Proton affinities of the anions of aromatic carboxylic acids measured by kinetic method

Bieńkowski, Tomasz; Świder, Paweł; Błaziak, Kacper; Danikiewicz, Witold

doi:10.1016/j.ijms.2013.10.006

Cited by 5 publications

(9 citation statements)

References 23 publications

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“…Molecules 2020, 25, x 8 of 16 [58,59]. These values are very close to available experimental data for pyridine (930 kJ/mol) [60,61], collidine (980 kJ/mol) [61], benzoate (1422 kJ/mol) and 2-nitrobenzoate (1383 kJ/mol) [62], formate (1445 kJ/mol) and acetate (1456 kJ/mol) [63], and fluoride (1550 kJ/mol) [64]. Figure 6 demonstrates the lower limits of the external electric field simulated the effect of CDF3/CDClF2 on 2-6 under the PCM (Figure 6a) and gas-phase (Figure 6b) approximations as a function of the PA of the involved conjugate bases.…”

Section: Discussionsupporting

confidence: 85%

“…The easiest way to estimate the proton-donating and proton-accepting powers is to calculate the gas-phase proton affinity (PA), Table 4 [58,59]. These values are very close to available experimental data for pyridine (930 kJ/mol) [60,61], collidine (980 kJ/mol) [61], benzoate (1422 kJ/mol) and 2-nitrobenzoate (1383 kJ/mol) [62], formate (1445 kJ/mol) and acetate (1456 kJ/mol) [63], and fluoride (1550 kJ/mol) [64].…”

Section: Discussionsupporting

confidence: 61%

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Adduct under Field—A Qualitative Approach to Account for Solvent Effect on Hydrogen Bonding

Shenderovich

Денисов

2020

Molecules

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The location of a mobile proton in acid-base complexes in aprotic solvents can be predicted using a simplified Adduct under Field (AuF) approach, where solute–solvent effects on the geometry of hydrogen bond are simulated using a fictitious external electric field. The parameters of the field have been estimated using experimental data on acid-base complexes in CDF3/CDClF2. With some limitations, they can be applied to the chemically similar CHCl3 and CH2Cl2. The obtained data indicate that the solute–solvent effects are critically important regardless of the type of complexes. The temperature dependences of the strength and fluctuation rate of the field explain the behavior of experimentally measured parameters.

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Section: Discussionsupporting

confidence: 85%

Section: Discussionsupporting

confidence: 61%

Adduct under Field—A Qualitative Approach to Account for Solvent Effect on Hydrogen Bonding

Shenderovich

Денисов

2020

Molecules

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“…Interactions of these charge sites give rise to a Coulomb energy, E Coul , that is given by where q i and q j are the protonation-dependent charges (− e , 0, or e ), with distances r ij . Unless noted otherwise, a dielectric constant of κ e = 1 was used. , An additional term arises from the proton affinities of the various sites (PA NT = 960 kJ mol –1 , PA ARG = 1029 kJ mol –1 , PA LYS = 937 kJ mol –1 , PA HIS = 958 kJ mol –1 , PA ASP‑ = 1450 kJ mol –1 , PA GLU‑ = 1450 kJ mol –1 , PA CT‑ = 1450 kJ mol –1 ). , These PA values give rise to the energy E PA where summation includes only protonated sites. These two terms result in a “total” energy …”

Section: Simulation Methodsmentioning

confidence: 99%

Collision-Induced Dissociation of Electrosprayed Protein Complexes: An All-Atom Molecular Dynamics Model with Mobile Protons

et al. 2016

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Electrospray ionization mass spectrometry (ESI-MS) has become an indispensable technique for examining noncovalent protein complexes. Collision-induced dissociation (CID) of these multiply protonated gaseous ions usually culminates in ejection of a single subunit with a disproportionately large amount of charge. Experiments suggest that this process involves subunit unfolding prior to separation from the residual complex, as well as H(+) migration onto the unravelling chain. Molecular dynamics (MD) simulations are a promising avenue for gaining detailed insights into these CID events. Unfortunately, typical MD algorithms do not allow for mobile protons. Here we address this limitation by implementing a strategy that combines atomistic force fields (such as OPLS/AA and CHARMM36) with a proton hopping algorithm, focusing on the tetrameric complexes transthyretin and streptavidin. Protons are redistributed over all acidic and basic sites in 20 ps intervals, subject to an energy function that reflects electrostatic interactions and proton affinities. Our simulations predict that nativelike conformers at the onset of collisional heating contain multiple salt bridges. Collisional heating initially causes subtle structural changes that lead to a gradual decline of these zwitterionic patterns. Many of the MD runs show gradual unfolding of a single subunit in conjunction with H(+) migration, culminating in subunit separation from the complex. However, there are also instances where two or more chains start to unfold simultaneously, giving rise to charge competition. The scission point where the "winning" subunit separates from the complex can be attained for different degrees of unfolding, giving rise to product ions in various charge states. The simulated product ion distributions are in close agreement with experimental CID data. Proton enrichment in the departing subunit is driven by charge-charge repulsion, but the combination of salt bridge depletion, charge migration, and proton affinity causes surprising compensation effects among the various energy terms. It appears that this work provides the most detailed account to date of the mechanism whereby noncovalent protein complexes disassemble during CID.

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“…With this option, the user can decide whether to run the proton redistribution code using the old point charge model that is based on eqs and or the new all-atom model that considers eqs –. In either case, intrinsic proton affinities were dealt with as described in eq , using the following PA int values (in kJ mol –1 ): ,, NT, 960; Arg, 1029; Lys, 937; His, 958; Asp – , 1450; Glu – , 1450; and CT – , 1450.…”

Section: Methodsmentioning

confidence: 99%

“…With this option, the user can decide whether to run the proton redistribution code using the old point charge model that is based on eqs 1 and 2 53 or the new all-atom model that considers eqs 6−8. In either case, intrinsic proton affinities were dealt with as described in eq 2, using the following PA int values (in kJ mol −1 ): 31,53,64 ■ RESULTS AND DISCUSSION Computational Cost. The goal of this study was to develop an improved mobile proton algorithm for MD studies on gaseous proteins.…”

Section: ■ Introductionmentioning

confidence: 99%

Molecular Dynamics Simulations on Gas-Phase Proteins with Mobile Protons: Inclusion of All-Atom Charge Solvation

Konermann

2017

J. Phys. Chem. B

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Molecular dynamics (MD) simulations have become a key tool for examining the properties of electrosprayed protein ions. Traditional force fields employ static charges on titratable sites, whereas in reality, protons are highly mobile in gas-phase proteins. Earlier studies tackled this problem by adjusting charge patterns during MD runs. Within those algorithms, proton redistribution was subject to energy minimization, taking into account electrostatic and proton affinity contributions. However, those earlier approaches described (de)protonated moieties as point charges, neglecting charge solvation, which is highly prevalent in the gas phase. Here, we describe a mobile proton algorithm that considers the electrostatic contributions from all atoms, such that charge solvation is explicitly included. MD runs were broken down into 50 ps fixed-charge segments. After each segment, the electrostatics was reanalyzed and protons were redistributed. Challenges associated with computational cost were overcome by devising a streamlined method for electrostatic calculations. Avidin (a 504-residue protein complex) maintained a nativelike fold over 200 ns. Proton transfer and side chain rearrangements produced extensive salt bridge networks at the protein surface. The mobile proton technique introduced here should pave the way toward future studies on protein folding, unfolding, collapse, and subunit dissociation in the gas phase.

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Proton affinities of the anions of aromatic carboxylic acids measured by kinetic method

Cited by 5 publications

References 23 publications

Adduct under Field—A Qualitative Approach to Account for Solvent Effect on Hydrogen Bonding

Adduct under Field—A Qualitative Approach to Account for Solvent Effect on Hydrogen Bonding

Collision-Induced Dissociation of Electrosprayed Protein Complexes: An All-Atom Molecular Dynamics Model with Mobile Protons

Molecular Dynamics Simulations on Gas-Phase Proteins with Mobile Protons: Inclusion of All-Atom Charge Solvation

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