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Structure and spectroscopy of bio- and nano-materials from first-principles simulations
KTH, School of Biotechnology (BIO), Theoretical Chemistry.ORCID iD: 0000-0002-6706-651X
2011 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

This thesis is devoted to first-principles simulations of bio- and nano-materials,focusing on various soft x-ray spectra, ground-state energies and structures of isolated largemolecules, bulk materials, and small molecules in ambient solutions.

K-edge near-edge x-ray absorption fine structure (NEXAFS) spectra, x-ray emission spectra, andresonant inelastic x-ray scattering spectra of DNA duplexes have been studied by means oftheoretical calculations at the density functional theory level. By comparing a sequence of DNAduplexes with increasing length, we have found that the stacking effect of base pairs has verysmall influence on all kinds of spectra, and suggested that the spectra of a general DNA can bewell reproduced by linear combinations of composed base pairs weighted by their ratio.

The NEXAFS spectra study has been extended to other realistic systems. We have used cluster modelswith increasing sizes to represent the infinite crystals of nucleobases and nucleosides, infinitegraphene sheet, as well as a short peptide in water solution. And the equivalent core holeapproximation has been extensively adopted, which provides an efficient access to these largesystems. We have investigated the influence of external perturbations on the nitrogen NEXAFSspectra of guanine, cytosine, and guanosine crystals, and clarified early discrepancies betweenexperimental and calculated spectra. The effects of size, stacking, edge, and defects to theabsorption spectra of graphene have been systematically analyzed, and the debate on theinterpretation of the new feature has been resolved. We have illustrated the influence of watersolvent to a blocked alanine molecule by using the snapshots generated from molecular dynamics.

Multi-scale computational study on four short peptides in a self-assembled cage is presented. It isshown that the conformation of a peptide within the cage does not corresponds to its lowest-energyconformation in vacuum, due to the Zn-O bond formed between the peptide and the cage, and theconfinement effect of the cage.

Special emphasis has been paid on a linear-scaling method, the generalized energy basedfragmentation energy (GEBF) approach. We have derived the GEBF energy equation at the Hartree-Focklevel with the Born approximation of the electrostatic potential. Numerical calculations for amodel system have explained the accuracy of the GEBF equation and provides a starting point forfurther refinements. We have also presented an automatic and efficient implementation of the GEBFapproach which is applicable for general large molecules.

Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology , 2011. , xvi, 74 p.
Series
Trita-BIO-Report, ISSN 1654-2312 ; 2011:05
Keyword [en]
soft x-ray spectroscopy, bio- and nano-materials, first-principles simulation, host-guest interaction, generalized energy-based fragmentation
National Category
Theoretical Chemistry Physical Chemistry
Research subject
SRA - Molecular Bioscience
Identifiers
URN: urn:nbn:se:kth:diva-31944ISBN: 978-91-7415-928-8OAI: oai:DiVA.org:kth-31944DiVA: diva2:407490
Public defence
2011-04-28, FA31, AlbaNova University Center, Roslagstullsbacken 21, Stockholm, 14:00 (English)
Opponent
Supervisors
Note
QC 20110404Available from: 2011-04-04 Created: 2011-03-30 Last updated: 2011-04-13Bibliographically approved
List of papers
1. Systematic Study of Soft X-ray Spectra of Poly(Dg)center dot Poly(Dc) and Poly(Da)center dot Poly(Dt) DNA Duplexes
Open this publication in new window or tab >>Systematic Study of Soft X-ray Spectra of Poly(Dg)center dot Poly(Dc) and Poly(Da)center dot Poly(Dt) DNA Duplexes
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2010 (English)In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, no 20, 7016-7021 p.Article in journal (Refereed) Published
Abstract [en]

In the present work, we have undertaken a combined experimental and theoretical study of X-ray spectroscopies for DNA base pairs, more precisely near-edge X-ray absorption, X-ray emission, and resonant inelastic X-ray scattering applied to poly(dG)center dot poly(dC) and poly(dA)center dot poly(dT) DNA duplexes. We have derived several conclusions on the nature of these X-ray spectra: the stacking of pairs has very little influence on the spectra; the spectra of a DNA composed of mixed Watson-Crick base pairs are well reproduced by linear combinations of GC and AT base pairs involved; the amine and imine nitrogens show noticeable differences as building blocks in the absorption, emission, and resonant emission spectra. The calculated spectra are in good agreement with experimental results. The ramifications of these conclusions for the use of X-ray spectroscopy for DNA are discussed.

Keyword
TRANSMISSION-GRATING SPECTROMETER, AMINO-ACIDS, ELECTRONIC-STRUCTURE, ABSORPTION SPECTRA, CORRELATION-ENERGY, SPECTROSCOPY, EDGE, APPROXIMATION, DENSITY, NUCLEOBASES
National Category
Chemical Sciences
Identifiers
urn:nbn:se:kth:diva-27576 (URN)10.1021/jp911199e (DOI)000277776800031 ()2-s2.0-77952702749 (ScopusID)
Note
QC 20101214Available from: 2010-12-14 Created: 2010-12-13 Last updated: 2011-04-04Bibliographically approved
2. Refinement of DNA Structures through Near-Edge X-ray Absorption Fine Structure Analysis: Applications on Guanine and Cytosine Nucleobases, Nucleosides, and Nucleotides
Open this publication in new window or tab >>Refinement of DNA Structures through Near-Edge X-ray Absorption Fine Structure Analysis: Applications on Guanine and Cytosine Nucleobases, Nucleosides, and Nucleotides
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2010 (English)In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, no 41, 13214-13222 p.Article in journal (Refereed) Published
Abstract [en]

In this work we highlight the potential of NEXAFS-near-edge X-ray absorption fine structure-analysis to perform refinements of hydrogen-bond structure in DNA. For this purpose we have carried out first-principle calculations of the N1s NEXAFS spectra of the guanine and cytosine nucleobases and their tautomers, nucleosides, and nucleotides in the gas phase, as well as for five crystal structures of guanine, cytosine, or guanosine. The spectra all clearly show imine (pi*(1)) and amine (pi*(2)) nitrogen absorption bands with a characteristic energy difference (Delta). Among all of the intramolecule covalent connections, the tautomerism of hydrogens makes the largest influence, around +/- 0.4-0.5 eV change of Delta, to the spectra due to a switch of single-double bonds. Deoxyribose and ribose sugars can cause at most 0.2 eV narrowing of Delta, while the phosphate groups have nearly negligible effects on the spectra. Two kinds of intermolecule interactions are analyzed, the hydrogen bonds and the stacking effect, by comparing "compressed" and "expanded" models. or by comparing models including or excluding the nearest stacking molecules. The shortening of hydrogen-bond length by 0.2-0.3 angstrom can result in the reduction of Delta by 0.2-0.8 eV. This is because the hydrogen bonds make the electrons more delocalized, and the amine and imine nitrogens become less distinguishable. Moreover, the hydrogen bond has a different ability to influence the spectra of different crystals, with guanine crystals as the largest (change by 0.8 eV) and the guanosine crystal as the smallest (change by 0.2 eV). The stacking has negligible effects on the spectra in all studied systems. A comparison of guanosine to guanine crystals shows that the sugars in the crystal could create "blocks" in the pi-and hydrogen bonds network of bases and thus makes the imine and amine nitrogens More distinguishable with a larger Delta. Our theoretical calculations offer a good match with experimental findings and explain earlier discrepancies in the NEXAFS analysis.

Keyword
SINGLE-STRANDED-DNA, NITROGEN K-EDGE, CRYSTAL STRUCTURE, ELECTRONIC-STRUCTURE, CORRELATION-ENERGY, BUILDING-BLOCKS, SPECTROSCOPY, SPECTRA, NEXAFS, DENSITY
National Category
Chemical Sciences
Identifiers
urn:nbn:se:kth:diva-26300 (URN)10.1021/jp1034745 (DOI)000282855100023 ()2-s2.0-77958039838 (ScopusID)
Note
QC 20101227Available from: 2010-12-27 Created: 2010-11-21 Last updated: 2011-04-04Bibliographically approved
3. X-ray absorption spectra of graphene from first-principles simulations
Open this publication in new window or tab >>X-ray absorption spectra of graphene from first-principles simulations
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2010 (English)In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 82, no 15, 155433- p.Article in journal (Refereed) Published
Abstract [en]

Near edge x-ray absorption fine-structure spectra of graphenes are calculated using hybrid density-functional theory with the equivalent core hole approximation, aiming to resolve the ongoing debate on the interpretation of corresponding experimental spectra. Effects of size, stacking, edges, and defects on the spectra have been analyzed in detail for both C 1s-pi* and C 1s-sigma* transitions. The infinite graphene sheet has been modeled by graphene nanoribbons of different size. The size dependence and convergence of the spectra have been revealed. It is found that the pi-pi interaction between layers have mainly effects on the C 1s-pi* transitions in two different energy regions. The stacking effect smears out the double-peaks structure of the first main pi* peak around 285 eV and results in blueshift of the second pi* structure by almost 2 eV. The calculations show that the pi spectrum of hydrogen saturated edge carbons is redshifted with respect to the central ones and that a new weak sigma* peak around 288 eV appears. The presence of defects can also introduce new spectral features in both pi and sigma regions.

National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Identifiers
urn:nbn:se:kth:diva-26251 (URN)10.1103/PhysRevB.82.155433 (DOI)000283049800016 ()2-s2.0-78149243806 (ScopusID)
Note
QC 20110129Available from: 2011-01-29 Created: 2010-11-21 Last updated: 2011-04-04Bibliographically approved
4. NEXAFS spectroscopies of blocked alanine in water solution from first-principles simulations
Open this publication in new window or tab >>NEXAFS spectroscopies of blocked alanine in water solution from first-principles simulations
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(English)Manuscript (preprint) (Other academic)
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-32061 (URN)
Note
QS 2011Available from: 2011-04-04 Created: 2011-04-04 Last updated: 2011-11-22Bibliographically approved
5. Understanding the Influence of Guest-Host Interactions on the Conformation of Short Peptides in a Hydrophobic Cavity: A Computational Study
Open this publication in new window or tab >>Understanding the Influence of Guest-Host Interactions on the Conformation of Short Peptides in a Hydrophobic Cavity: A Computational Study
2011 (English)In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 12, no 7, 1325-1333 p.Article in journal (Refereed) Published
Abstract [en]

We performed a computational investigation to understand the conformational preferences of four short peptides in a self-assembled cage based on the experimental work by Y. Hatakeyama et al. (Angew. Chem. Int. Ed. 2009, 48, 8695). For this purpose, we combined molecular dynamics simulations, Monte Carlo simulations, and quantum mechanical calculations to obtain energies and structures for several low-lying conformers of four peptides and the corresponding peptide-cage inclusion complexes. Our calculations at both B3LYP and MP2 levels show that for each peptide, the corresponding conformation within the host (as revealed by the crystal structure) does not represent the lowest-energy conformation of this peptide in vacuum. By comparing some low-lying conformers in vacuum and in the cavity (for the same peptide), we found that the cage has a significant influence on the conformational propensities of peptides. First, one carbonyl oxygen of each peptide tends to bind to one Zn (II) atom of the cage, forming a Zn-O bond. The formation of this bond leads to significant charge transfer from the cage to the peptide. Second, this Zn-O bond causes the peptide to go through some local conformational changes. For larger peptides, such as penta-and hexapeptides, our calculations also show that some of their conformers must undergo significant structural changes, due to the confinement of the host. This computational study reveals the noticeable influence of the guest-host interaction on the conformational preferences of short peptides.

Keyword
charge transfer, confinement, conformational propensity, host–guest interactions, peptides
National Category
Theoretical Chemistry
Research subject
SRA - Molecular Bioscience
Identifiers
urn:nbn:se:kth:diva-31955 (URN)10.1002/cphc.201001081 (DOI)000290471500017 ()2-s2.0-79955670870 (ScopusID)
Note
QC 20120822. Uppdaterad från Accepted till Published.Available from: 2011-03-30 Created: 2011-03-30 Last updated: 2012-08-22Bibliographically approved
6. Understanding the accuracy of the generalized energy-based fragmentation approach at the Hartree-Fock level by multipole expansion analysis
Open this publication in new window or tab >>Understanding the accuracy of the generalized energy-based fragmentation approach at the Hartree-Fock level by multipole expansion analysis
(English)Manuscript (preprint) (Other academic)
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-32063 (URN)
Note
QS 2011Available from: 2011-04-04 Created: 2011-04-04 Last updated: 2011-11-22Bibliographically approved
7. An Efficient Implementation of the Generalized Energy-Based Fragmentation Approach for General Large Molecules
Open this publication in new window or tab >>An Efficient Implementation of the Generalized Energy-Based Fragmentation Approach for General Large Molecules
2010 (English)In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 114, no 31, 8126-8134 p.Article in journal (Refereed) Published
Abstract [en]

An efficient implementation of the generalized energy-based fragmentation (GEBF) approach (Li, W.; Li, S.; Jiang, Y. J Phys. Chem. A 2007, 111, 2193) for treating a wide range of large molecules is presented. In this implementation, the fragmentation process can be automatically done for a general molecule, with only some functional groups defined by users. A new and fast scheme is designed for the generation of various subsystems and the derivation of their coefficients. The newly implemented GEBF approach has been applied to several large molecules including proteins, nucleic acids, and supermolecules with fused aromatic rings. Test calculations within the Hartree-Fock (HF) and density functional theory (DFT) framework demonstrate that the GEBF approach can provide reasonably accurate ground-state energies and optimized structures, which are in good agreement with those from conventional HF or DFT calculations. The GEBF approach implemented in this work can now be employed by nonexpert users to compute energies, optimized structures, and some molecular properties at various ab initio levels for a broad range of large molecules on ordinary PC workstations.

Keyword
LOCAL CORRELATION APPROACH, GROUND-STATE ENERGIES, ATOMIC ORBITAL BASIS, ELECTRON CORRELATION, COUPLED-CLUSTER, DENSITY-MATRIX, TAILORING APPROACH, WATER CLUSTERS, WEB-INTERFACE, LARGE SYSTEMS
National Category
Chemical Sciences
Identifiers
urn:nbn:se:kth:diva-29418 (URN)10.1021/jp103074f (DOI)000280523500014 ()2-s2.0-77955602217 (ScopusID)
Note
QC 20110215Available from: 2011-02-15 Created: 2011-02-02 Last updated: 2011-04-04Bibliographically approved

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