scholarly journals Competition of Intra- and Intermolecular Forces in Anthraquinone and Its Selected Derivatives

Molecules ◽  
2021 ◽  
Vol 26 (11) ◽  
pp. 3448
Author(s):  
Kamil Raczyński ◽  
Andrzej Pihut ◽  
Jarosław J. Panek ◽  
Aneta Jezierska
Keyword(s):  
Perturbation Theory ◽  
Hydrogen Bonds ◽  
Crystalline Phase ◽  
Density Functional ◽  
Environmental Influence ◽  
Topological Analysis ◽  
Intermolecular Forces ◽  
Intramolecular Proton Transfer ◽  
Td Dft ◽  
Electronic Ground

Intra- and intermolecular forces competition was investigated in the 9,10-anthraquinone (1) and its derivatives both in vacuo and in the crystalline phase. The 1,8-dihydroxy-9,10-anthraquinone (2) and 1,8-dinitro-4,5-dihydroxy-anthraquinone (3) contain Resonance-Assisted Hydrogen Bonds (RAHBs). The intramolecular hydrogen bonds properties were studied in the electronic ground and excited states employing Møller-Plesset second-order perturbation theory (MP2), Density Functional Theory (DFT) method in its classical formulation as well as its time-dependent extension (TD-DFT). The proton potential functions were obtained via scanning the OH distance and the dihedral angle related to the OH group rotation. The topological analysis was carried out on the basis of theories of Atoms in Molecules (AIM—molecular topology, properties of critical points, AIM charges) and Electron Localization Function (ELF—2D maps showing bonding patterns, calculation of electron populations in the hydrogen bonds). The Symmetry-Adapted Perturbation Theory (SAPT) was applied for the energy decomposition in the dimers. Finally, Car–Parrinello molecular dynamics (CPMD) simulations were performed to shed light onto bridge protons dynamics upon environmental influence. The vibrational features of the OH stretching were revealed using Fourier transformation of the autocorrelation function of atomic velocity. It was found that the presence of OH and NO2 substituents influenced the geometric and electronic structure of the anthraquinone moiety. The AIM and ELF analyses showed that the quantitative differences between hydrogen bonds properties could be neglected. The bridged protons are localized on the donor side in the electronic ground state, but the Excited-State Intramolecular Proton Transfer (ESIPT) was noticed as a result of the TD-DFT calculations. The hierarchy of interactions determined by SAPT method indicated that weak hydrogen bonds play modifying role in the organization of these crystal structures, but primary ordering factor is dispersion. The CPMD crystalline phase results indicated bridged proton-sharing in the compound 2.

Thermal-induced transformation of glutamic acid to pyroglutamic acid and self-cocrystallization: a charge–density analysis

2022 ◽  
Vol 78 (2) ◽  
Author(s):  
Sehrish Akram ◽  
Arshad Mehmood ◽  
Sajida Noureen ◽  
Maqsood Ahmed
Keyword(s):  
Hydrogen Bonds ◽  
Glutamic Acid ◽  
Single Crystal ◽  
Diffraction Data ◽  
Density Functional ◽  
Quantitative Estimation ◽  
Topological Analysis ◽  
Pyroglutamic Acid ◽  
X Ray Diffraction ◽  
X Ray

Thermal-induced transformation of glutamic acid to pyroglutamic acid is well known. However, confusion remains over the exact temperature at which this happens. Moreover, no diffraction data are available to support the transition. In this article, we make a systematic investigation involving thermal analysis, hot-stage microscopy and single-crystal X-ray diffraction to study a one-pot thermal transition of glutamic acid to pyroglutamic acid and subsequent self-cocrystallization between the product (hydrated pyroglutamic acid) and the unreacted precursor (glutamic acid). The melt upon cooling gave a robust cocrystal, namely, glutamic acid–pyroglutamic acid–water (1/1/1), C5H7NO3·C5H9NO4·H2O, whose structure has been elucidated from single-crystal X-ray diffraction data collected at room temperature. A three-dimensional network of strong hydrogen bonds has been found. A Hirshfeld surface analysis was carried out to make a quantitative estimation of the intermolecular interactions. In order to gain insight into the strength and stability of the cocrystal, the transferability principle was utilized to make a topological analysis and to study the electron-density-derived properties. The transferred model has been found to be superior to the classical independent atom model (IAM). The experimental results have been compared with results from a multipolar refinement carried out using theoretical structure factors generated from density functional theory (DFT) calculations. Very strong classical hydrogen bonds drive the cocrystallization and lend stability to the resulting cocrystal. Important conclusions have been drawn about this transition.

An analogy study on ESIPT reaction for 3BHC sensor between polar DMF and nonpolar toluene

2017 ◽  
Vol 95 (12) ◽  
pp. 1303-1307
Author(s):  
Dapeng Yang ◽  
Min Jia ◽  
Jingyuan Wu ◽  
Xiaoyan Song ◽  
Qiaoli Zhang
Keyword(s):  
Excited State ◽  
Density Functional ◽  
Emission Spectra ◽  
Dft Method ◽  
Intramolecular Proton Transfer ◽  
Nonpolar Solvent ◽  
State Behavior ◽  
Functional Theory ◽  
Td Dft ◽  
Intramolecular Hydrogen

A comparison about excited state intramolecular proton transfer (ESIPT) mechanism of a new sensor 3-(1,3-benzothiazol-2-yl)-2-hydroxynaphthalene-1-carbaldehyde (3BHC) in polar solvent dimethylformamide (DMF) and nonpolar solvent toluene have been investigated within the framework of the time-dependent density functional theory (TD-DFT) method. The reproduced previous experimental absorption and emission spectra via our calculations reveals the reasonability of the DFT and TD-DFT theoretical level. The staple bond lengths, bond angles, and corresponding infrared vibrational spectra demonstrate that the intramolecular hydrogen bond of 3BHC should be strengthened in both polar DMF and nonpolar toluene. Two kinds of ESIPT mechanisms for different solvents have been put forward; there is a low potential barrier in the ESIPT process in the DMF solvent, whereas there is almost a nonbarrier for the ESIPT process in the toluene solvent. Hence, we could conclude that the ESIPT process of 3BHC sensor is more likely to occur in the nonpolar solvent upon the photoexcitation, based on which, the excited state behavior of 3BHC could be controlled.

Intra- and intermolecular interactions in small bioactive molecules: cooperative features from experimental and theoretical charge-density analysis

2006 ◽  
Vol 62 (4) ◽  
pp. 612-626 ◽  
Author(s):  
Parthapratim Munshi ◽  
Tayur N. Guru Row
Keyword(s):  
Salicylic Acid ◽  
Hydrogen Bonds ◽  
Intermolecular Interactions ◽  
Density Functional ◽  
Theoretical Calculations ◽  
Topological Analysis ◽  
Van Der Waals Interactions ◽  
Bioactive Molecules ◽  
Topological Features ◽  
Weak Intermolecular Interactions

The topological features of the charge densities, ρ(r), of three bioactive molecules, 2-thiouracil [2,3-dihydro-2-thioxopyrimidin-4(1H)-one], cytosine [4-aminopyrimidin-2(1H)-one] monohydrate and salicylic acid (2-hydroxybenzoic acid), have been determined from high-resolution X-ray diffraction data at 90 K. The corresponding results are compared with the periodic theoretical calculations, based on theoretical structure factors, performed using DFT (density-functional theory) at the B3LYP/6-31G** level. The molecules pack in the crystal lattices via weak intermolecular interactions as well as strong hydrogen bonds. All the chemical bonds, including the intra- and intermolecular interactions in all three compounds, have been quantitatively described by topological analysis based on Bader's quantum theory of `Atoms In Molecules'. The roles of interactions such as C—H...O, C—H...S, C—H...π and π...π have been investigated quantitatively in the presence of strong hydrogen bonds such as O—H...O, N—H...O and N—H...S, based on the criteria proposed by Koch and Popelier to characterize hydrogen bonds and van der Waals interactions. The features of weak intermolecular interactions, such as S...S in 2-thiouracil, the hydrogen bonds generated from the water molecule in cytosine monohydrate and the formation of the dimer via strong hydrogen bonds in salicylic acid, are highlighted on a quantum basis. Three-dimensional electrostatic potentials over the molecular surfaces emphasize the preferable binding sites in the structure and the interaction features of the atoms in the molecules, which are crucial for drug–receptor recognition.

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.

Theoretical investigation on ESIPT mechanism for a novel Sal-3,4-benzophen system

2017 ◽  
Vol 16 (08) ◽  
pp. 1750073 ◽  
Author(s):  
Jian Lv ◽  
Dapeng Yang
Keyword(s):  
Excited State ◽  
Hydrogen Bonds ◽  
Potential Energy ◽  
Density Functional ◽  
Intramolecular Proton Transfer ◽  
Potential Energy Curves ◽  
State Process ◽  
The Density Functional Theory ◽  
Intramolecular Hydrogen ◽  
Excited State Process

In this work, we theoretically investigate the properties of excited state process for a novel salicylidene sal-3,4-benzophen (Sal-3,4-B) system, which contains two intramolecular hydrogen bonds (O1-H2[Formula: see text]N3 and O4-H5[Formula: see text]N6). Based on the density functional theory (DFT) and time-dependent DFT (TDDFT) methods, we find these two hydrogen bonds should be strengthened in the S1 state, while the O4-H5[Formula: see text]N6 one could be largely affected upon the excitation process. Analyses about infrared (IR) vibrational spectra about hydrogen bond moieties also confirm this viewpoint. Frontier molecular orbitals (MOs) depict the nature of electronic excited state and support the excited state intramolecular proton transfer (ESIPT) reaction.Two kinds of stepwise potential energy curves of Sal-3,4-B in the S1 state demonstrate that only one proton could be transferred. Also based on constructing potential energy curves, the synergetic situation could be eliminated. Due to the specific ESIPT mechanism for Sal-3,4-B, we successfully explain the previous experiment and provide a reasonable attribution to the second emission peak of experiment.

scholarly journals Computational Study on the Mechanism of the Photouncaging Reaction of Vemurafenib: Toward an Enhanced Photoprotection Approach for Photosensitive Drugs

Molecules ◽  
2021 ◽  
Vol 26 (7) ◽  
pp. 1846
Author(s):  
Abdulilah Dawoud Bani-Yaseen
Keyword(s):  
Anticancer Drug ◽  
Density Functional ◽  
Computational Study ◽  
Intramolecular Proton Transfer ◽  
Substantial Impact ◽  
Photochemical Behavior ◽  
Td Dft ◽  
Notable Increase ◽  
The Impact ◽  
Kinetics Of

The photochemical behavior of the photosensitive first-line anticancer drug vemurafenib (VFB) is of great interest due to the impact of such behavior on its pharmacological activity. In this work, we computationally elucidated the mechanism of the photoinduced release of VFB from the 4,5-dimethoxy-2-nitrobenzene (DMNB) photoprotecting group by employing various density functional theory (DFT)/time-dependent DFT (TD-DFT) approaches. The computational investigations included a comparative assessment of the influence of the position of the photoprotecting group as a substituent on the thermodynamics and kinetics of the photouncaging reactions of two VFB-DMNB prodrugs, namely pyrrole (NP) and sulfonamide (NS). With the aid of the DFT calculations concerning the activation energy barrier (∆G‡), the obtained results suggest that the step of the photoinduced intramolecular proton transfer of the DMNB moiety is not detrimental concerning the overall reaction profile of the photouncaging reaction of both prodrugs. However, the obtained results suggested that the position of the substitution position of the DMNB photoprotecting group within the prodrug structure has a substantial impact on the photouncaging reaction. In particular, the DMNB-Ns-VFB prodrug exhibited a notable increase in ∆G‡ for the key step of ring opining within the DMNB moiety indicative of potentially hindered kinetics of the photouncaging process compared with DMNB-Np-VFB. Such an increase in ∆G‡ may be attributed to the electronic influence of the NP fragment of the prodrug. The results reported herein elaborate on the mechanism of the photoinduced release of an important anticancer drug from photoprotecting groups with the aim of enhancing our understanding of the photochemical behavior of such photosensitive pharmaceutical materials at the molecular level.

scholarly journals Theoretical study of lumichrome, 1-methyl-lumichrome and lumiflavin binding ability with thymine

2021 ◽  
Vol 14 (1) ◽  
pp. 7-13
Author(s):  
Denisa Cagardová ◽  
Martin Michalík ◽  
Vladimír Lukeš
Keyword(s):  
Hydrogen Bonds ◽  
Density Functional ◽  
Fluorescence Spectra ◽  
Photophysical Properties ◽  
Theoretical Data ◽  
Binding Ability ◽  
Functional Theory ◽  
The Density Functional Theory ◽  
Electronic Ground ◽  
Experimental Absorption

Abstract Gas-phase geometry and electronic structure of lumichrome, 1-methyl-lumichrome and lumiflavin in the electronic ground state and their excited states were investigated using the Density Functional Theory. Their binding ability with thymine was estimated for model van der Waals dimers with two intermolecular hydrogen bonds. The influence of hydrogen bonds on their photophysical properties was analyzed. Obtained theoretical data were compared with available experimental absorption and fluorescence spectra.

Elaborating a new excited state intramolecular proton transfer (ESPT) mechanism for a new π-conjugated dye 2, 2′-((5-(2-(4-methoxyphenyl)ethenyl)-benzene-1,1-diyl)-bis-(nitrilomethylylidene)-diphenol)

2018 ◽  
Vol 96 (3) ◽  
pp. 351-357 ◽  
Author(s):  
Dapeng Yang ◽  
Min Jia ◽  
Xiaoyan Song ◽  
Qiaoli Zhang
Keyword(s):  
Hydrogen Bond ◽  
Excited State ◽  
Charge Transfer ◽  
Hydrogen Bonds ◽  
Proton Transfer ◽  
Density Functional ◽  
Dynamical Behavior ◽  
Intramolecular Proton Transfer ◽  
Intramolecular Hydrogen Bonds ◽  
Intramolecular Hydrogen

In this work, the excited state dynamical behavior of a novel π-conjugated dye 2,2′-((5-(2-(4-methoxyphenyl)ethenyl)-benzene-1,1-diyl)-bis-(nitrilomethylylidene)-diphenol) (C1) has been investigated. Two intramolecular hydrogen bonds of C1 are tested to pre-existing in the ground state via AIM and reduced density gradient. Using a time-dependent density functional theory (TDDFT) method, it has been substantiated that the intramolecular hydrogen bonds of C1 should be strengthened in the S1 state via analyzing fundamental bond length, bond angles, and corresponding infrared vibrational modes. The most obvious variation of these two hydrogen bonds is the O4–H5···N6 bond, which might play important roles in excited state behavior for the C1 system. Furthermore, based on electronic excitation, charge transfer could occur. Just due to this kind of charge re-distribution, two hydrogen bonds should be tighter in the first excited state, which is consistent with the variation of hydrogen bond lengths. Thus, the phenomenon of charge transfer is reasonable evidence for confirming the occurrence of the excited state proton transfer (ESPT) process in the S1 state. Our theoretically constructed potential energy surfaces of C1 show that excited state single proton transfer should occur along with the O4–H5···N6 hydrogen bond rather than the O1–H2···N3 bond. We not only clarify the ESIPT mechanism for C1 but put forward new affiliation and explain a previous experiment successfully.

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