Abstract:The calculation of anharmonic vibrational frequencies for a set of small molecules has been examined to explore the merit of applying such computationally expensive approaches for large molecules with density functional theory. The performance of different hybrid and gradient-corrected exchange-correlation functionals has been assessed for the calculation of anharmonic vibrational frequencies using second-order vibrational perturbation theory with two-and four-mode couplings and compared to the recently develo… Show more
“…Currently, modern computational chemistry yields results comparable to the most accurate experimental measurements [61]. Furthermore, the interpretation of experimental vibrational spectra is much easier and accurate owing to calculated harmonic and anharmonic [62] vibration transitions [63].
…”
2-carboxylic acids [3] and corresponding esters [4]. Pyrrole-2-carboxylates are also useful substrates for the preparation of more complex pyrrole containing systems [5] such as ketorolac, a drug with anti-inflammatory and analgesic properties [6]. It is noted that the 2-acylpyrrole motif is widespread in nature. There are many examples of 2-acylpyrrole based molecules (Figure 1) with various biological activities [7,8]. Representative examples are pyoluteorin and pyrrolomycin D, secondary metabolites produced by marine
Conformational Preferences of 2-Acylpyrroles in Light of FT-IR and DFT StudiesAlina T Dubis* Institute of Chemistry, University of Białystok, Hurtowa 1, Poland
AbstractConformations of alpha-substituted pyrroles have been effectively studied using spectroscopic methods assisted by theoretical calculations developed in the recent decade. The question of how to effectively study the conformation of 2-acylpyrrole no longer remains unanswered. The detailed spectroscopic studies conducted in the last decade and interpreted on the basis of theoretical calculations provide a satisfactory answer to that question. Based on the Density Functional Theory (DFT) calculations of conformational properties of 2-acylpyrroles, for which two stable rotameric forms were predicted, syn and anti-conformers have been studied either by experimental or theoretical methods. The family of 2-acylpyrroles have both a proton donor N-H group and a proton acceptor C=O group. This structure favors the formation of doubly hydrogen-bonded cyclic dimers connected by two N-H...O=C bonds. The tendency to form cyclic dimers stabilizes the syn-conformation. Due to these properties 2-acylpyrroles can be used as structural models for the conformational analysis of peptides.This review summarizes recent investigations of conformations of 2-acylpyrroles, with a particular emphasis on the hydrogen bonds forming within these systems. The influence of 2-substitution on different aspects of stability of these molecular systems and the usefulness of infrared spectroscopy supported by theoretical calculations in H-bonds and conformational studies are discussed. Among the molecular properties hydrogen bond energy, structural characteristics such as C=O bond length of dimers and unique spectral features of 2-acylpyrroles that can be used to predict and investigate the conformation and structure of proteins are considered.Graphical abstract. The potential energy diagram of 2-acylpyrroles as a function of the dihedral angle pyrrole ringcarbonyl group of bond rotation. Most stable conformer syn converts to conformer anti via the transition state TS1; less stable conformer anti converts to conformer syn via the transition state TS2. conformational research and can greatly support experimental work with quite good accuracy. Among the most useful parameters are geometrical parameters, relative conformational energies, barriers to internal rotation and vibrational frequencies for each conformer.
Journal of Physical Chemistry & BiophysicsEnergy differ...
“…Currently, modern computational chemistry yields results comparable to the most accurate experimental measurements [61]. Furthermore, the interpretation of experimental vibrational spectra is much easier and accurate owing to calculated harmonic and anharmonic [62] vibration transitions [63].
…”
2-carboxylic acids [3] and corresponding esters [4]. Pyrrole-2-carboxylates are also useful substrates for the preparation of more complex pyrrole containing systems [5] such as ketorolac, a drug with anti-inflammatory and analgesic properties [6]. It is noted that the 2-acylpyrrole motif is widespread in nature. There are many examples of 2-acylpyrrole based molecules (Figure 1) with various biological activities [7,8]. Representative examples are pyoluteorin and pyrrolomycin D, secondary metabolites produced by marine
Conformational Preferences of 2-Acylpyrroles in Light of FT-IR and DFT StudiesAlina T Dubis* Institute of Chemistry, University of Białystok, Hurtowa 1, Poland
AbstractConformations of alpha-substituted pyrroles have been effectively studied using spectroscopic methods assisted by theoretical calculations developed in the recent decade. The question of how to effectively study the conformation of 2-acylpyrrole no longer remains unanswered. The detailed spectroscopic studies conducted in the last decade and interpreted on the basis of theoretical calculations provide a satisfactory answer to that question. Based on the Density Functional Theory (DFT) calculations of conformational properties of 2-acylpyrroles, for which two stable rotameric forms were predicted, syn and anti-conformers have been studied either by experimental or theoretical methods. The family of 2-acylpyrroles have both a proton donor N-H group and a proton acceptor C=O group. This structure favors the formation of doubly hydrogen-bonded cyclic dimers connected by two N-H...O=C bonds. The tendency to form cyclic dimers stabilizes the syn-conformation. Due to these properties 2-acylpyrroles can be used as structural models for the conformational analysis of peptides.This review summarizes recent investigations of conformations of 2-acylpyrroles, with a particular emphasis on the hydrogen bonds forming within these systems. The influence of 2-substitution on different aspects of stability of these molecular systems and the usefulness of infrared spectroscopy supported by theoretical calculations in H-bonds and conformational studies are discussed. Among the molecular properties hydrogen bond energy, structural characteristics such as C=O bond length of dimers and unique spectral features of 2-acylpyrroles that can be used to predict and investigate the conformation and structure of proteins are considered.Graphical abstract. The potential energy diagram of 2-acylpyrroles as a function of the dihedral angle pyrrole ringcarbonyl group of bond rotation. Most stable conformer syn converts to conformer anti via the transition state TS1; less stable conformer anti converts to conformer syn via the transition state TS2. conformational research and can greatly support experimental work with quite good accuracy. Among the most useful parameters are geometrical parameters, relative conformational energies, barriers to internal rotation and vibrational frequencies for each conformer.
Journal of Physical Chemistry & BiophysicsEnergy differ...
“…30%‐40% additional Hartree‐Fock exchange, while anharmonic studies using VPT2 have shown that the B97‐1 functional outperforms B3LYP and that the optimum hybridization is ca. 20%, in line with the prediction of other molecular properties . Another method for checking the accuracy of harmonic calculations is therefore to compare the quality of the harmonic calculations with harmonic experimental frequencies that are extrapolated from vibrational spectra of small molecules.…”
Section: Resultsmentioning
confidence: 99%
“…Previous studies have shown that choice of basis set is of considerable importance when calculating accurate harmonic and anharmonic frequencies more generally . This can be such a significant source of computational cost and error, that basis sets tailored to specific vibrational coordinates are in development, and Pople basis sets are commonly used as a compromise between accuracy and computational cost, particularly during anharmonic calculations . At the same time, uncontracting the core basis functions in Pople‐type atom‐centered basis sets has been shown to improve calculations of core‐electron properties, such as core‐electron binding energies, and provides a systemic way of testing improvements in basis set quality when describing the core region of molecules as well as σ‐orbitals described by the additional s ‐functions, which are fewer in the Pople basis sets than other families of basis set …”
Section: Introductionmentioning
confidence: 99%
“…The functionals studied in this work have been chosen to reflect specific cases of interest. The B3LYP functional is known to perform particularly well for calculating scaled harmonic frequencies, and the B97‐1 functional is one of few functionals that outperforms B3LYP for calculating anharmonic frequencies . Two meta‐hybrid functionals were also chosen.…”
The effects that uncontracting the core 1s basis functions in the Pople basis sets have on the calculation of harmonic vibrational frequencies, scaling factors, and anharmonic frequencies are examined for a selection of hybrid and meta‐hybrid density functional theory methods across a wide range of molecules. Median improvements of around half a wavenumber indicate that uncontracting the core functions provides modest improvements for harmonic calculations. The importance of these core functions is found to increase when using meta‐hybrid or anharmonic methods. The core functions are also found to be particularly important for several types of vibrational coordinate, including some carbonyl and carbon‐nitrogen stretching modes, where interaction between the uncontracted 1s functions and triple‐ζ 2s functions appear to play a significant role. Extra core functions are also particularly important for anharmonic second‐order perturbation theory calculations involving alkyne molecule bending modes, where individual transitions can change by as much as 230 wavenumbers.
“…Harmonic frequencies were scaled using a scaling factor of 0.9682. 2,50,65 In principle it would be possible to derive scaling factors for different excited state methods. However, there is currently a lack of experimental data encompassing a wide range of functional groups to make this reliable, and we assume here that scaling factors derived for the ground state can be applied with no additional modifications following previous excited state frequency benchmarking studies.…”
In contrast to the ground state, the calculation of the infrared (IR) spectroscopy of molecular singlet excited states represents a substantial challenge. Here we use the structural IR fingerprint of the singlet excited states of a range of coumarin dyes to assess the accuracy of density functional theory based methods for the calculation of excited state IR spectroscopy.It is shown that excited state Kohn-Sham density functional theory provides a high level of accuracy and represents an alternative approach to time-dependent density functional theory for simulating the IR spectroscopy of the singlet excited states.
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