Density functional theory modeling and calculation of NMR parameters: An ab initio study of the polymorphs of bulk glycine (original) (raw)
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Journal of Molecular Structure, 1989
I3C NMR spectra of a variety of polypeptides containing I3C-enriched [l-13C]glycine [(Gly*)] residue as a minor component (<8%) in the solid state were recorded, in order to obtain the 13C chemical shifts of isotropic averaging and the principal values of chemical shift tensors (ull, u22, and u33) of glycine carbonyl carbon (Gly CO), taking antiparallel @-sheet, 31-helix, a-helix, and w-helix forms. The latter two conformations are achieved only when Gly residues are incorporated into the homoplypeptides, taking the respective conformations. It was found that the isotropic Gly CO chemical shifts are significantly displaced depending on conformational change. We also found that the magnitudes of displacements of chemical shifts upon conformational changes are larger for u2* and u33 than the isotropic chemical shift values, while ull is almost unchanged upon any conformational changes.
The role of explicit solvent molecules in the calculation of NMR chemical shifts of glycine in water
Theoretical Chemistry Accounts, 2018
We present the results of a computational study of the NMR properties of glycine in water solution at the level of density functional theory employing the B3LYP functional and the 6-31G(d,p) and pcSseg-2 basis sets, describing the solvent either via the PCM continuous solvation model or PCM with additional explicit water molecules hydrogen bonded to the solute. We observe that the solvent causes considerable changes in the predicted magnetic shieldings and that the results depend significantly on the number of solvent molecules included in the quantum mechanical treatment. Keywords Chemical shift • PCM • pcSseg-2 basis sets 1 Introduction Amino acids are some of the fundamental bricks of life carrying out much of the functions in cells and therefore in living organisms. Glycine, in particular,
Journal of Molecular Structure, 1991
CP-MAS and CP-static lSN NMR spectra were measured for a variety of solid oligopeptides containing the glycine residue, the crystal structures of which had already been determined by Xray diffraction. From the results of the observed 15N chemical shifts, it was found that the isotropic ~SN chemical shifts (a~o) of the glycine residues move downfield with a decrease of hydrogen bond length (RN...o) between the nitrogen and oxygen atoms in the amide groups, and that the principal value of aa3 moves linearly downfield with a decrease of RN...o. There is no relationship between the principal value of a~l or a22 and R N. --o" This indicates that such a linear downfield shift of a33 contributes predominantly to the downfield shift of a~o. Quantum chemical calculations of the ~SN shielding constant for the model compounds were carried out by the FPT-INDO method, and the relationship between lSN chemical shift and RN...o discussed.
1998
NGUYEN ET AL. amine group, presents a distinct challenge. The relative energy of this conformer is extremely sensitive to the basis set, the level of correlation, or the functional used. The widely used BP86, PP86, and BP91 nonlocal functionals overestimate the strength of the hydrogen bond and predict that this conformer is the lowest energy structure. This contradicts both experiment and high-level post-Ž. Hartree᎐Fock studies. The adiabatic connection method ACM and the BLYP functional yield the correct order. The ACM method, in particular, gives energies which are in reasonable agreement with MP2, although these are somewhat low as compared with experiment. Based on this study, ACM should perform well for this type of bioorganic application, with typical errors of a few tenths of a kilocaloriermole and only rarely exceeding 0.5 kcalrmol.
Journal of Chemical Theory and Computation, 2013
A state-of-the-art computational strategy for the evaluation of accurate molecular structures as well as thermodynamic and spectroscopic properties along with the direct simulation of infrared (IR) and Raman spectra is established, validated (on the basis of the experimental data available for the Ip glycine conformer) and then used to provide a reliable and accurate characterization of the elusive IVn/gtt and IIIp/tct glycine conformers. The integrated theoretical model proposed is based on accurate post-Hartree−Fock computations (involving composite schemes) of energies, structures, properties, and harmonic force fields coupled to DFT corrections for the proper inclusion of vibrational effects at an anharmonic level (as provided by general second-order perturbative approach). It is shown that the approach presented here allows the evaluation of structural, thermodynamic, and spectroscopic properties with an overall accuracy of about, or better than, 0.001 Å, 20 MHz, 1 kJ·mol −1 , and 10 cm −1 for bond distances, rotational constants, conformational enthalpies, and vibrational frequencies, respectively. The high accuracy of the computational results allows one to support and complement experimental studies, thus providing (i) an unequivocal identification of several conformers concomitantly present in the experimental mixture and (ii) data not available or difficult to experimentally derive.
Journal of Molecular Structure, 1990
i5N NMR spectra of a variety of solid oligopeptides (X-Gly-Gly) containing glycine residues have been measured, of which the crystal structures had already been determined by X-ray diffraction. The experimental 15N chemical shifts of the glycine residues were plotted against the N. --0 hydrogen bond length and the N-H bond length in the >C=O* --H-N< type hydrogen bond form, respectively. It was found that the decrease of the N-H bond length leads to a linear increase in i5N shielding, but there is no clear relationship between the i5N chemical shifts and the N* * -0 separation. Further, i5N chemical shift calculations were carried out using a model compound, by the FPT-INDO method, in order to further understand the nature of the hydrogen bond. The calculated results reasonably explain the experimental ones.
Journal of Mass Spectrometry, 2005
A new modification of pulsed-ionization high-pressure mass spectrometry (PHPMS) has been used to perform equilibrium thermochemical studies for relatively nonvolatile biomolecules such as amino acids. Binding enthalpy and entropy changes have been measured for proton-bound clusters of glycine, which are in good agreement with both theoretical (DFT) results of this work and a previous blackbody infrared dissociation experiment. Experimental data indicate that a number of conformers of the proton-bound dimer of glycine may coexist in the explored temperature range (360-460 K). Several new, conceptually different isomers (two of them zwitterionic) have been found by DFT calculations, one of which is 7 kJ mol −1 lower in energy than the structure previously reported to be the energy minimum.
Physical Chemistry Chemical Physics, 2013
The structures, relative stabilities, and infrared spectra of the six low-energy conformers of glycine have been characterized using a state-of-the-art quantum-mechanical approach allowing the bond distances, conformational enthalpies and vibrational frequencies to be determined well within the chemical accuracy. Transition state structures governing interconversion among the different energy minima have also been characterized. In detail, the gas-phase thermodynamic properties (at 15 K and 410 K) of the glycine conformers considered have been obtained with a 1 kJ mol À1 accuracy, and it has been shown that the employment of DFT geometries usually reduces such accuracy by at most 0.1 kJ mol À1 .
A density functional theory study of the hydrogen bond interactions in glycine dimers
Chemical Physics Letters, 2007
Crystal structures are usually described in geometric terms. However, it is the energetics of intermolecular interactions that determine the chemical and physical properties of molecular materials. 1 In this paper, we use density functional theory (DFT) in combination with numerical basis sets to analyze the hydrogen bonding interactions in a family of novel ionic molecular materials. We find that the calculated binding energies are consistent with those of other ionic hydrogen bonded systems. We also examine electron density distributions for the systems of interest to gain insight into the nature of the hydrogen bonding interaction and investigate the effects of different aspects of the crystal field on the geometry of the hydrogen bond.
15N NMR spectroscopy 14. Neighboring residue effects in glycine-containing polypeptides
1979
Gly-Gly), were synthesized by known methods, and their natural abundance "N NMR spectra were measured in trifluoroacetic acid. These spectra were compared with those of other previously described sequence polypeptides and with the corresponding homopolypeptides. The spectra of all sequence polypeptides exhibit neighboring residue effects, so that glycine nitrogen atoms acylated by other 2-(or w-)amino acids have chemical shifts different from that of the Gly-Gly bond. These neighboring residue effects cannot be summarized or explained by simple rules; however, they are useful for the characterization ofcopolypeptides. Such an application was tested in the case of four sequence polypeptides consisting of isomeric sequences of identical monomeric units. All isomeric sequences can be distinguished from each other, and the observed shift effects could be related to the neighboring residue effects of other copolypeptides.