Electronic states of general mixed crystals

Up to now molecular-orbital calculations of the electronic states of linear mixed crystals have been concerned only with binary systems such as AB, AB₂, and A₂B₂. The purpose of the present treatment is to extend this work to crystals whose elementary cells contain any number of different atoms in any ordered sequence. The formulation of this general theory is based on the resolvent method. Although the approach enables the general properties of delocalized and localized states to be discussed, the more simple cases already solved in the literature can still be easily derived from the general equations. Furthermore, the classification of Tamm and Shockley states retains its significance, even when other kinds of states can occur and various transitions between the clear cut cases can exist. As in earlier investigations, the chemisorption states are related to surface states and have similar properties. The resolvent method is summarized in the Appendix and its connection with the partition technique is shown.     

Solvation and structural effects on the stability of 10-X-2 ate-complexes: a computational study

The structures and energies of a variety of 10-X-2 ate-complexes derived from reaction of alkyllithiums and aryllithiums with the corresponding organohalides have been studied at the B3LYP/6-31+2G** theoretical level. The results of the calculations, which are in good agreement with the available experimental data, indicate that diaryl ate-complexes are more stable than their dialkyl counterparts. Fluorine substitution was found to confer substantial stability to both diaryl and dialkyl ate-complexes, and the calculations suggest that perfluoro dialkyl 10-X-2 ate-complexes should be experimentally observable species. One of the most important factors contributing to stability of a 10-X-2 ate-complex is removal of the formally cationic lithium from the vicinity of the ate-anion via coordination with a Lewis basic solvent.     

Triplet states in isotopically mixed anthracene crystals: High resolution optical spectroscopy

The triplet O,O transitions of guest and host in isotopically mixed anthracene crystals of various compositions (A-h₁₀, ¹³C-monosubstituted A-h₁₀, A-d₁h₉, A-d₂h_g in A-d₁₀ and A-d₁₀ in A-h₁₀) have been investigated using high resolution laser excitation spectroscopy. The guest aggregate spectra have been studied in polarized light as a function of guest concentration up to 15%. The analyses allow us to identify the monomer, dimer and trimer lines. From the dimer splittings the dominant resonance pair interactions are dedu The comparison of different mixed crystal systems with guest levels below and above the host exciton band reveals that quasiresonance and superexchange corrections are of minor importance. The experimental resonance pair interactions are used to calculate the triplet exciton band structure of anthracen and the observed guest polarization behaviour is interpreted quantitatively by the Rashba effect. Finally, the lower Davydov component of the host is s and broadened with increasing guest concentration. The shift is discussed using a theoretical model of Lifshitz.     

Two-photon excitation into low-energy singlet states of anthracene in mixed crystals

The two-photon excitation spectrum of the first excited state of anthracene in fluorene and biphenyl at 4.2 K has been measured. Intensity is induced into the origin by the static dipole moment of fluorene, and into b_1u vibrons through coupling to an A_g state near 29400 cm⁻¹; the nature of this A_g state is discussed.     

Localized excited triplet states in mixed charge-transfer single crystals: formation of excited multicomplexes

Single crystals of charge-transfer (CT) complexes between tetracyanobenzene as acceptor and different aromatic donors were doped with guest donors. The molecular arrangements of the guest CT complexes forming triple energy traps in the host crystal were determined from the triplet ESR spectra of the traps. A method for the determination of relative charge-transfer triplet energies is proposed. Extended electron delocalization over more than one donor-acceptor pair has been found.     

Solvation in mixed aqueous solvents from a thermodynamic cycle approach

A novel approach is presented for interpreting and potentially predicting values of the isothermal, isobaric transfer free energy, entropy, and enthalpy (Deltamicrotr2, Deltastr2, and Deltahtr2) for a solute between water and water-cosolvent mixtures. The approach explicitly accounts for volumetric properties of the solvent and solute (the equation of state, EoS) and casts the overall transfer process as a thermodynamic cycle with two stages: (1) isothermal solvent exchange from pure water to the cosolvent composition of interest at fixed mass density; (2) isothermal expansion or compression at the final solvent composition to recover the pressure of the initial state. Using molecular simulations with methane as the solute, the analysis is illustrated over a wide range of cosolvent concentrations for sorbitol-, ethanol-, and methanol-water binary mixtures. The EoS contribution semiquantitatively or quantitatively captures Deltamicrotr2, Deltastr2, and Deltahtr2 in almost all cases tested, highlighting the importance of considering the effects of changes in solvent density on the overall transfer process. The results also indicate that apolar solvation at these length scales is dominated by the work of cavity formation across a range of cosolvent species and concentrations.     

Atypical protonation states in the active site of HIV-1 protease: a computational study

The HIV protease (HIVP) is a prominent example for successful structure-based drug design. Besides its pharmaceutical impact, it is a well-studied system for which, as experimentally evidenced, protonation changes in the active site occur upon ligand binding. Therefore, it serves as an ideal candidate for a case study using our newly developed partial charge model, which was optimized toward the application of Poisson-Boltzmann based pK(a) calculations. The charge model suggests reliably experimentally determined protonation states in the active site of HIVP. Furthermore, we perform pKa calculations for two HIVP complexes with novel types of inhibitors developed and synthesized in our group. For these complexes, no experimental knowledge about the protonation states is given. For one of the compounds, containing a central pyrrolidine ring, the calculations predict that both catalytic aspartates should be deprotonated upon ligand binding.     

Nano structures of group 13-15 mixed heptamer clusters: a computational study

The structural and thermodynamic characteristics of lowest-energy structures of group 13-15 mixed heptamers in two distinct series [(HM)(k)(HM')(l)(NH)(7)] (M, M' = B, Al, Ga and k + l = 7) and [(HGa)(7)(YH)(m)(Y'H)(n)] (Y,Y' = N, P, As and m + n = 7) have been systematically investigated using the density functional approach. Our main goal is to get knowledge of the preferential bonding patterns of the first three rows of group 13-15 elements for the construction of mixed heptameric clusters. Structural parameters, thermodynamic properties of oligomerization reaction, band gaps, and dipole moments of the 18 lowest-energy structures of the studied heptamers in each series are compared to their corresponding binary parents, that is, [(HM)(7)(NH)(7)] and [(HGa)(7)(YH)(7)]. The stability of different isomer structures is discussed to reveal the competitiveness of group 13 and 15 bonding. Mixed heptamers are predicted to be thermodynamically more stable compared to a mixture of monomers. However, the favorability for the generation of mixed heptamers strongly depends on the nature of inserted metal and nonmetal pairs of group 13-15. Moreover, it is found that among all studied heptamers the smaller band gaps correspond to arsenic containing species which are close to the semiconducting regime, around 4.62-4.98 eV.     

A computational study of lithium enolate mixed aggregates

Ab initio calculations were performed to examine the formation of mixed dimer and trimer aggregates between the lithium enolate of acetaldehyde (lithium vinyloxide, LiOV) and lithium chloride, lithium bromide, and lithium amides. Gas-phase calculations showed that in the absence of solvation effects, the mixed trimer 2LiOV.LiX is the most favored species. Solvation in ethereal solvents was modeled by a combination of specific coordination of dimethyl ether ligands on each lithium and "dielectric solvation" (DSE, dielectric solvation energies), immersion of each molecule in a cavity within a continuous dielectric having the dielectric constant of THF at room temperature. DSE is less important for aggregates (reduced dipoles or quadrupoles) than monomers (dipoles) and is also reduced for the coordinatively solvated species. Both solvation terms reduce the exothermicity of aggregation. In many cases, lithium salts that are three- rather than four-coordinate have significant populations at room temperature. The strongly basic lithium amides prefer mixed aggregates with weaker bases than homoaggregates. The computational results are consistent with the limited experimental data available.     

Multipodal coordination of a tetracarboxylic crown ether with NH4(+): a vibrational spectroscopy and computational study

The elucidation of the structural requirements for molecular recognition by the crown ether (18-crown-6)-2,3,11,12-tetracarboxylic acid (18c6H(4)) and its cationic complexes constitutes a topic of current fundamental and practical interest in catalysis and analytical sciences. The flexibility of the central ether ring and its four carboxyl side arms poses important challenges to experimental and theoretical approaches. In this study, infrared action vibrational spectroscopy and quantum mechanical computations are employed to characterize the conformational structure of the isolated gas phase complex formed by the 18c6H(4) host with NH(4)(+) as guest. The results show that the most stable gas-phase structure is a barrel-like conformation sustained by tetrapodal H-bonding of the ammonia cation with two C=O side groups and with four oxygen atoms of the ether ring in a bifurcated arrangement. Interestingly, a similar structure had been proposed in previous crystallographic studies. The experiment also provides evidence for a significant contribution of a higher energy bowl-like conformer with features resembling those adopted by 18c6H(4) in the analogous complexes with secondary amines. Such a conformation displays H-bonding between confronted side carboxyl groups and tetrapodal binding of the NH(4)(+) with the ether ring and with one C=O group. Structures involving even more extensive intramolecular H-bonding in the 18c6H(4) substrate are found to lie higher in energy and are ruled out by the experiment.     

Degradation mechanism of methyl mercury selenoamino acid complexes: a computational study

Density functional theory (DFT) calculations have been carried out on the possible degradation/demethylation mechanism of methyl mercury (CH(3)Hg(+)) complexes with free cysteine and seleonocysteine. The binding of CH(3)Hg(+) ions with one (seleno)amino acid is thermodynamically favorable. However, the binding with another acid molecule is a highly unfavorable process. The CH(3)Hg-(seleno)cysteinate then degrades to bis(methylmercuric)sulphide (selenide for the Se-containing complex) which in turn forms dimethyl mercury and HgS/HgSe, the latter being precipitated out as nanoparticles. The dimethyl mercury interacts with water molecules and regenerates the CH(3)HgOH precursor. The calculated free energies of formation confirm the thermodynamic feasibility of every intermediate step of the degradation cycle and fully support earlier experimental results. In completing the cycle, one unit of mercury precipitates out from two units of sources, and thereby Se antagonizes the Hg toxicity. The degradation of CH(3)Hg-L-cysteinate is thermodynamically more favorable than the formation of CH(3)Hg-L-cysteinate. The preferred degradation of the CH(3)Hg-L-cysteinate suggests that another mechanism for CH(3)Hg to cross the blood-brain barrier should exist.     

Packing effects in organometallic compounds: A study of five mixed crystals

A series of cocrystals of an organometallic tungsten complex with organic small molecules has been prepared and studied by single-crystal X-ray diffraction. Comparison of the five structures thus obtained allowed the measurement of the effects of the crystal environment on the molecular structure under investigation. Not only soft torsional degrees of freedom but also bond angles, the point symmetry, and other geometrical features of the reference molecule have been found to vary significantly. It is concluded that parameters commonly ascribed to themolecular structure may in reality depend onintermolecular interactions.Dedicated to Prof. Dr. J. Strähle on the occasion of his 60th birthday.     

Solvation of p-coumaric acid in water

The photoactive yellow protein (PYP) is an important model protein for many (photoactive) signaling proteins. Key steps in the PYP photocycle are the isomerization and protonation of its chromophore, p-coumaric acid (pCA). In the ground state of the protein, this chromophore is in the trans configuration with its phenolic oxygen deprotonated. For this paper, we studied four different configurations of pCA solvated in water with ab initio molecular dynamics simulations as implemented in CP2K/Quickstep. We researched the influence of the protonation and isomerization state of pCA on its hydrogen-bonding properties and on the Mulliken charges of the atoms in the simulation. The chromophore isomerization state influenced the hydrogen-bonding less than its protonation state. In general, more charge yielded a higher hydrogen-bond coordination number. Where deprotonation increases both the coordination number and the residence time of the water molecules around the chromophore, protonation showed a somewhat lower coordination number on two of the three pCA oxygens but much higher residence times on all of them. This could be explained by the increased polarization of the OH groups of the molecule. The presence of the chromophore also influenced the charge and polarization of the water molecules around it. This effect was different in the four systems studied and mainly localized in the first solvation shell. We also performed a proton-transfer reaction from hydronium through various other water molecules to the chromophore. In this small charge-separated system, the protonation occurred within 6.5 ps. We identified the transition state for the final step in this protonation series.     

Stereodynamics of bond rotation in tertiary 1-naphthoic acid amides: a computational study

Computations sho that independent N-CO rotation is not possible in N,N-diethyl-1-naphthamide, and that the coalescence signal corresponding to methyl equivalence observed in the VT NMR spectrum of this system is caused by a complex process whose rate-determining step implies concerted N-CO, Ar-CO, and ethyl rotations. The calculated Gibbs energy barriers for these processes in solution are in good agreement with the experimental values.     

Preparation, solid-state characterization, and computational study of a crown ether attached to a squaramide

[structure: see text] Crystals of a disecondary squaramide covalently linked to a crown ether presents a great variety of inter- and intramolecular nonbonded interactions including C-H/pi contacts, C-H...O and N-H...O hydrogen bonds, and pi-pi stacking between squaramide rings. Latter interaction, the stacking between squaramide rings, can be considered as an experimental evidence for the proposed aromaticity of squaramide when it is forming hydrogen bonds, either as acceptor or donor.     

Solvation structure of coronene-transition metal complex: a RISM-SCF study

Coronene (C(24)H(12)) is a flat polyaromatic hydrocarbon consisting of seven peri-fused benzene rings and attracts lots of attention as a fragment of graphene. Using a hybrid method of quantum chemistry and statistical mechanics called RISM-SCF, which is an alternative to QM/MM, the electronic structure and solvation structure of a coronene-transition metal complex were computed in a self-consistent manner. The binding of a ruthenium complex ([C(5)H(5)Ru](+)) was extensively studied, especially the changing of the solvation structure.     

Structure-energy relationship in barbituric acid: a calorimetric, computational, and crystallographic study

This paper reports the value of the standard (p(o) = 0.1 MPa) molar enthalpy of formation in the gas phase at T = 298.15 K for barbituric acid. The enthalpies of combustion and sublimation were measured by static bomb combustion calorimetry and transference (transpiration) method in a saturated N2 stream and a gas-phase enthalpy of formation value of -(534.3 +/- 1.7) kJ x mol(-1) was determined at T = 298.15 K. G3-calculated enthalpies of formation are in very good agreement with the experimental value. The behavior of the sample as a function of the temperature was studied by differential scanning calorimetry, and a new polymorph of barbituric acid at high temperature was found. In the solid state, two anhydrous forms are known displaying two out of the six hydrogen-bonding patterns observed in the alkyl/alkenyl derivatives retrieved from the Cambridge Crystallographic Database. The stability of these motifs has been analyzed by theoretical calculations. X-ray powder diffraction technique was used to establish to which polymorphic form corresponds to the commercial sample used in this study and to characterize the new form at high temperature.     

Radiation-induced reactions via the lowest excited states in cinnamic acid crystals

Radiation-induced reactions of cinnamic acid derivatives have been examined and compared with photoreactions in the crystalline state; all the reaction products were exactly the same as those of the photoreactions, indicating that the reactions proceed only via the lowest excited state to give [2 + 2] cycloadducts, E/Z isomerization products, or starting molecules.