Tzonka Mineva

Solvation effects on reaction profiles by the polarizable continuum model coupled with the Gaussian density functional method

An efficient version of the polarizable continuum model for solvation has been implemented in the Gaussian density‐functional‐based code called deMon. Solvation free energies of representative compounds have been calculated as a preliminary test. The hydration effects on the reaction profile of the Cl−+CH3Cl→ClCH3+Cl− reaction and the thermodynamics of the Menschutkin reaction have also been investigated. Finally, the conformational behavior of the 1,2‐diazene cis–trans isomerization process in water was examined. Comparisons between the results obtained and the available experimental data and previous theoretical computations have been made. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 290–299, 1998

Interaction between n-Alkane Chains: Applicability of the Empirically Corrected Density Functional Theory for Van der Waals Complexes.

The geometries, interaction energies, and vibrational frequencies of a series of n-alkane dimers up to dodecane have been calculated using density functional theory (DFT) augmented with an empirical dispersion energy term (DFT-D). The results obtained from this method for ethane to hexane dimers are compared with those provided by the MP2 level of theory and the combined Gaussian-3 approach with CCSD(T) being the highest correlation method [G3(CCSD(T))]. Two types of dimer isomers have been studied. The most stable isomers have the two carbon chains in parallel planes, whereas the second ones have the two carbon chains in the same plane. Butane is found to be the shortest carbon chain to form dimers with similar properties, that is, a constant average distance between the monomer carbon skeletons, a similar increment per CH2 unit for the dimer interaction energy, and comparable dimer symmetric stretching frequencies. The values and trends obtained from the DFT-D approach agree very well with those obtained from MP2 for the geometries and vibrational frequencies and from the G3(CCSD(T)) method for the energies, validating the use of DFT-D for the study of large hydrocarbon complexes.

Investigation of the interface in silica-encapsulated liposomes by combining solid state NMR and first principles calculations.

In the context of nanomedicine, liposils (liposomes and silica) have a strong potential for drug storage and release schemes: such materials combine the intrinsic properties of liposome (encapsulation) and silica (increased rigidity, protective coating, pH degradability). In this work, an original approach combining solid state NMR, molecular dynamics, first principles geometry optimization, and NMR parameters calculation allows the building of a precise representation of the organic/inorganic interface in liposils. {(1)H-(29)Si}(1)H and {(1)H-(31)P}(1)H Double Cross-Polarization (CP) MAS NMR experiments were implemented in order to explore the proton chemical environments around the silica and the phospholipids, respectively. Using VASP (Vienna Ab Initio Simulation Package), DFT calculations including molecular dynamics, and geometry optimization lead to the determination of energetically favorable configurations of a DPPC (dipalmitoylphosphatidylcholine) headgroup adsorbed onto a hydroxylated silica surface that corresponds to a realistic model of an amorphous silica slab. These data combined with first principles NMR parameters calculations by GIPAW (Gauge Included Projected Augmented Wave) show that the phosphate moieties are not directly interacting with silanols. The stabilization of the interface is achieved through the presence of water molecules located in-between the head groups of the phospholipids and the silica surface forming an interfacial H-bonded water layer. A detailed study of the (31)P chemical shift anisotropy (CSA) parameters allows us to interpret the local dynamics of DPPC in liposils. Finally, the VASP/solid state NMR/GIPAW combined approach can be extended to a large variety of organic-inorganic hybrid interfaces.

Correction for dispersion and Coulombic interactions in molecular clusters with density functional derived methods: Application to polycyclic aromatic hydrocarbon clusters

The density functional based tight binding (DFTB) is a semiempirical method derived from the density functional theory (DFT). It inherits therefore its problems in treating van der Waals clusters. A major error comes from dispersion forces, which are poorly described by commonly used DFT functionals, but which can be accounted for by an a posteriori treatment DFT-D. This correction is used for DFTB. The self-consistent charge (SCC) DFTB is built on Mulliken charges which are known to give a poor representation of Coulombic intermolecular potential. We propose to calculate this potential using the class IV/charge model 3 definition of atomic charges. The self-consistent calculation of these charges is introduced in the SCC procedure and corresponding nuclear forces are derived. Benzene dimer is then studied as a benchmark system with this corrected DFTB (c-DFTB-D) method, but also, for comparison, with the DFT-D. Both methods give similar results and are in agreement with references calculations (CCSD(T) and symmetry adapted perturbation theory) calculations. As a first application, pyrene dimer is studied with the c-DFTB-D and DFT-D methods. For coronene clusters, only the c-DFTB-D approach is used, which finds the sandwich configurations to be more stable than the T-shaped ones.

Density Functional Theory-Based Conformational Analysis of a Phospholipid Molecule (Dimyristoyl Phosphatidylcholine)

The conformational space of the dimyristoyl phosphatidylcholine (DMPC) molecule has been studied using density functional theory (DFT), augmented with a damped empirical dispersion energy term (DFT-D). Fourteen ground-state isomers have been found with total energies within less than 1 kcal/mol. Despite differences in combinations of their torsion angles, all these conformers share a common geometric profile, which includes a balance of attractive, repulsive, and constraint forces between and within specific groups of atoms. The definition of this profile fits with most of the structural characteristics deduced from measured NMR properties of DMPC solutions. The calculated vibrational spectrum of the molecule is in good agreement with experimental data obtained for DMPC bilayers. These results support the idea that DMPC molecules preserve their individual molecular structures in the various assemblies.

14N and 81Br quadrupolar nuclei as sensitive NMR Probes of n-alkyltrimethylammonium bromide crystal structures. An experimental and theoretical study.

This is the first time a comprehensive study has been carried out on n-alkyltrimethylammonium bromide salts using (14)N and (81)Br solid state NMR, X-ray diffraction, and theoretical calculations. The investigation represents a necessary step toward further (14)N and (81)Br NMR characterization of the environment of cationic and anionic groups in materials, accounting for the amphiphilic properties of cationic surfactants. The NMR spectra of five C(x)H(2x+1)(CH(3))(3)N(+)Br(-) polycrystalline samples with different n-alkyl chain lengths (x = 1, 12, 14, 16, 18) were recorded and modeled. The (14)N and (81)Br quadrupolar coupling interaction parameters (C(Q), eta(Q)) were also estimated from spectrum modeling and from computer simulation. The obtained results were discussed in depth making use of the experimental and reoptimized crystal structures. In the study, both (14)N and (81)Br nuclei were found to be sensitive probes for small structural variations. The parameters which influence the NMR properties the most are mobility, deviation of C-N-C bond angles from T(d) angles, and variations in r(N-Br) distances.

Vibrational characterization of ethylene adsorption and its thermal evolution on Si(001)-(2×1): Identification of majority and minority species

The vibrational and structural properties of a single-domain Si(001)-(2 x 1) surface upon ethylene adsorption have been studied by density functional cluster calculations and high-resolution electron energy loss spectroscopy. The detailed analysis of the theoretically and the experimentally determined vibrational frequencies reveals two coexisting adsorbate configurations. The majority species consist of ethylene molecules which are di-sigma bonded to the two Si atoms of a single Si-Si dimer. The local symmetry of this adsorption complex is reduced to C(2) for ethylene saturation coverage as determined by surface selection rules for the vibrational excitation process. The symmetry reduction includes the rotation of the C-C bond around the surface normal and the twist of the methylene groups around the C-C axis. Experimentally, 17 ethylene-derived modes are found and assigned for the majority and the minority species based on a comparison with calculated vibrational frequencies. The minority species which can account up to 14% of the total ethylene coverage is spectroscopically identified for the first time. It is assigned to ethylene molecules di-sigma bonded to two adjacent Si-Si dimers (in an end-bridge configuration). One part of the minority species desorbs molecularly at 665 K, about 50 K higher than the majority species, whereas the remaining part dissociates to adsorbed acetylene at temperatures around 630 K. For the latter, a di-sigma end-bridge like bonding configuration is proposed based on a comparison with vibrational data for adsorbed acetylene on Si(100)-(2 x 1).

Drug nano-domains in spray-dried ibuprofen–silica microspheres

Silica microspheres encapsulating ibuprofen in separated domains at the nanometre scale are formed by spray-drying and sol-gel processes. A detailed (1)H and (13)C NMR study of these microspheres shows that ibuprofen molecules are mobile and are interacting through hydrogen bonds with other ibuprofen molecules. (1)H magnetisation exchange NMR experiments were employed to characterize the size of the ibuprofen domains at the nanometre scale. These domains are solely formed by ibuprofen, and their diameters are estimated to be ∼40 nm in agreement with TEM observations. The nature and formation of these particular texture and drug dispersion are discussed.

Lipid Thermodynamics: Melting is Molecular

[*] Dr. S. Krishnamurty, Dr. T. Mineva, Dr. S. Begu, Prof. J.M. Devoisselle, Dr. A. Goursot ICGM, UMR 5253 CNRS, Ecole de Chimie de Montpellier, 34296 Montpellier, France Dipl.Chem. M. Stefanov Institute of Catalysis, Bulgarian Academy of Sciences, Sofia, Bulgaria Dr. R. Zhu, Prof. D.R. Salahub Department of Chemistry and Institute for Biocomplexity and Informatics, University of Calgary, 2500 University Drive NW, Calgary, Alberta, Canada T2N 1N4 Fax: (+1) 440.... Email: dsalahub@ucalgary.ca

Density functional potential-energy hypersurface and reactivity indices in the isomerization of X3H+ (X = O, S, Se, Te)

Potential-energy hypersurfaces of protonated O 3 , S 3 , Se 3 and Te 3 systems have been investigated using the gradient-corrected density functional approximation. Both the open (C 2v ) and cyclic (D 3h ) X 3 structures have been considered in the protonation process. Results show that the relative stability of the cyclic form with respect to the trans-open one increases on going from O 3 to Se 3 and reverses for Te 3 . The calculated density functional potential-energy surfaces are consistent with those (for ozone and thiozone) obtained at the ab initio correlated level of theory. The order of stability and reactivity indices has been rationalized on the basis of orbital hardness values along the reaction paths.