ChemInform Abstract: Conformations and Relative Stabilities of the cis and trans Isomers in a Series of Isolated N‐Phenylamides

Manea, Victoria P.; Wilson, Kenneth J.; Cable, John

doi:10.1002/chin.199723031

Cited by 5 publications

(19 citation statements)

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“…56 The observed c-FA/t-FA abundance ratios have been rationalized by experimental estimates of their energy difference ranging from ΔD 0 trans−cis = 276 ± 84 58 to 350 ± 150 56 and ∼875 cm −1 . 61 These values are in accordance with the theoretical predictions. 54,56,61,62,68 Isomer-selective IR spectra of t-/c-FA recorded in the hydride stretch (amide A, ν NH , ν CH ) and fingerprint (amide I−II) ranges demonstrate the large structural differences of the amide groups in the two isomers.…”

Section: Introductionsupporting

confidence: 91%

“…61 These values are in accordance with the theoretical predictions. 54,56,61,62,68 Isomer-selective IR spectra of t-/c-FA recorded in the hydride stretch (amide A, ν NH , ν CH ) and fingerprint (amide I−II) ranges demonstrate the large structural differences of the amide groups in the two isomers. 59,60 Interestingly, clusters of FA with polar (L = H 2 O) and nonpolar ligands (L = Ar) have so far only been observed for the more stable t-FA rotamer.…”

Section: Introductionsupporting

confidence: 91%

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Stepwise Microhydration of Aromatic Amide Cations: Formation of Water Solvation Network Revealed by Infrared Spectra of Formanilide⁺–(H₂O)_n Clusters (n ≤ 5)

et al. 2015

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Hydration of peptides and proteins has a strong impact on their structure and function. Infrared photodissociation spectra (IRPD) of size-selected clusters of the formanilide cation, FA(+)-(H2O)n (n = 1-5), are analyzed by density functional theory calculations at the ωB97X-D/aug-cc-pVTZ level to determine the sequential microhydration of this prototypical aromatic amide cation. IRPD spectra are recorded in the hydride stretch and fingerprint ranges to probe the preferred interaction motifs and the cluster growth. IRPD spectra of cold Ar-tagged clusters, FA(+)-(H2O)n-Ar, reveal the important effects of temperature and entropy on the observed hydration motifs. At low temperature, the energetically most stable isomers are prominent, while at higher temperature less stable but more flexible isomers become increasingly populated because of entropy. In the most stable structures, the H2O ligands form a hydrogen-bonded solvent network attached to the acidic NH proton of the amide, which is stabilized by large cooperative effects arising from the excess positive charge. In larger clusters, hydration bridges the gap between the NH and CO groups (n ≥ 4) solvating the amide group rather than the more positively charged phenyl ring. Comparison with neutral FA-(H2O)n clusters reveals the strong impact of ionization on the acidity of the NH proton, the strength and topology of the interaction potential, and the structure of the hydration shell.

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Section: Introductionsupporting

confidence: 91%

Section: Introductionsupporting

confidence: 91%

Stepwise Microhydration of Aromatic Amide Cations: Formation of Water Solvation Network Revealed by Infrared Spectra of Formanilide⁺–(H₂O)_n Clusters (n ≤ 5)

et al. 2015

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“…The frequency positions of the S 0 -S 1 origins for A−D already provide some clue to the structures involved. The electronic origins of B−D are very red-shifted from that of tFA (36004 cm −1 ) and tAA (35902 cm −1 ), 27 while that for conformer A is shifted to the blue, as shown in Figure 3. Previous studies 28 have identified H 2 O complexes with tFA in which H 2 O acts either as a H-bond donor to the CO site or as a H-bond acceptor from the NH.…”

Section: Results and Analysismentioning

confidence: 89%

“…The amide group's conjugation with the phenyl ring produces a smaller than typical energy difference between trans-amide and cis-amide isomers, and in formanilide itself, both cis-and trans-isomers were observed in the expansion. 27 As a result, it was important also to explore this possibility in SAHA, where the cis-amide structure could potentially engage in hydrogen-bonding arrangements with the hydroxamic acid tail that are not available to trans-SAHA. However, the standard force field parameters in GAFF places an artificial barrier at the cis-amide configuration because in peptides, trans-amide structures are preferred over cis nearly exclusively.…”

Section: Discussionmentioning

confidence: 99%

Single Conformation Spectroscopy of Suberoylanilide Hydroxamic Acid: A Molecule Bites Its Tail

Zhang¹,

Blodgett

Zhu

et al. 2017

J. Phys. Chem. A

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Suberoylanilide hydroxamic acid (SAHA) is a histone deacetylase inhibitor that causes growth arrest and differentiation of many tumor types and is an approved drug for the treatment of cancer. The chemical structure of SAHA consists of formanilide "head" and a hydroxamic acid "tail" separated by an n-hexyl chain, CHNH(C═O)-(CH)-(C═O)NHOH. The alkyl chain's preference for extended structures is in competition with tail-to-head (T-H) or head-to-tail (H-T) hydrogen bonds between the amide and hydroxamic acid groups. Laser desorption was used to bring SAHA into the gas phase and cool it in a supersonic expansion before interrogation with mass-resolved resonant two-photon ionization spectroscopy. Single conformation UV spectra in the S-S region and infrared spectra in the hydride stretch and mid-IR regions were recorded using IR-UV hole-burning and resonant ion-dip infrared spectroscopy, respectively. Three conformers of SAHA were distinguished and spectroscopically characterized. Comparison of the experimental IR spectra with the predictions of density functional theory calculations (DFT, B3LYP D3BJ/6-31+G(d)) leads to assignments for the three conformers, all of which possess tightly folded alkyl chains that enable formation of a T-H (conformer A) or H-T (conformers B and C) hydrogen bonds. A modified version of the generalized Amber force field was developed to more accurately describe the hydroxamic acid OH internal rotor potential, leading to predictions for the relative energies in reasonable agreement with experiment. This force field was used to generate a disconnectivity graph for the low-energy portion of the potential energy landscape of SAHA. This disconnectivity graph contains more than one hundred minima and maps out the lowest-energy pathways between them, which could then be characterized via DFT calculations. This combination of force field and DFT calculations provides insight into the potential energy landscape and how population was funneled into the three observed conformers.

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“…As we know, acetanilide (AA), as one kind of N-phenylamide, has been exclusively observed in a trans configuration in the gas phase recently [70]. The trans-AA has a C s symmetry structure in which all the heavy atoms are lying in the aromatic plane [71].…”

Section: Introductionmentioning

confidence: 99%

Excited-state hydrogen-bonding dynamics oftrans-acetanilide in an aqueous environment: a theoretical study

Zhang

2012

Molecular Simulation

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In this work, the time-dependent density functional theory (TDDFT) method was carried out to study the hydrogen-bonding dynamics in both singlet and triplet excited states of trans-acetanilide (AA) -(H 2 O) complexes formed by trans-acetanilide in a water (H 2 O) solvent. The ground-state geometric structure optimisations were calculated by the density functional theory method, but the electronic excitation energies and corresponding oscillation strengths of the low-lying electronically excited states for isolated AA, H 2 O monomers and hydrogen-bonded AA(CO) -(H 2 O) 1 , AA(NH) -(H 2 O) 1 dimers as well as the dihydrogen-bonded AA -(H 2 O) 2 trimer were calculated by the TDDFT method. In our system, the intermolecular hydrogen bonds CvO· · ·HZO and NZH· · ·OZH can also be formed. From the TDDFT results, we depicted the changes of different hydrogen-bonded complexes in various electronic excited states. According to Zhao's rule on the relationship between the electronic spectral shift and excited-state hydrogen-bonding dynamics, hydrogen bond strengthening can bring the relative electronic spectra redshift, whereas hydrogen bond weakening can make the corresponding electronic spectra shift to blue. In addition, we also discussed the frontier molecular orbitals and the electron density transition.

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ChemInform Abstract: Conformations and Relative Stabilities of the cis and trans Isomers in a Series of Isolated N‐Phenylamides

Cited by 5 publications

References 1 publication

Stepwise Microhydration of Aromatic Amide Cations: Formation of Water Solvation Network Revealed by Infrared Spectra of Formanilide⁺–(H₂O)_n Clusters (n ≤ 5)

Stepwise Microhydration of Aromatic Amide Cations: Formation of Water Solvation Network Revealed by Infrared Spectra of Formanilide⁺–(H₂O)_n Clusters (n ≤ 5)

Single Conformation Spectroscopy of Suberoylanilide Hydroxamic Acid: A Molecule Bites Its Tail

Excited-state hydrogen-bonding dynamics oftrans-acetanilide in an aqueous environment: a theoretical study

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ChemInform Abstract: Conformations and Relative Stabilities of the cis and trans Isomers in a Series of Isolated N‐Phenylamides

Cited by 5 publications

References 1 publication

Stepwise Microhydration of Aromatic Amide Cations: Formation of Water Solvation Network Revealed by Infrared Spectra of Formanilide+–(H2O)n Clusters (n ≤ 5)

Stepwise Microhydration of Aromatic Amide Cations: Formation of Water Solvation Network Revealed by Infrared Spectra of Formanilide+–(H2O)n Clusters (n ≤ 5)

Single Conformation Spectroscopy of Suberoylanilide Hydroxamic Acid: A Molecule Bites Its Tail

Excited-state hydrogen-bonding dynamics oftrans-acetanilide in an aqueous environment: a theoretical study

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Stepwise Microhydration of Aromatic Amide Cations: Formation of Water Solvation Network Revealed by Infrared Spectra of Formanilide⁺–(H₂O)_n Clusters (n ≤ 5)

Stepwise Microhydration of Aromatic Amide Cations: Formation of Water Solvation Network Revealed by Infrared Spectra of Formanilide⁺–(H₂O)_n Clusters (n ≤ 5)