Theoretical studies on the stability of N-methylformamide in both liquid and gas phases

Cordeiro, João Manuel Marques; Cordeiro, Maria A. M.; Bosso, Antônio R.S.A.; Politi, José R. S.

doi:10.1016/j.cplett.2006.02.102

Cited by 19 publications

(6 citation statements)

References 23 publications

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“…The competition between intramolecular and intermolecular hydrogen bonds plays an important role in determining the energy landscape of alanine dipeptide (AD). − Thus, while in the gas phase cyclic structures forming intramolecular hydrogen bonds are found to be more stable, in particular C7 eq and C5 (β strand), in aqueous solution there is a destabilization of C7 eq in favor of PPII as it permits a better interaction with the solvent molecules. The same trend has been found in N -methylformamide, another molecule used as a model for the peptide bond. − As a consequence, simplified solvent models (dielectric continuum, Langevin dipoles, etc.) that neglect specific interactions seem, a priori, not to be adequate for this type of studies.…”

Section: Introductionmentioning

confidence: 99%

Conformational Changes of the Alanine Dipeptide in Water–Ethanol Binary Mixtures

Almeida

Cordeiro

Martı́n

et al. 2016

J. Chem. Theory Comput.

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Experimental work developed in the last years has evidenced the capacity of alcohols and polyalcohols to modify the energy landscape of peptides and proteins. However, the mechanism underlying this effect is not clear. Taking as a model system the alanine dipeptide (AD) we perform a QM/MM study in water, ethanol, and a 40-60% in volume water-ethanol mixture. The AD molecule was described at the MP2/aug-cc-pVDZ level. In polar solution, only αR and PPII conformers contribute in an appreciable way to the conformational equilibrium. The final in solution αR-PPII free energy difference is determined from the interplay between the internal energy of the dipeptide and the solute-solvent interaction free energy. Internal energy favors the formation of PPII, whereas, on the contrary, solute-solvent interaction is favorable to αR, so any factor that decreases the solute-solvent interaction free energy will increase the PPII population. The addition of ethanol increases the stability of the PPII conformer. Our results point to the presence of preferential solvation in this system, the composition of the first solvation shell in the binary mixture being dominated by water molecules. Remarkably, this fact does not affect the differential conformational stability that is controlled by long-range interactions. From the analysis of solvent density maps it is concluded that, in the water-ethanol mixture, ethanol molecules are more likely found around the alanine side chain and the carbonyl group, but while in PPII ethanol molecules interact mainly with the carbonyl group of the N-terminal end, in C5 the interaction is with the carbonyl group of the C-terminal end. In αR, ethanol interacts with both carbonyl groups.

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Section: Introductionmentioning

confidence: 99%

Conformational Changes of the Alanine Dipeptide in Water–Ethanol Binary Mixtures

Almeida

Cordeiro

Martı́n

et al. 2016

J. Chem. Theory Comput.

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“…In addition, DMSO can also work as cryo-protectant3132, cell fusogen333435, cell differentiation inducer3637, and membrane/skin permeation enhancer. To this end, the self-association structures of both NMF and NMA have common hydrogen bonds in the form of N−H···O = C, the same as in proteins3839. Studies on the interaction between DMSO and amides indicated that this aprotic solvent can break the N−H···O = C hydrogen bond between amide molecules by forming stronger N−H···O = S hydrogen bond404142.…”

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confidence: 99%

Evidences for Cooperative Resonance-Assisted Hydrogen Bonds in Protein Secondary Structure Analogs

Zhou

Deng

Zheng

et al. 2016

Sci Rep

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Cooperative behaviors of the hydrogen bonding networks in proteins have been discovered for a long time. The structural origin of this cooperativity, however, is still under debate. Here we report a new investigation combining excess infrared spectroscopy and density functional theory calculation on peptide analogs, represented by N-methylformamide (NMF) and N-methylacetamide (NMA). Interestingly, addition of the strong hydrogen bond acceptor, dimethyl sulfoxide, to the pure analogs caused opposite effects, namely red- and blue-shift of the N−H stretching infrared absorption in NMF and NMA, respectively. The contradiction can be reconciled by the marked lowering of the energy levels of the self-associates between NMA molecules due to a cooperative effect of the hydrogen bonds. On the contrary, NMF molecules cannot form long-chain cooperative hydrogen bonds because they tend to form dimers. Even more interestingly, we found excellent linear relationships between changes on bond orders of N−H/N−C/C = O and the hydrogen bond energy gains upon the formation of hydrogen bonding multimers in NMA, suggesting strongly that the cooperativity originates from resonance-assisted hydrogen bonds. Our findings provide insights on the structures of proteins and may also shed lights on the rational design of novel molecular recognition systems.

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“…Trans-NMF is more stable than cis-NMF, and is dominant at normal conditions [46,47]. The energy difference between trans-NMF and cis-NMF has been reported in literature to be between 4.2 and 7.87 kJ/mol [15,20,21,46]. Optimized geometry energies performed at the considered DFT calculation for the two isolated trans and cis isomers and hydrogen bonded NMF-(H 2 O) 2,3 complexes in this work are presented in Table 1.…”

Section: Resultsmentioning

confidence: 99%

“…1. The methyl and carbonyl moieties can adopt two configurations in NMF, trans-NMF and cis-NMF (trans and cis refer to the orientation of C@O and NAH bonds with respect to the CAN bond), [15,20,21,23] as shown in Fig. 1a and b, respectively.…”

Section: Resultsmentioning

confidence: 99%

“…In addition, classical ensemble treatments, such as molecular dynamics simulations [16] and Monte Carlo statistical investigations [17][18][19] have been performed for NMF. The pure liquid and aqueous solutions of NMF have been the subject of studies in recent years, both theoretically [20][21][22][23][24][25][26][27][28][29] and experimentally [30][31][32][33]. A structural investigation of liquid NMF by X-ray scattering at 298 K found that the hydrogen bond network occurs in NMF between C@O and NAH groups, which contributes to the origin of its unusual dielectric and thermodynamics properties [33].…”

Section: Introductionmentioning

confidence: 98%

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Intermolecular hydrogen bonding of N-methylformamide in aqueous environment: A theoretical study

Wang

Guo

Wei

et al. 2014

Computational and Theoretical Chemistry

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Theoretical studies on the stability of N-methylformamide in both liquid and gas phases

Cited by 19 publications

References 23 publications

Conformational Changes of the Alanine Dipeptide in Water–Ethanol Binary Mixtures

Conformational Changes of the Alanine Dipeptide in Water–Ethanol Binary Mixtures

Evidences for Cooperative Resonance-Assisted Hydrogen Bonds in Protein Secondary Structure Analogs

Intermolecular hydrogen bonding of N-methylformamide in aqueous environment: A theoretical study

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