The .gamma. turn: ab initio calculations on proline and N-acetylproline amide

Sapse, Anne‐Marie; Mallah-Levy, Lina; Daniels, Scott B.; Erickson, Bruce W.

doi:10.1021/ja00246a005

Cited by 59 publications

(36 citation statements)

References 4 publications

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“…This limits the conformational mobility of the N-H bond with respect to the carboxyl group, which is itself restricted in mobility by the pyrrolidine cycle [192]. This rigidity is one of the factors that determines the important role played by proline in the folding of proteins and peptides, where steric effects arising from the proline side chains help to determine the stabilities and positions of the protein folds [193]. It can also be expected to influence the way the molecule adsorbs and self-assembles at a metal surface.…”

Section: Prolinementioning

confidence: 99%

Adsorption and self-assembly of bio-organic molecules at model surfaces: A route towards increased complexity

Costa

Pradier

Tielens

et al. 2015

Surface Science Reports

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Understanding the bio-physical-chemical interactions at nanostructured biointerfaces and the assembling mechanisms of so-called hybrid nano-composites is nowadays a keyissue for nanoscience in view of the many possible applications foreseen. The contribution of surface science in this field is noteworthy since, using a bottom-up approach, it allows the investigation of the fundamental processes at the basis of complex interfacial phenomena and thus it helps to unravelthe elementary mechanisms governing them. Nowadays it is well demonstrated that a wide variety of different molecular assemblies can form upon adsorption of small biomolecules at surfaces. The geometry of such self-organized structures can often be tuned by a careful control of the experimental conditions during the deposition process. Indeed an impressive number of studies exist (both experimental and -to a lesser extendtheoretical), which demonstrate the ability of molecular self-assembly to create different structural motifs in a more or less predictable manner, by tuning the molecular building blocks as well as the metallic substrate. In this frame, amino acidsand small peptides at surfaces are key, basic, systems to be studied. The amino acidsstructure is simple enough to serve as a model for the chemisorption of biofunctional molecules, but their adsorption at surfaces has applications in surface functionalization, in enantiospecific catalysis, biosensing, nanoparticles shape control or in emerging fields such as "green" corrosion inhibition. In this paper we review the most recent advancements in this field. We will start from amino acids adsorption at metal surfaces and we will evolve then in the direction of more complex systems, in thelight of the latest improvements of surface science techniques and of computational methods. On one side, we will focus on amino acids adsorption at oxide surfaces, on the other on peptide adsorption both at metal and oxide substrates. Particular attention will be drawn to the added value provided by the combination of several experimental surface science techniques and to the precious contribution of advanced complementary computational methods to resolve the details of systems of increased complexity. Finally, some hints into experiments performed in the presence of water and then characterized in UHV and in the related theoretical work will be presented. This is a further step towards abetter approximation of real biological systems. However, since the methods employed are often not typical of surface science, this topic is not developed in details.2

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Section: Prolinementioning

confidence: 99%

Adsorption and self-assembly of bio-organic molecules at model surfaces: A route towards increased complexity

Costa

Pradier

Tielens

et al. 2015

Surface Science Reports

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“…[10] In the same study Reva et al [10] reported AM1 optimized geometries (resulting, unfortunately, in almost planar rings, similar to STO-3G and 6-31G RHF optimizations [14] ) and consequent relative energies, which all proved to be inadequate. The earliest ab initio study for proline, at the STO-3G and 6-31G restricted Hartree ± Fock (RHF) level, was performed by Sapse et al [14] This study used severe model restrictions, including the assumption of bondlength and -angle equalities: Figure 1 for labeling of the atoms of Pro), which result in an almost planar pyrrolidine ring. The corresponding results [14] quickly became outdated.…”

Section: Introductionmentioning

confidence: 98%

“…The earliest ab initio study for proline, at the STO-3G and 6-31G restricted Hartree ± Fock (RHF) level, was performed by Sapse et al [14] This study used severe model restrictions, including the assumption of bondlength and -angle equalities: Figure 1 for labeling of the atoms of Pro), which result in an almost planar pyrrolidine ring. The corresponding results [14] quickly became outdated. With the rapid development of computer resources several more elaborate theoretical investigations followed: Ramek et al [12] located ten distinct conformers of Pro at the 6-311G** RHF level and determined reaction paths and potential barriers connecting stationary points on the PES of Pro; Csa ¬ sza ¬ r et al [15] reported structural results for 12 conformers of neutral proline, including relative energies obtained at correlated levels of electronic structure theory; and Stepanian et al [17] determined 15 stable minima on the PES of Pro using density functional theory (DFT) and reassigned the vibrational spectra of unionized proline obtained from matrix-isolation IR spectroscopy.…”

Section: Introductionmentioning

confidence: 99%

Conformers of Gaseous Proline

Czinki

Császár

2003

Chemistry A European J

105

100

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Accurate geometries, relative energies, rotational and quartic centrifugal distortion constants, dipole moments, harmonic vibrational frequencies, and infrared intensities were determined from ab initio electronic structure calculations for eighteen conformers of the neutral form of the amino acid L-proline. Only four conformers have notable population at low and moderate temperature. The second most stable conformer is only 2+/-2 kJ mol(-1) above the global minimum, while the third and fourth conformers are nearly degenerate and have an excess energy of 7+/-2 kJ mol(-1) relative to the global minimum. All four conformers have one hydrogen bond: N.HO in the lower energy pair of conformers, and NH.O in the higher energy pair of conformers. The conformer pairs differ only in their ring puckering. The relative energies of the conformers include corrections for valence electron correlation, extrapolated to the complete basis set limit, as well as core correlation and relativistic effects. Structural features of the pyrrolidine ring of proline are discussed by using the concept of pseudorotation. The accurate rotational and quartic centrifugal distortion constants as well as the vibrational frequencies and infrared intensities should aid identification and characterization of the conformers of L-proline by rotational and vibrational spectroscopy, respectively. Bonding features of L-proline, especially intramolecular hydrogen bonds, were investigated by the atoms-in-molecules (AIM) technique.

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“…The pyrrolidine ring in proline was calculated to be almost planar at the RHF level with the STO-3G and 6-31G basis sets [34]. while, more elaborate electronic-structure results, especially those employing polarization functions in the basis set [35], show that the ring is considerably puckered in all conformers.…”

Section: Discussionmentioning

confidence: 98%

“…The structural features of pro and its derivatives have been studied by experimental techniques )X-ray crystallography [13][14][15], NMR [16], and IR [17,18] spectroscopy( and theretical molecular mechanics [15,19], perturbed configuration interaction with localized orbitals (PCILO) [20] and ab initio [19,[21][22][23][24] calculations.…”

Section: Introductionmentioning

confidence: 99%

Potential Energy Surface (PES) Scan of Gas-Phase L-Proline

Guerdaoui

Kahoui

Bourjila

et al. 2014

ILCPA

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We performed here a systematic ab initio calculations on neutral gas-phase L-proline. A total of 8 local minima were located by geometry optimization of the trial structures using density functional theory (DFT) with B3LYP three parameter hybrid potential coupled with the 6-31G)d( basis set. The absolute minimum obtained will be subject to a rigid potential energy surface (PES) scan by rotating its carboxylic group using the same method with more accurate basis set B3LYP/6-311++G(d,p), to get a deeper idea about its conformational stability. The main aim of the present work was the study of the rigidity of the L-proline structure and the puckering of its pyrrolidine ring.

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The .gamma. turn: ab initio calculations on proline and N-acetylproline amide

Cited by 59 publications

References 4 publications

Adsorption and self-assembly of bio-organic molecules at model surfaces: A route towards increased complexity

Adsorption and self-assembly of bio-organic molecules at model surfaces: A route towards increased complexity

Conformers of Gaseous Proline

Potential Energy Surface (PES) Scan of Gas-Phase L-Proline

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