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.     

H-bonded complexes between acetylacetone and two molecules of methanol: HF and DFT level study

Five stable H-bonded complexes (supersystems) between acetylacetone and two methanol molecules were investigated at the B3LYP and HF levels of theory using the 6-311G** and 6-11++G** basis sets. The most stable complex was found as the one with the highest relative bonding and interaction energies. All vibrational frequencies resulting from calculations with the 6-311++G** basis set were compared with the recorded IR spectrum of acetylacetone/methanol mixture in a molar ratio 1:2.     

Conformational stability and normal coordinate analyses for 1-halovinyl azides CH<Subscript>2</Subscript>=CX–NNN (X is F,Cl and Br)

The conformational behavior of 1-halovinyl azides CH2=CX-NNN (X=F, Cl and Br) were investigated by DFT-B3LYP and ab initio MP2 calculations with the 6-311++G** basis set. The molecules were predicted to exist predominantly in the trans (the vinyl CH2=CH- and the azide -NNN groups are trans to each other) conformation. The relative energy between cis and trans were calculated to decrease in order: bromide>chloride>fluoride. Full optimization was performed at the ground and transition states in the molecule at both MP2 and B3LYP levels. The barrier to internal rotation around the C-N single bond in the three molecules was calculated to be about 4-5 kcal mol(-1). The vibrational frequencies were computed at the DFT-B3LYP level and the calculated infrared and Raman spectra of the cis- trans mixture of the three molecules were plotted. Complete vibrational assignments were made on the basis of normal coordinate calculations for both stable conformers of the three molecules.     

Theoretical potential scans and vibrational spectra of vinyl selenonyl halides CH2=CH–SeO2X (X is F, Cl and Br)

The structure and conformational stability of vinyl selenonyl fluoride, chloride and bromide CH₂=CH–SeO₂X (X is F, Cl and Br) were investigated using density functional B3LYP/6-311+G** and ab initio MP2/6-311+G** calculations. From the calculations the molecules were predicted to exist only in the non-planar gauche conformation with the vinyl C=C group almost eclipsing one of the selenonyl Se=O bonds as a result of conjugation between the two moieties. Single-minimum potential scans were calculated at the DFT level for the molecules. The vibrational frequencies were computed using B3LYP/6-311+G**. Normal coordinate calculations were then carried out and potential energy distributions were calculated for the three molecules in the gauche conformation.Figure Potential function for the asymmetric torsion in vinyl selenonyl fluoride (dotted line), chloride (dashed line) and bromide (solid line) as determined at the DFT-B3LYP/6-311+G** level     

DFT studies on the intrinsic conformational properties of non-ionic pyrrolysine in gas phase

B3LYP/6-31G(d,p) level of theory is used to carry out a detailed gas phase conformational analysis of non-ionized (neutral) pyrrolysine molecule about its nine internal back-bone torsional angles. A total of 13 minima are detected from potential energy surface exploration corresponding to the nine internal back-bone torsional angles. These minima are then subjected to full geometry optimization and vibrational frequency calculations at B3LYP/6-31++G(d,p) level. Characteristic intramolecular hydrogen bonds present in each conformer, their relative energies, theoretically predicted vibrational spectra, rotational constants and dipole moments are systematically reported. Single point calculations are carried out at B3LYP/6-311++G(d,p) and MP2/6-31++G(d,p) levels. Six types of intramolecular H-bonds, viz. O…H–O, N…H-O, O…H–N, N…H–N, O…H–C and N…H–C, are found to exist in the pyrrolysine conformers; all of which contribute to the stability of the conformers. The vibrational frequencies are found to shift invariably toward the lower side of frequency scale corresponding to the presence of intramolecular H-bond interactions in the conformers.     

Normal coordinate analyses of 3,5-dichlorophenylcyanamide

The structure of 3,5-dichlorophenylcyanamide c-C₆H₃Cl₂–NHCN was investigated by DFT-B3LYP and ab initio MP2 calculations with the 6-311+G** basis set. The planar to perpendicular rotational barrier was calculated to be of about 5 kcal mol^–1 at both levels of calculation. The stability of the planar structure of the molecule was explained on the basis of conjugation effects between the cyanamide–NHCN moiety and the phenyl c-C₆H₅ ring in agreement with earlier NMR results. The CNC and the HNC bond angles were calculated to be about 120° especially by MP2 calculation, which is consistent with sp² (planar –NH–CN group) and not sp³ (pyramidal –NH–CN group) structure. The vibrational frequencies of the d₀, d₁ and d₃ species of 3,5-dichlorophenylcyanamide and the potential energy distributions among symmetry coordinates of the normal modes of the parent molecule were computed at the DFT-B3LYP level. The calculated infrared and Raman spectra of the molecule were plotted. Complete vibrational assignments were made on the basis of isotopic substitution and normal coordinate calculations.Figure Potential curves for the internal rotation in 3,5-dichlorophenylcyanamide as determined by DFT-B3LYP/6-311+G** (solid) and MP2/6-311+G** (dotted) calculations     

Molecular structure,vibrational spectra and HOMO,LUMO analysis of 4-piperidone by density functional theory and ab initio Hartree–Fock calculations

Vibrational frequencies and geometrical parameters of 4-piperidone (4-PID) in the ground state have been calculated by using the Hartree–Fock (HF) and density functional methods (B3LYP) with 6-311++G(d,p) and 6-311+G(3df,2p) basis sets. These methods are proposed as a tool to be applied in the structural characterisation of 4-PID (C₅H₉NO). The title molecule has C _s point group symmetry, thus providing useful support in the interpretation of experimental IR and Raman data. The DFT-B3LYP/6-311+G(3df,2p) calculations have been found more reliable than the ab initio HF/6-311++G(d,p) calculations for the vibrational study of 4-PID. The calculated highest occupied molecular orbital and lowest unoccupied molecular orbital energies show that charge transfer occurs within the molecule. The theoretical spectrograms for FT-IR and FT-Raman spectra of the title molecule have been constructed.     

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.     

Electronic structure simulations of 2,6-dimethyl-2,5-heptadien-4-one by FTIR,FT-Raman,NMR, UV–vis,NBO and density functional theory

Density functional theory (DFT) (B3LYP and B3PW91) calculations have been carried out for 2,6-dimethyl-2,5-heptadien-4-one (DMHD4O) using 6–311++ G** basis set. Complete vibrational assignment and analysis of the fundamental modes of the compound were carried out from the FTIR and FT-Raman spectral data. The theoretical electronic absorption has been calculated by using time-dependent DFT (TD-DFT) methods and compared with the experimental spectra. The theoretically computed Frontier energy gaps and TD-DFT calculations are in good agreement with the experimental UV–vis spectral absorption. The chemical hardness measured from the Frontier molecular orbital energies of DMHD4O is 0.0693 eV. Electronic stability of the compound arising from hyperconjugative interactions and charge delocalisation were also investigated based on the natural bond orbital (NBO) analysis. Effective stabilisation energy E ⁽²⁾ associated with the interactions of the π and the lone pair of electrons was determined by the NBO analysis. ¹³C and ¹H NMR chemical shifts of the compound have been calculated by means of Gauge-Invariant Atomic Orbital using B3LYP/6–311++ G** method. The partial ionic character of the carbonyl group due to resonance render a partially positive charge to the carbonyl carbon, and thus C4 chemical shift lie in the very downfield 191.6 ppm. Comparison between the experimental and the theoretical results indicates that B3LYP method is able to provide satisfactory results for predicting vibrational, electronic and NMR properties.     

Zwitterionic conformers of pyrrolysine and their interactions with metal ions—a theoretical study

A total of 16 pyrrolysine conformers in their zwitterionic forms are studied in gas and simulated aqueous phase using a polarizable continuum model (PCM). These conformers are selected on the basis of our study on the intrinsic conformational properties of non-ionic pyrrolysine molecule in gas phase [Das and Mandal (2013) J Mol Model 19:1695?1704]. In aqueous phase, the stable zwitterionic pyrrolysine conformers are characterized by full geometry optimization and vibrational frequency calculations using B3LYP/6-311++G(d,p) level of theory. Single point calculations are also carried out at MP2/6-311++G(d,p) level. Characteristic intramolecular hydrogen bonds present in each conformer, their relative energies, theoretically predicted vibrational spectra, rotational constants and dipole moments are systematically reported. The calculated relative energy range of the conformers at B3LYP/6-311++G(d,p) level is 5.19 kcal mol^?1 whereas the same obtained by single point calculations at MP2/6-311++G(d,p) level is 4.58 kcal mol^?1. A thorough analysis reveals that four types of intramolecular H-bonds are present in the conformers; all of which play key roles in determining the energetics and in imparting the observed conformations to the conformers. The vibrational frequencies are found to shift invariably toward the lower side of frequency scale corresponding to the presence of the H-bonds. This study also points out that conformers with diverse structural motifs may differ in their thermodynamical stability by a narrow range of relative energy. The effects of metal coordination on the relative stability order and structural features of the conformers are examined by complexing five zwitterionic conformers of pyrrolysine with Cu⁺² through their carboxylate groups. The interaction enthalpies and Gibbs energies, rotational constants, vibrational frequencies and dipole moments of the metal complexes calculated at B3LYP level are also reported. The zwitterionic conformers of pyrrolysine are not stable in gas phase; after geometry optimization they are converted to the non-ionic forms.     

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.     

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.     

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.

     

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.     

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.     

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.     

Low-energy conformers of pamidronate and their intramolecular hydrogen bonds: a DFT and QTAIM study

Extensive DFT and ab initio calculations were performed to characterize the conformational space of pamidronate, a typical pharmaceutical for bone diseases. Mono-, di- and tri-protic states of molecule, relevant for physiological pH range, were investigated for both canonical and zwitterionic tautomers. Semiempirical PM6 method were used for prescreening of the single bond rotamers followed by geometry optimizations at the B3LYP/6-31++G(d,p) and B3LYP/6-311++G(d,p) levels. For numerous identified low energy conformers the final electronic energies were determined at the MP2/6-311++G(2df,2p) level and corrected for thermal effects at B3LYP level. Solvation effects were also considered via the COSMO and C-PCM implicit models. Reasonable agreement was found between bond lengths and angle values in comparison with X-ray crystal structures. Relative equilibrium populations of different conformers were determined from molecular partition functions and the role of electronic, vibrational and rotational degrees of freedom on the stability of conformers were analyzed. For no level of theory is a zwitterionic structure stable in the gas-phase while solvation makes them available depending on the protonation state. Geometrically identified intramolecular hydrogen bonds were analyzed by QTAIM approach. All conformers exhibit strong inter-phosphonate hydrogen bonds and in most of them the alkyl-amine side chain is folded on the P-C-P backbone for further hydrogen bond formation.

Electronic structure and conformational properties of <Emphasis Type="Italic">1H</Emphasis>-indole-3-acetic acid

The conformational space of 1H-Indole-3-Acetic Acid (IAA) was scanned using molecular dynamics at semiempirical level, and complemented with functional density calculations at B3LYP/6-31G** level, 14 conformers of lowest energy were obtained. Electronic distributions were analyzed at a higher calculation level, thus improving the basis set (B3LYP/6-311++G**). A topological study based on Bader’s theory (AIM: atoms in molecules) and natural bond orbital (NBO) framework performed with the aim to analyze the stability and reactivity of the conformers allowed the understanding of electronic aspects relevant in the study of the antioxidant properties of IAA. Intramolecular hydrogen bonds were found and were characterized as blue-shifting hydrogen bonding interactions. Furthermore, molecular electrostatic potential maps (MEPs) were obtained and analyzed in the light of AIM and NBO results, thus showing subtle but essential features related not only to reactivity but also with intramolecular weak interactions, charge delocalization and structure stabilization.     

Molecular structure and effects of intermolecular hydrogen bonding on the vibrational spectrum of trifluorothymine, an antitumor and antiviral agent

In the present work, the experimental and the theoretical vibrational spectra of trifluorothymine were investigated. The FT-IR (400-4000?cm(-1)) and μ-Raman spectra (100-4000?cm(-1)) of trifluorothymine in the solid phase were recorded. The geometric parameters (bond lengths and bond angles) and vibrational frequencies of the title molecule in the ground state were calculated using ab initio Hartree-Fock (HF) method and density functional theory (B3LYP) method with the 6-31++G(d,p) and 6-311++G(d,p) basis sets for the first time. The optimized geometric parameters and the theoretical vibrational frequencies were found to be in good agreement with the corresponding experimental data and with results found in the literature. Vibrational frequencies were assigned based on the potential energy distribution using the VEDA 4 program. The dimeric form of trifluorothymine was also simulated to evaluate the effect of intermolecular hydrogen bonding on the vibrational frequencies. It was observed that the stretching modes shifted to lower frequencies, while the in-plane and out-of-plane bending modes shifted to higher frequencies due to the intermolecular N-H?O hydrogen bonds.