Reaction Field Model Research Articles

Solvent-induced 1H NMR chemical shifts of annulenes

We computationally investigate the effect of solvent polarity on the 1H NMR chemical shifts of a few annulenes using multiple DFT levels within the IEFPCM solvation formalism. The solvent polarity is parametrized by defining a dielectric function that can efficiently quantify the solvent-induced shift (SIS). Both the linear and the nonlinear SIS behavior are observed. As the polarity of the solvent increases, the value of SIS decreases for both the inner and the outer protons of [12]- and [30]annulenes as well as for the outer protons of [18]annulene. For the inner protons of C2 [18]annulene, the nonlinearity is primarily due to the anisotropic environment inside the annulenic ring cavity, i.e. due to the existence of an anisotropic reaction field. Interestingly, the SIS values computed using multiple DFT levels within the IEFPCM solvation directly fit into the relatively simple Onsager’s reaction field model.

Ionization Patterns and Chemical Reactivity of Cytosine-Guanine Watson-Crick Pairs.

Gas-phase and aqueous vertical ionization potentials, vIPgas and vIPaq respectively and measurements of the molecular electrostatic and local ionization maps calculated at the DFT/B3LYP-D3/ 6-311+G** level of theory and the C-PCM reaction field model for single- and double-stranded CpG and 5MeCpG pairs show that the vIPaq for single- and double-stranded pairs of C-G and 5MeC-G are practically the same, in the range of 5.79 to 5.81 eV. The aqueous adiabatic ionization potentials for single-stranded CpG and 5MeCpG are 5.52 eV and 5.51 eV respectively and they reflect the nuclear reorganization that takes place after the abstraction of the electron. The aqueous adiabatic ionization energy values that correspond to the CpG+. radical cation and the hydrated electron, e-,, being at infinite distance, adIPaq+Vo, are 3.92 eV and 3.91 eV respectively with (Vo=-1.6 eV) Analysis of data suggest that the HOMO-LUMO energy gap in the hard/soft-acid/base (HSAB) concept cannot be used a priori to determine the effect of cytosine methylation on the guanine enhanced oxidative damage in DNA.

A New Formulation for the Concerted Alchemical Calculation of van der Waals and Coulomb Components of Solvation Free Energies.

Alchemical free energy calculations via molecular dynamics have been widely used to obtain thermodynamic properties related to protein-ligand binding and solute-solvent interactions. Although soft-core modeling is the most common approach, the linear basis function (LBF) methodology [Naden, L. N.; et al. J. Chem. Theory Comput.2014, 10 (3), 1128; 2015, 11 (6), 2536] has emerged as a suitable alternative. It overcomes the end-point singularity of the scaling method while maintaining essential advantages such as ease of implementation and high flexibility for postprocessing analysis. In the present work, we propose a simple LBF variant and formulate an efficient protocol for evaluating van der Waals and Coulomb components of an alchemical transformation in tandem, in contrast to the prevalent sequential evaluation mode. To validate our proposal, which results from a careful optimization study, we performed solvation free energy calculations and obtained octanol-water partition coefficients of small organic molecules. Comparisons with results obtained via the sequential mode using either another LBF approach or the soft-core model attest to the effectiveness and correctness of our method. In addition, we show that a reaction field model with an infinite dielectric constant can provide very accurate hydration free energies when used instead of a lattice-sum method to model solute-solvent electrostatics.

Revealing Intra- and Intermolecular Interactions Determining Physico-Chemical Features of Selected Quinolone Carboxylic Acid Derivatives.

The intra- and intermolecular interactions of selected quinolone carboxylic acid derivatives were studied in monomers, dimers and crystals. The investigated compounds are well-recognized as medicines or as bases for further studies in drug design. We employed density functional theory (DFT) in its classical formulation to develop gas-phase and solvent reaction field (PCM) models describing geometric, energetic and electronic structure parameters for monomers and dimers. The electronic structure was investigated based on the atoms in molecules (AIM) and natural bond orbital (NBO) theories. Special attention was devoted to the intramolecular hydrogen bonds (HB) present in the investigated compounds. The characterization of energy components was performed using symmetry-adapted perturbation theory (SAPT). Finally, the time-evolution methods of Car–Parrinello molecular dynamics (CPMD) and path integral molecular dynamics (PIMD) were employed to describe the hydrogen bond dynamics as well as the spectroscopic signatures. The vibrational features of the O-H stretching were studied using Fourier transformation of the autocorrelation function of atomic velocity. The inclusion of quantum nuclear effects provided an accurate depiction of the bridged proton delocalization. The CPMD and PIMD simulations were carried out in the gas and crystalline phases. It was found that the polar environment enhances the strength of the intramolecular hydrogen bonds. The SAPT analysis revealed that the dispersive forces are decisive factors in the intermolecular interactions. In the electronic ground state, the proton-transfer phenomena are not favourable. The CPMD results showed generally that the bridged proton is localized at the donor side, with possible proton-sharing events in the solid-phase simulation of stronger hydrogen bridges. However, the PIMD enabled the quantitative estimation of the quantum effects inclusion—the proton position was moved towards the bridge midpoint, but no qualitative changes were detected. It was found that the interatomic distance between the donor and acceptor atoms was shortened and that the bridged proton was strongly delocalized.

Solvation of Potassium 5-Hydroxy Pentanoyl Trifluoroborate Salt in Aqueous Environment by Using FT-Raman and UV-Visible Spectra

The hydration process of potassium 5-hydroxypentanoyltrifluoroborate salt, K[C5H9BF3O2] and its 5-hydroxypentanoyltrifluoroborate [C5H9BF3O2]- anion have been studied by combining the experimental FT-Raman and ultraviolet-visible spectra in aqueous solution with hybrid B3LYP/6-311++G** calculations. Solvent effects have been considered with the self-consistent reaction field (SCRF) and solvation (SM) models. Here, the structures of [C5H9BF3O2].[H2O]n clusters of anion, with n from 1 to 5 implicit water molecules, were proposed in order to study the number of water molecules that could hydrate the anion. Calculations were performed in the gas phase and an aqueous solution to observe the effect of the medium on the dipole moment and volume values. Calculated solvation energies for all clusters were corrected by zero-point vibrational energy (ZPVE), non-electrostatic terms and by basis set superposition energy (BSSE). The dipole moment of salt in solution (10.19 D) suggests that the number of water molecules that could hydrate the anion vary between 3 and 4, in total agreement with the observed and predicted bands in the UV-Vis spectra for the salt and these two clusters in water between 180 and 400 nm. Comparisons among experimental and predicted Raman spectra show clearly the hydration effect because the bands attributed to OH, BF3 and C=O groups are shifted in solution, while, the predicted Raman spectra for all clusters in solution show strong changes in the intensities of many bands, in accordance with the corresponding experimental one. Evidently, the hydration occurs on the OH, BF3 and C=O groups.

Unusual blue to red shifting of C-H stretching frequency of CHCl3 in co-operatively P⋯Cl phosphorus bonded POCl3-CHCl3 heterodimers at low temperature inert matrixes.

Heterodimers of POCl3-CHCl3 were generated in Ne, Ar, and Kr matrixes at low temperatures and were studied using infrared spectroscopy. The remarkable role of co-operative pentavalent phosphorus bonding in the stabilization of the structure dictated by hydrogen bonding is deciphered. The complete potential energy surface of the heterodimer was scanned by ab initio and density functional theory computational methodologies. The hydrogen bond between the phosphoryl oxygen of POCl3 and C-H group of CHCl3 in heterodimers induces a blue-shift in the C-H stretching frequency within the Ne matrix. However, in Ar and Kr matrixes, the C-H stretching frequency is exceptionally red-shifted in stark contrast with Ne. The plausibility of the Fermi resonance by the C-H stretching vibrational mode with higher order modes in the heterodimers has been eliminated as a possible cause within Ar and Kr matrixes by isotopic substitution (CDCl3) experiments. To evaluate the influence of matrixes as a possible cause of red-shift, self-consistent Iso-density polarized continuum reaction field model was applied. This conveyed the important role of the dielectric matrixes in inducing the fascinating vibrational shift from blue (Ne) to red (Ar and Kr) due to the matrix specific transmutation of the POCl3-CHCl3 structure. The heterodimer produced in the Ne matrix possesses a cyclic structure stabilized by hydrogen bonding with co-operative phosphorus bonding, while in Ar and Kr the generation of an acyclic open structure stabilized solely by hydrogen bonding is promoted. Compelling justification regarding the dispersion force based influence of matrix environments in addition to the well-known dielectric influence is presented.

Investigation of host-guest interactions between polyester dendrimers and ibuprofen using density functional theory (DFT)

Polyester dendrimers are mostly non-toxic and this advantage besides biodegradability gives them a great chance of success in the field of drug delivery. This study investigates electronic and structural characteristics of ibuprofen complexation with polyester G1 dendrimer using DFT calculations. Optimized structural geometries, interaction energies, NMR, NBO, and AIM analyses, revealed that the stability of G1:Ibu complex could be attributed to the intermolecular hydrogen bonds formed between the functional groups of polyester G1 dendrimer and ibuprofen molecule. All calculations were repeated using a self-consistent reaction field (SCRF) and polarizable continuum model (PCM) to consider implicit solvent effects and the outcomes were in line with gas phase calculations.

Reaction-field model for the dielectric response of mixtures.

We present a new effective medium theory for the dielectric response of mixtures of molecules with molecular polarizability and a permanent dipole moment. This model includes the interaction of each local dipole moment with the dipolar reaction fields of neighboring dipolar molecules. This interaction leads to an enhancement of the dielectric response of the mixture and constitutes an alternative method to describe the correlated motion of dipoles in liquids compared to the models of Fröhlich and Kirkwood. The model requires as input parameters the volume fractions of the components contained in the mixture and the dielectric parameters of the pure components. The results of the model are compared with experimental data and with the results of previous effective-medium theories.

The structure of benzonitrile-water complex as unveiled by matrix isolation infrared spectroscopy: Is it linear or cyclic at low temperatures?

The hydrogen bonded interaction of benzonitrile (C6H5CN)-water (H2O) complexes have been studied experimentally using matrix isolation infrared spectroscopy to elucidate the structure(s) of the binary complexes produced at low temperatures. Computations performed at MP2 and B3LYP-D3 level of theory with aug-cc-pVDZ basis set predicted two complexes, of which global minimum complex A has a cyclic structure with the interactions occurring between ortho-hydrogen of C6H5CN and oxygen of H2O and the hydrogen of H2O with π-cloud of CN in C6H5CN. The linear acylic complex B, a local minimum is stabilized through a straight C-H⋯N interaction between nitrogen of C6H5CN and hydrogen of H2O and is present at a relative energy of ∼0.7 kcal/mol with respect to global minimum. While previous gas phase studies using a number of spectroscopic probes identify exclusively the cyclic global complex, our experiments performed under isolated conditions at low temperatures uniquely produced the acyclic linear C6H5CN-H2O complex, a local minimum in the potential energy surface. The CN stretching vibrational mode of C6H5CN was exploited as a unique marker to confirm the generation of local minimum. The effect of matrixes was simulated using Onsager self-consistent reaction field model and as a result, the linear complex (complex B) turned out to be energetically favored isomer under the influence of matrixes. The hydrogen bonding interaction in both the complexes was characterized using Atoms in Molecules, Natural Bond Orbital, Energy Decomposition and Non-Covalent Interaction analyses.

Discrete Solvent Reaction Field Calculations for One- and Two-Photon Absorptions of Solution-Phase Dimethylaminonitrostilbene Molecule.

Based on the configurations generated by molecular dynamics (MD) simulations using the on-the-fly density-functional tight-bonding (DFTB) force field, we investigated performance of the discrete solvent reaction field (DRF) model coupled to time-dependent density functional theory (TD-DFT) for solvatochromic effect of one- and two-photon absorption phenomena. Dimethylaminonitrostilbene (DANS) molecule solvated in chloroform, dichloromethane, and dimethyl sulfoxide solvents was selected as a model system for our research purpose. For every selected MD/DFTB configuration, within the context of the DRF, solute molecule is represented by TD-DFT and solvent molecules are described by atomic charges and polarizabilities. The calculated one-photon absorption energies reproduce well the positive solvatochromic behavior of solvated DANS and are in good agreement with available experimental data. For the two-photon absorption cross section, even though our approach overshot the experimental data by about 20% in absolute magnitude, experimentally observed solvatochromic change was captured qualitatively in this work. At last, we examined the contributions of atomic charges and polarizabilities of solvent molecules to the solvatochromic shifts of properties of interest.

Structural and spectroscopic differences among the potassium 5-hydroxypentanoyltrifluoroborate salt and the furoyl and isonicotinoyl salts

FT-IR, FT-Raman and ultraviolet–visible spectroscopies were used to characterize the potassium 5-hydroxypentanoyltrifluoroborate salt (HTFB) while the theoretical structures of this salt in gas and aqueous solution phases were studied by using hybrid B3LYP/6-311++G** calculations and the self consistent reaction field (SCRF) and solvation (SM) models because these models consider the solvent effects. Good concordance were obtained among the predicted 1H-, 13C and 19F-NMR chemical shifts for HTFB in aqueous solution with the corresponding experimental available data for this salt in CDCl3. The corrected solvation energy by using ZPVE and non electrostatic terms is higher for this salt (−103.73 kJ/mol) than those reported for furoyl (−84.72 kJ/mol) and isonicotinoyl (−95.05 kJ/mol). Evidently, the side chain in HTFB increase the solubility of this salt in water, as compared with furoyl and isonicotinoyl. The NBO analyses show that the potassium 2-isonicotinoyltrifluorborate salt in both media is most stable than hydroxypentanoyl and furoyl salts and, in particular, the side chain in HTFB generates a diminishing of its stability in aqueous solution. Probably, this low stability of HTFB in solution is due to the higher solvation energy and to the n→σ∗ transitions no observed in the other salts. The AIM studies support the high stability of isonicotinoyl than the other two salts and, also, reveal the ionic characteristics of the K--O and K--F interactions observed in those three salts. The comparisons of the gap values for the three species suggest that the most reactive salt is isonicotinoyl while furoyl salt is the less reactive. The descriptors show the importance of study these salts in different media because the values in solution are slightly different in the three salts from those computed in gas phase. In addition, the harmonic force fields and the scaled internal force constants for the salt in both media are reported together to their complete vibrational assignments.

Synthesis and spectral properties of halogen methyl-phenyl-pyrazoloquinoxaline fluorescence dyes: Experiment and DFT/TDDFT calculations

We report the synthesis and spectroscopic studies of two novel 6-substituted fluorine (FMPPQX) and chlorine (ClMPPQX) derivatives of 1-Methyl-3-phenyl-1H-pyrazolo[3,4-b]quinoxaline (MPPQX) core. The spectroscopic measurements have been performed in solvents of different polarity. Steady state and time-resolved spectroscopy provide photophysical characterization of FMPPQX and ClMPPQX dyes. The fluorescence transition moments exhibit evidently lower values compared to relevant absorption transition moments what is apparently related with formation of instantly twisted molecular conformations in the excited state due to rotation of the phenyl group singly bonded to pyrazolo-quinoxaline moiety. The optical absorption and fluorescence emission transition energies are compared with results of quantum-chemical calculations. Quantum-chemical modeling employs the density functional theory (DFT/TDDFT methods) basing on re-parameterized LRC-BLYP (ω=0.231Bohr−1) or CAM-B3LYP xc-functionals and is combined with self consistent reaction field models with linear response (LR) and two different state-specific (IBSF and CLR) solvation models. Re-parameterized functional LRC-BLYP in combination with CLR solvation exhibits the best performance providing most accurate prediction of both excitation and emission transition energies. Relevant quantum-chemical technique may be therefore of interest for chemical engineering dealing with design and synthesis of novel organic dyes. Newly synthesized 6-substituted fluorine and chlorine MPPQX dyes may be considered as prospective blue-green fluorescence emitters for luminescent and electroluminescent applications.

Synthesis and spectral properties of Methyl-Phenyl pyrazoloquinoxaline fluorescence emitters: Experiment and DFT/TDDFT calculations

Paper reports the synthesis and spectroscopic studies of two novel 1-Methyl-3-phenyl-1H-pyrazolo[3,4-b]quinoxaline (PQX) derivatives with 6-substituted methyl (MeMPPQX) or methoxy (MeOMPPQX) side groups. The optical absorption and fluorescence emission spectra are recorded in solvents of different polarity. Steady state and time-resolved spectroscopy provide photophysical characterization of MeMPPQX and MeOMPPQX dyes as materials for potential luminescence or electroluminescence applications. Measured optical absorption and fluorescence emission spectra are compared with quantum-chemical DFT/TDDFT calculations using long-range corrected xc-functionals, LRC-BLYP and CAM-B3LYP in combination with self-consistent reaction field model based on linear response (LR), state specific (SS) or corrected linear response (CLR) solvations. Performances of relevant theoretical models and approaches are compared. The reparameterized LRC-BLYP functional (ω = 0.231 Bohr−1) in combination with CLR solvation provides most accurate prediction of both excitation and emission energies. The MeMPPQX and MeOMPPQX dyes represent efficient fluorescence emitters in blue-green region of the visible spectra.

Application of discrete solvent reaction field model with self-consistent atomic charges and atomic polarizabilities to calculate the χ(1) and χ(2) of organic molecular crystals

We use the discrete solvent reaction field model to evaluate the linear and second-order nonlinear optical susceptibilities of 3-methyl-4-nitropyridine-1-oxyde crystal. In this approach, crystal environment is created by supercell architecture. A self-consistent procedure is used to obtain charges and polarizabilities for environmental atoms. Impact of atomic polarizabilities on the properties of interest is highlighted. This approach is shown to give the second-order nonlinear optical susceptibilities within error bar of experiment as well as the linear optical susceptibilities in the same order as experiment. Similar quality of calculations are also applied to both 4-N,N-dimethylamino-3-acetamidonitrobenzene and 2-methyl-4-nitroaniline crystals.

On the spectral properties of methyl and methoxy derivatives of 1,3-diphenyl-1H-pyrazolo[3,4-b]quinoxalines: Experiment and DFT/TDDFT calculations

Paper reports the synthesis and spectroscopic studies of two novel 1,3-diphenyl pyrazoloquinoxaline (PQX) derivatives with 6-substituted methyl (MePQX) or methoxy (MeOPQX) side groups. The optical absorption and fluorescence emission spectra are recorded in solvents of different polarity. Other photophysical constants, such as the fluorescence lifetime and quantum yield, radiationless and radiative rate constants, electronic transition dipole moments, give complete characterization of MePQX and MeOPQX dyes as materials for potential luminescence or electroluminescence applications. Measured optical absorption and fluorescence emission spectra are compared with the results of quantum-chemical analysis using density functional theory (DFT/TDDFT) methods based on hybrid and long range corrected (LRC) exchange-correlation (xc) functionals in combination with solvation self consistent reaction field model. Comparing to conventional hybrid xc-functionals, the DFT/TDDFT calculations using LRC xc-functionals yield considerably more accurate description of optical absorption and fluorescence emission spectra. The best description of the absorption-emission circle provides the model assuming that optical absorption takes place from preferably flat or weakly twisted molecular conformations in the ground state, as particularly is suggested by the geometrical DFT optimization, whereas the fluorescence emission would be expected from more twisted molecular conformations in the excited state.

Computational study of the 1,3-dipolar cycloaddition between methyl 2-trifluorobutynoate and substituted azides in terms of reactivity indices and activation parameters

The 1,3-dipolar cycloaddition of methyl 2-trifluorobutynoate with various azides has been studied in terms of several theoretical approaches at DFT/B3LYP/6-311++G(d,p) level of theory. The mechanism of regioselectivity of these reactions was investigated through the evaluation of the potential energy surface of the cycloaddition process calculations and density DFT-based reactivity indices. These approaches were successfully applied to prediction of preferable regio-isomers for various reactions of 1,3-dipolar cycloadditions. The reactions were followed by performing transition state optimization, calculation of Intrinsic Reaction Coordinate and activation energies. Analysis of the geometries of the corresponding transition structures shows that the cycloaddition takes place along a single elementary step (one-step mechanism) but asynchronous mechanism. The calculation of the activation energies and reaction energies show that the 1,5-regioisomer for substituted phenyl azides as dipoles and the 1,4-regioisomer for substituted benzyl azides as dipoles are thermodynamically in all the cycloadditions reactions. The solvent effect was also studied in the solvent tert-butyl alcohol using self-consistent reaction field model. The observed regioselectivity was explained by using developed DFT-based reactivity descriptors, such as Fukui and Parr functions. The results were compared with experimental data to find a good agreement.

Size-Specific ZnO Quantum Dots as Onsager Cavity in Ooshika–Mataga–Lippert Equation

The influence of the surrounding solvent medium to a solute molecule in solution can be treated within the framework of Onsager reaction field model which is based on the assumption that the solute is reduced to a point dipole at the center of a spherical cavity inside the solvent that can be described as the homogeneous, polarizable medium of specific dielectric constant. When the solute molecules are excited in solution of the polar solvent, the changes in the photophysical properties of the solute are manifested through shifts in the maxima of absorption and fluorescence spectra and the observation can be interpreted in terms of the Ooshika–Mataga–Lippert equation. Over several decades, a wide variety of organic molecules as fluoroprobes have been explored to reveal the polarity of their immediate solvent environment. However, while these molecular probes, with diameters less than 10 A, have been employed so far in the literature as Onsager cavities, the limiting value of their radii has not been restr...

Modification of the Onsager Reaction Field and Its Application on Spectral Parameters.

Solvent polarity is an important solvent property. The Onsager's theory of reaction field was the most classic model to describe solvent effects and was widely used in relating dielectric constant and other solvent polarity parameters. In this study, a modified semi-empirical reaction field was presented to relate electron transition energies or hyperfine coupling constants with the dielectric constants of solvents. In previous work, this relationship was well established by traditional Onsager reaction field for nonhydrogen-bonding systems but failed for hydrogen-bonding systems. In this modified reaction field model, the radius of the field was replaced by that of the primary solvation shell or the molecular fragment rather than that of the probe. In this way, the molecular volume of the solvent which contains information of the molecular size and overall interactions is involved in the reaction field. The 154 sets of electron transition energies and 44 sets of nitrogen isotropic hyperfine coupling constants were used to verify the modified model, indicating it works far better than the traditional model for hydrogen-bonding systems.

Solvation Reaction Field at the Interface Measured by Vibrational Sum Frequency Generation Spectroscopy.

Interfacial electric fields are important in several areas of chemistry, materials sciences, and device physics. However, they are poorly understood, partly because they are difficult to measure directly and model accurately. We present both a spectroscopic experimental investigation and a theoretical model for the interfacial field at the junction of a conductor and a dielectric. First, we present vibrational sum frequency generation (VSFG) results of the nitrile (CN) stretch of 4-mercaptobenzonitrile (4-MBN) covalently attached to a gold surface and in contact with a variety of liquid dielectrics. It is found that the CN stretch frequency red-shifts with increasing dielectric constant. Second, we build a model in direct analogy to the well-known Onsager reaction field theory, which has been successful in predicting vibrational frequency shifts in bulk dielectric media. Clearly, due to the asymmetric environment, with metal on one side and a dielectric on the other, the bulk Onsager model is not applicable at the interface. To address this, we apply the Onsager model to the interface accounting for the asymmetry. The model successfully explains the red-shift of the CN stretch as a function of the dielectric constant and is used to estimate the reaction field near the interface. We show the similarities and differences between the conventional bulk Onsager model and the interfacial reaction field model. In particular, the model emphasizes the importance of the metal as part of the solvation environment of the tethered molecules. We anticipate that our work will be of fundamental value to understand the crucial and often elusive electric fields at interfaces.

Application of discrete solvent reaction field to second-order susceptibility of organic molecular crystal

This article presents an assessment of methods to study the second harmonic generation (SHG) response of organic molecular crystal. We incorporated the discrete solvent reaction field model, density functional theory, and the local field approximation (designated as the LF-DRF/DFT) to investigate the SHG susceptibilities of the chromophore of 2-carboxylic acid-4-nitropyridine-1-oxide (POA). In experiment, the POA appears in two different polymorphic crystal structures easily identified by noticeable differences in the melting points and SHG susceptibilities. In this work, we tried to utilize the LF-DRF/DFT in a supermolecular framework to differentiate the two crystals. While focusing on the ratio of the calculated SHG susceptibilities for the two crystals, at optical wavelength of 1064 nm, the S12 g and SSB-D exchange–correlation functionals within a 5 × 5 × 5 extended architecture produced 2.16 and 2.08, differing from the experimental estimate of 2.16 by 0 and 3.7 %, respectively.