A comprehensive classification and nomenclature of carboxyl–carboxyl(ate) supramolecular motifs and related catemers: implications for biomolecular systems

D’Ascenzo, Luigi; Auffinger, Pascal

doi:10.1107/s205252061500270x

Cited by 66 publications

(64 citation statements)

References 75 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…It is noteworthy that expanded systems 6 and 7 have the same ratio syn to anti‐protonation, where the number of energetically less favorable anti‐protonation is larger compared to the favorable syn‐protonation.…”

Section: Resultsmentioning

confidence: 99%

“…significantly higher than the energy of system 3 leading to the fact that system 7 has again the highest energy. It is noteworthy that expanded systems 6 and 7 have the same ratio syn to anti-protonation, where the number of energetically less favorable anti-protonation [49] is larger compared to the favorable syn-protonation. Table 5 shows the information of proton transfer observed during geometry optimizations.…”

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Investigating the Structure and Dynamics of Apo‐Photosystem II

et al. 2019

View full text Add to dashboard Cite

Photosynthetic water oxidation is a model for future technologies employing solar energy to split water into hydrogen and oxygen. Natural water oxidation is carried out by a special manganese catalyst, the water‐oxidizing complex (WOC), located in photosystem II (PSII) of cyanobacteria, algae, and plants. Hence, there is great interest in the molecular structure as well as structural changes during catalytic activity and assembly/disassembly of the WOC. In particular, the light‐driven assembly during photosystem II repair under physiological conditions is poorly understood, and structural information about manganese depleted PSII (apo‐PSII) is required as a starting point for improving this understanding. Recently Zhang et al. (eLife 2017;6:e26933) showed that the cavity harboring the WOC in PSII remains largely intact upon manganese‐depletion and suggested that deprotonation of hydrogen‐bonding pairs enables the charge‐compensated insertion of the manganese cations without any major change of the cavity structure. By computational methods we have further investigated the structure of apo‐PSII and show how it can be stabilized by protons localized at the terminal carboxylate groups inside the remaining cavity. Ab‐initio molecular dynamics simulations suggest that not more than two water molecules fill the void left by manganese depletion.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Investigating the Structure and Dynamics of Apo‐Photosystem II

et al. 2019

View full text Add to dashboard Cite

show abstract

“…13 The anti state may also be important to consider when calculating solvation free energies. 14 Finally, the anti conformation is not insignificantly represented in structures from the Cambridge Structural Database, 15 supported by related crystallographic and theoretical charge density studies. 16,17 Past work investigating acetic acid in solvent predominantly considers the syn state such as in studies characterizing hydrogen-bonding interactions of acetic acid microhydrates using DFT-B3LYP calculations, 18 or assessing the dimer form in various stages of hydration theoretically 19,20 and experimentally.…”

Section: Introductionmentioning

confidence: 82%

Assessing the Conformational Equilibrium of Carboxylic Acid via Quantum Mechanical and Molecular Dynamics Studies on Acetic Acid

Lim

Bayly²,

Füsti-Molnár

et al. 2019

J. Chem. Inf. Model.

View full text Add to dashboard Cite

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 in silico 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 syn 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 syn conformation. We calculate and compare the relative energetic stabilities of syn and anti acetic acid using ab initio quantum mechanical calculations and atomistic molecular dynamics simulations. We show that while the syn conformation is the preferred state, the anti state may in some cases also be present under normal NPT conditions in solution.

show abstract

Section: Introductionmentioning

confidence: 82%

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

Lim¹,

Bayly²,

Füsti-Molnár³

et al. 2018

Preprint

View full text Add to dashboard Cite

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 in silico 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 syn 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 syn conformation. We calculate and compare the relative energetic stabilities of syn and anti acetic acid using ab initio quantum mechanical calculations and atomistic molecular dynamics simulations. We show that while the syn conformation is the preferred state, the anti state may in some cases also be present under normal NPT conditions in solution.

show abstract

A comprehensive classification and nomenclature of carboxyl–carboxyl(ate) supramolecular motifs and related catemers: implications for biomolecular systems

Abstract: The vast diversity of carboxyl–carboxyl(ate) arrangements is reduced to 17 supramolecular motifs and eight catemers. Examples of each, extracted from the CSD, are presented.

Cited by 66 publications

References 75 publications

Investigating the Structure and Dynamics of Apo‐Photosystem II

Investigating the Structure and Dynamics of Apo‐Photosystem II

Assessing the Conformational Equilibrium of Carboxylic Acid via Quantum Mechanical and Molecular Dynamics Studies on Acetic Acid

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

Contact Info

Product

Resources

About