International Journal of Molecular Sciences

Editorial

12 pages, 200 KiB

Open AccessEditorial

Ab Initio Study of the Prototropic Tautomerism of Cytosine and Guanine and Their Contribution to Spontaneous Point Mutations

by Yevgeniy Podolyan, Leonid Gorb and Jerzy Leszczynski

Int. J. Mol. Sci. 2003, 4(7), 410-421; https://doi.org/10.3390/i4070410 - 25 Jun 2003

Cited by 95 | Viewed by 10764

Abstract

High-level quantum-chemical and quantum-dynamics calculations are reported on the tautomerization equilibria and rate constants of isolated and monohydrated cytosine and guanine molecules. The results are used to estimate the fraction of the bases present in the cell during DNA synthesis as the unwanted [...] Read more.

High-level quantum-chemical and quantum-dynamics calculations are reported on the tautomerization equilibria and rate constants of isolated and monohydrated cytosine and guanine molecules. The results are used to estimate the fraction of the bases present in the cell during DNA synthesis as the unwanted tautomers that forms irregular base pairs, thus giving rise to a spontaneous GC → AT point mutation. A comparison of the estimated mutation frequencies with the observed frequency in E. coli is used to analyze two proposed mechanisms, differing in the degree of equilibration reached in the tautomerization reaction. It was found that the fraction of the rare tautomer in monohydrated complex of cytosine as well as guanine significantly exceed the amount responsible for the observed values of the GC → AT mutations. In the absence of water the equilibrium concentration of tautomeric forms is relatively large, but the barrier to their formation is high. It is possible that the mechanism in which a high tautomerization barrier keeps the tautomeric transformation far from a state of equilibrium is more likely than a mechanism in which water and/or polymerases produce a low equilibrium concentration of the tautomeric forms. Full article

(This article belongs to the Special Issue Proton Transfer Processes)

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2 pages, 108 KiB

Open AccessEditorial

Special Issue on Proton Transfer Processes

by Henryk Chojnacki

Int. J. Mol. Sci. 2003, 4(7), 408-409; https://doi.org/10.3390/i4070408 - 25 Jun 2003

Cited by 7 | Viewed by 5240

Abstract

It is well established that the hydrogen bond plays crucial role in many areas of physical, chemical and biological phenomena.[...] Full article

(This article belongs to the Special Issue Proton Transfer Processes)

Research

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5 pages, 137 KiB

Open AccessArticle

Studies on Electronic Charge of the Hydrogen Bond Proton in Model Molecular Systems

by Henryk Chojnacki

Int. J. Mol. Sci. 2003, 4(7), 481-485; https://doi.org/10.3390/i4070481 - 25 Jun 2003

Cited by 3 | Viewed by 6848

Abstract

The population analysis of the hydrogen bond atoms was analyzed within the different basis sets for model molecular systems for the ground and low-lying excited electronic states. The Mulliken, Lőwdin and Hirshfeld methods were used in our investigations. It has been shown that [...] Read more.

The population analysis of the hydrogen bond atoms was analyzed within the different basis sets for model molecular systems for the ground and low-lying excited electronic states. The Mulliken, Lőwdin and Hirshfeld methods were used in our investigations. It has been shown that normally the proton is transferred, however, in some excited electronic states the hydrogen atom displacement might be responsible for the tautomeric interconversion. Full article

(This article belongs to the Special Issue Proton Transfer Processes)

21 pages, 730 KiB

Open AccessArticle

Excited State Proton Transfer of Carbazole. A Convenient Way to Study Microheterogeneous Environments

by Nitin Chattopadhyay

Int. J. Mol. Sci. 2003, 4(7), 460-480; https://doi.org/10.3390/i4070460 - 25 Jun 2003

Cited by 20 | Viewed by 9280

Abstract

Excited state proton transfer of carbazole gives rise to dual fluorescence from the two prototropic species. Simultaneous consideration of the two emissions takes care of many of the instrumental artifacts. The relative intensity of the two emissions of carbazole is sensitive not only [...] Read more.

Excited state proton transfer of carbazole gives rise to dual fluorescence from the two prototropic species. Simultaneous consideration of the two emissions takes care of many of the instrumental artifacts. The relative intensity of the two emissions of carbazole is sensitive not only to the pH of the bulk medium but also the microenvironment around the probe. Hence, excited state proton transfer of carbazole has been well studied and exploited extensively to study the detail of microheterogeneous liquid environments like aqueous micelles, cyclodextrins etc. Effect of additive like urea has also been monitored via this photoreaction. Full article

(This article belongs to the Special Issue Proton Transfer Processes)

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15 pages, 915 KiB

Open AccessArticle

Model, First-Principle Calculation of Ammonia Dissociation on Si(100) Surface. Importance of Proton Tunneling

by Zorka K. Smedarchina and Marek Z. Zgierski

Int. J. Mol. Sci. 2003, 4(7), 445-459; https://doi.org/10.3390/i4070445 - 25 Jun 2003

Cited by 21 | Viewed by 9393

Abstract

The dissociation of an ammonia molecule on a cluster of Si atoms simulating the 100 silicon crystal structure with two Si dimers has been investigated by means of the DFT and an approximate instanton methods. The model corresponds to the low coverage limit [...] Read more.

The dissociation of an ammonia molecule on a cluster of Si atoms simulating the 100 silicon crystal structure with two Si dimers has been investigated by means of the DFT and an approximate instanton methods. The model corresponds to the low coverage limit of the surface. Absolute rate constants of two different dissociation paths are evaluated together with deuterium isotope effects. It is demonstrated that, even at room temperatures, the process is dominated by tunneling and that dissociation to a silicon atom of the adjacent dimer, rather than a silicon within the same dimer, is the prevailing mechanism. This leads to creation of a metastable structure which will slowly decay through a two-step hydrogen atom migration towards the absolute minimum on the potential energy surface corresponding to the NH2 group and the hydrogen atom residing in the same dimer. Full article

(This article belongs to the Special Issue Proton Transfer Processes)

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11 pages, 347 KiB

Open AccessArticle

Specific Features of Intramolecular Proton Transfer Reaction in Schiff Bases

by Aleksander Koll

Int. J. Mol. Sci. 2003, 4(7), 434-444; https://doi.org/10.3390/i4070434 - 25 Jun 2003

Cited by 48 | Viewed by 8878

Abstract

The differences between the intramolecular proton transfer in Mannich and Schiff bases are discussed. The tautomeric forms being in equilibrium in both types of molecules are seriously different. In Mannich bases there are in equilibrium the forms of phenols and phenolates. In Schiff [...] Read more.

The differences between the intramolecular proton transfer in Mannich and Schiff bases are discussed. The tautomeric forms being in equilibrium in both types of molecules are seriously different. In Mannich bases there are in equilibrium the forms of phenols and phenolates. In Schiff bases each of tautomers is strongly influenced by resonance between zwitterionic and keto structures. Despite the common opinion that the proton transfer forms in compounds with internal π-electronic coupling are mainly keto forms it is shown in this work, that in Schiff bases the content of keto structure is slightly less than zwitterionic one. Almost equal participation of both forms leads to effective resonance between them and stabilization of intramolecular hydrogen bond in this way. Full article

(This article belongs to the Special Issue Proton Transfer Processes)

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12 pages, 303 KiB

Open AccessArticle

Theoretical Study of Multidimensional Proton Tunnelling in Benzoic Acid Dimer

by Marek J. Wójcik, Krzysztof Szczeponek and Marek Boczar

Int. J. Mol. Sci. 2003, 4(7), 422-433; https://doi.org/10.3390/i4070422 - 25 Jun 2003

Cited by 17 | Viewed by 8355

Abstract

Ab initio B3LYP/6-311++G** calculations have been carried out for the benzoic acid dimer for the stable and saddle point structures. The energy barrier for the proton tunneling amounts to 6.5 kcal/mol. The normal mode frequencies have been computed including modes coupled to the [...] Read more.

Ab initio B3LYP/6-311++G** calculations have been carried out for the benzoic acid dimer for the stable and saddle point structures. The energy barrier for the proton tunneling amounts to 6.5 kcal/mol. The normal mode frequencies have been computed including modes coupled to the proton tunneling mode. Two-dimensional model potentials, formed from symmetric mode coupling potential and squeezed double well potential, have been fitted to the calculated energy barrier, geometries and frequencies, and used to analyze proton dynamics. The calculated proton tunneling energy splitting in the vibrationally ground states of the low-frequency modes is ~230 cm^-1. The two-dimensional model PES predict monotonic increase of the tunneling splitting with the excitation of the planar modes. Depending of the sign of the coupling parameter out-of-plane modes can either suppress or promote the splittings. Full article

(This article belongs to the Special Issue Proton Transfer Processes)

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