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PubMed2000

Moist and soft, dry and stiff: a review of neutron experiments on hydration-dynamics-activity relations in the purple membrane of Halobacterium salinarum.

Twenty-five years of neutron experiments on hydration and thermal dynamics in purple membranes of Halobacterium salinarum are reviewed. Neutron diffraction, elastic and quasielastic scattering, allowed to map the distribution of water and lipids and to measure thermal fluctuations and correlation times in the membranes, under various conditions of temperature, hydration and lipid environment. Strong correlations were established between dynamics parameters and the activity of bacteriorhodopsin (the purple membrane protein), as a light driven proton pump supporting the hypothesis that the influence of hydration on activity is in fact due to its effects on membrane thermal dynamics. Hydrogen-deuterium labelling experiments highlighted stiffer and softer parts in the bacteriorhodopsin structure. The soft parts would allow the conformational changes involved in activity, while the stiffer ones may control a valve-like function in vectorial proton transfer.

Bacteriorhodopsins↗
PubMed1987

Structure and hydration of purple membranes in different conditions.

The unit cell dimension of the bacteriorhodopsin lattice in purple membranes decreases by the same amount (2%) upon drying the membranes at room temperature as when they are cooled to liquid nitrogen temperatures. Neutron diffraction experiments with H2O:2H2O exchange, however, show that whereas in the dry membranes the lipid headgroups are dehydrated and the decrease in dimension is due to a smaller area occupied by the lipid molecules, the water of hydration remains in place in the cooled membranes, and the decrease in dimension is due to thermal contraction only. These data suggest a hypothesis that functional bacteriorhodopsin, in the wet state at room temperature, has a relatively soft environment that would allow large amplitude motions of the protein; in the dry membranes at room temperature (which are inactive), the amplitudes of protein motions would be inhibited by a more close-packed environment as they are reduced, due to thermal contraction, in the cold membranes.

Bacteriorhodopsins↗
PubMed1989

The structure of mineralized collagen fibrils.

A new model for the structure of mineralized bone collagen is presented which is compatible with neutron diffraction, electromicroscopic, crosslinking, and composition-density data. Mineralized collagen fibrils are comprised of azimuthally oriented, flexible molecules laterally arranged on a superlattice. Four nearest neighbors are longitudinally staggered by 67 nm and two neighbors by 2* 67 nm. In early stages of mineralization the molecules are parallel to the fibril axis with an average interaxis distance of 1.8 nm. In later stages they become flexed away from the fibril axis by an anisotropic lateral compression of molecules to an interaxis distance of 1.3 nm. Three quarters of the mineral in bone is disposed within the fibrils with a symmetry and habit reflecting the above organization of the collagen molecules.

Calcification, Physiologic↗
PubMed2002

Beta-amyloid 25 to 35 is intercalated in anionic and zwitterionic lipid membranes to different extents.

Neuronal plasma membranes are thought to be the primary target of the neurotoxic beta-amyloid peptides (Abeta) in the pathogenesis of the Alzheimer's disease. Histologically, Abeta peptides are observed as extracellular macroscopic senile plaques, and most biophysical techniques have indicated the presence of Abeta close to the lipid headgroup region but not in the core of the membrane bilayers. The focus of this study is an investigation of the interaction between Abeta and lipid bilayers from a structural point of view. Neutron diffraction with the use of selectively deuterated amino acids has allowed us to determine unambiguously the position of the neurotoxic fragment Abeta (25-35) in the membrane. Two populations of the peptide are detected, one in the aqueous vicinity of the membrane surface and the second inside the hydrophobic core of the lipid membrane. The location of the C terminus was studied in two different lipid compositions and was found to be dependent on the surface charge of the membrane. The localization of beta-amyloid peptides in cell membranes will offer new insights on their mechanism in the neurodegenerative process associated with Alzheimer's disease and might provide clues for therapeutic developments.

Alzheimer Disease↗
PubMed1995

Detergent structure in tetragonal crystals of OmpF porin.

BACKGROUND: The high-resolution structures of five porins have been solved by X-ray crystallography including the trigonal crystal form of the trimeric OmpF porin from Escherichia coli. In an accompanying article, the structure of the tetragonal form of OmpF porin is presented. In contrast to the trigonal crystal form, the protein surfaces normally in contact with lipids in the membrane are exposed and interact with amphiphiles in the tetragonal crystal. Thus, the tetragonal form can be used to investigate protein-detergent interactions. RESULTS: Using single-crystal neutron diffraction studies and two different detergents (one of them deuterated in its hydrophobic moiety), details of the amphiphile-protein interactions are revealed. Detergent molecules bind to the so-called hydrophobic zone that surrounds the OmpF porin trimer and which is exposed to lipid in the native environment. The aromatic rings on both sides of the hydrophobic zone coincide with the boundary between non-polar and polar moieties of the detergents. CONCLUSIONS: In the tetragonal crystal form of OmpF porin, the membrane-exposed area is accessible from the aqueous solution. It is coated by a film of detergent molecules, which presumably mimics the interactions of the protein with lipids in the biological membrane. In the trigonal form, protein-protein interactions predominate in the hydrophobic zone. These may reflect the tight interactions between trimers that are observed in the biological membrane.

Bacterial Outer Membrane Proteins↗
PubMed1996

Determination of protein and solvent volumes in protein crystals from contrast variation data.

By varying the relative values of protein and solvent scattering densities in a crystal, it is possible to obtain information on the shape and dimensions of protein molecular envelopes. Neutron diffraction methods are ideally suited to these contrast variation experiments because H/D exchange leads to large differential changes in the protein and solvent scattering densities and is structurally non-perturbing. Low resolution structure factors have been measured from cubic insulin crystals with differing H/D contents. Structure factors calculated from a simple binary density model, in which uniform scattering densities represent the protein and solvent volumes in the crystals, were compared with these data. The contrast variation differences in the sets of measured structure factors were found to be accurately fitted by this simple model. Trial applications to two problems in crystal structure determination illustrate how this fact may be exploited. (i) A translation function that employs contrast variation data gave a sharp minimum within 1-9A of the correctly positioned insulin molecule and is relatively insensitive to errors in the atomic model. (ii) An ab initio phasing method for the contrast variation data, based on analyzing histograms of the density distributions in trial maps, was found to recover the correct molecular envelope.

Citrate (si)-Synthase↗
PubMed1992

X-ray diffraction reconstruction of the inverted hexagonal (HII) phase in lipid-water systems.

The structure of the inverted hexagonal (HII) phase in biological lipid-water systems is studied to examine the physical interactions which drive the polymorphic phase behavior and which are also thought to play a relevant role in biological membrane function. A method is derived which yields the complex phase factors of the HII phase diffraction amplitudes from examination of a single sample. This method is applied to a low-resolution Fourier reconstruction of the HII phase in dioleoylphosphatidylethanolamine (DOPE) + water, specifically to examine deviations from the presumed circular model of the HII phase. It is found that the average radius of the water core, Rw, as determined from a Fourier reconstruction, is in good agreement with previously measured values of Rw obtained from more time-consuming traditional methods [Tate, M. W., & Gruner, S. M. (1989) Biochemistry 28, 4245]. In addition to the average value of Rw, the Fourier reconstruction also can be used to determine the true shape of the water core. It is found that the water core is circular to within 5% of Rw when the unit cell size is less than approximately 75 A. Above 75 A, however, a definite shape deformation becomes apparent, with radial noncircularities of 5-10%, probably in response to the increased entropic cost of packing the hydrocarbon chains into the anisotropic environment of the HII unit cell [Kirk, G. L., Gruner, S. M., & Stein D. E. (1984) Biochemistry 23, 1093]. As a more direct probe of the packing anisotropy, Fourier reconstructions of DOPE + dodecane and DOPE + squalene systems were compared with the reconstruction of DOPE. These oils are known to promote the low temperature occurrence of the HII phase, presumably by a reduction in the hydrocarbon packing stress. In support of this hypothesis, the alkanes were observed to relax the water core to a circular shape for even large lattices. In addition, anisotropy of the electron density near the end of the lipid chains is reduced when alkane is added, implying a more uniform hydrocarbon packing environment, consistent with the results of neutron diffraction upon the addition of deuterated decane [Turner, D. C., Gruner, S. M., & Huang, J. (1992) Biochemistry (following paper in this issue)].

Alkanes↗
PubMed1982

Linking regions between helices in bacteriorhodopsin revealed.

Three-dimensional electron-microscopic structural analysis requires the combination of many different tilted views of the same specimen. The relative difficulty of tilting the sample to high angles >60 degrees without introducing severe distortion due to different focal distances across the specimen entails that the observable range of electron diffraction data is often limited to this range of angles. Thus, it is generally not possible to observe the diffraction maxima that lie within the conical region of reciprocal space around the direction perpendicular to the electron microscope grid. The absence of data in this region leads to a predictable distortion in the object, and for +/-60 degrees tilting makes the resolution essentially twice as bad in the direction perpendicular to the grid as it is for the in-plane image. Constrained density map modification and refinement methods can significantly reduce these effects. A method has been developed, tested on model cases, and applied to the electron-microscopic structure determination of bacteriorhodopsin in order to visualize the location of linking regions between helices. Electron-microscopic structural analysis of bacteriorhodopsin (Henderson and Unwin. 1975 Nature [Lond.] 257:28-32.) showed that the molecule consists of seven rods of density each nearly spanning the lipid bilayer. Owing to the distortion introduced by the missing conical region of reciprocal space data, no density was visible for the polypeptide segments linking the alpha-helices. Density in the refined maps indicates the location of at least five of the extrahelical segments of the polypeptide. The total number of possible ways of interconnecting the helices is reduced from 7! (5,040) to the five most consistent possibilities without recourse to other considerations. In addition, the density for the helical regions is more uniform and cylindrical throughout their length, and the length of the helices increases from 35 to 45 A, close to the membrane thickness of 49 A obtained for membranes dried in vacuo. Only three of the five structures consistent with the location of observed linkers place the seventh helix, onto which the chromophore can be attached by reduction in the light, at a position consistent with the main peak for deuterated retinal in the structure, as derived from neutron diffraction analysis. Two of these models are also consistent with the possible location of some of the reduced chromophore on helix B, at lys 40/41 after reduction in the dark, as well as lys 216 on helix G.

Bacteriorhodopsins↗
PubMed1996

Neutron anatomy.

The familiar extremes of crystalline material are single-crystals and random powders. In between these two extremes are polycrystalline aggregates, not randomly arranged but possessing some preferred orientation and this is the form taken by constructional materials, be they steel girders or the bones of a human or animal skeleton. The details of the preferred orientation determine the ability of the material to withstand stress in any direction. In the case of bone the crucial factor is the orientation of the c-axes of the mineral content-the crystals of the hexagonal hydroxyapatite- and this can readily be determined by neutron diffraction. In particular it can be measured over the volume of a piece of bone, utilising distances ranging from 1 mm to 10 mm. The major practical problem is to avoid the intense incoherent scattering from the hydrogen in the accompanying collagen; this can best be achieved by heat-treatment and it is demonstrated that this does not affect the underlying apatite. These studies of bone give leading anatomical information on the life and activities of humans and animals-including, for example, the life history of the human femur, the locomotion of sheep, the fracture of the legs of racehorses and the life-styles of Neolithic tribes. We conclude that the material is placed economically in the bone to withstand the expected stresses of life and the environment. The experimental results are presented in terms of the magnitude of the 0002 apatite reflection. It so happens that for a random powder the 0002, 1121 reflections, which are neighbouring lines in the powder pattern, are approximately equal in intensity. The latter reflection, being of manifold multiplicity, is scarcely affected by preferred orientation so that the numerical value of the 0002/1121 ratio serves quite accurately as a quantitative measure of the degree of orientation of the c-axes in any chosen direction, for a sample of bone.

Anatomy↗
PubMed1986

Hydrostatic pressure induces hydrocarbon chain interdigitation in single-component phospholipid bilayers.

By use of neutron diffraction for structural analysis, the temperature-pressure phase diagrams of several fully hydrated single-component phospholipid bilayers have been explored up to hydrostatic pressures of 2 kbars. The gel to liquid-crystalline phase transition temperature Tm increases linearly with pressure over a 10(-3)-2 kbar range in accordance with the Clausius-Clapeyron relationship giving dTm/dP values of 23.0 degrees C/kbar for 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC) and 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (DPPC) and 28.0 degrees C/kbar for 1,2-distearoyl-sn-glycero-3-phosphatidylcholine (DSPC). The so-called pretransition was not observed in the isothermal pressure experiments, suggesting that no appreciable volume change occurs at this transition. These results are in good agreement with those reported using other techniques. In addition, at pressures higher than the isothermal liquid-crystalline to gel transition pressure, a new pressure-induced phase transition was observed for DPPC and DSPC in which the hydrocarbon chains from apposing monolayers become interdigitated with the chains occupying a cross-sectional area approximately equal to 5% less than in the gel phase. The temperature-pressure phase diagrams show the gel-interdigitated phase boundaries to be highly curved and the minimum pressure at which interdigitation occurs to decrease with increasing hydrocarbon chain length.

Gels↗
PubMed2005

Structure, thermodynamics, and liquid-vapor equilibrium of ethanol from molecular-dynamics simulations using nonadditive interactions.

We present a molecular-dynamics simulation study of the bulk and liquid-vapor interfacial properties of ethanol using a polarizable force field based on the fluctuating charge (FQ) formalism, as well as the nonpolarizable CHARMM22 force field. Both models are competitive with respect to the prediction of ambient liquid properties such as liquid density, enthalpy of vaporization, dielectric constant, and self-diffusion constants. The polarizable model predicts an average condensed-phase dipole moment of 2.2 D associated with an induced liquid-phase dipole moment of 0.6 D; though qualitatively in agreement with earlier nonadditive models as well as recent Car-Parinello calculations, the current FQ model underestimates the condensed-phase dipole moment. In terms of liquid structure, both models are in agreement with recent neutron-diffraction results of liquid ethanol structure, although the polarizable model predicts the hydroxyl-hydrogen-hydroxyl-hydrogen structure factor in closer agreement with the experimental data. In terms of interfacial properties, both models predict ambient surface tension to within 4% of the experimental value of 22.8 dyncm, while overestimating the surface excess entropy by almost a factor of 2. Both models display the characteristic preferential orientation of interfacial molecules. The polarizable model allows for a monotonic variation of the average molecular dipole moment from the bulk value to that of the vapor phase. Consequently, there is a dramatic difference in the surface potential predicted by the polarizable and nonpolarizable models. The polarizable model estimates a surface potential of -209+/-3 mV, while the nonpolarizable model yields a value of -944+/-10 mV. Finally, based on the vapor-liquid equilibrium simulation data from several temperatures, we estimate the critical properties of both models. As observed with other FQ models for associating fluids (such as water and methanol), and counter to what one would anticipate by modeling more physically the electrostatic response to local environment, the current FQ model underestimates the critical temperature and overestimates the critical density of ethanol; moreover, the FQ model is, in this respect, equivalent to the underlying fixed-charge model. These results further suggest the need to revisit polarizable models in terms of quantitative vapor-liquid equilibrium prediction.

Chemistry, Physical↗
PubMed1983

Comparisons of the interaction of propranolol and timolol with model and biological membrane systems.

The nonspecific interaction of the beta-adrenergic blocking drugs, propranolol and timolol, with model and biological membranes has been investigated. Radioisotope measurements of the association of these drugs with dimyristoyl lecithin (DMPC) bilayers showed that both propranolol and timolol had a significantly greater molar association (mole of drug per mole of lipid) with DMPC above its phase transition temperature than below. Timolol had a much lower molar association with DMPC as compared with propranolol both above and below the phase transition temperature. For the DMPC model membrane system, the molar association of propranolol as measured by radioisotope and inferred from calorimetric studies was similar. Neutron diffraction utilizing propranolol deuterated in the naphthalene moiety showed that the naphthalene moiety of propranolol partitions into the hydrocarbon core of the DMPC lipid bilayer, and that the charged amine side chain is most likely positioned in the aqueous phospholipid head group region. For timolol, the association as measured by radioisotope methods was apparently greater than the partitioning inferred from calorimetric studies using freezing point depression analysis, suggesting a more complex interaction of timolol as compared with propranolol with the DMPC lipid bilayer. The association of propranolol and timolol with sarcoplasmic reticulum vesicles (SR) was similar to that with highly purified protein-depleted SR lipids, and DMPC above its phase transition. The association of propranolol with the SR membrane (mole of propranolol per mole of SR phospholipid) correlated with its ability to inhibit calcium uptake, whereas only a fraction of the total association of timolol with the SR membrane appeared to lead to inhibition of calcium uptake. These results suggest that the major nonspecific interactions of propranolol and timolol are with the SR membrane lipids, and that the magnitude of their interactions depends on both the lipid solubility of the drug and the physical state of the fatty acyl chains of the membrane. Both propranolol and timolol appear to perturb the functional properties of the calcium pump protein in the SR membrane (inhibition of ATP-induced calcium uptake) indirectly by partitioning into the bulk lipid matrix of the SR lipid bilayer, although other sites of interaction cannot be excluded.

Animals↗
PubMed1984

Crystal structure of the nucleosome core particle at 16 A resolution.

The crystal structure of the nucleosome core particle has been studied by neutron diffraction to a resolution of 16 A. By using H2O/D2O solvent contrast variation, the structures of the DNA and histone core were analysed separately. The DNA, as seen at this resolution, forms a super-helix of pitch 25.8 A, radius 42.1 A and 1.8 turns in length. The histone core itself is approximately helical and follows the DNA along the inside of the super-helix, giving the nucleosome core particle an overall 2-fold axis of symmetry. Four regions can be distinguished in the protein density, which we interpret as dimers of histones within the octameric core. The dimers have been assigned on the basis of other evidence as being of two kinds, (H2A-H2B) and (H3-H4). Because solvent contrast variation can distinguish between hydrophobic and hydrophilic regions in the protein density, our results suggest that the interface between the monomers of each dimer is probably quite hydrophobic in character, while the interaction between dimers is weaker and/or more hydrophilic. The protein is in contact with most of the DNA and there are some regions where it may penetrate between the turns of the super-helix. In particular, the tetramer (H4-H3)-(H3-H4) is in close contact with the central part of the DNA, but significant contacts are seen also between the histones H3 and the extremities of the super-helix, thus explaining the stability of a nucleosome-like particle depleted of H2A and H2B. Significant departures from the molecular 2-fold axis of symmetry occur in the relative arrangements of the two (H2A-H2B) dimers.

Crystallography↗
PubMed1991

Structure of the detergent phase and protein-detergent interactions in crystals of the wild-type (strain Y) Rhodobacter sphaeroides photochemical reaction center.

Rhodobacter sphaeroides (strain Y) reaction center (RC) crystals were grown in the presence of n-octyl beta-glucoside (beta-OG). In order to determine the structure of the detergent phase in these crystals, low-resolution neutron diffraction experiments were performed at different contrasts obtained by varying the H2O/D2O ratio in the solvent. From the contrast variation data and from the RC atomic coordinates determined by X-ray diffraction [Arnoux, B., Ducruix, A., Reiss-Husson, F., Lutz, M., Norris, J., Schiffer, M., & Chang, C. H. (1989) FEBS Lett. 258, 47-50], a model was obtained for the structure of the detergent phase in the crystal. The detergent forms a ring-shaped micelle surrounding the most hydrophobic part of the transmembrane alpha helices of the RC. Each detergent ring is connected to two next-neighbor rings by intermicellar bridges. The detergent phase is organized thus in infinite zigzag chains parallel to the b axis of the P2(1)2(1)2(1) unit cell. The main interactions between beta-OG molecules and the RC molecules are hydrophobic and are localized at the level of the transmembrane alpha helices. This interaction replaces the phospholipid-protein interaction existing in vivo in the membrane and, to some extent, also the light harvesting complex-protein interaction. Secondary hydrophilic interactions are found between a few of the charged residues of the H subunit and the hydrophilic surface of the detergent ring from a neighboring RC molecule. A comparison with a previous study on Rhodopseudomonas viridis crystals [which grow in the presence of lauryldimethylamine N-oxide (LDAO) and belong to a different space group] [Roth, M., Lewit-Bentley, A., Michel, H., Deisenhofer, J., Huber, R., & Oesterhelt, D. (1989) Nature 340, 659-661] shows a quasi identity of shape and position of the beta-OG and LDAO rings around the transmembrane alpha helices. The secondary interactions, involving in both cases the external surface of the H subunit, differ because of the different molecular packing in the two space groups. The role and structural requirements of the detergent in the crystallization process are discussed.

Algorithms↗
PubMed2001

The charge density distribution in a model compound of the catalytic triad in serine proteases.

Combined low temperature (28(1) K) X-ray and neutron diffraction measurements were carried out on the co-crystallised complex of betaine, imidazole, and picric acid (1). The experimental charge density was determined and compared with ab initio theoretical calculations at the B3LYP/6-311G(d,p) level of theory. The complex serves as a model for the active site in, for example, the serine protease class of enzymes, the so-called catalytic triad. The crystal contains three short strong N-H...O hydrogen bonds (HBs) with dN...O < 2.7 A. The three HBs have energies above 13 kcalmol(-1), although the hydrogen atoms are firmly localized in the "nitrogen wells". This suggests that low-barrier hydrogen bonding in catalytic enzyme reactions may be a sufficient, but not a necessary, condition for obtaining transition-state stabilization. Structural analysis (e.g., covalent N-H bond lengthening) indicates that the hydrogen bond between H3A and 08 of imidazole and betaine respectively (HB2) is slightly stronger than the bond between H1A and O1A of imidazole and picric acid (HB1), although HB1 is shorter than HB2: (dN...O(HB1)= 2.614(1) A, dN...O(HB2) = 2.684(1) A, dH...O(HB1) = 1.630(1) A, dH...O(HB2)= 1.635(1) A, dN-H(HB1) = 1.046(1) A, dN-H(HB2) = 1.057(1) A). Furthermore, the charge density analysis reveals that HB2 has a larger covalent character than HB1, with considerable polarization of the density towards the acceptor atom. The Gatti and Bader source function (S) is introduced to the analysis of strong HBs. The source function is found to be a sensitive measure for the nature of a hydrogen bond, and comparison with low-barrier and single-well hydrogen bonding systems (e.g., benzoylacetone and nitromalonamide) shows that the low-barrier hydrogen bond (LBHB) state is characterized by an enormously increased hydrogen atom source contribution to the bond critical point in the HB. In this context, HB2 can be characterized as intermediate between localized HBs and delocalized LBHBs.

Binding Sites↗
PubMed1993

The location of amantadine hydrochloride and free base within phospholipid multilayers: a neutron and X-ray diffraction study.

Concomitant neutron and X-ray studies were undertaken in order to locate accurately the anti-influenza and Parkinson's disease drug amantadine in multilayers of 1,2-dioleoyl-sn-glycero-3-phosphocholine. The X-ray data were phased using the swelling series method and the neutron data were phased using D2O/H2O exchange and a variation of the isomorphous replacement technique. The sets of data complement each other and reveal two populations of amantadine within the bilayer. One site is close to the bilayer surface, the other is much deeper. The majority of the amantadine occupies the surface site. The relative occupancy, but not the position, of the two locations appears to be dependent upon the initial protonation state of the drug. No evidence of bilayer perturbation was observed with either the protonated or the deprotonated forms of amantadine.

Amantadine↗
PubMed2000

A novel energy-based stochastic method for positioning polar protons in protein structures from X-rays.

A novel automated method for the optimal placement of polar hydrogens in a protein structure is presented. The algorithm adds initially, to a protein data bank file of the protein, nonrotatable hydrogens such as peptide backbone hydrogens according to geometric considerations. Then, water protons and polar side chain protons of lysine, serine, threonine, tyrosine, aspartic acid, glutamic acid, and the C and N termini of a protein are added according to energy considerations. A unique stochastic approach has been developed to overcome a combinatorial explosion in the search for the lowest energy structure. First, the system is divided into ensembles. Each ensemble is treated separately: N conformations are sampled at random, their energies computed, whereas common components of high-energy combinations are gathered on one hand, and low-energy combinations on the other. Components that yield only high-energy conformations and do not contribute to any low energies are excluded. This is reiterated while the total amount of combinations is decreased along the iterative process. When the total number of combinations is lower than a user defined threshold, all remaining combinations are evaluated by exhaustive search. Energy evaluations use nonbonding energy expressions alone. The program was tested on five high-resolution crystal structures: bovine pancreatic trypsin inhibitor (Brookhaven Protein Data Bank file 5PTI), RNase-A (5RSA), trypsin (1NTP), and carbon monoxymyoglobin (2MB5), for which neutron diffraction structures are available, as well as phosphate binding protein (1IXH) for which very high resolution X-ray crystallography was used. The low RMS values prove the efficiency of this algorithm as a tool for positioning protons in proteins. It may be used for other biological structures.

Algorithms↗
PubMed2000

Electronic excitations in homopolyatomic bismuth cations: spectroscopic measurements in molten salts and an ab initio CI-singles study

The electronic excitations of the low-valence bismuth cluster cations Bi5(3+), Bi8(2+), and Bi9(5+) have been studied with experimental and theoretical techniques. The UV-visible spectra of the bismuth ions were measured in acidic chloroaluminate melts (mixture of 1-methyl-3-benzyl imidazolium chloride and AlCl3). The spectra of the Bi5(3+) and Bi8(2+) ions agree fairly well with previous reports, but also revealed additional low-energy absorptions. Ab initio methods were employed to assign the experimentally observed electronic transitions of these homopolyatomic bismuth cations. Structures were optimized at the RHF, MP2, and B3LYP levels of theory by using split-valence LANL2DZ basis sets that were augmented with one and two sets of pure d functions. The computed structures agree well with the results of neutron diffraction analyses of melts. Electronically excited states of the three clusters were treated by using the CI-Singles theory. The results of these calculations were used to explain the observed UV-visible spectra. The observed electronic excitations in the UV-visible range are all found to result from transitions involving the molecular orbitals formed by 6p-atomic-orbital overlap. This leads to the necessity of using basis sets that include d-type functions, which allow for an adequate description of the bonding that results from such p-orbital overlap. Spin-orbit coupling becomes increasingly important with increasing atomic number and its consideration is necessary when describing the electronic transitions in clusters of heavy atoms. The calculations show that singlet-triplet transitions, which are made accessible by strong spin-orbit coupling, are responsible for some of the observed absorptions.

Journal Article↗