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.

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.

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.

Improving the accuracy of interpolated potential energy surfaces by using an analytical zeroth-order potential function

2004 ◽  
Vol 120 (14) ◽  
pp. 6414-6422 ◽  
Author(s):  
Akio Kawano ◽  
Yin Guo ◽  
Donald L. Thompson ◽  
Albert F. Wagner ◽  
Michael Minkoff
Keyword(s):  
Potential Energy ◽  
Potential Function ◽  
Potential Energy Surfaces ◽  
Zeroth Order ◽  
Energy Surfaces

Empirical Potential-Energy Surfaces Fitting Using Feed forward Neural Networks

2012 ◽  
Author(s):  
Lionel Raff ◽  
Ranga Komanduri ◽  
Martin Hagan ◽  
Satish Bukkapatnam
Keyword(s):  
Potential Energy ◽  
Ab Initio ◽  
Potential Energy Surfaces ◽  
Force Fields ◽  
Pair Potential ◽  
Potential Surfaces ◽  
Empirical Potential ◽  
Functional Forms ◽  
Dynamics Simulations ◽  
Energy Surfaces

When the system of interest becomes too complex to permit the use of ab initio methods to obtain the system potential-energy surfaces (PES), empirical potential surfaces are frequently employed to represent the force fields present in the system under investigation. In most cases, the functional forms present in these potentials are selected on the basis of chemical and physical intuitions. The parameters of the surface are frequently adjusted to fit a very small set of experimental data that comprise bond energies, equilibrium bond distances and angles, fundamental vibrational frequencies, and perhaps measured barrier heights to reactions of interest. Such potentials generally yield only qualitative or semiquantitative descriptions of the system dynamics. Several research groups have significantly improved the accuracy of the values of the experimental properties computed using empirical potential surfaces by fitting the chosen functional form for the potential to the force fields obtained from trajectories using ab initio Car-Parrinello molecular dynamics simulations. The fitting to the force fields is usually done using a least-squares fitting approach. This method has been employed by Izvekov et al. to obtain effective non-polarizable three-site force fields for liquid water. Carré et al. have employed such a procedure to obtain a new pair potential for silica. In their investigation, the vector of potential parameters was fitted using an iterative Levenberg-Marquardt algorithm. Tangney and Scandolo have also developed an interatomic force field for liquid SiO2 in which the parameters were fitted to the forces, stresses, and energies obtained from ab initio calculations. Ercolessi and Adams have used a quasi-Newtonian procedure to fit an empirical potential for aluminum to data obtained from first-principals computations. Empirical potentials can be improved by making the parameters parameterized functions of the coordinates defining the instantaneous positions of the atoms of the system. This approach has been successfully employed by numerous investigators The difficulty with this procedure is that the number of parameters that must be adjusted increases rapidly. Appropriate fitting of these parameters requires a much more extensive database. Finally, the actual fitting process can often be tedious, difficult, and time-consuming.

Representation of potential energy surfaces by discrete polynomials: proton transfer in malonaldehyde

2000 ◽  
Vol 2 (18) ◽  
pp. 4095-4103 ◽  
Author(s):  
V. Aquilanti ◽  
G. Capecchi ◽  
S. Cavalli ◽  
C. Adamo ◽  
V. Barone
Keyword(s):  
Potential Energy ◽  
Proton Transfer ◽  
Potential Energy Surfaces ◽  
Discrete Polynomials ◽  
Energy Surfaces
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