scholarly journals Proton Transfer and Nitro Rotation Tuned Photoisomerization of Artificial Base Pair-ZP

2020 ◽  
Vol 8 ◽  
Author(s):  
Xixi Cui ◽  
Yu Zhao ◽  
Zhibing Li ◽  
Qingtian Meng ◽  
Changzhe Zhang
Keyword(s):  
Proton Transfer ◽  
Gas Phase ◽  
Base Pair ◽  
Potential Energy Surfaces ◽  
Photophysical Properties ◽  
Molecular Vibration ◽  
Base Pairs ◽  
Vibration Effect ◽  
Double Proton Transfer ◽  
Energy Surfaces

Recently, the successful incorporation of artificial base pairs in genetics has made a significant progress in synthetic biology. The present work reports the proton transfer and photoisomerization of unnatural base pair ZP, which is synthesized from the pyrimidine analog 6-amino-5-nitro-3-(1-β-D-2′-deoxyribo-furanosyl)-2 (1H)-pyridone (Z) and paired with its Watson-Crick complement, the purine analog 2-amino-8-(1′-β-D-2′- deoxyribofuranosyl)-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one (P). To explain the mechanism of proton transfer process, we constructed the relaxed potential energy surfaces (PESs) linking the different tautomers in both gas phase and solution. Our results show that the double proton transfer in the gas phase occurs in a concerted way both in S0 and S1 states, while the stepwise mechanism becomes more favorable in solution. The solvent effect can promote the single proton transfer, which undergoes a lower energy barrier in S1 state due to the strengthened hydrogen bond. In contrast to the excited state ultrafast deactivation process of the natural bases, there is no conical intersection between S0 and S1 states along the proton transfer coordinate to activate the decay mechanism in ZP. Of particular relevance to the photophysical properties, charge-transfer character is obviously related to the nitro rotation in S1 state. We characterized the molecular vibration effect on the electronic properties, which reveals the electronic excitation can be tuned by the rotation-induced structural distortion accompanied with the electron localization on nitro group.

A theoretical study of the potential energy surfaces for the double proton transfer reaction of model DNA base pairs

2017 ◽  
Vol 19 (6) ◽  
pp. 4802-4808 ◽  
Author(s):  
Chaozheng Li ◽  
Yonggang Yang ◽  
Donglin Li ◽  
Yufang Liu
Keyword(s):  
Proton Transfer ◽  
Potential Energy Surfaces ◽  
Proton Transfer Reaction ◽  
Base Pairs ◽  
Double Proton Transfer ◽  
Dna Base ◽  
Dna Base Pairs ◽  
Dna Base Pair ◽  
Energy Surfaces ◽  
The Double Proton Transfer

The excited-state double proton transfer (ESDPT) mechanism in a model DNA base pair, 7-azaindole (7AI) dimer, has been debated over the years.

Double Proton Transfer using Dissociable Force Fields

2004 ◽  
Vol 57 (12) ◽  
pp. 1223 ◽  
Author(s):  
Sven Lammers ◽  
Markus Meuwly
Keyword(s):  
Proton Transfer ◽  
Potential Energy Surfaces ◽  
Force Fields ◽  
Computing Time ◽  
Alternative Methods ◽  
Zeroth Order ◽  
Barrier Heights ◽  
Double Proton Transfer ◽  
Energy Scaling ◽  
Energy Surfaces

The construction, implementation, and use of dissociable classical force fields are discussed. Starting from zeroth-order interaction potentials for O2H5+ and N2H7+ calculated with MP2/6–311++G**, energy scaling of the potential energy surfaces allows adjustment of quantities such as the barrier heights to describe a range of physical situations observed in realistic systems. As an example, ‘potential morphing’ is used to investigate the dynamics of double proton transfer in 2-pyridone · 2-hydroxypyridine for which previous estimates of the barrier to tautomerization are available. Scaling factors to give barrier heights for double proton transfer between 3.6 and 17.6 kcal mol−1 are chosen to demonstrate the utility of the method to describe a range of different barrier heights and shapes. Considerable savings in computing time can be achieved compared to alternative methods such as mixed quantum/classical methods.

scholarly journals The influence of base pair tautomerism on single point mutations in aqueous DNA

2020 ◽  
Vol 10 (6) ◽  
pp. 20190120
Author(s):  
A. Gheorghiu ◽  
P. V. Coveney ◽  
A. A. Arabi
Keyword(s):  
Proton Transfer ◽  
Base Pair ◽  
Single Point ◽  
Point Mutations ◽  
Base Pairs ◽  
Single Proton ◽  
Double Proton Transfer ◽  
Wide Range ◽  
Single Point Mutations ◽  
The Double Proton Transfer

The relationship between base pair hydrogen bond proton transfer and the rate of spontaneous single point mutations at ambient temperatures and pressures in aqueous DNA is investigated. By using an ensemble-based multiscale computational modelling method, statistically robust rates of proton transfer for the A:T and G:C base pairs within a solvated DNA dodecamer are calculated. Several different proton transfer pathways are observed within the same base pair. It is shown that, in G:C, the double proton transfer tautomer is preferred, while the single proton transfer process is favoured in A:T. The reported range of rate coefficients for double proton transfer is consistent with recent experimental data. Notwithstanding the approximately 1000 times more common presence of single proton transfer products from A:T, observationally there is bias towards G:C to A:T mutations in a wide range of living organisms. We infer that the double proton transfer reactions between G:C base pairs have a negligible contribution towards this bias for the following reasons: (i) the maximum half-life of the G*:C* tautomer is in the range of picoseconds, which is significantly smaller than the milliseconds it takes for DNA to unwind during replication, (ii) statistically, the majority of G*:C* tautomers revert back to their canonical forms through a barrierless process, and (iii) the thermodynamic instability of the tautomers with respect to the canonical base pairs. Through similar reasoning, we also deduce that proton transfer in the A:T base pair does not contribute to single point mutations in DNA.

Serine–Ca2+ versus serine–Cu2+ complexes — A theoretical perspective

2010 ◽  
Vol 88 (8) ◽  
pp. 759-768 ◽  
Author(s):  
Al Mokhtar Lamsabhi ◽  
Otilia Mó ◽  
Manuel Yáñez
Keyword(s):  
Gas Phase ◽  
Electron Density ◽  
Potential Energy Surfaces ◽  
Metal Ion ◽  
Theoretical Perspective ◽  
Binding Energies ◽  
Interacting Systems ◽  
Intramolecular Hydrogen ◽  
Energy Surfaces ◽  
Doubly Charged

The association of Ca2+ and Cu2+ to serine was investigated by means of B3LYP DFT calculations. The [serine–M]2+ (M = Ca, Cu) potential energy surfaces include, as does the neutral serine, a large number of conformers, in which a drastic reorganization of the electron density of the serine moiety is observed. This leads to significant changes in the number and strength of the intramolecular hydrogen bonds existing in the neutral serine tautomers. In some cases, a proton is transferred from the carboxylic OH group to the amino group and accordingly, some of the more stable [serine–M]2+ complexes can be viewed as the result of the interaction of the zwiterionic form of serine with the doubly charged metal ion. Whereas the interaction between Ca2+ and serine is essentially electrostatic, that between Cu2+ and serine has a non-negligible covalent character, reflected in larger electron densities at the bond critical points between the metal and the base, in the negative values of the electron density between the two interacting systems, and in much larger Cu2+ than Ca2+ binding energies. More importantly, the interaction with Cu2+ is followed by a partial oxidation of the base, which is not observed when the metal ion is Ca2+. The main consequence is that in Cu2+ complexes a significant acidity enhancement of the serine moiety takes place, which strongly favors the deprotonation of the [serine–Cu]2+ complexes. This is not the case for Ca2+ complexes. Thus, [serine–Ca]2+ complexes, like those formed by urea, thiourea, selenourea, or glycine, should be detected in the gas phase. Conversely, the complexes with Cu2+ should deprotonate spontaneously and therefore only [(serine–H)–Cu]+ monocations should be experimentally accessible.

Effect of number and different types of proton donors on excited-state intramolecular single and double proton transfer in bipyridine derivatives: theoretical insights

2020 ◽  
Vol 44 (19) ◽  
pp. 8018-8031
Author(s):  
Komsun Chaihan ◽  
Nawee Kungwan
Keyword(s):  
Excited State ◽  
Proton Transfer ◽  
Vibrational Mode ◽  
Photophysical Properties ◽  
Reaction Energy ◽  
Topology Analysis ◽  
Double Proton Transfer ◽  
And Topology ◽  
Proton Donors ◽  
Different Types

Intra-HBs are strengthened upon photoexcitation, confirmed by red-shift in vibrational mode and topology analysis. Number and type of donors result in difference in photophysical properties. Occurrence of ESIPT depends on barrier and reaction energy.

Effects of π-expansion, an additional hydroxyl group, and substitution on the excited state single and double proton transfer of 2-hydroxybenzaldehyde and its relative compounds: TD-DFT static and dynamic study

2019 ◽  
Vol 43 (48) ◽  
pp. 19107-19119 ◽  
Author(s):  
Chanatkran Prommin ◽  
Khanittha Kerdpol ◽  
Tinnakorn Saelee ◽  
Nawee Kungwan
Keyword(s):  
Excited State ◽  
Proton Transfer ◽  
Photophysical Properties ◽  
Dynamic Study ◽  
Hydroxyl Group ◽  
Single Proton ◽  
Double Proton Transfer ◽  
Td Dft ◽  
The Double Proton Transfer

The effects of π-expansion, an extra hydroxyl group, and substituents on the photophysical properties, the excited state single proton transfer and the double proton transfer of 2-hydroxybenzaldehyde and its relatives have been theoretically investigated using TD-DFT.

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