Theoretical potential functions and vibrational analysis for halocarbonyl azides CXO-NNN (X=F,Cl and Br)

The structural stability of halocarbonyl azides CXO-NNN (X=F, Cl and Br) was investigated by DFT and MP2 calculations using the 6-311++G** basis set. From the calculations, the molecules were found to have an s-cis<--> s-trans conformational equilibrium with cis being the lower -energy form. Full energy optimizations were carried out for the transition states and the minima at the B3LYP/6 -311++G** and MP2/6 -311++G** levels, from which the rotational barriers were calculated to be of the order 8-10 kcal x mol(-1). The vibrational frequencies were computed at the DFT -B3LYP level and the vibrational assignments for the normal modes of the stable conformers were made on the basis of normal coordinate calculations.     

A B3LYP and MP2 theoretical investigation into host-guest interaction between calix[4]arene and Li+ or Na+

The DFT-B3LYP and MP2 methods with 6-311G** and 6-311++G** basis sets have been applied to study the complexation energies of the host-guest complexes between the cone calix[4]arene and Li⁺ or Na⁺ on the B3LYP optimized geometries. A comparison of the complexation energies obtained from the MP2(full) with those from MP2(fc) method is also carried out. The result shows that it is essential to introduce the diffuse basis set into the geometry optimizations and complexation energy calculations of the alkali-metal cation-π interaction complexes of calix[4]arene, and the D _e values show a maximum of 21.13 kJ mol⁻¹ (14.45% of relative error) between the MP2(full)/6-311++G** and MP2(fc)/6-311++G** method. For Li⁺ cation, the complexation is mainly energetically stabilized by the lower rim/cation (namely O–Li⁺) interaction. However, binding energies and NBO analyses confirm that Na⁺ cation prefers to enter the calix[4]arene cavity and the cation-π interaction is predominant, which contradicts the previous low-level theoretical studies. Furthermore, the complexation with Li⁺ is preferred over that with Na⁺ by at least 12.70 kJ mol⁻¹ at MP2(full)/6-311++G**//B3LYP/6-311++G** level.      

Quantum mechanical and NMR spectroscopy studies on the conformations of the hydroxymethyl and methoxymethyl groups in aldohexosides

The potential energy surfaces of the hydroxymethyl and methoxymethyl groups in methyl hexopyranosides have been extensively studied, employing quantum mechanical calculations and high resolution NMR data. The structure and energy of the C-5-C-6 rotamers were calculated at the B3LYP level of the density functional theory (DFT). For all, geometry optimizations were carried out for 264 conformers of 16 methyl D-gluco- and methyl D-galactopyranoside derivatives 1-16 at the B3LYP/6-31G** level. For all calculated minima, single-point calculations were performed at the B3LYP/6-311++G** level. Solvent effects were considered using a self-consistent reaction field method. Values of the vicinal coupling constants 3J(H-5-H-6R), 3J(H-5-H-6S), 3J(C-4-H-6R), and 3J(C-4-H-6S) for methyl D-glucopyranosides, methyl D-galactopyranosides and their 6-O-methyl derivatives 9-16 were measured in two solvents, methanol and water. The calculated gg, gt, and tg rotamer populations of the hydroxymethyl and methoxymethyl groups in 9-16 agreed well with experimental data. The results clearly showed that the population of gg, gt, and tg rotamers is sensitive to solvent effects. It was concluded that the preference of rotamers in 1-16 is due to the hydrogen bonding and solvent effects.     

Determination of the absolute configurations of synthetic daunorubicin analogues using vibrational circular dichroism spectroscopy and density functional theory

The absolute configurations of three synthesized anthracycline analogues have been determined using vibrational circular dichroism (VCD) spectroscopy and the density functional theory (DFT) calculations. The experimental VCD spectra of the three compounds have been measured for the first time in the film state, prepared from their CDCl₃ solutions. Conformational searches for the monomers and some dimers of the three compounds have been performed at the DFT level using the B3LYP functional and the 6‐311G** and 6‐311++G** basis sets. The corresponding vibrational absorption and VCD spectra have been calculated. The good agreement between the experimental and the calculated spectra allows one to assign the absolute configurations of the three compounds with high confidence. In addition, the dominant conformers of the three compounds have also been identified. Chirality, 2010. © 2010 Wiley‐Liss, Inc.     

Potential scans and potential energy distributions of normal vibrational modes of trichloroacetyl isocyanate

The conformational stability and vibrational infrared and Raman spectra of trichloroacetyl isocyanate (CCl3CONCO) were investigated by ab initio MP2 and density functional B3LYP calculations using the 6-311++G** basis set. From the potential energy scans of the internal rotations in both the halomethyl and the isocyanate rotors, the molecule was predicted to exist predominantly in the cis-cis conformation. The steric hindrance between the halomethyl group and the nitrogen lone-pair was found to favor the staggered configuration for the chlorine atom, while conjugation effects favor the planar configuration for the C=O and the NCO groups. Vibrational wavenumbers were computed for the molecule at the DFT-B3LYP/6-311++G** level. Normal coordinate calculations were carried out to obtain the potential energy distributions (PED) among the symmetry coordinates of the normal modes for the molecule. The theoretical vibrational assignments were compared with experimental ones and ratios of observed to calculated wavenumbers of about 0.97-1.04 were obtained.     

Density functional studies on the electron affinities of DNA and RNA bases

Influence of basis sets on electron affinities (EAs) of DNA and RNA bases has been investigated using density functional method (B3LYP functional) with different basis sets (6-31G, TZVP and 6-311+ + G**). Effect of some PBE functionals namely, PBEOP, PBELYP and PBEVWN, on EA values of the nucleobases was studied using basis set which predicted the most reliable values with B3LYP functional. Observation of the trends in the values of EA and dipole moment of the molecules enable us to identify the features of a basis set that shows the presence of dipole-bound state of some of the nucleobases. The vertical electron affinities with B3LYP and PBEOP functionals are close to the experimental values. The adiabatic electron affinities of uracil and thymine were found to be positive for basis set with diffuse functions using B3LYP functional. Adenine does not have a stable covalently bound anion at all levels of basis sets and functionals. The sign of adiabatic electron affinity value of cytosine is inconsistent with that of experimental value but in agreement with previous theoretical results. For guanine the adiabatic electron affinity value with 6-311+ + G** basis set was found to be very high as comparison with other two basis sets confirming the formation of mixed covalent-dipole character.     

Catalytic mechanism of the inverting N-acetylglucosaminyltransferase I: DFT quantum mechanical model of the reaction pathway and determination of the transition state structure

The complex N-glycan structures on glycoproteins play important roles in cell adhesion and recognition events in metazoan organisms. A critical step in the biosynthetic pathway leading from high mannose to these complex structures includes the transfer of N-acetylglucosamine (GlcNAc) to a mannose residue by the inverting N-acetylglucosaminyltransferase I (GnT-I). The catalytic mechanism of this enzymatic reaction is explored herein using DFT quantum chemical methods. The computational model used to follow the reaction is based on the X-ray crystallographic structure of GnT-I and contains 127 atoms that represent fragments of residues critical for the substrate binding and catalysis. The mechanism of the catalytic reaction was monitored by means of a 2D potential energy map calculated as a function of predefined reaction coordinates at the B3LYP/6-31G** level. This potential energy surface revealed one transition state associated with a reaction pathway following a concerted mechanism. The reaction barrier was estimated, and the structure of the transition state was characterized at the B3LYP/6-311++G**// B3LYP/6-31G** level.     

Investigation of the intermolecular proton transfer in the supersystems adenine-methanol/ethanol/i-propanol: MP2 and DFT levels study

Twelve H-bonded supersystems constructed between the adenine tautomers and methanol, ethanol, and i-propanol were studied at the B3LYP and MP2 levels of theory using 6-311G(d,p) and 6-311++G(d,p) basis functions. The thermodynamic parameters of the complex formations were calculated in order to estimate the exact stability of the supersystems. It was proven that the calculated energy barriers of the alcohol-assisted proton transfers are about 60% lower than those of the intramolecular proton transfers in adenine found earlier (Gu and Leszczynski in J Phys Chem A 103:2744–2750, 1999). Figure H-bonded complex between i-propanol and adenine     

DFT studies on the structural and vibrational properties of polyenes

Detailed density functional theory (DFT) calculations on the structure and harmonic frequencies of model all-trans and all-cis polyenes were undertaken. For the first time, we report on the convergence of selected B3LYP/6-311++G** and BLYP/6-311++G** calculated structural parameters resulting from a systematic increase in polyene size (chains containing 2 to 14 C?=?C units). The limiting values of the structural parameters for very long chains were estimated using simple three-parameter empirical formulae. BLYP/6-311++G** calculated ν(C?=?C) and ν(C–C) frequencies for all-trans and all-cis polyenes containing up to 14 carbon–carbon double bonds were used to estimate these values for very long chains. Correction of raw, unscaled vibrational data was performed by comparing theoretical and experimental wavenumbers for polyenes chains containing 3 to 12 conjugated C?=?C units with both ends substituted by tert-butyl groups. The corrected ν(C?=?C) and ν(C–C) wavenumbers for all-trans molecules were used to estimate the presence of 9 – 12 C?=?C units in all-trans polyene pigment in red coral.

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Graphical abstract Detailed density functional theory (DFT) calculations on the structure and harmonic frequencies of model all-trans and all-cis polyenes were undertaken. For the first time, we report on the convergence of selected B3LYP/6-311++G** and BLYP/6-311++G** calculated structural parameters resulting from a systematic increase in polyene size (chains containing 2 to 14 C=C units). The limiting values of the structural parameters for very long chains were estimated using simple three-parameter empirical formulae.

     

B3LYP/6-311++G** study of structure and spin-spin coupling constant in methyl 2-O-sulfo-alpha-L-iduronate

Structures of three most stable conformers ((1)C4, (4)C1, (2)S0) of methyl 2-O-sulfo-alpha-L-iduronate monosodium salt have been analyzed by DFT using the B3LYP/6-311++G** method. The optimized geometries confirmed the influence of both 2-O-sulfate and carboxylate groups upon the pyranose ring geometry. The computed energies showed that the chair (1)C4 form is the most stable one. Time-averaged DFT-calculated proton-proton and proton-carbon spin-spin coupling constants agree with the experimental data and indicate that only two chair forms contribute to the conformational equilibrium of methyl 2-O-sulfo-alpha-L-iduronate monosodium salt. The influence of the charged groups upon the magnitudes of spin-spin coupling constants is also discussed.     

Structural characterization of the (MeSH)4 potential energy surface

A random walk on the PES for (MeSH)₄ clusters produced 50 structural isomers held together by hydrogen-bonding networks according to calculations performed at the B3LYP/6–311++G** and MP2/6–311++G** levels. The geometric motifs observed are somewhat similar to those encountered for the methanol tetramer, but the interactions responsible for cluster stabilization are quite different in origin. Cluster stabilization is not related to the number of hydrogen bonds. Two distinct, well-defined types of hydrogen bonds scattered over a wide range of distances are predicted.

Basis set validation for polyatomic cation-water interactions

A study of the effects of counterpoise (CP) corrections in polyatomic cation-water interactions is added to the systematic analysis performed in the past of the basis set superposition error (BSSE) in neutral and anionic adducts. The interaction with water of the ammonium cation and its methyl and -CHO derivatives is considered due to the need to model accurately this functional group, which is common in biological molecules. The basis sets employed are the STO-3G and MINI-1 minimal basis sets and the 3-21G, 4-31G and 6-31G** extended ones. In addition, the 6-311++G (2d,p) and 6-311++G (3d, 2p) basis sets have been used for the smallest system, at the SCF and MP2 levels, both without and with CP correction. These basis sets give an equilibrium distance slightly larger and an interaction energy less favourable than the 6-31G** basis set at the corresponding level, while the inclusion of correlation corrections produces a stronger H-bond at a shorter distance. The results confirm the previous hint of a lower incidence of BSSEs in medium size cationic systems, at a different extent for the various basis sets. While the STO-3G basis set is sharply affected by BSSEs in both the equilibrium distance and the interaction energy, the MINI-1 basis set shows a small BSSE, though its trend is not completely satisfactory because the charge transfer component has an anomalous behaviour with respect to our reference basis set. The 4-31G basis set is the only one able to hold comparison with the 6-31G**, even though the interaction energy produced is slightly overestimated. The 3-21G basis set, when corrected, almost parallels the 4-31G one in this set of compounds. The reliability of the CPED correction is checked and discussed.     

Molecular modeling of dipeptide and its analogous systems with water

Intermolecular hydrogen-bond interactions in the monohydrated complexes of formamide, N-methylacetamide and glycylglycine have been studied using ab initio and DFT methods. The geometries were optimized using second-order Møller–Plesset perturbation theory and the B3LYP DFT functional with the 6-311++G** basis set. It is observed that hydrogen-bond interactions at the carbonyl group of the peptide moiety are stronger than those at the amino group of the formamide and N-methylacetamide molecules. Because of the presence of cyclic hydrogen-bonding interactions in glycylglycine, the interaction at the amino group is higher than at the carbonyl. The ¹³C and ¹⁵N NMR shielding values were calculated for the non-hydrated and monohydrated complexes. Condensed Fukui functions have also been calculated for non-hydrated formamide, N-methylacetamide and glycylglycine molecules at the B3LYP/6-311++G** level of theory, and the results are discussed.Figure Structure of hydrated glycylglycine dipeptide     

Many-body energies during proton transfer in an aqueous system

The energetics of the mechanism of proton transfer from a hydronium ion to one of the water molecules in its first solvation shell are studied using density functional theory and the Møller–Plesset perturbation (MP2) method. The potential energy surface of the proton transfer mechanism is obtained at the B3LYP and MP2 levels with the 6-311++G** basis set. Many-body analysis is applied to the proton transfer mechanism to obtain the change in relaxation energy, two-body, three-body and four-body energies when proton transfer occurs from the hydronium ion to one of the water molecules in its first solvation shell. It is observed that the binding energy (BE) of the complex decreases during the proton transfer process at both levels of theory. During the proton transfer process, the % contribution of the total two-body energy to the binding energy of the complex increases from 62.9 to 68.09% (39.9 to 45.95%), and that of the total three-body increases from 25.9 to 27.09% (24.16 to 26.17%) at the B3LYP/6-311++G** (MP2/ 6-311++G**) level. There is almost no change in the water–water–water three-body interaction energy during the proton transfer process at both levels of theory. The contribution of the relaxation energy and the total four-body energy to the binding energy of the complex is greater at the MP2 level than at the B3LYP level. Significant differences are found between the relaxation energies, the hydronium–water interaction energies and the four-body interaction energies at the B3LYP and MP2 levels.     

Theoretical investigation on the structure and thermodynamic properties of the 2,4-dinitroimidazole complex with methanol

The structure and thermodynamic properties of the 2, 4-dinitroimidazole complex with methanol were investigated using the B3LYP and MP2(full) methods with the 6-31++G(2d,p) and 6-311++G(3df,2p) basis sets. Four types of hydrogen bonds [N–H?O, C–H?O, O–H?O (nitro oxygen) and O–H?π] were found. The hydrogen-bonded complex having the highest binding energy had a N–H?O hydrogen bond. Analyses of natural bond orbital (NBO) and atoms-in-molecules (AIM) revealed the nature of the intermolecular hydrogen-binding interaction. The changes in thermodynamic properties from monomers to complexes with temperatures ranging from 200.0 to 800.0 K were investigated using the statistical thermodynamic method. Hydrogen-bonded complexes of 2,4-dinitroimidazole with methanol are fostered by low temperatures.

Theoretical investigation of cyromazine tautomerism using density functional theory and Møller–Plesset perturbation theory methods

A computational chemistry analysis of six unique tautomers of cyromazine, a pesticide used for fly control, was performed with density functional theory (DFT) and canonical second-order Møller–Plesset perturbation theory (MP2) methods to gain insight into the contributions of molecular structure to detection properties. Full geometry optimisation using the 6-311++G** basis set provided energetic properties, natural charges, frontier orbitals and vibrational modes. Excitation energies were obtained using time-dependent DFT. Hydrogen location and bond order contribute significantly to the electronic properties. The common cyromazine tautomer possesses the lowest energy, highest band gap energy and highest excitation energy. B3LYP/6-31G** dynamics simulations indicate each tautomer possesses a stable structure with limited rotation about the single bonds. Tautomerisation involving intramolecular hydrogen transfer influences the natural charges of neighbouring atoms and the frontier orbital properties. The excitation energies are highly correlated with band gap energies of the frontier orbitals. The calculated infrared and Raman spectra are suitable for vibrational assignments associated with the chemical structure. The tautomeric forms of cyromazine possess similar spatial properties and significant variation in electronic properties.     

Ab initio and DFT study of the inner mechanism and dynamic stereochemistry of electrophilic addition reaction of bromine to bisbenzotetracyclo[6.2.2.23,6.02,7]tetradeca-4,9,11,13-tetraene

The inner mechanism and dynamic stereochemistry of electrophilic addition of bromine to bisbenzotetracyclo[6.2.2.2(3,6).0(2,7)]tetradeca-4,9,11,13-tetraene(BBTT) molecule have been investigated by the methods of quantum chemistry. The structure of the BBTT molecule has been studied by ab initio and DFT/B3LYP methods using the 6-31G(d) and 6-311G(d) basis sets. The double bonds of BBTT molecule are endo-pyramidalized. The structure and stability of the cationic intermediates and products of the addition reaction have been investigated by HF/6-311G(d), HF/6-311G(d,p), B3LYP/6-311G(d) and B3LYP/6-311++G(2d,p)//B3LYP/6-311G(d) methods. The bridged bromonium cation isomerized into the more stable nonclassical delocalized N- and U-type cations and the difference between the stability of these cations is small. For the determination of the direction of addition reaction and the stereochemistry of the products, the stability of nonclassical delocalized N- and U-type ions and the structure of their cationic centres play a vital role. Since the cationic centre of the N-type ion is in interaction with the benzene ring from the exo face, the nucleofilic attackof the bromide anion to this centre occurs from the endo face and the exo,endo-isomer of the N-type product is obtained. The attack of bromide anion, towards the cationic centre of U-type ion from the endo face is sterically hindered by the hydrogen atom therefore the attack occurs from the exo face, which interacts with the benzene ring and the more stable exo,exo-isomer of U-type product is formed. Although, the U-type cation was 2.232 kcal mol(-1) more stable than the N-type cation, the U-type product was 0.587 kcal mol(-1) less stable than the N-type product.     

Vibrational assignments and derived potential energy distributions for tri- and difluoromethyl ketene by density functional calculations

The structures of 3,3,3-trifluoromethyl ketene and 3,3-difluoromethyl ketene were studied by utilizing ab initio calculations with the 6-311++G** basis set at the (B3LYP) Density Functional level. Full optimization was performed for both molecules in their ground and transition states. Energy optimization of the systems under investigation shows that trifluoromethyl ketene exists only in the cis conformation (fluorine atom eclipses the ketene group). Difluoromethyl ketene was predicted to have two stable conformations: the cis (hydrogen atom eclipses the ketene group) and the gauche (fluorine atom eclipses the ketene group) form. The conformational stability of the molecules was found to be governed mainly by electrostatic and molecular orbital interactions. The vibrational frequencies were computed and complete assignments were provided on the basis of normal coordinate calculations and comparison with similar molecules. The potential energy distributions (PED) among symmetry coordinates were derived for the stable conformations of the two molecules.