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     

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.      

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     

Ab initio study of phenyl benzoate: structure,conformational analysis,dipole moment,IR and Raman vibrational spectra

The molecular structure (bond distances and angles), conformational properties, dipole moment and vibrational spectroscopic data (vibrational frequencies, IR and Raman intensities) of phenyl benzoate were calculated using Hartree–Fock (HF), density functional (DFT), and second order Møller–Plesset perturbation theory (MP2) with basis sets ranging from 6-31G* to 6-311++G**. The theoretical results are discussed mainly in terms of comparisons with available experimental data. For geometric data, good agreement between theory and experiment is obtained for the MP2, B3LYP and B3PW91 levels with basis sets including diffuse functions. The B3LYP/6-31+G* theory level estimates the shape of the experimental functions for phenyl torsion around the Ph–O and Ph–C bonds well, but reproduces the height of the rotational barriers poorly. The B3LYP/6-31+G* harmonic force constants were scaled by applying the scaled quantum mechanical force field (SQM) technique. The calculated vibrational spectra were interpreted and band assignments were reported. They are in excellent agreement with experimental IR and Raman spectra.Figure Calculated and experimental (GED) potential energy functions for torsional motion of phenyl benzoate relative to the minimum value. a The potential function for torsion about the O₃–C₄ bond. b The potential function for torsion about the C₂–C₁₀ bond.     

An ab initio study of di- and trifluorobenzene–benzene complexes as relevant to carbonic anhydrase II–drug interactions

Ab initio calculations at the MP2/6-31G* level have shown that variously substituted di- and trifluorobenzenes form non-covalent complexes with benzene that adopt either aromatic–aromatic or H---F binding, the choice being determined by the pattern of fluorination. The binding energies of these structures are from 3.4 to 4.5 kcal mol^–1. This range is large enough to account for observed variations in the binding affinity of a library of fluoroaromatic inhibitors of carbonic anhydrase. This enzyme has an aromatic amino acid at a central position in the active site. The diverse modes of binding of the dimers also suggest that aggregates of fluorobenzenes might adopt specified 3-dimensional shapes in the solid state. Figure Observed structure for 1,2-difluorobenzene     

Direct ab initio dynamics studies of the hydrogen abstraction reactions of hydrogen atom with n-propyl radical and isopropyl radical

The kinetics of the hydrogen abstraction reactions of hydrogen atom with n-propyl radical and isopropyl radical were studied using the direct ab initio dynamics approach. BHandHLYP/cc-pVDZ method was employed to optimize the geometries of stationary points as well as the points on the minimum energy path (MEP). The energies of all the points for the two reactions were further refined at the QCISD(T)/cc-pVTZ level of theory. No barrier was found at the QCISD(T)/cc-pVTZ//BHandHLYP/cc-pVDZ level of theory for both reactions. The forward and reverse rate constants were evaluated with both canonical variational transition state theory (CVT) and microcanonical variational transition state theory ( VT) in the temperature range of 300–2,500 K. The fitted three-parameter Arrhenius expression of the calculated CVT rate constants at the QCISD(T)/cc-pVTZ//BHandHLYP/cc-pVDZ level of theory are k^CVT (n – C₃H₇)=1.68×10^–14 T^0.84 e^(319.5/T) cm³ molecule^–1 s^–1 and k^CVT (iso-C₃H₇)=4.99×10^–14 T^0.90 e^(159.5/T) cm³ molecule^–1 s^–1 for reactions of n-C₃H₇ + H and iso-C₃H₇ + H, respectively, which are in good agreement with available literature data. The variational effects were analysed.Figure Comparison of the calculated forward rate constants at the QCISD(T)/cc-pVTZ//BHandHLYP/cc-pVDZ level of theory and the available experimental and theoretical data of the reaction vs 1,000/T for the two reactions.     

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.     

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.     

Determination of fuzzy logic membership functions using genetic algorithms: application to structure–odor modeling

Fuzzy logic has been used as a tool in structure–camphoraceous odor relationships. The data base studied included 99 molecules. The rules used to discriminate between camphor and non camphor molecules lead to 77% correct discrimination. Such rules account for the shape and the size of the molecule. Their adjustment by means of genetic algorithms led to 84% correct discrimination between camphor and non-camphor molecules.Figure Membership function for the chosen variables     

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.     

Reinvestigation of molecular structure and barrier to internal rotation of pyridinium N-phenolate betaine dye

In the present paper, the results of a systematic theoretical study of the molecular structure of 4-(1-pyridinium-1-yl)phenolate betaine are reported. The ground-state molecular structure and the barrier to internal rotation of the betaine dye molecule were calculated ab inito (with Hartree–Fock theory and the second-order of Möller–Plesset method) and with density functional theory (DFT). In order to estimate the complete basis set limit, the calculations of barriers to internal rotations were performed using correlation–consistent basis sets with a maximal cardinal number of four. It was determined that electron correlation is crucial in order to obtain reliable geometries and rotational barriers of the molecule investigated. For the sake of comparison, the results of calculations using the AM1 Hamiltonian are also presented.Figure Investigated betaine dye.     

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.     

Structures and stability of N<Subscript>13</Subscript><Superscript>+</Superscript> and N<Subscript>13</Subscript><Superscript>−</Superscript> clusters

The structures and stabilities of eleven N₁₃ ⁺ and N₁₃ ^– isomers have been investigated with second-order Møller–Plesset (MP2) and density functional theory (DFT) methods. Five N₁₃ ⁺ isomers and six N₁₃ ^– isomers are all reasonable local minima on their potential energy hypersurfaces. The most stable N₁₃ ⁺ cation is structure C-2 with C_2v symmetry, which contains a pentazole ring and two N₄ open chains. It is different from those of the N₇ ⁺ and N₉ ⁺ clusters, but similar to the N₁₁ ⁺ cluster. Meanwhile, the most stable N₁₃ ^– structure A-2 is composed of a pentazole ring and a six-membered ring connected by two nitrogen atoms. It is not only different from those of the N₇ ^– and N₉ ^– clusters, but also from the N₁₁ ^– cluster. The decomposition pathways of structures C-2 and A-2 were investigated at the B3LYP/(aug)-cc-pVDZ level. From the barrier heights of the structures C-2 and A-2 decomposition processes, it is suggested that C-2 is difficult to observe experimentally and A-2 may be observed as a short-lived species. Figure Optimized geometrical parameters of N₁₃ ⁺ isomer C-2      

A Comparative Semiempirical, Ab initio and DFT Study of Decarbonylation of Cyclic Ketones Part 1: Thermal Fragmentation of Cyclopropanone

Calculations using different quantum mechanical methods including semiempirical (MNDO,AM1 and PM3), ab initio (RHF and MP2 calculations using the 6-311G and 6-311++G^** basis sets), and density functional theory (LSDA, BP, MIXBP and B3LYP, i.e., B3LYP/6-311+G**//B3LYP/6-31G*) have been performed on the thermal fragmentation of cyclopropanone to ethylene and carbon monoxide. All RHF calculations predict a concerted single step mechanism for this conversion. The estimated activation energies vary from 34.4 to 54.6 kcal·mol^-1, mainly localized around 37±2 kcal·mol^-1, depending on the method. Whereas the calculated RHF reaction energies also varied from 14.5 to -33.3 kcal·mol^-1, the B3LYP/6-311+G**//B3LYP/6-31G* method predicts the experimental value (-17.7 kcal·mol^-1) within experimental uncertainties. Remarkably, semiempirical AM1 and PM3 methods and simple DFT calculations, LSDA, predict comparable results to the more advanced methods. UHF ab initio calculations predict the same single step mechanism, whereas a multistep biradical mechanism with an unrealistically low activation energy is favored by the semiempirical methods. Structures of the activated complex of the single step mechanism, estimated by different methods, are very similar and consistent with a nonlinear cheletropic [_2s + _2a] reaction, as predicted by the orbital symmetry rules and earlier EHT calculations.Electronic Supplementary Material available.     

Looking for high energy density compounds among polynitraminepurines

A series of purine derivatives with nitramine groups are calculated by using density functional theory (DFT). The molecular theory density, heats of formation, bond dissociation energies and detonation performance are investigated at DFT-B3LYP/6-311G** level. The isodesmic reaction method is employed to calculate the HOFs of the energies obtained from electronic structure calculations. Results show that the position of nitramine groups can influence the values of HOFs. The bond dissociation energies and the impact sensitivity are analyzed to investigate the thermal stability of the purine derivatives. The calculated bond dissociation energies of ring-NHNO₂ and NH-NO₂ bond show that the NH-NO₂ bond should be the trigger bond in pyrolysis processes. The H₅₀ of most compounds are larger than that of CL-20 and RDX.     

Ab initio and DFT study on the electrophilic addition reaction of bromine to tetracyclo[5.3.0.02,6.03,10]deca–4,8–diene

The electronic and geometric structures of tetracyclo[5.3.0.0^2,6.0^3,10]deca-4,8-diene (hypostrophene) have been investigated by ab initio and DFT/B3LYP methods using the 6-31G* and 6-311G* basis sets. The double bonds of hypostrophene are endo-pyramidalized. The cationic intermediates and products formed in the addition reaction have been investigated using the HF/6-311G*, HF/6-311G**, and B3LYP/6-311G* methods. The bridged bromonium cation was more stable than the U-type cation. Considering that the bridged cation does not isomerize to the less stable U-type cation, it is not possible for the U-type product to be obtained in the reaction. The bridged bromonium cation transformed into the more stable N-type cation and the N-type product was obtained via this cation. The thermodynamic stability of the exo, exo and exo, endo isomers of the N-type dibromide molecule were almost identical. The N-type product was 16.6 kcal mol⁻¹ more stable than the U-type product. Figure General energy diagram of the hypostrophene–bromine (HS–Br₂) system (kcal mol⁻¹) (MP2/6-311G*//HF/6-311G*)     

Theoretical investigations into the intermolecular hydrogen-bonding interactions of <Emphasis Type="Italic">N</Emphasis>-(hydroxymethyl)acetamide dimers

The structures of the N-(hydroxymethyl)acetamide (model molecule of ceramide) dimers have been fully optimized at B3LYP/6–311++G** level. The intermolecular hydrogen bonding interaction energies have been calculated using the B3LYP/6–311++G**, B3LYP/6–311++G(2df,2p), MP2(full)/6–311++G** and MP2(full)/6–311++G(2df,2p) methods, respectively. The results show that the O–H···O, N–H···O, O–H···N, and C–H···O hydrogen bonding interactions could exist in N-(hydroxymethyl)acetamide dimers, and the O–H···O, N–H···O, and O–H···N hydrogen bonding interactions could be stronger than C–H···O. The three-dimensional network structure formed by ceramide molecules through intermolecular hydrogen bonding interactions may be the main reason why the stratum corneum of skin could prevent foreign substances from entering our body, as is in accordance with the experimental results. The stability of hydrogen-bonding interactions follow the order of (a)?>?(b)?≈?(c)?>?(d)?>?(e)?≈?(f)?>?(g)?>?(h). The analyses of the energy decomposition, frequency, atoms in molecules (AIM), natural bond orbital (NBO), and electron density shift are used to further reveal the nature of the complex formation. In the range of 263.0–328.0 K, the complex is formed via an exothermic reaction, and the solvent with lower temperature and dielectric constant is favorable to this process.

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Graphical abstract The structures and the O–H···O=C, N–H···O=C and C–H···O=C H-bonding interactions in the N-(hydroxymethyl)acetamide (model molecule of ceramide) dimers were investigated using the B3LYP and MP2(full) methods.

     

A quantitative structure–antifungal activity relationship study of oxygenated aromatic essential oil compounds using data structuring and PLS regression analysis

Twenty two oxygenated aromatic essential oil compounds were chosen for the study of the antifungal activity against two wood-decaying fungi, the white-rot Trametes versicolor, which mainly metabolizes lignin, and the brown-rot Coniophoha puteana, which digests cellulose in plant cell walls. Minimal inhibitory concentrations (MICs) were determined by the agar dilution method, using dimethyl sulfoxide (DMSO) as the solvent for the selected compounds and potato-dextrose agar (PDA) as the growth medium for both fungi. The MICs were then used to generate a tree structure, which represents the structuring of the essential oil compounds by the nature and position of the substituents in their aromatic rings, and as dependent variables (log(1/MIC)) in the QSAR analysis. Data structuring proved that a relationship between the molecular structures of the essential oil compounds and their antifungal activity exists, and the hypotheses derived therefrom were complemented by performing a QSAR analysis using the partial least squares (PLS) method. Statistically significant PLS models were obtained with the 1-octanol–water partition coefficient (C log P), the energy of the highest occupied molecular orbital (E _HOMO), and the number of hydrogen-bond donor atoms in the molecules of the compounds studied (Donor) for T. versicolor and with C log P and the fractional negative surface area (FNSA1) for C. puteana.Figure Tree structure representing the structuring of the oxygenated aromatic essential-oil compounds by the position and nature of their substituents in the aromatic ring     

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.