# Structure and Energy of Non-Canonical Basepairs: Comparison of Various Computational Chemistry Methods with Crystallographic Ensembles

01 Dec 2011-Journal of Biomolecular Structure & Dynamics (Taylor & Francis Group)-Vol. 29, Iss: 3, pp 541-556

TL;DR: The energetics and geometry of 32 most frequently observed basepairs in the functional RNA crystal structures are analyzed using different popular empirical, semi-empirical and ab initio quantum chemical methods and their optimized geometry with the crystal data indicate that the most of the polar basepair along with few non-polar ones act as seed for RNA folding while few may act as some conformational switch in the RNA.

Abstract: Different types of non-canonical basepairs, in addition to the Watson-Crick ones, are observed quite frequently in RNA. Their importance in the three dimensional structure is not fully understood, but their various roles have been proposed by different groups. We have analyzed the energetics and geometry of 32 most frequently observed basepairs in the functional RNA crystal structures using different popular empirical, semi-empirical and ab initio quantum chemical methods and compared their optimized geometry with the crystal data. These basepairs are classified into three categories: polar, non-polar and sugar-mediated, depending on the types of atoms involved in hydrogen bonding. In case of polar basepairs, most of the methods give rise to optimized structures close to their initial geometry. The interaction energies also follow similar trends, with the polar ones having more attractive interaction energies. Some of the C-H…O/N hydrogen bond mediated non-polar basepairs are also found to be sig...

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22 Jan 2013

TL;DR: Premises of creation of Internet portal designed to provide access to participants of educational and scientific process for the joint creation, consolidation, concentration and rapid spreading of educationaland scientific information resources in its own depository are considered.

Abstract: Premises of creation of Internet portal designed to provide access to participants of educational and scientific process for the joint creation, consolidation, concentration and rapid spreading of educational and scientific information resources in its own depository are considered. CMS-based portal content management systems’ potentiality is investigated. Architecture for Internet portal of MES of Ukraine’s information resources is offered.

969 citations

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TL;DR: The positive values of Grunenberg’s compliance constants prove that the CH···O/N contacts in nucleobase pairs are stabilizing interactions unlike electrostatic repulsion and anti-H-bonds, and it is asserted that the most reliable descriptors of the H-bonding are the electron density ρ at the Â£1,000/mol critical points and the NBO calculated stabilization energy E(2).

Abstract: This study aims to cast light on the physico-chemical nature and energetic of the non-conventional CH···O/N H-bonds in the biologically important natural nucleobase pairs using a comprehensive quan...

118 citations

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TL;DR: Theoretical studies of these isolated base pairs using ab initio quantum chemical methods as well as molecular dynamics simulations of larger fragments have established that many of these non-canonical base pairs are as stable as the canonical Watson-Crick base pairs.

Abstract: RNA is now known to possess various structural, regulatory and enzymatic functions for survival of cellular organisms. Functional RNA structures are generally created by three-dimensional organization of small structural motifs, formed by base pairing between self-complementary sequences from different parts of the RNA chain. In addition to the canonical Watson–Crick or wobble base pairs, several non-canonical base pairs are found to be crucial to the structural organization of RNA molecules. They appear within different structural motifs and are found to stabilize the molecule through long-range intra-molecular interactions between basic structural motifs like double helices and loops. These base pairs also impart functional variation to the minor groove of A-form RNA helices, thus forming anchoring site for metabolites and ligands. Non-canonical base pairs are formed by edge-to-edge hydrogen bonding interactions between the bases. A large number of theoretical studies have been done to detect and analyze these non-canonical base pairs within crystal or NMR derived structures of different functional RNA. Theoretical studies of these isolated base pairs using ab initio quantum chemical methods as well as molecular dynamics simulations of larger fragments have also established that many of these non-canonical base pairs are as stable as the canonical Watson–Crick base pairs. This review focuses on the various structural aspects of non-canonical base pairs in the organization of RNA molecules and the possible applications of these base pairs in predicting RNA structures with more accuracy.

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TL;DR: The finding suggests that gold nanoparticle-quercetin complex can pass through the membranes of human red blood cells and provides evidences how capping is important in stabilizing the gold nanoparticles and further enhances its interaction with other molecules, such as drugs.

Abstract: Quercetin and several other bioflavonoids possess antioxidant property. These biomolecules can reduce the diabetic complications, but metabolize very easily in the body. Nanoparticle-mediated delivery of a flavonoid may further increase its efficacy. Gold nanoparticle is used by different groups as vehicle for drug delivery, as it is least toxic to human body. Prior to search for the enhanced efficacy, the gold nanoparticle-flavonoid complex should be prepared and well characterized. In this article, we report the interaction of gold nanoparticle with quercetin. The interaction is confirmed by different biophysical techniques, such as Scanning Electron Microscope (SEM), Circular Dichroism (CD), Fourier-Transform InfraRed (FT-IR) spectroscopy and Thermal Gravimetric Analysis (TGA) and cross checked by quantum chemical calculations. These studies indicate that gold clusters are covered by citrate groups, which are hydrogen bonded to the quercetin molecules in the complex. We have also provided evidences how capping is important in stabilizing the gold nanoparticle and further enhances its interaction with other molecules, such as drugs. Our finding also suggests that gold nanoparticle-quercetin complex can pass through the membranes of human red blood cells.

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TL;DR: All the available RNA structures from PDB are classified through a programmatic approach into nine functional classes and it would be now a simple assignment to regularly update the classification as and when new structures are released.

Abstract: One of the important goals of most biological investigations is to classify and organize the experimental findings so that they are readily useful for deriving generalized rules. Although there is a huge amount of information on RNA structures in PDB, there are redundant files, ambiguous synthetic sequences etc. Moreover, a systematic hierarchical organization, reflecting RNA classification, is missing in PDB. In this investigation, we have classified all the available RNA crystal structures from PDB through a programmatic approach. Hence, it would be now a simple assignment to regularly update the classification as and when new structures are released. The classification can further determine (i) a non-redundant set of RNA structures and (ii) if available, a set of structures of identical sequence and function, which can highlight structural polymorphism, ligand-induced conformational alterations etc. Presently, we have classified the available structures (2095 PDB entries having RNA chain longer than 9 nucleotides solved by X-ray crystallography or NMR spectroscopy) into nine functional classes. The structures of same function and same source are mostly seen to be similar with subtle differences depending on their functional complexation. The web-server is available online at http://www.saha.ac.in/biop/www/HD-RNAS.html and is updated regularly.

26 citations

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##### References

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TL;DR: A simple derivation of a simple GGA is presented, in which all parameters (other than those in LSD) are fundamental constants, and only general features of the detailed construction underlying the Perdew-Wang 1991 (PW91) GGA are invoked.

Abstract: Generalized gradient approximations (GGA’s) for the exchange-correlation energy improve upon the local spin density (LSD) description of atoms, molecules, and solids. We present a simple derivation of a simple GGA, in which all parameters (other than those in LSD) are fundamental constants. Only general features of the detailed construction underlying the Perdew-Wang 1991 (PW91) GGA are invoked. Improvements over PW91 include an accurate description of the linear response of the uniform electron gas, correct behavior under uniform scaling, and a smoother potential. [S0031-9007(96)01479-2] PACS numbers: 71.15.Mb, 71.45.Gm Kohn-Sham density functional theory [1,2] is widely used for self-consistent-field electronic structure calculations of the ground-state properties of atoms, molecules, and solids. In this theory, only the exchange-correlation energy EXC › EX 1 EC as a functional of the electron spin densities n"srd and n#srd must be approximated. The most popular functionals have a form appropriate for slowly varying densities: the local spin density (LSD) approximation Z d 3 rn e unif

117,932 citations

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TL;DR: In this article, a semi-empirical exchange correlation functional with local spin density, gradient, and exact exchange terms was proposed. But this functional performed significantly better than previous functionals with gradient corrections only, and fits experimental atomization energies with an impressively small average absolute deviation of 2.4 kcal/mol.

Abstract: Despite the remarkable thermochemical accuracy of Kohn–Sham density‐functional theories with gradient corrections for exchange‐correlation [see, for example, A. D. Becke, J. Chem. Phys. 96, 2155 (1992)], we believe that further improvements are unlikely unless exact‐exchange information is considered. Arguments to support this view are presented, and a semiempirical exchange‐correlation functional containing local‐spin‐density, gradient, and exact‐exchange terms is tested on 56 atomization energies, 42 ionization potentials, 8 proton affinities, and 10 total atomic energies of first‐ and second‐row systems. This functional performs significantly better than previous functionals with gradient corrections only, and fits experimental atomization energies with an impressively small average absolute deviation of 2.4 kcal/mol.

80,847 citations

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TL;DR: Numerical calculations on a number of atoms, positive ions, and molecules, of both open- and closed-shell type, show that density-functional formulas for the correlation energy and correlation potential give correlation energies within a few percent.

Abstract: A correlation-energy formula due to Colle and Salvetti [Theor. Chim. Acta 37, 329 (1975)], in which the correlation energy density is expressed in terms of the electron density and a Laplacian of the second-order Hartree-Fock density matrix, is restated as a formula involving the density and local kinetic-energy density. On insertion of gradient expansions for the local kinetic-energy density, density-functional formulas for the correlation energy and correlation potential are then obtained. Through numerical calculations on a number of atoms, positive ions, and molecules, of both open- and closed-shell type, it is demonstrated that these formulas, like the original Colle-Salvetti formulas, give correlation energies within a few percent.

77,776 citations

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TL;DR: The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource are described.

Abstract: The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules. This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the future development of the resource.

30,190 citations

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TL;DR: In this paper, a detailed study of correlation effects in the oxygen atom was conducted, and it was shown that primitive basis sets of primitive Gaussian functions effectively and efficiently describe correlation effects.

Abstract: In the past, basis sets for use in correlated molecular calculations have largely been taken from single configuration calculations. Recently, Almlof, Taylor, and co‐workers have found that basis sets of natural orbitals derived from correlated atomic calculations (ANOs) provide an excellent description of molecular correlation effects. We report here a careful study of correlation effects in the oxygen atom, establishing that compact sets of primitive Gaussian functions effectively and efficiently describe correlation effects i f the exponents of the functions are optimized in atomic correlated calculations, although the primitive (s p) functions for describing correlation effects can be taken from atomic Hartree–Fock calculations i f the appropriate primitive set is used. Test calculations on oxygen‐containing molecules indicate that these primitive basis sets describe molecular correlation effects as well as the ANO sets of Almlof and Taylor. Guided by the calculations on oxygen, basis sets for use in correlated atomic and molecular calculations were developed for all of the first row atoms from boron through neon and for hydrogen. As in the oxygen atom calculations, it was found that the incremental energy lowerings due to the addition of correlating functions fall into distinct groups. This leads to the concept of c o r r e l a t i o n c o n s i s t e n t b a s i s s e t s, i.e., sets which include all functions in a given group as well as all functions in any higher groups. Correlation consistent sets are given for all of the atoms considered. The most accurate sets determined in this way, [5s4p3d2f1g], consistently yield 99% of the correlation energy obtained with the corresponding ANO sets, even though the latter contains 50% more primitive functions and twice as many primitive polarization functions. It is estimated that this set yields 94%–97% of the total (HF+1+2) correlation energy for the atoms neon through boron.

24,491 citations