shows that the ADPs in the cold crystals of HEWL reflect frozen-in disorder rather than thermal vibrations of the atoms. Directly generalizing the results of multipole studies on small-molecule crystals, the important consequence for electron-density analysis of protein crystals is that multipole parameters cannot be independently varied in a meaningful way in structure refinements. Instead, a multipole model for HEWL has been developed by refinement of atomic coordinates and ADPs against the X-ray diffraction data of Wang and coworkers [Wang et al. (2007), Acta Cryst. D63, 1254-1268], while multipole parameters were fixed to the values for transferable multipole parameters from the ELMAM2 database [Domagala et al. (2012), Acta Cryst. A68, 337-351] . Static and dynamic electron densities based on this multipole model are presented. Analysis of their topological properties according to the QTAIM shows that the covalent bonds possess similar properties to the covalent bonds of small molecules. Hydrogen bonds of intermediate strength are identified for the Glu35 and Asp52 residues, which are considered to be essential parts of the active site of HEWL. Furthermore, a series of weak C-HÁ Á ÁO hydrogen bonds are identified by means of the existence of bond critical points (BCPs) in the multipole electron density. It is proposed that these weak interactions might be important for defining the tertiary structure and activity of HEWL. The deprotonated state of Glu35 prevents a distinction between the Phillips and Koshland mechanisms.

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Experimental Charge Density of α-Glycine at 23 K

Cited by 120 publications

References 45 publications

Dipole and quadrupole moments of molecules in crystals: A novel approach based on integration over Hirshfeld surfaces

Dipole and quadrupole moments of molecules in crystals: A novel approach based on integration over Hirshfeld surfaces

Dependence of the Intermolecular Electrostatic Interaction Energy on the Level of Theory and the Basis Set

The active site of hen egg-white lysozyme: flexibility and chemical bonding

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