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1.
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. 相似文献
2.
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. 相似文献
3.
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. 相似文献
4.
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. 相似文献
5.
Hakan Kayi 《Journal of molecular modeling》2010,16(5):1029-1038
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. 相似文献
6.
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. 相似文献
7.
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. 相似文献
8.
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 相似文献
9.
10.
Many lineages of land plants (from lycopsids to angiosperms) have non-photosynthetic life cycle phases that involve obligate
mycoheterotrophic arbuscular mycorrhizal (AM) associations where the plant host gains organic carbon through glomalean symbionts.
Our goal was to isolate and phylogenetically identify the AM fungi associated with both the autotrophic and underground mycoheterotrophic
life cycle phases of Psilotum nudum. Phylogenetic analyses recovered 11 fungal phylotypes in four diverse clades of Glomus A that form AM associations with P. nudum mycoheterotrophic gametophytes and autotrophic sporophytes, and angiosperm roots found in the same greenhouse pots. The correspondence
of identities of AM symbionts in P. nudum sporophytes, gametophytes and neighboring angiosperms provides compelling evidence that photosynthetic heterospecific and
conspecific plants can serve as the ultimate sources of fixed carbon for mycoheterotrophic gametophytes of P. nudum, and that the transfer of carbon occurs via shared fungal networks. Moreover, broader phylogenetic analyses suggest greenhouse
Psilotum populations, like field-surveyed populations of mycoheterotrophic plants, form AM associations with restricted clades of
Glomus A. The phylogenetic affinities and distribution of Glomus A symbionts indicate that P. nudum greenhouse populations have the potential to be exploited as an experimental system to further study the physiology, ecology
and evolution of mycoheterotrophic AM associations.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
11.
Jaroslav Fulneček Roman Matyášek Aleš Kovařík 《Molecular genetics and genomics : MGG》2009,281(4):407-420
The widespread occurrence of epigenetic alterations in allopolyploid species deserves scrutiny that DNA methylation systems
may be perturbed by interspecies hybridization and polyploidization. Here we studied the genes involved in DNA methylation
in Nicotiana tabacum (tobacco) allotetraploid containing S and T genomes inherited from Nicotiana sylvestris and Nicotiana tomentosiformis progenitors. To determine the inheritance of DNA methyltransferase genes and their expression patterns we examined three
major DNA methyltransferase families (MET1, CMT3 and DRM) from tobacco and the progenitor species. Using Southern blot hybridization and PCR-based methods (genomic CAPS), we found
that the parental loci of these gene families are retained in tobacco. Homoeologous expression was found in all tissues examined
(leaf, root, flower) suggesting that DNA methyltransferase genes were probably not themselves targets of uniparental epigenetic
silencing for over thousands of generations of allotetraploid evolution. The level of CG and CHG methylation of selected high-copy
repeated sequences was similar and high in tobacco and its diploid progenitors. We speculate that natural selection might
favor additive expression of parental DNA methyltransferase genes maintaining high levels of DNA methylation in tobacco, which
has a repeat-rich heterochromatic genome.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.
Nucleotide sequence data reported are available in the DDBJ/EMBL/GenBank databases under the accession numbers AM946602–AM946620
and FM872474–FM872476. 相似文献
12.
Ulf Grunwald Wenbing Guo Kerstin Fischer Stanislav Isayenkov Jutta Ludwig-Müller Bettina Hause Xiaolong Yan Helge Küster Philipp Franken 《Planta》2009,229(5):1023-1034
A microarray carrying 5,648 probes of Medicago truncatula root-expressed genes was screened in order to identify those that are specifically regulated by the arbuscular mycorrhizal
(AM) fungus Gigaspora rosea, by Pi fertilisation or by the phytohormones abscisic acid and jasmonic acid. Amongst the identified genes, 21% showed a common
induction and 31% a common repression between roots fertilised with Pi or inoculated with the AM fungus G. rosea, while there was no obvious overlap in the expression patterns between mycorrhizal and phytohormone-treated roots. Expression
patterns were further studied by comparing the results with published data obtained from roots colonised by the AM fungi Glomus mosseae and Glomus intraradices, but only very few genes were identified as being commonly regulated by all three AM fungi. Analysis of Pi concentrations in plants colonised by either of the three AM fungi revealed that this could be due to the higher Pi levels in plants inoculated by G. rosea compared with the other two fungi, explaining that numerous genes are commonly regulated by the interaction with G. rosea and by phosphate. Differential gene expression in roots inoculated with the three AM fungi was further studied by expression
analyses of six genes from the phosphate transporter gene family in M. truncatula. While MtPT4 was induced by all three fungi, the other five genes showed different degrees of repression mirroring the functional differences
in phosphate nutrition by G. rosea, G. mosseae and G. intraradices.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
13.
Genomic and genetic analysis of Myb-related genes that regulate anthocyanin biosynthesis in grape berry skin 总被引:2,自引:0,他引:2
Azuma A Kobayashi S Mitani N Shiraishi M Yamada M Ueno T Kono A Yakushiji H Koshita Y 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2008,117(6):1009-1019
14.
15.
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. 相似文献
16.
17.
Annotated maps of the IGH, IGK, and IGL loci in the gray, short-tailed opossum Monodelphis domestica were generated from analyses of the available whole genome sequence for this species. Analyses of their content and organization
confirmed a number of previous conclusions based on characterization of complementary DNAs encoding opossum immunoglobulin
heavy and light chains and limited genomic analysis, including (a) the predominance of a single immunoglobulin heavy chain
variable region (IGHV) subgroup and clan, (b) the presence of a single immunoglobulin (Ig)G subclass, (c) the apparent absence
of an IgD, and (d) the general organization and V gene complexity of the IGK and IGL light chain loci. In addition, several unexpected discoveries were made including the presence of a partial V to D, germline-joined
IGHV segment, the first germline-joined Ig V gene to be found in a mammal. In addition was the presence of a larger number
of IGKV subgroups than had been previously identified. With this report, annotated maps of the major histocompatibility complex,
T-cell receptor, and immunoglobulin loci have been completed for M. domestica, the only non-eutherian mammalian species for which this has been accomplished, strengthening the utility of this species
as a model organism.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
18.
Marie J. E. Charpentier Cathy V. Williams Christine M. Drea 《Conservation Genetics》2008,9(6):1605-1615
The consequences of inbreeding have been well studied in a variety of taxa, revealing that inbreeding has major negative impacts
in numerous species, both in captivity and in the wild; however, as trans-generational health data are difficult to obtain
for long-lived, free-ranging species, similar analyses are generally lacking for nonhuman primates. Here, we examined the
long-term effects of inbreeding on numerous health estimates in a captive colony of ring-tailed lemurs (Lemur catta), housed under semi-natural conditions. This vulnerable strepsirrhine primate is endemic to Madagascar, a threatened hotspot
of biodiversity; consequently, this captive population represents an important surrogate. Despite significant attention to
maintaining the genetic diversity of captive animals, breeding colonies invariably suffer from various degrees of inbreeding.
We used neutral heterozygosity as an estimate of inbreeding and showed that our results reflect genome-wide inbreeding, rather
than local genetic effects. In particular, we found that genetic diversity affects several fitness correlates, including the
prevalence and burden of Cuterebra parasites and a third (N = 6) of the blood parameters analyzed, some of which reflect immunocompetence. As a final validation of inbreeding depression
in this captive colony, we showed that, compared to outbred individuals, inbred lemurs were more likely to die earlier from
diseases. Through these analyses, we highlight the importance of monitoring genetic variation in captive animals—a key objective
for conservation geneticists—and provide insight into the potential negative consequences faced by small or isolated populations
in the wild.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
19.
Stewart JJ 《Journal of molecular modeling》2007,13(12):1173-1213
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. 相似文献
20.
The objective of this study was to determine patterns of ectomycorrhizas (ECM) and arbuscular mycorrhizas (AM) colonization associated with Alnus acuminata (Andean alder), in relation to soil parameters (electrical conductivity, field H2O holding capacity, pH, available P, organic matter, and total N) at two different seasons (autumn and spring). The study was conducted in natural forests of A. acuminata situated in Calilegua National Park (Jujuy, Argentina). Nine ECM morphotypes were found on A. acuminata roots. The ECM colonization was affected by seasonality and associated positively with field H2O holding capacity, pH, and total N and negatively associated with organic matter. Two morphotypes (Russula alnijorullensis and Tomentella sp. 3) showed significant differences between seasons. Positive and negative correlations were found between five morphotypes (Alnirhiza silkacea, Lactarius omphaliformis, Tomentella sp. 1, Tomentella sp. 3, and Lactarius sp.) and soil parameters (total N, pH, and P). A significant negative correlation was found between field H2O holding capacity and organic matter with AM colonization. Results of this study provide evidence that ECM and AM colonization of A. acuminata can be affected by some soil chemical edaphic parameters and indicate that some ECM morphotypes are sensitive to changes in seasonality and soil parameters. 相似文献