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1.
Plant Cell Rep ; 43(6): 136, 2024 May 06.
Artigo em Inglês | MEDLINE | ID: mdl-38709311

RESUMO

KEY MESSAGE: In our study, we discovered a fragment duplication autoregulation mechanism in 'ZS-HY', which may be the reason for the phenotype of red foliage and red flesh in grapes. In grapes, MYBA1 and MYBA2 are the main genetic factors responsible for skin coloration which are located at the color loci on chromosome 2, but the exact genes responsible for color have not been identified in the flesh. We used a new teinturier grape germplasm 'ZhongShan-HongYu' (ZS-HY) which accumulate anthocyanin both in skin and flesh as experimental materials. All tissues of 'ZS-HY' contained cyanidin 3-O-(6″-p-coumaroyl glucoside), and pelargonidins were detected in skin, flesh, and tendril. Through gene expression analysis at different stage of flesh, significant differences in the expression levels of VvMYBA1 were found. Gene amplification analysis showed that the VvMYBA1 promoter is composed of two alleles, VvMYBA1a and 'VvMYBA1c-like'. An insertion of a 408 bp repetitive fragment was detected in the allele 'VvMYBA1c-like'. In this process, we found the 408 bp repetitive fragment was co-segregated with red flesh and foliage phenotype. Our results revealed that the 408 bp fragment replication insertion in promoter of 'VvMYBA1c-like' was the target of its protein, and the number of repeat fragments was related to the increase of trans-activation of VvMYBA1 protein. The activation of promoter by VvMYBA1 was enhanced by the addition of VvMYC1. In addition, VvMYBA1 interacted with VvMYC1 to promote the expression of VvGT1 and VvGST4 genes in 'ZS-HY'. The discovery of this mutation event provides new insights into the regulation of VvMYBA1 on anthocyanin accumulation in red-fleshed grape, which is of great significance for molecular breeding of red-fleshed table grapes.


Assuntos
Antocianinas , Regulação da Expressão Gênica de Plantas , Fenótipo , Proteínas de Plantas , Regiões Promotoras Genéticas , Fatores de Transcrição , Vitis , Vitis/genética , Vitis/metabolismo , Regiões Promotoras Genéticas/genética , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo , Antocianinas/metabolismo , Antocianinas/genética , Pigmentação/genética , Frutas/genética , Frutas/metabolismo , Alelos
2.
Int J Mol Sci ; 24(7)2023 Mar 30.
Artigo em Inglês | MEDLINE | ID: mdl-37047480

RESUMO

Very long-chain fatty acid (VLCFA) synthesis in plants, is primarily rate-limited by the enzyme 3-ketoacyl CoA synthase (KCS), which also controls the rate and carbon chain length of VLCFA synthesis. Disruption of VLCFA during pollen development, may affect the pollen wall formation and ultimately lead to male sterility. Our study identified 24 grapevine KCS (VvKCS) genes and provided new names based on their relative chromosome distribution. Based on sequence alignment and phylogenetic investigation, these genes were grouped into seven subgroups, members of the same subgroup having similar motif structures. Synteny analysis of VvKCS genes, showed that the segmental duplication events played an important role in expanding this gene family. Expression profiles obtained from the transcriptome data showed different expression patterns of VvKCS genes in different tissues. Comparison of transcriptome and RT-qPCR data of the male sterile grape 'Y-14' and its fertile parent 'Shine Muscat', revealed that 10 VvKCS genes were significantly differentially expressed at the meiosis stage, which is a critical period of pollen wall formation. Further, joint analysis by weighted gene co-expression network analysis (WGCNA) and Kyoto Encyclopedia of Genes and Genomes (KEGG), revealed that five of these VvKCS (VvKCS6/15/19/20/24) genes were involved in the fatty acid elongation pathway, which may ultimately affect the structural integrity of the pollen wall in 'Y-14'. This systematic analysis provided a foundation for further functional characterization of VvKCS genes, with the aim of grapevine precision breeding improvement.


Assuntos
Genes de Plantas , Infertilidade Masculina , Masculino , Humanos , Filogenia , Melhoramento Vegetal , Perfilação da Expressão Gênica , Transcriptoma , Infertilidade Masculina/genética , Ácidos Graxos/genética , Regulação da Expressão Gênica de Plantas
3.
Int J Mol Sci ; 23(14)2022 Jul 13.
Artigo em Inglês | MEDLINE | ID: mdl-35887065

RESUMO

Anthocyanins are synthesized in the endoplasmic reticulum and then transported to the vacuole in plants. Glutathione S-transferases (GSTs) are thought to play a key role in anthocyanin transport. To clarify the mechanism of GST genes in the accumulation and transport of anthocyanin in the early fruit stage, we analyzed and characterized the GST family in the flesh of 'Zhongshan-HongYu' (ZS-HY) based on the transcriptome. In this study, the 92 GST genes identified through a comprehensive bioinformatics analysis were unevenly present in all chromosomes of grapes, except chromosomes 3, 9 and 10. Through the analysis of the chromosomal location, gene structure, conserved domains, phylogenetic relationships and cis-acting elements of GST family genes, the phylogenetic tree divided the GST genes into 9 subfamilies. Eighteen GST genes were screened and identified from grape berries via a transcriptome sequencing analysis, of which 4 belonged to the phi subfamily and 14 to the tau subfamily, and the expression levels of these GST genes were not tissue-specific. The phylogenetic analysis indicated that VvGST4 was closely related to PhAN9 and AtTT19. This study provides a foundation for the analysis of the GST gene family and insight into the roles of GSTs in grape anthocyanin transport.


Assuntos
Antocianinas , Vitis , Antocianinas/metabolismo , Regulação da Expressão Gênica de Plantas , Glutationa Transferase/metabolismo , Filogenia , Proteínas de Plantas/metabolismo , Vitis/genética , Vitis/metabolismo
4.
Proc Natl Acad Sci U S A ; 115(50): E11578-E11585, 2018 12 11.
Artigo em Inglês | MEDLINE | ID: mdl-30463943

RESUMO

The Kohn-Sham potential [Formula: see text] is the effective multiplicative operator in a noninteracting Schrödinger equation that reproduces the ground-state density of a real (interacting) system. The sizes and shapes of atoms, molecules, and solids can be defined in terms of Kohn-Sham potentials in a nonarbitrary way that accords with chemical intuition and can be implemented efficiently, permitting a natural pictorial representation for chemistry and condensed-matter physics. Let [Formula: see text] be the maximum occupied orbital energy of the noninteracting electrons. Then the equation [Formula: see text] defines the surface at which classical electrons with energy [Formula: see text] would be turned back and thus determines the surface of any electronic object. Atomic and ionic radii defined in this manner agree well with empirical estimates, show regular chemical trends, and allow one to identify the type of chemical bonding between two given atoms by comparing the actual internuclear distance to the sum of atomic radii. The molecular surfaces can be fused (for a covalent bond), seamed (ionic bond), necked (hydrogen bond), or divided (van der Waals bond). This contribution extends the pioneering work of Z.-Z. Yang et al. [Yang ZZ, Davidson ER (1997) Int J Quantum Chem 62:47-53; Zhao DX, et al. (2018) Mol Phys 116:969-977] by our consideration of the Kohn-Sham potential, protomolecules, doubly negative atomic ions, a bond-type parameter, seamed and necked molecular surfaces, and a more extensive table of atomic and ionic radii that are fully consistent with expected periodic trends.

5.
Int J Mol Sci ; 21(12)2020 Jun 18.
Artigo em Inglês | MEDLINE | ID: mdl-32570751

RESUMO

The glycogen synthase kinase 3/shaggy kinase (GSK3) is a serine/threonine kinase that plays important roles in brassinosteroid signaling, abiotic stress responses, cell division, and elongation, etc. In this study, we characterized seven grape GSK3 genes, showing high similarities with homologs from other species including Arabidopsis, white pear, apple, orange, and peach. Gene chip microarray data derived from an online database revealed very diverse developmental and tissue-specific expression patterns of VvSKs. VvSK3 and VvSK7 showed much higher expression levels in almost every tissue compared with other members. VvSK7 was highly enriched in young tissues like berries before the veraison stage, young leaves and green stems, etc., but immediately downregulated after these tissues entered maturation or senescence phases. Prediction of cis-elements in VvSK promoters indicated that VvSKs might be sensitive to light stimulation, which is further confirmed by the qPCR data. Constitutive overexpression of VvSK7 in Arabidopsis leads to dwarf plants that resembles BR-deficient mutants. The photosynthetic rate was significantly reduced in these plants, even though they accumulated more chlorophyll in leaves. Transient overexpression of VvSKs in tomatoes delayed the fruit ripening process, consistent with the observation in grapevine which blocks VvSKs by EBR- or BIKININ-promoted berry expansion and soluble solids accumulation. Data presented in the current study may serve as a theoretical basis for the future application of BRs or related compounds in quality grape production.


Assuntos
Quinase 3 da Glicogênio Sintase/genética , Proteínas de Plantas/genética , Vitis/fisiologia , Clorofila/metabolismo , Evolução Molecular , Regulação da Expressão Gênica no Desenvolvimento , Regulação da Expressão Gênica de Plantas , Quinase 3 da Glicogênio Sintase/metabolismo , Especificidade de Órgãos , Fotossíntese , Filogenia , Proteínas de Plantas/metabolismo , Regiões Promotoras Genéticas , Vitis/genética
6.
Molecules ; 25(11)2020 Jun 02.
Artigo em Inglês | MEDLINE | ID: mdl-32498235

RESUMO

Volatile compounds are considered to be essential for the flavor and aroma quality of grapes. Thidiazuron (TDZ) is a commonly used growth regulator in grape cultivation that stimulates larger berries and prevents fruit drop. This study was conducted to investigate the effect of TDZ on the production of aroma volatiles and to identify the key genes involved in the terpene biosynthesis pathways that are affected by this compound. Treatment with TDZ had a negative effect on the concentration of volatile compounds, especially on monoterpenes, which likely impacts the sensory characteristics of the fruit. The expression analysis of genes related to the monoterpenoid biosynthesis pathways confirmed that treatment with TDZ negatively regulated the key genes DXS1, DXS3, DXR, HDR, VvPNGer and VvPNlinNer1. Specifically, the expression levels of the aforementioned genes were down-regulated in almost all berry development stages in the TDZ-treated samples. The novel results from the present study can be used to aid in the development of food products which maintain the flavor quality and sensory characteristics of grape. Furthermore, these findings can provide the theoretical basis that can help to optimize the utilization of TDZ for the field production of grapes at a commercial scale.


Assuntos
Monoterpenos/metabolismo , Compostos de Fenilureia/farmacologia , Proteínas de Plantas/genética , Tiadiazóis/farmacologia , Vitis/crescimento & desenvolvimento , Regulação para Baixo , Perfilação da Expressão Gênica , Regulação da Expressão Gênica no Desenvolvimento/efeitos dos fármacos , Regulação da Expressão Gênica de Plantas/efeitos dos fármacos , Odorantes/análise , Vitis/química , Vitis/genética , Compostos Orgânicos Voláteis/metabolismo
7.
Int J Mol Sci ; 20(14)2019 Jul 18.
Artigo em Inglês | MEDLINE | ID: mdl-31323865

RESUMO

Hydrogen cyanamide (HC) is an agrochemical compound that is frequently used to break bud dormancy in grapevines grown under mild winter conditions globally. The present study was carried out to provide an in-depth understanding of the molecular mechanism associated with HC releasing bud dormancy in grapevines. For this purpose, RNA-seq based transcriptomic and tandem mass tag (TMT)-based proteomic information was acquired and critically analyzed. The combined results of transcriptomic and proteomic analysis were utilized to demonstrate differential expression pattern of genes at the translational and transcriptional levels. The outcome of the proteomic analysis revealed that a total of 7135 proteins (p-value ≤ 0.05; fold change ≥ 1.5) between the treatments (HC treated versus control) were identified, out of which 6224 were quantified. Among these differentially expressed proteins (DEPs), the majority of these proteins were related to heat shock, oxidoreductase activity, and energy metabolism. Metabolic, ribosomal, and hormonal signaling pathways were found to be significantly enriched at both the transcriptional and translational levels. It was illustrated that genes associated with metabolic and oxidoreductase activity were mainly involved in the regulation of bud dormancy at the transcriptomic and proteomic levels. The current work furnishes a new track to decipher the molecular mechanism of bud dormancy after HC treatment in grapes. Functional characterization of key genes and proteins will be informative in exactly pinpointing the crosstalk between transcription and translation in the release of bud dormancy after HC application.


Assuntos
Flores/metabolismo , Vitis/metabolismo , Flores/genética , Regulação da Expressão Gênica de Plantas/genética , Regulação da Expressão Gênica de Plantas/fisiologia , Dormência de Plantas/genética , Dormência de Plantas/fisiologia , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Proteômica/métodos , Transcriptoma/genética , Vitis/genética
8.
J Chem Phys ; 148(7): 074110, 2018 Feb 21.
Artigo em Inglês | MEDLINE | ID: mdl-29471641

RESUMO

Nanostructures can be bound together at equilibrium by the van der Waals (vdW) effect, a small but ubiquitous many-body attraction that presents challenges to density functional theory. How does the binding energy depend upon the size or number of atoms in one of a pair of identical nanostructures? To answer this question, we treat each nanostructure as a whole object, not as a collection of atoms. Our calculations start from an accurate static dipole polarizability for each considered nanostructure, and an accurate equilibrium center-to-center distance for the pair (the latter from experiment or from the vdW-DF-cx functional). We consider the competition in each term -C2k/d2k (k = 3, 4, 5) of the long-range vdW series for the interaction energy, between the size dependence of the vdW coefficient C2k and that of the 2kth power of the center-to-center distance d. The damping of these vdW terms can be negligible, but in any case, it does not affect the size dependence for a given term in the absence of non-vdW binding. To our surprise, the vdW energy can be size-independent for quasi-spherical nanoclusters bound to one another by vdW interaction, even with strong nonadditivity of the vdW coefficient, as demonstrated for fullerenes. We also show that, for low-dimensional systems, the vdW interaction yields the strongest size-dependence, in stark contrast to that of fullerenes. We illustrate this with parallel planar polycyclic aromatic hydrocarbons. The size dependences of other morphologies or bonding types lie between, as shown by sodium clusters.

9.
BMC Plant Biol ; 17(1): 18, 2017 01 19.
Artigo em Inglês | MEDLINE | ID: mdl-28103799

RESUMO

BACKGROUND: Bud dormancy is an important biological phenomenon of perennial plants that enables them to survive under harsh environmental circumstances. Grape (Vitis vinifera) is one of the most grown fruit crop worldwide; however, underlying mechanisms involved in grape bud dormancy are not yet clear. This work was aimed to explore the underlying molecular mechanism regulating bud dormancy in grape. RESULTS: We have performed transcriptome and differential transcript expression analyses of "Shine Muscat" grape buds using the Illumina RNA-seq system. Comparisons of transcript expression levels among three stages of dormancy, paradormancy (PD) vs endodormancy (ED), summer buds (SB) vs ED and SB vs PD, resulted in the detection of 8949, 9780 and 3938 differentially expressed transcripts, respectively. Out of approximately 78 million high-quality generated reads, 6096 transcripts were differentially expressed (log2 ratio ≥ 1, FDR ≤ 0.001). Grape reference genome was used for alignment of sequence reads and to measure the expression level of transcripts. Furthermore, findings obtained were then compared using two different databases; Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), to annotate the transcript descriptions and to assign a pathway to each transcript. KEGG analysis revealed that secondary metabolites biosynthesis and plant hormone signaling was found most enriched out of the 127 total pathways. In the comparisons of the PD vs ED and SB vs ED stages of grape buds, the gibberellin (GA) and abscisic acid (ABA) pathways were found to be the most enriched. The ABA and GA pathways were further analyzed to observe the expression pattern of differentially expressed transcripts. Transcripts related to the PP2C family (ABA pathway) were found to be up-regulated in the PD vs ED comparison and down-regulated in the SB vs ED and SB vs PD comparisons. GID1 family transcripts (GA pathway) were up-regulated while DELLA family transcripts were down-regulated during the three dormancy stages. Differentially expressed transcripts (DEGs) related to redox activity were abundant in the GO biological process category. RT-qPCR assay results for 12 selected transcripts validated the data obtained by RNA-seq. CONCLUSION: At this stage, taking into account the results obtained so far, it is possible to put forward a hypothesis for the molecular mechanism underlying grape bud dormancy, which may pave the way for ultimate improvements in the grape industry.


Assuntos
Proteínas de Plantas/genética , RNA de Plantas/genética , Vitis/genética , Flores/genética , Flores/crescimento & desenvolvimento , Flores/metabolismo , Perfilação da Expressão Gênica , Regulação da Expressão Gênica no Desenvolvimento , Regulação da Expressão Gênica de Plantas , Dormência de Plantas , Proteínas de Plantas/metabolismo , RNA de Plantas/metabolismo , Vitis/crescimento & desenvolvimento , Vitis/metabolismo
10.
Phys Chem Chem Phys ; 19(32): 21707-21713, 2017 Aug 16.
Artigo em Inglês | MEDLINE | ID: mdl-28776618

RESUMO

Recently, Tao and Mo proposed a meta-generalized gradient approximation for the exchange-correlation energy with remarkable accuracy for molecules, solids, and surfaces. To better understand this functional, in this work, we make a comparative study of the TM and TMTPSS functionals, the latter of which is a combination of the TM exchange with the original TPSS correlation functional, on atoms, molecules, and hydrogen-bonded complexes by the use of eight well-known databases. Our calculations show that, while the TMTPSS functional achieves better accuracy for atomization energies or enthalpies of formation, harmonic vibrational frequencies, and atomic excitation energies than the TM functional, it is less accurate for proton affinities, molecular bond lengths, and in particular hydrogen-bonded complexes.

11.
J Chem Phys ; 146(23): 234102, 2017 Jun 21.
Artigo em Inglês | MEDLINE | ID: mdl-28641440

RESUMO

Excitation energy plays an important role in energy conversion, biological processes, and optical devices. In this work, we apply the Tao-Mo (TM) nonempirical meta-generalized gradient approximation and the combination TMTPSS (TMx + TPSSc), with TPSSc being the correlation part of the original TPSS (Tao-Perdew-Staroverov-Scuseria) to study excitation energies of small molecules and oligomers. Our test set consists of 17 molecules with 134 total excited states, including singlet, triplet, valence, and Rydberg excited states. Our calculation shows that both the TMTPSS and TM functionals yield good overall performance, with mean absolute errors (MAEs) of 0.37 eV and 0.42 eV, respectively, outperforming commonly used semilocal functionals LSDA (MAE = 0.55 eV), PBE (MAE = 0.58 eV), and TPSS (MAE = 0.47 eV). In particular, TMTPSS can yield nearly the same accuracy of B3LYP (MAE = 0.36 eV), with lower computational cost. The accuracy for semilocal density functional theory continues to hold for conjugated oligomers, but they become less accurate than hybrid functionals, due to the insufficient nonlocality.

12.
Plant Cell Physiol ; 57(3): 540-57, 2016 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-26858283

RESUMO

Anther development is a very precise and complicated process. In Arabidopsis, the AtMYB80 transcription factor regulates genes involved in pollen development and controls the timing of tapetal programmed cell death (PCD). In this study, we isolated and characterized cDNA for VviMYB80 expressed in flower buds of male-sterile Vitis vinifera L. cv. 'Zhong Shan Hong', a late-maturing cultivar derived from self-progeny of cv. 'Wink'. VviMYB80 belongs to the MYB80 subfamily and clusters with AtMYB35/TDF1 in a distinct clade. We found that in flower buds, expression of the VviMYB80 gene in cv. 'Zhong Shan Hong' sharply increased at the tetrad stage, resulting in a higher and earlier transcript level than that found in cv. 'Wink'. Expression of the VviMYB80 gene, driven by the 35S promoter, caused pleiotropic effects on the stamens, including smaller and shriveled anthers, delayed dehiscence, fewer seeds, shorter anther filaments, distorted pollen shape and a lack of cytoplasm, with the tapetum exhibiting hypertrophy in transformed tobacco. These results suggest that VviMYB80 may play an important role in stamen development and that expression of VviMYB80 driven by the 35S promoter in tobacco induces male sterility.


Assuntos
Regulação da Expressão Gênica de Plantas , Genes de Plantas , Nicotiana/genética , Infertilidade das Plantas/genética , Proteínas de Plantas/genética , Regiões Promotoras Genéticas , Vitis/genética , Vias Biossintéticas/genética , Parede Celular/metabolismo , DNA Complementar/genética , DNA Complementar/isolamento & purificação , Flores/citologia , Flores/crescimento & desenvolvimento , Flores/ultraestrutura , Regulação da Expressão Gênica no Desenvolvimento , Germinação , Fenótipo , Filogenia , Proteínas de Plantas/metabolismo , Plantas Geneticamente Modificadas , Propanóis/metabolismo , Análise de Sequência de DNA , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo
13.
Phys Rev Lett ; 117(7): 073001, 2016 Aug 12.
Artigo em Inglês | MEDLINE | ID: mdl-27563956

RESUMO

Most density functionals have been developed by imposing the known exact constraints on the exchange-correlation energy, or by a fit to a set of properties of selected systems, or by both. However, accurate modeling of the conventional exchange hole presents a great challenge, due to the delocalization of the hole. Making use of the property that the hole can be made localized under a general coordinate transformation, here we derive an exchange hole from the density matrix expansion, while the correlation part is obtained by imposing the low-density limit constraint. From the hole, a semilocal exchange-correlation functional is calculated. Our comprehensive test shows that this functional can achieve remarkable accuracy for diverse properties of molecules, solids, and solid surfaces, substantially improving upon the nonempirical functionals proposed in recent years. Accurate semilocal functionals based on their associated holes are physically appealing and practically useful for developing nonlocal functionals.

14.
J Chem Phys ; 144(3): 031102, 2016 Jan 21.
Artigo em Inglês | MEDLINE | ID: mdl-26801013

RESUMO

Due to the absence of the long-range van der Waals (vdW) interaction, conventional density functional theory (DFT) often fails in the description of molecular complexes and solids. In recent years, considerable progress has been made in the development of the vdW correction. However, the vdW correction based on the leading-order coefficient C6 alone can only achieve limited accuracy, while accurate modeling of higher-order coefficients remains a formidable task, due to the strong non-additivity effect. Here, we apply a model dynamic multipole polarizability within a modified single-frequency approximation to calculate C8 and C10 between small molecules. We find that the higher-order vdW coefficients from this model can achieve remarkable accuracy, with mean absolute relative deviations of 5% for C8 and 7% for C10. Inclusion of accurate higher-order contributions in the vdW correction will effectively enhance the predictive power of DFT in condensed matter physics and quantum chemistry.

15.
J Chem Phys ; 145(23): 234306, 2016 Dec 21.
Artigo em Inglês | MEDLINE | ID: mdl-28010100

RESUMO

Recently, Tao and Mo derived a meta-generalized gradient approximation functional based on a model exchange-correlation hole. In this work, the performance of this functional is assessed on standard test sets, using the 6-311++G(3df,3pd) basis set. These test sets include 223 G3/99 enthalpies of formation, 99 atomization energies, 76 barrier heights, 58 electron affinities, 8 proton affinities, 96 bond lengths, 82 harmonic vibrational frequencies, 10 hydrogen-bonded molecular complexes, and 22 atomic excitation energies. Our calculations show that the Tao-Mo functional can achieve high accuracy for most properties considered, relative to the local spin-density approximation, Perdew-Burke-Ernzerhof, and Tao-Perdew-Staroverov-Scuseria functionals. In particular, it yields the best accuracy for proton affinities, harmonic vibrational frequencies, hydrogen-bond dissociation energies and bond lengths, and atomic excitation energies.

16.
J Chem Phys ; 142(16): 164302, 2015 Apr 28.
Artigo em Inglês | MEDLINE | ID: mdl-25933759

RESUMO

Sublimation energy is one of the most important properties of molecular crystals, but it is difficult to study, because the attractive long-range van der Waals (vdW) interaction plays an important role. Here, we apply efficient semilocal density functional theory (DFT), corrected with the dynamically screened vdW interaction (DFT + vdW), the Rutgers-Chalmers nonlocal vdW-DF, and the pairwise-based dispersion-corrected DFT-D2 developed by Grimme and co-workers, to study the sublimation of fullerenes. We find that the short-range part, which accounts for the interaction due to the orbital overlap between fullerenes, is negligibly small. Our calculation shows that there exists a strong screening effect on the vdW interaction arising from the valence electrons of fullerenes. On the other hand, higher-order contributions can be as important as the leading-order term. The reasons are that (i) the surface of fullerene molecules is metallic and thus highly polarizable, (ii) the band gap of fullerene solids is small (less than 2 eV), and (iii) fullerene molecules in the solid phase are so densely packed, yielding the high valence electron density and small equilibrium intermolecular distances (the first nearest neighbor distance is only about 10 Å for C60). However, these two effects make opposite contributions, leading to significant error cancellation between these two contributions. We demonstrate that, by considering higher-order contributions and the dynamical screening, the DFT + vdW method can yield sublimation energies of fullerenes in good agreement with reference values, followed by vdW-DF and DFT-D2. The insights from this study are important for a better understanding of the long-range nature of vdW interactions in nanostructured solids.

17.
J Chem Phys ; 142(2): 024312, 2015 Jan 14.
Artigo em Inglês | MEDLINE | ID: mdl-25591358

RESUMO

Van der Waals (vdW) coefficients can be accurately generated and understood by modelling the dynamic multipole polarizability of each interacting object. Accurate static polarizabilities are the key to accurate dynamic polarizabilities and vdW coefficients. In this work, we present and study in detail a hollow-sphere model for the dynamic multipole polarizability proposed recently by two of the present authors (JT and JPP) to simulate the vdW coefficients for inhomogeneous systems that allow for a cavity. The inputs to this model are the accurate static multipole polarizabilities and the electron density. A simplification of the full hollow-sphere model, the single-frequency approximation (SFA), circumvents the need for a detailed electron density and for a double numerical integration over space. We find that the hollow-sphere model in SFA is not only accurate for nanoclusters and cage molecules (e.g., fullerenes) but also yields vdW coefficients among atoms, fullerenes, and small clusters in good agreement with expensive time-dependent density functional calculations. However, the classical shell model (CSM), which inputs the static dipole polarizabilities and estimates the static higher-order multipole polarizabilities therefrom, is accurate for the higher-order vdW coefficients only when the interacting objects are large. For the lowest-order vdW coefficient C6, SFA and CSM are exactly the same. The higher-order (C8 and C10) terms of the vdW expansion can be almost as important as the C6 term in molecular crystals. Application to a variety of clusters shows that there is strong non-additivity of the long-range vdW interactions between nanoclusters.

18.
Proc Natl Acad Sci U S A ; 109(1): 18-21, 2012 Jan 03.
Artigo em Inglês | MEDLINE | ID: mdl-22205765

RESUMO

The van der Waals interaction is a weak, long-range correlation, arising from quantum electronic charge fluctuations. This interaction affects many properties of materials. A simple and yet accurate estimate of this effect will facilitate computer simulation of complex molecular materials and drug design. Here we develop a fast approach for accurate evaluation of dynamic multipole polarizabilities and van der Waals (vdW) coefficients of all orders from the electron density and static multipole polarizabilities of each atom or other spherical object, without empirical fitting. Our dynamic polarizabilities (dipole, quadrupole, octupole, etc.) are exact in the zero- and high-frequency limits, and exact at all frequencies for a metallic sphere of uniform density. Our theory predicts dynamic multipole polarizabilities in excellent agreement with more expensive many-body methods, and yields therefrom vdW coefficients C(6), C(8), C(10) for atom pairs with a mean absolute relative error of only 3%.

19.
Phys Rev Lett ; 112(10): 106101, 2014 Mar 14.
Artigo em Inglês | MEDLINE | ID: mdl-24679308

RESUMO

van der Waals (vdW) interactions between particles and surfaces are critical for the study of physical adsorption. In this work, we develop a method to calculate the leading- and higher-order coefficients, describing the dependence of vdW interaction on height above the surface. We find that the proposed method can produce the vdW coefficients for atoms on surfaces of metals and semiconductors, with a mean absolute relative deviation of about 5%. As an important application, we study the adsorption energies for rare-gas atoms on noble-metal surfaces by combining the present method, which accounts for the long-range part, with semilocal density functional theory (DFT), which accounts for the short-range part. This combined DFT+vdW approach yields adsorption energies in excellent agreement (5%) with experiments. This suggests that the present method may serve as a useful dispersion correction to density functional approximations.

20.
J Phys Chem A ; 118(40): 9310-8, 2014 Oct 09.
Artigo em Inglês | MEDLINE | ID: mdl-25188223

RESUMO

A spin-forbidden reaction is a reaction in which the total electronic spin-state changes. The standard transition-state theory that assumes a reaction occurs on a single potential energy surface with spin-conservation cannot be applied to a spin-forbidden reaction directly. In this work, we derive the crossing coefficient based on the Wentzel-Kramers-Brillouin (WKB) theory to quantify the effect of intersystem crossing on the kinetics of spin-forbidden reactions. Acrylates and methacrylates, by themselves, can generate free radicals that initiate polymerization at temperatures above 120 °C. Previous studies suggest that a triplet diradical is a key intermediate in the self-initiation. The formation of a triplet diradical from two closed-shell monomer molecules is a spin-forbidden reaction. This study provides a quantitative analysis of singlet-triplet spin crossover of diradical species in self-initiation of acrylates and methacrylates, taking into account the effect of intersystem crossing. The concept of crossing control is introduced and demonstrated computationally to be a new likely route to generate monoradicals via monomer self-initiation in high temperature polymerization.

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