Molecular geometry as a source of chemical information. 3. How H-bonding affects aromaticity of the ring in the case of phenol and p-nitrophenol complexes: a B3LYP/6-311+G study

Molecular geometries of phenol and p-nitrophenol (ArOH) interacting with fluoride were optimized at the B3LYP/6-311+G level of theory taking as constraints the planarity of the systems and the linearity of the O...H...F moiety. For p-nitrophenol complexes, the substituent effect stabilization energy (SESE) was computed, and for all systems aromaticity indices, HOMA, and out-of-plane components of NICS(1) and NICS(1)(zz)() were calculated. SESE values depend strongly on the O...F distance, the same as both aromaticity indices. Variation in HOMA values for the studied ArOH...F(-) complexes is within the range of 0.55 to approximately 1.0 and for NICS(1)(zz)() between -12 and -26 ppm. It was also found that a decrease in aromaticity is well correlated with the variations of C-O bond length.     

Statistical analysis of (13)C and (15)N NMR chemical shifts from GIAO/B3LYP/6-311 + + G** calculated absolute shieldings

The (13)C and (15)N absolute shieldings of 28 compounds have been calculated at the GIAO/B3LYP/6-311 + + G** level to complete a collection of data already published. This has allowed us to devise new equations relating delta and sigma for these nuclei based on 461 points ((13)C) and 70(72) points ((15)N).     

How H-bonding affects aromaticity of the ring in variously substituted phenol complexes with bases. 4. Molecular geometry as a source of chemical information

Aromaticity of the ring of variously substituted phenols in their H-bonded complexes with various bases was a subject of analysis based on 664 geometries retrieved from CSD and by use of the aromaticity index HOMA. GEO and EN, the components of the HOMA index, describing a decrease of aromaticity due to an increase of bond alternation (GEO term) and bond elongation (EN term), were also studied. There is an approximate monotonic dependence of HOMA and GEO on the H-bond strength estimated by the C-O bond length of the hydroxyl group in phenols.     

Simulation of proton migration pathways in phenolsulfonic acid-based membranes by B3LYP/6-31G** DFT calculations

Geometrical and energetic characteristics of clusters simulating crystal hydrates of phenolsulfonic acid (PSA) and its complexes with poly(vinyl alcohol) (PVA) and the pathways of proton transport therein were determined using the DFT (B3LYP) theory with the 6-31G** basis set. In the formation of proton-conducting PVA—PSA-based membranes, it is energetically favorable to have at least one water molecule in close proximity of the SO₃H fragment. In water-free media, the proton migration along the SO₃H group is hindered by a barrier of 30–34 kcal mol⁻¹. In the presense of water, the proton conductivity follows the relay mechanism with the activation barrier of 5–8 kcal mol⁻¹, which is close to the experimetally observed barrier of 4–6 kcal mol⁻¹. Thus, the relay mechanism of proton transfer in a sulfonic acid—water complex is energetically the most favorable. The most energetically favorable isomer is the one with the PSA and PVA fragments H-bonded through a water molecule. The deficiency of water causes the PVA OH protons to be involved in hydrogen bonding as well. The role of PVA is to align the acid molecules and participate in the relay proton transfer. Introduction of an aldehyde into the membrane results in significant improvement of its physical properties. The aldehyde reacts with the hydroxyl groups of PVA. At high humidity, one may expect little effect of the degree of cross-linking on the proton mobility.     

DFT B3LYP/6-311+G* calculation study of a new nonclassical mechanism of electrophilic functionalization of aromatic C–H bond via aryl cation formation

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Substituent effects on the thermochemistry of thiophenes. a theoretical (G3(MP2)//B3LYP and G3) study

Very good linear correlations between experimental and calculated enthalpies of formation in the gas phase (G3(MP2)//B3LYP and G3) for 48 thiophene derivatives have been obtained. These correlations permit a correction of the calculated enthalpies of formation in order to estimate more reliable "experimental" values for the enthalpies of formation of substituted thiophenes, check the reliability of experimental measurements, and also predict the enthalpies of formation of new thiophenes that are not available in the literature. Moreover, the difference between the enthalpies of formation of isomeric thiophenes with the same substituent in positions 2 and 3 of the ring has been analyzed. Likewise, a comparison of the substituent effect in the thiophene and benzene rings has been established.     

Fourier-transform infrared spectrum of aspartate hydroxo-aqua nickel (II) complex and DFT-B3LYP/3-21G and 6-311G structural and vibrational calculations

Aspartate hydroxo-aqua nickel (II) complex was synthesized and the structural analysis was carried out through the following methods: determination of the C, N, O and H contents, thermogravimetry and infrared spectrum. Several hypothetic structures were calculated by means of DFT: B3LYP/3-21G and B3LYP/6-311G quantum mechanical method. For [Ni(Asp)(OH)(H(2)O)] we have obtained the minimum of energy and no imaginary frequencies in the calculated infrared spectrum. Moreover, the experimental FT-infrared spectrum shows that the two N-H stretching follow the Bellamy-Williams relation proposed for primary amines. Coordination water bands were also observed in the infrared spectrum. For reasons of accomplishment, the Fourier transforms infrared and Raman spectra of acid aspartic were also discussed.     

New scale factors for harmonic vibrational frequencies using the B3LYP density functional method with the triple-zeta basis set 6-311+G(d,p)

We have calculated optimal frequency scaling factors for the B3LYP/ 6-311+G(d,p) method for fundamental vibrational frequencies on the basis of a set of 125 molecules. Using the new scaling factor, the vibrational frequencies calculated with the triple-zeta basis set 6-311+G(d,p) give significantly better accuracy than those calculated with the double-zeta 6-31G(d) basis set. Scale factors were also determined for low-frequency vibrations using the molecular set of 125 molecules and for zero-point energies using a smaller set of 40 molecules. We have studied the effect on the calculated vibrational frequencies for various combinations of diffuse and polarization functions added to the triple-zeta 6-311G basis set. The 6-311+G(d,p) basis set is found to give almost converged frequencies for most molecules, and we conclude that our optimum scaling factors are valid for the basis sets 6-311G(d,p) to 6-311++G(3df,3pd). The new scale factors are 0.9679 for vibrational frequencies, 1.0100 for low-frequency vibrations, and 0.9877 for zero-point vibrational energies.     

Fourier transform infrared spectrum, vibrational analysis and structural determinations of the trans-bis(glycine)nickel(II) complex by means of the RHF/6-311G and DFT:B3LYP/6-31G and 6-311G methods

The trans-bis(glycine)nickel(II) complex was synthesized, and the Fourier transform infrared spectra in the regions 4000-370 cm(-1) and 700-30 cm(-1) were measured. Band deconvolution analysis and the second derivative of the infrared spectrum were also performed. The determination of the geometrical structure in the trans position of the glycine ligands around Ni(II) for the trans-bis(glycine)nickel(II) complex as well as the vibrational assignment were assisted by RHF/6-311G and by Density Functional Theory calculations, DFT:B3LYP/6-31G and 6-311G basis sets. A full discussion of the framework vibrational modes was done using as criteria the geometry study of distorted structures generated for the vibrational modes. Incidentally, Normal Coordinate Analysis was carried out for the Ni(N)(2)(O)(2) structural fragment. The calculated DFT spectra in the high- and low-energy regions agree with the observed ones.     

Novel H-bonded base dimers as repeat units for information-bearing self-associative duplexes: a B3LYP/6-31G* search

Density functional theory at the B3LYP/6-31G* level with counterpoise correction has been employed to study six sets of nitrogenous bases for the capacity of each to form H-bonded dimers restricted to a chosen pairing configuration. These results are augmented by MP2/6-311++G(d,p) single point calculations on the B3LYP/6-31G* optimized geometries. Each set has two bases, including substituted azoles, imidazoles, pyrimidines, and fused ring systems. This study aims to determine the suitability of each set to furnish H-bonded base pairs which may serve as repeat units for self-associative H-bonded macromolecular duplexes with the capacity to store and replicate information at the molecular level. Out of the various possibilities tested here, a set of two substituted pyrimidines best satisfies the prescribed criteria and may be put forward as a good candidate to yield isomorphic repeat units for designing such synthetic information-bearing macromolecular duplexes. The optimized configurations of these chosen base pairs as calculated at the B3LYP/6-31G* level compare well with those calculated at the B3LYP/6-31++G(d,p) and MP2/6-31G(d,p) levels, and indicate that isomorphism of the two base pairs is independent of method used. Assuming a one-to-one correspondence for encoding information in the macromolecule, such a set of two bases can allow the macromolecule to encode up to 8 types of encrypted species.     

Lennard-Jones parameters for the combined QM/MM method using the B3LYP/6-31G*/AMBER potential

A combined DFT quantum mechanical and AMBER molecular mechanical potential (QM/MM) is presented for use in molecular modeling and molecular simulations of large biological systems. In our approach we evaluate Lennard-Jones parameters describing the interaction between the quantum mechanical (QM) part of a system, which is described at the B3LYP/6-31+G* level of theory, and the molecular mechanical (MM) part of the system, described by the AMBER force field. The Lennard-Jones parameters for this potential are obtained by calculating hydrogen bond energies and hydrogen bond geometries for a large set of bimolecular systems, in which one hydrogen bond monomer is described quantum mechanically and the other is treated molecular mechanically. We have investigated more than 100 different bimolecular systems, finding very good agreement between hydrogen bond energies and geometries obtained from the combined QM/MM calculations and results obtained at the QM level of theory, especially with respect to geometry. Therefore, based on the Lennard-Jones parameters obtained in our study, we anticipate that the B3LYP/6-31+G*/AMBER potential will be a precise tool to explore intermolecular interactions inside a protein environment.     

FT-IR vibrational spectrum and DFT:B3LYP/6-311G structure and vibrational analysis of bis-serinenickel(II) complex: [Ni(Ser)2

The bis-serinenickel(II) complex was synthesized, and the Fourier-transforms infrared spectra in the regions 4000-370 and 700-30 cm(-1) was measured. The second derivative spectra and band deconvolution analysis was also obtained. Density functional theory calculations, DFT:B3LYP/6-311G, were performed for the determination of geometrical structure and vibrational assignment for the bis-serinenickel(II) complex. A full discussion of the framework vibrational modes was done using as criteria the geometry study of distorted structures generated for the vibrational modes. Incidentally, the normal coordinate analysis was carried out for the Ni(N)2(O)2 structural fragment. The calculated DFT spectra in the high and low energy regions agree well with the observed ones.     

Vibrational assignments for 7-methyl-4-bromomethylcoumarin, as aided by RHF and B3LYP/6-31G* calculations

Infrared (4000-400 cm(-1)) and Raman (3500-50 cm(-1)) spectral measurements have been made for the solid sample of 7-methyl-4-bromomethylcoumarin. Electronic structure calculations at RHF/6-31G* and B3LYP/6-31G* levels of theory have been performed, giving equilibrium geometries, harmonic vibrational spectra and normal modes. Different orientations of bromomethyl group have yielded only two conformers, of which the most stable one lying lower from the other conformer by approximately 7.99 kJ/mol, is non-planar with no symmetry. A complete assignment of the vibrational modes, aided by the calculations, has been proposed. Coupled vibrations are manifest in many modes. Some spectral features, compared to 6-methyl-4-bromomethylcoumarin, show changes across both IR and Raman spectra, involving mainly skeletal vibrations, and to a lesser degree, methyl and bromomethyl vibrations. Low-frequency vibrations below 150 cm(-1) are assigned to lattice modes.     

IR and Raman Vibrational Assignments for Metal-free Phthalocyanine from Density Functional B3LYP／6-31G（d） Method

Vibrational (IR and Raman) spectra for the metal-free phthalocyanine (H2Pc) have been comparatively investigated through experimental and theoretical methods. The frequencies and intensities were calculated at density functional B3LYP level using the 6-3 IG(d) basis set. The calculated vibrational frequencies were scaled by the factor 0.9613 and compared with the experimental result. In the IR spectrum, the characteristic IR band at 1008.cm^-1 is interpreted as C-N (pyrrole) in-plane bending vibration, in contrast with the traditional assigned N-H in-plane or out-of-plane bending vibration. The band at 874 cm^-1 is attributed to the isoindole deformation and aza vibration. In the Raman spectrum, the bands at 540, 566, 1310, 1340, 1425, 1448 and 1618 cm^-1 are also re-interpreted. Assignments of vibrational bands in the IR and Raman spectra are given based on density functional calculations for the first time. The present work provides valuable information to the traditional empirical assignment and will be helpful for further investigation of the vibration spectra of phthalocyanine analogues and their metal complexes.     

DFT/B3LYP study of the substituent effect on the reaction enthalpies of the individual steps of single electron transfer-proton transfer and sequential proton loss electron transfer mechanisms of phenols antioxidant action

The reaction enthalpies related to the individual steps of two phenolic antioxidants action mechanisms, single electron transfer-proton transfer (SET-PT) and sequential proton loss electron transfer (SPLET), for 30 meta and para-substituted phenols (ArOH) were calculated using DFT/B3LYP method. These mechanisms represent the alternative ways to the extensively studied hydrogen atom transfer (HAT) mechanism. Except the comparison of calculated reaction enthalpies with available experimental and/or theoretical values, obtained enthalpies were correlated with Hammett constants. We have found that electron-donating substituents induce the rise in the enthalpy of proton dissociation (PDE) from ArOH+* radical cation (second step in SET-PT) and in the proton affinities of phenoxide ions ArO- (reaction enthalpy of the first step in SPLET). Electron-withdrawing groups cause the increase in the reaction enthalpies of the processes where electron is abstracted, i.e., in the ionization potentials of ArOH (first step in SET-PT) and in the enthalpy of electron transfer from ArO- (second step in SPLET). Found results indicate that all dependences of reaction enthalpies on Hammett constants of the substituents are linear. The calculations of liquid-phase reaction enthalpies for several para-substituted phenols indicate that found trends hold also in water, although substituent effects are weaker. From the thermodynamic point of view, entering SPLET mechanism represents the most probable process in water.     

Dissociation Energies and Rotational Barriers About CC Single,Double, and Triple Bonds: A Hybrid HF-DFT Approach (Becke3LYP/6-311++G**)

Structural Chemistry -     

H-Atom abstraction from CH(3)NHNH(2) by NO(2): CCSD(T)/6-311++G(3df,2p)//MPWB1K/6-31+G(d,p) and CCSD(T)/6-311+G(2df,p)//CCSD/6-31+G(d,p) calculations

Stationary points of paths for H atom abstraction from CH(3)NHNH(2) (monomethylhydrazine) by NO(2) were characterized via CCSD(T)/6-311++G(3df,2p)//MPWB1K/6-31+G(d,p) and CCSD(T)/6-311+G(2df,p)//CCSD/6-31+G(d,p) calculations. Five transition states connecting CH(3)NHNH(2)-NO(2) complexes to a manifold that includes CH(3)NHNH-HONO, CH(3)NNH(2)-HONO, CH(3)NNH(2)-HNO(2), and CH(3)NHNH-HNO(2) complexes were identified. Transition states that connect CH(3)NHNH-HONO, CH(3)NNH(2)-HONO, CH(3)NNH(2)-HNO(2), and CH(3)NHNH-HNO(2) complexes to each other via H atom exchange and/or hindered internal rotation were also identified. The high point in the minimum energy path from the CH(3)NHNH(2) + NO(2) reactant asymptote to the manifold of HONO-containing product states is a transition state 8.6 kcal/mol above the reactant asymptote. From a kinetics standpoint, this value is considerably higher than the 5.9 kcal/mol value that was estimated for it based on theoretical results for H atom abstraction from NH(3) by NO(2).     

Matrix-isolation FT-IR spectroscopic study and theoretical DFT(B3LYP)/6-31++G** calculations of the vibrational and conformational properties of tyrosine

The complicated conformational isomerism of tyrosine is studied by experimental matrix-isolation FT-IR spectroscopy combined with theoretical DFT(B3LYP)/6-31++G** calculations. Not less than 18 possible conformations of tyrosine have been considered theoretically. The results revealed that the most and the less stable forms of neutral tyrosine have the same conformation of the main part of amino acid (conformation II) but they differ in orientation of the phenyl ring. The calculated values of the relative energies suggest that all conformations would be detectable in the experimental spectrum. However, it appeared that it is not possible to distinguish in the experimental spectrum between the bands due to the forms with the same conformation of the main part of amino acid but a different orientation of the phenol ring.     

DFT:B3LYP ab initio molecular dynamics study of the Zundel and Eigen proton complexes, H5O2+ and H9O4+, in the triplet state in gas phase and solution

DFT:B3LYP ab initio molecular dynamics (MD) approach is used to elucidate the properties of the Zundel and Eigen, H5O2+ and H9O4+, proton complexes in the triplet state. The simulation considers the complexes in the gas phase (isolated complexes) and inside the clusters composed of 32, 64, and 128 water molecules, mimicking the behavior of aqueous solutions. MD simulations reveal three distinct periods. For the complex in solutions, the periods are smoothed out. The H5O2+ and H9O4+ complexes in the triplet state undergo structural rearrangements, which eventually result in hydrogen elimination. For the H5O2+, the hydrogen is eliminated from the center of the water cluster, whereas for the H9O4+ it is removed from a near-surface water molecule. The rate of hydrogen elimination decreases with increasing the number of water molecules surrounding the complex.