Coluci, VR; Galvao, DS; Baughman, RH
Theoretical investigation of electromechanical effects for graphyne carbon nanotubes Journal Article
In: The Journal of chemical physics, vol. 121, no. 7, pp. 3228–3237, 2004.
@article{coluci2004theoretical,
title = {Theoretical investigation of electromechanical effects for graphyne carbon nanotubes},
author = {Coluci, VR and Galvao, DS and Baughman, RH},
url = {http://scitation.aip.org/content/aip/journal/jcp/121/7/10.1063/1.1772756},
year = {2004},
date = {2004-01-01},
journal = {The Journal of chemical physics},
volume = {121},
number = {7},
pages = {3228--3237},
publisher = {AIP Publishing},
abstract = {We present a theoretical study of the electronic and mechanical properties of graphyne-based nanotubes (GNTs). These semiconducting nanotubes result from the elongation of one-third of the covalent interconnections of graphite-based nanotubes by the introduction of yne groups. The effect of charge injection on the dimensions of GNTs was investigated using tight-binding calculations. Low amounts of electron injection are predicted to cause qualitatively different responses for armchair and zigzag graphyne nanotubes. Although the behavior is qualitatively similar to the usual carbon nanotubes, the charge-induced strains are predicted to be smaller for the GNTs than for ordinary single walled carbon nanotubes.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Braga, Scheila Furtado; Galvao, Douglas Soares
A structure-activity study of taxol, taxotere, and derivatives using the electronic indices methodology (EIM) Journal Article
In: Journal of chemical information and computer sciences, vol. 43, no. 2, pp. 699–706, 2003.
@article{braga2003structure,
title = {A structure-activity study of taxol, taxotere, and derivatives using the electronic indices methodology (EIM)},
author = {Braga, Scheila Furtado and Galvao, Douglas Soares},
url = {http://pubs.acs.org/doi/abs/10.1021/ci025640v},
year = {2003},
date = {2003-01-01},
journal = {Journal of chemical information and computer sciences},
volume = {43},
number = {2},
pages = {699--706},
publisher = {American Chemical Society},
abstract = {Among the new families of effective anticancer drugs, the natural product paclitaxel (Taxol/Bristol-MyersSquibb)
and its semisynthetic derivative docetaxel (Taxotere/Rhone-Poulenc Rorer) are probably the most
promising agents under investigation. Surprisingly considering their importance no detailed quantum
mechanical studies have been carried out for these drugs. In this work we report the first structure-activity
relationship (SAR) studies for 20 taxoid structures using molecular descriptors from all-electron quantum
methods. The used methods were the pattern-recognition Principal Component Analysis (PCA), Hierarchical
Clustering Analysis (HCA), and the recently developed Electronic Indices Methodology (EIM). The combined
use of EIM with PCA/HCA methodologies was able to correctly classify active and inactive taxoids with
100% of accuracy using only a few “universal” quantum molecular descriptors. It was possible to identify
the electronic features defining active molecules. This information can be used to select and design new
active compounds. The combined use of EIM with PCA/HCA can be a new and very efficient tool in the
field of computer assisted drug design.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
and its semisynthetic derivative docetaxel (Taxotere/Rhone-Poulenc Rorer) are probably the most
promising agents under investigation. Surprisingly considering their importance no detailed quantum
mechanical studies have been carried out for these drugs. In this work we report the first structure-activity
relationship (SAR) studies for 20 taxoid structures using molecular descriptors from all-electron quantum
methods. The used methods were the pattern-recognition Principal Component Analysis (PCA), Hierarchical
Clustering Analysis (HCA), and the recently developed Electronic Indices Methodology (EIM). The combined
use of EIM with PCA/HCA methodologies was able to correctly classify active and inactive taxoids with
100% of accuracy using only a few “universal” quantum molecular descriptors. It was possible to identify
the electronic features defining active molecules. This information can be used to select and design new
active compounds. The combined use of EIM with PCA/HCA can be a new and very efficient tool in the
field of computer assisted drug design.
Del Nero, J; Galvao, DS; Laks, B
Electronic structure investigation of biosensor polymer Journal Article
In: Optical Materials, vol. 21, no. 1, pp. 461–466, 2003.
@article{del2003electronic,
title = {Electronic structure investigation of biosensor polymer},
author = {Del Nero, J and Galvao, DS and Laks, B},
url = {http://www.sciencedirect.com/science/article/pii/S0925346702001830},
year = {2003},
date = {2003-01-01},
journal = {Optical Materials},
volume = {21},
number = {1},
pages = {461--466},
publisher = {Elsevier},
abstract = {We report a theoretical study of the ground, excited and ionic states of 3-methyl pyrrole-4-carboxilic acid (MPC) oligomers and related compounds which present conformational defects. Our results reveal the existence of differentiated electronic behavior for MPC with relation to oligopyrrole derivatives. These electronic features might explain why MPC works properly as a biosensor for cytochrome C while no voltametric response is observed for unsubstituted poly(pyrrole).},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Coluci, VR; Braga, SF; Legoas, SB; Galvao, DS; Baughman, RH
Families of carbon nanotubes: Graphyne-based nanotubes Journal Article
In: Physical Review B, vol. 68, no. 3, pp. 035430, 2003.
@article{coluci2003families,
title = {Families of carbon nanotubes: Graphyne-based nanotubes},
author = {Coluci, VR and Braga, SF and Legoas, SB and Galvao, DS and Baughman, RH},
url = {http://journals.aps.org/prb/abstract/10.1103/PhysRevB.68.035430},
year = {2003},
date = {2003-01-01},
journal = {Physical Review B},
volume = {68},
number = {3},
pages = {035430},
publisher = {APS},
abstract = {New families of carbon single-walled nanotubes are proposed and their electronic structures are investigated. These nanotubes, called graphynes, result from the elongation of covalent interconnections of graphite-based nanotubes by the introduction of yne groups. Analogously to ordinary nanotubes, armchair, zigzag, and chiral graphyne nanotubes are possible. We here predict the electronic properties of these unusual nanotubes using tight-binding and ab initio density functional methods. Of the three graphyne nanotube families analyzed here, two provide metallic behavior for armchair tubes and either metallic or semiconducting behavior for zigzag nanotubes. A diameter- and chirality-independent band gap is predicted for the other investigated graphyne family, as well as an oscillatory dependence of the effective mass on nanotube diameter.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Coluci, VR; Braga, SF; Legoas, SB; Galvao, DS; Baughman, RH
Graphyne Nanotubes: New Families of Carbon Nanotubes Proceedings
Warrendale, Pa.; Materials Research Society; 1999, vol. 739, 2003.
@proceedings{coluci2003graphyne,
title = {Graphyne Nanotubes: New Families of Carbon Nanotubes},
author = {Coluci, VR and Braga, SF and Legoas, SB and Galvao, DS and Baughman, RH},
url = {http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=8031794},
year = {2003},
date = {2003-01-01},
journal = {MATERIALS RESEARCH SOCIETY SYMPOSIUM PROCEEDINGS},
volume = {739},
pages = {175--180},
publisher = {Warrendale, Pa.; Materials Research Society; 1999},
abstract = {Fundamentally new families of carbon single walled nanotubes are proposed. These nanotubes, called graphynes, result from the elongation of covalent interconnections of graphite-based nanotubes by the introduction of yne groups. Similarly to ordinary nanotubes, armchair, zig-zag, and chiral graphyne nanotubes are possible. We present here results for the electronic properties of graphyne based tubes obtained from tight-binding and ab initio density functional methods.},
keywords = {},
pubstate = {published},
tppubtype = {proceedings}
}
Giro, R; Galvao, DS
Semiempirical studies of the electronic structure of polyphenylene sulfide phenyleneamine Journal Article
In: International journal of quantum chemistry, vol. 95, no. 3, pp. 252–259, 2003.
@article{giro2003semiempirical,
title = {Semiempirical studies of the electronic structure of polyphenylene sulfide phenyleneamine},
author = {Giro, R and Galvao, DS},
url = {http://onlinelibrary.wiley.com/doi/10.1002/qua.10722/full},
year = {2003},
date = {2003-01-01},
journal = {International journal of quantum chemistry},
volume = {95},
number = {3},
pages = {252--259},
publisher = {Wiley Subscription Services, Inc., A Wiley Company},
abstract = {Polyphenylene sulfide (PPS) and polyaniline (PANI) are heteroatom-containing polymers with unique properties. While PPS provides a good level of chemical and thermal stability, PANI is important due to its ability to form electrically conducting films. A combination of PPS and PANI, with alternating phenyleneamine and phenylene sulfide blocks, resulted in a new material combining the structural features of PPS and PANI. This copolymer is known as polyphenylene sulfide–phenyleneamine (PPSA). In this work we present geometric and spectroscopic studies on PPSA oligomers using the well-known semiempirical methods PM3 (parametric method 3) and ZINDO-S/CI (Zerner's intermediate neglect of differential overlap/spectroscopic-configuration interaction). PM3 results show that long PPSA oligomers present alternating in- and out-of-plane rings with torsion angles about 60°. The ZINDO-simulated spectra compare well with the available experimental data. The origin of the low PPSA conductivity is addressed in terms of electronic features presented by isolated polymeric chains. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem 95: 252–259, 2003},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Braga, SF; Galvao, DS
A semiempirical study on the electronic structure of 10-deacetylbaccatin-III Journal Article
In: Journal of Molecular Graphics and Modelling, vol. 21, no. 1, pp. 57–70, 2002.
@article{braga2002semiempirical,
title = {A semiempirical study on the electronic structure of 10-deacetylbaccatin-III},
author = {Braga, SF and Galvao, DS},
url = {http://www.sciencedirect.com/science/article/pii/S1093326302001213},
year = {2002},
date = {2002-01-01},
journal = {Journal of Molecular Graphics and Modelling},
volume = {21},
number = {1},
pages = {57--70},
publisher = {Elsevier},
abstract = {We performed a conformational and electronic analysis for 10-deacetylbaccatin-III (DBAC) using well-known semiempirical methods (parametric method 3 (PM3) and Zerner’s intermediate neglect of differential overlap (ZINDO)) coupled to the concepts of total and local density of states (LDOS). Our results indicate that regions presented by paclitaxel (Taxol®) as important for the biological activity can be traced out by the electronic features present in DBAC. These molecules differ only by a phenylisoserine side chain. Compared to paclitaxel, DBAC has a simpler structure in terms of molecular size and number of degrees of freedom (d.f.). This makes DBAC a good candidate for a preliminary investigation of the taxoid family. Our results question the importance of the oxetane group, which seems to be consistent with recent experimental data.
},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Giro, R; Cyrillo, M; Galvao, DS
Designing conducting polymers using genetic algorithms Journal Article
In: Chemical Physics Letters, vol. 366, no. 1, pp. 170–175, 2002.
@article{giro2002designing,
title = {Designing conducting polymers using genetic algorithms},
author = {Giro, R and Cyrillo, M and Galvao, DS},
url = {http://www.sciencedirect.com/science/article/pii/S0009261402015476},
year = {2002},
date = {2002-01-01},
journal = {Chemical Physics Letters},
volume = {366},
number = {1},
pages = {170--175},
publisher = {North-Holland},
abstract = {We have developed a new methodology to design conducting polymers with pre-specified properties. The methodology is based on the use of genetic algorithms (GAs) coupled to Negative Factor Counting technique. We present the results for a case study of polyanilines, one of the most important families of conducting polymers. The methodology proved to be able of generating automatic solutions for the problem of determining the optimum relative concentration for binary and ternary disordered polyaniline alloys exhibiting metallic properties. The methodology is completely general and can be used to design new classes of materials.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Galvao, DS; Braga, SF; Barone, PMVB; Dantas, SO
Dual-Mode Optical Molecular Switching Systems for Organic Memories Proceedings
Cambridge Univ Press, vol. 708, 2002.
@proceedings{galvao2002dual,
title = {Dual-Mode Optical Molecular Switching Systems for Organic Memories},
author = {Galvao, DS and Braga, SF and Barone, PMVB and Dantas, SO},
url = {http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=8214320},
year = {2002},
date = {2002-01-01},
journal = {MATERIALS RESEARCH SOCIETY SYMPOSIUM PROCEEDINGS},
volume = {708},
pages = {335--340},
publisher = {Cambridge Univ Press},
abstract = {The synthesis of dual-mode optical molecular switching systems has been recently achieved. These systems were based on chiral helical-shaped alkenes in which the chirality can be reversibly modulated by light. In this work we report a theoretical study on the geometric and spectroscopic properties of these structures using the well-known semi-empirical methods PM3 (Parametric Method 3) and ZINDO/S-CI (Zerner's Intermediate Neglect of Differential Overlap -Spectroscopic - Configuration Interaction). Our results show that there are two stable conformers very close in energy for each possible molecular helicity presenting a barrier of ∼40 kcal/mol for bond rotation along the main molecular axis. Under protonation these barriers increase significantly and might explain why the protonation leads to the blocking of the switching process. We propose a scheme for the switching mechanism based on charge transfer and conformational changes during the isomer interconversion.},
keywords = {},
pubstate = {published},
tppubtype = {proceedings}
}
Coluci, V R; Braga, SF; Legoas, Sergio B; Galvao, Douglas S; Baughman, RH
New families of carbon nanotubes Journal Article
In: arXiv preprint cond-mat/0207085, 2002.
@article{coluci2002new,
title = {New families of carbon nanotubes},
author = {Coluci, V R and Braga, SF and Legoas, Sergio B and Galvao, Douglas S and Baughman, RH},
url = {http://arxiv.org/abs/cond-mat/0207085},
year = {2002},
date = {2002-01-01},
journal = {arXiv preprint cond-mat/0207085},
abstract = {Fundamentally new families of carbon single walled nanotubes are proposed. These nanotubes, called graphynes, result from the elongation of covalent interconnections of graphite-based nanotubes by the introduction of yne groups. Similarly to ordinary nanotubes, arm-chair, zig-zag, and chiral graphyne nanotubes are possible. Electronic properties, predicted using tight-binding and ab initio density functional methods, show a rich variety of metallic and semiconducting behaviors.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Legoas, Sergio B; Galvao, Douglas S; Rodrigues, Varlei; Ugarte, Daniel
Origin of anomalously long interatomic distances in suspended gold chains Journal Article
In: Physical Review Letters, vol. 88, no. 7, pp. 076105, 2002.
@article{legoas2002origin,
title = {Origin of anomalously long interatomic distances in suspended gold chains},
author = {Legoas, Sergio B and Galvao, Douglas S and Rodrigues, Varlei and Ugarte, Daniel},
url = {http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.88.076105},
year = {2002},
date = {2002-01-01},
journal = {Physical Review Letters},
volume = {88},
number = {7},
pages = {076105},
publisher = {American Physical Society},
abstract = {The discovery of long bonds in gold atom chains has represented a challenge for physical interpretation. In fact, interatomic distances frequently attain 3.0–3.6 Å values, and distances as large as 5.0 Å may be occasionally observed. Here we studied gold chains by transmission electron microscopy and performed theoretical calculations using cluster ab initio density functional formalism. We show that the insertion of two carbon atoms is required to account for the longest bonds, while distances above 3 Å may be due to a mixture of clean and one C atom contaminated bonds.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Vendrame, R; Coluci, VR; Braga, RS; Galvao, DS
Structure--activity relationship (SAR) studies of the tripos benchmark steroids Journal Article
In: Journal of Molecular Structure: THEOCHEM, vol. 619, no. 1, pp. 195–205, 2002.
@article{vendrame2002structure,
title = {Structure--activity relationship (SAR) studies of the tripos benchmark steroids},
author = {Vendrame, R and Coluci, VR and Braga, RS and Galvao, DS},
url = {http://www.sciencedirect.com/science/article/pii/S016612800200578X},
year = {2002},
date = {2002-01-01},
journal = {Journal of Molecular Structure: THEOCHEM},
volume = {619},
number = {1},
pages = {195--205},
publisher = {Elsevier},
abstract = {We report here qualitative structure–activity relationship (SAR) studies for the molecular set called Tripos or Cramer steroid data set. These compounds are known to bind to corticosteroid binding globulin (CBG). In the present work we have used the electronic indices methodology (EIM). The EIM is based on Boolean relational rules exploring the concepts of local density of states and critical values for energy separation involving frontier orbitals. We have also carried out comparative principal component analysis (PCA) and hierarchical clustering analysis (HCA) studies with molecular descriptors obtained from EIM calculations. EIM, PCA and HCA correctly predict (100% accuracy) the steroid's biological activity. The present studies reinforce the universal applicability of the EIM descriptors and show that the combined use of EIM coupled to PCA can be a new efficient and powerful SAR tool.
},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Legoas, Sergio B; Galvao, Douglas S; Rodrigues, Varlei; Ugarte, Daniel
The Role of Carbon Contamination in Suspended Gold Nanowires Journal Article
In: MRS Proceedings, vol. 738, pp. G14–6, 2002.
@article{legoas2002role,
title = {The Role of Carbon Contamination in Suspended Gold Nanowires},
author = {Legoas, Sergio B and Galvao, Douglas S and Rodrigues, Varlei and Ugarte, Daniel},
url = {http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=8031754&fileId=S1946427400148249},
year = {2002},
date = {2002-01-01},
journal = {MRS Proceedings},
volume = {738},
pages = {G14--6},
publisher = {Cambridge University Press},
abstract = {Metallic nanowires represent very interesting systems due to new phenomena such as quantum conductance and unexpected long interatomic distances attaining 0.3–0.5 nm. These large distances represent a challenge for physical interpretation. In this work we present experimental data from transmission electron microscopy and results from ab initio density functional calculations for suspended gold chains. We show that large distances as 0.5 nm can be easily explained by the presence of carbon atoms as contaminants, while distances ranging from 0.29 up to 0.36 nm might be explained as resulting of a mixture of clean stressed and contaminated linear chains.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
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