Hydrogen abstraction from biphenyl, acenaphthylene, naphthalene and phenanthrene by atomic hydrogen and methyl radical: DFT and G3(MP2)-RAD data

Can Small Polyaromatics Describe Their Larger Counterparts for Local Reactions? A Computational Study on the H-Abstraction Reaction by an H-Atom from Polyaromatics

Hydrogen abstraction is one of the crucial initial key steps in the combustion of polycyclic aromatic hydrocarbons. For an accurate theoretical prediction of heterogeneous combustion processes, larger systems need to be treated as compared to pure gas phase reactions. We address here the question on how transferable activation and reaction energies computed for small molecular models are to larger polyaromatics. The approximate transferability of energy contributions is a key assumption for multiscale modeling approaches. To identify efficient levels of accuracy, we start with accurate coupled-cluster and density functional theory (DFT) calculations for different sizes of polyaromatics. More approximate methods as the reactive force-field ReaxFF and the extended semi-empirical tight binding (xTB) methods are then benchmarked against these data sets in terms of reaction energies and equilibrium geometries. Furthermore, we analyze the role of bond-breaking and relaxation energies, vibrational contributions, and post-Hartree-Fock correlation corrections on the reaction, and for the activation energies, we analyze the validity of the Bell-Evans-Polanyi and Hammond principles. First, we find good transferability for this process and that the predictivity of small models at high theoretical levels is way superior than any approximate method can deliver. Second, ReaxFF can serve as a qualitative exploration method, whereas GFN2-xTB in combination with GFN1-xTB appears as a favorable tool to bridge between DFT and ReaxFF so that we propose a multimethod scheme with employing ReaxFF, GFN1/GFN2-xTB, DFT, and coupled cluster to cope effectively with such a complex reactive system.

Benzo-Fused Periacenes or Double Helicenes? Different Cyclodehydrogenation Pathways on Surface and in Solution

Controlling the regioselectivity of C-H activation in unimolecular reactions is of great significance for the rational synthesis of functional graphene nanostructures, which are called nanographenes. Here, we demonstrate that the adsorption of tetranaphthyl- p-terphenyl precursors on metal surfaces can completely change the cyclodehydrogenation route and lead to obtaining planar benzo-fused perihexacenes rather than double [7]helicenes during solution synthesis. The course of the on-surface planarization reactions is monitored using scanning probe microscopy, which unambiguously reveals the formation of dibenzoperihexacenes and the structures of reaction intermediates. The regioselective planarization can be attributed to the flattened adsorption geometries and the reduced flexibility of the precursors on the surfaces, in addition to the different mechanism of the on-surface cyclodehydrogenation from that of the solution counterpart. We have further achieved the on-surface synthesis of dibenzoperioctacene by employing a tetra-anthryl- p-terphenyl precursor. The energy gaps of the new nanographenes are measured to be approximately 2.1 eV (dibenzoperihexacene) and 1.3 eV (dibenzoperioctacene) on a Au(111) surface. Our findings shed new light on the regioselectivity in cyclodehydrogenation reactions, which will be important for exploring the synthesis of unprecedented nanographenes.

On-the-fly kinetics of hydrogen abstraction from polycyclic aromatic hydrocarbons by methyl/ethyl radicals

This work provides a rigorous procedure, within the framework of the Reaction Class Transition State Theory (RC-TST) and the Structure-Activity Relationship (SAR), for predicting reliable thermal rate constants on-the-fly for hydrogen abstraction reactions by methyl/ethyl radicals from Polycyclic Aromatic Hydrocarbons (PAHs) in a temperature range of 300-3000 K. All necessary RC-TST parameters were derived from ab initio calculations for a representative set of 36 reactions on which different error analyses and comparisons with available literature data were carried out. In addition to the good agreement between the RC-TST rate constants and the literature data, the detailed error analyses show that RC-TST/SAR, utilizing either the Linear Energy Relationship (LER) where only the reaction energy is needed or Barrier Height Grouping (BHG) where no additional data is needed, can predict the thermal rate constants for any reaction in the title reaction class with an average systematic error of less than 50% when compared to the explicit rate calculations. Therefore, the constructed RC-TST procedure can be confidently used to obtain reliable rate constants on the fly in an attempt to effectively construct detailed kinetic mechanisms for PAH-related fuels.

Exploring the driving forces behind the structural assembly of biphenylthiolates on Au(111)

In this contribution, we use dispersion-corrected density functional theory to study inter- and intramolecular interactions in a prototypical self-assembled monolayer (SAM) consisting of biphenylthiolates bonded to Au(111) via thiolate groups. The goal is to identify the nature of the interactions that drive the monolayer into a specific conformation. Particular focus is laid on sampling realistic structures rather than high symmetry model configurations. This is achieved by studying conceptually different local minimum structures of the SAM that are obtained via exploring the potential energy surface from systematically varied starting geometries. The six obtained packing motifs differ in the relative arrangement of the two molecules in the unit cell (co-planar versus herringbone) and in the intramolecular configuration (twisted versus planar rings). We find that van der Waals interactions within the organic adsorbate and between the adsorbate and substrate are the main reason that these molecular assemblies can form stable structures at all. The van der Waals interactions are, however, very similar for all observed motifs; by analyzing various types of interactions in the course of three notional SAM-formation steps, we find that the main driving force stabilizing the actual global minimum structure originates from electrostatic interactions between the molecules.

Reaction kinetics of hydrogen abstraction from polycyclic aromatic hydrocarbons by H atoms

We studied how the PAH structure, site, and size affect the rate constants of hydrogen abstraction reactions of PAH systematically.

Spectroscopic (FT-IR/FT-Raman) and computational (HF/DFT) investigation and HOMO/LUMO/MEP analysis on 1,1-difluoro-2-vinyl-cyclopropane

All the computational calculations were made in the ground state using the HF and DFT (B3LYP) methods with 6-31++G (d,p) and 6-311++G (d,p) basis sets. Making use of the recorded data, the complete vibrational assignments were made and analysis of the observed fundamental bands of molecule was carried out. The shifting of the frequencies in the vibrational pattern of the title molecule due to the substitutions; CHCH₂ and F were deeply investigated by the vibrational analysis. Moreover, (13)C NMR and (1)H NMR chemical shifts were calculated by using the gauge independent atomic orbital (GIAO) method with HF/B3LYP methods with 6-311++G (d,p). A study on the electronic properties, such as HOMO and LUMO energies, were performed by time-dependent DFT (TD-DFT) approach. Mulliken charges of the 1DF2VCP were also calculated and interpreted. The thermodynamic properties (heat capacity, entropy, and enthalpy) of the title compound at different temperatures were calculated in gas phase.

Spectroscopic (FT-IR/FT-Raman) and computational (HF/DFT) investigation and HOMO/LUMO/MEP analysis on 2-amino-4-chlorophenol

The spectra (FT-IR and FT-Raman) of the present compound; 2-amino-4-chlorophenol (2A4CP) were recorded in the range of 4000-100 cm(-1). All the computational calculations were made in the ground state using the HF and DFT (B3LYP and B3PW91) methods with 6-31++G(d,p) and 6-311++G(d,p) basis sets. From potential energy surface calculation, there are two conformers, Rot-1 and Rot-2 for this molecule. The computational results detected that Rot-1 form is the most stable conformer. Making use of the recorded data, the complete vibrational assignments were made and analysis of the observed fundamental bands of molecule is carried out. The complete assignments were performed on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQMs) method and PQS program. The shifting of the frequencies in the vibrational pattern of the title molecule due to the substitutions; NH(2) and Cl were deeply investigated by the vibrational analysis. Moreover, (13)C NMR and (1)H NMR chemical shifts were calculated by using the gauge independent atomic orbital (GIAO) method with HF/B3LYP/B3PW91 methods with 6-311++G(d,p). A study on the electronic properties, such as HOMO and LUMO energies, were performed by time-dependent DFT (TD-DFT) approach. Besides frontier molecular orbitals (FMOs), molecular electrostatic potential (MEP) was performed. NLO properties and Mulliken charges of the 2A4CP were also calculated and interpreted. The thermodynamic properties (heat capacity, entropy, and enthalpy) of the title compound at different temperatures were calculated in gas phase.

Chain-length and mode-delocalization dependent amide-I anharmonicity in peptide oligomers

The diagonal anharmonicities of the amide-I mode in the alanine oligomers are examined in the normal-mode basis by ab initio calculations. The selected oligomers range from dimer to heptamer, in either the α-helical or β-sheet conformations. It is found that the anharmonicity varies from mode to mode within the same oligomer. For a given amide-I mode, the anharmonicity is closely related to the delocalization extent of the mode: the less it delocalizes, the larger the anharmonicity it has. Thus, the single-mode potential energy distribution (PED(max)) can be used as an indicator of the magnitude of the anharmonicity. It is found that as the peptide chain length increases, the averaged diagonal anharmonicity generally decreases; however, the sum of the averaged diagonal and off-diagonal anharmonicities within a peptide roughly remains a constant for all the oligomers examined, indicating the excitonic characteristics of the amide-I modes. Excitonic coupling tends to decrease the diagonal anharmonicities in a coupled system with multiple chromophores, which explains the observed behavior of the anharmonicities. The excitonic nature of the amide-I band in peptide oligomers is thus verified by the anharmonic computations. Isotopic substitution effect on the anharmonicities and mode localizations of the amide-I modes in peptides is also discussed.

Vibrational spectroscopic investigation (FT-IR and FT-Raman) on 1,2-dibromobenzene by HF and hybrid (LSDA and B3LYP) calculations

The FT-IR and FT-Raman spectra of the compound 1,2-dibromobenzene have been recorded in the region 4000-100cm(-1). The vibrational analysis has been made using HF and DFT (B3LYP and LSDA) level of theory by employing 6-31 +G (d, p) and 6-311 ++G (d, p) basis sets. Optimized geometrical parameters have been calculated, interpreted and compared with the reported experimental values of some halogen-substituted benzene. The experimental geometrical parameters show satisfactory agreement with the theoretical prediction of HF and DFT. The geometrical structure of the compound is fractured by the substitutions of couple of Br in the ring. From the vibrational assignments it is observed that, the vibrational pattern of the fundamental modes is realigned slightly with respect to the substitutions. The simulated FT-IR and FT-Raman spectra of the compound for different methods are compared with the experimental spectra. The impact of Br in the vibrational assignments of the molecule is also investigated.

Comparative vibrational analysis of 1,2-Dinitro benzene and 1-Fluoro-3-nitro benzene: a combined experimental (FT-IR and FT-Raman) and theoretical study (DFT/B3LYP/B3PW91)

In this work, the comparative analysis is made on the structure and vibrational spectra of 1,2-Dinitro benzene (1,2-DNB) and 1-Fluoro-3-nitro benzene (1-F-3-NB) molecules. The FT-IR and FT-Raman experimental spectra of the molecules have been recorded using Bruker IFS 66 V spectrometer in the range of 4000-100 cm(-1). Making use of the recorded data, the complete vibrational assignments are made and analyses of the observed fundamental bands of molecules are carried out. The experimental determinations of vibrational frequencies are compared with those obtained theoretically from ab-initio Hartree-fock (HF) and DFT (B3LYP and B3PW91) methods with 6-31++G (d, p) and 6-311++G (d, p) basis sets. The differences between the observed and scaled wave number values of most of the fundamentals of the molecules are very small in B3LYP than HF. The geometries and normal modes of vibrations obtained from ab-initio HF and B3LYP/B3PW91 calculations are compared with the experimentally observed data. Comparison of the simulated spectra of the molecules provides important information regarding the difference and similarity of the vibrational characteristics between the molecules. The impact of substitutions on the structures between the molecules is also investigated.

Vibrational spectroscopy (FT-IR and FT-Raman) investigation, and hybrid computational (HF and DFT) analysis on the structure of 2,3-naphthalenediol

The FT-IR and FT-Raman vibrational spectra of 2,3-naphthalenediol (C(10)H(8)O(2)) have been recorded using Bruker IFS 66V spectrometer in the range of 4000-100 cm(-1) in solid phase. A detailed vibrational spectral analysis has been carried out and the assignments of the observed fundamental bands have been proposed on the basis of peak positions and relative intensities. The optimized molecular geometry and vibrational frequencies in the ground state are calculated by using the ab initio Hartree-Fock (HF) and DFT (LSDA and B3LYP) methods with 6-31+G(d,p) and 6-311+G(d,p) basis sets. There are three conformers, C1, C2 and C3 for this molecule. The computational results diagnose the most stable conformer of title molecule as the C1 form. The isotropic computational analysis showed good agreement with the experimental observations. Comparison of the fundamental vibrational frequencies with calculated results by HF and DFT methods. Comparison of the simulated spectra provides important information about the capability of computational method to describe the vibrational modes. A study on the electronic properties, such as absorption wavelengths, excitation energy, dipole moment and Frontier molecular orbital energies, are performed by time dependent DFT approach. The electronic structure and the assignment of the absorption bands in the electronic spectra of steady compounds are discussed. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecule. On the basis of the thermodynamic properties of the title compound at different temperatures have been calculated. The statistical thermodynamic properties (standard heat capacities, standard entropies, and standard enthalpy changes) and their correlations with temperature have been obtained from the theoretical vibrations.

FT-IR and FT-Raman, UV spectroscopic investigation of 1-bromo-3-fluorobenzene using DFT (B3LYP, B3PW91 and MPW91PW91) calculations

The FT-IR and FT-Raman spectra of 1-bromo-3-fluorobenzene (C(6)H(4)FBr) molecule have been recorded using Bruker IFS 66V spectrometer in the range of 4000-100 cm(-1). The molecular geometry and vibrational frequencies in the ground state are calculated using the DFT (B3LYP, B3PW91 and MPW91PW91) methods with 6-31++G(d,p) and 6-311++G(d,p) basis sets. The computed values of frequencies are scaled using a suitable scale factor to yield good coherence with the observed values. The isotropic DFT (B3LYP, B3PW91 and MPW1PW91) analysis showed good agreement with the experimental observations. Comparison of the fundamental vibrational frequencies with calculated results by B3LYP methods. The complete data of this molecule provide the information for future development of substituted benzene. The influence of bromine and fluorine atom on the geometry of benzene and its normal modes of vibrations has also been discussed. A study on the electronic properties, such as absorption wavelengths, excitation energy, dipole moment and frontier molecular orbital energies, was performed by time dependent DFT (TD-DFT) approach. The electronic structure and the assignment of the absorption bands in the electronic spectra of steady compounds were discussed. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecule. On the basis of the thermodynamic properties of the title compound at different temperatures have been calculated in gas phase, revealing the correlations between standard heat capacities (C) standard entropies (S), standard enthalpy changes (H) and temperatures.

Experimental (FT-IR and FT-Raman) and theoretical (HF and DFT) investigation, IR intensity, Raman activity and frequency estimation analyses on 1-bromo-4-chlorobenzene

The FT-IR and FT-Raman spectra of 1-bromo-4-chlorobenzene (1-Br-4-CB) have been recorded using Bruker IFS 66V spectrometer in the region of 4000-100 cm(-1). Ab-initio-HF (HF/6-311+G (d, p)) and DFT (B3LYP/6-31++G (d, p)/6-311++G (d, p)) calculations have been performed giving energies, optimized structures, harmonic vibrational frequencies, depolarization ratios, IR intensities, Raman activities. The vibrational frequencies are calculated and scaled values are compared with FT-IR and FT-Raman experimental values. Comparison of simulated spectra with the experimental spectra provides important information, the computational method have the ability to describe the vibrational methods. The frequency estimation analysis on HF and DFT is made. The impact of di-substituted halogens on the benzene molecule has also been discussed.

Molecular Structure and Vibrational Analysis of 1-Bromo-2-Chlorobenzene Using ab initio HF and Density Functional Theory (B3LYP) Calculations

The FT-Raman and FT-IR spectra for 1-bromo-2-chlorobenzene (1B2CB) have been recorded in the region 4000–100 cm−1 and compared with the harmonic vibrational frequencies calculated using HF/DFT (B3LYP) method by employing 6-31+G (d, p) and 6-311++G (d, p) basis set with appropriate scale factors. IR intensities and Raman activities are also calculated by HF and DFT (B3LYP) methods. Optimized geometries of the molecule have been interpreted and compared with the reported experimental values of some substituted benzene. The experimental geometrical parameters show satisfactory agreement with the theoretical prediction from HF and DFT. The scaled vibrational frequencies at B3LYP/6-311++G (d, p) seem to coincide with the experimentally observed values with acceptable deviations. The theoretical spectrograms (IR and Raman) have been constructed and compared with the experimental FT-IR and FT-Raman spectra. Some of the vibrational frequencies of the benzene are affected upon profusely with the halogen substitutions in comparison to benzene, and these differences are interpreted.

FT-IR and FT-Raman spectra and vibrational investigation of 4-chloro-2-fluoro toluene using ab initio HF and DFT (B3LYP/B3PW91) calculations

FT-IR (4000-100 cm(-1)) and FT-Raman (4000-100 cm(-1)) spectra of solid sample of 4-chloro-2-fluoro toluene (4Cl2FT) have been recorded using Bruker IFS 66 V spectrometer. Ab initio-HF (HF/6-311++G (d, p)) and DFT (B3LYP/6-311++G and B3PW91/6-311++G (d, p)) calculations have been performed giving energies, optimized structures, harmonic vibrational frequencies, depolarization ratios, IR intensities, Raman activities. The vibrational frequencies are calculated and scaled values are compared with FT-IR and FT-Raman experimental values. The isotropic HF and DFT analyses showed good agreement with experimental observations. The differences between the observed and scaled wave number values of most of the fundamentals are very small in B3LYP than HF. Comparison of the simulated spectra provides important information about the ability of the computational method (B3LYP) to describe the vibrational modes. The influences of substitutions on the geometry of molecule and its normal modes of vibrations have also been discussed. The changes made by substitutions on the benzene are much responsible for the non-linearity of the molecule. This is an attractive entity for the future studies of non-linear optics.

Vibrational spectroscopy (FTIR and FTRaman) investigation using ab initio (HF) and DFT (B3LYP and B3PW91) analysis on the structure of 2-amino pyridine

The FTIR and FTRaman spectra of 2-amino pyridine (2-AP) molecule have been recorded using Bruker IFS 66 V spectrometer in the range of 4000-100 cm(-1). The molecular geometry and vibrational frequencies in the ground state are calculated by using the ab initio Hartree-Fock (HF) and DFT (B3LYP and B3PW91) methods with 6-31++G (d, p) and 6-311++G (d, p) basis sets. The computed values of frequencies are scaled using a suitable scale factor to yield good coherence with the observed values. Making use of the recorded data, the complete vibrational assignments are made and analysis of the observed fundamental bands of molecule is carried out. The geometries and normal modes of vibrations obtained from ab initio HF and B3LYP/B3PW91 calculations are in good agreement with the experimentally observed data. The differences between the observed and scaled wave number values of most of the fundamentals are very small in B3LYP than HF. The influence of N atom and amine group in the skeletal ring vibrations of the title molecule has also been discussed.