A theoretical study of hydration effects on structural stability and hydrogen-bonding dynamics of 2′-deoxyguanosine 5′-monophosphate with different negative charges

2013 ◽  
Vol 91 (2) ◽  
pp. 169-175
Author(s):  
Weiping Zhang ◽  
Xiaoyu Zhang
Keyword(s):  
Density Functional Theory ◽  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Density Functional ◽  
Negative Charge ◽  
Solvation Shell ◽  
Excitation Energies ◽  
Functional Theory ◽  
Hydrogen Bonding Dynamics

The effects of hydration on the ground-state structural stability and excited-state hydrogen-bonding dynamics of 2′-deoxyguanosine 5′-monophosphate (dGMP) carrying different negative charges were investigated with B3LYP/6–31+G(d,p) using density functional theory (DFT) and time-dependent density functional theory (TDDFT) methods, respectively. Particularly, we not only considered the solvent effects by the polarizible continuum model (PCM), but also the first solvation shell was included explicitly. We demonstrated that the intramolecular hydrogen bond O2–H1···O3 will be weakened with the strengthening of the hydration. From the view of bond length, we can make a valid presumption that the site of negative charge will be the more preferable site of the hydration, and the preferable site may be changed because of the presence of other hydrogen bonds. Furthermore, we found that the first solvation shell had very little effect on the geometric structures except for the hydrogen bond P–O5···H5. By comparing the excitation energies, one important finding is that the changes in different electronic states are not obvious with the increase in n value when considering the PCM. Another finding is that the average interactions of hydrogen bonds may be strengthened with an increase of negative charge because of a decrease in excitation energies.

TIME-DEPENDENT DENSITY FUNCTIONAL THEORY STUDY ON DYNAMICS OF HYDROGEN BONDING IN EXCITED STATES OF TRANS-ACETANILIDE IN METHANOL SOLVENT

2012 ◽  
Vol 11 (02) ◽  
pp. 421-435 ◽  
Author(s):  
XIAOYU ZHANG ◽  
WEIPING ZHANG ◽  
FANKAI MENG
Keyword(s):  
Density Functional Theory ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Excited States ◽  
Electronic Spectra ◽  
Density Functional ◽  
Excitation Energies ◽  
Intermolecular Hydrogen Bonds ◽  
Functional Theory ◽  
Tddft Method

The hydrogen-bonding dynamics in both singlet and triplet excited states of the trans-acetanilide ( AA ) in methanol ( MeOH ) solvent was investigated using the time-dependent density functional theory (TDDFT) method. Geometric optimizations of the hydrogen-bonded AA–MeOH complexes considered here as well as the isolated AA and MeOH molecules were performed using density functional theory (DFT) method. At the same time, the TDDFT method was performed to calculate the electronic transition energies and corresponding oscillation strengths of all the compounds in the low-lying electronically excited states. In this study, only the intermolecular hydrogen bonds C=O⋯H–O and N–H⋯O–H can be formed. A theoretical forecast that changes of hydrogen bonds in the low-lying electronic excited states was proposed. We discussed not only ground-state geometric structures and electronic excitation energies but also frontier molecular orbitals and electron density transition. The intermolecular hydrogen bonds between AA and MeOH molecules play an important role in the geometric structures and electronic excitation energies. Zhao et al. have put forward the relationship between the electronic spectra and hydrogen bonding dynamics for the first time. According to Zhao's rule, a redshift of the relevant electronic spectra will appear if hydrogen bond is strengthened, while the hydrogen bond weakening can make an electronic spectra shift to blue.

Time-dependent density functional theory study on the electronic excited-state hydrogen bonding dynamics of BHC-nicotinamide in MeOH solution

2013 ◽  
Vol 91 (4) ◽  
pp. 248-254 ◽  
Author(s):  
Jinling Cheng ◽  
Di Liu
Keyword(s):  
Density Functional Theory ◽  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Excited State ◽  
Ground State ◽  
Density Functional ◽  
Time Dependent ◽  
Functional Theory ◽  
Hydrogen Bonding Dynamics ◽  
Hydrogen Bond Strengthening

The density functional theory (DFT) and time-dependent density functional theory (TDDFT) methods were performed to investigate the electronic excited-state hydrogen bonding dynamics of the hydrogenbonded complex formed by BHC-nicotinamide (BHCN) and methanol (MeOH). The ground-state geometry optimizations, electronic transition energies, corresponding oscillation strengths of the low-lying electronically excited states, and the optimized S1 excited-state geometry for the isolated BHCN and MeOH monomers, the hydrogen-bonded BHCN–MeOH dimers, and BHCN–2MeOH trimer complexes have been calculated by using the DFT and TDDFT methods, respectively. We have demonstrated that the intermolecular hydrogen bond C10=O14···H40−O39−Me is weaker than C16=O17···H46−O45−Me in the hydrogen-bonded dimers and trimer no matter whether in the ground state or the excited state. In addition, our results are consistent with the relationship between the electronic spectral shifts and excited-state hydrogen bonding dynamics: hydrogen bond strengthening can induce the relative electronic spectra redshift, whereas a blueshift will be induced. In addition, we focused our attention on the frontier molecular orbital and the results could reasonably explain the hydrogen bond strengthening or weakening mechanism.

Structural polymorphism of pyrazinium hydrogen sulfate: extending chemistry of the pyrazinium salts with small anions

2010 ◽  
Vol 66 (4) ◽  
pp. 451-457 ◽  
Author(s):  
Armand Budzianowski ◽  
Mariana Derzsi ◽  
Piotr J. Leszczyński ◽  
Michał K. Cyrański ◽  
Wojciech Grochala
Keyword(s):  
Density Functional Theory ◽  
Hydrogen Bond ◽  
Dipole Moment ◽  
Hydrogen Bonds ◽  
Dft Calculations ◽  
Density Functional ◽  
Hydrogen Sulfate ◽  
Structural Polymorphism ◽  
Functional Theory ◽  
First Time

Two polymorphs (α, β) of pyrazinium hydrogen sulfate (pyzH+HSO_4^-, abbreviated as PHS) with distinctly different hydrogen-bond types and topologies but close electronic energies have been synthesized and characterized for the first time. The α-polymorph (P212121) forms distinct blocks in which the pyzH+ and HSO_4^- ions are interconnected through a network of NH...O and OH...O hydrogen bonds. The β-form (P\bar 1) consists of infinite chains of alternating pyzH+ and HSO_4^- ions connected by NH...O and OH...N hydrogen bonds. Density functional theory (DFT) calculations indicate the possible existence of a hypothetical polar P1 form of the β-polymorph with an unusually high dipole moment.

scholarly journals Theoretical Researches On Binding Modes and Stability of Hydrogen Bonds Between Uracil and Formic Acid

2021 ◽  
Author(s):  
Qian Tang ◽  
Ting Huang ◽  
Ruisi Huang ◽  
Hongyu Cao ◽  
Lihao Wang ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Formic Acid ◽  
Density Functional ◽  
Implicit Solvent ◽  
Binding Modes ◽  
Functional Theory ◽  
Hydrogen Bond Formation ◽  
Vibration Absorption

Abstract The hydrogen bond formation with formic acid would affect the complementary pair of bases between uracil and adenine, but the binding modes and spectral properties of hydrogen bonds are still obscure. Density functional theory and time-dependent density functional theory were applied to investigate the intermolecular hydrogen bonds between uracil and formic acid. The reduced density gradient (RDG), bond lengths and vibration absorption frequencies revealed that the most probable uracil-formic acid (U-FA) interaction mode formed in the position c of FA and the site 1 of U, that is, the mode 1c. The theoretical parameters in excited state complexes manifested that the variety of hydrogen bond configurations led to different degrees of strengthening or weakening of molecular interaction. In the implicit solvent (water), the formations of O-H∙∙∙O in the uracil-formic acid complexes were promoted obviously. These theoretical studies would positively affect the researches of life science and medicinal chemistry.

scholarly journals Hydrogen-bonding study of photoexcited 4-nitro-1,8-naphthalimide in hydrogen-donating solvents

Open Physics ◽  
2016 ◽  
Vol 14 (1) ◽  
pp. 621-627
Author(s):  
Jianfang Cao ◽  
Hongmei Wu ◽  
Yue Zheng ◽  
Fangyuan Nie ◽  
Ming Li ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Hydrogen Bond ◽  
Excited States ◽  
Density Functional ◽  
Intermolecular Hydrogen Bond ◽  
Excitation Energies ◽  
Hydrogen Bond Acceptor ◽  
Functional Theory ◽  
Electronically Excited ◽  
Hydrogen Bonded

AbstractThe solute–solvent interactions of 4-nitro-1,8-naphthalimide (4NNI) as a hydrogen bond acceptor in hydrogen donating methanol (MeOH) solvent in electronic excited states were investigated by means of the time-dependent density functional theory(TDDFT). We calculated the S0 state geometry optimizations, electronic transition energies and corresponding oscillation strengths of the low-lying electronically excited states for the isolated 4NNi and hydrogen-bonded 4NNi-(MeOH)1,4 complexes using the density functional theory (DFT) and TDDFT methods. The electronic excitation energies of the hydrogen-bonded complexes are correspondingly decreased compared to that of the isolated 4NNi, which revealed that the intermolecular hydrogen bond C=O···H–O and N=O···H–O in the hydrogen-bonded 4NNi-(MeOH)1,4 are strengthened in the electronically excited state. The calculated results are consistent with the mechanism that hydrogen bond strengthening will induce a redshift of the corresponding electronic spectra, while hydrogen bond weakening will cause a blueshift. Furthermore, we believe that the deduction we used to depict the trend of the hydrogen bond changes in excited states exists in many other fuorescent dyes in solution.

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