Showing papers in "ChemPhysChem in 2006"
TL;DR: Several systems of seemingly quite different nature and of increasing complexity, such as Grotthuss diffusion in water, excited-state proton-transfer in solution, phase transitions in ice, and protonated water networks in the membrane protein bacteriorhodopsin, are discussed in the realms of a unifying viewpoint.
Abstract: In the last decade, ab initio simulations and especially Car-Parrinello molecular dynamics have significantly contributed to the improvement of our understanding of both the physical and chemical properties of water, ice, and hydrogen-bonded systems in general. At the heart of this family of in silico techniques lies the crucial idea of computing the many-body interactions by solving the electronic structure problem "on the fly" as the simulation proceeds, which circumvents the need for pre-parameterized potential models. In particular, the field of proton transfer in hydrogen-bonded networks greatly benefits from these technical advances. Here, several systems of seemingly quite different nature and of increasing complexity, such as Grotthuss diffusion in water, excited-state proton-transfer in solution, phase transitions in ice, and protonated water networks in the membrane protein bacteriorhodopsin, are discussed in the realms of a unifying viewpoint.
775 citations
TL;DR: The many studies that have demonstrated the enhanced syntheses of nanoporous oxides are reviewed and proposals to explain differences in microwave reactions are analyzed, as it explains the discrepancies between many microwave studies.
Abstract: Studies in the last decade suggest that microwave energy may have a unique ability to influence chemical processes. These include chemical and materials syntheses as well as separations. Specifically, recent studies have documented a significantly reduced time for fabricating zeolites, mixed oxide and mesoporous molecular sieves by employing microwave energy. In many cases, microwave syntheses have proven to synthesize new nanoporous structures. By reducing the times by over an order of magnitude, continuous production would be possible to replace batch synthesis. This lowering of the cost would make more nanoporous materials readily available for many chemical, environmental, and biological applications. Further, microwave syntheses have often proven to create more uniform (defect-free) products than from conventional hydrothermal synthesis. However, the mechanism and engineering for the enhanced rates of syntheses are unknown. We review the many studies that have demonstrated the enhanced syntheses of nanoporous oxides and analyze the proposals to explain differences in microwave reactions. Finally, the microwave reactor engineering is discussed, as it explains the discrepancies between many microwave studies.
559 citations
TL;DR: A critical review of recent FRET investigations using luminescent QDs that focused on addressing basic fundamental questions, as well as developing targeted applications with potential use in biology, including sensor design and protein conformation studies are provided.
Abstract: Forster resonance energy transfer (FRET), which involves the nonradiative transfer of excitation energy from an excited donor fluorophore to a proximal ground-state acceptor fluorophore, is a well-characterized photophysical tool. It is very sensitive to nanometer-scale changes in donor-acceptor separation distance and their relative dipole orientations. It has found a wide range of applications in analytical chemistry, protein conformation studies, and biological assays. Luminescent semiconductor nanocrystals (quantum dots, QDs) are inorganic fluorophores with unique optical and spectroscopic properties that could enhance FRET as an analytical tool, due to broad excitation spectra and tunable narrow and symmetric photoemission. Recently, there have been several FRET investigations using luminescent QDs that focused on addressing basic fundamental questions, as well as developing targeted applications with potential use in biology, including sensor design and protein conformation studies. Herein, we provide a critical review of those developments. We discuss some of the basic aspects of FRET applied to QDs as both donors and acceptors, and highlight some of the advantages offered (and limitations encountered) by QDs as energy donors and acceptors compared to conventional dyes. We also review the recent developments made in using QD bioreceptor conjugates to design FRET-based assays.
541 citations
TL;DR: Several findings show that the superoxide ion does not undergo transformations into charged atomic oxygen at the surface, and represents a dead-end form of low-temperature oxygen adsorption on reduced metal oxide.
Abstract: Tin dioxide is the most commonly used material in commercial gas sensors based on semiconducting metal oxides. Despite intensive efforts, the mechanism responsible for gas-sensing effects on SnO(2) is not fully understood. The key step is the understanding of the electronic response of SnO(2) in the presence of background oxygen. For a long time, oxygen interaction with SnO(2) has been treated within the framework of the "ionosorption theory". The adsorbed oxygen species have been regarded as free oxygen ions electrostatically stabilized on the surface (with no local chemical bond formation). A contradiction, however, arises when connecting this scenario to spectroscopic findings. Despite trying for a long time, there has not been any convincing spectroscopic evidence for "ionosorbed" oxygen species. Neither superoxide ions O(2)(-), nor charged atomic oxygen O,(-) nor peroxide ions O(2)(2-) have been observed on SnO(2) under the real working conditions of sensors. Moreover, several findings show that the superoxide ion does not undergo transformations into charged atomic oxygen at the surface, and represents a dead-end form of low-temperature oxygen adsorption on reduced metal oxide.
397 citations
376 citations
TL;DR: This Review first summarizes the currently available DNA tile toolboxes and further emphasizes recent developments toward self-assembling DNA nanostructures with increasing complexity.
Abstract: DNA tile based self-assembly provides an attractive route to create nanoarchitectures of programmable patterns. It also offers excellent scaffolds for directed self-assembly of nanometer-scale materials, ranging from nanoparticles to proteins, with potential applications in constructing nanoelectronic/nanophotonic devices and protein/ligand nanoarrays. This Review first summarizes the currently available DNA tile toolboxes and further emphasizes recent developments toward self-assembling DNA nanostructures with increasing complexity. Exciting progress using DNA tiles for directed self-assembly of other nanometer scale components is also discussed.
367 citations
324 citations
TL;DR: This finding is in agreement with DFT (gas phase) calculations, which show a preference for ion pairs H-bonded via C(2)H as a result of the acidic C( 2)H bond.
Abstract: The structures and ion-pair formation in the ionic liquid (IL) 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide are studied by a combination of FTIR measurements and DFT calculations. We could clearly distinguish imidazolium cations that are completely H-bonded to anions from those that are single H-bonded in ion pairs. Ion-pair formation already occurs in the neat IL and rises with temperature. Ion-pair formation is strongly promoted by dilution of the IL in chloroform. In these weakly polar environments ion pairs H-bonded via C(2)H are strongly favored over those H-bonded via C(4,5)H. This finding is in agreement with DFT (gas phase) calculations, which show a preference for ion pairs H-bonded via C(2)H as a result of the acidic C(2)H bond.
294 citations
TL;DR: This Review discusses some of the topics of highest interest in current smectic liquid crystal research, and address application-relevant research (de Vries-type tilting transitions without defect generation and high-tilt antiferroelectric liquid crystals with perfect dark state) as well as more curiosity-driven research.
Abstract: Interest in the smectic liquid-crystalline state of matter received a substantial boost with the discovery by Meyer in the mid-1970s that a chiral smectic C (SmC*) phase exhibits a spontaneous electric polarization, and with the subsequent demonstration by Clark and Lagerwall of the surface-stabilized SmC* ferroelectric liquid crystal at the beginning of the 1980s. Since then, chiral smectic phases and their plethora of polar effects have dominated the research in this field, which today has reached a mature state where the first commercial microdisplay applications are now shipping in millions-per-year quantities. In this Review we discuss some of the topics of highest interest in current smectic liquid crystal research, and address application-relevant research (de Vries-type tilting transitions without defect generation and high-tilt antiferroelectric liquid crystals with perfect dark state) as well as more curiosity-driven research (the nature and origin of the chiral smectic C subphases and their intermediate frustrated states between ferro- and antiferroelectricity).
285 citations
TL;DR: A combination of atomic force microscopy imaging, force measurements, confocal fluorescence imaging and two-focus scanning fluorescence correlation spectroscopy to obtain structural and dynamical information about this model membrane system is presented.
Abstract: Dioleoylphosphatidylcholine/sphingomyetin/cholesterol (DOPC/ SM/cholesterol) model membranes exhibit liquid-liquid phase separation and therefore provide a physical model for the putative liquid-ordered domains present in cells. Here we present a combination of atomic force microscopy (AFM) imaging, force measurements, con focal fluorescence imaging and two-focus scanning fluorescence correlation spectroscopy (two-focus SFCS) to obtain structural and dynamical information about this model membrane system. Partition coefficients and diffusion coefficients in the different phases were measured with two-focus SFCS for numerous fluorescent lipid analogues and proteins, while being directly related to the lateral organization of the membrane and Its mechanical properties probed by AFM. Moreover we show how the combination of these different approaches is effective in reducing artifacts resulting from the use of a single technique.
206 citations
TL;DR: It is demonstrated via voltammetric and X-ray photoelectron spectroscopy (XPS) analysis that oxygenated species formed at edge plane sites/defects decrease the electron transfer kinetics of ferrocyanide but that the rates for potassium hexachloroiridate(III), hexaammineruthenium(III) chloride and TMPD are insensitive to the oxygenatedspecies.
Abstract: The electron transfer kinetics of ferrocyanide, potassium hexachloroiridate(III), hexaammineruthenium(III) chloride, and N,N,N',N'-tetramethyl-p-phenylenediamine (TMPD) have been examined at basal plane and edge plane pyrolytic graphite electrodes which have been allowed to oxidise in air for various periods of time. It is demonstrated via voltammetric and X-ray photoelectron spectroscopy (XPS) analysis that oxygenated species formed at edge plane sites/defects decrease the electron transfer kinetics of ferrocyanide but that the rates for potassium hexachloroiridate(III), hexaammineruthenium(III) chloride and TMPD are insensitive to the oxygenated species. The behaviour of the ferro-/ferricyanide couple contrasts with that seen on single-walled carbon nanotubes where oxygenation of the tube ends is known to speed up the electron transfer kinetics (A. Chou, T. Bocking, N. K. Singh, J. J. Gooding, Chem. Commun. 2005, 842); the possible reasons for this contrasting behaviour are discussed.
TL;DR: The results to date for the electrodeposition of metals and semiconductors in the most popular air- and water-stable ionic liquids are presented.
Abstract: In addition to their stability, the advantages of air- and water-stable ionic liquids over chloroaluminate ionic liquids, which were intensively investigated in the past, are that they are easy to dry, purify, and handle. Moreover, some of these ionic liquids have an extremely large electrochemical window of more than 5 V, and hence they give access to the electrodeposition of many metals and semiconductors, such as Ta, Ti, Si, and Ge. The results to date for the electrodeposition of metals and semiconductors in the most popular air- and water-stable ionic liquids are presented.
TL;DR: It was found that nanocrystalline aluminium can be electrodeposited in the ionic liquid [BMP]Tf2N saturated with AlCl3, and deposits obtained are generally uniform, dense, shining, and adherent with very fine crystallites in the nanometer size regime.
Abstract: The present work shows, for the first time, a comparative experimental study on the electrodeposition of aluminium in three different water and air stable ionic liquids, namely 1-butyl-1-methylpyrrolidinium-bis(trifluoromethylsulfonyl)imide ([BMP]Tf2N), 1-ethyl-3-methylimidazolium-bis(trifluoromethylsulfonyl)imide ([EMIm] Tf2N), and trihexyl-tetradecyl-phosphoniumbis(trifluoromethylsulfonyl)imide (P(14,6,6,6) Tf2N). The ionic liquids [BMP]Tf2N and [EMIm]Tf2N show biphasic behaviour in the AlCl3 concentration range from 1.6 to 2.5 mol L(-1) and 2.5 to 5 mol L(-1), respectively. The biphasic mixtures become monophasic at temperatures >/=80 degrees C. It was found that nanocrystalline aluminium can be electrodeposited in the ionic liquid [BMP]Tf2N saturated with AlCl3. The deposits obtained are generally uniform, dense, shining, and adherent with very fine crystallites in the nanometer size regime. However, coarse cubic-shaped aluminium particles in the micrometer range are obtained in the ionic liquid [EMIm]Tf2N. In this liquid the particle size significantly increases as the temperature rises. A very thin, mirrorlike aluminium film containing very fine crystallites of about 20 nm is obtained in the ionic liquid [trihexyl-tetradecyl-phosphonium]Tf(2)N at room temperature. At 150 degrees C, the average grain size is found to be 35 nm.
TL;DR: DFT predictions of the energetics support the experimental observation that the reduced surfaces are energetically more favorable than the unreduced surfaces for oxygen adsorption and reduction.
Abstract: Interactions between O(2) and CeO(2) are examined experimentally using in situ Raman spectroscopy and theoretically using density-functional slab-model calculations. Two distinct oxygen bands appear at 825 and 1131 cm(-1), corresponding to peroxo- and superoxo-like species, respectively, when partially reduced CeO(2) is exposed to 10 % O(2). Periodic density-functional theory (DFT) calculations aid the interpretation of spectroscopic observations and provide energetic and geometric information for the dioxygen species adsorbed on CeO(2). The O(2) adsorption energies on unreduced CeO(2) surfaces are endothermic (0.91
TL;DR: The results indicate that the interaction between the electronegative oxygen atoms of the oxyethylene units in TX-100 and the electropositive imidazolium ring may be the driving force for the solubilization of bmimBF4 into the core of the TX- 100 aggregates, suggesting the formation of IL/O microemulsions.
Abstract: The ionic liquid (IL) 1-butyl-3-methylimidazolium tetrafluoroborate (bmimBF4) forms nonaqueous microemulsions with p-xylene, with the aid of the nonionic surfactant TX-100. The phase behavior of the ternary system is investigated, and three microregions of the microemulsions-ionic liquid-in-oil (IL/O), bicontinuous, and oil-in-ionic liquid (O/IL)-are identified by conductivity measurements, according to percolation theory. On the basis of a phase diagram, a series of IL/O microemulsions are chosen and characterized by dynamic light scattering (DLS). The size of aggregates increases on increasing the amount of added polar component (bmimBF(4)), which is a similar phenomenon to that observed for typical water-in-oil (W/O) microemulsions, suggesting the formation of IL/O microemulsions. The microstructural characteristics of the microemulsions are investigated by FTIR and 1H NMR spectroscopy. The results indicate that the interaction between the electronegative oxygen atoms of the oxyethylene (OE) units in TX-100 and the electropositive imidazolium ring may be the driving force for the solubilization of bmimBF4 into the core of the TX-100 aggregates. In addition, the micropolarity of the microemulsions is investigated by using methyl orange (MO) as a UV/Vis spectroscopic probe. A relatively constant polarity of the microemulsion droplets is obtained in the IL microemulsion. Finally, a plausible structure for the IL/O microemulsion is presented.
TL;DR: The use of a trifluorotris(pentafluoroethyl)phosphate-based ionic liquid, specifically, as supporting electrolyte in acetonitrile solutions affords a wider anodic window, which is attributed to the high stability of the anionic component of these intrinsically conductive and thermally robust compounds.
Abstract: The electrochemical windows of acetonitrile solutions doped with 0.1 M concentrations of several ionic liquids were examined by cyclic voltammetry at gold and platinum microelectrodes. These results were compared with those observed in the commonly used 0.1 M tetrabutylammonium perchlorate/acetonitrile system as well as with neat ionic liquids. The use of a trifluorotris(pentafluoroethyl)phosphate-based ionic liquid, specifically, as supporting electrolyte in acetonitrile solutions affords a wider anodic window, which is attributed to the high stability of the anionic component of these intrinsically conductive and thermally robust compounds.
TL;DR: The CCSD(T) calculations for single-configuration-dominated transition metal complexes such as ferrocene appear to have an accuracy comparable to that observed for molecules containing only first- and second-row atoms, and to be of a quality similar to that obtained experimentally.
Abstract: The molecular structures of ferrocene in the eclipsed (equilibrium) and staggered (saddle-point) conformations have been determined by full geometry optimizations at the levels of second-order Moller–Plesset (MP2) theory, coupled-cluster singles-and-doubles (CCSD) theory, and CCSD theory with a perturbative triples correction [CCSD(T)] in a TZV2P+f basis set. Existing experimental results are reviewed. The agreement between the CCSD(T) results and experiment is in all cases excellent; the calculated structure parameters and the barrier to internal rotation of the ligand rings differ from the most accurate experimental values by less than two estimated standard deviations. The CCSD(T) calculations for single-configuration-dominated transition metal complexes such as ferrocene thus appear to have an accuracy comparable to that observed for molecules containing only first- and second-row atoms, and to be of a quality similar to that obtained experimentally. A comparison with previous DFT results indicates that the B3LYP model gives overall the best DFT results, with a deviation of around 2 pm for the metal–carbon distance and smaller errors for the cyclopentadienyl rings.
TL;DR: The findings show that the reduction of a cylindrical quartz pellet at certain potentials is mainly determined by the diffusion of the O(2-) ions and also the ohmic polarisation in the reduction-generated porous silicon layer.
Abstract: The electrochemical reduction of solid SiO 2 (quartz) to Si is studied in molten CaCl 2 at 1173 K. Experimental observations are compared and agree well with a novel penetration model in relation with electrochemistry at the dynamic conductor insulator electrolyte three-phase interlines. The findings show that the reduction of a cylindrical quartz pellet at certain potentials is mainly determined by the diffusion of the O 2- ions and also the ohmic polarisation in the reduction-generated porous silicon layer. The reduction rate increases with the ove, potential to a maximum after which the process is retarded, most likely due to precipitation of CaO in the reaction region (cathodic passivation). Data are reported on the reduction rate, current efficiency and energy consumption during the electroreduction of quartz under potentiostatic conditions. These theoretical and experimental findings form the basis for an in-depth discussion on the optimisation of the electroreduction method for the production of silicon.
TL;DR: In this paper, the interplay between three important noncovalent interactions involving aromatic rings is studied by means of high level ab initio calculations, and it is shown that very strong synergic effects are present in complexes where either cation-π or anion-π and π--π interactions coexist.
Abstract: The interplay between three important noncovalent interactions involving aromatic rings is studied by means of high level ab initio calculations. They demonstrate that very strong synergic effects are present in complexes where either cation–π or anion–π and π--π interactions coexist. These strong synergic effects have been studied using the “atoms in molecules” theory and the physical nature of the interactions investigated by means of the molecular interaction potential with polarization (MIPp).
TL;DR: The emission properties of nanocrystalline ZnO particles prepared following an organometallic synthetic method are investigated and the shape of the particles and the ligands used are shown to influence the luminescence properties in the visible domain.
Abstract: The emission properties of nanocrystalline ZnO particles prepared following an organometallic synthetic method are investigated. Spherical particles and nanorods are studied. The shape of the particles and the ligands used are shown to influence the luminescence properties in the visible domain. Two different emissions are observed at 440 nm (approximately 2.82 eV) and at 580 nm (approximately 2.14 eV) that are associated with the presence of surface defects on the particles. The first emission corresponds to the well-known yellow emission located at 580 nm (approximately 2.14 eV) with a lifetime of 1850 ns for 4.0 nm size ZnO nanoparticles. The second emission at 440 nm (approximately 2.82 eV) is observed when amine functions are present. This strong blue emission is associated with an excitation energy less than that associated with the yellow emission displaying a lifetime of nine nanoseconds. A possible hole trapping effect by the amine groups on the surface of the ZnO particles is discussed as the origin of this emission. The modification of the intensities between the two visible emissions for different particle shapes is proposed to be related to a specific location of the amine ligands on the surface of the particles.
TL;DR: This approach is applied on benchmark diatomic and triatomic molecules, and on TiF3 and Cu(NH3)4(2+) using either CASPT2 or CCSD(T) methods to calculate the spin-free states and SO-RASSI to calculate spin-orbit coupling.
Abstract: Starting from the formula proposed by Gerloch and McMeeking in 1975, the electronic g-matrix is expressed as a sum of two matrices called Lambda and Sigma describing the orbital and spin contributions respectively. This approach is applied on benchmark diatomic and triatomic molecules, and on TiF3 and Cu(NH3)4(2+) using either CASPT2 or CCSD(T) methods to calculate the spin-free states and SO-RASSI to calculate spin-orbit coupling. Results compare very well to experimental data and to previous theoretical work; and, for each molecule, the anisotropy of the g-matrix is modeled by the mean of a few parameters.
TL;DR: It is suggested that PVA segments adsorb to the primary and secondary prism faces of ice parallel to the c axis with a linear misfit parameter of only 2.7 %, most likely via multiple hydrogen bonds.
Abstract: The effects of poly(vinyl alcohol) (PVA) on the Ostwald ripening of polycrystalline ice samples are studied. At -6 degrees C, ice recrystallization in sucrose solutions is inhibited at PVA concentrations down to 0.005 mg mL(-1), with a recrystallization inhibition constant of 48.9 mL mg(-1). Ice growth-habit experiments reveal molecular recognition of the arrangement of water molecules in the ice by PVA molecules, and indicate that PVA molecules adsorb to the primary and secondary prism faces of hexagonal ice, Ih. Based on these observations, together with an analysis of the O-atom pattern in ice and the conformation of OH groups in PVA, an adsorption model is proposed. We suggest that PVA segments adsorb to the primary and secondary prism faces of ice parallel to the c axis with a linear misfit parameter of only 2.7 %, most likely via multiple hydrogen bonds. The proposed adsorption mechanism is discussed in the light of recent thermal hysteresis and scanning tunneling microscopy experiments.
TL;DR: The systematic preparation of metal nanotube arrays is presented and the growth mechanism, termed current-directed tubular growth (CDTG), for template-based electrodeposition technology is put forward.
Abstract: Nanotubes composed of layered or nonlayered materials have been synthesized through various methods, among which template-based electrodeposition technology provides a versatile technique for synthesizing one-dimensional nanostructured materials. However, the growth mechanism of nanotubes using the template method is seldom clarified. Herein, we present the systematic preparation of metal nanotube arrays and put forward the growth mechanism, termed current-directed tubular growth (CDTG), for template-based electrodeposition. There are competitive growth rates for metal atoms entering the crystal lattice, that is, v( parallel) (growth rate parallel to current direction) and v( perpendicular) (growth rate perpendicular to current direction). Metal nanotubes can be obtained at v( parallel)>>v( perpendicular), while nanowires can be obtained at v( parallel) approximately v( perpendicular). The as-synthesized metal (Fe, Co, Ni) nanotubes are constructed from nonlayered materials, which are of body-centered cubic iron structure, hexagonal close packed cobalt structure, and face-centered cubic nickel structure, respectively. The CDTG mechanism is expected to have applications in designing and synthesizing other metal nanotubes and even compound nanotubes via template-based electrodeposition technology.
TL;DR: The increased concentration range obtained with TEAOH is further used to facilitate thiol exchange which occurs at a greater extent than would be achieved in NaOH solution.
Abstract: The solubility of charged nanoparticles is critically dependent on pH. However, the concentration range available with bases such as NaOH is quite narrow, since the particles precipitate due to compression of the electric double layer when the ionic strength is increased. The stability of mercaptoundecanoic acid-capped Au nanoparticles is studied at a set pH using the hydroxide as base and different cations of various sizes. The counterions used are sodium (Na(+)), tetramethylammonium (TMA(+)), tetraethylammonium (TEA(+)), and tetrabutylammonium (TBA(+)). The particles precipitate in the 70-90 mM range with Na(+) as the counterion, but with quaternary ammonium hydroxides the particles are stable even in concentrations exceeding 1 M. The change in solubility is linked to a strongly adsorbed layer on the surface of the ligand shell of the nanoparticles. The increased concentration range obtained with TEAOH is further used to facilitate thiol exchange which occurs at a greater extent than would be achieved in NaOH solution.
TL;DR: It is shown that for different systems (defined by the cluster size, the support, experimental conditions, etc.) the reaction mechanism differs and, hence, no generalized explanation for the catalytic driving force of small gold particles can be given.
Abstract: Recent progress in the understanding of the fascinating catalysis of CO combustion by supported gold particles is summarized. Focusing on aize-selected gold clusters consisting of only a few atoms, that is, the size regime with properties nonscalable from the bulk properties, we discuss the current knowledge of the different factors controlling the reactivity at the molecular level. These factors include the role of the oxide support, its defects, cluster charging as well as the structural fluxionality of clusters, the cluster size dependency, and the promotional effect of water. By combining experimental results with quantum mechanical ab initio calculations, a detailed picture of the reaction mechanism emerges. While similar mechanisms might be active for gold nanoparticles in in the scalable size rgime, it si shown that for different systems (defined by the cluster size, the support, experimental conditions, etc.) the reaction mechanism differs and, hence, no generalized explanation for the catalytic driving force of small gold particles can be given.
TL;DR: The dominant interaction between carborane and biomolecules is the formation of unconventional proton-hydride hydrogen bonds (dihydrogen bonds) characterized by a short distance between hydrogen atoms, which can be used to explain the specificity of inhibition of HIV protease by carboranes.
Abstract: Noncovalent interactions of the polyhedral carborane 1-carba-closo-dodecaborane (CB(11)H(12))(-) with building blocks of biomolecules, modelled by glycine (GLY), serine (SER), phenylalanine (PHE), glutamic acid (GLU), lysine (LYS) and arginine (ARG), were investigated in vacuo by molecular dynamics simulations with the UFF empirical potential. Selected structures were further studied by accurate ab initio quantum chemical procedures. Interactions with a peptide bond (GLY-SER dipeptide) and a nucleic acid building block (guanine) were also considered. The RESP and NPA charges of carboranes and small model systems are compared and their use is discussed. The dominant interaction between carboranes and biomolecules is the formation of unconventional proton-hydride hydrogen bonds (dihydrogen bonds) characterized by a short distance between hydrogen atoms (as close as 1.8 A) and an average strength in the range of 4.2-5.8 kcal mol(-1). The total stabilization energy of complexes investigated is rather large, and the largest value (approximately 15 kcal mol(-1)) was found for the carborane complexes with ARG and the GLY-SER dipeptide. These interactions are ubiquitous under geometrical constraints influencing the strength of the interaction. The carborane forms dihydrogen bonds with biomolecules preferably with the hydrogen atoms of its lower hemisphere (i.e. the part of the cage opposite to the carbon atom). These two geometrical factors can be used to explain the specificity of inhibition of HIV protease by carboranes.