Theoretical Study on the Properties of Linear and Cyclic Amides in Gas Phase and Water Solution

Aparicio-Martinez, Santiago; Kr, Hall; Pb, Balbuena

doi:10.1021/jp0611166

Cited by 11 publications

(13 citation statements)

References 45 publications

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“…The cis‐trans isomerization of the peptide band is crucial factor that influences three‐dimensional structure of proteins and peptides, and thus it maintains to be highly discussed topic 39–48. Secondary amides are known to occur predominantly in a trans configuration in peptides and proteins 49, 50.…”

Section: Resultsmentioning

confidence: 99%

The cis‐trans isomerization of N‐methyl‐α,β‐dehydroamino acids

et al. 2012

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Dehydroamino acids with the methylated N-terminal peptide group occur in natural small cyclic peptides. The structural analysis was used to investigate the cis-trans isomerization of the N-terminal tertiary amide group of diamides: Ac-(Z)-Δ(Me)Abu-NHMe (1), Ac-(Z)-Δ(Me)Phe-NHMe (2), Ac-(E)-Δ(Me)Phe-NHMe (3), Ac-Δ(Me)Ala-NHMe (4), and Ac-(Me)Ala-NHMe (5). The compounds were analyzed in the solid state by an X-ray crystallography (1-3), and in the solution by FTIR (MeCN and CHCl(3) ) and NMR (DMSO-d6 and CDCl(3) ) methods (1-5). In the solid state, the studied compounds adopt the cis configuration of N-terminal amide. In solution, this configuration also prevails for the dehydroamino acids 1-4, in contrast to the saturated analog 5. The results indicate that N-methyldehydroamino acids present a promising tool to induce the cis configuration of the amide bond.

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Section: Resultsmentioning

confidence: 99%

The cis‐trans isomerization of N‐methyl‐α,β‐dehydroamino acids

et al. 2012

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“…Putting a water molecule in the vicinity of these hydrogen bond donors and acceptors, results in 3 conformations for each monomer: aa_a , aa_b , aa_c and maa_a , maa_b , maa_c , see Figure and Table . Both static and dynamic studies on the solvation of acrylamide in water, performed by Balbuena et.al., , show that the acrylamide carbonyl oxygen coordinates with water hydrogen and that the bridge-type interactions aa_a and maa_a are the most stable. These findings are confirmed here for various electronic structure methods.…”

Section: Resultsmentioning

confidence: 99%

“…An acrylamide-derived monomer such as NIPAM is one of the most studied monomers as a result of its peculiar lower critical solution behavior. Several studies on the solvation of acrylamide have shown that acrylamide exists as a hydrogen-bonded complex with one or more water molecules. , This interaction will certainly play a role in the behavior of the reacting monomers and should be incorporated in the molecular model in order to completely account for them in the evaluation of the propagation reaction rate coefficients. An other aspect of acrylamide solvation is the result of the presence of the hydrophobic vinyl bond.…”

Section: Introductionmentioning

confidence: 99%

Solvent Effects on Free Radical Polymerization Reactions: The Influence of Water on the Propagation Rate of Acrylamide and Methacrylamide

et al. 2009

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The polymerization of acrylamide (AA) and methacrylamide (MAA) was studied by an extensive set of computational methods with a particular focus on the possible influence of water molecules on the propagation reaction. An extensive set of electronic structure methods was tested, consisting of B3LYP, BMK, MPWB1K, MP2, and B2-PLYP of which some include dispersion effects. The effect of water on the transition state is modeled in two different ways. Explicit water molecules are added to the system, showing that replacing the hydrogen bond that dominates the transition state structure by a water-mediated hydrogen bond, results in more stable, more feasible transition states. This effect is the largest for AA polymerization, a monomer that is known to experience a larger solvent effect than MAA. Additionally, a conductor-like polarizable continuum model (C-PCM) is applied on both the transition states in gas phase and the ones bearing explicit water molecules. This model has a dramatic effect on all the propagation rates, raising them by about 3 orders of magnitude. The inclusion of explicit water molecules gives insight into the role of water molecules and the formation of prereactive complexes. The relative rate of polymerization of AA with regard to MAA is well reproduced for a trimeric propagating radical with inclusion of explicit water molecules or by using an implicit solvation model at the BMK and MPWB1K level of theory.

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“…The interesting structural and conformational problems presented by the two N-vinylamides motivated the present MW research, which has been augmented with quantum chemical calculations performed at a much higher level of theory than previously employed 42 to obtain information that could be useful for the assignment of the MW spectra and for investigating properties of the potential energy hypersurface. ■ RESULTS AND DISCUSSION ■ EXPERIMENTAL SECTION Compound and MW Experiment.…”

Section: ■ Introductionmentioning

confidence: 99%

Microwave Spectra, Planarity, and Conformational Preferences of cis- and trans-N-Vinylformamide

Møllendal

Samdal

2012

J. Phys. Chem. A

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The microwave spectra of a mixture of cis- and trans-H-N-C-O forms of N-vinylformamide, (H(2)C═CHNHC(═O)H), have been measured at room temperature in the 18-75 GHz spectral range. The spectra of two forms were assigned. The first of these forms has a cis arrangement for the H-N-C-O chain of atoms, whereas the second form has a trans arrangement. The C-C-N-C chain of atoms is antiperiplanar (180°) in both forms. The inertial defect of the ground vibrational state of cis is -0.142(5) × 10(-20) u m(2), whereas this parameter is -0.087098(26) × 10(-20) u m(2) for trans. It is concluded that the equilibrium structures of both cis and trans are completely planar. The dipole moment determined from Stark effect measurements is μ(a) = 9.96(8), μ(b) = 2.22(3), μ(c) = 0 (by symmetry), and μ(tot) = 10.20(8) × 10(-30) C m [3.06(2) D], for cis, and μ(a) = 7.64(16), μ(b) = 9.24(10), μ(c) = 0 (by symmetry), and μ(tot) = 12.0(2) × 10(-30) C m [3.59(5) D] for trans. The spectrum of one vibrationally excited state, presumably the first excited state of the torsion about the C-N bond of cis, was assigned and the frequency of this state was determined to be 76(15) cm(-1) by relative intensity measurements. The spectra of two vibrationally excited states of trans were assigned. These states are assumed to be the first excited state of the torsion about the C-N bond, and a low bending vibration. Relative intensity measurements yielded 101(20) and ca. 300 cm(-1), respectively, for the frequencies of these normal vibrations. Accurate values of the quartic centrifugal distortion constants, the dipole moments, and the vibration-rotation constants have been obtained for both cis and trans. The experimental work has been augmented by high-level quantum chemical calculations at the B3LYP/cc-pVTZ and CCSD(T)/cc-pVTZ levels of theory. The theoretical calculation performed without symmetry restrictions correctly predict that cis and trans are both planar. The CCSD(T) rotational constants are in excellent agreement with their experimental counterparts, whereas the B3LYP quartic centrifugal distortion constants and the vibration-rotation constants are in fairly good agreement with experiments. The CCSD(T) dipole moments deviate more than expected from the experimental dipole moments. It is estimated that further conformers of cis and trans must be at least 4 kJ/mol higher in energy.

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Theoretical Study on the Properties of Linear and Cyclic Amides in Gas Phase and Water Solution

Cited by 11 publications

References 45 publications

The cis‐trans isomerization of N‐methyl‐α,β‐dehydroamino acids

The cis‐trans isomerization of N‐methyl‐α,β‐dehydroamino acids

Solvent Effects on Free Radical Polymerization Reactions: The Influence of Water on the Propagation Rate of Acrylamide and Methacrylamide

Microwave Spectra, Planarity, and Conformational Preferences of cis- and trans-N-Vinylformamide

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