AM1* parameters for aluminum, silicon, titanium and zirconium

Our extension of the AM1 semiempirical molecular orbital technique, AM1*, has been parameterized for the elements Al, Si, Ti and Zr. The basis sets for all four metals contain a set of d-orbitals. Thus, AM1* parameters are now available for H, C, N, O and F (which use the original AM1 parameters), Al, Si, P, S, Cl, Ti, Mo and Zr. Special attention was paid to reproducing homolytic and heterolytic bond-dissociation energies correctly. Such bond-energy data help to avoid eccentricities in the parameterization caused by inaccurate experimental heats of formation. The performance and typical errors of AM1* for the newly parameterized elements are discussed. Generally, the new method performs less well than established techniques for heats of formation but considerably better for the heats of reaction. Electronic Supplementary Material Supplementary material is available for this article at     

AM1* parameters for cobalt and nickel

We report the parameterization of AM1* for the elements Co and Ni. The basis sets for both metals contain one set each of s-, p- and d-orbitals. AM1* parameters are now available for H, C, N, O and F (which use the original AM1 parameters), Al, Si, P, S, Cl, Ti, V, Cr, Co, Ni, Cu, Zn, Br, Zr, Mo and I. The performance and typical errors of AM1* are discussed for Co and Ni and compared with available NDDO Hamiltonians.     

AM1* parameters for gold

We report the parameterisation of AM1* for gold. The basis set for gold contains one set each of s-, p- and d-orbitals. AM1* parameters are now available for H, C, N, O and F (which use the original AM1 parameters), Al, Si, P, S, Cl, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Br, Zr, Mo, I and Au. The performance and typical errors of AM1* for gold are discussed.     

AM1* parameters for manganese and iron

We report the parameterization of AM1* for the elements manganese and iron. The basis sets for both metals contain one set each of s-, p- and d-orbitals. AM1* parameters are now available for H, C, N, O and F (which use the original AM1 parameters), Al, Si, P, S, Cl, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Br, Zr, Mo, I and Au. The performance and typical errors of AM1* are discussed for Mn and Fe, and are compared with available NDDO Hamiltonians.     

AM1* parameters for palladium and silver

We report the parameterization of AM1* for the elements palladium and silver. The basis sets for both metals contain one set each of s-, p- and d-orbitals. AM1* parameters are now available for H, C, N, O and F (which use the original AM1 parameters), Al, Si, P, S, Cl, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Br, Zr, Mo, Pd, Ag, I and Au. The performance and typical errors of AM1* are discussed for Pd and Ag and compared with the PM6 Hamiltonian.     

AM1* parameters for vanadium and chromium

Our extension of the AM1 semiempirical molecular orbital technique, AM1*, has been parameterized for the elements V and Cr. The basis sets for both metals contain one set each of s-, p- and d-orbitals. AM1* parameters are now available for H, C, N, O and F (which use the original AM1 parameters), Al, Si, P, S, Cl, Ti, V, Cr, Cu, Zn, Br, Zr, Mo and I. The performance and typical errors of AM1* are discussed for V and Cr and compared with available NDDO Hamiltonians. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

AM1* parameters for copper and zinc

Our extension of the AM1 semiempirical molecular orbital technique, AM1*, has been parameterized for the elements Cu and Zn. The basis sets for both metals contain a set of d-orbitals. The zinc parameterization uses a filled d-shell to give 12 valence electrons. Thus, AM1* parameters are now available for H, C, N, O and F (which use the original AM1 parameters), Al, Si, P, S, Cl, Ti, Cu, Zn, Zr and Mo. The performance and typical errors of AM1* are discussed for the newly parameterized elements. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

AM1* parameters for bromine and iodine

Our extension of the AM1 semiempirical molecular orbital technique, AM1*, has been parameterized for the elements Br and I. The basis sets for both halogens contain a set of d-orbitals as polarization functions. AM1* performs as well as other MNDO-like methods that use d-orbitals in the basis, and better than those that rely on an sp-basis. Thus, AM1* parameters are now available for H, C, N, O and F (which use the original AM1 parameters), Al, Si, P, S, Cl, Ti, Cu, Zn, Br, Zr, Mo and I. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Chloride ligation in inorganic manganese model compounds relevant to Photosystem II studied using X-ray absorption spectroscopy

Chloride ions are essential for proper function of the photosynthetic oxygen-evolving complex (OEC) of Photosystem II (PS II). Although proposed to be directly ligated to the Mn cluster of the OEC, the specific structural and mechanistic roles of chloride remain unresolved. This study utilizes X-ray absorption spectroscopy (XAS) to characterize the Mn–Cl interaction in inorganic compounds that contain structural motifs similar to those proposed for the OEC. Three sets of model compounds are examined; they possess core structures Mn^IV₃O₄X (X=Cl, F, or OH) that contain a di--oxo and two mono--oxo bridges or Mn^IV₂O₂X (X=Cl, F, OH, OAc) that contain a di--oxo bridge. Each set of compounds is examined for changes in the XAS spectra that are attributable to the replacement of a terminal OH or F ligand, or bridging OAc ligand, by a terminal Cl ligand. The X-ray absorption near edge structure (XANES) shows changes in the spectra on replacement of OH, OAc, or F by Cl ligands that are indicative of the overall charge of the metal atom and are consistent with the electronegativity of the ligand atom. Fourier transforms (FTs) of the extended X-ray absorption fine structure (EXAFS) spectra reveal a feature that is present only in compounds where chloride is directly ligated to Mn. These FT features were simulated using various calculated Mn–X interactions (X=O, N, Cl, F), and the best fits were found when a Mn–Cl interaction at a 2.2–2.3 Å bond distance was included. There are very few high-valent Mn halide complexes that have been synthesized, and it is important to make such a comparative study of the XANES and EXAFS spectra because they have the potential for providing information about the possible presence or absence of halide ligation to the Mn cluster in PS II.Electronic Supplementary Material Supplementary material is available in the online version of this article at http://dx.doi.org/10.1007/s00775-003-0520-1Abbreviations bpea N,N-bis(2-pyridylmethyl)ethylamine - EXAFS extended X-ray absorption fine structure - FT Fourier transform - IPE inflection point energy - OEC oxygen evolving complex - PS II Photosystem II - tacn 1,4,7-triazacyclononane - XANES X-ray absorption near edge structure - XAS X-ray absorption spectroscopy - XRD X-ray diffraction     

Multipole electrostatic potential derived atomic charges in NDDO-methods with <Emphasis Type="Italic">spd</Emphasis>-basis sets

The recently introduced multipole approach for computing the molecular electrostatic potential (MEP) within the semiempirical neglect of diatomic differential overlap (NDDO) framework [Horn AHC, Lin Jr-H., Clark T (2005) Theor Chem Acc 114:159–168] has been used to obtain atomic charges of nearly ab initio quality by scaling the semiempirical MEP. The parameterization set comprised a total of 797 compounds and included not only the newly parameterized AM1* elements Al, Si, P, S, Cl, Ti, Zr, and Mo but also the standard AM1 elements H, C, N, O and F. For comparison, the ZDO-approximated MEP was also calculated analytically in the spd-basis. For the AM1*-optimized structures, single-point calculations at the B3LYP, HF and MP2 levels with the 6-31G(d) and LanL2DZP basis sets were performed to obtain the MEP. The regression analysis of all 12 combinations of semiempirical and ab initio MEP data yielded correlation coefficients of at least 0.99 in all cases. Scaling the analytical and multipole-derived semiempirical MEP by the regression coefficients yielded mean unsigned errors below 2.6 and 1.9 kcal mol⁻¹, respectively. Subsequently, for 22 drug molecules from the World Drug Index, atomic charges were computed according to the RESP procedure using XX/6-31G(d) (XX=B3LYP, HF, MP2) and scaled AM1* multipole MEP; the correlation coefficients obtained are 0.83, 0.85 and 0.83, respectively. Figure: Schematic representation of the atomic charge generation: The molecular electrostatic potential (MEP) is calculated using the AM1* Hamiltonian; then the semiempirical MEP is scaled to DFT or ab initio level, and atomic charges are generated subsequently by the restraint electrostatic potential (RESP) fit method. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible to authorized users. Proceedings of “Modeling Interactions in Biomolecules II”, Prague, September 5th–9th, 2005.     

Theoretical investigation of the structure and acid–base properties of potential 2-thiolumazine tautomeric forms using the AM1 semiempirical method

The relative stabilities of potential tautomers, in both gas and aqueous phases, have been calculated taking into account the entropy effects over the tautomeric equilibria, in order to determine the structure and acid–base properties of the most stable tautomers of 2-thiolumazine in different pH conditions. In each medium, the tautomer with the lowest energy must be the most representative form at the corresponding pH. Knowledge of the effect of the medium in the tautomerization energies allows us to evaluate the possible effect of the medium on the molecular stability. Clearly, the results show that in the gas phase the basicity of the potential donor atoms is N5<N8<O4<S2<N1<N3, and in the aqueous phase S2<(O4N5)<N8<N1<N3, with the higher basicity of N3 and N1 being common to the two phases. In the aqueous phase, the sulfur atom is usually found in the thiol form, whereas the oxygen atom is in the keto form only in the most stable species. Moreover the acid–base character of 2-thiolumazine in aqueous solution has been evaluated from the corresponding AM1 thermodynamic parameters. The results agree well with the experimental data. Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00894-002-0094-9Electronic Supplementary Material available.     

Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements

Several modifications that have been made to the NDDO core-core interaction term and to the method of parameter optimization are described. These changes have resulted in a more complete parameter optimization, called PM6, which has, in turn, allowed 70 elements to be parameterized. The average unsigned error (AUE) between calculated and reference heats of formation for 4,492 species was 8.0 kcal mol⁻¹. For the subset of 1,373 compounds involving only the elements H, C, N, O, F, P, S, Cl, and Br, the PM6 AUE was 4.4 kcal mol⁻¹. The equivalent AUE for other methods were: RM1: 5.0, B3LYP 6–31G*: 5.2, PM5: 5.7, PM3: 6.3, HF 6–31G*: 7.4, and AM1: 10.0 kcal mol⁻¹. Several long-standing faults in AM1 and PM3 have been corrected and significant improvements have been made in the prediction of geometries. Figure Calculated structure of the complex ion [Ta₆Cl₁₂]²⁺ (footnote): Reference value in parenthesis Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Nonorthogonal tight-binding model with H–C–N–O parameterisation

A parametric nonorthogonal tight-binding model (NTBM1) with the set of parameters for H–C–N–O systems is presented. This model compares well with widely used semi-empirical AM1 and PM3/PM7 models but contains less fitting parameters per atom. All NTBM1 parameters are derived based on a criterion of the best agreement between the calculated and experimental values of bond lengths, valence angles and binding energies for various H–C–N–O molecules. Results for more than 200 chemical compounds are reported. Parameters are currently available for hydrogen, carbon, nitrogen, oxygen atoms and corresponding interatomic interactions. The model has a good transferability and can be used for both relaxation of large molecular systems (e.g., high-molecular compounds or covalent cluster complexes) and long-timescale molecular dynamics simulation (e.g., modelling of thermal decomposition processes). The program package based on this model is available for download at no cost from http://ntbm.info.     

Biophysical characterization and molecular modeling of the coordinative-intercalative DNA monoadduct of a platinum-acridinylthiourea agent in a site-specifically modified dodecamer

The guanine-N7 monoadduct of [Pt(en)Cl(ACRAMTU)](NO₃)₂ (PT-ACRAMTU; en=ethane-1,2-diamine, ACRAMTU=1-[2-(acridin-9-ylamino)ethyl]-1,3-dimethylthiourea), a dual metalating/intercalating cytotoxic agent, was generated in a double-stranded dodecamer, d(CCTCTCG*TCTCC/GGAGACGAGAGG) (III*), and isolated by preparative reverse-phase high-performance liquid chromatography (HPLC). The adduct was characterized using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), circular-dichroism spectropolarimetry (CD), UV-melting curves, and NMR spectroscopy. In addition, a molecular mechanics/restrained molecular dynamics (MM/rMD) study was performed for this adduct using the AMBER force field. Monoadduction of the sequence leads to a pronounced increase in melting temperature, T_m=T_m(III*)–T_m(III)=9.7 °C. Because there is complete enthalpy–entropy compensation, binding occurs without noticeable thermodynamic destabilization. This feature and the CD (induced-ligand circular dichroism) and NMR (upfield shifts of aromatic acridine proton signals) data are indicative of a unique, nondenaturing dual-binding mode that involves partial intercalation of the acridine chromophore. An energy-minimized AMBER model of III* demonstrates that platination of G7-N7 of guanine in the major groove and partial insertion of the acridine moiety into the C6G19/G7C18 base step on the 5 face of the modified purine base is feasible and supportive of the experimental results. Differences in the biophysical properties between III* and duplexes containing adducts of the clinical-drug cisplatin are outlined, and possible biological consequences are discussed.Electronic Supplementary Material Supplementary material is available in the online version of this article at http://dx.doi.org/10.1007/s00775-004-0534-3Abbreviations ACRAMTU 1-[2-(acridin-9-ylamino)ethyl]-1,3-dimethylthiourea - dGuo 2-deoxyguanosine - dGuo* [Pt(en)(ACRAMTU-S)(dGuo-N7)]³⁺ - en ethane-1,2-diamine - ICD Induced circular dichroism - MALDI-TOF MS Matrix-assisted laser desorption ionization time-of-flight mass spectrometry - MM Molecular mechanics - PIPES 1,4-piperazinediethanesulfonic acid - PT-ACRAMTU [Pt(en)Cl(ACRAMTU)](NO₃)₂ - rMD Restrained molecular dynamics     

Solution conformation of human big endothelin-1

Summary The solution conformation of human big endothelin-1, a 38-residue peptide which serves as the putative precursor to the potent vasoconstrictor endothelin-1 has been examined by¹H NMR. NOEs were utilized as distance restraints in the distance geometry program DSPACE to generate initial structures. Further refinement of these structures was accomplished through molecular mechanics/molecular dynamics in an iterative process involving the incorporation of stereospecific assignments of prochiral centers and the use of back-calculation of NOESY spectra. A family of structures consisting of a type 11 -turn for residues 5–8 and an -helix extending from residues 9–16 constitute a well-defined region, as reflected by the atomic root-mean-square (RMS) difference of 1.56 Å about the mean coordinate positions of the backbone atoms (N, C, Ca and O). This core region (residues 1-15) is very similar to the core residues of endothelin-1 (Donlan, M. et al. (1991)J. Cell. Biochemistry, S15G, 85). While the evidence from NOESY and coupling constant data suggests that the C-terminal region, residues 17–34, is not a mixture of randomly distributed chain conformations, it is also not consistent with a single chain conformation. Under the conditions studied, residues 17–38 in human big endothelin-1 in water at pH 3.0 between 20–30°C appear to be represented by a series of conformers in dynamic equilibrium.     

Activation by a new synthetic acyltripeptide and its analogs entrapped in liposomes of rat alveolar macrophages to the tumor cytotoxic state

Summary FK-565 (heptanoyl--d-Glu-(l-meso-a, -A₂pm (l)-d-AlaOH) is a synthetic acyltripeptide closely resembling cell wall peptidoglycan peptides of Streptomyces in structure. Alveolar macrophages (AM) lavaged from lungs of F344 rats were activated by in vitro treatment with FK-565 and its derivatives at concentrations of 1–50 g/ml medium, and the activated AM killed syngeneic mammary adenocarcinoma cells. When FK-565 and related compounds were encapsulated in multilamellar (MLV) liposomes composed of phosphatidyl-choline and phosphatidylserine, dose-response experiments showed that they were about 800 times more effective than the free compounds in activating AM. Liposome-encapsulated FK-565 and its analogs caused significant activation of AM within 4 h. These data indicated that acyltripeptide and its analogs encapsulated in liposomes are more efficient than the free compounds in rendering AM tumoricidal.     

Secondary structure of β-hydroxydecanoyl thiol ester dehydrase, a 39-kDa protein, derived from Hα, Cα, Cβ and CO signal assignments and the Chemical Shift Index: Comparison with the crystal structure

Summary Nearly complete backbone ¹H, ¹⁵N and ¹³C signal assignments are reported for -hydroxydecanoyl thiol ester dehydrase, a 39-kDa homodimer containing 342 amino acids. Although ¹⁵N relaxation data show that the protein has a rotational correlation time of 18 ns, assignments were derived from triple-resonance experiments recorded at 500 MHz and pH 6.8, without deuteration. The Chemical Shift Index, CSI, identified two long helices and numerous -strands in dehydrase. The CSI predictions are in close agreement with the secondary structure identified in the recently derived crystal structure, particularly when one takes account of the numerous bulges in the -strands. The assignment of dehydrase and a large deuterated protein [Yamazaki et al. (1994) J. Am. Chem. Soc., 116, 11655–11666] suggest that assignment of 40–60 kDa proteins is feasible. Hence, further progress in understanding the chemical shift/structure relationship could open the way to determine the structures of such large proteins. Supplementary Material is available on request, comprising Table S1 listing the spectral parameters; Table S2 listing the assignments; Fig. S1 showing the 2D ¹H–¹⁵N HSQC spectrum; Fig. S2 showing sequential NOEs, secondary shifts, H-exchange and ³J_HN data; and Fig. S3 showing plots of the H, C, CO and C Chemical Shift Indexes.To whom correspondence should be addressed.     

Removal of inorganic nitrogen sources from water by the algal biofilm of the aerial microalga Trentepohlia aurea

Removal of inorganic nitrogen sources by cells of the aerial microalga Trentepohlia aurea grown on the surface of substrate, such as filter paper, has been investigated in a batch system. When the alga grew on the paper dampened with medium, it actively ingested inorganic nitrogenous compounds in the medium. Immobilized cells on the filter papers were called algal biofilm in this study. When the algal biofilms were soaked in modified Bold's Basal medium (using 1 g NH₄Cl l^–1 as a N source), the removal rate was 4.25 mg ammonium-N l^–1 day^–1 in 40 days. In modified medium with added 26 mg nitrite-N, the removal rate of the total inorganic N ion by the biofilms reached 5.11 mg N l^–1 day^–1. This removal rate of total N ion was higher than that in the medium by addition of 26 mg nitrate-N. In addition, we tried to examine simultaneous removal of ammonium, nitrate, and nitrite ions and growth inhibition of cyanobacteria in the medium by using the algal biofilms. Consequently, it was demonstrated that the algal biofilms of T. aurea could be utilized as a biofunctional material for the purification of wastewater.     

Assignments of1H−15N magnetic resonances and identification of secondary structure elements of the λ-cro repressor

Summary The assignments of¹H–¹⁵N magnetic resonances of the -cro repressor are presented. Individual¹⁵N-amino acids were incorporated into the protein, or it was uniformly labeled with¹⁵N. For the¹³C–¹⁵N double-labeling experiments,¹³C-amino acids were incorporated into the uniformly¹⁵N-labeled protein. All the amide¹H–¹⁵N resonances could be assigned with such specific labeling, and sequential connectivities obtained by two-dimensional (2D)¹H–¹⁵N reverse correlation spectroscopies and three-dimensional (3D)¹H/¹⁵N NOESY-HMQC spectroscopy. Conventional 2D¹H–¹H correlation spectroscopies were applied to the assignment of the side-chain protons. Some of the¹H resonance assignments are inconsistent with those previously reported [Weber, P.L., Wemmer, D.E. and Reid, B.R. (1985)Biochemistry,24, 4553–4562]. The sequential NOE connectivities and H-D exchange rates indicate several elements of the secondary structure, including -helices consisting of residues 8–15, 19–25 and 28–37, and three extended strands consisting of residues 4–7, 39–45 and 49–55. Based on several long-range NOEs, the three extended strands could be combined to form an antiparallel -sheet. The amide proton resonances of the C-terminal residues except Ala⁶⁶ (residues 60–65) were hardly observed at neutral pH, indicating that the arm is flexible. The identified secondary structure elements in solution show good agreement with those in the crystal structure of the cro protein [Anderson, W.F., Ohlendorf, D.H., Takeda, Y. and Matthews, B.W. (1981)Nature,290, 754–758].     

Characterization of a protein-generated O₂ binding pocket in PqqC, a cofactorless oxidase catalyzing the final step in PQQ production

PQQ is an exogenous, tricyclic, quino-cofactor for a number of bacterial dehydrogenases. The final step of PQQ formation is catalyzed by PqqC, a cofactorless oxidase. This study focuses on the activation of molecular oxygen in an enzyme active site without metal or cofactor and has identified a specific oxygen binding and activating pocket in PqqC. The active site variants H154N, Y175F,S, and R179S were studied with the goal of defining the site of O(2) binding and activation. Using apo-glucose dehydrogenase to assay for PQQ production, none of the mutants in this "O(2) core" are capable of PQQ/PQQH(2) formation. Spectrophotometric assays give insight into the incomplete reactions being catalyzed by these mutants. Active site variants Y175F, H154N, and R179S form a quinoid intermediate (Figure 1) anaerobically. Y175S is capable of proceeding further from quinoid to quinol, whereas Y175F, H154N, and R179S require O(2) to produce the quinol species. None of the mutations precludes substrate/product binding or oxygen binding. Assays for the oxidation of PQQH(2) to PQQ show that these O(2) core mutants are incapable of catalyzing a rate increase over the reaction in buffer, whereas H154N can catalyze the oxidation of PQQH(2) to PQQ in the presence of H(2)O(2) as an electron acceptor. Taken together, these data indicate that none of the targeted mutants can react fully to form quinone even in the presence of bound O(2). The data indicate a successful separation of oxidative chemistry from O(2) binding. The residues H154, Y175, and R179 are proposed to form a core O(2) binding structure that is essential for efficient O(2) activation.