Correlation between computed gas-phase and experimentally determined solution-phase infrared spectra: models of the iron-iron hydrogenase enzyme active site

Gas-phase density functional theory calculations (B3LYP, double zeta plus polarization basis sets) are used to predict the solution-phase infrared spectra for a series of CO- and CN-containing iron complexes. It is shown that simple linear scaling of the computed C--O and C--N stretching frequencies yields accurate predictions of the the experimentally determined nu(CO) and nu(CN) values for a variety of complexes of different charges and in solvents of varying polarity. As examples of the technique, the resulting correlation is used to assign structures to spectroscopically observed but structurally ambiguous species in two different systems. For the (mu-SCH2CH2CH2S)[Fe(CO)3]2 complex in tetrahydrofuran solution, our calculations show that the initial electrochemical reduction process leads to a simple one-electron reduced product with a structure very similar to the (mu-SCH2CH2CH2S)[Fe(CO)3]2 parent complex. For the iron-iron hydrogenase enzyme active site, our computations show that the absence or presence of a water molecule near the distal iron center (the iron center further from the [4Fe4S] cluster and protein backbone) has very little effect on the predicted infrared spectra.     

Interplay of stereoelectronic and enviromental effects in tuning the structural and magnetic properties of a prototypical spin probe: further insights from a first principle dynamical approach

The nitrogen isotropic hyperfine coupling constant (hcc) and the g tensor of a prototypical spin probe (di-tert-butyl nitroxide, DTBN) in aqueous solution have been investigated by means of an integrated computational approach including Car-Parrinello molecular dynamics and quantum mechanical calculations involving a discrete-continuum embedding. The quantitative agreement between computed and experimental parameters fully validates our integrated approach. Decoupling of the structural, dynamical, and environmental contributions acting onto the spectral observables allows an unbiased judgment of the role played by different effects in determining the overall experimental observables and highlights the importance of finite-temperature vibrational averaging. Together with their intrinsic interest, our results pave the route toward more reliable interpretations of EPR parameters of complex systems of biological and technological relevance.     

Synthesis, spectroscopic characterizations and quantum chemical computational studies of (Z)-4-[(E)-(4-fluorophenyl)diazenyl]-6-[(3-hydroxypropylamino)methylene]-2-methoxycyclohexa-2,4-dienone

In this study, the molecular structure and spectroscopic properties of the title compound were characterized by X-ray diffraction, FT-IR and UV-vis spectroscopies. These properties were also investigated using DFT method. The most convenient conformation of title compound was firstly determined. The geometry optimizations in gas phase and solvent media were performed by DFT methods with B3LYP adding 6-31G(d) basis set. The differences between crystal and computational structures are due to crystal packing in which hydrogen bonds play an important role. UV-vis spectra were recorded in different organic solvents. The results show that title compound exists in both keto and enol forms in DMSO, EtOH but it tends to shift towards enol form in benzene. The polar solvents facilitate the proton transfer by decreasing the activation energy needed for Transition State. The formation of both keto and enol forms in DMSO and EtOH is due to decrease in the activation energy. TD-DFT calculations starting from optimized geometry were carried out in both gas and solution phases to calculate excitation energies of the title compound. The non-linear optical properties were computed at the theory level and the title compound showed a good second order non-linear optical property. In addition, thermodynamic properties were obtained in the range of 100-500K.     

Hydrogen bond geometries from electron paramagnetic resonance and electron-nuclear double resonance parameters: density functional study of quinone radical anion-solvent interactions

Density functional theory was used to study the impact of hydrogen bonding on the p-benzosemiquinone radical anion BQ(*-) in coordination with water or alcohol molecules. After complete geometry optimizations, (1)H, (13)C, and (17)O hyperfine as well as (2)H nuclear quadrupole coupling constants and the g-tensor were computed. The suitability of different model systems with one, two, four, and 20 water molecules was tested; best agreement between theory and experiment could be obtained for the largest model system. Q-band pulse (2)H electron-nuclear double resonance (ENDOR) experiments were performed on BQ(*-) in D(2)O. They compare very well with the spectra simulated by use of the theoretical values from density functional theory. For BQ(*-) in coordination with four water or alcohol molecules, rather similar hydrogen-bond lengths between 1.75 and 1.78 A were calculated. Thus, the computed electron paramagnetic resonance (EPR) parameters are hardly distinguishable for the different solvents, in agreement with experimental findings. Furthermore, the distance dependence of the EPR parameters on the hydrogen-bond length was studied. The nuclear quadrupole and the dipolar hyperfine coupling constants of the bridging hydrogens show the expected dependencies on the H-bond length R(O.H). A correlation was obtained for the g-tensor. It is shown that the point-dipole model is suitable for the estimation of hydrogen-bond lengths from anisotropic hyperfine coupling constants of the bridging (1)H nuclei for H-bond lengths larger than approximately 1.7 A. Furthermore, the estimation of H-bond lengths from (2)H nuclear quadrupole coupling constants of bridging deuterium nuclei by empirical relations is discussed.     

The weak hydrogen bond in the fluorobenzene-ammonia van der Waals complex: Insights into the effects of electron withdrawing substituents on pi versus in-plane bonding

The fluorobenzene-ammonia van der Waals complex has been studied using a combination of two-color resonance enhanced multiphoton ionization (REMPI) spectroscopy, counterpoise corrected RICC2 ab initio molecular orbital calculations, and multidimensional Franck-Condon analysis. The experimental REMPI spectrum is characterized by a dominant, blueshifted band origin, and weak activity in intermolecular vibrational modes. RICC2 geometry optimizations and numerical vibrational frequency calculations of the neutral ground and first excited states have been performed on a number of different structural isomers of the complex using basis sets ranging from augmented double-zeta to quadruple-zeta level. Ground state basis set superposition error corrected zero-point binding energies show the in-plane sigma complex, forming a pseudo-six-membered ring connecting the fluorine atom and ortho-hydrogen, to be consistently the most stable of all six conformations considered, at all levels of theory. Comparison of computed zero-point excitation energies for the most stable pi and sigma conformers with fluorobenzene show that the sigma complex is the only conformer predicted to exhibit a spectral blueshift upon electronic excitation. The computed neutral ground and first excited state geometries and frequencies were used to perform multidimensional Franck-Condon simulations of the S(1)-S(0) vibronic spectrum for each of the most stable conformers. These simulations yielded null spectra for transitions involving the most stable of the pi complexes, pi(bridge); a spectrum rich in strong intermolecular vibrational structure for the second of the pi complexes, in complete contrast to the experimental spectrum; and for the sigma complex, a spectrum exhibiting weak intermolecular activity in line with that observed experimentally. This last simulation allowed an almost complete vibrational assignment of the intermolecular structure in the REMPI spectrum. The agreement between computational results and experiment overwhelmingly favors assignment of the spectrum to the in-plane sigma complex.     

西红花酸二甲酯电子吸收光谱与热力学性质的理论研究

使用密度泛函理论B3LYP方法,对西红花酸二甲酯的结构、电子吸收光谱、热力学性质进行理论计算研究,并基于Tomasi的极化统一场模型(PCM)讨论溶剂效应.结果显示,溶剂对西红花酸二甲酯的前线分子轨道特征几乎无影响,溶剂作用使该分子的最大吸收波长红移约42 nm,红移程度与溶剂极性无关.西红花酸二甲酯分子的气态热力学性质与温度的关系式分别为:Cm p=189.782+0.925T,S m=457.503+1.366T,H m=1164.899+0.195T+4.671×10-4T2,Gm=1164.899-0.263T-8.989×10-4T2.298 K时,西红花酸二甲酯分子的气态标准摩尔生成焓和标准摩尔生成自由能分别为-1180.67和-733.23 kJ·mol-1.     

Theoretical study of absorption and emission properties of green and yellow emitting iridium(III) complexes

Iridium(III) complexes are among the most used phosphorescent materials for the development of organic light emitting diodes (OLEDs). In this work, the photophysical properties of a family of complexes based on phenyldiazine ligands were studied. Their ground state geometric and electronic structures as well as their absorption and emission spectra were investigated by the means of density functional theory (DFT) and time-dependent DFT (TD-DFT). An extremely good agreement between the computed and experimental values is obtained, thus suggesting that the computational protocol here applied could be used for the in silico screening and design of new Ir-based emitting complexes.     

STUDIES ON FLAVINS IN ORGANIC SOLVENTS-I*. SPECTRAL CHARACTERISTICS OF RIBOFLAVIN,RIBOFLAVIN TETRABUTYRATE AND LUMICHROME

Abstract— The absorption and fluorescence spectra of riboflavin, riboflavin tetrabutyrate and lumichrome have been studied in organic solvents of different polarity including ethanol, acetone, dioxane, pyridine, acetic acid and in cyclohexane-dioxane mixtures. The molar extinction coefficients of the compounds were measured and the character of solvent sensitive changes observed in the absorption spectra are discussed. The effect of hydrogen bonding and/or intramolecular charge transfer complex are proposed as possible explanation. Changes in the shape of fluorescence emission spectra are less evident; in the case of riboflavin tetrabutyrate, mirror symmetry to the shape of the longest wavelength maximum was observed in low-polar solvents. Quantum yields of fluorescence are higher the lower the polarity of the solvent used; the value for riboflavin tetrabutyrate is greater than for riboflavin. Changes were also observed in the fluorescence emission spectra of lumichrome in solvents of different polarity. Fairly good agreement was demonstrated for positions of the observed absorption maxima of riboflavin in 98% dioxane, riboflavin tetrabutyrate and lumichrome in 80% cyclohexane in mixture with dioxane and the values calculated from energies of molecular orbitals of flavins computed by B. Pullman and A. Pullman.     

17O solid-state NMR and first-principles calculations of sodium trimetaphosphate (Na3P3O9), tripolyphosphate (Na5P3O10), and pyrophosphate (Na4P2O7)

The assignment of high-field (18.8 T) (17)O MAS and 3QMAS spectra has been completed by use of first-principles calculations for three crystalline sodium phosphates, Na 3P 3O 9, Na 5P 3O 10, and Na 4P 2O 7. In Na 3P 3O 9, the calculated parameters, quadrupolar constant ( C Q), quadrupolar asymmetry (eta Q), and the isotropic chemical shift (delta cs) correspond to those deduced experimentally, and the calculation is mandatory to achieve a complete assignment. For the sodium tripolyphosphate Na 5P 3O 10, the situation is more complex because of the free rotation of the end-chain phosphate groups. The assignment obtained with ab initio calculations can however be confirmed by the (17)O{ (31)P} MAS-J-HMQC spectrum. Na 4P 2O 7 (17)O MAS and 3QMAS spectra show a complex pattern in agreement with the computed NMR parameters, which indicate that all of the oxygens exhibit very similar values. These results are related to structural data to better understand the influence of the oxygen environment on the NMR parameters. The findings are used to interpret those results observed on a binary sodium phosphate glass.     

Unambiguous NMR spectral assignments of salvinorin A

The complete assignments of the (1)H and (13)C NMR spectra of the hallucinogenic neoclerodane diterpenoid salvinorin A were determined in three different NMR solvents using HSQC, HMBC and COSY. Solvent systems are described that allow the resolution of all (1)H signals. Virtual coupling was observed for the protons at C-2, C-3 and C-4 in the 600 MHz (1)H spectrum in CDCl(3). The complete assignments of the (1)H and (13)C NMR spectra of salvinorin B are also reported.     

Experimental and computational study of HXeY...HX complexes (X, Y = Cl and Br): an example of exceptionally large complexation effect

The complexes of xenon hydrides HXeY (Y = Cl and Br) with hydrogen halides HX (X = Cl and Br) have been studied both computationally and experimentally in a xenon matrix. The experiments revealed three new complexes: HXeBr...HBr, HXeBr...HCl, and HXeCl...HCl. The experimental assignments were done on the basis of the strong H-Xe stretching absorption of HXeY (Y = Cl and Br) molecules and supported by theoretical results. We experimentally obtained monomer-to-complex blue-shifts of this vibrational mode for all the studied systems (up to approximately 150 cm (-1)). The electronic structure calculations revealed three local structures for each HNgY...HX complexes and their computed interaction energies varied between -460 and -2800 cm (-1). The computational estimates of the vibrational shifts were in agreement with the experimental values. We also found possible experimental absorption belonging to HXeBr...(HBr) 2 trimer and its vibrational shift (+245 cm (-1)) is similar to the computational estimate of a cyclic ternary complex (+252 cm (-1)).     

Axial and equatorial hydrogen-bond conformers between (CH2)3S and H(D)F: Fourier transform infrared spectroscopy and ab initio calculations

The coexistence of axial and equatorial hydrogen-bonded conformers of 1?:?1 (CH(2))(3)S-HF (and -DF) has been observed in the same adiabatic expansion of a supersonic jet seeded with argon and in a static absorption cell at room temperature. High level calculations computed the axial conformer to be the most stable one with a small energy difference with respect to the equatorial one, in full agreement with previous microwave experiments. On the grounds of band contour simulations of FTIR spectra and ab initio energetic and anharmonic vibrational calculations, two pairs of ν(s) HF donor stretching bands, observed in a series of jet-FTIR spectra at 3457.9 and 3480.5 cm(-1) have been respectively assigned to the axial and equatorial forms of the 1?:?1 complex. In the jet-FTIR spectra series with HF, the assignment of an additional broad band (about 200 cm(-1) higher in frequency with respect to ν(s)) to a 1?:?2 complex has been supported by theoretical investigations. Experimental detection of both axial and equatorial forms of a cyclic trimer has been confirmed by calculated energetic and vibrational properties. The nature of hydrogen bonding has been examined within topological frameworks. The energetic partitioning within the 1?:?1 dimers has been elucidated with SAPT techniques. Interestingly, the interconversion pathway between two 1?:?1 structures has been explored and it was seen that the formation of the 1?:?1 complex affects the interconversion barrier on the ring puckering motion. The band contour analysis of gas phase FTIR experiments provided a consistent set of vibrational frequencies and anharmonic coupling constants, in good agreement with ab initio anharmonic vibrational calculations. Finally, from a series of cell-FTIR spectra recorded at different partial pressures of (CH(2))(3)S and HF monomers, the absorption signal of the 1?:?1 complex could be isolated which enabled to estimate the equilibrium constant K(p) = 0.023 at 298 K for the dimerization.     

Effects of the 3- and 4-methoxy and acetamide substituents and solvent environment on the electronic properties of N-substituted 1,8-naphthalimide derivatives

The photophysical properties of polar molecules in solution with an intramolecular charge-transfer effect in the excited state depend strongly on the polarity and proticity of the solvents. UV-visible spectra of 1,8-naphthalimide and some N-substituted derivatives in acetic acid, acetonitrile, dichloromethane, and p-dioxane were carried out. Several molecular cluster geometries formed with N-substituted 1,8-naphthalimide derivatives and a large set of random positioning of some solvent molecules in their environment were optimized by a semiempirical method. It provided a complete screening of possible solute-solvent configurations and resulted in a multiple minima hypersurface of the supramolecular systems. With such local minima energies, the main thermodynamic association functions were found. They also provided selected cluster geometries for calculations of vertical electronic transitions with a time-dependent density functional theory (TD-DFT), if the lowest energy structures were considered. Calculated vertical electronic transition energies at the TD-DFT level were compared with experimental data. The experimental absorption UV-visible spectra for the six compounds in the four solvents were performed in our laboratory. Moreover, X-ray photoelectron spectroscospy of the 1,8-naphthalimide was carried out in the ICP-CSIC laboratory. Thermodynamic function values show different association energies between each solvent and the molecules, in correlation with the possibility of hydrogen bond formation and the polarity and dielectric constant of the solvents. The 3- and 4-acetamide 1,8-naphthalimide derivatives have the highest conformer number and the most negative Gibbs free association energy values for a determined solvent. This indicates the importance of the entropic factors.     

Ab initio calculations of anharmonic vibrational spectroscopy for hydrogen fluoride (HF)n (n = 3, 4) and mixed hydrogen fluoride/water (HF)n(H2O)n (n = 1, 2, 4) clusters

Anharmonic vibrational frequencies and intensities are computed for hydrogen fluoride clusters (HF)n, with n = 3, 4 and mixed clusters of hydrogen fluoride with water (HF)n(H2O)n where n = 1, 2. For the (HF)4(H2O)4 complex, the vibrational spectra are calculated at the harmonic level, and anharmonic effects are estimated. Potential energy surfaces for these systems are obtained at the MP2/TZP level of electronic structure theory. Vibrational states are calculated from the potential surface points using the correlation-corrected vibrational self-consistent field method. The method accounts for the anharmonicities and couplings between all vibrational modes and provides fairly accurate anharmonic vibrational spectra that can be directly compared with experimental results without a need for empirical scaling. For (HF)n, good agreement is found with experimental data. This agreement shows that the M?ller-Plesset (MP2) potential surfaces for these systems are reasonably reliable. The accuracy is best for the stiff intramolecular modes, which indicates the validity of MP2 in describing coupling between intramolecular and intermolecular degrees of freedom. For (HF)n(H2O)n experimental results are unavailable. The computed intramolecular frequencies show a strong dependence on cluster size. Intensity features are predicted for future experiments.     

Prediction of solid solution formation in a family of diastereomeric salts. A molecular modeling study

The possibility of solid solution behavior of diastereomeric salts, containing multiple resolving agents of the same family (Dutch Resolution), is predicted by molecular modeling. Super-cells containing different ratios of resolving agents in the diastereomeric salt are constructed and optimized, and their lattice energy is computed. The energy difference between these "simulated solid solutions" and the native structures is related in an understandable fashion to the probability of solid solution formation. This procedure is applied to a family of diastereomeric salts of ephedrine and cyclic phosphoric acids, for which the ternary diagrams have been determined experimentally at 25 degrees C in ethanol. Good agreement between experimental and computational results indicates that this relatively simple and fast method could predict the stable character of solid solution behavior in binary systems.     

Theoretical and spectroscopic study of the reaction of diethylhydroxylamine on silicon(100)-2 x 1

Incorporating diversity into structures constructed from the organic modification of silicon surfaces requires the use of molecules that contain multiple substituents of different types. In this work we examine the possible dissociation pathways of diethylhydroxylamine (DEHA, (C(2)H(5))(2)NOH) on the surface of clean silicon(100)-2x1 using cluster and planewave computational methods and high resolution electron energy loss spectroscopy. Our computational results show that DEHA initially forms a strongly-bound complex with the surface via a dative N-Si bond. A low-barrier O-H bond scission then occurs yielding a surface silicon dimer capped by the (C(2)H(5))(2)NO and H fragments. Calculated and measured vibrational spectra support the computed reaction mechanism.     

Density functional calculations of 9-diphenylaminoacridine fluorescent indicator and its interactions with analyte molecules: I. Structures of complexes in the ground electronic states and absorption spectra

The interaction of 9-diphenylaminoacridine dye (indicator) with several small analyte molecules (methanol, acetonitrile, acetone, tetrahydrofuran, benzene, ammonia, formaldehyde, and acetaldehyde) has been theoretically studied in relation to the problem of the development of optical chemosensors based on organic dyes. The structures of the resulting complexes and the absorption spectra of 9-diphenylaminoacridine and its complexes with analytes were calculated using density functional theory (DFT) with the PBE0 functional and the 6-31G(d,p) basis set. It was demonstrated that complexes of two types with different mutual arrangements of molecules corresponding to the lateral and stacking structures can be formed for each analyte. The calculated absorption spectrum only weakly changes upon complex formation, which is in agreement with experimental data on the absorption spectra of 2,7-dimethyl-9-ditolylaminoacridine in solutions of corresponding solvents. The method for the calculation of excited states that was used in this work can be applied to the calculation of the fluorescence spectra of 9-diphenylaminoacridine complexes.     

Atom accurate structure determination of alprazolam/cyclodextrin inclusion complexes by ROESY and computational approaches

A lot of interest has been seen in computational methods that provide reliable atom accurate structures of different molecular systems. In this article, we describe the complexation of alprazolam (ALP) with three cyclodextrins, i.e., α-, β- and γ-CD. ROESY spectra showed that no complex was formed between ALP and α-CD however, ring A of ALP formed ICs with β- and γ-CD. Therefore, structures of ALP/β-CD and ALP/γ-CD were obtained by a combination of NMR (2D-ROESY) and computational methods by a quantitative ROESY approach. Here we determined the structures of CD ICs by a method recently used in our laboratory and then the structures were obtained independently by DFT (B3LYP functional and def2-TZVP basis set). The structures obtained by both methods were compared with each other. Results demonstrated that our method provides reasonable structures comparable to DFT, and can be used to obtain highly atom accurate structures of CD inclusion complexes. Quantitative ROESY analysis of MM and MD structures consume less time and are cheap as compared to DFT, which is highly CPU demanding and time taking. Negative values of binding energy showed that the process of inclusion was spontaneous and complexes formed were stable. The large negative value of binding energy for ALP/β-CD as compared to ALP/γ-CD showed a higher binding affinity of ALP towards β-CD. FMO studies also revealed the higher HOMO-LOUMO gap for inclusion complexes as compared to pure ALP. Intermolecular H-bonds formed in both the complexes are also one of the forces responsible for inclusion complex formation.     

Molecular structure and vibrational spectra of 1,3-bis(4-pyridyl)propane by quantum chemical calculations

The experimental and theoretical study on the structures and vibrations of 1,3-bis(4-pyridyl)propane are presented. The FT-IR and Raman spectra of molecule have been measured. The optimized geometric bond lengths have been obtained by DFT show the best agreements with experimental values. The harmonic vibrational frequencies were calculated and scaled values have been compared with experimental FT-IR and FT-Raman spectra. Majority of the computed wavenumbers were found to be in good agreement with experimental observations. A complete assignment of the fundamentals was proposed based on the total energy distribution (TED) calculation.     

Experimental and theoretical study of two new pyrazoline derivatives based on dibenzofuran

Two novel pyrazoline derivatives, named 2,8-bis(1,3-diphenyl-pyrazoline-5-yl)dibenzofuran (A) and 2,8-bis(1-(4-bromophenyl)-3-phenyl-pyrazoline-5-yl)dibenzofuran (B), were synthesized and characterized by elemental analysis, NMR, MS and thermogravimetric analysis. The absorption and emission spectra of them were determined by experimental methods in different polar solvents and were computed using the density functional theory (DFT) and the time-dependent density functional theory (TDDFT) at the same time. The calculated absorption and emission wavelengths are in good agreement with the experimental data. The fluorescence quantum yields and fluorescence lifetimes of them in different polar solvents were studied by means of steady state and time resolved fluorescence. The calculated reorganization energy for hole and electron indicates that the two compounds are in favor of hole transport than electron transport. The results show the two compounds present high fluorescence quantum yields and excellent thermal stability. It makes them of great interest as novel fluorescent probes and optoelectronic materials.