The geometries, energies, and electronic properties of the two possible configurations of bis-[dibenzo[a.i]fluorenylidene] were investigated theoretically by density functional theory DFT B3LYP at the UB3LYP/6-311?+?G(2d,p) // UB3LYP/6-31?+?G(d,p) level of theory. According to the performed calculations, it was found that the singlet is 3.4?kcal?mol-1 lower in energy compared to triplet state at room temperature. This gap is compared with those of other alkenes like ethylene, (61.9?kcal?mol-1) tetra-tert-butyethylene, (6.4?kcal?mol-1) and bis-fluorenylidene (19.5?kcal?mol-1). These results confirm the experimental findings of the paramagnetic properties determined by Franzen and Joschek. The low singlet-triplet gap in the case of bis-[dibenzo[a.i]fluorenylidene] is the result of a steric destabilization of the singlet due to strain and stabilization of the triplet electronic state by delocalization of each free electron within each aromatic moiety. This correlates with the special electronic structure of the triplet state of this compound, where facial interaction of two hydrogen atoms lying close to the lobes of each p-orbital occupied with a single electron at the distorted double bond in the triplet electronic state.
Figure
a) The singlet form of bis-dibenzo[a.i]fluorenylidene. b) The triplet form of bis-dibenzo[a.i]fluorenylidene. The central dihedral angle around the C=C double bond changes from 53.2° in the singlet electronic structure to 90.0° in the triplet electronic structure. Of great interest is the very low singlet-triplet gap of this electronic system which equals to 3.4 kcal/mol according to calculation by DFT UB3LYP/6-311+G(2d,p) // UB3LYP/6-31+G(d,p) level of theory. 相似文献
Full geometric optimization of endo,endo-tetracyclo[4.2.1.13,6.02,7]dodeca-4,9-diene (TTDD) has been carried out by ab initio and DFT/B3LYP methods and the structure of the molecule investigated. The double bonds of TTDD molecule are endo pyramidalized. The structure of π-orbitals and their mutual interactions for TTDD molecule were investigated. The cationic
intermediates and products obtained as a result of the addition reaction have been studied using the HF/6-311G(d), HF/6-311G(d,p)
and B3LYP/6-311G(d) methods. The bridged bromonium cation isomerized into the more stable N- and U-type cations and the difference
between the stability of these cations is small. The N- and U-type reaction products are obtained as a result of the reaction,
which takes place via the cations in question. The stability of exo, exo and exo, endo isomers of N-type product are nearly the same and the formation of both isomers is feasible. The U-type product basically
formed from the exo, exo-isomer. Although the U-type cation was 0.68 kcal mol−1 more stable than the N-type cation, the U-type product was 4.79 kcal mol−1 less stable than the N-type product.
Figure The energy diagram of TTDD–Br2 system (kcal mol−1)(MP2/6-311G*//HF/6-311G*) 相似文献
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.
Figure
Two distinct types of hydrogen bonds are predicted for the Methanethiol tetramers 相似文献
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.
Figure
Molecular structures and bond critical points of 2,4-dinitroimidazole complexes at MP2(full)/6-311++G(3df,2p) level. Structure and thermodynamic property of the 2,4-dinitroimidazole complex with methanol are 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) are found. For the hydrogen-bonded complex having the highest binding energy, there is a N–H…O hydrogen bond. The complex formed by the N–H…O hydrogen bond can be produced spontaneously at room temperature and the equilibrium constant is predicted to be 6.354 and 1.219 at 1 atm with the temperature of 268.0 and 298.15 K, respectively. 相似文献
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. 相似文献
The changes of bond dissociation energy (BDE) in the C–NO2 bond and nitro group charge upon the formation of the molecule-cation interaction between Na+ and the nitro group of 14 kinds of nitrotriazoles or methyl derivatives were investigated using the B3LYP and MP2(full) methods with the 6-311++G**, 6-311++G(2df,2p) and aug-cc-pVTZ basis sets. The strength of the C–NO2 bond was enhanced in comparison with that in the isolated nitrotriazole molecule upon the formation of molecule-cation interaction. The increment of the C–NO2 bond dissociation energy (ΔBDE) correlated well with the molecule-cation interaction energy. Electron density shifts analysis showed that the electron density shifted toward the C-NO2 bond upon complex formation, leading to the strengthened C-NO2 bond and the possibly reduced explosive sensitivity.
Figure
C1-N2 bond turns strong upon molecule-cation interaction formation, leading to a possibly reduced explosive sensitivity. 相似文献
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.
Figure
The most stable conformers of pamidronate at different protonation states in gas-phase and solution. 相似文献
The electronic and geometric structures of tetracyclo[5.3.0.02,6.03,10]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*) 相似文献
Increase of the atmospheric concentration of halogenated organic compounds is partially responsible for a change of the global climate. In this work we have investigated the interaction between halogenated ether and water, which is one of the most important constituent of the atmosphere. The structures of the complexes formed by the two most stable conformers of enflurane (a volatile anaesthetic) with one and two water molecules were calculated by means of the counterpoise CP-corrected gradient optimization at the MP2/6–311++G(d,p) level. In these complexes the CH…Ow hydrogen bonds are formed, with the H…Ow distances varying between 2.23 and 2.32 Å. A small contraction of the CH bonds and the blue shifts of the ν(CH) stretching vibrations are predicted. There is also a weak interaction between one of the F atoms and the H atom of water, with the Hw…F distances between 2.41 and 2.87 Å. The CCSD(T)/CBS calculated stabilization energies in these complexes are between ?5.89 and ?4.66 kcal?mol?1, while the enthalpies of formation are between ?4.35 and ?3.22 kcal?mol?1. The Cl halogen bonding between enflurane and water has been found in two complexes. The intermolecular (Cl···O) distance is smaller than the sum of the corresponding van der Waals radii. The CCSD(T)/CBS stabilization energies for these complexes are about ?2 kcal?mol?1.
Figure
Complex between enflurane and water molecules 相似文献
The structural and thermodynamic properties of an anthraquinone derivative were studied by means of quantum-chemical calculations. Conformational analysis using ab initio and density functional theory methods revealed 14 low-energy conformers. In order to discuss similarities and differences in entropy of the conformers, the rotational and vibrational contributions to entropy were correlated with changes in conformer structure. The component of the moment of inertia perpendicular to the molecular plane gives significant input to ΔSrot, whereas the largest contributions to the ΔSvib have vibrations associated with the τS1C20 coordinate.
Figure
Optimized B3LYP/6-311++G(d,p) geometry of 1-[(2-mercaptoethyl)amino]-9,10-anthraquinone (MEAA) and vibrational contributions to entropy (ΔSvib, in J mol?1?K?1) relative to the most stable conformer 相似文献
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.
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.
The electronic features of anti-tumor agent, temozolomide, and its degradation products (MTIC and metabolite AIC) have been traced by means of UV absorption spectroscopy in vacuo and aqueous media. For comparison, electronic spectra of related structures and drugs (e.g., dacarbazine) were also investigated. These investigations were carried out using time-dependent density functional theory (TD-DFT) method while the conductor like screening model (COSMO) were applied for the inclusion of solvent effects in electronic spectra. From functional benchmarking, two methods; B3LYP and O3LYP were selected among several other methods with 6-311+G(2d,p) basis set aiming to get the best results in accord with the experimental values. An assessment of the obtained spectra has shown that O3LYP functional gives a mean absolute error (MAE) from experimental absorption peaks of 4.3 nm compared to the 7.2 nm MAE value at B3LYP level in aqueous media. Furthermore, since the structural and tautomeric conformers affect the electronic spectra, conformational preferences have been analyzed in temozolomide, dacarbazine, and their related structures. Temozolomide structure possesses two rotamers that differ in the orientation of carboxamide moiety with a small energy difference (energy difference of 1.39 kcal mol?1 in vacuo and 0.35 kcal mol?1 in aqueous media at B3LYP/6-311++G(2df,3pd). The more stable and meta-stable TMZ rotamer have shown their absorption maxima at 329–334 nm, respectively, at O3LYP level in aqueous media. Applying statistical calculation according to Boltzmann population formula at 25 °C and computed weighed mean estimates the λmax of temozolomide at 331 nm, which is in notable agreement with the experimental value (330 nm). Moreover, molecular orbital composition analysis has been conducted in order to interpret these findings.
In this work we investigated the outside binding mode between a cationic porphyrin and a nucleotide pair of DNA, adenine-thymine and guanine-cytosine, in a supramolecular assembly. We used two structural models (semi-extended, extended) that differ in the size of porphyrin, two kinds of theoretical methods: a three layer ONIOM (B3LYP/6-31G(d)/PM3/UFF), and DFT B3LYP/6-31G(d,p), and three cationic porphyrins. ONIOM method was first tested on the semi-extended model that was calculated in four environments: gas phase, solution phase using an explicit solvent model (H2O), in the presence of a sodium cation (Na+) and in both (H2O + Na+). From interaction energy results, we found that the affinity of the cationic substituent by the adenine nucleotide is favored upon the thymine nucleotide. The extended model that considers the whole porphyrin was applied in the gas phase to the four nucleotides. All the cationic porphyrins showed affinity by the nucleotides in the order adenine > guanine > thymine > cytosine. The interaction energy values for outside binding showed a strong porphyrin-nucleotide interaction (≈-90 kcal?mol-1), that slightly varies between the nucleotides suggesting that this kind of cationic porphyrin has a little selectivity for some of them. We also found that the effect of the nature of the cationic substituent (chain length) in the porphyrin on the outside binding is small (≈2–13 kcal?mol-1). Coherence between the results showed that ONIOM is a useful tool to get a reasonable molecular geometry to be used as a starting point in calculations of density functional theory.
Figure
A three-layer ONIOM model for the outside binding of cationic porphyrins and nucleotide pair DNA 相似文献
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 De 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.
相似文献
The electronic structure of the two most stable isomers of squaric acid and their complexes with BeH2 were investigated at the B3LYP/6-311?+?G(3df,2p)// B3LYP/6-31?+?G(d,p) level of theory. Squaric acid forms rather strong beryllium bonds with BeH2, with binding energies of the order of 60 kJ?mol?1. The preferential sites for BeH2 attachment are the carbonyl oxygen atoms, but the global minima of the potential energy surfaces of both EZ and ZZ isomers are extra-stabilized through the formation of a BeH···HO dihydrogen bond. More importantly, analysis of the electron density of these complexes shows the existence of significant cooperative effects between the beryllium bond and the dihydrogen bond, with both becoming significantly reinforced. The charge transfer involved in the formation of the beryllium bond induces a significant electron density redistribution within the squaric acid subunit, affecting not only the carbonyl group interacting with the BeH2 moiety but significantly increasing the electron delocalization within the four membered ring. Accordingly the intrinsic properties of squaric acid become perturbed, as reflected in its ability to self-associate.
Figure
The ability of squaric acid to self-associate is significantly enhanced when this molecule forms beryllium bonds with BeH2相似文献
The interactions of L-aminoglucosidic stereoisomers such as rhodostreptomycins A (Rho A) and B (Rho B) with cations (Mg2+, Ca2+, and H+) were studied by a quantum mechanical method that utilized DFT with B3LYP/6-311G**. Docking studies were also carried out in order to explore the surface recognition properties of L-aminoglucoside with respect to Mg2+ and Ca2+ ions under solvated and nonsolvated conditions. Although both of the stereoisomers possess similar physicochemical/antibiotic properties against Helicobacter pylori, the thermochemical values for these complexes showed that its high affinity for Mg2+ cations caused the hydration of Rho B. According to the results of the calculations, for Rho A–Ca2+(H2O)6, ΔH = ?72.21 kcal?mol?1; for Rho B–Ca2+(H2O)6, ΔH = ?72.53 kcal?mol?1; for Rho A–Mg2+(H2O)6, ΔH = ?72.99 kcal?mol?1 and for Rho B–Mg2+(H2O)6, ΔH = ?95.00 kcal?mol?1, confirming that Rho B binds most strongly with hydrated Mg2+, considering the energy associated with this binding process. This result suggests that Rho B forms a more stable complex than its isomer does with magnesium ion. Docking results show that both of these rhodostreptomycin molecules bind to solvated Ca2+ or Mg2+ through hydrogen bonding. Finally, Rho B is more stable than Rho A when protonation occurs.
Figure
Rho B–H showed higher stability since it is considered a proton pump inhibitor, and is therefore a stronger inhibitor of Helicobacter pylori 相似文献
The changes of bond dissociation energy (BDE) in the C–NO2 bond and nitro group charge upon the formation of the intermolecular hydrogen-bonding interaction between HF and the nitro group of 14 kinds of nitrotriazoles or methyl derivatives were investigated using the B3LYP and MP2(full) methods with the 6-311++G**, 6-311++G(2df,2p) and aug-cc-pVTZ basis sets. The strength of the C–NO2 bond was enhanced and the charge of nitro group turned more negative in complex in comparison with those in isolated nitrotriazole molecule. The increment of the C–NO2 bond dissociation energies correlated well with the intermolecular H-bonding interaction energies. Electron density shifts analyses showed that the electron density shifted toward the C–NO2 bond upon complex formation, leading to the strengthened C–NO2 bond and the possibly reduced explosive sensitivity.
Figure
C1-N2 bond turns strong upon H-bond formation, leading to a possibly reduced explosive sensitivity 相似文献
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. 相似文献
A theoretical analysis of the nature of the interactions in dibenzo[24]crown-8 (DB24C8)-n-dibutylammonium (DBM)—pseudorotaxane complex at the MP2 and DFT levels shows that the main contribution to the binding energy is the electrostatic interaction with moderate (20–25%) correlation stabilization. The total binding energy in the DB24C8-DBM complex represents a sum of the binding energies of two NH–O and one CH–O hydrogen bonds and the latter constitutes about 25% of the total interaction energy, giving the total binding energy of −41.2 kcal mol−1 at the BHandHLYP/6-311++G** level. Deprotonation of the DB24C8-DBM complex reduces the binding energy by some 50 kcal mol−1, giving metastable complexes DB24C8-DBA-1 or DB24C8-DBA-2, which will dissociate to give free crown ether and n-dibutylamine because of the strong exchange repulsion that prevails in neutral complexes.
Figure
Formation of DB24C8-DBM pseudorotoxane complex 相似文献