quantum computing
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Practical challenges in simulating quantum systems on classical computers have been widely recognized in the quantum physics and quantum chemistry communities over the past century. Although many approximation methods have been introduced, the complexity of quantum mechanics remains hard to appease. The advent of quantum computation brings new pathways to navigate this challenging and complex landscape. By manipulating quantum states of matter and taking advantage of their unique features such as superposition and entanglement, quantum computers promise to efficiently deliver accurate results for many important problems in quantum chemistry, such as the electronic structure of molecules. In the past two decades, significant advances have been made in developing algorithms and physical hardware for quantum computing, heralding a revolution in simulation of quantum systems. This Review provides an overview of the algorithms and results that are relevant for quantum chemistry. The intended audience is both quantum chemists who seek to learn more about quantum computing and quantum computing researchers who would like to explore applications in quantum chemistry.
It has been already three decades, since the fluorescent nanocrystals called quantum dots (QDs) appeared and attracted attention of a broad scientific community. Their excellent not only optical but also electronic properties predetermined QDs for utilization in a variety of areas. Besides lasers, solar cells, and/or computers, QDs have established themselves in the field of (bio)chemical labeling as well as medical imaging. However, due to the numerous application possibilities of QDs, there are high demands on their properties that need to be precisely controlled and characterized. CE with its versatile modes and possibilities of detection was found to be an effective tool not only for characterization of QDs size and/or surface properties but also for monitoring of their interactions with other molecules of interest. In this minireview, we are giving short insight in analysis of QDs by CE, and summarizing the advantages of this method for QDs characterization.
- MeSH
- elektroforéza kapilární metody MeSH
- kvantové tečky chemie MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- přehledy MeSH
We combined atomistic molecular-dynamics simulations with quantum-mechanical calculations to investigate the sequence dependence of the stretching behavior of duplex DNA. Our combined quantum-mechanical/molecular-mechanical approach demonstrates that molecular-mechanical force fields are able to describe both the backbone and base-base interactions within the highly distorted nucleic acid structures produced by stretching the DNA from the 5' ends, which include conformations containing disassociated basepairs, just as well as these force fields describe relaxed DNA conformations. The molecular-dynamics simulations indicate that the force-induced melting pathway is sequence-dependent and is influenced by the availability of noncanonical hydrogen-bond interactions that can assist the disassociation of the DNA basepairs. The biological implications of these results are discussed. Copyright 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.
Complex molecular shapes of ribosomal RNA molecules are stabilized by recurrent types of tertiary interactions involving highly specific and conserved non-Watson-Crick base pairs, triplets, and quartets. We analyzed the intrinsic structure and stability of the P-motif and the four basic types of A-minor interactions (types I, II, III, and 0), which represent the most prominent RNA tertiary interaction patterns refined in the course of evolution. In the studied interactions, the electron correlation component of the stabilization usually exceeds the Hartree-Fock (HF) term, leading to a strikingly different balance of forces as compared to standard base pairing stabilized primarily by the HF term. In other words, the A-minor and P-interactions are considerably more influenced by the dispersion energy as compared to canonical base pairs, which makes them particularly suitable to zip the folded RNA structures that are substantially hydrated even in their interior. Continuum solvent COSMO calculations confirm that the stability of the canonical GC base pair is affected (reduced) by the continuum solvent screening considerably more than the stability of the A-minor interaction. Among the studied systems, the strong A-minor II and weak A-minor III interactions require water molecules to stabilize the experimental geometry. Gas-phase optimization of the canonical A-minor II A/CG triplet without water results in a geometry that is clearly inconsistent with the RNA structure. The gas-phase structure of the P-interaction and the most stable A-minor I interaction nicely agrees with the geometries occurring in the ribosome. A-minor I can also adopt an alternative water-mediated substate rather often observed in X-ray and molecular dynamics studies. The A-minor I water bridge, however, does not appear to stabilize the tertiary contact, and its role is to provide structural flexibility to this binding pattern within the context of the RNA structure. Interestingly, the insertion of a polar water molecule in the A-minor I A/CG tertiary contact occurring in the A/C tertiary pair is stabilized primarily by the HF (electrostatic) interaction energy, while the dispersion-controlled A/G contact remains firmly bound. Thus, the intrinsic balance of forces as revealed by quantum mechanics (QM) calculations nicely correlates with many behavioral aspects of the studied interactions inside RNA. The comparison of interaction energies computed using quantum chemistry and an AMBER force field reveals that common molecular mechanics calculations perform rather well, except that the strength of the P-interaction is modestly overestimated. We also briefly discuss the non-negligible methodological differences when evaluating simple base-base nucleic acids base pairs and the complex RNA tertiary base pairing patterns using QM procedures.
[1st ed.] xvi, 387 s. : il. + 1 optický disk
Trans Hoogsteen/sugar edge (H/SE) RNA base pairs form one of the six families of RNA base pairs that utilize the 2'-hydroxyl group of ribose for base pairing and play key roles in stabilizing folded RNA molecules. Here, we provide a detailed quantum chemical characterization of intrinsic structures and interaction energies of this base pair family, along with the evaluation of solvent screening effects by a continuum solvent approach. We report DFT-optimized geometries and MP2 interaction energies for all 10 crystallographically identified members of the family, for a representative set of them, using complete basis set extrapolation. For 6 of the 10 base pairs, we had to apply geometric constraints to keep the geometries relevant to RNA. We confirm that the remaining, hitherto undetected, possible members of this family do not have appropriate steric features required to establish stable base pairing in the trans H/SE fashion. The interaction patterns in the trans H/SE family are highly diverse, with gas-phase interaction energies in the range from -1 to -17 kcal/mol. Except for the C/rC and G/rG trans H/SE base pairs, the interaction energy is roughly evenly distributed between the HF and correlation components. Thus, in the trans H/SE base pairs, the relative importance of electron correlation is noticeably smaller than in the cis WC/SE or cis and trans SE/SE base pairs, but still larger than in canonical base pairs. The trans H/SE A/rG base pair is the intrinsically most stable member of this family. This base pair is also known as the sheared AG base pair and belongs to the most prominent set of RNA base pairs utilized in molecular building blocks of functional RNAs. For all trans H/SE base pairs that we identified, in addition to conventional base pairing, viable alternative structures were stabilized by amino-acceptor interactions. In the QM calculations, these amino-acceptor complexes appear to be equally as stable as those with common H-bonds, and more importantly, the switch to amino-acceptor interaction does not require any significant geometrical rearrangement of the base pairs. Such interactions are worthy of further investigations, as X-ray crystallography cannot unambiguously distinguish between conventional and amino-acceptor interactions involving the 2'-hydroxyl group, formation of such interactions is usually not considered, and molecular modeling force fields do not include such interactions properly as a result of neglect of aminogroup pyramidalization.
In this review primarily written for non-experts we explain basic methodological aspects and interpretation of modern quantum chemical (QM) computations applied to nucleic acids. We introduce current reference QM computations on small model systems consisting of dozens of atoms. Then we comment on recent advance of fast and accurate dispersion-corrected density functional theory methods, which will allow computations of small but complete nucleic acids building blocks in the near future. The qualitative difference between QM and molecular mechanics (MM, force field) computations is discussed. We also explain relation of QM and molecular simulation computations to experiments.
For the first time, the combination of molecularly imprinted polymer (MIP) technology with laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) is presented with focus on an optimization of the LA-ICP-MS parameters such as laser beam diameter, laser beam fluence, and scan speed using CdS quantum dots (QDs) as a template and dopamine as a functional monomer. A non-covalent imprinting approach was employed in this study due to the simplicity of preparation. Simple oxidative polymerization of the dopamine that creates the self-assembly monolayer seems to be an ideal choice. The QDs prepared by UV light irradiation synthesis were stabilized by using mercaptosuccinic acid. Formation of a complex of QD-antibody and QD-antibody-antigen was verified by using capillary electrophoresis with laser-induced fluorescence detection. QDs and antibody were connected together via an affinity peptide linker. LA-ICP-MS was employed as a proof-of-concept for detection method of two types of immunoassay: 1) antigen extracted from the sample by MIP and subsequently overlaid/immunoreacted by QD-labelled antibodies, 2) complex of antigen, antibody, and QD formed in the sample and subsequently extracted by MIP. The first approach provided higher sensitivity (MIP/NIP), however, the second demonstrated higher selectivity. A mixture of proteins with size in range 10-250 kDa was used as a model sample to demonstrate the capability of both approaches for detection of IgG in a complex sample.
- MeSH
- elektroforéza kapilární MeSH
- fluorescence MeSH
- hmotnostní spektrometrie * MeSH
- imunoanalýza metody MeSH
- imunoglobulin G analýza MeSH
- kvantové tečky chemie MeSH
- laserová terapie * MeSH
- molekulový imprinting * MeSH
- myši MeSH
- počítačové zpracování signálu MeSH
- polymery chemie MeSH
- proteiny analýza MeSH
- sloučeniny kadmia chemie MeSH
- sulfidy chemie MeSH
- zvířata MeSH
- Check Tag
- myši MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
