The Role of a Short and Strong Hydrogen Bond on the Double Proton Transfer in the Formamidine−Formic Acid Complex:  Theoretical Studies in the Gas Phase and in Solution

Kim, Yong-Ho; Lim, Sangbae; Kim, Yangsoo

doi:10.1021/jp990398p

Cited by 63 publications

(77 citation statements)

References 43 publications

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“…(2). The hydrogen bonds between groups with net charge are well accepted in chemistry and biology [30][31][32], especially when the proton donor is positively charged. In our data (Fig.…”

Section: The Donor-acceptor Types In Hydrogen Bondsmentioning

confidence: 99%

Hydrogen Bonds and Hydrophobic Interactions of Porphyrins in Porphyrin-Containing Proteins

Stojanovic¹,

Zarić²

2009

TOSBJ

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Structures of porphyrin-containing proteins from the Protein Data Bank (PDB) Select January 2007, were searched in order to find and systematically characterize hydrogen bonds and hydrophobic interactions of porphyrins in proteins. The results revealed that every porphyrin is involved in at least one hydrogen bond, most of the porphyrins form several, while some of them form up to thirteen hydrogen bonds. In most of the hydrogen bonds propionate groups of porphyrins interact with side-chains of residues. The most frequently observed donor is side chain of arginine. Histidine, lysine, threonine, serine and tyrozine form substantial number of hydrogen bonds too. The study has revealed that hydrophobic interactions are common between porphyrin and protein. Side-chains hydrophobic interactions are more frequent than those with backbone. The average conservation score for the amino acids making hydrogen bonds (7.2) and hydrophobic interactions (7.3) is statistically significantly higher than for the amino acids that are not involved in noncovalent interactions (5.7) with the porphyrin, indicating importance of hydrogen bonds and hydrophobic interactions with the porphyrin.

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“…(2). The hydrogen bonds between groups with net charge are well accepted in chemistry and biology [30][31][32], especially when the proton donor is positively charged. In our data (Fig.…”

Section: The Donor-acceptor Types In Hydrogen Bondsmentioning

confidence: 99%

Hydrogen Bonds and Hydrophobic Interactions of Porphyrins in Porphyrin-Containing Proteins

Stojanovic¹,

Zarić²

2009

TOSBJ

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“…7 Therefore, the barrier height of FA-FN complex is much smaller than those of other complexes. M06-2X method underestimated the barrier height for all cyclic complexes, whereas the G3* and MCCM-UT-CCSD values agreed very well with the BMC-CCSD results within1 kcal/mol of energy difference.…”

Section: Optimized Structures Of Fa-hmentioning

confidence: 97%

“…The DPT in FA-FN complex occurs asynchronously through an intermediate. 7 The value of the calculated barrier height (note that there are two transition states, but because of the C 2v symmetry of the molecule, they are equivalent) depends very much on the computational level. The DPT in FM dimer occurs concertedly.…”

Section: 4mentioning

confidence: 99%

Quantum Mechanical Studies for Structures and Energetic of Double Proton Transfer in Biologically Important Hydrogen-bonded Complexes

Park¹,

Kim²,

Kim³

et al. 2011

Bulletin of the Korean Chemical Society

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We have performed quantum mechanical calculations to study the geometries and binding energies of biologically important, cyclic hydrogen-bonded complexes, such as formic acid + H 2 O, formamidine + H 2 O, formamide + H 2 O, formic acid dimer, formamidine dimer, formamide dimer, formic acid + formamide, formic acid + formamidine, formamide + formamidine, and barrier heights for the double proton transfer in these complexes. Various ab initio, density functional theory, multilevel methods have been used. Geometries and energies depend very much on the level of theory. In particular, the transition state symmetry of the proton transfer in formamidine dimer varies greatly depending on the level of theory, so very high level of theory must be used to get any reasonable results.

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“…This changes the strength of the hydrogen bonds in the order OH-N > OH-O > NH-O > NH-N. The calculated equilibrium structures and transition states for four analogs of the formic acid dimer, calculated at the DFT-B3LYP/6-31G(d,p) level [43][44][45][46], are illustrated in Fig. 29.7.…”

Section: Dimeric Formic Acid and Related Dimersmentioning

confidence: 99%

Multiple Proton Transfer: From Stepwise to Concerted

Smedarchina

Siebrand

Fernández‐Ramos

2006

Hydrogen‐Transfer Reactions

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It is well recognized that reactions involving the transfer of a proton or hydrogen atom are special in that these particles can tunnel through classically forbidden regions [1]. The wave-like properties also add a new element to reactions in which two or more protons transfer, since under appropriate conditions, they may allow the protons to move as a single particle. In this contribution we review the dynamics of such reactions [2], focusing on double proton transfer for simplicity. In particular, we probe how the motion of one proton influences that of the other and which conditions lead to weak or strong correlation between their motions. Generally speaking, no correlation results in independent transfer and weak correlation in stepwise transfer. Strengthening the correlation will ultimately lead to concerted transfer and may give rise to synchronous transfer if the transferred particles are equivalent.While proton-proton correlation is a unifying concept that allows us to classify and understand the various multiproton transfer mechanisms, it is not a quantity that is easily measured or calculated. In dealing with a specific reaction, one tends to use a simpler approach based on the search for a transition state, i.e. a configuration along the transfer path characterized by a first-order saddle point representing a vibrational force field with one imaginary frequency. More generally, the presence of two mobile particles implies that the potential energy surface contains stationary states with zero, one, or two imaginary frequencies, representing, respectively, a stable intermediate, a transition state, and a state with a secondorder saddle point.A stable intermediate roughly halfway along the trajectory implies barriers separating it from the equilibrium configurations. Such a potential favors stepwise transfer under conditions where the intermediate is thermally accessible. This basically reduces the dynamics to that appropriate for single proton transfer, but leaves open the question of how to deal with transfer at low temperature. A barrier corresponding to a single transition state, similar to that observed for single proton transfer, implies concerted transfer of the two protons. This again can Hydrogen-Transfer Reactions. Edited by be treated by the methods developed for single proton dynamics [1,3]. However, if, instead, this barrier corresponds to a second-order saddle point, it represents concerted motion along two proton coordinates. This situation does not immediately reveal the nature of the corresponding transfer process, but it drives home the point that the presence of two mobile protons allows at least two transfer mechanisms. On a potential energy surface with more than one saddle point, there will in general be multiple pathways along which the potential has a doubleminimum profile. To analyze the transfer dynamics governed by such a potential, we need an approach that goes beyond the question whether the transfer is concerted or stepwise.To elucidate the effect of proton-proton correlation...

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The Role of a Short and Strong Hydrogen Bond on the Double Proton Transfer in the Formamidine−Formic Acid Complex: Theoretical Studies in the Gas Phase and in Solution

Cited by 63 publications

References 43 publications

Hydrogen Bonds and Hydrophobic Interactions of Porphyrins in Porphyrin-Containing Proteins

Hydrogen Bonds and Hydrophobic Interactions of Porphyrins in Porphyrin-Containing Proteins

Quantum Mechanical Studies for Structures and Energetic of Double Proton Transfer in Biologically Important Hydrogen-bonded Complexes

Multiple Proton Transfer: From Stepwise to Concerted

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