Molecular Structure Calculations Research Articles

Ab initio and density functional theory calculations of molecular structure and vibrational spectra of 4-(2-Hydroxyethyl) piperazine-1-ethanesulfonic acid

The FTIR and FT-Raman spectra of 4-(2-Hydroxyethyl) piperazine-1-ethanesulfonic acid were recorded and the structural and spectroscopic data of the molecule in the ground state were calculated using Hartree–Fock and Density Functional Method (B3LYP). The most stable conformer was optimized and the structural and vibrational parameters were determined. With the observed FTIR and FT-Raman data, a complete vibrational band assignment and analysis of the fundamental modes of the compound were carried out. Thermodynamic properties, Mulliken and natural atomic charge distribution were calculated using both Hartree–Fock and Density Functional Method and compared. UV–Visible and HOMO–LUMO analysis were carried out. 1H and 13C NMR chemical shifts of the molecule were calculated using gauge including atomic orbital method and were compared with experimental results. Stability of the molecule arising from hyperconjugative interactions and charge delocalization has been analyzed using natural bond orbital analysis. The first order hyperpolarizability (β) and molecular electrostatic potential of the molecule was computed using DFT calculations. The electron density based local reactivity descriptor such as Fukui functions were calculated to explain the chemically reactive site in the molecule.

Crystal, Molecular Structure and DFT Study of 2,6,7-Trimethyl-3-p-tolylquinoxaline and 2-(4-Methoxyphenyl)-3,6,7-trimethylquinoxaline

The molecular structure of 2,6,7-trimethyl-3-p-tolylquinoxaline (hereafter denoted I) was confirmed by single crystal X-ray structure analysis. In the title compound, C18H18N2, I, the quinoxaline ring system is essentially planar. The phenyl ring at the 2-position makes a dihedral angle of 40.23° with the quinoxaline mean plane. In the crystal, molecules are linked into layers mainly by H2C–H···π and (π)C–H···π interactions. Stacking π···π interactions are absent in the structure. The experimental and theoretical structural aspects of I and the recently reported methoxy derivative, 2-(4-methoxyphenyl)-3,6,7-trimethylquinoxaline, II, have been investigated and compared. Experimental geometric parameters (bond lengths and bond angles and dihedral angles) were compared with computed values from density functional theory with B3LY6−31G(d,p) basis set. Results show that values are in good agreement. The highest occupied molecular orbitals (HOMO) and lowest unoccupied molecular orbitals (LUMO) energies have been also calculated and used to determine the charge transfer within the molecule. MEP surfaces analyses were performed by the DFT method. From the MEP map, negative region is mainly localized over the electronegative nitrogen atoms (in I), and the nitrogen and oxygen atoms (in II) and the maximum positive region is localized on the methyl groups. These surfaces seem to correlate well with the intermolecular interactions in the lattice. Time-dependent density functional theory has been carried out to study the UV spectra of both molecules in gas phase and in methanol using polarizable continuum model and the results are presented and discussed. Crystal, molecular structure, crystal supramolecularity and DFT calculations of 2,6,7-Trimethyl-3-p-tolylquinoxaline and 2-(4-Methoxyphenyl)-3,6,7-trimethylquinoxaline are reported.

Design and synthesis of novel ROR inverse agonists with a dibenzosilole scaffold as a hydrophobic core structure

Molecular structure calculations indicated that the dibenzosilole skeleton could be well superposed on phenanthridinone, which is a structural component of ligands of retinoic acid receptor-related orphan receptors (RORs). Therefore, we designed, synthesized and biologically evaluated a series of novel ROR ligands based on the dibenzosilole scaffold as a hydrophobic core structure. Dibenzosilole derivatives bearing a hexafluoro-2-hydroxypropyl group on the benzene ring exhibited significant ROR-inhibitory activity, comparable to that of the lead phenanthridinone derivative 5. Our results indicate that the dibenzosilole skeleton would be a useful scaffold for developing novel biologically active compounds, and that cis-amide structure can be replaced by an alkylsilyl functionality.

Molecular structure, spectroscopic characterization and DFT calculations of a novel (Z)-1-[(2-Ethylphenylamino)methylene]naphthalene-2(1H)-one

A novel Schiff base compound (Z)-1-[(2-Ethylphenylamino)methylene]naphthalene-2(1H)-one was synthesized from the reaction of 2-hydroxy-1-naphthaldehyde with 2-ethylaniline. The structural properties of the compound have been characterized by using FT-IR, 1H and 13C NMR, UV–vis and X-ray single-crystal methods. According to X-ray diffraction result, the title compound exists in the keto-amine tautomeric form. The molecular geometry, vibrational frequencies, electronic absorption spectra and gauge including atomic orbital (GIAO) 1H and 13C NMR chemical shift values of the title compound in the ground state have been calculated by using density functional theory (DFT/B3LYP) method with 6-311G++(d,p) basis set, and compared with the experimental data. The obtained results indicate that optimized geometry can well reflect the crystal structural parameters. The theoretical values are in good agreement with the experimental ones. The energetic behavior of the compound in solvent media has been examined using B3LYP method with the 6-311G++(d,p) basis set by applying the polarizable continuum model (PCM). The total energy of the compound decreases with increasing polarity of the solvent. The molecular electrostatic potential (MEP), HOMO–LUMO energy gap and non-linear optical (NLO) properties of the compound were investigated using theoretical calculations.

Dissociative recombination and vibrational excitation of CO+: model calculations and comparison with experiment

The latest molecular data—potential energy curves and Rydberg/valence interactions—characterizing the super-excited electronic states of CO are reviewed, in order to provide inputs for the study of their fragmentation dynamics. Starting from this input, the main paths and mechanisms for CO+ dissociative recombination are analyzed; its cross sections are computed using a method based on multichannel quantum defect theory. Convoluted cross sections, giving both isotropic and anisotropic Maxwellian rate coefficients, are compared with merged-beam and storage-ring experimental results. The calculated cross sections underestimate the measured ones by a factor of two, but display a very similar resonant shape. These facts confirm the quality of our approach for the dynamics, and call for more accurate and more extensive molecular structure calculations.

Formation of H2 from internally heated polycyclic aromatic hydrocarbons: excitation energy dependence.

We have investigated the effectiveness of molecular hydrogen (H2) formation from Polycyclic Aromatic Hydrocarbons (PAHs) which are internally heated by collisions with keV ions. The present and earlier experimental results are analyzed in view of molecular structure calculations and a simple collision model. We estimate that H2 formation becomes important for internal PAH temperatures exceeding about 2200 K, regardless of the PAH size and the excitation agent. This suggests that keV ions may effectively induce such reactions, while they are unlikely due to, e.g., absorption of single photons with energies below the Lyman limit. The present analysis also suggests that H2 emission is correlated with multi-fragmentation processes, which means that the [PAH-2H](+) peak intensities in the mass spectra may not be used for estimating H2-formation rates.

Stable and easily accessible functional dyes: dihydrotetraazaanthracenes as versatile precursors for higher acenes.

A series of new dihydrotetraazaanthracenes and one new dihydrotetraazatetracene as substances for applications in organoelectronic devices and as suitable building blocks for higher azaacenes was synthesised. The condensation of aromatic diamines with dichlorodicyanopyrazine led to these tricyclic/tetracyclic compounds. Syntheses of N-substituted phenylenediamines were developed to enable the introduction of multiple functional groups such as ester, amino, or nitro groups on the chromophoric system. Relationships between the structure and the spectroscopic properties could be derived from UV/Vis absorption and fluorescence spectroscopy, as well as by DFT and TD-DFT calculations of molecular and aggregate structures. The absorption spectra are dominated by π-π* transitions of the single molecules, whereas aggregation needs to be taken into account to obtain reasonable agreement between theory and experiment in certain cases. Single-crystal X-ray analyses were carried out to examine the morphology and solid packing effects. Finally, a dihydrotetraazaanthracene was used as a building-block to create a mesoionic octaazapentacene.

Density functional calculations of molecular structures of arsenic-binding β-domain of metallothioneins-2

Arsenic is part of the most serious hazards whose detoxification in organisms is mainly performed by its binding to some metalloproteins such as metallothioneins (MTs). It is of great physiological significance to detect the molecular structures of arsenic-binding MTs for understanding its detoxification mechanism. But there is no definite density functional method in geometry descriptions of arsenic-binding βMT2, which contains 384 atoms. In this work, six arsenic complexes were used to estimate the performance of 21 density functionals. Moreover, eight different basis sets were also considered. The computed structure parameters were compared to the experimental data. It is shown that the combination of the functional SOGGA/basis set TZVP shows a highest ratio of cost performance in predicting molecular structures of arsenic complexes. Using the combination of SOGGA with TZVP, we have successfully predicted the optimal structures and theoretical absorption spectra of As3+-binding β domain of rabbit liver metallothioneins-2. The confirmed calculation method will be helpful for our further understanding on the molecular structures of arsenic-containing systems.

A weight averaged approach for predicting amide vibrational bands of a sphingomyelin bilayer.

Infrared (IR) and Raman spectra of a sphingomyelin (SM) bilayer have been calculated for the amide I, II and A modes and the double-bonded CC stretching mode by a weight averaged approach, based on an all-atom molecular dynamics (MD) simulation and a vibrational structure calculation. Representative structures and statistical weights of SM clusters connected by hydrogen bonds (HBs) are observed in MD trajectories. After constructing smaller fragments from the SM clusters, the vibrational spectra of the target modes were calculated by normal mode analysis with a correction for anharmonicity, using density functional theory. The final IR and Raman spectra of a SM bilayer were obtained as the weight averages over all SM clusters. The calculated Raman spectrum is in excellent agreement with a recent measurement, providing a clear assignment of the peak in question observed at 1643 cm(-1) to the amide I modes of a SM bilayer. The analysis of the IR spectrum has also revealed that the amide bands are sensitive to the water content inside the membrane, since their band positions are strongly modulated by the HB between SM and water molecules. The present study suggests that the amide I band serves as a marker to identify the formation of SM clusters, and opens a new way to detect lipid rafts in the biological membrane.

Concept of effective states of atoms in compounds to describe properties determined by the densities of valence electrons in atomic cores

A new approach for describing the effective electronic states of "atoms in compounds" to study the properties of molecules and condensed matter which are circumscribed by the operators heavily concentrated in atomic cores is proposed. Among the properties are hyperfine structure, space parity (P) and time reversal invariance (T) nonconservation effects, chemical shifts of x-ray emission lines (XES), M\"{o}ssbauer effect, etc. Advantage of the approach is that a good quantitative agreement of predicted and experimental data can be attained even for such difficult cases as XES chemical shifts providing correct quantum-mechanical interpretation of the experimental data. From computational point of view the method can be quite efficient being implemented in the framework of the relativistic pseudopotential theory [Int.J. Quantum Chem. 71, 359 (1999)] and procedures of recovering the wave functions in heavy-atom cores [Int.J. Quantum Chem. 104, 223 (2005)] after a molecular, cluster or periodic structure calculation performed on the basis of pseudoorbitals smoothed near the nuclei within the pseudopotential approximation. We report results of our studies of a number of atomic and molecular systems to demonstrate the capabilities of the approach.

Unimolecular reactions of 1,1,1-trichloroethane, 1,1,1-trichloropropane, and 3,3,3-trifluoro-1,1,1-trichloropropane: determination of threshold energies by chemical activation.

The recombination of CCl3 radicals with CH3, CH3CH2, and CF3CH2 radicals was used to generate CH3CCl3, CH3CH2CCl3, and CF3CH2CCl3 molecules with approximately 87 kcal mol(-1) of vibrational energy in a bath gas at room temperature. The competition between collisional deactivation and unimolecular reaction by HCl elimination was used to obtain the experimental rate constants for each molecule. These experimental rate constants were matched to calculated statistical unimolecular rate constants to assign threshold energies to the three HCl elimination reactions. The models needed for the calculations of the rate constants were obtained from molecular structure calculations using density functional theory (DFT) with the hybrid density-functional MO6-2X recommended by Truhlar for transition states. The assigned threshold energies are 52 ± 2, 50 ± 2, and 52 ± 2 kcal mol(-1) for CH3CCl3, CH3CH2CCl3, and CF3CH2CCl3, respectively, and the CH3 and CF3 groups have only a minor effect on the threshold energies for HCl elimination. The DFT calculated threshold energies are in agreement with the experimentally assigned values. The addition of Cl atoms to the same carbon atom lowers the threshold energy for HCl elimination in the CH3CH2Cl, CH3CHCl2, and CH3CCl3 series. This trend, which is the opposite of that for CH3CH2F, CH3CHF2, and CH3CF3, is discussed in terms of transition-state structure and correlated with the relative stabilities of CH3CH2(+), CH3CHCl(+), and CH3CCl2(+) ions; the relative stabilities are based on the hydride affinities obtained from calculations. Comparison of the reactions of CH3CCl3 and CH2ClCHCl2 shows that the threshold energy is much higher for the isomer with chlorine atoms on both carbon atoms.

Role of Protonation State and Solvation on the pH Dependent Optical Properties of Bromocresol Green.

pH sensors play a key role in many industrial and diagnostic applications. Mostly their usage is based on experience, and in many cases the working mechanisms of these sensors are not known in detail, thereby hindering a systematic improvement of such sensors for specific applications. In this report, we present results from combined quantum chemical and molecular mechanics calculations of molecular structures and optical absorption properties of bromocresol green (BRG) in aqueous solution with varying pH value. In the acidic pH range, this chromophore has an intense band with absorption maximum at 444 nm and in the basic pH regime the absorption spectra show a redshift toward 613 nm. In order to identify the molecular structures responsible for this pH dependent optical behavior the closed and open forms of BRG are studied using static approaches considering in each case the three possible protonated states namely, neutral, anionic, and dianionic. For the most significant forms, i.e. the open forms of BRG, extensive modeling based on the integrated approach has been carried out, where the structure and dynamics were studied using hybrid QM/MM molecular dynamics, while the excitation energy calculations were carried out using time dependent density functional theory wherein the surrounding solvent was described as polarizable continuum, semicontinuum, or via a molecular mechanics force-field. The anionic and dianionic forms of BRG have been recognized as molecular forms responsible for its acidic and basic pH behavior, respectively. In contrast to the case of solvatochromic probes, the different protonation states determine the optical behavior in different pH values for pH probes. Hence, the level of solvent description appears to be of minor importance. Independent of the level of theory used to describe the solvent, all models reproduce the spectral features of BRG in different pH and also the pH induced redshift in good agreement with experiment.

Molecular structure, spectroscopic properties and quantum chemical calculations of a novel 2,2′-Dicarboxy-4,4′-(propane-2,2-di-yl)diphenol

The synthesis, spectroscopic (IR, 1H and 13C NMR chemical shifts) investigations of 2,2′-Dicarboxy-4,4′-(propane-2,2-di-yl)diphenol molecule have been confirmed. Molecular geometry, vibrational frequencies and gauge including atomic orbital (GIAO) 1H and 13C NMR chemical shift values of the compound in the ground state have been calculated using the density functional method (DFT) with 6-311G++(d,p) basis set. The calculated values are in good agreement with the experimental values. The energetic behavior of the compound in solvent media has been examined using B3LYP method with the 6-311G++(d,p) basis set by applying the polarizable continuum model (PCM). The total energy of the compound decreases with increasing polarity of the solvent. Besides, molecular electrostatic potential (MEP), non-linear optical (NLO) properties of the compound have been investigated by using theoretical calculations.

Evaluation of log Po/w values of drugs from some molecular structure calculation softwares

Predictive software packages to estimate the lipophilicity of molecules have become key tools in the new drug design. Six different well-known computational programs including the classical BioByte-clogP and the GALAS algorithm offered by ACDlabs were evaluated through a set of 103 drugs with different structures and functionalities. To evaluate the predictions accuracy, reliable experimental log Po/w values for the whole testing set were carefully selected. The best estimations are performed by GALAS/logP based on the fragmental method, corrected according to the similarity with compounds included in the software training set.

Molecular structure, spectroscopic properties (FT-IR, Micro-Raman, and UV-vis), and DFT calculations of minaprine

Molecular geometry, experimental vibrational wavenumbers, electronic properties, and quantum chemical calculations of minaprine (C17H22N4O · 2HCl), (with synonym, dihydrochloride salt of N-(4-methyl-6-phenyl-3-pyridazinyl)-4-morpholineethamine) which is widely used as a psychotropic drug at medicinal treatment, in the ground state by using density functional theory (DFT/B3LYP) method with 6–31++G(d,p) basis set have been presented for the first time. The comparison of the observed fundamental vibrational frequencies were in a very good agreement with the experimental data. Furthermore, UV-vis TD-DFT calculations, the highest occupied molecular orbitals (HOMO-1, HOMO), lowest unoccupied molecular orbitals (LUMO, LUMO + 1), molecular electrostatic potential (MEP) surface, atomic charges and thermodynamic properties of minaprine molecule have been theoretically calculated and simulated at the mentioned level.

Using of DFT method for calculation of molecular structures of metalmacrocyclic 3d-element chelates forming at “self-assembly”

Using density functional theory (DFT) at the OPBE/TZP level, the calculation of the geometric parameters of the molecular structures of M(II) (5656)macrotetracyclic complexes with a tetradentate macrocyclic ligand with (NNNN)-coordination of donor centers, resulting from “self-assembly” process in M(II)– dithiooxamide– propandiol-1,3 ternary systems, where M= Mn, Fe, Co, Ni, Cu, Zn was performed. The calculation of the molecular structure of this ligand itself was also carried out. The values of the bond lengths, bond and torsion angles in the resulting complexes and macrocyclic ligand indicated above, are presented. The values of the standard enthalpy, entropy and Gibbs free energy of formation of these compounds were also calculated.

Quantum-chemical calculation of molecular structures of (5656)macrotetracyclic 3d-metal complexes “self-assembled” in quaternary systems M(II) ion-ethanedithioamide-formaldehyde-ammonia by the density functional theory method

The geometric parameters of (5656)macrotetracyclic complexes of Mn(II), Fe(II), Co(II), Ni(II), Cu(II), and Zn(II) with the NNNN-coordination of donor sites of the chelant formed by the template reactions in the M(II)-ethanedithioamide-formaldehyde-ammonia systems have been calculated by the OPBE/TZVP hybrid density functional theory (DFT) method with the use of the Gaussian09 program package. In all complexes, five-membered chelate rings (almost identical to each other in each complex) are nonplanar. For all M(II) ions under consideration, two additional six-membered nonplanar chelate rings formed as a result of template “cross-link” are turned at considerable angles with respect to the five-membered rings. The six-membered rings are located on different sides of the NNNN plane of the nitrogen donor atoms.

A suggestion for a new algorithm for the calculation of molecular structures

Algorithms available for the calculation of molecular structures of biomolecules only deliver reasonable results in a few cases. In particular, for complex biomolecules as proteins and nucleic acids, the results are only partly usable. Thus, molecular structures of immunological relevant molecules can only be determined experimentally by methods as X–ray analysis and nuclear magnetic resonance (NMR) spectroscopy. Perhaps, the difficulties with the algorithms used so far are that a large number of interactions are ignored. So far, electrostatic interactions as in hydrogen bonds have been considered, with addition of van der Waals interactions and hydrophobic forces. This work considers mass–charge interactions in addition to the Coulombic interactions as pure charge–charge interactions. This new type of interaction has recently been proposed, and turns out to be useful in the calculation of molecular structures. An efficient method of calculating molecular structures would lead to a better understanding of structures and would be a developmental leap for computational biology.

Molecular Structure, Spectroscopic Properties (FT-IR, Micro-Raman and UV-vis) and DFT Calculations of Minaprine

Molecular Structure, Spectroscopic Properties (FT-IR, Micro-Raman and UV-vis) and DFT Calculations of Minaprine

Chiral Modification of Platinum by Co‐Adsorbed Cinchonidine and Trifluoroacetic Acid: Origin of Enhanced Stereocontrol in the Hydrogenation of Trifluoroacetophenone

Cinchonidine (CD) adsorbed onto a platinum metal catalyst leads to rate acceleration and induces strong stereocontrol in the asymmetric hydrogenation of trifluoroacetophenone. Addition of catalytic amounts of trifluoroacetic acid (TFA) significantly enhances the enantiomeric excess from 50 to 92%. The origin of the enantioselectivity bestowed by co-adsorbed CD and TFA is investigated by using in situ attenuated total reflection infrared spectroscopy and modulation excitation spectroscopy. Molecular interactions between the chiral modifier (CD), acid additive (TFA) and the trifluoro-activated substrate at the solid-liquid interface are elucidated under conditions relevant to catalytic hydrogenations, that is, on a technical Pt/Al2O3 catalyst in the presence of H2 and solvent. Monitoring of the unmodified and modified surface during the hydrogenation provides an insight into the phenomenon of rate enhancement and the crucial interactions of CD with the ketone, corresponding product alcohol, and TFA. Comparison of the diastereomeric interactions occurring on the modified surface and in the liquid solution shows a striking difference for the chiral preferences of CD. The spectroscopic data, in combination with calculations of molecular structures and energies, sheds light on the reaction mechanism of the heterogeneous asymmetric hydrogenation of trifluoromethyl ketones and the involvement of TFA in the diastereomeric intermediate surface complex: the quinuclidine N atom of the adsorbed CD forms an N-H-O-type hydrogen-bonding interaction not only with the trifluoro-activated ketone but also with the corresponding alcohol and the acid additive. Strong evidence is provided that it is a monodentate acid/base adduct in which the carboxylate of TFA resides at the quinuclidine N-atom of CD, which imparts a better stereochemical control.