scholarly journals Assessing the Conformational Equilibrium of Carboxylic Acid via QM and MD Studies on Acetic Acid

2018 ◽  
Author(s):  
Victoria T. Lim ◽  
Christopher I. Bayly ◽  
Laszlo Fusti-Molnar ◽  
David Mobley
Keyword(s):  
Acetic Acid ◽  
Molecular Modeling ◽  
Carboxylic Acids ◽  
Functional Group ◽  
Careful Examination ◽  
Hydrogen Atoms ◽  
Biomolecular Systems ◽  
General Belief ◽  
Dynamics Simulations ◽  
Carboxyl Functional Group

Accurate hydrogen placement in molecular modeling is crucial for studying the interactions and dynamics of biomolecular systems. It is difficult to locate hydrogen atoms from many experimental structural characterization approaches, such as due to the weak scattering of x-ray radiation. Hydrogen atoms are usually added and positioned <i>in silico</i> when preparing experimental structures for modeling and simulation. The carboxyl functional group is a prototypical example of a functional group that requires protonation during structure preparation. To our knowledge, when in their neutral form, carboxylic acids are typically protonated in the <i>syn</i> conformation by default in classical molecular modeling packages, with no consideration of alternative conformations, though we are not aware of any careful examination of this topic. Here, we investigate the general belief that carboxylic acids should always be protonated in the <i>syn</i> conformation. We calculate and compare the relative energetic stabilities of <i>syn</i> and <i>anti</i> acetic acid using <i>ab initio</i> quantum mechanical calculations and atomistic molecular dynamics simulations. We show that while the <i>syn</i> conformation is the preferred state, the <i>anti</i> state may in some cases also be present under normal NPT conditions in solution.

scholarly journals Assessing the Conformational Equilibrium of Carboxylic Acid via QM and MD Studies on Acetic Acid

2018 ◽  
Author(s):  
Victoria T. Lim ◽  
Christopher I. Bayly ◽  
Laszlo Fusti-Molnar ◽  
David Mobley
Keyword(s):  
Acetic Acid ◽  
Molecular Modeling ◽  
Carboxylic Acids ◽  
Functional Group ◽  
Careful Examination ◽  
Hydrogen Atoms ◽  
Biomolecular Systems ◽  
General Belief ◽  
Dynamics Simulations ◽  
Carboxyl Functional Group

Accurate hydrogen placement in molecular modeling is crucial for studying the interactions and dynamics of biomolecular systems. It is difficult to locate hydrogen atoms from many experimental structural characterization approaches, such as due to the weak scattering of x-ray radiation. Hydrogen atoms are usually added and positioned <i>in silico</i> when preparing experimental structures for modeling and simulation. The carboxyl functional group is a prototypical example of a functional group that requires protonation during structure preparation. To our knowledge, when in their neutral form, carboxylic acids are typically protonated in the <i>syn</i> conformation by default in classical molecular modeling packages, with no consideration of alternative conformations, though we are not aware of any careful examination of this topic. Here, we investigate the general belief that carboxylic acids should always be protonated in the <i>syn</i> conformation. We calculate and compare the relative energetic stabilities of <i>syn</i> and <i>anti</i> acetic acid using <i>ab initio</i> quantum mechanical calculations and atomistic molecular dynamics simulations. We show that while the <i>syn</i> conformation is the preferred state, the <i>anti</i> state may in some cases also be present under normal NPT conditions in solution.

scholarly journals Site-specific Umpolung amidation of carboxylic acids via triplet synergistic catalysis

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yunyun Ning ◽  
Shuaishuai Wang ◽  
Muzi Li ◽  
Jie Han ◽  
Chengjian Zhu ◽  
...  
Keyword(s):  
Carboxylic Acids ◽  
Functional Group ◽  
Amide Bond ◽  
Coupling Reagents ◽  
Complex Molecules ◽  
Bond Forming ◽  
Synergistic Catalysis ◽  
Wide Range ◽  
Amidation Reaction ◽  
Forming Methods

AbstractDevelopment of catalytic amide bond-forming methods is important because they could potentially address the existing limitations of classical methods using superstoichiometric activating reagents. In this paper, we disclose an Umpolung amidation reaction of carboxylic acids with nitroarenes and nitroalkanes enabled by the triplet synergistic catalysis of FeI2, P(V)/P(III) and photoredox catalysis, which avoids the production of byproducts from stoichiometric coupling reagents. A wide range of carboxylic acids, including aliphatic, aromatic and alkenyl acids participate smoothly in such reactions, generating structurally diverse amides in good yields (86 examples, up to 97% yield). This Umpolung amidation strategy opens a method to address challenging regioselectivity issues between nucleophilic functional groups, and complements the functional group compatibility of the classical amidation protocols. The synthetic robustness of the reaction is demonstrated by late-stage modification of complex molecules and gram-scale applications.

Molecular dynamics simulations of isotope compounds of hydrogen atoms: prospects and progress

2002 ◽  
Vol 580 (1-3) ◽  
pp. 33-38
Author(s):  
Cristina P. Gonçalves ◽  
Flávia Rolim ◽  
Vinı́cius C. Mota ◽  
José R. Mohallem
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Hydrogen Atoms ◽  
Dynamics Simulations

Molecular modeling of organic and biomolecular systems usingBOSS andMCPRO

2005 ◽  
Vol 26 (16) ◽  
pp. 1689-1700 ◽  
Author(s):  
William L. Jorgensen ◽  
Julian Tirado-Rives
Keyword(s):  
Molecular Modeling ◽  
Biomolecular Systems

scholarly journals Computational notes on the electronic properties of carboxylic acid

2020 ◽  
Vol 9 (2) ◽  
pp. 1079-1082
Keyword(s):  
Acetic Acid ◽  
Carboxylic Acid ◽  
Electronic Properties ◽  
Carboxylic Acids ◽  
Normal Mode ◽  
Normal Modes ◽  
Carboxyl Groups ◽  
Vibrational Characteristics ◽  
Vibrational Features ◽  
Acetic Acids

The present work describing the electronic properties and vibrational characteristics of carboxylic acids. Acetic acid is chosen as model molecules then optimized at B3LYP/6-31g(d,p) level of theory. The vibrational frequencies were calculated at the same level of theory. Band assignments which were calculated as 18 normal modes were assigned as one compare the normal mode coordinates with original one. Band assignments were described indicating the directions of normal modes in terms the vibrating atoms of the acetic acids. It could be concluded that DFT could be a useful tool for elucidation both the structural and vibrational features of carboxylic acids and then further utilized for assignment of the structures contains carboxyl groups which are known as most reactive structures in chemistry, biology and environment.

scholarly journals Heterogeneous chemistry of monocarboxylic acids on α-Al<sub>2</sub>O<sub>3</sub> at ambient condition

2010 ◽  
Vol 10 (2) ◽  
pp. 3937-3974 ◽  
Author(s):  
S. R. Tong ◽  
L. Y. Wu ◽  
M. F. Ge ◽  
W. G. Wang ◽  
Z. F. Pu
Keyword(s):  
Acetic Acid ◽  
Formic Acid ◽  
Carboxylic Acids ◽  
Propionic Acid ◽  
Ambient Condition ◽  
Heterogeneous Reactions ◽  
Dust Particles ◽  
Monocarboxylic Acids ◽  
Al2o3 Particles ◽  
Α Al2o3

Abstract. A study of the atmospheric heterogeneous reactions of formic acid, acetic acid, and propionic acid on dust particles (α-Al2O3) was performed at ambient condition by using a diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) reactor. From the analysis of the spectral features, observations of carboxylates formation provide strong evidence for an efficient reactive uptake process. Comparison of the calculated and experimental vibrational frequencies of adsorbed carboxylates establishes the bridging coordinated structures on the surface. The uptake coefficients of formic acid, acetic acid, and propionic acid on α-Al2O3 particles are (2.07±0.26)×10−3, (5.00±0.69)×10−3, and (3.04±0.63)×10−3, respectively (using geometric area). Besides, the effect of various relative humid (RH) on this heterogeneous reactions was studied. The uptake coefficients of monocarboxylic acids on α-Al2O3 particles increase initially (RH<20%) and then decrease with the increased RH (RH>20%) which was due to the effect of water on carboxylic acids solvation, particles surface hydroxylation, and competition on reactive site. On the basis of the results of experimental simulation, the mechanism of heterogeneous reaction of dust with carboxylic acids at ambient condition was discussed. The loss of atmospheric monocarboxylic acids due to reactive uptake on available mineral dust particles can be competitive with homogeneous loss pathways, especially in dusty urban and desertified environments.

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