Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 26
Filtrar
Mais filtros










Base de dados
Intervalo de ano de publicação
1.
Phys Chem Chem Phys ; 22(9): 5211-5219, 2020 Mar 04.
Artigo em Inglês | MEDLINE | ID: mdl-32091055

RESUMO

A key challenge in conformer sampling is finding low-energy conformations with a small number of energy evaluations. We recently demonstrated the Bayesian Optimization Algorithm (BOA) is an effective method for finding the lowest energy conformation of a small molecule. Our approach balances between exploitation and exploration, and is more efficient than exhaustive or random search methods. Here, we extend strategies used on proteins and oligopeptides (e.g. Ramachandran plots of secondary structure) and study correlated torsions in small molecules. We use bivariate von Mises distributions to capture correlations, and use them to constrain the search space. We validate the performance of our new method, Bayesian Optimization with Knowledge-based Expected Improvement (BOKEI), on a dataset consisting of 533 diverse small molecules, using (i) a force field (MMFF94); and (ii) a semi-empirical method (GFN2), as the objective function. We compare the search performance of BOKEI, BOA with Expected Improvement (BOA-EI), and a genetic algorithm (GA), using a fixed number of energy evaluations. In more than 60% of the cases examined, BOKEI finds lower energy conformations than global optimization with BOA-EI or GA. More importantly, we find correlated torsions in up to 15% of small molecules in larger data sets, up to 8 times more often than previously reported. The BOKEI patterns not only describe steric clashes, but also reflect favorable intramolecular interactions such as hydrogen bonds and π-π stacking. Increasing our understanding of the conformational preferences of molecules will help improve our ability to find low energy conformers efficiently, which will have impact in a wide range of computational modeling applications.

2.
J Cheminform ; 11(1): 49, 2019 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-31372768

RESUMO

Rapidly predicting an accurate three dimensional geometry of a molecule is a crucial task for cheminformatics and across a wide range of molecular modeling. Consequently, developing a fast, accurate, and open implementation of structure prediction is necessary for reproducible cheminformatics research. We introduce a fragment-based coordinate generation implementation for Open Babel, a widely-used open source toolkit for cheminformatics. The new implementation improves speed and stereochemical accuracy, while retaining or improving accuracy of bond lengths, bond angles, and dihedral torsions. Input molecules are broken into fragments by cutting at rotatable bonds. The coordinates of fragments are set according to a fragment library, prepared from open crystallographic databases. Since the coordinates of multiple atoms are decided at once, coordinate prediction is accelerated over the previous rules-based implementation in Open Babel, as well as the widely-used distance geometry methods in RDKit. This new implementation will be beneficial for a wide range of applications, including computational property prediction in polymers, molecular materials and drug design.

3.
J Cheminform ; 11(1): 32, 2019 May 21.
Artigo em Inglês | MEDLINE | ID: mdl-31115707

RESUMO

Generating low-energy molecular conformers is a key task for many areas of computational chemistry, molecular modeling and cheminformatics. Most current conformer generation methods primarily focus on generating geometrically diverse conformers rather than finding the most probable or energetically lowest minima. Here, we present a new stochastic search method called the Bayesian optimization algorithm (BOA) for finding the lowest energy conformation of a given molecule. We compare BOA with uniform random search, and systematic search as implemented in Confab, to determine which method finds the lowest energy. Energetic difference, root-mean-square deviation, and torsion fingerprint deviation are used to quantify the performance of the conformer search algorithms. In general, we find BOA requires far fewer evaluations than systematic or uniform random search to find low-energy minima. For molecules with four or more rotatable bonds, Confab typically evaluates [Formula: see text] (median) conformers in its search, while BOA only requires [Formula: see text] energy evaluations to find top candidates. Despite using evaluating fewer conformers, 20-40% of the time BOA finds lower-energy conformations than a systematic Confab search for molecules with four or more rotatable bonds.

4.
J Chem Theory Comput ; 14(11): 5553-5566, 2018 Nov 13.
Artigo em Inglês | MEDLINE | ID: mdl-30281307

RESUMO

Gas-phase electric properties of molecules can be computed routinely using wave function methods or density functional theory (DFT). However, these methods remain computationally expensive for high-throughput screening of the vast chemical space of virtual compounds. Therefore, empirical force fields are a more practical choice in many cases, particularly since force field methods allow one to routinely predict the physicochemical properties in the condensed phases. This work presents Drude polarizable models, to increase the physical realism in empirical force fields, where the core particle is treated as a point charge and the Drude particle is treated either as a 1 s-Gaussian or a ns-Slater ( n = 1, 2, 3) charge density. Systematic parametrization to large high-quality quantum chemistry data obtained from the open access Alexandria Library ( https://doi.org/10.5281/zenodo.1004711 ) ensures the transferability of these parameters. The dipole moments and isotropic polarizabilities of the isolated molecules predicted by the proposed Drude models are in agreement with experiment with accuracy similar to DFT calculations at the B3LYP/aug-cc-pVTZ level of theory. The results show that the inclusion of explicit polarization into the models reduces the root-mean-square deviation with respect to DFT calculations of the predicted dipole moments of 152 dimers and clusters by more than 50%. Finally, we show that the accuracy of the electrostatic interaction energy of the water dimers can be improved systematically by the introduction of polarizable smeared charges as a model for charge penetration.

5.
J Phys Chem B ; 121(44): 10269-10275, 2017 11 09.
Artigo em Inglês | MEDLINE | ID: mdl-29035526

RESUMO

Many biomaterials are piezoelectric (i.e., mechanically deform under an applied electric field); however, the molecular origin of this phenomenon remains unclear. In the case of protein-based scaffolds, one possibility involves flexible response of local folding motifs to the applied field. Here, we test this hypothesis by examining the piezoresponse in a series of helical peptide-based oligomers. Control over folding propensity is exerted through systematic variation in both side-chain sequence and backbone composition. Piezoresponse is quantified by piezo-force microscopy on polar self-assembled monolayers. The results indicate backbone rigidity is an important determinant in peptide electromechanical responsiveness.


Assuntos
Materiais Biocompatíveis/química , Peptídeos/química , Sequência de Aminoácidos , Materiais Biocompatíveis/síntese química , Peptídeos/síntese química , Dobramento de Proteína , Teoria Quântica
6.
Macromol Rapid Commun ; 37(11): 882-7, 2016 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-27079687

RESUMO

To investigate the sequence effect on donor-acceptor conjugated oligomers and polymers, the trimeric isomers PBP and BPP, comprising dialkoxy phenylene vinylene (P), benzothiadiazole vinylene (B), and alkyl endgroups with terminal olefins, are synthesized. Sequence effects are evident in the optical/electrochemical properties and thermal properties. Absorption maxima for PBP and BPP differ by 41 nm and the electrochemical band gaps by 0.1 V. The molar emission intensity is five times greater in PBP than BPP. Both trimers are crystalline and the melting points differ by 17 °C. The PBP and BPP trimers are used as macromonomers in an acyclic diene metathesis polymerization to give PolyPBP and PolyBPP. The optical and electrochemical properties are similar to those of their trimer precursors-sequence effects are still evident. These results suggest that sequence is a tunable variable for electronic materials and that the polymerization of oligomeric sequences is a useful approach to introducing sequence into polymers.


Assuntos
Técnicas Eletroquímicas , Temperatura Alta , Modelos Químicos , Polímeros/química , Polímeros/síntese química
7.
J Phys Chem A ; 118(35): 7404-10, 2014 Sep 04.
Artigo em Inglês | MEDLINE | ID: mdl-24576213

RESUMO

Organic piezoelectric materials are promising targets in applications such as energy harvesting or mechanical sensors and actuators. In a recent paper (Werling, K. A.; et al. J. Phys. Chem. Lett. 2013, 4, 1365-1370), we have shown that hydrogen bonding gives rise to a significant piezoelectric response. In this article, we aim to find organic hydrogen bonded systems with increased piezo-response by investigating different hydrogen bonding motifs and by tailoring the hydrogen bond strength via functionalization. The largest piezo-coefficient of 23 pm/V is found for the nitrobenzene-aniline dimer. We develop a simple, yet surprisingly accurate rationale to predict piezo-coefficients based on the zero-field compliance matrix and dipole derivatives. This rationale increases the speed of first-principles piezo-coefficient calculations by an order of magnitude. At the same time, it suggests how to understand and further increase the piezo-response. Our rationale also explains the remarkably large piezo-response of 150 pm/V and more for another class of systems, the "molecular springs" (Marvin, C.; et al. J. Phys. Chem. C 2013, 117, 16783-16790.).

8.
J Phys Chem B ; 117(16): 4528-35, 2013 Apr 25.
Artigo em Inglês | MEDLINE | ID: mdl-23189962

RESUMO

Here, we report an unusual oxidation-induced photoluminescence (PL) turn-on response of a poly(3-alkoxythiophene), poly(3-{2-[2-(2-ethoxyethoxy)ethoxy]ethoxy}thiophene) (PEEEET). PEEEET shows a significantly red-shifted absorption spectrum compared to polyalkylthiophenes and is almost nonfluorescent (quantum yield ≪ 1%) in its pristine state. The introduction of sulfonyl defects along the polymer backbone by the oxidation of PEEEET with meta-chloroperbenzoic acid (m-CPBA) increased the emission quantum yield with the intensity increasing with the degree of oxidation. Molecular modeling data indicated that the oxidation-induced PL increase cannot be explained by the nature of monomer units and radiative rate changes. We attributed the enhanced fluorescence to the reduced nonradiative rate caused by the increased band gap, according to the energy gap law, which is consistent with the observed blue shifts in absorption and PL spectra accompanied by the PL increase.

9.
J Phys Chem Lett ; 4(9): 1365-70, 2013 May 02.
Artigo em Inglês | MEDLINE | ID: mdl-26282286

RESUMO

The piezoelectric properties of 2-methyl-4-nitroaniline crystals were explored qualitatively and quantitatively using an electrostatically embedded many-body (EE-MB) expansion scheme for the correlation energies of a system of monomers within the crystal. The results demonstrate that hydrogen bonding is an inherently piezoelectric interaction, deforming in response to the electrostatic environment. We obtain piezo-coefficients in excellent agreement with the experimental values. This approach reduces computational cost and reproduces the total resolution of the identity (RI)-Møller-Plesset second-order perturbation theory (RI-MP2) energy for the system to within 1.3 × 10(-5)%. Furthermore, the results suggest novel ways to self-assemble piezoelectric solids and suggest that accurate treatment of hydrogen bonds requires precise electrostatic evaluation. Considering the ubiquity of hydrogen bonds across chemistry, materials, and biology, a new electromechanical view of these interactions is required.

10.
J Phys Chem Lett ; 4(10): 1613-23, 2013 May 16.
Artigo em Inglês | MEDLINE | ID: mdl-26282968

RESUMO

There has been increasing interest in rational, computationally driven design methods for materials, including organic photovoltaics (OPVs). Our approach focuses on a screening "pipeline", using a genetic algorithm for first stage screening and multiple filtering stages for further refinement. An important step forward is to expand our diversity of candidate compounds, including both synthetic and property-based measures of diversity. For example, top monomer pairs from our screening are all donor-donor (D-D) combinations, in contrast with the typical donor-acceptor (D-A) motif used in organic photovoltaics. We also find a strong "sequence effect", in which the average HOMO-LUMO gap of tetramers changes by ∼0.2 eV as a function of monomer sequence (e.g., ABBA versus BAAB); this has rarely been explored in conjugated polymers. Beyond such optoelectronic optimization, we discuss other properties needed for high-efficiency organic solar cells, and applications of screening methods to other areas, including non-fullerene n-type materials, tandem cells, and improving charge and exciton transport.

11.
J Phys Chem Lett ; 4(1): 36-42, 2013 Jan 03.
Artigo em Inglês | MEDLINE | ID: mdl-26291208

RESUMO

The effect of morphology on charge transport in organic photovoltaics is assessed using Monte Carlo. In isotopic two-phase morphologies, increasing the domain size from 6.3 to 18.3 nm improves the fill factor by 11.6%, a result of decreased tortuosity and relaxation of Coulombic barriers. Additionally, when small aggregates of electron acceptors are interdispersed into the electron donor phase, charged defects form in the system, reducing fill factors by 23.3% on average, compared with systems without aggregates. In contrast, systems with idealized connectivity show a 3.31% decrease in fill factor when domain size was increased from 4 to 64 nm. We attribute this to a decreased rate of exciton separation at donor-acceptor interfaces. Finally, we notice that the presence of Coulomb interactions increases device performance as devices become smaller. The results suggest that for commonly found isotropic morphologies the Coulomb interactions between charge carriers dominates exciton separation effects.

12.
Chemistry ; 18(45): 14497-509, 2012 Nov 05.
Artigo em Inglês | MEDLINE | ID: mdl-23011958

RESUMO

Electron delocalization of new mixed-valent (MV) systems with the aid of lateral metal chelation is reported. 2,2'-Bipyridine (bpy) derivatives with one or two appended di-p-anisylamino groups on the 5,5'-positions and a coordinated [Ru(bpy)(2)] (bpy = 2,2'-bipyridine), [Re(CO)(3)Cl], or [Ir(ppy)(2)] (ppy = 2-phenylpyridine) component were prepared. The single-crystal molecular structure of the bis-amine ligand without metal chelation is presented. The electronic properties of these complexes were studied and compared by electrochemical and spectroscopic techniques and DFT/TDDFT calculations. Compounds with two di-p-anisylamino groups were oxidized by a chemical or electrochemical method and monitored by near-infrared (NIR) absorption spectral changes. Marcus-Hush analysis of the resulting intervalence charge-transfer transitions indicated that electron coupling of these mixed-valent systems is enhanced by metal chelation and that the iridium complex has the largest coupling. TDDFT calculations were employed to interpret the NIR transitions of these MV systems.

13.
J Cheminform ; 4(1): 17, 2012 Aug 13.
Artigo em Inglês | MEDLINE | ID: mdl-22889332

RESUMO

BACKGROUND: The Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible, high quality rendering, and a powerful plugin architecture. Typical uses include building molecular structures, formatting input files, and analyzing output of a wide variety of computational chemistry packages. By using the CML file format as its native document type, Avogadro seeks to enhance the semantic accessibility of chemical data types. RESULTS: The work presented here details the Avogadro library, which is a framework providing a code library and application programming interface (API) with three-dimensional visualization capabilities; and has direct applications to research and education in the fields of chemistry, physics, materials science, and biology. The Avogadro application provides a rich graphical interface using dynamically loaded plugins through the library itself. The application and library can each be extended by implementing a plugin module in C++ or Python to explore different visualization techniques, build/manipulate molecular structures, and interact with other programs. We describe some example extensions, one which uses a genetic algorithm to find stable crystal structures, and one which interfaces with the PackMol program to create packed, solvated structures for molecular dynamics simulations. The 1.0 release series of Avogadro is the main focus of the results discussed here. CONCLUSIONS: Avogadro offers a semantic chemical builder and platform for visualization and analysis. For users, it offers an easy-to-use builder, integrated support for downloading from common databases such as PubChem and the Protein Data Bank, extracting chemical data from a wide variety of formats, including computational chemistry output, and native, semantic support for the CML file format. For developers, it can be easily extended via a powerful plugin mechanism to support new features in organic chemistry, inorganic complexes, drug design, materials, biomolecules, and simulations. Avogadro is freely available under an open-source license from http://avogadro.openmolecules.net.

14.
J Cheminform ; 3: 33, 2011 Oct 07.
Artigo em Inglês | MEDLINE | ID: mdl-21982300

RESUMO

BACKGROUND: A frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language) and de facto standards have arisen (for example, SMILES format), the need to interconvert formats is a continuing problem due to the multitude of different application areas for chemistry data, differences in the data stored by different formats (0D versus 3D, for example), and competition between software along with a lack of vendor-neutral formats. RESULTS: We discuss, for the first time, Open Babel, an open-source chemical toolbox that speaks the many languages of chemical data. Open Babel version 2.3 interconverts over 110 formats. The need to represent such a wide variety of chemical and molecular data requires a library that implements a wide range of cheminformatics algorithms, from partial charge assignment and aromaticity detection, to bond order perception and canonicalization. We detail the implementation of Open Babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion. CONCLUSIONS: Open Babel presents a solution to the proliferation of multiple chemical file formats. In addition, it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching. For developers, it can be used as a programming library to handle chemical data in areas such as organic chemistry, drug design, materials science, and computational chemistry. It is freely available under an open-source license from http://openbabel.org.

15.
J Cheminform ; 3(1): 37, 2011 Oct 14.
Artigo em Inglês | MEDLINE | ID: mdl-21999342

RESUMO

BACKGROUND: The Blue Obelisk movement was established in 2005 as a response to the lack of Open Data, Open Standards and Open Source (ODOSOS) in chemistry. It aims to make it easier to carry out chemistry research by promoting interoperability between chemistry software, encouraging cooperation between Open Source developers, and developing community resources and Open Standards. RESULTS: This contribution looks back on the work carried out by the Blue Obelisk in the past 5 years and surveys progress and remaining challenges in the areas of Open Data, Open Standards, and Open Source in chemistry. CONCLUSIONS: We show that the Blue Obelisk has been very successful in bringing together researchers and developers with common interests in ODOSOS, leading to development of many useful resources freely available to the chemistry community.

16.
J Cheminform ; 3: 8, 2011 Mar 16.
Artigo em Inglês | MEDLINE | ID: mdl-21410983

RESUMO

BACKGROUND: Many computational chemistry analyses require the generation of conformers, either on-the-fly, or in advance. We present Confab, an open source command-line application for the systematic generation of low-energy conformers according to a diversity criterion. RESULTS: Confab generates conformations using the 'torsion driving approach' which involves iterating systematically through a set of allowed torsion angles for each rotatable bond. Energy is assessed using the MMFF94 forcefield. Diversity is measured using the heavy-atom root-mean-square deviation (RMSD) relative to conformers already stored. We investigated the recovery of crystal structures for a dataset of 1000 ligands from the Protein Data Bank with fewer than 1 million conformations. Confab can recover 97% of the molecules to within 1.5 Å at a diversity level of 1.5 Å and an energy cutoff of 50 kcal/mol. CONCLUSIONS: Confab is available from http://confab.googlecode.com.

17.
Chem Cent J ; 2: 24, 2008 Dec 03.
Artigo em Inglês | MEDLINE | ID: mdl-19055766

RESUMO

BACKGROUND: Open Source cheminformatics toolkits such as OpenBabel, the CDK and the RDKit share the same core functionality but support different sets of file formats and forcefields, and calculate different fingerprints and descriptors. Despite their complementary features, using these toolkits in the same program is difficult as they are implemented in different languages (C++ versus Java), have different underlying chemical models and have different application programming interfaces (APIs). RESULTS: We describe Cinfony, a Python module that presents a common interface to all three of these toolkits, allowing the user to easily combine methods and results from any of the toolkits. In general, the run time of the Cinfony modules is almost as fast as accessing the underlying toolkits directly from C++ or Java, but Cinfony makes it much easier to carry out common tasks in cheminformatics such as reading file formats and calculating descriptors. CONCLUSION: By providing a simplified interface and improving interoperability, Cinfony makes it easy to combine complementary features of OpenBabel, the CDK and the RDKit.

18.
Chem Cent J ; 2: 5, 2008 Mar 09.
Artigo em Inglês | MEDLINE | ID: mdl-18328109

RESUMO

BACKGROUND: Scripting languages such as Python are ideally suited to common programming tasks in cheminformatics such as data analysis and parsing information from files. However, for reasons of efficiency, cheminformatics toolkits such as the OpenBabel toolkit are often implemented in compiled languages such as C++. We describe Pybel, a Python module that provides access to the OpenBabel toolkit. RESULTS: Pybel wraps the direct toolkit bindings to simplify common tasks such as reading and writing molecular files and calculating fingerprints. Extensive use is made of Python iterators to simplify loops such as that over all the molecules in a file. A Pybel Molecule can be easily interconverted to an OpenBabel OBMol to access those methods or attributes not wrapped by Pybel. CONCLUSION: Pybel allows cheminformaticians to rapidly develop Python scripts that manipulate chemical information. It is open source, available cross-platform, and offers the power of the OpenBabel toolkit to Python programmers.

19.
Langmuir ; 22(25): 10554-63, 2006 Dec 05.
Artigo em Inglês | MEDLINE | ID: mdl-17129030

RESUMO

The redox reactions of DMcT at PEDOT-modified glassy carbon electrodes (GCEs) in acetonitrile (AN) have been investigated via cyclic voltammetry (CV) and the electrochemical quartz crystal microbalance (EQCM) in order to elucidate the redox reaction mechanism. A redox couple at -0.29 V versus Ag/Ag+ was assigned to the dimerization process of singly protonated DMcT (DMcT-1H), and a second couple observed at +0.42 V was assigned to the polymerization process of the protonated DMcT dimer. Our investigations revealed further that the anodic current response at +0.55 V (polymerization process) has a shoulder at +0.38 V ascribed to the dimerization process of doubly protonated DMcT (DMcT-2H), indicating that the redox couple at +0.42 V is the overlapping response of the polymerization of the protonated DMcT dimer and the dimerization of the DMcT-2H monomer. It was also confirmed that the dimerization process of DMcT-1H at -0.29 V proceeded not only at the surface of a PEDOT film but also inside the film as previously suggested. Moreover, the thermodynamics of these redox reactions at PEDOT-modified GCEs are dependent on the basicity (or acidity) of the solution, as anticipated and previously shown at unmodified GCEs. The oxidation of DMcT occurs at less positive potentials and the reduction occurs at more negative potentials in the presence of base. On the basis of the results obtained, the full redox reaction scheme for DMcT at a PEDOT-modified GCE is proposed.


Assuntos
Compostos Bicíclicos Heterocíclicos com Pontes/química , Fontes de Energia Elétrica , Lítio/química , Polímeros/química , Tiadiazóis/química , Ânions/química , Eletroquímica , Eletrodos , Estrutura Molecular , Oxirredução , Propriedades de Superfície , Termodinâmica
20.
J Chem Inf Model ; 46(3): 991-8, 2006.
Artigo em Inglês | MEDLINE | ID: mdl-16711717

RESUMO

The Blue Obelisk Movement (http://www.blueobelisk.org/) is the name used by a diverse Internet group promoting reusable chemistry via open source software development, consistent and complimentary chemoinformatics research, open data, and open standards. We outline recent examples of cooperation in the Blue Obelisk group: a shared dictionary of algorithms and implementations in chemoinformatics algorithms drawing from our various software projects; a shared repository of chemoinformatics data including elemental properties, atomic radii, isotopes, atom typing rules, and so forth; and Web services for the platform-independent use of chemoinformatics programs.


Assuntos
Química , Internet , Algoritmos , Fenômenos Químicos , Informática , Software
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA