scholarly journals Solvent Effect on the Stability and Reverse Substituent Effect in Nitropurine Tautomers

Symmetry ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1223
Author(s):  
Anna Jezuita ◽  
Paweł A. Wieczorkiewicz ◽  
Halina Szatylowicz ◽  
Tadeusz M. Krygowski
Keyword(s):  
Solvent Effect ◽  
Nitro Group ◽  
Density Functional ◽  
Polarizable Continuum Model ◽  
Proximity Effects ◽  
Intramolecular Interactions ◽  
Solvation Energies ◽  
Wide Range ◽  
The Stability ◽  
Reverse Substituent Effect

The solvent effect on the stability and electron-accepting properties (EA) of the nitro group attached to the C2, C6, or C8 position of nitropurine NH tautomers is investigated. For this purpose, the density functional theory (DFT) and the polarizable continuum model (PCM) of solvation in a wide range of solvents (1 < ε < 109) are used. We show that the EA properties of the NO2 group, described by the charge of the substituent active region (cSAR) model, are linearly dependent on the reciprocal of the solvent dielectric constant; in all cases, solvation enhances the EA properties of this group. Furthermore, the sensitivity of EA properties of the nitro group to the solvent effect depends on the proximity effects. It has been shown that the proximity of two endocyclic N atoms (two repulsive interactions) results in higher sensitivity than the asymmetric proximity of the endocyclic N atom and NH group (one repulsive and one attractive interaction). To explain this phenomenon, the geometry of the nitro group in coplanar form and after forcing its rotation around the CN bond is discussed. Relative stabilities of nitropurine tautomers in different solvents are also presented. Differences in the stabilities and solvation energies are explained by aromaticity, electronic structure, and intramolecular interactions of the nitropurine tautomers.

A DFT-D study on the stability and intramolecular interactions of the salts of 1,2,3- and 1,2,4-triazoles

2014 ◽  
Vol 92 (11) ◽  
pp. 1111-1117
Author(s):  
Xueli Zhang ◽  
Xuedong Gong
Keyword(s):  
Hydrogen Bonds ◽  
Density Functional ◽  
Energy Gap ◽  
Lattice Energy ◽  
Intramolecular Interactions ◽  
Dispersion Energy ◽  
Functional Theory ◽  
Formation Reaction ◽  
The Stability ◽  
Intramolecular Hydrogen

Nitrogen-rich 1,2,4-triazole (1) and 1,2,3-triazole (2) react as bases with the oxygen-rich acids HNO3 (a), HN(NO2)2 (b), and HClO4 (c) to produce energetic salts (1a, 1b, and 1c and 2a, 2b, and 2c, respectively) potentially applicable to composite explosives and propellants. In this study, these salts were studied with the dispersion-corrected density functional theory. For the isomers such as 1a and 2a, the more negative ΔrGm of the formation reaction leads to a higher thermally stable salt. The ability to form intramolecular hydrogen bonds predicted with the quantum theory of atoms in molecules has the order of 2 > 1. Different hydrogen bonds result in different second-order perturbation energies, redshifts in IR, and electron density differences. The charge transfer, binding energy, dispersion energy, lattice energy, and energy gap between frontier orbits in the salts of 1 are larger than those of 2, which is helpful for stabilizing the former, and 1 is more obviously stabilized than 2 by formation of salts. Different conformations of 1 and 2 hardly affect the frontier orbital distributions. Base 1 is a more preferred base than 2 to form salts.

scholarly journals Assessing the stability of Pd-exchanged sites in zeolites with the aid of a high throughput quantum chemistry workflow

2021 ◽  
Author(s):  
Hassan Aljama ◽  
Martin Head-Gordon ◽  
Alexis Bell
Keyword(s):  
High Throughput ◽  
High Throughput Screening ◽  
Active Sites ◽  
Density Functional ◽  
Functional Materials ◽  
No Adsorption ◽  
Functional Theory ◽  
Wide Range ◽  
The Stability ◽  
Shed Light

Abstract Cation exchanged-zeolites are functional materials with a wide range of applications from catalysis to sorbents. They present a challenge for computational studies using density functional theory due to the numerous possible active sites. From Al configuration, to placement of extra framework cation(s), to potentially different oxidation states of the cation, accounting for all these possibilities is not trivial. To make the number of calculations more tractable, most studies focus on a few active sites. We attempt to go beyond these limitations by implementing a workflow for a high throughput screening, designed to systematize the problem and exhaustively search for feasible active sites. We use Pd-exchanged CHA and BEA to illustrate the approach. After conducting thousands of individual calculations, we identify the sites most favorable for the Pd cation and discuss the results in detail. The high throughput screening identifies many energetically favorable sites that are non-trivial. Lastly, we employ these results to examine NO adsorption in Pd-exchanged CHA, which is a promising passive NOx adsorbent (PNA) during the cold start of automobiles. The results shed light on critical active sites for NOx capture that were not previously studied.

Encapsulation of Thiotepa and Altretamine as neurotoxic anticancer drugs in Cucurbit[n]uril (n=7, 8) nanocapsules: A DFT study

2016 ◽  
Vol 15 (07) ◽  
pp. 1650056 ◽  
Author(s):  
Keyumars Hassanzadeh ◽  
Keivan Akhtari ◽  
Sara Sheikh Esmaeili ◽  
Azin Vaziri ◽  
Hedyeh Zamani ◽  
...  
Keyword(s):  
Anticancer Drugs ◽  
Chemical Stability ◽  
Density Functional ◽  
Water Solubility ◽  
Polarizable Continuum Model ◽  
Basis Set ◽  
Molecular Characteristics ◽  
The Stability ◽  
Global And Local ◽  
Physical And Chemical

The encapsulation of Altretamine (ALT) and Thiotepa (THI) as neurotoxic anticancer drugs in Cucurbit[[Formula: see text]]uril (CB[[Formula: see text]]) family of macrocycles ([Formula: see text],8) have been investigated and their potential in drug delivery, ability to provide physical and chemical stability, improving water solubility and decreasing the side effects have been studied using density functional theory (DFT) approach with B3LYP and the dispersion corrected functional WB97XD methods by employing the 3-21G* basis set. All the calculations were evaluated for gas phase and water as a pharmaceutical and biological solvent according to the polarizable continuum model (PCM). The non-covalent inter-molecular interactions between the host and guest parts were visualized using reduced density gradient analysis. The molecular characteristics for drugs, CB[[Formula: see text]] and their complexes calculated and the global and local descriptors were employed to study the chemical stability of the host–guest complexes. The results show that the encapsulation of THI and ALT for both CB[7] and CB[8] energetically favorable and this can decrease the central nervous system (CNS) neurotoxicity, and increase the stability of THI in electrophilic and nucleophilic. Beside the CNS neurotoxicity reduction and increasing the stability in electrophilic and nucleophilic attacks, the solubility in water for ALT was improved.

A DFT-D study on the stability and intramolecular interactions of the energetic salts of 3,6-dihydrazido-1,2,4,5-tetrazine

2016 ◽  
Vol 94 (1) ◽  
pp. 28-34
Author(s):  
Xueli Zhang ◽  
Xuedong Gong
Keyword(s):  
Hydrogen Bond ◽  
Density Functional ◽  
Lattice Energy ◽  
Intramolecular Interactions ◽  
Bond Energies ◽  
Dispersion Energy ◽  
Linear Relationships ◽  
The Stability ◽  
Intramolecular Hydrogen ◽  
Hydrogen Bond Energies

Structures of the salts I–IV formed by 3,6-dihydrazido-1,2,4,5-tetrazine with HNO3, HN(NO2)2, HClO4, and HC(NO2)3, respectively, were studied using dispersion-corrected density functional theory. The intramolecular hydrogen bond energies of I–IV were estimated using the quantum theory of atoms in molecules. The total hydrogen bond energies (EH,tot) have the order of I (65.60 kcal/mol) > II (46.24 kcal/mol) > III (39.13 kcal/mol) > IV (19.68 kcal/mol). In addition, the charge transfer (q), binding energy (Eb), lattice energy (HL), dispersion energy (Edis), and second-order perturbation energy (E2) were evaluated for studying the intramolecular interactions between the cation and anion. Linear relationships exist between any two of EH,tot, qtot, Eb, and E2,tot. HLs have the same variation trend as h50s (characteristic height) and may be used as the indicator of impact sensitivity. The HOMOs and LUMOs of I–IV are derived from the HOMOs of the isolated anions and the LUMOs of the isolated cations, respectively. Ultraviolet spectra of I–IV have the strongest absorptions at around 442, 445, 427, and 587 nm, respectively. The excitations HOMO→LUMO to HOMO–7→LUMO play important roles in the first three excited states.

A theoretical study of 3,5-diazido-1,2,4-triazole: the role of the hydrogen bonding interaction in stabilizing the molecular system

2014 ◽  
Vol 92 (9) ◽  
pp. 896-903 ◽  
Author(s):  
Junqing Yang ◽  
Xuedong Gong ◽  
Guixiang Wang
Keyword(s):  
Hydrogen Bonding ◽  
Proton Transfer ◽  
Density Functional ◽  
Molecular System ◽  
Polarizable Continuum Model ◽  
Proton Donor ◽  
Proton Acceptor ◽  
Good Thermal Stability ◽  
The Stability ◽  
Dynamics Simulations

3,5-Diazido-1, 2, 4-triazole (DATZ) is a compound that has a good thermal stability and can be used to produce high energetic ionic salts. The conformations of DATZ were searched by the molecular dynamics simulations and optimized by the molecular mechanics and dispersion-corrected density functional theory methods. The dimer and trimer of DATZ were constructed from the most stable monomer. The hydrogen bonding interactions, which were found to be critically important in increasing the stability of the dimer and trimer, were investigated with the help of the natural bond orbital and the quantum theory of atoms in molecules analyses. The changes in thermodynamic functions, stabilization interaction energies, and hydrogen-bonding energies show that the trimer is most likely the existing form of DATZ. The intramolecular, intermolecular, and water catalytic proton transfer processes were simulated to investigate the proton transfer mechanism. The intermolecular transfer process requires the lowest activation energy (42.56 kJ mol−1) and is the most likely process of proton transfer. DATZ is not only a proton acceptor but also a proton donor. Its weak acidity was quantified as pKa = 10.16. The solvation energy estimated using the conductor-like polarizable continuum model in water is the largest (−99.96 kJ mol−1), revealing that DATZ is more stable in water than in another seven solvents.

scholarly journals Microsolvation of Histidine—A Theoretical Study of Intermolecular Interactions Based on AIM and SAPT Approaches

Symmetry ◽  
2020 ◽  
Vol 12 (7) ◽  
pp. 1153
Author(s):  
Beata Kizior ◽  
Jarosław J. Panek ◽  
Aneta Jezierska
Keyword(s):  
Gas Phase ◽  
Density Functional ◽  
Heterocyclic Ring ◽  
Polarizable Continuum Model ◽  
Water Molecules ◽  
Implicit Solvent ◽  
Actual Interaction ◽  
The Stability ◽  
Explicit Water ◽  
The Impact

Histidine is unique among amino acids because of its rich tautomeric properties. It participates in essential enzymatic centers, such as catalytic triads. The main aim of the study is the modeling of the change of molecular properties between the gas phase and solution using microsolvation models. We investigate histidine in its three protonation states, microsolvated with 1:6 water molecules. These clusters are studied computationally, in the gas phase and with water as a solvent (Polarizable Continuum Model, PCM) within the Density Functional Theory (DFT) framework. The structural analysis reveals the presence of intra- and intermolecular hydrogen bonds. The Atoms-in-Molecules (AIM) theory is employed to determine the impact of solvation on the charge flow within the histidine, with emphasis on the similarity of the two imidazole nitrogen atoms—topologically not equivalent, they are revealed as electronically similar due to the heterocyclic ring aromaticity. Finally, the Symmetry-Adapted Perturbation Theory (SAPT) is used to examine the stability of the microsolvation clusters. While electrostatic and exchange terms dominate in magnitude over polarization and dispersion, the sum of electrostatic and exchange term is close to zero. This makes polarization the factor governing the actual interaction energy. The most important finding of this study is that even with microsolvation, the polarization induced by the presence of implicit solvent is still significant. Therefore, we recommend combined approaches, mixing explicit water molecules with implicit models.

High-throughput computational material screening of the cycloalkane-based two-dimensional Dion–Jacobson halide perovskites for optoelectronics

2021 ◽  
Author(s):  
Guoqi Zhao ◽  
Jiahao Xie ◽  
Kun Zhou ◽  
Bangyu Xing ◽  
Xinjiang Wang ◽  
...  
Keyword(s):  
High Throughput ◽  
Density Functional ◽  
Perovskite Solar Cells ◽  
Two Dimensional ◽  
Photovoltaic Properties ◽  
Wide Range ◽  
Stability Issue ◽  
Halide Perovskites ◽  
The Stability ◽  
Inorganic Framework

Abstract Two-dimensional (2D) layered perovskites have emerged as potential alternates to traditional 3D analogs to solve the stability issue of perovskite solar cells. In recent years, many efforts have been spent on manipulating the interlayer organic spacing cation to improve the photovoltaic properties of Dion–Jacobson (DJ) perovskites. In this work, a serious of cycloalkane (CA) molecules were selected as the organic spacing cation in 2D DJ perovskites, which can widely manipulate the optoelectronic properties of DJ perovskites. The underlying relationship between the CA interlayer molecules and the crystal structures, thermodynamic stabilities, and electronic properties of 58 DJ perovskites has been investigated by using automatic high-throughput workflow cooperated with density-functional (DFT) calculations. We have found that these CA-based DJ perovskites are all thermodynamic stable. The sizes of the cycloalkane molecules can influence the degree of inorganic framework distortion and further tune the bandgaps with a wide range of 0.9~2.1 eV. These findings indicate the cycloalkane molecules are suitable for spacing cation in 2D DJ perovskites and provide a useful guidance in designing novel 2D DJ perovskites for optoelectronic applications.

Intrinsic Stacking Interactions of Natural and Artificial Nucleobases

2019 ◽  
Author(s):  
Drew P. Harding ◽  
Laura J. Kingsley ◽  
Glen Spraggon ◽  
Steven Wheeler
Keyword(s):  
Gas Phase ◽  
Electrostatic Interactions ◽  
Density Functional ◽  
Molecular Descriptors ◽  
Stacking Interactions ◽  
Interaction Energies ◽  
Functional Theory ◽  
Binding Partner ◽  
Heavy Atoms ◽  
Wide Range

The intrinsic (gas-phase) stacking energies of natural and artificial nucleobases were explored using density functional theory (DFT) and correlated ab initio methods. Ranking the stacking strength of natural nucleobase dimers revealed a preference in binding partner similar to that seen from experiments, namely G > C > A > T > U. Decomposition of these interaction energies using symmetry-adapted perturbation theory (SAPT) showed that these dispersion dominated interactions are modulated by electrostatics. Artificial nucleobases showed a similar stacking preference for natural nucleobases and were also modulated by electrostatic interactions. A robust predictive multivariate model was developed that quantitively predicts the maximum stacking interaction between natural and a wide range of artificial nucleobases using molecular descriptors based on computed electrostatic potentials (ESPs) and the number of heavy atoms. This model should find utility in designing artificial nucleobase analogs that exhibit stacking interactions comparable to those of natural nucleobases. Further analysis of the descriptors in this model unveil the origin of superior stacking abilities of certain nucleobases, including cytosine and guanine.

Performance of Electronic Structure Methods for the Description of Hückel-Möbius Interconversions in Extended π-Systems

2019 ◽  
Author(s):  
Tatiana Woller ◽  
Ambar Banerjee ◽  
Nitai Sylvetsky ◽  
Xavier Deraet ◽  
Frank De Proft ◽  
...  
Keyword(s):  
Electronic Structure ◽  
Basis Set ◽  
Dft Methods ◽  
Molecular Switching ◽  
Wide Range ◽  
Electronic Structure Methods ◽  
Explicitly Correlated ◽  
Relative Errors ◽  
The Stability ◽  
Basis Set Expansion

<p>Expanded porphyrins provide a versatile route to molecular switching devices due to their ability to shift between several π-conjugation topologies encoding distinct properties. Taking into account its size and huge conformational flexibility, DFT remains the workhorse for modeling such extended macrocycles. Nevertheless, the stability of Hückel and Möbius conformers depends on a complex interplay of different factors, such as hydrogen bonding, p···p stacking, steric effects, ring strain and electron delocalization. As a consequence, the selection of an exchange-correlation functional for describing the energy profile of topological switches is very difficult. For these reasons, we have examined the performance of a variety of wavefunction methods and density functionals for describing the thermochemistry and kinetics of topology interconversions across a wide range of macrocycles. Especially for hexa- and heptaphyrins, the Möbius structures have a pronouncedly stronger degree of static correlation than the Hückel and figure-eight structures, and as a result the relative energies of singly-twisted structures are a challenging test for electronic structure methods. Comparison of limited orbital space full CI calculations with CCSD(T) calculations within the same active spaces shows that post-CCSD(T) correlation contributions to relative energies are very minor. At the same time, relative energies are weakly sensitive to further basis set expansion, as proven by the minor energy differences between MP2/cc-pVDZ and explicitly correlated MP2-F12/cc-pVDZ-F12 calculations. Hence, our CCSD(T) reference values are reasonably well-converged in both 1-particle and n-particle spaces. While conventional MP2 and MP3 yield very poor results, SCS-MP2 and particularly SOS-MP2 and SCS-MP3 agree to better than 1 kcal mol<sup>-1</sup> with the CCSD(T) relative energies. Regarding DFT methods, only M06-2X provides relative errors close to chemical accuracy with a RMSD of 1.2 kcal mol<sup>-1</sup>. While the original DSD-PBEP86 double hybrid performs fairly poorly for these extended p-systems, the errors drop down to 2 kcal mol<sup>-1</sup> for the revised revDSD-PBEP86-NL, again showing that same-spin MP2-like correlation has a detrimental impact on performance like the SOS-MP2 results. </p>

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