Modified interfacial statistical associating fluid theory: a perturbation density functional theory for inhomogeneous complex fluids

A density functional theory based on Wertheim's first order perturbation theory is developed for inhomogeneous complex fluids. The theory is derived along similar lines as interfacial statistical associating fluid theory [S. Tripathi and W. G. Chapman, J. Chem. Phys. 122, 094506 (2005)]. However, the derivation is more general and applies broadly to a range of systems, retaining the simplicity of a segment density based theory. Furthermore, the theory gives the exact density profile for ideal chains in an external field. The general avail of the theory has been demonstrated by applying the theory to lipids near surfaces, lipid bilayers, and copolymer thin films. The theoretical results show excellent agreement with the results from molecular simulations.     

Investigation of inter-ion interactions in N,N,N',N'-tetramethylethylenediammonium dithiocyanate via experimental and theoretical charge density studies

The crystal structure of the N,N,N',N'-tetramethylethylenediammonium dithiocyanate salt has been examined by experimental charge density studies from high-resolution X-ray diffraction data. The corresponding results are compared with multipole refinements, using theoretical structure factors obtained from a periodic density functional theory calculation at the B3LYP level with a 6-31G(**) basis set. The salt crystallizes in space group P and contains only a single ion pair with an inversion center in the cation. The salt has thus one unique classical N+-H...(NCS)(-) hydrogen bond but also has six other weaker interactions: four C-H...S, one C-H...N, and one C-H...C(pi). The nature of all these interactions has been examined topologically using Bader's quantum theory of "atoms in molecules" and all eight of the Koch-Popelier criteria. The experimental and theoretical approaches agree well and both show that the inter-ion interactions, even in this simplest of systems, play an integrated and complex role in the packing of the ions in the crystal. Electrostatic potential maps are derived from experimental charge densities. This is the first time such a system has been examined in detail by these methods.     

Structural, electronic, and bonding properties of zeolite Sn-beta: a periodic density functional theory study

The structural, electronic, and the bonding properties of the zeolite Sn-beta (Sn-BEA) have been investigated by using the periodic density functional theory. Each of the nine different T-sites in BEA were substituted by Sn atoms and all the nine geometries were completely optimized by using the plane-wave basis set in conjunction with the ultra-soft pseudopotential. On the basis of the structural and the electronic properties, it has been demonstrated that the substitution of Sn atoms in the BEA framework is an endothermic process and hence the incorporation of Sn in the BEA is limited. The lowest unoccupied molecular orbitals (LUMO) energies have been used to characterize the Lewis acidity of each T-site. On the basis of the relative cohesive energy and the LUMO energy, the T2 site is shown to be the most favorable site for the substitution Sn atoms in the BEA framework.     

A perturbation density functional theory for the competition between inter and intramolecular association

Using the framework of Wertheim's thermodynamic perturbation theory we develop the first density functional theory which accounts for intramolecular association in chain molecules. To test the theory new Monte Carlo simulations are performed at a fluid solid interface for a 4 segment chain which can both intra and intermolecularly associate. The theory and simulation results are found to be in excellent agreement. It is shown that the inclusion of intramolecular association can have profound effects on interfacial properties such as interfacial tension and the partition coefficient.     

Structure, spectroscopy, and reactivity properties of porphyrin pincers: a conceptual density functional theory and time-dependent density functional theory study

Porphyrin and pincer complexes are both important categories of compounds in biological and catalytic systems. The idea to combine them is computationally investigated in this work. By employment of density functional theory (DFT), conceptual DFT, and time-dependent DFT approaches, structure, spectroscopy, and reactivity properties of porphyrin pincers are systematically studied for a selection of divalent metal ions. We found that the porphyrin pincers are structurally and spectroscopically different from their precursors and are more reactive in electrophilic and nucleophilic reactions. A few quantitative linear/exponential relationships have been discovered between bonding interactions, charge distributions, and DFT chemical reactivity indices. These results are implicative in chemical modification of hemoproteins and understanding chemical reactivity in heme-containing and other biologically important complexes and cofactors.     

Matrix isolation infrared spectroscopic and density functional theory studies on the reactions of yttrium and lanthanum hydrides with dinitrogen

Laser-ablated yttrium and lanthanum hydrides have been codeposited at 4 K with dinitrogen in excess argon. Products, HY(N2), HYNN, H2YNN, HLaNN, and H2LaNN, have been formed in the present experiments and characterized by using infrared spectroscopy on the basis of the results of the isotopic shifts, mixed isotopic splitting patterns, stepwise annealing, and comparison with theoretical predictions. Density functional theory calculations have been performed on these molecules. The agreement between the experimental and calculated vibrational frequencies, relative absorption intensities, and isotopic shifts supports the identification of these molecules from the matrix infrared spectra. Plausible reaction mechanisms have been proposed for the formation of these molecules.     

Structural, electronic, and vibrational characterization of Fe-HNO porphyrinates by density functional theory

A recent report of the structural and vibrational properties of heme-bound HNO in myoglobin, MbHNO, revealed a long Fe-N(HNO) bond with the hydrogen atom bonded to the coordinated N atom. The Fe-N(H)-O moiety was reported to exhibit an unusually high Fe-N(HNO) stretching frequency relative to those of the corresponding [FeNO]6 and [FeNO]7 porphyrinates, despite the Fe-N(HNO) bond being longer than either of its Fe-N(NO) counterparts. Herein, we present results from density functional theory calculations of an active site model of MbHNO that support the previous assignment and clarify this seemingly contradictory result. The results are consistent with the experimental evidence for a ground-state Fe-N(H)-O structure having a long Fe-N(HNO) bond and a uniquely high nu(Fe)(-)(N(HNO)) frequency. This high frequency is the result of the correspondingly low reduced mass of the normal mode, which is largely attributable to significant motion of the N-bound hydrogen atom. Additionally, the calculations show the Fe-N(H)O bonding in this complex to be remarkably insensitive to whether the HNO and ImH ligand planes are parallel or perpendicular. This is attributed to insensitivities of the Fe-L(axial) characters of molecular orbitals to the relative HNO and ImH orientation in both the parallel and perpendicular conformers.     

Infrared spectra of metal-free, N',N-dideuterio, and magnesium porphyrins: density functional calculations

Infrared frequencies and intensities for the metal-free porphyrin (H2Por), N',N-dideuterio porphyrin (D2Por), and magnesium porphyrin complex (MgPor) have been calculated at density functional B3LYP level using the 6-31G(d) basis set. Detailed assignments of the NH and NM vibrational bands in the IR spectra have been made on the basis of comparison between the calculated data and the experimental results. The previous empirical controversial assignments for the bands at 1224, 1110 and 771 cm(-1) for metal-free porphyrin are also clearly interpreted.     

Matrix isolation infrared spectroscopic and density functional theory studies on the reactions of yttrium and lanthanum hydrides with carbon monoxide

Laser-ablated yttrium and lanthanum hydrides have been co-deposited at 4 K with carbon monoxide in excess argon. Products, such as HYCO, (HY)2CO, HLaCO, HLa(CO)2, and H2LaCO, have been formed in the present experiments and characterized using infrared spectroscopy on the basis of the results of the isotopic shifts, mixed isotopic splitting patterns, stepwise annealing, the change of reagent concentration and laser energy, and the comparison with theoretical predictions. Density functional theory calculations have been performed on these molecules. The agreement between the experimental and calculated vibrational frequencies, relative absorption intensities, and isotopic shifts supports the identification of these molecules from the matrix infrared spectra. Plausible reaction mechanisms have been proposed to account for the formation of these molecules.     

Thermochemistry and infrared spectroscopy of neutral and cationic iron-polycyclic aromatic hydrocarbon complexes of astrophysical interest: fundamental density functional theory studies

This paper reports extensive calculations on the structural, thermodynamic, and mid-infrared spectroscopic properties of neutral and cationic model iron-polycyclic aromatic hydrocarbon (PAH) complexes of astrophysical interest for three PAHs of increasing size, namely, naphthalene (C10H8), pyrene (C16H10), and coronene (C24H12). Geometry optimizations and frequency calculations were performed using hybrid Hartree-Fock/density functional theory (DFT) methods. The use of DFT methods is mandatory in terms of computational cost and efficiency to describe the electronic and vibrational structures of such large organometallic unsaturated species that present several low-energy isomers of different structures and electronic and spin states. The calculated structures for the low-energy isomers of the model Fe-PAH and Fe-PAH+ complexes are presented and discussed. Iron-PAH binding energies are extracted, and the consequences of the coordination of iron on the infrared spectra of neutral and cationic PAHs are shown with systematic effects on band intensities and positions being demonstrated. The first results are discussed in terms of astrophysical implications. This work is the first step of an ongoing effort in our group to understand the photophysics and spectroscopy of iron-PAH complexes in the conditions of the interstellar medium using a synergy between observations, laboratory experiments, and theory.     

Importance of entropy in the conformational equilibrium of phenylalanine: a matrix-isolation infrared spectroscopy and density functional theory study

The conformational behavior and infrared spectrum of l-phenylalanine were studied by matrix-isolation infrared spectroscopy and DFT [B3LYP/6-311++G(d,p)] calculations. The fourteen most stable structures were predicted to differ in energy by less than 10 kJ mol(-1), eight of them with abundances higher than 5% at the temperature of evaporation of the compound (423 K). Experimental results suggest that six conformers contribute to the spectrum of the isolated compound, whereas two conformers (IIb(3) and IIIb(3)) relax in matrix to a more stable form (IIb(2)) due to low energy barriers for conformational isomerization (conformational cooling). The two lowest-energy conformers (Ib(1), Ia) differ only in the arrangement of the amino acid group relative to the phenyl ring; they exhibit a relatively strong stabilizing intramolecular hydrogen bond of the O-H...N type and the carboxylic group in the trans configuration (O=C-O-H dihedral angle ca. 180 degrees ). Type II conformers have a weaker H-bond of the N-H...O=C type, but they bear the more favorable cis arrangement of the carboxylic group. Being considerably more flexible, type II conformers are stabilized by entropy and the relative abundances of two conformers of this type (IIb(2) and IIc(1)) are shown to significantly increase with temperature due to entropic stabilization. At 423 K, these conformers are found to be the first and third most abundant species present in the conformational equilibrium, with relative populations of ca. 15% each, whereas their populations could be expected to be only ca. 5% if entropy effects were not taken into consideration. Indeed, phenylalanine can be considered a notable example of a molecule where entropy plays an essential role in determining the relative abundance of the possible low-energy conformational states and then, the thermodynamics of the compound, even at moderate temperatures. Upon UV irradiation (lambda > 235 nm) of the matrix-isolated compound, unimolecular photodecomposition of phenylalanine is observed with production of CO(2) and phenethylamine.     

Fourier transform infrared and Raman spectra, vibrational assignment and density functional theory calculations of naphthazarin

FT Raman and FTIR spectra of Naphthazarin (5,8-dihydroxy-1,4-naphthoquinone) and its deuterated analogue are recorded. Comparison between the spectra obtained by two techniques, a series of density functional theory (DFT) calculations and the spectral behavior upon deuteration were used for the assignment of the vibrational spectra of this compound. The calculated vibrational frequencies by the B3LYP, B3PW91, G96LYP, G96P86, and MPWLYP density functionals are generally consistent with the observed spectra. Infrared and Raman vibrational transitions predicted by B3LYP/6-311++G** are reported for the titled compound and its deuterated analogous and the assignments are discussed. All experimental and theoretical results support a relatively weak hydrogen bond in naphthazarin (NZ), compared with that in the enol form of normal beta-diketones. The observed nuOH/nuOD and gammaOH/gammaOD appear at about 3060/2220 and 790/560 cm(-1), respectively, which are consistent with the calculated hydrogen bond geometry and proton chemical shift results. Two bands at about 350 and 290 cm(-1) are assigned to the O...O stretching modes belong to A1 and B2 species, respectively.     

Azide functional monolayers grafted to a germanium surface: model substrates for ATR-IR studies of interfacial click reactions

High-quality azide-functional substrates are prepared by a low temperature reaction of 11-bromoundecyltrichlorosilane with UV-ozone-treated germanium ATR-IR plates followed by nucleophilic substitution of the terminal bromine by addition of sodium azide. The resulting monolayer films are characterized by atomic force microscopy (AFM), contact angle analysis, X-ray photoelectron spectroscopy (XPS), attenuated total reflectance infrared spectroscopy (ATR-IR), and ellipsometry. XPS and ellipsometric thickness data correspond well to the results of molecular model calculations confirming the formation of a densely packed azide-functional monolayer. These azide-functional substrates enable interfacial "click" reactions with complementary alkyne-functional molecules to be studied in situ by ATR-IR. To illustrate their potential utility for kinetic studies we show that, in the presence of copper(I) catalyst, the azide-modified surfaces react rapidly and quantitatively with 5-chloro-pentyne to form triazoles via a 1,3-dipolar cycloaddition reaction. Time-resolved ATR-IR measurements indicate that the interfacial click reaction is initially first order in azide concentration as expected from the reaction mechanism, with a rate constant of 0.034 min(-1), and then transitions to apparent second order dependence, with a rate constant of 0.017 min(-1)/(chains/nm(2)), when the surface azide and triazole concentrations become similar, as predicted by Oyama et al. The reaction achieves an ultimate conversion of 50% consistent with the limit expected due to steric hindrance of the 5-chloro-pentyne reactant at the surface.     

Comparative studies on the structures,infrared spectrum,and thermodynamic properties of phthalocyanine using ab initio Hartree–Fock and density functional theory methods

The molecular structure, vibrational spectrum, standard thermodynamic functions, and enthalpy of formation of free base phthalocyanine (Pc) have been studied using the density functional theory B3LYP procedure, as well as the ab initio Hartree–Fock method. Various basis sets 3‐21G, 6‐31G*, and LANL2DZ have been employed. The results obtained at various levels are discussed and compared with each other and with the available experimental data. It is shown that calculations performed at the Hartree–Fock level cannot produce a reliable geometry and related properties such as the dipole moment of Pc and similar porphyrin‐based systems. Electron correlation must be included in the calculations. The basis set has comparatively less effect on the calculated results. The results derived at the B3LYP level using the smaller 3‐21G and LANL2DZ basis sets are very close to those produced using the medium 6‐31G* basis set. The geometry of Pc obtained at the B3LYP level has D_2h symmetry and the diameter of the central macrocycle is about 4 Å. The enthalpy of formation of Pc in the gas phase has been predicted to be 1518.50 kJ/mol at the B3LYP/6‐311G(2d,2p)//B3LYP/6‐31G* level via an isodesmic reaction. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

Criteria for determining the hydrogen-bond structures of a tyrosine side chain by fourier transform infrared spectroscopy: density functional theory analyses of model hydrogen-bonded complexes of p-cresol

Fourier transform infrared (FTIR) spectroscopy is a powerful method to investigate the structures of key Tyr residues involved in various protein reactions. In this study, we have performed density functional theory (DFT) calculations for various hydrogen-bonded complexes of p-cresol, a simple model of a Tyr side chain, in different hydrogen-bond forms to develop explicit criteria for determining the hydrogen-bond structures of Tyr using FTIR spectroscopy. The CO stretching (nuCO) and COH bending (deltaCOH) vibrations were focused as markers and calculated results were compared with experimental data of p-cresol and Tyr. The calculated and experimental nuCO frequencies appeared at 1280-1260, 1260-1250, 1255-1235, and 1240-1220 cm-(1) in the hydrogen-bond donor, free, donor-acceptor, and acceptor forms, respectively. These frequencies, which showed little overlap between the individual hydrogen-bond forms, had a negative linear correlation with the CO lengths in optimized geometries. The deltaCOH frequencies were found at 1255-1210 cm-(1) in the donor form, while the free and acceptor forms showed relatively low deltaCOH frequencies at 1185-1165 and 1190-1160 cm-(1), respectively. In the donor-acceptor form, the vibrational mode with a considerable deltaCOH contribution was found at 1280-1255 cm-(1) with a weak IR intensity. This frequency and the nuCO frequency in the donor-acceptor form are similar to the nuCO and deltaCOH frequencies, respectively, of the donor form, making it difficult to discriminate the two forms. These two forms can be clearly distinguished by detecting a strong nuCO(D) band in p-cresol-OD or Tyr-OD, in which the deltaCOD vibration largely downshifts to approximately 1000 cm-(1). The nuCO(D) frequency of the donor-acceptor form was found at 1260-1240 cm-(1), while that of the donor form was at 1270-1255 cm-(1). Practically, plotting the frequency of the lower-frequency strong IR band (nuCO of the donor-acceptor form or deltaCOH of the donor form) of undeuterated species against the nuCO(D) frequency is convenient for accurate discrimination. Because the donor form shows a positive linear correlation between deltaCOH and nuCO(D) frequencies, the two forms exhibited distinct areas in this plot. The effects of hydrogen-bond interactions on other potential IR and Raman markers are also discussed.     

Molecular conformations of a partially halogenated ether: A study based on infrared spectroscopy and density functional theory calculations

A new partially halogenated ether (ClCF₂CF(CF₃)OCF₂CH₃) has been synthesized and characterized using DSC, GC, ¹H and ¹⁹F NMR, IR. The experimental infrared spectra of this “flexible” molecule have been successfully interpreted on the basis of reliable Density Functional Theory calculations. An efficient method useful for the identification of the many stable conformers has been developed and applied. Infrared spectra of the stable conformers have been simulated after full geometry optimization. The results obtained allow detection of conformation-sensitive bands, making possible the interpretation of fine details in the spectra.     

Synergistic interactions in the mixed micelles of cationic gemini with zwitterionic surfactants: fluorescence and Krafft temperature studies

Pyrene fluorescence and Krafft temperature measurements have been carried out for various combinations of cationic gemini (m-2-m) with zwitterionic surfactants by changing the length of the hydrophobic tail over the whole mixing range. The results have been evaluated by using the regular solution theory. All the mixtures of cationic gemini+zwitterionic surfactants indicate the presence of synergistic interactions which largely decrease at higher hydrophobicity of both components. A greater amount of gemini component in the mixed micelles induces stronger synergism which reduces with the increase in the length of hydrophobic tail of the gemini component. The Krafft temperature measurements also indicate the presence of strong synergistic interactions, which decrease with increase in the length of hydrophobic tail of both components.