Pub Date : 2019-01-30DOI: 10.5772/INTECHOPEN.80491
Ruby Srivastava
Molecular computing devices composed of biological substances, such as nucleic acid and ribonucleic acid plays a key role for the logical processing of a variety of inputs and viable outputs in the cellular machinery of all living organisms. These devices are directly dependent on the advancement in DNA and RNA technology. RNA nanoparticles can be engineered into a programmable and logically acting “Ribocomputing Devices”; a breakthrough at the interface of nanotechnology and synthetic biology. It opens a new path to the synthetic biologists to design reliable synthetic biological circuits which can be useful as the electronic circuits. In this emerging field, a number of challenges persist; as how to translate a variety of nucleic acid based logic gates developed by numerous research laboratories into the realm of silicon-based computing. So in this chapter we will discuss the advances in ribonucleic acid (RNA) based computing and it’s potential to serve as an alternative to revolutionize silicon-based technology by theoretical means. Also the results of the calculated parameters with computational tools using Density functional theory and the designed device circuits will be analyzed. chemical modification into nucleotides without significant alteration of the RNA property in folding and self-assembly; tuning the immunogenic properties of synthetic RNA constructs for in vivo applications; role of 2D, 3D, 4D structure and intermolecular interaction of RNA molecules; developing methods to control shape, size, and stoichiometry of RNA nanoparticles; regulation and processing functions of RNA in cells; cost in RNA production by biochemical synthesis; and safety of using RNA due to its therapeutic modality for cancer and other diseases without affecting the other organs.
{"title":"Role of Density Functional Theory in “Ribocomputing Devices”","authors":"Ruby Srivastava","doi":"10.5772/INTECHOPEN.80491","DOIUrl":"https://doi.org/10.5772/INTECHOPEN.80491","url":null,"abstract":"Molecular computing devices composed of biological substances, such as nucleic acid and ribonucleic acid plays a key role for the logical processing of a variety of inputs and viable outputs in the cellular machinery of all living organisms. These devices are directly dependent on the advancement in DNA and RNA technology. RNA nanoparticles can be engineered into a programmable and logically acting “Ribocomputing Devices”; a breakthrough at the interface of nanotechnology and synthetic biology. It opens a new path to the synthetic biologists to design reliable synthetic biological circuits which can be useful as the electronic circuits. In this emerging field, a number of challenges persist; as how to translate a variety of nucleic acid based logic gates developed by numerous research laboratories into the realm of silicon-based computing. So in this chapter we will discuss the advances in ribonucleic acid (RNA) based computing and it’s potential to serve as an alternative to revolutionize silicon-based technology by theoretical means. Also the results of the calculated parameters with computational tools using Density functional theory and the designed device circuits will be analyzed. chemical modification into nucleotides without significant alteration of the RNA property in folding and self-assembly; tuning the immunogenic properties of synthetic RNA constructs for in vivo applications; role of 2D, 3D, 4D structure and intermolecular interaction of RNA molecules; developing methods to control shape, size, and stoichiometry of RNA nanoparticles; regulation and processing functions of RNA in cells; cost in RNA production by biochemical synthesis; and safety of using RNA due to its therapeutic modality for cancer and other diseases without affecting the other organs.","PeriodicalId":211304,"journal":{"name":"Density Functional Theory","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127609821","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2019-01-14DOI: 10.5772/INTECHOPEN.81772
Sergio Ricardo de Lazaro, L. Lacerda, R. Ribeiro
In the last few years, the multiferroic materials have represented a very important research topic on the design of new technological devices. A better description for this kind of materials involves two or more forms of ferroic orders coupled in a single crystalline structure. The great number of studies in this field is focused on candidates that present the coupling between a magnetic order and ferroelectricity. However, these material classes are a challenging topic on first-principles calculations due to the strong correlation that arose from the unpaired electrons. Furthermore, the partial filling of d or f orbitals reduces a high localization and a strong interaction causing failures on the electronic structure prediction. The investigation of multiferroic materials aims at their application on the development of devices such as actuators, magnetic readers, sensors and data storage. Multiferroic materials are also alternatives to the production of technological applications based on spintronic. Our proposal is to show our experience in DFT simulations for magnetic states applied in oxides of ilmenites and corundum-ordered structures. Theoretical results reported for our group until now showed a good agreement with experimental results for half-metallicity, reduced band-gap, and/or ferromagnetic ordering.
{"title":"Magnetic Ordering in Ilmenites and Corundum-Ordered Structures","authors":"Sergio Ricardo de Lazaro, L. Lacerda, R. Ribeiro","doi":"10.5772/INTECHOPEN.81772","DOIUrl":"https://doi.org/10.5772/INTECHOPEN.81772","url":null,"abstract":"In the last few years, the multiferroic materials have represented a very important research topic on the design of new technological devices. A better description for this kind of materials involves two or more forms of ferroic orders coupled in a single crystalline structure. The great number of studies in this field is focused on candidates that present the coupling between a magnetic order and ferroelectricity. However, these material classes are a challenging topic on first-principles calculations due to the strong correlation that arose from the unpaired electrons. Furthermore, the partial filling of d or f orbitals reduces a high localization and a strong interaction causing failures on the electronic structure prediction. The investigation of multiferroic materials aims at their application on the development of devices such as actuators, magnetic readers, sensors and data storage. Multiferroic materials are also alternatives to the production of technological applications based on spintronic. Our proposal is to show our experience in DFT simulations for magnetic states applied in oxides of ilmenites and corundum-ordered structures. Theoretical results reported for our group until now showed a good agreement with experimental results for half-metallicity, reduced band-gap, and/or ferromagnetic ordering.","PeriodicalId":211304,"journal":{"name":"Density Functional Theory","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123141131","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-11-22DOI: 10.5772/INTECHOPEN.80922
Alejandro Pérez-Mendoza, R. Ribadeneira
Material properties and process modeling with density functional theory (DFT) is an accurate method to facilitate the study and the design of materials computationally for the development of different electrochemical technologies such as fuel cells, solar cells, and batteries, among others, mainly to achieve alternative ways for energy conversion and storage. Considering the relevance of DFT in the development of these alternative technologies for energy generation and storage, in this chapter, the application of DFT to study catalytic alloys and their reactivity processes to develop polymer membrane fuel cells (PEMFCs) is presented. In this sense, firstly, a brief review of the application of DFT to develop catalysts for PEMFCs and the relation with the concept of chemi- cal descriptors is presented. Secondly, the main chemical descriptors for this task are presented and discussed. Finally, a summary of the main findings of the modeling with DFT and chemical descriptors approach of catalytic alloys for PEMFCs is presented and analyzed.
{"title":"Modeling with DFT and Chemical Descriptors Approach for the Development of Catalytic Alloys for PEMFCs","authors":"Alejandro Pérez-Mendoza, R. Ribadeneira","doi":"10.5772/INTECHOPEN.80922","DOIUrl":"https://doi.org/10.5772/INTECHOPEN.80922","url":null,"abstract":"Material properties and process modeling with density functional theory (DFT) is an accurate method to facilitate the study and the design of materials computationally for the development of different electrochemical technologies such as fuel cells, solar cells, and batteries, among others, mainly to achieve alternative ways for energy conversion and storage. Considering the relevance of DFT in the development of these alternative technologies for energy generation and storage, in this chapter, the application of DFT to study catalytic alloys and their reactivity processes to develop polymer membrane fuel cells (PEMFCs) is presented. In this sense, firstly, a brief review of the application of DFT to develop catalysts for PEMFCs and the relation with the concept of chemi- cal descriptors is presented. Secondly, the main chemical descriptors for this task are presented and discussed. Finally, a summary of the main findings of the modeling with DFT and chemical descriptors approach of catalytic alloys for PEMFCs is presented and analyzed.","PeriodicalId":211304,"journal":{"name":"Density Functional Theory","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115859802","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-11-05DOI: 10.5772/INTECHOPEN.80267
M. Antuch, P. Millet
The energetic needs of a rising human population have led to the search for alternative energy sources. A promising route for the large-scale storage of renewable energy is water electrolysis, which is performed with a proton-conducting polymer electrolyte. However, only platinum group metal electrocatalysts have the adequate properties to minimize the overvoltages associated with either hydrogen or oxygen evolution reactions. Alternative materials based on transition metals are scarce, but molecular electrochemistry offers some alternatives. In particular, transition metal clathrochelates exhibit an interesting activity with regard to the hydrogen evolution reaction (HER). However, such complexes form a vast family, and there is a need to implement screening approaches to identify the most performing ones. Theoretical studies on molecular electrocatalysts are adequate for this purpose, since density functional theory (DFT) has a strong predicting capability to provide clues for the improvement of practical devices. This chapter describes the most recent theoretical methods applied to several members of the clathrochelate family. We describe the computation of their common spectroscopic and electrochemical properties. In addition, DFT analysis is used to decipher the multistep reaction mechanism of a model Co clathrochelate with regard to the hydrogen evolution reaction in the homogeneous phase.
{"title":"The Use of Density Functional Theory to Decipher the Electrochemical Activity of Metal Clathrochelates with Regard to the Hydrogen Evolution Reaction in the Homogeneous Phase","authors":"M. Antuch, P. Millet","doi":"10.5772/INTECHOPEN.80267","DOIUrl":"https://doi.org/10.5772/INTECHOPEN.80267","url":null,"abstract":"The energetic needs of a rising human population have led to the search for alternative energy sources. A promising route for the large-scale storage of renewable energy is water electrolysis, which is performed with a proton-conducting polymer electrolyte. However, only platinum group metal electrocatalysts have the adequate properties to minimize the overvoltages associated with either hydrogen or oxygen evolution reactions. Alternative materials based on transition metals are scarce, but molecular electrochemistry offers some alternatives. In particular, transition metal clathrochelates exhibit an interesting activity with regard to the hydrogen evolution reaction (HER). However, such complexes form a vast family, and there is a need to implement screening approaches to identify the most performing ones. Theoretical studies on molecular electrocatalysts are adequate for this purpose, since density functional theory (DFT) has a strong predicting capability to provide clues for the improvement of practical devices. This chapter describes the most recent theoretical methods applied to several members of the clathrochelate family. We describe the computation of their common spectroscopic and electrochemical properties. In addition, DFT analysis is used to decipher the multistep reaction mechanism of a model Co clathrochelate with regard to the hydrogen evolution reaction in the homogeneous phase.","PeriodicalId":211304,"journal":{"name":"Density Functional Theory","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116706549","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-11-05DOI: 10.5772/INTECHOPEN.80698
Siwarut Siwaipram, Sarawoot Impeng, P. Bopp, S. Bureekaew
Theoretical methods have become indispensable tools in many fields of chemistry and materials research. Metal-organic frameworks (MOFs) are porous materials; they have been intensively developed due to their diverse properties suitable for a wide range of applications. Theoretical approaches have thus been frequently employed toward the design and characterization of MOFs. We focus here in particular on theoretical studies of single-site catalytic reactions that occur inside the cavities of MOFs. The density func tional method (DFT) has been the main approach used for such studies. We briefly review the uses of DFT to examine the catalytic reactions in MOFs. We note that DFT methods are versatile and can be made to work for different purposes such as, e.g., force-field development for molecular simulations. We shall, however, cover this field only very succinctly to put it into context with our main topic. functionalized groups on different linkers as using the anion. The concluded that the of the d-orbital was significantly by the The 3d orbital energy of Fe correlated with the electron-donating strength of the functional groups on the linkers. The results reveal that linkers with ▬ NH 2 groups reduce the enthalpic barrier for the most endothermic step in the oxidation pathway. This illustrates the use of to understand intensive The activ might by selecting which might useful for upgrading certain hydrocarbon
{"title":"Density Functional Theory Studies of Catalytic Sites in Metal- Organic Frameworks","authors":"Siwarut Siwaipram, Sarawoot Impeng, P. Bopp, S. Bureekaew","doi":"10.5772/INTECHOPEN.80698","DOIUrl":"https://doi.org/10.5772/INTECHOPEN.80698","url":null,"abstract":"Theoretical methods have become indispensable tools in many fields of chemistry and materials research. Metal-organic frameworks (MOFs) are porous materials; they have been intensively developed due to their diverse properties suitable for a wide range of applications. Theoretical approaches have thus been frequently employed toward the design and characterization of MOFs. We focus here in particular on theoretical studies of single-site catalytic reactions that occur inside the cavities of MOFs. The density func tional method (DFT) has been the main approach used for such studies. We briefly review the uses of DFT to examine the catalytic reactions in MOFs. We note that DFT methods are versatile and can be made to work for different purposes such as, e.g., force-field development for molecular simulations. We shall, however, cover this field only very succinctly to put it into context with our main topic. functionalized groups on different linkers as using the anion. The concluded that the of the d-orbital was significantly by the The 3d orbital energy of Fe correlated with the electron-donating strength of the functional groups on the linkers. The results reveal that linkers with ▬ NH 2 groups reduce the enthalpic barrier for the most endothermic step in the oxidation pathway. This illustrates the use of to understand intensive The activ might by selecting which might useful for upgrading certain hydrocarbon","PeriodicalId":211304,"journal":{"name":"Density Functional Theory","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132644298","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-11-05DOI: 10.5772/INTECHOPEN.80280
P. Geerlings, S. Fias, T. Stuyver, P. Ayers, R. Balawender, Frank De Proft
An overview is given of our recent work on the linear response function (LRF) χ r ; r 0 ð Þ and its congener, the softness kernel s r ; r 0 ð Þ , the second functional derivatives of the energy E and the grand potential Ω with respect to the external potential at constant N and μ , respectively. In a first section on new insights into the LRF in the context of conceptual DFT, the mathematical and physical properties of these kernels are scrutinized through the concavity of the E ¼ E N ; v ½ (cid:2) and Ω ¼ Ω μ ; v (cid:1) (cid:3) functionals in v r ð Þ resulting, for example, in the negative semidefiniteness of χ . As an example of the analogy between the CDFT functionals and thermodynamic state functions, the analogy between the stability condi- tions of the macroscopic Gibbs free energy function and the concavity conditions for Ω is established, yielding a relationship between the global and local softness and the softness kernel. The role of LRF and especially the softness kernel in Kohn ’ s nearsightedness of electronic matter (NEM) principle is highlighted. The first numerical results on the soft- ness kernel for molecules are reported and scrutinized for their nearsightedness, reconcil-ing the physicists ’ NEM view and the chemists ’ transferability paradigm. The extension of LRF in the context of spin polarized conceptual DFT is presented. Finally, two sections are devoted to ‘ new horizons ’ for the LRF. The role of LRF in (evaluating) alchemical derivatives is stressed, the latter playing a promising role in exploring the chemical compound space. Examples for the transmutation of N 2 and the CC ! BN substitution pattern in 2D and 3D carbocyclic systems illustrate the computational efficiency of the use of alchemical derivatives in exploring nearest neighbours in the chemical compound space. As a second perspective, the role of LRF in evaluating and interpreting molecular conductivity is described. Returning to its forerunner, Coulson ’ s atom-atom polarizability, it is shown how in conjugated π systems (and within certain approximations) a remarkable integral-integrand relationship between the atom-atom polarizability and the transmission proba- bility between the atoms/contacts exists, leading to similar trends in both properties. A simple selection rule for transmission probability in alternating hydrocarbons is derived based on the sign of the atom-atom polarizability.
{"title":"New Insights and Horizons from the Linear Response Function in Conceptual DFT","authors":"P. Geerlings, S. Fias, T. Stuyver, P. Ayers, R. Balawender, Frank De Proft","doi":"10.5772/INTECHOPEN.80280","DOIUrl":"https://doi.org/10.5772/INTECHOPEN.80280","url":null,"abstract":"An overview is given of our recent work on the linear response function (LRF) χ r ; r 0 ð Þ and its congener, the softness kernel s r ; r 0 ð Þ , the second functional derivatives of the energy E and the grand potential Ω with respect to the external potential at constant N and μ , respectively. In a first section on new insights into the LRF in the context of conceptual DFT, the mathematical and physical properties of these kernels are scrutinized through the concavity of the E ¼ E N ; v ½ (cid:2) and Ω ¼ Ω μ ; v (cid:1) (cid:3) functionals in v r ð Þ resulting, for example, in the negative semidefiniteness of χ . As an example of the analogy between the CDFT functionals and thermodynamic state functions, the analogy between the stability condi- tions of the macroscopic Gibbs free energy function and the concavity conditions for Ω is established, yielding a relationship between the global and local softness and the softness kernel. The role of LRF and especially the softness kernel in Kohn ’ s nearsightedness of electronic matter (NEM) principle is highlighted. The first numerical results on the soft- ness kernel for molecules are reported and scrutinized for their nearsightedness, reconcil-ing the physicists ’ NEM view and the chemists ’ transferability paradigm. The extension of LRF in the context of spin polarized conceptual DFT is presented. Finally, two sections are devoted to ‘ new horizons ’ for the LRF. The role of LRF in (evaluating) alchemical derivatives is stressed, the latter playing a promising role in exploring the chemical compound space. Examples for the transmutation of N 2 and the CC ! BN substitution pattern in 2D and 3D carbocyclic systems illustrate the computational efficiency of the use of alchemical derivatives in exploring nearest neighbours in the chemical compound space. As a second perspective, the role of LRF in evaluating and interpreting molecular conductivity is described. Returning to its forerunner, Coulson ’ s atom-atom polarizability, it is shown how in conjugated π systems (and within certain approximations) a remarkable integral-integrand relationship between the atom-atom polarizability and the transmission proba- bility between the atoms/contacts exists, leading to similar trends in both properties. A simple selection rule for transmission probability in alternating hydrocarbons is derived based on the sign of the atom-atom polarizability.","PeriodicalId":211304,"journal":{"name":"Density Functional Theory","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123724944","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-11-05DOI: 10.5772/INTECHOPEN.79558
F. Ruiz
32 pags., 6 figs., 2 tabs. -- Open Access funded by Creative Commons Atribution Licence 3.0
32 pags。， 6图。， 2个标签。——由知识共享署名许可3.0资助的开放获取
{"title":"The Application of Periodic Density Functional Theory to the Study of Uranyl-Containing Materials: Thermodynamic Properties and Stability","authors":"F. Ruiz","doi":"10.5772/INTECHOPEN.79558","DOIUrl":"https://doi.org/10.5772/INTECHOPEN.79558","url":null,"abstract":"32 pags., 6 figs., 2 tabs. -- Open Access funded by Creative Commons Atribution Licence 3.0","PeriodicalId":211304,"journal":{"name":"Density Functional Theory","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131946542","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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