Conductor-like Polarizable Continuum Model Research Articles

TD-DFT Study on Thiacalix[4]arene, the Receptor of a Fluorescent Chemosensor for Cu2.

The electronic and spectral properties of p-tert-butylthiacalix[4]arene (TCA) and its Cu2+ complexes (CuTCA and Cu2TCA) were characterized by time-dependent density functional theory (TD-DFT). Geometries of TCA, CuTCA, and Cu2TCA were optimized at the CAM-B3LYP/6-31+G(d,p) level of theory in water using the conductor-like polarizable continuum model. The absorption spectra of TCA, CuTCA, and Cu2TCA were demonstrated by TD-DFT method. The quenching mechanism of perylene as the fluorophore of a chemosensor based on thiacalix[4]arene was discussed. The addition of Cu2+ to TCA introduced a series of low-lying excited states involving copper d orbitals. The overlap between absorption of TCA complexes and emission of perylene indicated that the quenching of perylene fluorescence is due to fluorescence resonance energy transfer.

An integrated theoretical and experimental investigation of insensitive munition compounds adsorption on cellulose, cellulose triacetate, chitin and chitosan surfaces

This manuscript reports results of combined computational chemistry and batch adsorption investigation of insensitive munition compounds, 2,4-dinitroanisole (DNAN), triaminotrinitrobenzene (TATB), 1,1-diamino-2,2-dinitroethene (FOX-7) and nitroguanidine (NQ), and traditional munition compound 2,4,6-trinitrotoluene (TNT) on the surfaces of cellulose, cellulose triacetate, chitin and chitosan biopolymers. Cellulose, cellulose triacetate, chitin and chitosan were modeled as trimeric form of the linear chain of 4C1 chair conformation of β-d-glucopyranos, its triacetate form, β-N-acetylglucosamine and D-glucosamine, respectively, in the 1➔4 linkage. Geometries were optimized at the M062X functional level of the density functional theory (DFT) using the 6-31G(d,p) basis set in the gas phase and in the bulk water solution using the conductor-like polarizable continuum model (CPCM) approach. The nature of potential energy surfaces of the optimized geometries were ascertained through the harmonic vibrational frequency analysis. The basis set superposition error (BSSE) corrected interaction energies were obtained using the 6-311G(d,p) basis set at the same theoretical level. The computed BSSE in the gas phase was used to correct interaction energy in the bulk water solution. Computed and experimental results regarding the ability of considered surfaces in adsorbing the insensitive munitions compounds are discussed.

Insight into substituent effects on the hydrolysis of amidines by a microhydration model

The hydrolysis of substituted amidines XN′=CH–N(Y)2 (X = alkyl, nucleoside, aryl; Y = methyl, benzyl) is studied by use of computational techniques. For each substituted system, two possible pathways, N′-Path and N-Path, are considered, in which the proton transfer to N′ and N, respectively, after the nucleophilic attack of H2O to C=N′ double bond. The geometry optimizations of the stationary states are carried out to map out the hydrolysis pathways at the density functional theory B3LYP/6-311+G(d,p) level. Single-point MP2 calculations (MP2/6-311++G(d,p)//B3LYP/6-311+G(d,p)) are performed to obtain more credible energy information. A microhydration surrounding is constructed to describe the effect of water molecules in the first hydration shell on the energy barrier from radial distribution functions, g(R). The bulk solvent effects are examined by using the conductor-like polarizable continuum model (CPCM). The calculated results indicate that the hydrolysis of N,N-disubstituted formamidines is more favored for Y = methyl than for Y = benzyl. Furthermore, for N′-substituted formamidines, the hydrolysis reactivity increases in the following order: X = aryl < X = nucleoside < X = alkyl. In addition, the substituent effects on the proton transfer manner after the nucleophilic attack of H2O to C=N′ double bond are discussed. The preference of proton transfer to N′ or N atom depends on the different nucleophilicity of each nitrogen atom bearing different substituents in the intermediate (IM). Our computational results are in agreement with the available experimental conclusion and will allow for a better understanding of the hydrolysis mechanism of amidines.

Computational assisted electrochemical studies for 1,4-diazabicyclo[2,2,2]octane determination at multiwalled carbon nanotube paste electrode

A multiwalled carbon nanotube-modified carbon paste electrode (MWCNT-PE) was used for determination of 1,4-diazabicyclo[2,2,2]octane (DABCO or TEDA) in 0.1 M phosphate buffer solutions (pH 10.25). Cyclic voltammetry(CV) and differential pulse voltammetry (DPV) techniques were used to investigate the electrocatalytic oxidation of DABCO at the surface of modified electrode. The results shown that the oxidation peak current of DABCO at the surface of MWCNT-PE was 2.40 times larger than that at the bare electrode. The experimental formal redox potential (E°') of DABCO was obtained 986 mV versus SHE (Standard Hydrogen Electrode). Density functional theory (DFT) method at B3LYP/6-311++G** level of theory and a conductor-like Polarizable Continuum Model (CPCM) was used to calculate the E°' values. The highest occupied molecular orbital (E HOMO), lowest unoccupied molecular orbital (E LUMO) and some thermodynamic parameters such as Gibbs free energy of DABCO and its oxidation forms were calculated. Both direct and indirect methods were used to calculate the theoretical standard electrode potential for DABCO and the results were found to be in good agreement with the experimental values.

Hydrolysis theory based on density functional studies for cytotoxic Pt(II) and Pd(II) complexes with benzimidazole derivative

The hydrolysis processes of cytotoxic Pt(II) and Pd(II) complexes bearing benzimidazole moieties were explored combining density functional theory with conductor-like polarisable continuum model (CPCM) approach. Pentacoordinated transition state (TS) structures as well as the other stationary points for two distinct paths were optimized and characterized. The computed potential energy surfaces reveal the rate-limiting step as the second aquation, suggesting that the monohydrated complex is most likely to react with the DNA bases. The results give detailed energy profiles for the hydrolysis mechanism, which may assist in understanding the interaction of such anticancer agents with their ultimate cellular target.

Electroanalytical Measurement of TEDA (Triethylenediamine) in the Masks of War

In this paper, for the first time, the electroanalytical study of Triethylenediamine, TEDA was done on a typically graphene modified carbon paste electrode (Gr/CPE) in pH=10.5 of phosphate buffer solutions (PBS). The surface morphology of the bare and modified electrodes was characterized by scanning electron microscopy (SEM), electrochemical impedance spectroscopy (EIS) and cyclic voltammetry (CV). The electro-oxidation of TEDA was investigated at the surface of modified electrode. The results revealed that the oxidation peak current of TEDA at the surface of Gr/CPE is 2.70 times than that shown at bare-CPE. A linear calibration plot was observed in the range of 1.0 to 202.0 ppm. In this way, the detection limit was found to be 0.18 ppm. The method was then successfully applied to determination of TEDA in aqueous samples obtained from two kinds of activated carbon from the masks of war. On the other hand, density functional theory (DFT) method at B3LYP/6-311++G** level of theory and a conductor-like Polarizable Continuum Model (CPCM) was used to calculate the pKa values of TEDA. The energies of lowest unoccupied molecular orbital (ELUMO) and highest occupied molecular orbital (EHOMO), gap energy (ΔE) and some thermodynamic parameters such as Gibbs free energy of TEDA and its conjugate acid (HT+) were calculated. The results of calculated pKa were found to be in good agreement with the experimental values. Keywords: TEDA, Graphene, Differential pulse voltammetry, War mask, Acidity constant, Density functional theory

Quantum mechanics investigation of initial reaction pathways and early ring-opening reactions in thermal decomposition of liquid-phase RDX

Cyclotrimethylene trinitramine (RDX) is a commonly used ingredient in solid propellants and explosives. As a result, RDX has been the subject of many experimental and theoretical investigations to elucidate its liquid-phase and gas-phase decomposition. In our experimental effort involving Fourier Transform Infrared (FTIR) spectroscopy and time-of-flight mass spectrometry (ToFMS) of fast thermolysis of RDX, the results indicate that ring-opening occurs very early due to the presence of carbon-containing species among the detected gas-phase species, such as HCN, H2CO, CO and CO2. Two existing pathways – 1) HONO elimination and 2) NNO2 homolysis – are re-examined for liquid-phase decomposition and early ring-opening reactions have been identified after a lengthy search using quantum mechanics. Three additional pathways – 1) reaction with NO and formation of ONDNTA, 2) prompt oxidation via HONO and ONNO2 addition, and 3) hydrogen abstraction via NO2– are also identified along with early ring-opening reactions in each pathway. The quantum mechanics investigation is based on using density functional theory (DFT) at the B3LYP/6-311++G(d,p) level. The liquid-phase studies use the Conductor-like Polarizable Continuum Model (CPCM) for solvation with water as solvent within the Gaussian program package. Intrinsic reaction coordinate calculations have also been performed to verify that the reactants indeed are connected to the expected products. Results explain the mechanistic details of the formation of early carbon containing species, simultaneous formation of formaldehyde and N2O, as well as the formation of minor species such as HNCO and HOCN. Proposed reactions can account for the experimentally observed autocatalytic behavior and can assist in the development of a detailed chemical kinetics mechanism of nitramine propellants containing RDX and possibly HMX.

Effective Polarization in Pairwise Potentials at the Graphene-Electrolyte Interface.

At the graphene-electrolyte interface, the polarizability of both the surface and the solution plays a major role in defining the interfacial structure and dynamics of the ions. Current molecular models predict different ion adsorption behavior at the interface depending on whether surface or solution polarization is included in the model. Here, we propose a simple method to parametrize the ion-carbon interaction from density functional theory, implicitly modeling the solution using the conductor-like polarizable continuum model. The new model simultaneously takes into account the polarizability of both the graphene sheet and the solution without the need to use time-consuming polarizable potentials and can predict the ion adsorption trend so far only achievable using first-principles simulations. Simulations performed with 1 M electrolyte solutions of different ions show that cations are strongly adsorbed onto the graphene surface with a trend (Li+ < Na+ < K+) opposite to that predicted by the gas-phase calculations and different from that obtained from the single-ion simulations.

Prediction of 1H NMR chemical shifts for clusters of imidazolium-based ionic liquids.

Nuclear magnetic resonance (NMR) has been widely used to elucidate the bulk structure of ionic liquids. In this work, we calculated 1H NMR chemical shifts of 1-ethyl-3-methylimidazolium (C2mim+) ionic liquids combined with various anions such as chloride (Cl), tetrafluoroborate (BF4), hexafluorophosphate (PF6), acetate (OAc), trifluoroacetate (TFA), and dicyanamide (DCA). The previously established level of theory, HF/6-311G+(3df,2p), was used for the accurate prediction of NMR chemical shifts both in gas phase and in solvents with varying dielectric constant such as CHCl3 and ethanol. The following factors affecting the predicted proton chemical shifts were considered. Firstly, ionic clusters consisting of 2, 8 and 16 ion pairs were optimized to model interionic interactions present in the bulk of ionic liquids. In larger clusters the distribution of the calculated chemical shifts of individual protons in the C2mim+ cation was examined with respect to the position of the cation in the cluster. We further confirmed that electronic properties of ionic liquids such as magnetic shielding had local nature, thus allowing us to accurately predict proton NMR chemical shifts of ionic liquids from relatively small-sized clusters. Secondly, solvent effects in single ion pairs as well as larger ionic clusters were accounted through a Conductor-like Polarisable Continuum Model (CPCM). Solvent effects generated through a dielectric constant of either chloroform or ethanol were found to be important in single ion pairs due to improved description of interionic distances. With increasing cluster size the difference between gas-phase and CPCM optimized structures became minimal, thus resulting in similar values for calculated 1H NMR chemical shifts. We also established that the model size that produced the best results for imidazolium ionic liquids strongly depended on the anion type. Strongly coordinating anions such as chloride and acetate require calculations of clusters consisting of at least 8 ion pairs, whereas weakly coordinating anions produce excellent accuracy for single ion pairs optimized in the presence of solvent. The polarity of the solvent was found to play a minor role.

Theoretical study on the investigation of antioxidant properties of some hydroxyanthraquinones

ABSTRACTAnthraquinones are located in an important class of natural compounds having antioxidant properties. Quantum chemical calculations based on the density functional theory were employed to study the relationship between the structure and the antioxidant activity of four hydroxyanthraquinones. The solvation effects on the antioxidant activity were taken into account by using the conductor-like polarisable continuum model with different dielectric constants (ε = 2.25, C6H6; ε = 78.39, H2O). The three antioxidant action mechanisms, hydrogen atom transfer (HAT), single electron transfer-proton transfer and sequential proton loss electron transfer (SPLET) were elucidated. The reaction enthalpies related to the steps in these mechanisms were computed in gas phase and solvents. The calculated results are in line with experimental values. The results showed that HAT was the most favourable mechanism for describing the antioxidant activity of hydroxyanthraquinones in the gas phase and in benzene, whereas in aqueous solution, SPLET represented the most thermodynamically plausible reaction pathway.

A DFT Approach to the Mechanistic Study of Hydrozone Hydrolysis.

Hydrazone chemistry is widely utilized in biomedical field as a means of bioconjugation protocol, especially in drug delivery field due to pH labile nature of this linkage. In the light of kinetics studies, the generally accepted mechanism for the hydrolysis of hydrazones involves two main steps, namely, nucleophilic addition of water molecule to the hydrazone molecule to form carbinolamine intermediate and subsequent decomposition of this intermediate into the hydrazine and aldehyde/ketone moieties. Hydrolysis of hydrazones is catalyzed in the acidic environments and is thought to proceed through several proton transfer steps. To the best of our knowledge, in the literature no detailed theoretical study has been reported related to the mechanism of hydrolysis. In this study, we evaluated the proposed mechanism with DFT calculations with M06-2X functional at the 6-311+g(d,p) level including conductor-like polarizable continuum model solvation model. We also analyzed possible proton transfer pathways and assessed energetics of each step.

A machine learning correction for DFT non-covalent interactions based on the S22, S66 and X40 benchmark databases.

Background Non-covalent interactions (NCIs) play critical roles in supramolecular chemistries; however, they are difficult to measure. Currently, reliable computational methods are being pursued to meet this challenge, but the accuracy of calculations based on low levels of theory is not satisfactory and calculations based on high levels of theory are often too costly. Accordingly, to reduce the cost and increase the accuracy of low-level theoretical calculations to describe NCIs, an efficient approach is proposed to correct NCI calculations based on the benchmark databases S22, S66 and X40 (Hobza in Acc Chem Rev 45: 663–672, 2012; Řezáč et al. in J Chem Theory Comput 8:4285, 2012).ResultsA novel type of NCI correction is presented for density functional theory (DFT) methods. In this approach, the general regression neural network machine learning method is used to perform the correction for DFT methods on the basis of DFT calculations. Various DFT methods, including M06-2X, B3LYP, B3LYP-D3, PBE, PBE-D3 and ωB97XD, with two small basis sets (i.e., 6-31G* and 6-31+G*) were investigated. Moreover, the conductor-like polarizable continuum model with two types of solvents (i.e., water and pentylamine, which mimics a protein environment with ε = 4.2) were considered in the DFT calculations. With the correction, the root mean square errors of all DFT calculations were improved by at least 70 %. Relative to CCSD(T)/CBS benchmark values (used as experimental NCI values because of its high accuracy), the mean absolute error of the best result was 0.33 kcal/mol, which is comparable to high-level ab initio methods or DFT methods with fairly large basis sets. Notably, this level of accuracy is achieved within a fraction of the time required by other methods. For all of the correction models based on various DFT approaches, the validation parameters according to OECD principles (i.e., the correlation coefficient R2, the predictive squared correlation coefficient q2 and q_{cv}^{2} from cross-validation) were >0.92, which suggests that the correction model has good stability, robustness and predictive power.ConclusionsThe correction can be added following DFT calculations. With the obtained molecular descriptors, the NCIs produced by DFT methods can be improved to achieve high-level accuracy. Moreover, only one parameter is introduced into the correction model, which makes it easily applicable. Overall, this work demonstrates that the correction model may be an alternative to the traditional means of correcting for NCIs.Graphical abstractA machine learning correction model efficiently improved the accuracy of non-covalent interactions(NCIs) calculated by DFT methods. The application of the correction model is easy and flexible, so it may be an alternative correction means for NCIs by first-principle calculations.Electronic supplementary materialThe online version of this article (doi:10.1186/s13321-016-0133-7) contains supplementary material, which is available to authorized users.

Quantum chemical approach for condensed-phase thermochemistry (III): Accurate evaluation of proton hydration energy and standard hydrogen electrode potential

Gibbs free energy of hydration of a proton and standard hydrogen electrode potential were evaluated using high-level quantum chemical calculations. The solvent effect was included using the cluster-continuum model, which treated short-range effects by quantum chemical calculations of proton–water complexes, and the long-range effects by a conductor-like polarizable continuum model. The harmonic solvation model (HSM) was employed to estimate enthalpy and entropy contributions due to nuclear motions of the clusters by including the cavity–cluster interactions. Compared to the commonly used ideal gas model, HSM treatment significantly improved the contribution of entropy, showing a systematic convergence toward the experimental data.

Theoretical studies on the hydrolysis mechanism of acetamiprid

The possible hydrolysis mechanisms for acetamiprid (AAP) with H3O+, H2O and OH− in the gas phase were studied by employing the B3LYP/6-311+G(d,p) and MP2/6-311+G(d,p) levels. In each case, two different pathways were taken into account in our calculations. Moreover, the solvent effect of water was estimated at the B3LYP/6-311+G(d,p) level by using the conductor-like polarizable continuum model (CPCM). The calculated results clearly showed that hydrolysis of AAP with OH− could readily take place in comparison with hydrolysis with H3O+, H2O. The most favorable pathway in the gas phase is the proton transfer toward the N atom in the single bond of AAP in the hydrolysis with OH−. The solvent effect does not significantly change the conclusion. The free energy barrier height of 25.74 kcal/mol (107.6 kJ/mol) is in excellent agreement with the available experimental value (106.3 kJ/mol).

Aggregation of photosensitizers: the role of dispersion and solvation on dimer formation energetics

A detailed account for the dimer formation energetics is computed for two commonly used photosensitizers: metal-free phthalocyanine (Pc) and methylene blue (MB), a cationic phenothiazine. Gas-phase calculations were performed using the density functional theory augmented with dispersion corrections using both the dispersion-correcting atom-centred potentials and the D2/D3 methods. SCS-MP2/CBS results were also provided for comparison. Hydration free energies were determined using continuum methodologies: namely the conductor-like polarizable continuum model, the solvation model density and a reparametrized version of the polarizable continuum model. For methylene blue, the Langevin dipole model was also used. Our results showed that the nature of aggregation is remarkably different for these two molecules, being dispersion driven for Pc while solvent driven for MB. For water and ethanol our results are in good agreement with the experimental data available for MB. We also provide quantitative estimates to the popular explanation put out by Mukerjee and Ghosh more than 40 years ago that aggregation arises from solvent entropic and inter-species enthalpic contributions.

Quantum chemical modeling of the structure and vibrational spectra of two melatonin catabolites: N-γ-acetyl-N-formyl-5-methoxykynuramine and N-γ-acetyl-5-methoxykynuramine

Quantum chemical calculations for possible conformers of the melatonin molecule (N-acetyl–5-methoxytryptamine) and its two catabolites, (N-γ-acetyl-N-formyl-5-methoxykynuramine (AFMK) and N-γ-acetyl-5-methoxykynuramine (AMK)), are performed at different theoretical levels with inclusion of the macrohydration effects within the conductor-like polarizable continuum model (CPCM). The influence of the used in biochemical studies CD3-labels on the vibrational spectra of molecules is considered. It is demonstrated that the theoretical (B3LYP/6-31+G**) vibrational spectra and geometric parameters of the most stable melatonin conformers are in good agreement with the experimental data. On a base of analysis of the theoretical frequency shifts in the theoretical B3LYP/6-31+G** vibrational spectra of different conformations of melatonin catabolites and of the influence of the aqueous surrounding and isotopic substitution, the conclusion is made that the region of nitrogen–hydrogen stretching can be proposed for identification of considered compounds.

Physical Absorption Of CO2 in Protic and Aprotic Ionic Liquids: An Interaction Perspective.

The physical absorption of CO2 by protic and aprotic ionic liquids such as 1-ethyl-3-methyl-imidazolium tetrafluoroborate was examined at the molecular level using symmetry adapted perturbation theory (SAPT) and density functional techniques through comparison of interaction energies of noncovalently bound complexes between the CO2 molecule and a series of ionic liquid ions and ion pairs. These energies were contrasted with those for complexes with model amines such as methylamine, dimethylamine, and trimethylamine. Detailed analysis of the five fundamental forces that are responsible for stabilization of the complexes is discussed. It was confirmed that the nature of the anion had a greater effect upon the physical interaction energy in non functionalized ionic liquids, with dispersion forces playing an important role in CO2 solubility. Hydrogen bonding with protic cations was shown to impart additional stability to the noncovalently bound CO2···IL complex through inductive forces. Two solvation models, the conductor-like polarizable continuum model (CPCM) and the universal solvation model (SMD), were used to estimate the impact of solvent effects on the CO2 binding. Both solvent models reduced interaction energies for all types of ions. These interaction energies appeared to favor imidazolium cations and carboxylic and sulfonic groups as well as bulky groups (e.g., NTf2) in anions for the physical absorption of CO2. The structure-reactivity relationships determined in this study may help in the optimization of the physical absorption process by means of ionic liquids.

An insight into hydration structure of sodium glycinate from ab initio quantum chemical study.

The hydration structure of sodium glycinate (Na(+)GL(-)) is probed by the Monte-Carlo multiple minimum (MCMM) method combined with quantum mechanical (QM) calculations at the MP2/6-311++G(d,p) level. In the gas phase, the energy of [Na(+)GL(-)]β is more than 30 kJ mol(-1) higher than [Na(+)GL(-)]α. With higher degrees of hydration, our results indicate that the most stable conformers of [Na(+)GL(-)]∙(H2O)8 were derived from [Na(+)GL(-)]β instead of [Na(+)GL(-)]α. The stable conformers determined by the conductor-like polarizable continuum model (CPCM) also show that [Na(+)GL(-)]β is more stable than [Na(+)GL(-)]α in the liquid phase. By analyzing the hydration process, water…water hydrogen bonding interaction will be more preferable than ion…water interaction as the number of water molecules increases. According to the electronic density at the bond critical point on the Na-X bonds (X = O1, O2, N) in the low-energy conformers, Na(+)GL(-) will be dissociated as Na(+) and GL(-) in the bulk water, which is not predicted by the CPCM model. The structure features and the charge redistribution of Na(+)GL(-) will provide a physical explanation for the weakening Na-O1 interaction.

The 6,6-dicyanopentafulvene core: a template for the design of electron-acceptor compounds.

The electron-accepting ability of 6,6-dicyanopentafulvenes (DCFs) can be varied extensively through substitution on the five-membered ring. The reduction potentials for a set of 2,3,4,5-tetraphenyl-substituted DCFs, with varying substituents at the para-position of the phenyl rings, strongly correlate with their Hammett σp-parameters. By combining cyclic voltammetry with DFT calculations ((U)B3LYP/6-311+G(d)), using the conductor-like polarizable continuum model (CPCM) for implicit solvation, the absolute reduction potentials of a set of twenty DCFs were reproduced with a mean absolute deviation of 0.10 eV and a maximum deviation of 0.19 eV. Our experimentally investigated DCFs have reduction potentials within 3.67-4.41 eV, however, the computations reveal that DCFs with experimental reduction potentials as high as 5.3 eV could be achieved, higher than that of F4-TCNQ (5.02 eV). Thus, the DCF core is a template that allows variation in the reduction potentials by about 1.6 eV.

Simulation of the resonance Raman spectra for 5-halogenated (F, Cl, and Br) uracils.

The resonance Raman spectra of the 5-halogenated (F, Cl, and Br) uracils are simulated via the Herzberg-Teller (HT) short-time dynamics formalism. The gradient of the S1 excited state is computed at the CAMB3LYP/aug-cc-pVTZ level of theory in the conductor-like polarizable continuum model for water (C-PCM, H2O), based on the equilibrium geometry determined using PBE0/aug-cc-pVTZ in H2O (C-PCM). The simulated resonance Raman spectra show good agreement with the experimental spectra in terms of both peak positions and intensities. The differences between the resonance Raman spectra of the three 5-halogenated uracils, caused by the effect of halogen substitution, are examined in terms of ground-state normal-mode eigenvectors and excited-state Cartesian gradients, according to the HT formalism. The differences in the normal-mode eigenvectors and excited-state Cartesian gradients between 5-fluorouracil and 5-chlorouracil are used to interpret the dissimilarity between their resonance Raman spectra. Meanwhile, the similarity between the spectra of 5-chlorouracil and 5-bromouracil is explained by the correspondence between their normal modes and excited-state gradients.