A neutron diffraction study of the structure of L-glutamic acid.HCl

Pressure-induced phase transitions in DL-glutamic acid monohydrate crystal

DL-glutamic acid monohydrate crystal was synthesized from an aqueous solution by slow evaporation technique. The crystal was submitted to high-pressure (1 atm-14.3 GPa) to investigate its vibrational behavior and the occurrence of phase transitions. We performed Raman spectroscopy as probe and through the analysis of the spectra we discovered three structural phase transitions. The first one occurs around 0.9 GPa. In this phase transition, glutamic acid molecules suffer modifications in their conformations while water molecules are less affected. The second phase transition at 4.8 GPa involves conformational changes related to CO₂^-, NH₃⁺ units and the water molecules, while the third one, between 10.9 and 12.4 GPa, involves motions of several parts of the glutamic acid as well as the water molecules. Considering the dynamic of high pressure, the second phase of DL-glutamic acid monohydrate crystal presented a better stability compared with the second phase of its polymorphs α and β L-glutamic acid. In addition, water molecules seem to play important role on this structural stability. All changes are reversible.

Intermolecular hydrogen bond energies in crystals evaluated using electron density properties: DFT computations with periodic boundary conditions

The hydrogen bond (H-bond) energies are evaluated for 18 molecular crystals with 28 moderate and strong O-H···O bonds using the approaches based on the electron density properties, which are derived from the B3LYP/6-311G** calculations with periodic boundary conditions. The approaches considered explore linear relationships between the local electronic kinetic G(b) and potential V(b) densities at the H···O bond critical point and the H-bond energy E(HB). Comparison of the computed E(HB) values with the experimental data and enthalpies evaluated using the empirical correlation of spectral and thermodynamic parameters (Iogansen, Spectrochim. Acta Part A 1999, 55, 1585) enables to estimate the accuracy and applicability limits of the approaches used. The V(b)-E(HB) approach overestimates the energy of moderate H-bonds (E(HB) < 60 kJ/mol) by ~20% and gives unreliably high energies for crystals with strong H-bonds. On the other hand, the G(b)-E(HB) approach affords reliable results for the crystals under consideration. The linear relationship between G(b) and E(HB) is basis set superposition error (BSSE) free and allows to estimate the H-bond energy without computing it by means of the supramolecular approach. Therefore, for the evaluation of H-bond energies in molecular crystals, the G(b) value can be recommended to be obtained from both density functional theory (DFT) computations with periodic boundary conditions and precise X-ray diffraction experiments.

A solid-state 35/37Cl NMR study of a chloride ion receptor and a GIPAW-DFT study of chlorine NMR interaction tensors in organic hydrochlorides

The results of a 35/37Cl solid-state nuclear magnetic resonance (SSNMR) study of the 1-butyl-3-methylimidazolium chloride complex of meso-octamethylcalix[4]pyrrole (1) are reported. Line shapes obtained from magic-angle-spinning and stationary powder samples collected at 9.4 and 21.1 T are analyzed to provide the 35/37Cl quadrupolar tensor and chemical shift (CS) tensor and their relative orientation. The relatively high symmetry of the chloride ion coordination environment is manifested in the small value of the quadrupole coupling constant, CQ(35Cl) = 1.0 MHz. The isotropic chemical shift of 120 ppm (with respect to NaCl(s)) is at the upper edge of the typical range seen for organic hydrochlorides. Consideration of chemical shift anisotropy (span, Ω = 50 ppm) and non-coincidence of the quadrupolar and CS tensors were essential to properly simulate the experimental spectra. The utility of gauge-including projector-augmented wave density functional theory (GIPAW-DFT) calculations of chlorine quadrupolar and CS tensors in organic chlorides was explored by validation against available benchmark experimental data for solid amino acid hydrochlorides. The calculations are shown to systematically overestimate the value of the 35Cl quadrupole coupling constant. Additional calculations on various hydrated and solvated models of 1 are consistent with a structure in which solvent and water of hydration are absent.

Crystal structure of l-leucine nitrate

l-leucine nitrate, C6H14NO2 + · NO3 −, M = 194.187, triclinic, P1, a = 5.662(6), b = 8.445(4), c = 10.867(6) Å, α = 75.79(4), β = 95.45(6), γ = 99.82(6)°, V = 495.57 Å3, Dm = 1.307 gm/cc (flotation), Dc = 1.301 gm/cc, Z = 2, μ = 1.06 cm−1, λ (MoKα) = 0.71073 Å, F(000) = 208, T = 293 K.

The structure was solved by direct, Fourier and difference Fourier methods, refined to R = 0.045 and wR = 0.050 for 1934 observed reflections with intensity greater than 3σ(I). Since the structure has a pseudo 21-axis parallel to the a-axis, all the hydrogen atoms were located by geometric consideration and fixed at their calculated positions. The pseudo-symmetry is present even at the final stage of refinement. All available hydrogen atoms are involved in hydrogen bonding.

l-Glutamic acid hydro-chloride at 153 K

THE TITLE COMPOUND [SYSTEMATIC NAME: (S)-1,3-dicarboxy-propanaminium chloride], C(5)H(10)NO(4) (+)·Cl(-), has been investigated previously by Dawson [Acta Cryst. (1953). 6, 81-83], with R = 0.106 and without the location of H atoms, and then by Sequeira, Rajagopal & Chidambaram [Acta Cryst. (1972). B28, 2514-2519] using neutron diffraction with R = 0.043. The present determination at 153 K has R = 0.017 and all the H atoms are located. There are obvious differences in some C-C bond lengths between the present and previous studies. In the present structure, l-glutamic acid is protonated and is linked to the Cl(-) anion by an O-H⋯Cl hydrogen bond. The crystal structure is established by a three-dimensional network of O-H⋯O, N-H⋯O and N-H⋯Cl hydrogen bonds.

QTAIM study of strong H-bonds with the O-H...a fragment (A=O, N) in three-dimensional periodical crystals

The relationship between the d(H...A) distance (A=O, N) and the topological properties at the H...A bond critical point of 37 strong (short) hydrogen bonds occurring in 26 molecular crystals are analyzed using the quantum theory of atoms in molecules (QTAIM). Ground-state wave functions of the three-dimensional periodical structures representing the accurate experimental geometries calculated at the B3LYP/6-31G** level of approximation were used to obtain the QTAIM electron density characteristics. The use of an electron-correlated method allowed us to reach the quantitatively correct values of electron density rhob at the H...A bond critical point. However, quite significant differences can appear for small absolute values of the Laplacian (<0.5 au). The difference between the H...O and H...N interactions is described using the rhob versus d(H...A) dependence. It is demonstrated that the values of parameters in this dependence are defined by the nature of the heavy atom forming the H...A bond. An intermediate (or transit) region separating the shared and closed-shell interactions is observed for the H-bonded crystals in which the bridging proton can move from one heavy atom to another. The crystalline environment changes the location of the bridging proton in strong H-bonded systems; however, the d(O-H)/d(H...O) ratio is approximately the same for both the gas-phase complexes and molecular crystals with a linear or near-linear O-H...O bond.

Chlorine-35/37 NMR Spectroscopy of Solid Amino Acid Hydrochlorides: Refinement of Hydrogen-Bonded Proton Positions Using Experiment and Theory

Trends in the chlorine chemical shift (CS) tensors of amino acid hydrochlorides are investigated in the context of new data obtained at 21.1 T and extensive quantum chemical calculations. The analysis of chlorine-35/37 NMR spectra of solid L-tryptophan hydrochloride obtained at two magnetic field strengths yields the chlorine electric field gradient (EFG) and CS tensors, and their relative orientations. The chlorine CS tensor is also determined for the first time for DL-arginine hydrochloride monohydrate. The drastic influence of 1H decoupling at 21.1 T on the spectral features of salts with particularly small 35Cl quadrupolar coupling constants (CQ) is demonstrated. The chlorine CS tensor spans (Omega) of hydrochloride salts of hydrophobic amino acids are found to be larger than those for salts of hydrophilic amino acids. A new combined experimental-theoretical procedure is described in which quantum chemical geometry optimizations of hydrogen-bonded proton positions around the chloride ions in a series of amino acid hydrochlorides are cross-validated against the experimental chlorine EFG and CS tensor data. The conclusion is reached that the relatively computationally inexpensive B3LYP/3-21G* method provides proton positions which are suitable for subsequent higher-level calculations of the chlorine EFG tensors. The computed value of is less sensitive to the proton positions. Following this cross-validation procedure, /CQ(35Cl)/ is generally predicted within 15% of the experimental value for a range of HCl salts. The results suggest the applicability of chlorine NMR interaction tensors in the refinement of proton positions in structurally similar compounds, e.g., chloride ion channels, for which neutron diffraction data are unavailable.

Solid-State 35/37Cl NMR Spectroscopy of Hydrochloride Salts of Amino Acids Implicated in Chloride Ion Transport Channel Selectivity: Opportunities at 900 MHz

The results of a detailed systematic chlorine solid-state NMR study of several hydrochloride salts of amino acids implicated in chloride ion transport channel selectivity are reported. (35)Cl and (37)Cl NMR spectra have been obtained for stationary and/or magic-angle spinning powdered samples of the following compounds on 500 and/or 900 MHz spectrometers: DL-arginine HCl monohydrate, L-lysine HCl, L-serine HCl, L-glutamic acid HCl, L-proline HCl, L-isoleucine HCl, L-valine HCl, L-phenylalanine HCl, and glycine HCl. Spectral analyses provide information on the anisotropic properties and relative orientations of the chlorine electric field gradient and chemical shift (CS) tensors, which are intimately related to the local molecular and electronic structure. Data obtained at 900 MHz provide unique examples of the effects of CS anisotropy on the NMR spectrum of a quadrupolar nucleus. The range of chlorine quadrupolar coupling constants (C(Q)) measured, -6.42 to 2.03 MHz, demonstrates the sensitivity of this parameter to the chloride ion environment and suggests the applicability of chlorine solid-state NMR as a novel experimental tool for defining chloride binding environments in larger ion channel systems. Salts of hydrophobic amino acids are observed to tend to exhibit larger values of C(Q) than salts of hydrophilic amino acids. A simple model for rationalizing the observed trend in C(Q) is proposed. For salts for which neutron diffraction structures are available, we identify a quantum chemical method which reproduces experimental values of C(Q) with a root-mean-square deviation of 0.1 MHz and a correlation coefficient of 0.9998. On the basis of this, chlorine NMR tensors are predicted for the Cl(-) binding site in ClC channels.

A review of oxygen-17 solid-state NMR of organic materials--towards biological applications

17O solid state NMR of organic materials is developing rapidly. This article provides a snapshot of the current state of development of this field. The NMR techniques and enrichment protocols that are driving this progress are outlined. The (17)O parameters derived from solid-state NMR experiments are summarized and the structural sensitivity of the approach to effects such as hydrogen bonding highlighted. The prospects and challenges for (17)O solid-state NMR of biomolecules are discussed.

Two-dimensional (17)O multiple quantum magic-angle spinning NMR of organic solids

We report two-dimensional (2D) (17)O multiple-quantum magic-angle spinning (MQMAS) NMR spectra for four (17)O-labeled organic compounds: [(17)O(2)]-D-alanine (1), potassium hydrogen [(17)O(4)]dibenzoate (2), [(17)O(4)]-D,L-glutamic acid.HCl (3) and [2,4-(17)O(2)]uracil (4). The high spectral resolution observed in the 2D (17)O MQMAS NMR spectra allows extraction of precise (17)O NMR parameters for all crystallographically distinct oxygen sites. We demonstrate that rotor synchronization is important in obtaining high-quality (17)O MQMAS spectra for organic compounds. Several issues related to the potential of (17)O MQMAS NMR for large biomolecular systems are also discussed.

Strong hydrogen bonding interactions involving a buried glutamic acid in the transmembrane sequence of the neu/erbB-2 receptor

The receptor tyrosine kinase encoded by the neu/erbB-2 proto-oncogene is constitutively activated by a single valine to glutamic acid substitution at position 664 in the predicted membrane-spanning sequence of the receptor. We have explored the structural changes involved in receptor activation with polarized FTIR and magic angle spinning NMR spectroscopy. The hydrophobic transmembrane sequence folds into a well-defined alpha-helical structure spanning the membrane bilayer. Measurements of the pKa and 13C chemical shift anisotropy of Glu 664 reveal that the side chain carboxyl group is protonated and strongly hydrogen bonded. These studies provide direct evidence for glutamate hydrogen-bonding interactions in the mechanism of receptor dimerization and activation.

Amino acid side-chain populations in aqueous and saline solution: bis-penicillamine enkephalin

The potentials of mean force (pmfs) for rotation around the chi 1 aromatic side-chain dihedrals of the zwitterionic bis-penicillamine enkephalin pentapeptide have been determined in both aqueous and saline solution. These side chains are known to be associated with the pharmacophore and their conformational populations are thought to be critical for activity. It is found that the association between chloride ions and the peptide in saline solution simulations has profound effects on the relative energies of the g-, g+, and t conformations, and also the barriers between them. Using the pmfs we have also calculated the respective Boltzmann-weighted 3J alpha beta vicinal coupling constants. The agreement between the calculated and experimentally determined coupling constants is poor for the pmf in pure water, but substantially improved for the pmf determined in saline solution. Reasons for these differences appear to be related to the experimental conditions.

Representation of DNA sequences by use of helical wheels to identify pattern formation with protein binding potential

Similar to the protein segments with helical potential the three-dimensional structures of DNA sequences can be represented by a two-dimensional projection along the axis of the double helix. We will call this projection according to Schiffer and Edmundson "helical wheel". In the first place the wheels are employed here as graphical restatements of known sequences which represent binding sites of restriction-modification enzymes. Specific recognition of these sites has to be based on sequence related multi contact interactions of weak bonds. Because of the spatial and directional characteristics of H-bonds we will utilize the pattern formation of H-bond donor--and acceptor groups protruding into the major groove of the helix to identify the particular sequences. The characteristics of these patterns can be readily visualized and compared by examination of these wheels.

Hydrogen bonds in crystal structures of amino acids, peptides and related molecules

The results of a survey of 439 hydrogen bonds in 95 recently determined crystal structures of amino acids, peptides and related molecules suggest that the following generalizations hold true for linear (angle X-H---Y greater than 150 degrees) hydrogen bonds. (1) The charge on the acceptor group does not influence the length of a hydrogen bond. (2) For a given acceptor group, the hydrogen bond lengths increase in the order imidazolium N--H less than ammonium N-H less than guanidinium N-H; this order holds true for oxygen anion acceptor groups. Cl-ions and the uncharged oxygen of water molecules. (3) The uncharged imidazole N-H group forms shorter hydrogen than the amide N-H GROUP. (4) The carboxyl O-H groups form shorter hydrogen bonds than other hydroxyl groups. (5) The hydrogen bonds involving a halogen ion are longer than hydrogen bonds with other acceptors when corrected for their longer van der Walls radii. The observed differences between the lengths of hydrogen bonds formed by different donor and acceptor groups in amino acids and peptides, imply differences in the energetics of their formation.

The molecular and crystal structure of 2-imino-4-oxo-1,3-thiazolidine hydrochloride

The crystal structure of 2-imino-4-oxo-1,3-thiazolidine hydrochloride C3H5N2SOCl has been determined by x-ray diffraction methods by three-dimensional Patterson synthesis using heavy-atom method for solving the phase problem. The crystals are orthorhombic with space group Pbca – D 2h 15, having cell dimensions a = 9.53(1)Å, b = 17.61(5) Å, and c = 7.71(1) Å. There are eight molecules per unit cell giving a calculated density of 1.566 g · cm−3. The refinement by least-squares method with anisotropic temperature factors for non-hydrogen atoms led to a final R value of 12.3% for 706 reflections. Excepting chlorine the molecule is planar. Bond lengths and bond angles are calculated and discussed.