First-principles simulations of the chemical functionalization of (5,5) boron nitride nanotubes

We perform density functional theory studies to investigate structural and electronic properties of the (5,5) boron nitride nanotubes (BNNTs) with surfaces and ends functionalized by thiol (SH) and hydroxyl (OH) groups. The exchange-correlation energies are treated according to the functional of Hamprecht-Cohen-Tozer-Handy within the generalized gradient approximation (HCTH-GGA). We use the base function with double polarization DNP. To determine the (5,5) BNNT-SH and (5,5) BNNT-OH relaxed structures the minimum energy criterion is applied considering six different geometries depending upon the SH and OH functional groups orientation: (C1) The adsorbed functional group is oriented toward the N atom, (C2) the functional group is oriented toward the B atom, (C3) the functional group is at the central hexagon of the BNNT surface. The (C4) fourth and (C5) fifth configurations are formed by allowing bonds (of S or O) with B or N atoms at one end of the nanotube. (C6) The sixth geometry is obtained by placing the functional group at the center of one end of the BNNT. The (5,5) BNNT-SH system, in vacuum, suffers a semiconductor to metal transition while the (5,5) BNNT-OH system retains the semiconductor behavior. When structures are solvated in water these systems behave as semiconductors. The polarity increases as a consequence of the functional group-nanotube interactions no matter if they are in vacuum or in solvation situation, which indicates the possible solubility and dispersion. According to the work function the best option to construct a device is with the BNNT-OH system.     

A density functional theory analysis for the adsorption of the amine group on graphene and boron nitride nanosheets

In this paper first principles total energy calculations to study the adsorption of amine group (NH₂) on graphene (G) and boron nitride (hBN) nanosheets are developed; the density functional theory, within the local density approximation and Perdew-Wang functional was employed. The sheets were modeled with a sufficiently proved C_nH_m-like cluster with armchair edge. The optimized geometry was obtained following the minimum energy criterion, searching on four positions for each nanosheet: perpendicular to the carbon atom, on the hexagon, inside the hexagon and on the bridge C–C, for the G-amine interaction; and, perpendicular to the B, perpendicular to the N, on the hexagon, and inside the hexagon, for the hBN-amine interaction. A physisorption, with amine parallel to the C–C–C bond with a distance graphene-amine of 2.56 Å, was found. For the case of BN a B–N bond, with bond length equal to 1.56 Å, was found; the amine lies perpendicular to the nanosheet. When the graphene is doped with B and Al atoms a chemisorption with B–N (1.57 Å) and Al–N (1.78 Å) bonds is observed; the bond angle in the amine group is also incremented, 5.5° and 8.1°, respectively. In the presence of point defects (monovacancies) of B in the hBN-amine and C in the G-amine, there exists chemisorption, increasing the reactivity of the sheets.     

A theoretical study of red-shifting and blue-shifting hydrogen bonds occurring between imidazolidine derivatives and PEG/PVP polymers

A theoretical study is presented with the aim to investigate the molecular properties of intermolecular complexes formed by the monomeric units of polyvinylpyrrolidone (PVP) or polyethyleneglycol (PEG) polymers and a set of four imidazolidine (hydantoine) derivatives. The substitution of the carbonyl groups for thiocarbonyl in the hydantoin scaffold was taken into account when analyzing the effect of the hydrogen bonds on imidazolidine derivatives. B3LYP/6-31G(d,p) calculations and topological integrations derived from the quantum theory of atoms in molecules (QTAIM) were applied with the purpose of examining the N–H⋯O hydrogen bond strengths formed between the amide group of the hydantoine ring and the oxygen atoms of PVP and PEG polymers. The effects caused by the N–H⋯O interaction fit the typical evidence for hydrogen bonds, which includes a variation in the stretch frequencies of the N–H bonds. These frequencies were identified as being vibrational red-shifts because their values decreased. Although the values of such calculated interaction energies are between 12 and 33 kJ mol⁻¹, secondary intermolecular interactions were also identified. One of these secondary interactions is formed through the interaction of the benzyl hydrogen atoms with the oxygen atoms of the PVP and PEG structures. As such, we have analyzed the stretch frequencies on the C–H bonds of the benzyl groups, and blue-shifts were identified on these bonds. In this sense, the intermolecular systems formed by hydantoine derivatives and PVP/PEG monomers were characterized as a mix of red-shifting and blue-shifting hydrogen-bonded complexes.     

The effect of ring size on vibrational spectroscopy and hydrogen bonding properties for the complexes between small ring carbonyl compounds with HF and HCl: Theoretical analysis

The effect of the molecular structure on the properties of C = O…HX (X = F, Cl) bonds was investigated in a set of small cyclic carbonyl compounds, using vibrational spectroscopy and B3LYP/6–311G** calculations. Two main effects were studied: the size of the ring and the inclusion of oxygen atoms in the ring. In these complexes the C = O and H–X participating bonds in the hydrogen–bond are elongated, while others bonds are compressed. The calculated vibrational spectra were interpreted and band assignments were reported. Surface potential energy calculations are carried out with scanning HCl and HF near oxygen atom.     

DFT studies of the phenol adsorption on boron nitride sheets

We perform first principles total energy calculations to investigate the atomic structures of the adsorption of phenol (C₆H₅OH) on hexagonal boron nitride (BN) sheets. Calculations are done within the density functional theory as implemented in the DMOL code. Electron-ion interactions are modeled according to the local-spin-density-approximation (LSDA) method with the Perdew-Wang parametrization. Our studies take into account the hexagonal h-BN sheets and the modified by defects d-BN sheets. The d-BN sheets are composed of one hexagon, three pentagons and three heptagons. Five different atomic structures are investigated: parallel to the sheet, perpendicular to the sheet at the B site, perpendicular to the sheet at the N site, perpendicular to the central hexagon and perpendicular to the B-N bond (bridge site). To determine the structural stability we apply the criteria of minimum energy and vibration frequency. After the structural relaxation phenol molecules adsorb on both h-BN and d-BN sheets. Results of the binding energies indicate that phenol is chemisorbed. The polarity of the system increases as a consequence of the defects presence which induces transformation from an ionic to covalent bonding. The elastic properties on the BN structure present similar behavior to those reported in the literature for graphene.     

Effect of N,N′-bis (alkyldimethyl)-α,ω-alkanediammonium dibromides on bacteria of the genusclostridium

Antibacterial effect of 17 ammonium compounds of the type of N,N′-bis(alkyldimethyl)-α,ω-alkanediammonium dibromides was tested on anaerobically sporulating bacteria of the genusClostridium. A sizable antibacterial activity was displayed by five N,N′-bis(alkyldimethyl)-1,6-hexanediammonium dibromides and by four N,N′-bis(decyldimethyl)-α,ω-alkanediammonium dibromides. These compounds exhibited activity higher than, or comparable with, that of the reference standards Ajatin and Septonex. The maximum antibacterial activity was found in compounds whose alkyl chain contained 9–12 carbon atoms. Compounds with a lower number of carbon atoms in the chain (less than 8) exhibited a low activity.     

Density functional theory study on (LiNH<Subscript>2</Subscript>)<Subscript>n</Subscript> (<Emphasis Type="Italic">n</Emphasis> = 1–5) clusters

Geometrical structures and relative stabilities of (LiNH₂)_n (n = 1–5) clusters were studied using density functional theory (DFT) at the B3LYP/6-31G* and B3LYP/6-31++G* levels. The electronic structures, vibrational properties, N–H bond dissociation energies (BDE), thermodynamic properties, bond properties and ionization potentials were analyzed for the most stable isomers. The calculated results show that the Li–N and Li–Li bonds can be formed more easily than those of the Li–H or N–H bonds in the clusters, in which NH₂ is bound to the framework of Li atomic clusters with fused rings. The average binding energies for each LiNH₂ unit increase gradually from 142 kJ mol⁻¹ up to about 180 kJ mol⁻¹ with increasing n. Natural bond orbital (NBO) analysis suggests that the bonds between Li and NH₂ are of strong ionicity. Three-center–two-electron Li–N–Li bonding exists in the (LiNH₂)₂ dimer. The N–H BDE values indicate that the change in N–H BDE values from the monomer a1 to the singlet-state clusters is small. The N–H bonds in singlet state clusters are stable, while the N–H bonds in triplet clusters dissociate easily. A study of their thermodynamic properties suggests that monomer a1 forms clusters (b1, c1, d2 and e1) easily at low temperature, and clusters with fewer numbers of rings tend to transfer to ones with more rings at low temperature. E _g, E _HOMO and E _av decrease gradually, and become constant. Ring-like (LiNH₂)_3,4 clusters possess higher ionization energy (VIE) and E _g, but lower values of E _HOMO. Ring-like (LiNH₂)_3,4 clusters are more stable than other types. A comparison of structures and spectra between clusters and crystal showed that the NH₂ moiety in clusters has a structure and spectral features similar to those of the crystal.     

Molecular modeling of zinc and copper binding with Alzheimer’s amyloid β-peptide

Aggregation of the amyloid β-peptide (Aβ) into insoluble fibrils is a key pathological event in Alzheimer’s disease. Cu(II) and Zn(II) ions were reported to be able to induce Aβ aggregation at nearly physiological concentrations in vitro. In this study, the binding modes of Cu(II) and Zn(II) in this process were explored by molecular modeling. In the pre-associated Aβ, Nτ atom of imidazole ring of His14, O atom of carbonyl of main-chain and two O atoms of water occupied the four ligand positions of the complex. While in the aggregated form of Aβ, the His13(N)–Metals–His14(N) bridges were formed through metal cross-linking action. These results would be helpful to put insight on revealing the formation mechanism of pathogenic Aβ aggregates in brain.     

Effects of fertigation scheme on N uptake and N use efficiency in cotton

While fertigation can increase fertilizer use efficiency, there is an uncertainly as to whether the fertilizer should be introduced at the beginning of the irrigation or at the end, or introduced during irrigation. Our objective was to determine the effect of different fertigation schemes on nitrogen (N) uptake and N use efficiency (NUE) in cotton plants. A pot experiment was conducted under greenhouse conditions in year 2004 and 2005. According to the application timing of nitrogen (N) fertilizer solution and water (W) involved in an irrigation cycle, four nitrogen fertigation schemes [nitrogen applied at the beginning of the irrigation cycle (N–W), nitrogen applied at the end of the irrigation cycle (W–N), nitrogen applied in the middle of the irrigation cycle (W–N–W) and nitrogen applied throughout the irrigation cycle (N&W)] were employed in a completely randomized design with four replications. Cotton was grown in plastic containers with a volume of 84 l, which were filled with a clay loam soil and fertilized with 6.4 g of N per pot as unlabeled and ¹⁵N-labeled urea for 2004 and 2005, respectively. Plant total dry matter (DM) and N content in N–W was significantly higher than in N&W in both seasons, but these were not consistent for W–N and W–N–W treatments. In year 2005, a significantly higher nitrogen derived from fertilizer (NDFF) for the whole plant was found in W–N and N–W than that in W–N–W and N&W. Fertigation scheme had a consistent effect on total NUE: N–W had the highest NUE for the whole plant, but this was not significantly different from W–N. Treatments W–N and W–N–W had similar total NUE, and N&W had the lowest total NUE. After harvesting, the total residual fertilizer N in the soil was highest in W–N, lowest in N–W, but this was not significantly different from N&W and W–N–W treatments. Total residual NO₃–N in the soil in N&W and W–N treatments was 20.7 and 21.2% higher than that in N–W, respectively. The total ¹⁵N recovery was not statistically significant between the four fertigation schemes. In this study, the fertigation scheme N–W (nitrogen applied at the beginning of an irrigation cycle) increased DM accumulation, N uptake and NUE of cotton. This study indicates that Nitrogen application at the beginning of an irrigation cycle has an advantage on N uptake and NUE of cotton. Therefore, NUE could be enhanced by optimizing fertilization schemes with drip irrigation.     

On the relative stability of tetragonal and trigonal Cu(II) complexes with relevance to the blue copper proteins

 The role of the cysteine thiolate ligand for the unusual copper coordination geometry in the blue copper proteins has been studied by comparing the electronic structure, geometry, and energetics of a number of small Cu(II) complexes. The geometries have been optimised with the density functional B3LYP method, and energies have been calculated by multiconfigurational second-order perturbation theory (the CASPT2 method). Most small inorganic Cu(II) complexes assume a tetragonal geometry, where four ligands make σ bonds to a Cu 3d orbital. If a ligand lone-pair orbital instead forms a π bond to the copper ion, it formally occupies two ligand positions in a square coordination, and the structure becomes trigonal. Large, soft, and polarisable ligands, such as SH^– and SeH^–, give rise to covalent copper-ligand bonds and structures close to a tetrahedron, which might be trigonal or tetragonal with approximately the same stability. On the other hand, small and hard ligands, such as NH₃, OH₂, and OH^–, give ionic bonds and flattened tetragonal structures. It is shown that axial type 1 (blue) copper proteins have a trigonal structure with a π bond to the cysteine sulphur atom, whereas rhombic type 1 and type 2 proteins have a tetragonal structure with σ bonds to all strong ligands. The soft cysteine ligand is essential for the stabilisation of a structure that is close to a tetrahedron (either trigonal or tetragonal), which ensures a low reorganisation energy during electron transfer. Received: 9 July 1997 / 26 November 1997     

Time-dependent density functional theory study of the excited-state dihydrogen bonding: clusters of 2-pyridone with diethylmethylsilane and triethylgermanium

Density functional theory (DFT) was carried out to identify the existence of intermolecular dihydrogen bonds of the 2-pyridone (2PY)-diethylmethylsilane (DEMS) and 2PY-triethylgermanium (TEGH) clusters in the ground state. The H···H distances of both clusters are shorter than the sum of their van der Waals radii. Thus, intermolecular dihydrogen bonds N–H•••H–Si and N–H•••H–Ge exist in the 2PY-DEMS and 2PY-TEGH clusters, respectively. Based on the ground-state conformations, intermolecular dihydrogen bonds N–H•••H–Si and N–H•••H–Ge in the electronically excited state of the 2PY-DEMS and 2PY-TEGH clusters were also investigated using time-dependent density functional theory (TDDFT). Electronic transition of the 2PY-DEMS cluster resembles that of the 2PY-TEGH cluster. Their S₁ state is a locally excited (LE) state centered on 2PY moiety. The H•••H distances of the 2PY-DEMS and 2PY-TEGH clusters both stretch in the S₁ state compared to those in the ground state. Upon electronic excitation, intermolecular dihydrogen bonding N–H•••H–Si and N–H•••H–Ge can weaken with decreasing dihydrogen bonding energies.     

Reaction of [Pt(Gly-Gly-N,N',O)I]- with the N-acetylated dipeptide L-methionyl-L-histidine: selective platination of the histidine side chain by intramolecular migration of the platinum(II) complex

The reaction of the monofunctional [Pt(Gly-Gly-N,N′,O)I]⁻ complex, in which Gly-Gly is the dipeptide glycyl-glycine coordinated through two nitrogen and oxygen atoms, with the N-acetylated dipeptide l-methionyl-l-histidine (MeCOMet-His) studied by ¹H NMR spectroscopy. All reactions were carried out in 50 mM phosphate buffer at pD 7.4 and at 25 °C. In the initial stage of the reaction, the platinum(II) complex forms the kinetically favored [Pt(Gly-Gly-N,N′,O)(MeCOMet-His-S)]⁻ complex, with unidentate coordination of the MeCOMet-His dipeptide through the sulfur atom of the methionine residue. In the second stage of the reaction, complete intramolecular migration of the [Pt(Gly-Gly-N,N′,O)] unit from the sulfur to the N3 nitrogen atom of imidazole was observed and a new platinum(II)-peptide complex, [Pt(Gly-Gly-N,N′,O)(MeCOMet-His-N3)]⁻ was formed. In comparison with previous results obtained for the reaction of [Pt(dien)Cl]⁺ with different methionine- and histidine-containing peptides, this migration reaction was sufficiently fast and strongly selective to the N3 atom of the imidazole ring of the histidine side chain. This study is an important step in the development of new platinum(II) complexes for selective covalent modification of peptides and proteins.     

Blue shifts <Emphasis Type="Italic">vs</Emphasis> red shifts in σ-hole bonding

σ-Hole bonding is a noncovalent interaction between a region of positive electrostatic potential on the outer surface of a Group V, VI, or VII covalently-bonded atom (a σ-hole) and a region of negative potential on another molecule, e.g., a lone pair of a Lewis base. We have investigated computationally the occurrence of increased vibration frequencies (blue shifts) and bond shortening vs decreased frequencies (red shifts) and bond lengthening for the covalent bonds to the atoms having the σ-holes (the σ-hole donors). Both are possible, depending upon the properties of the donor and the acceptor. Our results are consistent with models that were developed earlier by Hermansson and by Qian and Krimm in relation to blue vs red shifting in hydrogen bond formation. These models invoke the derivatives of the permanent and the induced dipole moments of the donor molecule. Figure Computed electrostatic potential on the molecular surface of Cl-NO₂. Color ranges, in kcal mol⁻¹, are: red, greater than 25; yellow, between 10 and 25; green, between 0 and 10; blue, between −4 and 0; purple, more negative than −4. The chlorine is facing the viewer, to the right. Note the yellow region of positive potential on the outer side of the chlorine, along the extension of the N–Cl bond. The blue region shows the sides of the chlorine to have negative potentials. The calculations were at the B3PW91/6–31G(d,p) level.     

Infrared and Raman spectra and vibrational analyses calculated with Moeller–Plesset perturbation theory of second order of nitrosoethylene and its chloro-derivatives

The conformational and structural stabilities of nitrosoethylene CH₂=CH–N=O, chloronitrosoethylene CH₂=CCl–N=O, and Dichloronitrosoethylene CCl₂=CH–N=O were investigated by ab initio Moeller–Plesset perturbation theory of second order (MP2) calculations using the 6−311+G^** basis set to include electron correlation. From the calculations all three were predicted to exist predominantly in the planar trans structure (C=C and N=O bonds are trans to each other) with high trans-cis rotational barriers of about 9 kcal mol⁻¹ as a result of pronounced conjugation between C=C and N=O bonds. The vibrational frequencies were computed for the three molecules, and also the d ₁ and d ₂ deuterated variants for the parent molecule at the MP2 level. Normal coordinate analyses were carried out and the potential energy distributions (PED), among the symmetry coordinates of the normal modes of the molecule were computed. Complete vibrational assignments were made on the basis of normal coordinate analyses for the molecules. The two chlorinated derivatives of nitrosoethylene were also investigated in the same way. As expected, we then find high Raman and infrared intensities in all modes that contain a high content of chlorine movements because vibrations of C–Cl bonds lead to large changes in polarizability, as well as to a large change in dipole moment. However, modes involving double bonds also have quite large intensities. An appreciable number of modes in these molecules are more or less pure symmetry coordinates.     

A B3LYP and MP2(full) theoretical investigation into explosive sensitivity upon the formation of the molecule-cation interaction between the nitro group of 3,4-dinitropyrazole and H+, Li+, Na+, Be2+ or Mg2+

The explosive sensitivity upon the formation of molecule-cation interaction between the nitro group of 3,4-dinitropyrazole (DNP) and H⁺, Li⁺, Na⁺, Be²⁺ or Mg²⁺ has been investigated using the B3LYP and MP2(full) methods with the 6-311++G** and 6-311++G(2df,2p) basis sets. The bond dissociation energy (BDE) of the C3–N7 trigger bond has also been discussed for the DNP monomer and the corresponding complex. The interaction between the oxygen atom of nitro group and H⁺ in DNP…H⁺ is partly covalent in nature. The molecule-cation interaction and bond dissociation energy of the C3–N7 trigger bond follow the order of DNP…Be²⁺ > DNP…Mg²⁺ > DNP…Li⁺ > DNP…Na⁺. Except for DNP…H⁺, the increment of the trigger bond dissociation energy in comparison with the DNP monomer correlates well with the molecule-cation interaction energy, natural charge of the nitro group, electron density ρ _BCP(C3–N7), delocalization energy E ⁽²⁾ and NBO charge transfer. The analyses of atoms in molecules (AIM), natural bond orbital (NBO) and electron density shifts have shown that the electron density of the nitro group shifts toward the C3–N7 trigger bond upon the formation of the molecule-cation interaction. Thus, the trigger bond is strengthened and the sensitivity of DNP is reduced.     

Crystal structure and conformational analysis of s-cis-(acetylacetonato)(ethylenediamine-N,N′-diacetato)-chromium(III)

The crystal structure of [Cr(edda)(acac)] (edda = ethylediamine-N,N′-diacetate; acac = acetylacetonato) has been determined by a single crystal X-ray diffraction study at 150 K. The chromium ion is in a distorted octahedral environment coordinated by two N and two O atoms of chelating edda and two O atoms of acac, resulting in s-cis configuration. The complex crystallizes in the space group P2₁/c of the monoclinic system in a cell of dimensions a = 10.2588(9), b = 15.801(3), c = 8.7015(11) ?, β =101.201(9)° and Z = 4. The mean Cr-N(edda), Cr-O(edda) and Cr-O(acac) bond distances are 2.0829(14), 1.9678(11) and 1.9477(11) ? while the angles O-Cr-O of edda and O-Cr-O of acac are 171.47(5) and 92.72(5)°, respectively. The crystal structure is stabilized by N–H⋯O hydrogen bonds linking [Cr(edda)(acac)] molecules in distinct linear strands. The visible electronic and IR spectroscopic properties are also discussed. An improved, physically more realistic force field, Vibrationally Optimized Force Field (VOFF), capable of reproducing structural and vibrational properties of [Cr(edda)(acac)] was developed and its transferability demonstrated on selected chromium(III) complexes with similar ligands.     

Greater Soil Carbon Sequestration under Nitrogen-fixing Trees Compared with <Emphasis Type="Italic">Eucalyptus</Emphasis> Species

Forests with nitrogen-fixing trees (N–fixers) typically accumulate more carbon (C) in soils than similar forests without N–fixing trees. This difference may develop from fundamentally different processes, with either greater accumulation of recently fixed C or reduced decomposition of older soil C. We compared the soil C pools under N–fixers with Eucalyptus (non–N–fixers) at four tropical sites: two sites on Andisol soils in Hawaii and two sites on Vertisol and Entisol soils in Puerto Rico. Using stable carbon isotope techniques, we tracked the loss of the old soil organic C from the previous C₄ land use (SOC₄) and the gain of new soil organic C from the C₃, N–fixer, and non–N–fixer plantations (SOC₃). Soils beneath N–fixing trees sequestered 0.11 ± 0.07 kg m⁻² y⁻¹ (mean ± one standard error) of total soil organic carbon (SOC_T) compared with no change under Eucalyptus (0.00 ± 0.07 kg m⁻² y⁻¹; P = 0.02). About 55% of the greater SOC_T sequestration under the N–fixers resulted from greater retention of old SOC₄, and 45% resulted from greater accretion of new SOC₃. Soil N accretion under the N–fixers explained 62% of the variability of the greater retention of old SOC₄ under the N–fixers. The greater retention of older soil C under N–fixing trees is a novel finding and may be important for strategies that use reforestation or afforestation to offset C emissions. Received 12 March 2001; accepted 5 October 2001.     

First-principle study of interfacial properties between γ-TiAl and TiC,VN

The adhesion, wettability, atomic bonding and electronic structure of γ-TiAl(110)/TiC(100) and γ-TiAl(110)/VN(100) interfaces were performed and investigated using first-principle calculations. Surface energy of γ-TiAl, TiC and VN with low crystal indices was calculated and compared, respectively. The three Al-terminated γ-TiAl(110)/ceramic(100) interface models were investigated to illustrate the interfacial bonding nature. The structure of Al atom placed on the top of the metalloid C and N atoms at the interface is the preferred interfacial structure with the larger work of adhesion. The electronic structure results show that the structure with metalloid site exists with the stronger polar covalent bonding between the interfacial Al and metalloid atom. The interfacial structure with metal site exhibits a mixture of the metallic features with some degree of covalent features. The simulation results are in agreement with the experimental results, in which the γ-TiAl/TiC interface exhibits the better wettability and stronger bonding than the γ-TiAl/VN interface.     

Multiplicity of cadmium binding sites in nucleotides: X-ray evidence for the involvement of O2'' and O3'' as well as phosphate and N7 in inosine 5''-monophosphate.

Single-crystal X-ray methods have been used to characterize a hydrated polymeric cadmium derivative of inosine 5'-monophosphate. In the structure there are two independent cadmium atoms, one of which binds to two ribose oxygen atoms, an N7 position on a base, and to three water molecules. The second metal atom binds to a phosphate oxygen, three water molecules, and to two N7 atoms, which are in cis-positions. For these last; the Cd-N bonds are appreciably out of the planes of the hypoxanthine bases so that the angle between these planes is only 31.4 degrees.     

The three-dimensional structure of bovine calcium ion-bound osteocalcin using 1H NMR spectroscopy

Structural information on osteocalcin or other noncollagenous bone proteins is very limited. We have solved the three-dimensional structure of calcium bound osteocalcin using (1)H 2D NMR techniques and proposed a mechanism for mineral binding. The protons in the 49 amino acid sequence were assigned using standard two-dimensional homonuclear NMR experiments. Distance constraints, dihedral angle constraints, hydrogen bonds, and (1)H and (13)C chemical shifts were all used to calculate a family of 13 structures. The tertiary structure of the protein consisted of an unstructured N terminus and a C-terminal loop (residues 16-49) formed by long-range hydrophobic interactions. Elements of secondary structure within residues 16-49 include type III turns (residues 20-25) and two alpha-helical regions (residues 27-35 and 41-44). The three Gla residues project from the same face of the helical turns and are surface exposed. The genetic algorithm-molecular dynamics simulation approach was used to place three calcium atoms on the NMR-derived structure. One calcium atom was coordinated by three side chain oxygen atoms, two from Asp30, and one from Gla24. The second calcium atom was coordinated to four oxygen atoms, two from the side chain in Gla 24, and two from the side chain of Gla 21. The third calcium atom was coordinated to two oxygen atoms of the side chain of Gla17. The best correlation of the distances between the uncoordinated Gla oxygen atoms is with the intercalcium distance of 9.43 A in hydroxyapatite. The structure may provide further insight into the function of osteocalcin.