Gas-phase Calculations Research Articles

Electrochemical Atomic Force Microscopy and First-Principles Calculations of Ferriprotoporphyrin Adsorption and Polymerization.

The adsorption and subsequent electrooxidative polymerization of ferriprotoporphyrin IX chloride (hemin; FePPCl) was investigated on highly ordered pyrolytic graphite, glassy carbon, and polycrystalline Pt electrodes using electrochemical atomic force microscopy, first-principles calculations, and cyclic voltammetry. Hemin was shown to readily adsorb to all three surfaces; however, it was more continuous over the carbon surfaces compared to the Pt surface. This disparity in adsorption appears to be a major contributing factor to differences observed between the electrodes following hemin electropolymerization. Despite differences in roughness and morphology, hemin polymerized as a continuous layer over each electrode surface. Periodic density functional theory calculations were used to model FePP (without Cl) on both the Pt(111) and graphite surfaces using the vdW-DF-optPBE functional to account for the dispersion interactions. Our calculations suggest that the FePP molecule chemisorbs to the Pt surface while at the same time exhibiting intramolecular hydrogen bonding between the carboxylic acid groups, which are extended away from the surface. In contrast to FePP-Pt chemisorption, FePP was found to physisorb to graphite. The preferred spin state upon adsorption was found to be S = 2 on Pt(111), whereas on graphite, the high and intermediate spin states were nearly isoenergetic. Additionally, gas-phase calculations suggest that much of the surface roughness observed microscopically for the polymerized porphyrin layer may originate from the nonparallel stacking of porphyrin molecules, which interact with each other by forming four intermolecular hydrogen bonds and through dispersion interactions between the stacked porphyrin rings. Regardless of polymer thickness, the underlying electrode appears to be able to participate in at least some redox processes. This was observed for the hemin-polymerized Pt electrode using the 2H+/H2 redox couple and was suspected to be due to some Pt surface atoms not being specifically coordinated to the hemin molecules and therefore available to react with H+ that was small enough to diffuse through the polymer layer.

5-Methyl-2-thiophenecarboxaldehyde: Experimental and TD/DFT study

The 5-Methyl-2-thiophenecarboxaldehyde (MTC) and its derivatives present a wide range of biological activities. In this regard a combined experimental and theoretical analysis for MTC and its derivatives can help to understand the electronic factors involved in the mode of action in biological systems. In the present work we used FT-IR and UV–vis techniques to investigate the spectroscopic properties of MTC. The conformational and vibrational analyses were theoretically explored using DFT calculation at DFT/B3LYP/6–311++G(d,p) level. A full electronic analysis of compound was performed using TD-DFT/B3LYP/6–311++G(d,p) calculations in gas phase and in ethanol solvent with the CPCM model. The NLO parameters (β, γ and χ(3)) and FMO energies for MTC were calculated at the same level of theory. The relation between linear polarizability (α) and refractive index (n) were used to describe the polarization behavior of MTC in ethanol solvent. Our results indicate that MTC can be considered as a candidate to microscopic third−order NLO material.

Unveiling Noncovalent Interactions in Imidazolium, Pyrrolidinium, or Quaternary Ammonium Cation and Acetate Anion Based Protic Ionic Liquids: Structure and Spectral Characteristics.

In the present work protic ionic liquids (PILs) composed of imidazolium-, quaternary ammonium-, or pyrrolidinium-dications and acetate (OAc-) anion have been modeled as the dication-anion complexes through the M06-2x based density functional theory. It has been shown that cation-anion interaction energies are larger for the PILs containing the quaternary ammonium cation, which can be attributed to strong hydrogen bonding from the terminal ammonium protons. Underlying N-H···O and C-H···O hydrogen bonding, electrostatic, and van der Waals interactions are unraveled using the natural bond orbital analyses in conjunction with the quantum theory of atoms in molecules (QTAIM) and noncovalent interaction index reduced density gradient methods. The ramifications of noncovalent binding to 1H NMR and vibrational spectra are presented. The calculations further demonstrate a linear correlation of the kinetic energy density parameter G( r) in QTAIM analysis with the characteristic frequency shift of -NH3+ stretching in the dication-anion complexes. Moreover, the chemical shifts (δH) in 1H NMR spectra from theory reveal larger deshielding; the corresponding δH value correlates well with proton affinities and cation-anion binding energies as well. Effect of solvent (DMSO) on structure, binding energies, and 1H NMR are presented. The shifts of the characteristic carbonyl and the terminal ammonium stretching vibrations accompanying the dication-anion complexes from gas phase calculations are in consonance with the self-consistent reaction field theory.

Conformational study of melamine crosslinkers and spectroscopical comparison of HMMM molecules by practical measurements and quantum chemical calculations

To understand and improve network formation processes and performance properties makes structural molecular studies critically important for the coil-coating industry. Crosslinking agents such as hexamethoxymethylmelamine (HMMM) or less methylated derivatives, e.g. methoxymethylmelamine (MMM), are often added to industrial coating formulations. For molecules with considerably fewer atoms and accordingly less rotational freedom (such as MMM) it is readily accessible to identify principal conformations. Thus, an MMM conformer study is straightforward and serves as orientation concerning HMMM conformer studies. For HMMM molecules an extensive computation method was developed to investigate the conformational distribution average and probably most likely molecular structures. Using the density functional theory (DFT) B3LYP-D3BJ method with Dunning's correlation basis set, calculations were performed to investigate the three-dimensional structural geometries of HMMM (basis set cc-pVDZ) and MMM (basis set cc-pVTZ). Beginning with 1500 conformations for HMMM and using various cut-off filters we focused on final residual 22 conformers for solvent phase calculations and 16 conformers for gas phase calculations. To the best of our knowledge, this is the first time that chemical properties for melamine crosslinkers were presented under consideration of conformational population distribution. Thus, computations of fully optimized structural geometries, energies and vibrational states indicate that preferred structural alignments for the methoxymethyl (MM) group in melamine molecules exist. Nevertheless, we suppose that as a matter of principle the MM group of MMM molecules can easily perform rotations by itself and all conformational structure geometries of MMM will exist. Concerning the MM groups position compared to triazine plane HMMM molecules have two main configurations,”3up-3down” and “4up-2down”, as dominant conformer species. Computations of weighted and averaged IR and Raman spectra of final conformations for HMMM monomers, dimers and trimers at ambient temperature are novel and in good agreement with experiment. Prediction of a final UV–Vis spectrum of top ten Boltzmann-weight and averaged monomeric HMMM conformers is in perfect agreement with practical measurement of commercially available HMMM.

Dipolar Relaxation in Functionalized Poly-p-phenylenes Bearing Ultrastrong Dipoles Perpendicular to the Backbone

Local polymer dynamics are studied in polymers bearing dipoles rigidly attached to the backbone. The compounds are based on cyano-substituted dihydrobenzimidazoles bearing ultrastrong dipole moments (∼12 D per repeat unit) incorporated in a poly-p-phenylene backbone, giving rise to polymers with rigid dipoles perpendicular to the chain. They belong to type B polymers according to the Stockmayer classification. They are ideal model systems for studying rotational isomers in the gas phase and the self-assembly and local dynamics in the solid state. Gas phase calculations (DFT) provided the dipole moments, the energetic barriers, and the backbone conformation as a function of the dipole strength and dipole separation. Calculated dipole moments show an odd–even effect as a function of dipole separation. Specific rotational isomers that maximize the dipole moment are obtained. In the solid state, dielectric spectroscopy and site-specific NMR techniques revealed that packing through intermolecular forces such as van der Waals, π–π, and dipole–dipole interactions dictates the dynamics. Dielectric spectroscopy further identified two modes, both with Arrhenius temperature dependence and activation energies of 20–23 kcal/mol. Combined results attribute the faster process to a libration motion of the highly polar group reorienting only the nonplanar five-membered ring and the slower process to larger amplitude and/or correlated motions of the polar groups. These dynamic results are in agreement with structural investigations (X-ray diffraction) demonstrating that type B polymers in the bulk have rigid backbones.

1H–pyrazole–3–carboxylic acid: Experimental and computational study

The FT–IR and UV–Vis spectra for 1H–pyrazole–3–carboxylic acid (H2pc) were recorded in methanol solvent. The optimized molecular structure, vibrational frequencies and NMR chemical shifts of the title molecule in methanol solvent and gas phase were obtained by using DFT/B3LYP and DFT/HSEh1PBE methods with 6–311++G(d,p) basis set. TD–DFT calculations in methanol solvent and gas phase were used to investigate UV–Vis absorption wavelengths. Furthermore, the NLO parameters and FMO energies of the molecule were calculated by using B3LYP and HSEh1PBE methods with 6–311++G(d,p) basis set. In order to investigate intermolecular hydrogen bonds and π–π interactions, NBO study was fulfilled by the same levels. To sum up, the fact that the title compound used frequently in coordination chemistry field has encouraged us to do experimental and theoretical characterizations of H2pc

Neutral derivatives of Thioflavin T do not exhibit viscosity-dependent fluorescence

Fluorescent molecular rotors (FMR) have wide range of applications due to high sensitivity of their emission intensity to microenvironment viscosity. Thioflavin T (ThT), which exhibits FMR properties, is widely used as fluorescent probe for in vitro detection of amyloid fibrils (AF) due to its high affinity and “light-up” feature (fluorescence quantum yield of ThT changes by ∼3 orders of magnitude upon binding to AF). At physiological pH, ThT is positively charged and, therefore, it does not cross blood-brain barrier (BBB). It has been proposed that neutral derivatives of ThT are more likely to cross BBB, which should make them suitable for in vivo applications. However, for in vivo applications as fluorescent imaging agents, the neutral ThT derivatives must retain the FMR properties of ThT.In this paper, we examined whether neutral ThT derivatives exhibit FMR properties by studying the effect of solvent viscosity on their fluorescence intensity and decay lifetime. We observed that while the cationic ThT derivatives possess FMR properties, the neutral forms behave as regular highly-emitting fluorophores. Further, quantum chemical calculations in gas phase showed significant differences in the shape of excited state potential energy surfaces for the neutral and cationic derivatives of ThT. While, for charged ThT derivatives, the E(S1*) energy is minimal for the twisted conformation with dihedral angle φ = 90° between molecular fragments, the coplanar conformation with φ = 0° (or 180°) is more favorable for the neutral derivatives. From our experimental and theoretical studies we conclude that the neutral ThT derivatives lack FMR properties as their photoexcitation does not induce twisting motion coupled with internal charge transfer and, therefore, their specificity as fluorescent imaging agents for AF detection is lower than that of parent ThT.

Improvement of Anion Transport Systems by Modulation of Chalcogen Interactions: The influence of solvent.

A series of potential anion transporters, dithieno[3,2-b;2',3'-d]thiophenes (DTT), involving anion-chalcogen interactions have been studied by analyzing the interaction energy, geometry, and charge transfer. It was found that gas phase calculations show very negative interaction energies with short anion-chalcogen distances, but when solvent effects are considered, the interaction energy values decreased drastically concomitantly with an elongation on the interatomic distances. To enhance the chalcogen interaction between the DTT derivatives and the anion, increasing the anion transporter capacity, bisisothioazole moiety was considered; i.e., the σ-hole of the chalcogen atom was modulated by substitution of the adjacent carbon by a nitrogen atom in the S-C axis, increasing the depth of the σ-hole and therefore the interaction between the chalcogen and anion. Finally, different anions were analyzed within the complexes, finding that F- and NO3- would be the best candidates to form complexes and possibly displace other anions such as Cl- or Br-.

Correction: Developing force fields when experimental data is sparse: AMBER/GAFF-compatible parameters for inorganic and alkyl oxoanions.

Correction for 'Developing force fields when experimental data is sparse: AMBER/GAFF-compatible parameters for inorganic and alkyl oxoanions' by Sadra Kashefolgheta et al., Phys. Chem. Chem. Phys., 2017, 19, 20593-20607.

A Polarizable Atomic Multipole-Based Force Field for Molecular Dynamics Simulations of Anionic Lipids.

In all of the classical force fields, electrostatic interaction is simply treated and explicit electronic polarizability is neglected. The condensed-phase polarization, relative to the gas-phase charge distributions, is commonly accounted for in an average way by increasing the atomic charges, which remain fixed throughout simulations. Based on the lipid polarizable force field DMPC and following the same framework as Atomic Multipole Optimized Energetics for BiomoleculAr (AMOEBA) simulation, the present effort expands the force field to new anionic lipid models, in which the new lipids contain DMPG and POPS. The parameters are compatible with the AMOEBA force field, which includes water, ions, proteins, etc. The charge distribution of each atom is represented by the permanent atomic monopole, dipole and quadrupole moments, which are derived from the ab initio gas phase calculations. Many-body polarization including the inter- and intramolecular polarization is modeled in a consistent manner with distributed atomic polarizabilities. Molecular dynamics simulations of the two aqueous DMPG and POPS membrane bilayer systems, consisting of 72 lipids with water molecules, were then carried out to validate the force field parameters. Membrane width, area per lipid, volume per lipid, deuterium order parameters, electron density profile, electrostatic potential difference between the center of the bilayer and water are all calculated, and compared with limited experimental data.

Polymer Segments at the Folding Limit: Raman Scattering for the Diglyme Benchmark.

Methyl-capped polyethers model flexible polar polymer chains. Their intrinsic all-trans conformational preference gives way to folded conformations if the chain is sufficiently long. We find by Raman cryospectroscopy in the gas phase and quantum chemical calculations that diglyme still prefers the stretched state, although folded variants come very close in energy. Three-body dispersion correction or higher-order electron correlation is important to match experiments, despite the polar character of C-O bonds. This turns oligoglymes into challenging benchmark systems for a balanced description of intra-chain torsion and inter-segment van der Waals attraction.

Benchmarking of Computational Methods for Creation of Retention Models in Quantitative Structure-Retention Relationships Studies.

Quantitative structure-retention relationship (QSRR) models are powerful techniques for the prediction of retention times of analytes, where chromatographic retention parameters are correlated with molecular descriptors encoding chemical structures of analytes. Many QSRR models contain geometrical descriptors derived from the three-dimensional (3D) spatial coordinates of computationally predicted structures for the analytes. Therefore, it is sensible to calculate these structures correctly, as any error is likely to carry over to the resulting QSRR models. This study compares molecular modeling, semiempirical, and density functional methods (both B3LYP and M06) for structure optimization. Each of the calculations was performed in a vacuum, then repeated with solvent corrections for both acetonitrile and water. We also compared Natural Bond Orbital analysis with the Mulliken charge calculation method. The comparison of the examined computational methods for structure calculation shows that, possibly due to the error inherent in descriptor creation methods, a quick and inexpensive molecular modeling method of structure determination gives similar results to experiments where structures are optimized using an expensive and time-consuming level of computational theory. Also, for structures with low flexibility, vacuum or gas phase calculations are found to be as effective as those calculations with solvent corrections added.

Partial density of states ligand field theory (PDOS-LFT): Recovering a LFT-like picture and application to photoproperties of ruthenium(II) polypyridine complexes

Gas phase density-functional theory (DFT) and time-dependent DFT (TD-DFT) calculations are reported for a data base of 98 ruthenium(II) polypyridine complexes. Comparison with X-ray crystal geometries and with experimental absorption spectra measured in solution show an excellent linear correlation with the results of the gas phase calculations. Comparing this with the usual chemical understanding based upon ligand field theory (LFT) is complicated by the large number of molecular orbitals present and especially by the heavy mixing of the antibonding metal e*$_{g}$ orbitals with ligand orbitals. Nevertheless, we show that a deeper understanding can be obtained by a partial density-of-states (PDOS) analysis which allows us to extract approximate metal t$_{2g}$ and e*$_{g}$ and ligand \pi* orbital energies in a well-defined way, thus providing a PDOS analogue of LFT (PDOS-LFT). Not only do PDOS-LFT energies generate a spectrochemical series for the ligands, but orbital energy differences provide good estimates of TD-DFT absorption energies. Encouraged by this success, we use frontier-molecular-orbital-theory-like reasoning to construct a model which allows us in most, but not all, of the cases studied to use PDOS-LFT energies to provide a semiquantitative relationship between luminescence lifetimes at room temperature and liquid nitrogen temperature.

PCM/DFT investigation of the hydrogen-bonds capability of 4-[4-(dimethylamino)phenyl]-2-oxo-1,2,5,6-tetrahydrobenzo[h]quinoline-3-carbonitrile (MAPC)

Quinoline-3-carbonitrile is an important constituent in a variety of pharmaceutical compounds. DFT/CAM-B3LYP with 6-311++G(d,p) basis set calculations in gas phase and in solvents using the PCM for newly synthesized 4-[4-(dimethylamino) phenyl]-2-oxo-1,2,5,6 tetrahydrobenzo[h]quinoline-3-carbonitrile (MAPC) have been performed. Efforts to simulate the complex formation of MAPC with water have also been performed. The electron density and its Laplacian have been computed at H-bonds BCP of water-MAPC complexes. The protonation and deprotonation of MAPC as important chemical and biochemical processes are examined. Their forms and energies are computed, analysed and discussed. The NBO analysis and the stabilization energy of the MAPC in their neutral, cation and anion forms due to their internal donor–acceptor orbital interactions were analysed. The 1,3-intramolecular proton transfer between the keto-enol interconversion has been investigated and the thermodynamic parameters of the process have been analysed.

Prediction of the lowest charge-transfer excited-state energy at the donor-acceptor interface in a condensed phase using ground-state DFT calculations with generalized Kohn-Sham functionals.

Knowledge of the charge (electron) transfer process at the donor-acceptor interface is required to understand the working mechanisms of different organic photovoltaic materials. Investigating the lowest charge-transfer state in organic donor-acceptor solar cells is important as it allows the destruction/formation of excitons and polarons to be studied, and is directly related to the open circuit voltage. By performing low-cost and feasible calculations of ground-state electronic structures using the Mulliken rule as well as the optimally tuned range-separated hybrid (OTRSH) density functional and a regular long-range corrected functional, the lowest charge-transfer (CT) state energies of a series of dimers containing functionalized anthracene (the donor) and tetracyanoethylene (the acceptor) were obtained. The jumping distances of excited electrons during CT were calculated. The polarizable continuum model was applied to account for the effects of the solvent methylene chloride (CH2Cl2) on the lowest CT state energies obtained from gas-phase calculations. The calculated lowest CT state energies of the dimers were close to the corresponding experimental results, with a root mean square deviation (RMSD) of 0.22eV.

Photophysical behavior of a potential drug candidate, trans-[2-(4-methoxystyryl)]quinoline-1-oxide tuned by environment effects

Styryl and/or quinoline structural fragments, present in a large number of bioactive substances, inspired the design of various new drug candidates. In this paper, we describe the photophysical behavior of trans-[2-(4-methoxystyryl)]quinoline-1-oxide (trans-MSQNO) on the basis of X-ray analysis data, theoretical calculations as well as steady state and time-resolved spectroscopy experiments in various media. The molecule crystallizes in orthorhombic unit cell containing eight molecules of N-oxide, space group Pbca. The NO bond is substantially shorter in comparison with the NO bond in the ZnTPP unit [1.3052(11) Å vs. 1.335(2) Å]. Variation of emission colors from the violet (~450nm) through blue (480nm), green (525nm) and yellow (575nm) is observed in different environments. Comparable values of lifetimes estimated both at ambient temperature and at 77K suggest that excited state dynamics in this case is viscosity independent. DFT and TD DFT B3LYP/6-31G(d, p) calculations performed for four different trans-MSQNO rotamers in the gas phase, as well as nonpolar and polar media (PCM model) suggest that an equilibrium between them can be significantly altered even by a relatively weak interactions with the environment. It is suggested that varying intensity ratios of experimental absorption bands in different media may be due to the dominant share of one or more rotamers of the excited trans-MSQNO molecule. Gas phase calculations show also that the vertical ππ*, S0→S1, transition resulting from the HOMO→LUMO electronic configuration exhibits only a partial CT nature. On the other hand, in polar media, a substantial increment of excited state dipole moment of all rotamers compared to the ground state, its increase with increasing solvent polarity and a significant red shift in the absorption and emission spectra, point to the enhanced CT nature of the S1 excited state. Hence, the trans-MSQNO molecule may be considered a subsequent styrylquinoline drug candidate where the CT drug-receptor interactions are of a high importance.

Complexation of nicotinic acid with first generation poly(amidoamine) dendrimers: A microscopic view from density functional theory

This study explains some electronic and structural parameters of niacin (NA) encapsulation into PAMAM-G1 dendrimer using DFT calculations. Optimized structural geometries, interaction energies, NMR, NBO, and AIM analyses, in accordance with experiment, revealed that the stability of G1@NA complex can be attributed to the five intermolecular hydrogen bonds formed between the functional groups of G1 and NA. Because of nearing to the experimental results, all the calculations repeated again using a self-consistent reaction field (SCRF) and the polarizable continuum model (PCM) to address the implicit solvent effects and the obtained results were in line with the calculations in gas phase.

Terahertz investigations on photoisomerisable compounds

ABSTRACTWe performed computational terahertz studies on organometallic photoisomerisable compounds, employing both gas phase and solid phase calculations. The calculations demonstrate the potential of employing terahertz techniques on photoisomerisable compounds. In particular, the trans-ligand, counterion and crystal effects are evaluated via the density functional theory calculations. In order to fully understand the terahertz responses of the photoisomerisable compounds, their experimental terahertz spectra were obtained and compared to the calculations. The calculated spectra generally predict the experimentally observed absorption peaks, while combined gas phase and solid phase calculations offer better agreement with the experiments. The first principles calculations also reveal the sensitivity of terahertz signal on the photoisomerisation processes, suggesting a photo-terahertz set-up that could be built in the future to fast screen and fully understand the photoisomerisable compounds, for related applications such as photo-transducer and photo-switch that require photoinduced geometrical changes.

Quantum chemical study of NH2 functionalized boron phosphide (BP) and aluminum phosphide (AlP) nanocones for chemical sensing of bromine (Br2) in the gas phase and ethanol

The Br2 molecule adsorption on BP-NC and AlP-NC surfaces was investigated by using density functional theory calculations in gas phase. The effects of NH2 functionalization and ethanol on the adsorption of Br2 gas on BP-NC and AlP-NC surfaces were investigated. Results reveal that adsorptions of Br2 on studied nanocones are exothermic and experimentally possible from the energetic viewpoint. Results show that, E ad value of Br2 on AlP-NC surface are more negative than corresponding values of BP-NC. Results reveal that, NH2 functionalization and ethanol increase and decrease the absolute E ad values of Br2 on studied nanocones, respectively. These results show that, there are good linearity dependencies between E ad and orbital energy values of studied nanocones. Therefore we can conclude the E ad and orbital energy values of studied nanocones can consider as important parameters to propose suitable nanocones with enhanced Br2 adsorption potential.

Double differential cross sections for liquid water ionization by fast electron impact

In this work we study theoretically the single ionization of liquid water by impact of energetic electrons. A realistic description of the wavefunction for an isolated water molecule in the liquid phase is made by means of a Wannier orbital formalism. We develop a first order model within the framework of an independent electron approximation in which the relaxation of the target is not taken into account. The double differential cross sections are computed and compared with experimental data and theoretical calculations for gas phase.