Carbohydrate-protein recognition probed by density functional theory and ab initio calculations including dispersive interactions

Carbohydrate-protein recognition has been studied by electronic structure calculations of complexes of fucose and glucose with toluene, p-hydroxytoluene and 3-methylindole, the latter aromatic molecules being analogues of phenylalanine, tyrosine and tryptophan, respectively. We use mainly a density functional theory model with empirical corrections for the dispersion interactions (DFT-D), this method being validated by comparison with a limited number of high level ab initio calculations. We have calculated both binding energies of the complexes as well as their harmonic vibrational frequencies and proton NMR chemical shifts. We find a range of minimum energy structures in which the aromatic group can bind to either of the two faces of the carbohydrate, the binding being dominated by a combination of OH-pi and CH-pi dispersive interactions. For the fucose-toluene and alpha-methyl glucose-toluene complexes, the most stable structures involve OH-pi interactions, which are reflected in a red shift of the corresponding O-H stretching frequency, in good quantitative agreement with experimental data. For those structures where CH-pi interactions are found we predict a corresponding blue shift in the C-H frequency, which parallels the predicted proton NMR shift. We find that the interactions involving 3-methylindole are somewhat greater than those for toluene and p-hydroxytoluene.     

An ab initio study of O2 and CO2 transport by perfluorocarbons

Fluorocarbons have been successfully applied as oxygen carriers replacing blood. In order to understand the nature of the interaction between fluorocarbons and hydrocarbons on the one hand and O₂, N₂ and CO₂ on the other, STO-3G calculations have been performed on their complexes. The very slight energies of interaction that were obtained seem to substantiate the contention that O₂, N₂ and CO₂ are physically dissolved in fluorocarbons. This energy of interaction is, however, distinctly larger for fluorocarbons than for hydrocarbons. Electrostatic potentials have been computed around several fluorocarbons. They make it possible to predict the geometries of the complexes that are formed.     

Molecular structure and vibrational spectra of phenobaraitone by density functional theory and ab initio hartree-Fock calculations

Quantum chemistry calculations have been performed using Gaussian03 program to compute optimized geometry, harmonic vibrational frequency along with intensities in IR and Raman spectra at RHF/6-31++G** and B3LYP/6-31++G** levels for phenobarbitone (C₁₂H₁₂N₂O₃) in the ground state. The scaled harmonic vibrational frequencies have been compared with experimental FT-IR and FT-Raman spectra. Theoretical vibrational spectra of the title compound were interpreted by means of potential energy distributions (PEDs) using MOLVIB program. A detailed interpretation of the infrared spectra of the title compound is reported. On the basis of the agreement between the calculated and observed results, the assignments of fundamental vibrational modes of phenobarbitone were examined and some assignments were proposed. The theoretical spectrograms for FT-IR and FT-Raman spectra of the title compound have been constructed.     

Molecular structure, IR spectra of 2-mercaptobenzothiazole and 2-mercaptobenzoxazole by density functional theory and ab initio Hartree–Fock calculations

Quantum chemistry calculations have been performed using Gaussian03 program to compute optimized geometry, harmonic vibrational frequency along with intensities in IR and Raman spectra and atomic charges at RHF/6-31+G*, B3LYP/6-31+G* and B3LYP/6-31++G* levels for 2-mercaptobenzothiazole (MBT, C₇H₅NS₂) and 2-mercaptobenzoxazole (MBO, C₇H₅NOS) in the ground state. The scaled harmonic vibrational frequencies have been compared with experimental FT-IR and FT-Raman spectra. The results show that the scaled theoretical vibrational frequencies is very good agreement with the experimental values. A detailed interpretation of the infrared and Raman spectra of 2-mercaptobenzothiazole and 2-mercaptobenzoxazole was reported. Comparison of calculated spectra with the experimental spectra provides important information about the ability of the computational method to describe the vibrational modes.     

Molecular structure, IR and NMR spectra of 2,6 distyrylpyridine by density functional theory and ab initio Hartree-Fock calculations

Vibrational frequencies and gauge including atomic orbital (GIAO) 13C NMR and 1H NMR chemical shift values of 2,6 distyrylpyridine (C21H17N) in the ground state have been calculated by using the Hartree-Fock (HF) and density functional method (B3LYP) with 6-31G(d) basis set. These methods are proposed as a tool to be applied in the structural characterization of 2,6 distyrylpyridine (C21H17N). The title compound has C2v point group, thus providing useful support in the interpretation of experimental IR data. In addition, obtained results were related to the linear correlation plot of experimental 13C NMR, 1H NMR chemical shifts values and IR data.     

Dissociation of sulfur oxoacids by two water molecules studied using ab initio and density functional theory calculations

Using ab initio [SCS‐MP2 and CCSD(T)] and density functional theory (M062X) calculations, we have studied the geometries and energies of sulfur oxoacids H₂S_mO₆ (m = 2–4) and their monohydrated and dihydrated clusters. When including the results from previously reported disulfuric acid (H₂S₂O₇) cases, the gas phase acidity is ordered as H₂S₂O₆ < H₂S₃O₆ < H₂S₂O₇ < H₂S₄O₆. The intramolecular H‐bonding, which may indicate the degree of structural flexibility in this molecular series, is an important factor for the order of the gas phase acidity. All these sulfur oxoacids show dissociated (or deprotonated) geometries with only two water molecules, although the energies of the dissociated conformers are ranked differently. All of the dissociated conformers form a unique H‐bonding network structure in which the protonated first water (H₃O⁺) is triply H‐bonded to each oxygen atom of two SO₃ moieties as well as the second water, which in turn is H‐bonded to a SO₃ moiety. H₂S₃O₆ has the best molecular flexibility for adopting such an H‐bonding network structure, and thereby all the low‐lying conformers of H₂S₃O₆(H₂O)₂ are dissociated. In contrast, the least flexible H₂S₂O₆ forms such a structure with a high strain, and dissociation of H₂S₂O₆(H₂O)₂ is found from the third lowest conformer. Although the gas phase acidity of H₂S₄O₆ is the highest in this series, the lowest dissociated conformer and the lowest undissociated conformer of H₂S₄O₆(H₂O)₂ are very close in energy. This is because forming the H‐bonding network structure is somewhat difficult due to the large distance between the two SO₃ moieties.     

FT-IR, NIR-FT-Raman and gas phase infrared spectra of 3-aminoacetophenone by density functional theory and ab initio Hartree-Fock calculations

The gas phase infrared spectrum of 3-aminoacetophenone (3AAP) was measured in the range 5000-500cm(-1) and with a resolution of 0.5cm(-1). The Fourier transform Raman (FT-Raman) and Fourier transform infrared (FT-IR) spectra of 3AAP were recorded in the solid phase. Geometry optimizations were done without any constraint and several thermodynamic parameters were calculated for the minimum energy conformer at ab initio and density functional theory (DFT) levels invoking 6-311G(2df 2p) basis set and the results are compared with the experimental values. Harmonic-vibrational wavenumber was also calculated for the minimum energy conformer at ab initio and DFT levels using 6-31G(d,p) basis set and the results are compared with related molecules. With the help of specific scaling procedures, the observed vibrational wavenumbers in gas phase, FT-IR and FT-Raman spectra were analyzed and assigned to different normal modes of the molecule. Most of the modes have wavenumbers in the expected range, the error obtained was in general very low. The appropriate theoretical spectrogram for the FT-IR spectra of the title molecule is also constructed.     

High level ab initio and density functional theory calculations of the dissociation energies,ionization energies,geometrical variations,and vibrational modes of ground and excited CO2, CO2+, and CO22+

The potential energy surface of CO₂²⁺ ( ³Σ_g^?) is investigated with HF, MP2, MP4, CBS‐Q, G1, G2MP2, G2, G3B3, and B3LYP/6‐311++G(3df,3pd) methods. Density functional theory shows the lowest dissociation channel of this compound to be the formation of CO⁺ ( ²Σ⁺)+O⁺ ( ⁴S_u) and to have a barrier of around 2 eV as well as a dissociation energy of around ?3.2 eV. Thus we propose that with enough correlation it is possible to accurately predict the energies of dissociation and barrier widths and heights to test for the stability of a particular molecular species. We also propose a refinement of current understanding by observing HOMO–LUMO gaps, Lowdin and Mulliken bond orders (to test for bond orbital overlap and hence qualitatively describe bonding and fragmentation in these complexes) and predicted spectrum for such studies as ZEKE spectroscopy (to study cationic states) and REMPI (to study the first excited states) of these class of molecules and, we hope, provide future insight into larger and more interesting systems. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

Electronic states of F2CO as studied by electron energy-loss spectroscopy and ab initio calculations

This paper reports on the first measurements of the electron impact electronic excitation cross-sections for carbonyl fluoride, F(2)CO, measured at 30 eV, 10° and 100 eV, 5° scattering angle, while sweeping the energy loss over the range 5.0-18.0 eV. The electronic-state spectroscopy has been investigated and the assignments are supported by quantum chemical calculations. The energy bands above 9.0 eV and the vibrational progressions superimposed upon it have been observed for the first time. Vibronic coupling has been shown to play an important role dictating the nature of the observed excited states, especially for the low-lying energy region (6.0-8.0 eV). New experimental evidence for the 6(1)B(2) state proposed to have its maximum at 12.75 eV according to the vibrational excitation reported in this energy region (11.6-14.0 eV). The n = 3 members of the Rydberg series have been assigned converging to the lowest ionization energy limits, 13.02 eV ((2)B(2)), 14.09 eV ((2)B(1)), 16.10 ((2)B(2)), and 19.15 eV ((2)A(1)) reported for the first time and classified according to the magnitude of the quantum defects (δ).     

Molecular structures and vibrational frequencies of 2-, 3- and 4-pyridine carboxaldehydes by ab initio Hartree-Fock and density functional theory calculations

The optimised molecular structures, vibrational frequencies and corresponding vibrational assignments of the cis and trans conformers of 2-, 3- and 4-pyridine carboxaldehydes have been calculated using ab initio Hartree-Fock (HF) and density functional theory (B3LYP) methods with 6-311++G(d, p) basis set. The calculations were adapted to the C(S) symmetries of all the molecules. The mean vibrational deviations between the vibrational frequency values of the two conformers of all the compounds have been seen to increase while the relative energies increase and it was concluded the more different the molecular structure of the two conformers is the higher the relative energy is between them, and thus a bigger mean vibrational deviation.     

ab initio molecular orbital and density functional analysis of acetylene + O2 reactions with CHEMKIN evaluation

A number of researchers have indicated that a direct reaction of acetylene with oxygen needs to be included in detailed reaction mechanisms in order to model observed flame speeds and induction times. Four pathways for the initiation of acetylene oxidation to chain propagation are considered and the rate constants are compared with values used in the mechanisms:

• 1 ³O₂ + HCCH to triplet adduct and reaction on the triplet surface
• 2 ³O₂ + HCCH to triplet adduct, conversion of triplet adduct to singlet adduct via collision in the reaction environment, with further reaction of the singlet adduct
• 3 ¹O₂ + HCCH to singlet adduct
• 4 Isomerization of HCCH to vinylidene and then vinylidene insertion reaction with ³O₂

Elementary reaction pathways for oxidation of acetylene by addition reaction of O₂(³Σ) on the triplet surface are analyzed. ab initio molecular orbital and density functional calculations are employed to estimate the thermodynamic properties of the reactants, transition states, and products in this system. Acetylene oxidation reaction over the triplet surface is initiated by addition of molecular oxygen, O₂(³Σ), to a carbon atom, forming a triplet peroxy‐ethylene biradical. The reaction path to major products, either two formyl radicals or glyoxal radical plus hydrogen atom, involves reaction through three transition states: O₂(³Σ) addition to acetylene (TS1), peroxy radical addition at the ipso‐carbon to form a dioxirane (TS2), and cleavage of O O bond in a three‐member ring (TS3). Single‐point QCISD(T) and B3LYP calculations with large basis sets were performed to try to verify barrier heights on important transition states. A second pathway to product formation is through spin conversion of the triplet peroxy‐ethylene biradical to the singlet by collision with bath gas. Rapid ring closure of the singlet peroxy‐ethylene biradical to form a four‐member ring is followed by breaking of the peroxy bond to form glyoxal, which further dissociates to either two formyl radicals or a glyoxal radical plus hydrogen atom. The overall forward rate constant through this pathway is estimated to be k_f = 2.21 × 10⁷ T^1.46e^{−33.1(kcal/mol)/RT}. Two additional pathways from the literature, HCCH + O₂(¹Δ) and pressure‐dependent isomerization of acetylene to vinylidene and then vinylidene reaction with O₂(³Σ), are also evaluated for completeness. CHEMKIN modeling on each of the four proposed pathways is performed and concentration profiles from these reactions are evaluated at 0.013 atm and 1 atm over 35 milliseconds. Through reaction on the triplet surface is evaluated to be not important. Formation of the triplet adduct with conversion (via collision) to a singlet and the vinylidene paths show similar and lower rates than those used in mechanisms, respectively. Our implementation of the HCCH + O₂(¹Δ) pathway of Benson suggests the need to include: (i) reverse reaction, (ii) barriers to further reaction of the initial adduct plus (iii) further evaluation of the O₂(¹Δ) addition barrier. The pathways from triplet adduct with conversion to singlet and from vinylidene are both recommended for initiation of acetylene oxidation. © 2000 John Wiley & Sons, Inc. Int J Chem Kinet 32: 623–641, 2000     

MP2, DFT and ab initio calculations on thioxanthone

Density functional theory (DFT), HF and MP2 calculations have been carried out to investigate thioxanthone molecule using the standard 6-31+G(d,p) basis set. The results of MP2 calculations show a butterfly structure for thioxanthone. The calculated results show that the predicted geometry can well reproduce the structural parameters. The predicted vibrational frequencies were assigned and compared with experimental IR spectra. A good harmony between theory and experiment is found. The theoretical electronic absorption spectra have been calculated using CIS method. ¹³C and ¹H NMR of the title compound have been calculated by means of B3LYP density functional method with 6-31+G(d,p) basis set. The comparison of the experimental and the theoretical results indicate that density functional B3LYP method is able to provide satisfactory results for predicting NMR properties.     

Molecular structure, vibrational spectra and HOMO, LUMO analysis of yohimbine hydrochloride by density functional theory and ab initio Hartree-Fock calculations

Yohimbine hydrochloride (YHCl) is an aphrodisiac and promoted for erectile dysfunction, weight loss and depression. The optimized geometry, total energy, potential energy surface and vibrational wavenumbers of yohimbine hydrochloride have been determined using ab initio, Hartree–Fock (HF) and density functional theory (DFT/B3LYP) method with 6-311++G(d,p) basis set. A complete vibrational assignment is provided for the observed Raman and IR spectra of YHCl. The UV absorption spectrum was examined in ethanol solvent and compared with the calculated one in gas phase as well as in solvent environment (polarizable continuum model, PCM) using TD-DFT/6-31G basis set. These methods are proposed as a tool to be applied in the structural characterization of YHCl. The calculated highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) with frontier orbital gap are presented.     

Theoretical ab initio study of NO and CO depollution reaction catalyzed by copper

The reaction between NO and CO leading to N₂ and CO₂ is the most studied depollution process of the former molecules. An ab initio study of a multistage mechanism of this reaction catalyzed by copper was performed at SCF level. Many intermediates intervene in the proposed mechanism, such as CuCO, CuNO, CuO, and NCO. Geometrical parameters, atomic charge, dipole moment, vibrational normal mode wave number, and dissociation energy of intervening molecules were calculated. Thermochemistry parameters (ΔH, ΔG, ΔS) were also obtained. Transition state has also been determined and has allowed us to discuss the reaction mechanism. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

Differences between ab initio and density functional electron densities

We analyzed the energy contributions and the spatial distribution differences of several electron densities of atoms and small molecules. The results show the insensitivity of local spin density correlation functionals in respect to differences in the electron densities. On the other hand, significant changes in one-electron and two-electron energy contributions are observed, although both compensate each other. The projection of the differences between these electron densities, referred to as the Hartree-Fock density, shows a qualitative resemblance between multideterminantal and Kohn-Sham wavefunctions. Finally, a comparative analysis of the optimized conformational parameters obtained using several methods shows that the inclusion of the correlation energy in SCF or in post-SCF procedures gives similar results and that the exchange potential is more important than is the correlation potential to improve these conformational parameters. © 1997 John Wiley & Sons, Inc.     

Molecular structure and vibrational spectra of three substituted 4-thioflavones by density functional theory and ab initio Hartree-Fock calculations

The vibrational frequencies of three substituted 4-thioflavones in the ground state have been calculated using the Hartree-Fock and density functional method (B3LYP) with 6-31G* and 6-31+G** basis sets. The structural analysis shows that there exists H-bonding in the selected compounds and the hydrogen bond lengths increase with the augment of the conjugate parameters of the substituent group on the benzene ring. A complete vibrational assignment aided by the theoretical harmonic wavenumber analysis was proposed. The theoretical spectrograms for FT-IR spectra of the title compounds have been constructed. In addition, it is noted that the selected compounds show significant activity against Shigella flexniri. Several electronic properties and thermodynamic parameters were also calculated.     

FTIR, Raman spectra and ab initio calculations of 2-mercaptobenzothiazole

FTIR and Raman spectra of a rubber vulcanization accelerator, 2-mercaptobenzothiazole (MBT), were recorded in the solid phase. The harmonic vibrational wavenumbers, for both the toutomeric forms of MBT, as well as for its dimeric complex, have been calculated, using ab initio RHF and density functional B3LYP methods invoking different basis sets upto RHF/6-31G** and B3LYP/6-31G** and the results were compared with the experimental values. Conformational studies have been also carried out regarding its toutomeric monomer forms and its dimer form. With all the basis sets the thione form of MBT (II) is predicted to be more stable than thiol form (I) and dimeric conformation (III) is predicted to be more stable with monomeric conformations (I) and (II). Vibrational assignments have been made, and it has been found that the calculated normal mode frequencies of dimeric conformation (III) are required for the analysis of IR and Raman bands of the MBT. The predicted shift in NH- stretching vibration towards the lower wave number side with the B3LYP/6-31G** calculations for the most stable dimer form (III), is in better agreement with experimental results. The intermolecular sulfur-nitrogen distance in N-H...S hydrogen bond was found to be 3.35 angstroms from these calculations, is also in agreement to the experimental value.     

FTIR and FT Raman, molecular geometry, vibrational assignments, ab initio and density functional theory calculations for 1,5-methylnaphthalene

The FTIR and FT Raman vibrational spectra of 1,5-methylnaphthalene (1,5-MN) have been recorded using Brunker IFS 66 V Spectrometer in the range 3600-10 cm(-1) in the solid phase. A detailed vibrational spectral analysis has been carried out and assignments of the observed fundamental bands have been proposed on the basis of peak positions and relative intensities. The Optimized molecular geometry, harmonic frequencies, electronic polarizability, atomic charges, dipole moment, rotational constants and several thermodynamic parameters in the ground state were calculated using ab initio Hartree Fock (HF) and density functional B3LYP methods (DFT) with 6-311++ G(d) basis set. With the help of different scaling factors, the observed vibrational wavenumbers in FTIR and FT Raman spectra were analyzed and assigned to different normal modes of the molecule. Most of the modes have wavenumbers in the expected range. The results of the calculations were applied to simulated infrared and Raman spectra of the title compound which showed excellent agreement with the observed spectra.