Elena E. Zvereva

Ab Initio and DFT Predictions of Infrared Intensities and Raman Activities

Relative infrared (IR) intensities and relative Raman activities have been computed for vibrations of test molecules, including from two to nine heavy atoms, using second-order Moller-Plesset perturbation theory (MP2), and three hybrid density functionals (B3LYP, M05, and M05-2X). The basis set convergence of vibrational properties is discussed. Our results demonstrate that B3LYP offers the most cost-effective choice for the prediction of molecular vibrational properties, but the predictions of another two tested hybrid functionals are very similar and in very good agreement with experimental data. MP2 shows good performance for the IR intensities, whereas the quality of prediction of the relative Raman activities should be characterized as only moderate. B3LYP calculations of the relative IR intensities using highly compact Sadlejs Z3PolX basis set retain the high accuracy of the more CPU expensive Sadlejs pVTZ and much more expensive aug-cc-pVTZ calculations. Relative Raman activities are more sensitive to basis set effects and require at least Sadlejs pVTZ to obtain quantitative results.

Rationalization of Solvation and Stabilization of Palladium Nanoparticles in Imidazolium-Based Ionic Liquids by DFT and Vibrational Spectroscopy

A combined DFT/vibrational spectroscopy approach is used to determine the interactions of the 1,3-dimethylimidazolium ([Mmim](+)) and 1-ethyl-3-methylimidazolium ([Emim](+)) cations and [BF(4)](-) anions with each other in the liquid state and with Pd nanoparticles (NPs) immersed in ionic liquids (ILs) composed of these ions. Formation of aggregates of the counter-ions in the liquid does not have a strong influence on the interaction energy of the IL components with the palladium clusters used to model NPs, which is smaller than the energy of addition of a Pd atom to the cluster. Stronger Pd-Pd interactions in comparison to the interactions of the palladium cluster with the IL suggest kinetic stabilisation of Pd-NPs in 1,3-dialkylimidazolium tetrafluoroborates rather than thermodynamic stabilisation. Moreover, the palladium clusters interact more strongly with the anions than with the cations, and this suggests an important role of the anions in formation and stabilisation of Pd-NP in ILs. At the same time, binding between an isolated Pd atom and [Mmim](+) cation is stronger than Pd-[BF(4)](-) binding. IR and Raman spectral simulations reveal that surface-enhanced Raman spectroscopy is much less sensitive to interactions of Pd-NPs with the [BF(4)](-) anion compared to interactions with [Mmim](+) cations. In contrast, IR spectroscopy is better suited to study the anion-metal interactions, whereas IR spectral manifestations of the cation-metal interactions are rather modest. The splitting of the strong ν(as)(BF(4)(-)) IR band into three components appears to be a convenient spectroscopic marker for Pd-[BF(4)](-) interactions, which is confirmed by actual spectra of Pd-NPs stabilised by [Emim][BF(4)]. The IR spectra and their assignment with quantum chemical computations suggest that both the anions and cations of [Emim][BF(4)] interact with the Pd-NP surface in the IL. The cation ring orientation close to the surface normal appears to be the dominant interaction. The anion is bound to the surface through either two or three fluorine atoms.

Application of time-dependent density functional theory and optical spectroscopy toward the rational design of novel 3,4,5-triaryl-1-R-1,2-diphospholes.

Twenty 3,4,5-triaryl-1-R-1,2-diphospholes were studied within the framework of density functional theory (DFT) and experimentally by UV/vis spectroscopy to check their suitability for opto-electronic applications. Time-dependent DFT (TD-DFT) calculations employing the PBE0 hybrid density functional combined with moderately sized def-TZVP basis set were shown to excellently reproduce the experimental absorption spectra of various 1,2-diphospholes. Frontier molecular orbital analysis reveals that HOMO and LUMO are mainly localized on the diphosphole ring and, to some extent, on the aryl moieties. The HOMO-LUMO energy gap can be easily tuned by variation of substituents introduced in para-positions of the aryl moieties and, to a lesser extent, by modification of the R group at phosphorus atom. As a result, both position and intensity of the absorption bands with highest wavelength are strongly influenced by the above structural changes. The UV-spectra simulations reveal that the introduction of donor groups like para-OMe, para-NMe2, and para-N(H)Ph, which are in n-π conjugation with the aryl moieties, should result in absorption of visible light by the corresponding 1,2-diphospholes, thus making them promising candidates for new functional materials.

A simple physical model for the simultaneous rationalisation of melting points and heat capacities of ionic liquids

The analysis of potential energy surfaces of ion pairs within the framework of an anharmonic oscillator model allows rationalization and prediction of melting points (T(mp)) and heat capacities (C(p)) of ionic liquids (ILs) comprising di- and trialkylimidazolium or tetraalkylphosphonium cations and weakly coordinating BF(4), PF(6), or Tf(2)N anions. Multiple short contacts between the counterions are demonstrated to be typical for the imidazolium based ILs. Differences in the types of contacts result in moderate changes of melting points of the ILs, comparable with differences in T(mp) experimentally determined for the same crystal. The theoretical evaluation of IL heat capacities additionally requires a consideration of conformational behaviour of the corresponding cations. A similar conformational composition of 1-butyl-3-methylimidazolium hexafluorophosphate and tetrafluoroborate at ambient temperature is demonstrated by the combined DFT-vibrational spectroscopy approach. A rough proportionality of C(p) to 1/T(mp) of ionic liquids is suggested, provided that the conformational composition of the ILs does not change on crystal-to-liquid transition.

The Mechanism of Citryl-Coenzyme A Formation Catalyzed by Citrate Synthase

The enzyme citrate synthase is used by all living cells to catalyze the first step of the citric acid cycle. In this work, we have investigated the enolization and condensation steps catalyzed by citrate synthase, using ab initio (B3LYP/def2-TZVP and MP2/aug-cc-pVDZ) quantum chemical/molecular mechanical hybrid potentials in conjunction with reaction-path-location algorithms and molecular dynamics free energy simulations. The results of the latter indicate that the catalytic His238 residue is in its neutral form, and also argue strongly for the presence of a water molecule in the enzymes catalytic center. Such a water is observed in some, but not all, of the experimentally resolved structures of the protein. The mechanism itself starts with an enolization that proceeds via an enolate intermediate rather than the enol form, which is much more unstable. This is in agreement with the results of other workers. For the condensation step, we investigated two mechanisms in which there is a direct nucleophilic attack of the enolate intermediate on the oxaloacetate carbonyl carbon, and found the one in which there is no proton transfer from the neighboring arginine to be preferred. Although this residue, Arg329, is not implicated directly in the reaction, it helps to stabilize the negative citryl-CoA formed during the condensation step.

New Method for the Preparation of Octathiotetraphosphetanes on the Basis of Elemental Phosphorus and Sulfur: Structure and Properties

Abstract New octathiotetraphosphetane ammonium salts are obtained based on the reaction of white phosphorus (Р4) and elemental sulfur with aliphatic mercaptans in the presence of amines (morpholine, methylmorpholine, pyrrolidine, and N,N-dimethylbenzylamine). The salts of octathiotetraphosphetane are characterized by IR/Raman spectroscopy. Several common IR and Raman bands can be used as structural markers for establishing the structures of [P4S8]4− anion in new compounds.

Conjugation effects and optical spectra of 1,2-diphosphole cycloadducts

Quantum chemical calculations and a comparative analysis of Raman spectra of 3,4,5-triphenyl-1-propyl-1,2-diphosphole (1), anti-endo-4,7,8,9-tetraphenyl-10-propyl-4-aza-1,10-diphosphatricyclo[5.2.1.02,6]deca-8-ene-3,5-dione (2) and 1,2,6,7-tetraphospha-3,4,5,8,9,10-hexaphenyltricyclo[5.3.0.02,6]deca-3,9-diene (3) made it possible to explain considerable differences in the UV absorption spectra of these compounds. The phenyl groups in the compounds under study, despite the steric factor, are conjugated with the π-system of the heterocycle, which in the case of diphosphole 1 comprises π-electrons of the C=C and P=C bonds. The disturbance of this diene system in molecules 2 and 3 decreases the effective length of conjugation of phenyl groups with the attached double bonds of the phosphorus-containing ring, that results in the hypsochromic shift of the π—π* electron transition bands in the UV absorption spectrum from 411 to 312 nm. The formation in molecule 3 of the four-membered ring P4, which is a new chromophore group, leads to the appearance of an additional absorption band with the maximum at ∼342 nm.

Coordination Features of P,S-Ligands Based on the Phosphorus Derivatives with I and Viii Group Metals

Abstract Continuing the study of the coordination ability of P,S-ligands, we have investigated the behavior of some P(IV)-S-phosphorus derivatives, in particular, trialkyltetrathiophosphates (R = i-Pr, Bu) and piperidinium and triethylammonium salts of octathiotetraphosphetane in reaction with Cu(I), Ag(I), Co(II), and Fe(II) halides. The series of complexes were obtained and characterized by the X-ray single crystal diffraction and IR/Raman spectroscopy. GRAPHICAL ABSTRACT

IR and NMR spectra, intramolecular hydrogen bonding and conformations of para-tert-butyl-aminothiacalix[4]arene in solid state and chloroform solution.

It is demonstrated that dissolution of aminothiacalix[4]arene in chloroform results in transformation of 1,3-alternate conformation, adopted in single-crystal and bulk polycrystalline solids, to the pinched-cone form. This conformer is stabilised by the intramolecular hydrogen bonds of two distal amino-groups acting as H-donors with another two amino moieties that appear as H-acceptors. The H-bonds cause quite small (ca. 10-20 cm(-1)) red shift of the IR bands of the NH(2) stretching vibrations, which suggests rather weak NHcdots, three dots, centeredN hydrogen bonding. This latter is sufficient to stabilize the pinched-cone conformation in the chloroform solution, but the energy gap between the pinched-cone and other conformations is small, and solid-state intermolecular forces easily overcome it, leading to realisation of the 1,3-alternate conformer. The comparison of the DFT computed and experimental vibrational and NMR spectra demonstrates good quality of present quantum-chemical computations, allows complete interpretation of the spectra and reveals simple IR and NMR spectroscopic markers of the conformers of aminothiacalix[4]arenes.

IR and Raman spectra, hydrogen bonds, and conformations of N -(2-hydroxyethyl)-4,6-dimethyl-2-oxo-1,2-dihydropyrimidine (drug Xymedone)

Hydrogen bonds and structure of drug Xymedone in different phase and aggregate states were studied using IR and Raman spectroscopy, IR microscopy, quantum chemical calculations (B3LYP/6-31G*), X-ray powder diffractometry, and DSC and TGA methods. It was found that the synthesized specimen of Xymedone powder is a mixture of two gauche-conformers. First one is bound by intermolecular hydrogen bonds and second one is stabilized by an intramolecular hydrogen bond. Upon the dissolution of Xymedone the conformational equilibrium shifted in favor of conformers of the first or second type depending on the solvent nature.