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 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 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.     

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 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 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.     

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.     

AM1* parameters for phosphorus,sulfur and chlorine

An extension of the AM1 semiempirical molecular orbital technique, AM1*, is introduced. AM1* uses AM1 parameters and theory unchanged for the elements H, C, N, O and F. The elements P, S and Cl have been reparameterized using an additional set of d orbitals in the basis set and with two-center core–core parameters, rather than the Gaussian functions used to modify the core–core potential in AM1. Voityuk and Röschs AM1(d) parameters have been adopted unchanged for AM1* with the exception that new core–core parameters are defined for Mo–P, Mo–S and Mo–Cl interactions. Thus, AM1* gives identical results to AM1 for compounds with only H, C, N, O, and F, AM1(d) for compounds containing Mo, H, C, N, O and F only, but differs for molybdenum compounds containing P, S or Cl. The performance and typical errors of AM1* are discussed.Electronic Supplementary Material Supplementary material is available in the online version of this article at . Tables 2 and 4–7 and a full list (Tables S1, S2) of geometrical parameters and barrier heights are given in the supplementary material.This revised version was published online in September 2003.     

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.     

Significance of Trace Element Profile of Blood of Persons with Multiple Caries versus Sound Teeth

In order to determine any possible relation between chemical composition of a person’s blood to formation of dental caries, whole blood was analyzed for 35 inorganic elements (Si, Al, Fe, Ca, Mg, K, Mn, Ti, P, Li, Be, B, V, Cr, Co, Ni, Cu, Zn, As, Sr, Y, Nb, Mo, Ag, Cd, Sn, Sb, Ba, La, Ce, W, Pb, Bi, Zr, and F) in the 15 people having sound teeth as well as an equal number of those having multiple caries. The results showed the absence of 13 elements (Si, Al, Mn, Ti, Be, Co, As, Y, Cd, Ba, La, Ce, and Zr) in the blood of both groups. Of the remaining 22 elements, the results of only seven elements (Fe, P, B, V, Sr, Sn, and F) were significantly different between the two groups. The most remarkable finding of this study was significantly decreased amount of phosphorus, strontium, and fluorine and perhaps increased boron in the blood of persons with caries.     

Optimization of parameters for semiempirical methods IV: extension of MNDO,AM1, and PM3 to more main group elements

The NDDO semiempirical methods MNDO, AM1, and PM3 have been extended to all the remaining non-radioactive elements of the main group, excluding the noble gases. Most of the new elements are of Groups I and II. 44 sets of parameters are presented for the following methods and elements. MNDO: Na, Mg, K, Ca, Ga, As, Se, Rb, Sr, In, Sb, Te, Cs, Ba, Tl, and Bi; AM1: Li, Be, Na, Mg, K, Ca, Ga, As, Se, Rb, Sr, In, Sn, Sb, Te, Cs, Ba, Tl, Pb, and Bi; PM3: B, Na, K, Ca, Rb, Sr, Cs, and Ba. Average errors are presented for heats of formation, molecular geometries, etc.     

Comparison of the accuracy of semiempirical and some DFT methods for predicting heats of formation

A comparison is made of the relative accuracy of some NDDO semiempirical methods and the DFT functionals LYP and PW91 using both double and triple zeta basis sets. The comparison is between the calculated heat of formation and that reported in the NIST database.Electronic Supplementary Material Parameters for the tailored method are available in the supplementary material; these are suitable for use with MOPAC2002. All raw data (experimental heats of formation, geometries, total energies and heats of formation for the various methods, etc.) are also provided in CAChe format. Supplementary material is available for this article if you access the article at . A link in the frame on the left on that page takes you directly to the supplementary material.     

Characterization of suspended solids in Lake Biwa by measuring their elemental composition of Al,Si, P,S, K,Ca, Ti,Mn, and Fe

We investigated the concentrations of particulate Al, Si, P, S, K, Ca, Ti, Mn, and Fe at various areas of Lake Biwa, such as the limnetic zone in the northern basin, the offshore zone, the dredged area and Akanoi Bay in the southern basin, and reed community areas in the shore. In the wide and deep northern basin, the density of suspended solids was low, and substantial fractions of particulate Si, P, S, and Ca were biogenic matter produced by phytoplankton. In the offshore zone in the narrow and shallow southern basin, the concentration ratios of particulate Si, K, Ca, Ti, and Fe against particulate Al were almost constant throughout the year and were similar to those found in crusts. Therefore, these elements are most likely derived from terrigenous clay matter. In the dredged area where the hypolimnion became anoxic during the stratification period, the concentrations of particulate Fe, Mn, P, S, and Ca increased because of the formation of hydrous Fe and Mn oxides and Fe sulfide. In Akanoi Bay, the ratios of Mn/Al and Fe/Al were high because of the stirring of sediments enriched with Mn and Fe oxides. In the reed community areas, the concentration of suspended solids correlated well with particulate Fe and P, but not with Al or chlorophyll a; therefore these areas seem to be rich in humic organic matter enriched with P and Fe due to microbial activity. Thus, the elemental composition of suspended solids reflects the chemical, biological, and physical processes in the lake and gives us useful indices of the characteristics of the water. Received: February 5, 2001 / Accepted: August 28, 2001     

Theoretical investigation of the role of clay edges in prebiotic peptide bond formation

Amino acid activation by anhydride formation in model tetrahedral silicate and aluminate sites in clays and neutral phosphates have been studied by semi-empirical molecular orbital calculations. the results have been compared to previousab initio studies on the reactant species and were found to be in good agreement. The geometries of all species were totally optimized and heats of formation obtained. Relative heats of formation of the anhydrides indicate the extent of anhydride formation to be Al > Si > P which is the same order as the stability of hydrolysis. The relative efficacy of the anhydrides in promoting peptide bond formation has been evaluated using both thermodynamic and chemical reactivity criteria. Heats of reaction for model reactions were calculated from calculated enthalpies of formation of the products and reactants. The electrophilicity of the carbonyl carbon and the nucleophilicity of the oxygen were specifically used as indicators of chemical reactivity towards dipeptide formation by the activated amino acids. Our results indicate that if the reaction mechanism is dominated by the nucleophilic character of the oxygen, tetrahedral Al sites should be more active than Si, and if the electrophilic character dominates, the order would be reversed.     

Using elemental profiling to determine intrinsic markers to track the dispersal of Prostephanus truncatus,a pest of stored grain with alternative natural hosts

Detecting sources of insects attacking grain stores can help to develop more effective pest management tools. This study considers combinations of chemical elements as intrinsic markers for tracing resource use by Prostephanus truncatus (Horn) (Coleoptera: Bostrichidae), a pest of stored maize (Zea mays L., Poaceae) which occurs in natural environments where alternative hosts may support reservoirs of infestation. Prostephanus truncatus were laboratory‐reared on maize or field‐caught in pheromone‐baited flight‐traps. Beetles and hosts were screened for multiple elements using inductively coupled plasma atomic emission spectrometry (ICP‐AES). For elements above detection limits, we tested relationships between determinations for various host plants, and for beetles according to environment where captured. An alternative host, Spondias purpurea L. (Anacardiaceae), contained more Al, B, Ca, Cu, Fe, Mg, Si, and Sr than maize, and less P and Zn. Elemental profiles of beetles were associated with environment, with significantly lower Al, Ca, Cu, Cr, Fe, P, S, Si, Sr, Ti, and Zn determinations in maize‐reared beetles than in beetles captured in agricultural or natural environments. Additionally, Al, Ba, K, P, Sr, and Ti determinations of field beetles captured in agricultural vs. natural environments were significantly different. This suggests Al, Sr, and Ti as candidate markers for environment, and possibly others as elemental concentrations (except B, Ba, Ni, and P) were significantly different in comparisons of all field‐collected vs. maize‐reared beetles. We present a robust practical solution which successfully identified combinations of elemental markers for remotely tracing resource use and dispersal by P. truncatus. We discuss the application of chemical characterisation for identifying intrinsic markers of pests, particularly species with alternative hosts. We discuss how to manage the low replication and unbalanced sample sizes inherent in insect elemental screening, particularly when rarer elements are potential markers.     

What proportion of household dust is derived from outdoor soil?

This report estimated the amount of outdoor soil in indoor dust in the Calabrese et al. (1989) children soil ingestion study via the use of statistical modelling. The estimate used data on outdoor soil and indoor dust in the homes of 60 children with eight tracer elements (Al, Ba, Mn, Si, Ti, V, Y, and Zr). The model estimated that 31.3% of indoor dust had an origin of outdoor soil. Based on a previous report (Stanek and Calabrese, 1992) on differential soil from dust ingestion in the Calabrese et al. (1989) study and the data of the present analysis, the median outdoor soil ingestion of the Calabrese et al. (1989) study should be revised downward by 35%. For the three most reliable tracers, the median soil ingestion estimates would be reduced from 29 to 19 mg/d for Al, 55 to 36 mg/d for Ti, and 16 to 10 mg/d for, Zr.     

铝、硒、硅和磷复合处理对水稻幼苗生长的影响

采用二次正交旋转组合设计,以铝(Al)、硒(Se)、硅(Si)、磷(P)为处理因子,建立了多因子复合处理对水稻品种金优725幼苗存活率、百株苗鲜质量、百株根鲜质量和根脯氨酸含量影响的回归模型,并分析了各因子的主效应和互作效应.结果表明：在供试条件下,影响水稻幼苗生长的单因子主效应大小为Al>P>Se>Si.其中,Al表现为负效应,而P、Se和Si表现为正效应;除Al与Si的互作外,各因子间的互作效应均未达到显著水平.模拟寻优结果表明,Al在0.587～0.913 mmol·L^-1、Se在0.478～0.564 mg·L^-1、Si在0.613～1.069 mmol·L^-1、P在2.252～2.657 mmol·L^-1浓度范围时,可使水稻幼苗在一个存在铝胁迫的营养液环境下达到一个较佳的生长状态.     

Determination of Major and Minor Elements in the <Emphasis Type="Italic">Malva sylvestris</Emphasis> L. from Turkey Using ICP-OES Techniques

In this work, Malva sylvestris var. mauritiana (L.) leaves were collected from different points in Muradiye region of Manisa-Turkey. The leaves were dissolved by wet digestion method using a mixture of mineral acid. Concentrations of Ag, Al, B, Ba, Bi, Ca, Cd, Co, Cr, Cu, Fe, K, La, Mg, Mn, Na, Ni, Pb, Sn, Sr, Sb, Si, Ti, U, Zn, and Zr in prepared solutions were determined by using inductively coupled plasma optical emission spectrometry (ICP-OES). High Ca (13,848 mg/kg) and Mg (1,936 mg/kg) concentrations were found at the leaves. Obtained values were compared with the internationally permitted (standard) values. The results of elements were analyzed statistically (analysis of variance test). For different leaf sizes, concentration factors were calculated.     

Morgane, a new LTR retrotransposon group, and its subfamilies in wheats

Transposable elements are the main components of grass genomes, especially in Triticeae species. In a previous analysis, we identified a very short element, Morgane_CR626934-1; here we describe more precisely this unusual element. Morgane_CR626934-1 shows high sequence identity (until 98%) with ESTs belonging to other possible small elements, expressed under abiotic and biotic stress conditions. No putative functional polyprotein could be identified in all of these different Morgane-like sequences. Moreover, elements from the Morgane_CR626934-1 subfamily are found only in wheats and Agropyrum genomes and among these species, only Ae. tauschii and T. aestivum present a high copy number of these elements. They are highly conserved in wheat genomes (95.5%). Based on the uncommon characteristics of the described Morgane-like elements, we proposed to classify them in a new group within the Class I LTR retrotransposon, the Morgane group. Electronic Supplementary Material Supplementary material is available for this article at