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.

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 A theoretical study on the red- and blue-shift hydrogen bonds of cis-trans formic acid dimer in excited states

2013 ◽  
Vol 11 (2) ◽  
pp. 171-179 ◽  
Author(s):  
Dapeng Yang ◽  
Yonggang Yang ◽  
Yufang Liu
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Formic Acid ◽  
Excited States ◽  
Density Functional ◽  
Blue Shift ◽  
Red Shift ◽  
Functional Theory ◽  
Photophysical Study ◽  
Tddft Method

AbstractThe excited states of cis-trans formic acid dimer and its monomers have been investigated by time-dependent density functional theory (TDDFT) method. The formation of intermolecular hydrogen bonds O1-H1...O2=C2 and C2-H2...O4=C1 induces bond length lengthening of the groups related to the hydrogen bond, while that of the C2-H2 group is shortened. It is demonstrated that the red-shift hydrogen bond O1-H1...O2=C2 and blue-shift hydrogen bond C2-H2...O4=C1 are both weakened when excited to the S1 state. Moreover, it is found that the groups related to the formation of red-shift hydrogen bond O1-H1...O2=C2 are both strengthened in the S1 state, while the groups related to the blue-shift hydrogen bond C2-H2...O4=C1 are both weakened. This will provide information for the photochemistry and photophysical study of red- and blue-shift hydrogen bond.

Microsolvation of the formic acid dimer — (HCOOH)2(H2O)n clusters with n = 1, . . ., 5

2010 ◽  
Vol 88 (8) ◽  
pp. 736-743 ◽  
Author(s):  
Cara M. Nordstrom ◽  
Alaina J. McGrath ◽  
Ajit J. Thakkar
Keyword(s):  
Density Functional Theory ◽  
Perturbation Theory ◽  
Hydrogen Bonds ◽  
Formic Acid ◽  
Density Functional ◽  
Water Molecules ◽  
Spin Component ◽  
Functional Theory ◽  
Moller Plesset ◽  
Plesset Perturbation Theory

Density functional theory and spin-component-scaled Møller–Plesset perturbation theory calculations are used to examine the microsolvation of the formic acid dimer. The lowest energy structures with n water molecules consist of a n-water cluster, not necessarily of lowest energy, with two formic acid molecules attached to its surface by hydrogen bonds. The total number of hydrogen bonds does not correlate directly with relative stability.

scholarly journals Theoretical Study of Hydrogen Bond Formation in Trimethylene Glycol-Water Complex

2012 ◽  
Vol 2012 ◽  
pp. 1-12 ◽  
Author(s):  
Snehanshu Pal ◽  
T. K. Kundu
Keyword(s):  
Density Functional Theory ◽  
Hydrogen Bond ◽  
Density Functional ◽  
Bond Formation ◽  
Proton Donor ◽  
Basis Set ◽  
Functional Theory ◽  
Hydrogen Bond Formation ◽  
Water Complex ◽  
Trimethylene Glycol

A detailed quantum chemical calculation based study of hydrogen bond formation in trimethylene glycol- (TMG-) water complex has been performed by Hatree-Fock (HF) method, second-order Møller-Plesset perturbation theory (MP2), density functional theory (DFT), and density functional theory with dispersion function (DFT-D) using 6-31++G(d,p) basis set. B3LYP DFT-D, WB97XD, M06, and M06-2X functionals are used to capture highly dispersive hydrogen bond formation. Geometrical parameters, interaction energy, deviation of potential energy curve of hydrogen-bonded O–H from that of free O–H, natural bond orbital (NBO), atom in molecule (AIM), charge transfer, and red shift are investigated. It is observed that hydrogen bond between TMG and water molecule is stronger in case of TMG acting as proton donor compared to that of water acting as proton donor, and dilute TMG solution would inhibit water cluster formation.

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.

Characterization of low-barrier hydrogen bonds. 3. Hydrogen maleate. An ab initio and DFT investigation

1997 ◽  
Vol 75 (9) ◽  
pp. 1195-1202 ◽  
Author(s):  
Michael A. McAllister
Keyword(s):  
Density Functional Theory ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Proton Transfer ◽  
Ab Initio ◽  
Bond Energy ◽  
Density Functional ◽  
Hydrogen Bond Energy ◽  
Functional Theory ◽  
Low Barrier Hydrogen Bonds

High-level ab initio molecular orbital and density functional theory calculations predict the existence of a very short-strong hydrogen bond in the monoanion of maleic acid (hydrogen maleate). At all levels of theory (HF, MP2, BLYP, and B3LYP) except B3PW91 the potential energy surface is predicted to contain two minima, and hence resembles a double well. The barrier to proton transfer via a symmetrical transition state is calculated to be very small at all levels of theory. In all cases the calculated zero point vibrational energy available to the system is larger than the calculated barrier for proton transfer, thus the resulting hydrogen bond formed in hydrogen maleate is predicted to be symmetrical. Using the B3PW91 functional and the 6-31 + G(d,p) basis set results in a single-well potential and a symmetrically positioned hydrogen. All correlated methods predict the gas phase hydrogen bond energy to be approximately 27 kcal/mol. Effects due to solvents were estimated using solvent cavity methods. Approximating the solvent as a dielectric continuum reduces the calculated hydrogen bond energy by roughly 6 kcal/mol at all levels of theory. Keywords: low-barrier hydrogen bonds, short-strong hydrogen bonds, hydrogen maleate, ab initio, density functional theory.

scholarly journals Study on the interaction between catechin and cholesterol by the density functional theory

2020 ◽  
Vol 18 (1) ◽  
pp. 357-368
Author(s):  
Kaiwen Zheng ◽  
Kai Guo ◽  
Jing Xu ◽  
Wei Liu ◽  
Junlang Chen ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Hydrogen Bond ◽  
Charge Transfer ◽  
Density Functional ◽  
Antioxidant Properties ◽  
Micelle Formation ◽  
Aromatic Rings ◽  
Hydrogen Bond Interaction ◽  
Functional Theory ◽  
The Density Functional Theory

AbstractCatechin – a natural polyphenol substance – has excellent antioxidant properties for the treatment of diseases, especially for cholesterol lowering. Catechin can reduce cholesterol content in micelles by forming insoluble precipitation with cholesterol, thereby reducing the absorption of cholesterol in the intestine. In this study, to better understand the molecular mechanism of catechin and cholesterol, we studied the interaction between typical catechins and cholesterol by the density functional theory. Results show that the adsorption energies between the four catechins and cholesterol are obviously stronger than that of cholesterol themselves, indicating that catechin has an advantage in reducing cholesterol micelle formation. Moreover, it is found that the molecular interactions of the complexes are mainly due to charge transfer of the aromatic rings of the catechins as well as the hydrogen bond interactions. Unlike the intuitive understanding of a complex formed by hydrogen bond interaction, which is positively correlated with the number of hydrogen bonds, the most stable complexes (epicatechin–cholesterol or epigallocatechin–cholesterol) have only one but stronger hydrogen bond, due to charge transfer of the aromatic rings of catechins.

scholarly journals Spectroscopic, X-ray Diffraction and Density Functional Theory Study of Intra- and Intermolecular Hydrogen Bonds in Ortho-(4-tolylsulfonamido)benzamides

Molecules ◽  
2021 ◽  
Vol 26 (4) ◽  
pp. 926
Author(s):  
Malose J. Mphahlele ◽  
Eugene E. Onwu ◽  
Marole M. Maluleka
Keyword(s):  
Density Functional Theory ◽  
Solid State ◽  
Hydrogen Bonds ◽  
Density Functional ◽  
Tetrahedral Geometry ◽  
Hindered Rotation ◽  
Hydrogen Bond Acceptor ◽  
Functional Theory ◽  
Vis Spectroscopy ◽  
Hydrogen Bonded

The conformations of the title compounds were determined in solution (NMR and UV-Vis spectroscopy) and in the solid state (FT-IR and XRD), complemented with density functional theory (DFT) in the gas phase. The nonequivalence of the amide protons of these compounds due to the hindered rotation of the C(O)–NH2 single bond resulted in two distinct resonances of different chemical shift values in the aromatic region of their 1H-NMR spectra. Intramolecular hydrogen bonding interactions between the carbonyl oxygen and the sulfonamide hydrogen atom were observed in the solution phase and solid state. XRD confirmed the ability of the amide moiety of this class of compounds to function as a hydrogen bond acceptor to form a six-membered hydrogen bonded ring and a donor simultaneously to form intermolecular hydrogen bonded complexes of the type N–H···O=S. The distorted tetrahedral geometry of the sulfur atom resulted in a deviation of the sulfonamide moiety from co-planarity of the anthranilamide scaffold, and this geometry enabled oxygen atoms to form hydrogen bonds in higher dimensions.

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