Polarizable Continuum Method Research Articles

Theoretical study of the absorption and emission spectra of 1,2-Bis(9-anthryl)acetylene in cyclohexane and acetonitrile

In this work we use TD-DFT combined with Polarizable Continuum Method and QM/MM approach to analyze the absorption and emission spectra of 1,2-bis(9-anthryl)acetylene in cyclohexane and acetonitrile. The absorption band located at 250 nm is found to be composed by several absorption transitions contributing to its high intensity. Solvent effects are found to be mild in the positions of the absorption and emission bands but influence the relaxation of the excited state. We thus corroborate the experimental contention of a charge-transfer excited state with symmetry-break after the absorption in polar acetonitrile and leading to an emission transition at 510 nm.

Efficiency of CuCr2O4/Titanium dioxide nanoparticles composite for organic dye removal in aqueous solutions

Semiconductor metal oxide with TiO2 nanoparticles removes hazardous compounds from environmental samples. TiO2 nanoparticles have shown potential as an efficient photocatalyst by being employed as a nano-catalyst for the breakdown of organic contaminants in wastewater samples. To separate substances from contaminated samples, combined UV and visible light irradiation has been used. Sol-gel synthesis was used to produce a copper chromite-titanium nanocomposite, which was then evaluated using analytical methods, such as XRD, BET, DRS-UV, and FT-IR. Using visible light, the photocatalytic activity of a nanocomposite made of CuCr2O4 and TiO2 was investigated for its role in the breakdown of malachite green. The effects of several parameters, including pH change, anions presence, contact time, catalyst amount, concentration variation, and the kinetics of photocatalytic degradation were investigated. The magnitude of transition energy calculated using UV-DRS spectra was found to be 3.1 eV for CuCr2O4−TiO2 nanocomposite. Maximum degradation was observed at pH 7.0. The surface area and pore volume of the co-doped samples of Cr2O4 – TiO2 obtained from BET were found to be 6.1213 m2/g and 0.045063 cm3/g respectively. The average particle size of the catalyst of the nano-catalysts calculated from XRD was found to be 8 nm for TiO2 and 66 nm for TiO2–CuCrO4. The peaks obtained in FTIR between the range of 900-500 cm−1 were due to the presence of an aromatic compound. The binding mechanism of a dye molecule to the surface of CuCr2O4–TiO2 nanocomposite was analysed using quantum chemical calculations with the self-consistent reaction field technique employing integral equation formalism for the polarized continuum method and the UFF atomic radii set.

A Theoretical Study of Solvent Effects on the Structure and UV-vis Spectroscopy of 3-Hydroxyflavone (3-HF) and Some Simplified Molecular Models.

Solvent effects on the UV-vis spectra of 3-hydroxyflavone and other structurally related molecules (3-hydroxychromen-4-one, 3-hydroxy-4-pyrone, and 4-pyrone) have been studied by combining time-dependent density functional theory (TDDFT) and the polarizable continuum method (PCM). Among the first five excited states of the four considered molecules, electronic states of n → π* and π → π* nature appear. In general, the stability of the n → π* states decreases as the π space becomes larger in such a way that only for 4-pyrone and 3-hydroxy-4-pyrone are they the first excited states. In addition, they become less stabilized in ethanol solution than the ground state, and this causes blueshift transitions in solution. The opposite trend is found for the π → π* excited states. They are less energetic with the π-system size and when passing from gas phase to solution. The solvent shift also depends strongly on the size of the π systems and on the formation of an intramolecular hydrogen bond; thus, it decreases when going from 4-pyrone to 3-hydroxyflavone. The performance of the three versions (cLR, cLR2, and IBSF) of the specific-state PCM method in predicting transition energies are compared.

Theoretical prediction of superatom molecular orbitals (SAMOs) in the ice-like cluster (H2O)10 and its impact in the supramolecular chemistry and function of nanostructured water

Superatom molecular orbitals (SAMOs) are atom-like molecular orbitals that have been observed in the buckminsterfullerene C60 molecule. We studied the ice-like water cluster (H2O)10 that is expected to be ubiquitous in nature in nanoscale microenvironments at ambient temperatures due to the nanoconfinement effect. We report for the first time the theoretical prediction of the existence of SAMOs in the adamantanoid nanostructured water cluster (H2O)10. The geometry of the adamantanoid water cluster (H2O)10 was optimized using the Restricted Hartree-Fock method and the ab-initio second-order Møller-Plesset perturbation theory (MP2) method, as well as the aqueous solvent phase polarizable continuum method (PCM). The optimized (H2O)10 structure is a distorted adamantanoid that closely matches the crystal structure of (H2O)10 that was previously reported. The theoretical studies using Hartree-Fock (HF), MP2, or Density Functional Theory (DFT) predict that the adamantanoid water cluster (H2O)10 exhibits SAMOs in the low-lying LUMOs. The orbital energies calculated with these methods are reported. The lowest-lying SAMOs in the water cluster (H2O)10 is the most intriguing SAMO due to its s-orbital character and potential to delocalize electrons in a large area that surrounds the cluster. The electron affinity of the water cluster (H2O)10 was calculated using HF, MP2, and DFT methods and the values obtained from each method were (kJ/mol) +74.71, -770.58, and -48.57, respectively. The existence of SAMOs in low-lying LUMO levels indicate of possible supramolecular chemistry of the water clusters with interfacial implications in nanoconfined spaces. Overall, these theoretical results predict new fundamental properties of water clusters that may have deep implications and impact in biological and nanotechnology systems that involve nanostructured water in confined spaces.

Radical-scavenging activity characterization of a series of synthetic 3-phenylcoumarins

A series of synthetic hydroxyl derivatives of 3-phenylcoumarin with already assessed radical-scavenging activity were modeled and treated with quantum-chemistry methods in order to get insight into the structural and energy changes occurring during dissociation of OH bonds by different mechanisms. The enthalpy changes of each step were calculated and the role of the OH-group positions in the molecules, as well as the influence of the second hydroxyl group on the reactivity were evaluated. The geometry of each intermediate structure was optimized using B3LYP/DFT functional and the standard 6-311++G(d,p) orbital basis set. Solvent effects were accounted for using the SCRF method, via the polarized continuum method.

Perspective for aggregation-induced delayed fluorescence mechanism: A QM/MM study**Project supported by the National Natural Science Foundation of China (Grant Nos. 11874242, 11974216, and 11904210), Shandong Provincial Natural Science Foundation, China (Grant No. ZR2019MA056), Taishan Scholar Project of Shandong Province, China, and the China Postdoctoral Science Foundation (Grant No. 2018M642689).

To enhance the potential application of thermally activated delayed fluorescence (TADF) molecular materials, new functions are gradually cooperated to the TADF molecules. Aggregation induced emission can effectively solve the fluorescence quenching problem for TADF molecules in solid phase, thus aggregation-induced delayed fluorescence (AIDF) molecules were recently focused. Nevertheless, their luminescent mechanisms are not clear enough. In this work, excited state properties of an AIDF molecule DMF-BP-DMAC [reported in Chemistry–An Asian Journal 14 828 (2019)] are theoretically studied in tetrahydrofuran (THF) and solid phase. For consideration of surrounding environment, the polarizable continuum method (PCM) and the combined quantum mechanics and molecular mechanics (QM/MM) method were applied for solvent and solid phase, respectively. Due to the increase of the transition dipole moment and decrease of the energy difference between the first single excited state (S1) and the ground state (S0), the radiative rate is increased by about 2 orders of magnitude in solid phase. The energy dissipation of the non-radiative process from S1 to S0 is mainly contributed by low-frequency vibrational modes in solvent, and they can be effectively suppressed in aggregation, which may lead to a slow non-radiation process in solid phase. Both factors would induce enhanced luminescence efficiency of DMF-BP-DMAC in solid phase. Meanwhile, the small energy gap between S1 and triplet excited states results in high reverse intersystem crossing (RISC) rates in both solvent and solid phase. Therefore, TADF is confirmed in both phases. Aggregation significantly influences both the ISC and RISC processes and more RISC channels are involved in solid state. The enhanced delayed fluorescence should be induced by both the enhanced fluorescent efficiency and ISC efficiency. Our calculation provides a reasonable explanation for experimental measurements and helps one to better understand the luminescence mechanism of AIDF molecules.

Theoretical investigations on the HOMO–LUMO gap and global reactivity descriptor studies, natural bond orbital, and nucleus-independent chemical shifts analyses of 3-phenylbenzo[d]thiazole-2(3H)-imine and its para-substituted derivatives: Solvent and substituent effects

Natural bond orbital analysis, salvation, and substituent effects of electron-releasing (–CH3, –OH) and electron-withdrawing (–Cl, –NO2, –CF3) groups at para positions on the molecular structure of synthesized 3-phenylbenzo[ d]thiazole-2(3 H)-imine and its derivatives in selected solvents (acetone, toluene, and ethanol) and in the gas phase by employing the polarizable continuum method model are studied using the M06-2x method and 6-311++G(d,p) basis set. The relative stability of the studied compounds is influenced by the possibility of intramolecular interactions between substituents and the electron donor–acceptor centers of the thiazole ring. Furthermore, atomic charges, electron density, chemical thermodynamics, energetic properties, dipole moments, and nucleus-independent chemical shifts of the studied compounds and their relative stability are considered. The dipole moment values and the highest occupied molecular orbital–lowest unoccupied molecular orbital energy gaps reveal different charge-transfer possibilities within the considered molecules. Finally, natural bond orbital analysis is carried out to picture the charge transfer between the localized bonds and lone pairs.

DFT study on tautomerism and natural bond orbital analysis of 4-substituted 1,2,4-triazole and its derivatives: solvation and substituent effects.

Density functional theory investigations at the DFT-B3LYP/6-311++G** theoretical level employed to determine the tautomerism, substituent effects of 4-substituted 4-amino-5-methyl-2,4-dihydro-3H-1,2,4-triazole-3-thione, and its derivatives (4-R-H, 4-R-CH3, 4-R-F, 4-R-NO2) in the selected solvent (acetone, acetonitrile, and dichloromethane) and gas phases using the polarizable continuum method (PCM) model. The substituted 1,2,4-triazoles have two main different tautomers namely N2-H and S7-H. For considered derivatives, thione forms are more energetically stable and dominant form in the studied solvent and gas phases. In addition, geometrical parameters, charges on atoms, dipole moments, energetic properties, and the nucleus-independent chemical shifts (NICS) are investigated. It has been seen that these molecular features of the studied compound and its derivatives are mostly solvent dependent. For electron-releasing and -withdrawing derivatives in the solution and gas phases, 2-H forms are the more stable and dominant form. The relative stability of the C4-substituted 1,2,4-triazole tautomerism is influenced by the possibility for intramolecular interactions between substituent and electron-donor or electron-acceptor centers of the triazole ring.

DFT study and NBO analysis of solvation/substituent effects of 3-phenylbenzo[d]thiazole-2(3H)-imine derivatives

In this work, to determine natural bond orbital (NBO) analysis, solvation and substituent effects for electron-releasing substituents (CH3, OH) and electron-withdrawing derivatives (Cl, NO2, CF3) in para positions on the molecular structure of the synthesized 3-phenylbenzo[d]thiazole-2(3H)-imine derivatives 1?6 (H (1), CH3 (2), Cl (3), OH (4), CF3 (5), NO2 (6)) in the selected solvents (acetone, toluene, and ethanol) and gas-phase employing polarizable continuum method (PCM) model were studied at the M06-2x/6- -311++G(d,p) level of theory. The relative stability of the studied compounds was affected by the possibility of intramolecular interactions between substituents and the electron donor/acceptor centers of the thiazole ring. Furthermore, atomic charges electron density, chemical thermodynamics, energetic properties, dipole moments, and the nucleus-independent chemical shifts (NICS) of the studied compounds and their relative stability are considered. The dipole moment values and the HOMO?LUMO energy gap reveal the different charge transfer possibilities within the considered molecules. Frontier molecular orbital (FMO) analysis revealed that compound 6 has very small HOMO-LUMO energy gaps in the considered phases, and thus is kinetically less stable. The obtained HOMO-LUMO energy gap corresponds to intramolecular hyperconjugative interactions ?? ?*. Finally, NBO analysis is carried out to demonstrate the charge transfer between localized bonds and lone pairs.

Optical and electronic properties of nickel(II) coordinated to chiral amino-alcohols. An experimental and theoretical study

Abstract In this work it was investigated the experimental and theoretical properties of chiral acetyl aminoalcohols and their octahedral coordination compounds with nickel(II). Structural relaxation to determine the ground state (GS) were based on their X-ray crystal structures. DFT (Density Functional Theory) was applied for electronic exchange and correlation, PCM (polarizable continuum method) for the simulation of water solvent effects. The experimental circular dichroism (CD) for the studied diasteromers [Ni(S,S(+)Hcpse)2] 6 and [Ni(R,S(−) Hceph)2]∙7 compounds, with two chiral C atoms, presented CD spectra with mirror images and opposite Cotton effects. This was confirmed by the theoretical calculations, TD-DFT (Time-Dependent DFT), which allowed to assign the observed electronic transitions. The influence of the spatial orientation of the substituents at the chiral carbon atom, which may produce marked effects on the electronic properties, was analyzed by means of these two approaches. A similar study was carried on for the [Ni(R(−) Hcphen)2] 8 compound, with only one chiral C atom, as the C-methyl group is replaced by a C–H, in order to investigate the differences on the electronic properties of 6 and 7. The differences of 6, 7 and 8 are reflected on the dipole moments, stereochemistry and compositions of the orbitals involved in the electronic transitions in the CD spectra.

Analytical calculation of pressure for confined atomic and molecular systems using the eXtreme-Pressure Polarizable Continuum Model.

We show that the pressure acting on atoms and molecular systems within the compression cavity of the eXtreme-Pressure Polarizable Continuum method can be expressed in terms of the electron density of the systems and of the Pauli-repulsion confining potential. The analytical expression holds for spherical cavities as well as for cavities constructed from van der Waals spheres of the constituting atoms of the molecular systems. © 2018 Wiley Periodicals, Inc.

Solvent effect on the intermolecular proton transfer of the Watson and Crick guanine-cytosine and adenine-thymine base pairs: a polarizable continuum model study.

Herein we present our results on the study of the double proton transfer (DPT) mechanism in the adenine-thymine (AT) and guanine-cytosine (GC) base pairs, both in gas phase and in solution. The latter was modeled using the polarizable continuum method (PCM) in different solvents. According to our DFT calculations, the DPT may occur for both complexes in a stepwise mechanism in condensate phase. In gas phase only the GC base pair exhibits a concerted DPT mechanism. Using the Wigner's tunneling corrections to the transition state theory we demonstrate that such corrections are important for the prediction of the rate constants of both systems in gas and in condensate phase. We also show that (i) as the polarity of the medium decreases the equilibrium constant of the DPT reaction increases in both complexes, and (ii) that the equilibrium constant in the GC complex is four orders of magnitude larger than in AT. This observation suggests that the spontaneous mutations in DNA base pairs are more probable in GC than in AT.

(Keynote) Electroreduction of Nitrocyclopropanes and Nitrophenyl Cyclopropanes: Mechanism of Cleavage of the Radical Anion

There are three possible mechanisms of cleavage of a nitrocyclopropane radical anion: homolytic cleavage to a cyclopropyl radical and a nitrite anion, homolytic cleavage to a distonic radical anion, and heterolytic cleavage to a different distonic radical anion. With the models synthesized so far, only products of the first mechanism were observed. On the other hand, only two cleavage mechanisms are possible for a nitrophenyl cyclopropane radical anion: homolytic cleavage to a distonic radical anion and heterolytic cleavage to a different distonic radical anion. The isolation and characterization of the products resulting from the cleavage of the nitrophenyl radical anion do not allow to distinguish between the two cleavage mechanisms. To shed light on the mechanisms of cleavage of those radical anions, density functional (DFT) quantum chemical calculations (B3LYP 6-31+G(d)) were carried out, including solvation energies in acetonitrile, computed using the polarizable continuum method.

(Keynote) Electroreduction of Nitrocyclopropanes and Nitrophenyl Cyclopropanes: Mechanism of Cleavage of the Radical Anion

There are three possible mechanisms of cleavage of a nitrocyclopropane radical anion 1•‾, mechanisms A (homolytic cleavage to a cyclopropyl radical 2• and a nitrite anion), B (homolytic cleavage to a distonic radical anion 3•‾ ), and C (heterolytic cleavage to a distonic radical anion 4•‾ [1]. With the models synthesized so far (Y = Z= alkyl, H = COOCH3), only products of mechanism A have been observed [1]. On the other hand, only two cleavage mechanisms are possible for a nitrophenyl cyclopropane radical anion 5•‾, mechanisms D (homolytic cleavage to the distonic radical anion 6•‾ ) and E (heterolytic cleavage to the distonic radical anion 7•‾ ) [1]. The isolation and characterization of the products resulting from the cleavage of the nitrophenyl radical anion 5•‾ do not allow to distinguish between the two cleavage mechanisms D (homolytic cleavage) and E (heterolytic cleavage) leading to the distonic radical anions 6•‾ and 7•‾ respectively. To shed light on the mechanisms of cleavage of those radical anions, density functional (DFT) quantum chemical calculations were carried out on species 1-3 (B3LYP 6-31+G(d), including solvation energies in acetonitrile computed using the polarizable continuum method. The results clearly favor mechanism B and species 3 over mechanisms A and C for the decomposition of anion radicals 1•‾ whenZ = Y = alkyl and X = H. [1] F. Couture-Martin, A. Sardashti, C. Cristea, J.M. Chapuzet, J. Lessard, ECS Transactions, 2008, 13, 13-19. Figure 1

Electronic structure and absorption spectra of fluorescent nucleoside analogues.

This work presents a systematic investigation of the electronic and conformational properties of five new fluorescent nucleobases belonging to the alphabet based on the isothiazole[4,3-d]pyrimidine molecule, very recently synthesized. This is of particular importance in the characterization of the main electronic aspects of these fluorescent nucleosides. The solvent effects of 1,4-dioxane and water were included combining the Sequential Monte Carlo/CASPT2 and the Free Energy Gradient (FEG) methods. For comparison, the Polarizable Continuum method was also used. The geometries of all compounds were optimized in solvent with the largest effects observed in water using the average solvent electrostatic configuration (ASEC) and the FEG approaches. Statistical analysis of the solute-solvent hydrogen bonds is performed and their effect on the absorption spectra analyzed. The dipole moments were calculated and the value obtained from the ASEC-FEG method in water follows the same trend as the natural canonical bases (adenine → uracil → guanine → cytosine). The theoretical results for the absorption spectra obtained from CASPT2(18,13) calculations using the geometries obtained with the ASEC-FEG procedure are in very good agreement with the experimental data. A detailed elucidation of the main aspects of the absorption spectra of the five new fluorescent nucleoside analogues is successfully attempted.

Polyoxomolybdate formation – A thermodynamic analysis from density functional/PCM calculations

Polyoxomolybdates have been intensely investigated, but their mechanisms of formation are not completely understood. The complex equilibrium of different species is affected by concentration, pH, ionic strength and temperature. It is a challenging system to model using computational chemistry. In the present work, density functional calculations were carried out using the polarizable continuum method to include solvent effects in an effort to provide insight into the mechanism of polyoxomolybdate formation in aqueous solution. We establish a possible sequence of reactions for the formation of small polyoxomolybdates containing up to 8 Mo by addition of the monomeric unit [MoO4]2−.

Replacement of Oxygen by Sulfur in Small Organic Molecules. 2. Theoretical Studies on the Tautomeric Equilibria of the 5-OH Substituted Oxazole, Thiazole, Isoxazole, and Isothiazole in the Isolated State and in Solution

Heterocycles are frequently appearing structure-building elements in drug candidates. The present paper investigates the consequences of the replacement of the oxygen atom by a sulfur atom in the isomeric rings of 5OH-oxazole and 5OH-isoxazole. Theoretical calculations at the B97D/aug-cc-pvqz level (with five additional “d” functions on the S atom) and considering the CCSD(T) level at the complete basis set limit followed the structural and concomitant free energy changes for the four title molecules in the isolated state, and in dichloromethane and water solvents. The selected species are subject to both conformational and tautomeric transformations. The polarizable continuum method (PCM) was applied for in-solution geometry optimization and estimation of the free energy components. In addition, explicit solvent Monte Carlo simulations were performed to calculate the relative solvation free energies of selected tautomers. This latter method allows for presenting solute atom - solvent atom radial distribution functions and the estimation of the number solute-solvent hydrogen bonds. The tautomeric preferences for the oxygen and sulfur containing species, which are sometimes different, were discussed and the calculated results were compared with experimental measurements for the structure composition available for 5OH-isoxazole and its methyl derivatives of in water. Potential of mean force curves were calculated for the 5-one tautomers of 5OH-isothiazole in dichloromethane and the possible tautomeric pathways for this solute in a non-protic solvent was discussed. Keywords: Conformational/tautomeric equilibria, Monte Carlo, PCM, potential of mean force, solution structure, tautomerization mechanism.

Mechanism of Thiol-Induced Nitrogen(II) Oxide Donation by Furoxans: a Quantum-Chemical Study

Quantum-chemical calculations according to DFT with UB3LYP functional in the 6-311++G** basis set, and accounting for solvation effects by the polarized continuum method were used to study the mechanisms of thiol-induced fragmentation of unsubstituted and annulated furoxans with the elimination of nitrogen(II) oxide. A preference for NO formation according to the radical mechanism involving an attack by sulfanyl radical (HS˙) on the carbon atom bonded to the N-oxide group was demonstrated for all systems. Anionic mechanisms involving HS– anions were not feasible in any of the cases due to high endothermic effects.

Study of the stepwise deprotonation reactions of glyphosate and the corresponding pKa values in aqueous solution.

Glyphosate (N-(phosphonomethyl)glycine) (Gph) is a herbicide that is broadly used in several countries. Its application to eliminate weeds may have the undesired effect of diminishing the metallic cations found in the soil (e.g., Ni(2+) and Zn(2+)), due to a complexation reaction that depends on the soil's pH. To better understand the molecular structures of glyphosate that are involved in such a complexation reaction, we have studied all possible glyphosate conformations in aqueous solution that may be involved in deprotonation reactions in the pH range from 2 to 11 using the polarizable continuum method (PCM). We have also compared direct (or absolute) methods to calculate pKa values, the cluster-continuum model and the proton-exchange scheme, using different thermodynamic cycles. The best result was achieved when using a proton-exchange scheme, which was able to properly reproduce three glyphosate experimental pKa values predicted for the glyphosate structures and conformations previously determined.

Molecular structure, spectroscopic properties, NLO, HOMO–LUMO and NBO analyses of 6-hydroxy-3(2H)-pyridazinone

The molecular structure and relative stabilities of the six possible isomers of 6-hydroxy-3(2H)-pyridazinone (DHP) in the gas phase and in solutions of different polarities are predicted using the B3LYP/6-311++G(d,p) method. The oxo-hydroxo isomer is the most stable form in the gas phase and in solution. These results agree with our reported X-ray structure. The effect of solvents on the spectroscopic properties of the most stable isomer has been studied using the polarized continuum method (PCM) at the same level of theory. The vibrational spectra of the compound studied are calculated and compared with the experimentally measured FTIR spectra. The electronic spectra in gas phase and in solution were calculated using the TD-DFT method. The most intense absorption band is predicted at 312.4nm and belongs mainly to a π→π* transition. In polar solvents, this spectral band undergoes a hypsochromic shift. Two stable dimer forms were calculated at same level of theory. Dimer A is more stable than dimer B, by 6.66kcalmol−1. The former is stabilized by stronger OH⋯O H-bonds compared to the weaker NH⋯O interactions in the latter. The effect of these H-bonding interactions on the molecular structure and vibrational spectra of these compounds are predicted. NBO analyses were carried out to investigate the stabilization energy of various inter- and intramolecular charge transfer interactions within the systems studied.