scholarly journals Molecular relaxation processes in calf-thymus DNA, in the presence of Mn2+and Na+ions: A Raman spectroscopic study

2008 ◽  
Vol 22 (5) ◽  
pp. 345-359 ◽  
Author(s):  
Cristina M. Muntean ◽  
Ioan Bratu
Keyword(s):  
Molecular Dynamics ◽  
Structural Changes ◽  
Vibrational Energy ◽  
Raman Band ◽  
Relaxation Times ◽  
Ion Concentration ◽  
Calf Thymus Dna ◽  
Relaxation Processes ◽  
Molecular Relaxation ◽  
Calf Thymus

In this paper the Raman total half bandwidths of calf-thymus DNA vibrations have been measured as a function of Mn2+ion concentration (0–600 mM), in the presence of two concentrations of Na+cations, respectively. The dependencies of the half bandwidths and of the global relaxation times on DNA molecular subgroup structure, on Mn2+and Na+ions concentrations, respectively, are reported. It is shown that changes in the (sub)picosecond dynamics of molecular subgroups in calf-thymus DNA can be monitored with Raman spectroscopy.In this study the Raman band parameters for the vibrations at 729 cm-1(dA), 787 cm-1(dC), 1094 cm-1(PO2-), 1376 cm-1(dA, dG, dT, dC), 1489 cm-1(dG, dA) and 1578 cm-1(dG, dA) of calf thymus DNA are presented. The full-widths at half-height (FWHH) of the bands in calf-thymus DNA are typically in the wavenumber range from 9 to 33.5 cm-1. It can be observed that the molecular relaxation processes studied in this work, have a global relaxation time smaller than 1.179 ps and larger than 0.317 ps.Mn2+-induced DNA structural changes result for the vibrations at 729 cm-1and 787 cm-1in smaller global relaxation times, and larger half bandwidths, respectively, as compared to the starting value of 0 mM Mn2+. The vibrational energy transfer processes of these two subgroups (dA, dC), respectively, are slower in the case of DNA samples at 10 mM NaCl, as compared to the corresponding DNA samples at 150 mM NaCl. However, the behaviour of the global relaxation times characteristic to the bands at 729 and 787 cm-1is similar with respect to manganese(II) ions concentration, in the case of the two values of Na+ions content, respectively.On the contrary, the molecular dynamics is slower for the base vibrations at 1376, 1489 and 1578 cm-1, in the case of DNA samples at 150 mM NaCl, as compared to the corresponding samples at lower Na+concentration, in almost all Mn2+ions concentration range. The molecular relaxation processes in these three cases, respectively, are quite different for the corresponding samples with different Na+ions content, upon increasing divalent manganese ions concentration.The molecular dynamics characterizing the band near 1094 cm-1of the DNA backbone PO2-symmetric stretching vibration is faster upon increasing the Mn2+ions concentration between 0–600 mM and seems not to be influenced by the Na+ions content, specific to our experimental conditions.

scholarly journals Molecular dynamics in calf-thymus DNA, at neutral and low pH, in the presence of Na+, Ca2+and Mg2+ions: A Raman microspectroscopic study

2007 ◽  
Vol 21 (4) ◽  
pp. 193-204 ◽  
Author(s):  
Cristina M. Muntean ◽  
Ioan Bratu
Keyword(s):  
Molecular Dynamics ◽  
Vibrational Energy ◽  
Divalent Cations ◽  
Relaxation Times ◽  
Helical Structure ◽  
Low Ph ◽  
Calf Thymus Dna ◽  
Relaxation Processes ◽  
Molecular Subgroup ◽  
Calf Thymus

In this paper the Raman total half bandwidths of calf-thymus DNA vibrations have been measured as a function of pH, monovalent and divalent cations' type and concentration. The dependence of different band parameters on DNA molecular subgroup structure, on pH and on Na+, Ca2+and Mg2+ions concentrations, respectively, are reported. It is shown that changes in (sub)picosecond dynamics of molecular subgroups in calf-thymus DNA can be monitored with confocal Raman microspectroscopy.The half bandwidths and the global relaxation times for the vibrations at 728 cm−1(dA), 785 cm−1(dC), 1094 cm−1(PO2−), 1377 cm−1(dA, dG, dT, dC), 1488 cm−1(dG, dA) and 1580 cm−1(dG, dA) of calf-thymus DNA are presented. The full-widths at half-height (FWHH) of the bands in calf-thymus DNA are typically in the wavenumber range from 7.4 to 31 cm−1. The bandwidths in the Raman spectra are sensitive to a dynamics active on a time scale from 0.34 to 1.44 ps.Low pH-induced melting of double helical structure in calf-thymus DNA results for some bands in shorter global relaxation times, as a consequence of the increased interaction of the base moieties with the solvent molecules.The molecular dynamics characterizing the 785, 1094, 1377 and 1580 cm−1vibrations, is faster in the case of high divalent cations DNA sample (pH 7), as compared to the respective low divalent cations DNA sample (pH 7), for both Ca2+and Mg2+ions. The vibrational energy transfer process of the guanine band at 1488 cm−1is slower for the high salt DNA sample, pH 7 as compared to the corresponding low salt DNA sample, pH 7, for both Ca2+and Mg2+. Molecular dynamics characterizing the vibration at 1488 cm−1is faster for DNA sample at high Na+ions (pH 7), as compared to the DNA sample at low Na+ions (pH 7).As far as the CaDNA and MgDNA complexes are concerned (pH 7), the global relaxation times of some base vibrations decrease for the case of magnesium ions, as compared to the case of the same concentration of calcium ions. The different ionic radius of the two types of metal cations (0.72 Å for Mg and 0.99 Å for Ca) were considered in explaining these results.Molecular relaxation processes of DNA subgroups, upon lowering the pH, in the presence of Na+, Ca2+and Mg2+ions are presented. Particularly, at low Ca2+concentration, upon lowering the pH, the molecular dynamics of DNA subgroups corresponding to vibrations at 728, 1376, 1488 and 1580 cm−1is much faster, probably due to the denaturation process of the double helical DNA.

scholarly journals Raman spectroscopic study on the subpicosecond dynamics in calf-thymus DNA, upon lowering the pH and in the presence of Mn2+ions

2008 ◽  
Vol 22 (6) ◽  
pp. 475-489 ◽  
Author(s):  
Cristina M. Muntean ◽  
Ioan Bratu
Keyword(s):  
Relaxation Time ◽  
Vibrational Energy ◽  
Raman Band ◽  
Relaxation Times ◽  
Low Ph ◽  
Calf Thymus Dna ◽  
Relaxation Processes ◽  
Molecular Subgroups ◽  
Limit Values ◽  
Calf Thymus

In this paper the Raman total half bandwidths of calf-thymus DNA vibrations have been measured as a function of pH (3.45–6.4), in the presence of Mn2+ions, respectively. The dependencies of the half bandwidths and of the global relaxation times, on DNA molecular subgroup structure and on pH, are reported. It is shown that changes in the subpicosecond dynamics of molecular subgroups in calf-thymus DNA can be monitored with Raman spectroscopy.Particularly, the Raman band parameters for the vibrations at 728 cm–1(dA), 787 cm–1(dC), 1093 cm–1(PO2–), 1376 cm–1(dA, dG, dT, dC), 1489 cm–1(dG, dA) and 1578 cm–1(dG, dA) of MnDNA complexes, at reduced and low pH values, are presented. In our study, the full widths at half-maximum (FWHM) of the bands in calf-thymus DNA are typically in the wavenumber range from 11 to 27 cm–1. It can be observed that the molecular relaxation processes studied in this work, have a global relaxation time smaller than 0.965 ps and larger than 0.393 ps. The limit values are characteristic for dA and dC residues, respectively (vibrations at 728 and 787 cm–1).Low pH-induced melting of double helical structure in calf-thymus DNA, in the presence of Mn2+ions, results for some bands in smaller global relaxation times, and larger bandwidths, respectively, as a consequence of the increased interaction of the base moieties with the solvent molecules. This behaviour is most evident for the bands at 787 cm–1up to pH 3.8, at 1578 cm–1up to pH 3.45 and is partially confirmed for the DNA backbone PO2–symmetric stretching vibration at 1093 cm–1.The fastest molecular dynamics was obtained for the adenine band at 728 cm–1in the pH interval 3.45–3.8 (global relaxation time 0.885 ps), for the cytosine ring breathing mode near 787 cm–1around the pH 3.8 (global relaxation time 0.393 ps), for the band at 1093 cm–1in the pH interval 3.8–4.4 (global relaxation time 0.518 ps) and for the vibration near 1578 cm–1at pH 3.45 (global relaxation time 0.544 ps).A comparison between different time scales of the vibrational energy transfer processes, characterizing the protonated MnDNA structural subgroups has been given.We have found that metal ion's type and concentration are modulators for the (sub)picosecond dynamics of protonated DNA molecular subgroups.

scholarly journals Subpicosecond dynamics in calf-thymus DNA, in the presence of Zn2+ions: A Raman spectroscopic study

2009 ◽  
Vol 23 (3-4) ◽  
pp. 141-154 ◽  
Author(s):  
Cristina M. Muntean ◽  
Ioan Bratu ◽  
Konstantinos Nalpantidis ◽  
Monica A. P. Purcaru
Keyword(s):  
Vibrational Energy ◽  
Raman Band ◽  
Relaxation Times ◽  
Calf Thymus Dna ◽  
Relaxation Processes ◽  
Molecular Subgroups ◽  
Molecular Subgroup ◽  
Limit Values ◽  
Calf Thymus ◽  
Solvent Molecules

In this paper the Raman total half bandwidths of calf-thymus DNA vibrations have been measured as a function of Zn2+ions concentration, in the presence of a constant concentration of Na+ions, respectively. The dependencies of the total half bandwidths and of the global relaxation times, on DNA molecular subgroup structure and on Zn2+ions concentration, are reported. It is shown that changes in the subpicosecond dynamics of molecular subgroups in ZnDNA complexes can be monitored with Raman spectroscopy.Particularly, the Raman band parameters for the vibrations at 729 cm−1(dA), 792 cm−1(dC, dT and 5'-C–O–P–O–C-3' network), 1094 cm−1(DNA backbone PO2−symmetric stretching), 1377 cm−1(dA, dT, dC), 1489 cm−1(the guanine N-7 and adenine rings) and 1581 cm−1(dG, dA) of ZnDNA complexes, in the presence of Zn2+ions concentrations that varied between 0 and 250 mM, are presented. In our study, the full widths at half-maximum (FWHM) of the bands in calf-thymus DNA complexes are typically in the wavenumber range from 10 to 50 cm−1. It can be observed that the molecular relaxation processes studied in this work, have a global relaxation time smaller than 0.94 ps and larger than 0.21 ps. The limit values are characterizing the dA and dG residues, respectively (vibrations at 729 cm−1and 1489 cm−1).Binding of Zn2+ions to double helical calf-thymus DNA results for some vibrations in smaller global relaxation times and larger bandwidths, respectively, possible as a consequence of the increased interaction of the base moieties with the solvent molecules in unstacked structures.The fastest and the slowest dynamics for different DNA structural subgroups and different Zn2+ions concentrations, respectively, have been analyzed.A comparison between different time scales of the vibrational energy transfer processes, characterizing the ZnDNA structural subgroups has been given.We have found that metal ion's type and concentration are modulators for the (sub)picosecond dynamics of calf thymus DNA molecular subgroups.

scholarly journals FT-Raman study of the (sub)picosecond dynamics in genomic DNA from plant tissues

2009 ◽  
Vol 23 (5-6) ◽  
pp. 281-289 ◽  
Author(s):  
Cristina M. Muntean ◽  
Ioan Bratu
Keyword(s):  
Relaxation Time ◽  
Genomic Dna ◽  
Vibrational Energy ◽  
Raman Band ◽  
Dynamical Behavior ◽  
Relaxation Processes ◽  
Molecular Subgroups ◽  
Molecular Relaxation ◽  
Leaf Tissues ◽  
Genomic Dnas

In this paper the Raman total half bandwidths of eight genomic DNAs from leaf tissues [potato (Solanum tuberosumL.), sword fern (Nephrolepis exaltataL.), scopolia (Scopolia carniolicaJacq.), redwood (Sequoia sempervirensD. Don. Endl.), orchids (Cymbidium × hybrida), chrysanthemum (Dendranthema grandifloraRamat.) and common sundew (Drosera rotundifoliaL.)] have been measured. The dependencies of the total half bandwidths and of the global relaxation times, on DNA molecular subgroup structure and on the type of genomic plant DNA, are reported. It is shown that changes in the (sub)picosecond dynamics of molecular subgroups in genomic DNAs from leaf tissues can be monitored with Raman spectroscopy.Particularly, the Raman band parameters for the vibrations at 879 cm−1(deoxyribose, dA), 1047 cm−1(CO stretching C‒O‒P‒O‒C, dG), 1089 cm−1(P—O symmetric stretching of PO2‒), 1124 cm−1(dA), 1272 cm−1(dC, dG, dT), 1276 cm−1(dC), 1455 cm−1(deoxyribose, dA, dC, dT) and 1482 cm−1(dG, dA) of genomic leaf tissues DNAs are presented. In our study, the full widths at half-maximum (FWHM) of the bands in genomic DNAs from leaf tissues are typically in the wavenumber range from 7.8 to 23.1 cm−1. It can be observed that the molecular relaxation processes studied in this work, have a global relaxation time smaller than 1.36 ps and larger than 0.46 ps.The fastest and the slowest relaxation processes of different DNA structural subgroups, for several types of genomic DNA extracted from leaf tissue, have been analyzed. Particularly, the slowest dynamics corresponding to the vibration near 1272 cm−1takes place in the case of DNA extracted from common sundew (global relaxation time 1.36 ps).A comparison between different time scales of the vibrational energy transfer processes, characterizing several DNA complexes, has been given.We have found that the bands at 879 cm−1(deoxyribose, phosphodiester, dA) and 1455 cm−1(deoxyribose, dA, dC, dT) are suitable for the study of dynamical behavior of molecular subgroups in genomic DNA extracted from leaf tissues.Specific molecular relaxation processes, depending on the type of genomic DNA extracted from leaf tissues has been observed.

scholarly journals A Bis-Monophospholyl Dysprosium Cation Showing Magnetic Hysteresis at 48 Kelvin

2019 ◽  
Author(s):  
Peter Evans ◽  
Daniel Reta ◽  
George F. S. Whitehead ◽  
Nicholas Chilton ◽  
David Mills
Keyword(s):  
Data Storage ◽  
Single Molecule ◽  
Structural Changes ◽  
Elevated Temperatures ◽  
Spin Dynamics ◽  
Magnetic Hysteresis ◽  
Relaxation Times ◽  
Magnetic Memory ◽  
Relaxation Processes ◽  
Potential Applications

Single-molecule magnets (SMMs) have potential applications in high-density data storage, but magnetic relaxation times at elevated temperatures must be increased to make them practically useful. <i>Bis</i>-cyclopentadienyl lanthanide sandwich complexes have emerged as the leading candidates for SMMs that show magnetic memory at liquid nitrogen temperatures, but the relaxation mechanisms mediated by aromatic C<sub>5</sub> rings have not been fully established. Here we synthesise a <i>bis</i>-monophospholyl dysprosium SMM [Dy(Dtp)<sub>2</sub>][Al{OC(CF<sub>3</sub>)<sub>3</sub>}<sub>4</sub>] (<b>1</b>, Dtp = {P(C<sup>t</sup>BuCMe)<sub>2</sub>}) by the treatment of <i>in situ</i>-prepared “[Dy(Dtp)<sub>2</sub>(C<sub>3</sub>H<sub>5</sub>)]” with [HNEt<sub>3</sub>][Al{OC(CF<sub>3</sub>)<sub>3</sub>}<sub>4</sub>]. SQUID magnetometry reveals that <b>1</b> has an effective barrier to magnetisation reversal of 1,760 K (1,223 cm<sup>–1</sup>) and magnetic hysteresis up to 48 K. <i>Ab initio</i> calculation of the spin dynamics reveal that transitions out of the ground state are slower in <b>1</b> than in the first reported dysprosocenium SMM, [Dy(Cp<sup>ttt</sup>)<sub>2</sub>][B(C<sub>6</sub>F<sub>5</sub>)<sub>4</sub>] (Cp<sup>ttt</sup> = C<sub>5</sub>H<sub>2</sub><sup>t</sup>Bu<sub>3</sub>-1,2,4), however relaxation is faster in <b>1</b> overall due to the compression of electronic energies and to vibrational modes being brought on-resonance by the chemical and structural changes introduced by the <i>bis</i>-Dtp framework. With the preparation and analysis of <b>1</b> we are thus able to further refine our understanding of relaxation processes operating in <i>bis</i>-C<sub>5</sub>/C<sub>4</sub>P sandwich lanthanide SMMs, which is the necessary first step towards rationally achieving higher magnetic blocking temperatures in these systems in future.

scholarly journals A Bis-Monophospholyl Dysprosium Cation Showing Magnetic Hysteresis at 48 Kelvin

2019 ◽  
Author(s):  
Peter Evans ◽  
Daniel Reta ◽  
George F. S. Whitehead ◽  
Nicholas Chilton ◽  
David Mills
Keyword(s):  
Data Storage ◽  
Single Molecule ◽  
Structural Changes ◽  
Elevated Temperatures ◽  
Spin Dynamics ◽  
Magnetic Hysteresis ◽  
Relaxation Times ◽  
Magnetic Memory ◽  
Relaxation Processes ◽  
Potential Applications

Single-molecule magnets (SMMs) have potential applications in high-density data storage, but magnetic relaxation times at elevated temperatures must be increased to make them practically useful. <i>Bis</i>-cyclopentadienyl lanthanide sandwich complexes have emerged as the leading candidates for SMMs that show magnetic memory at liquid nitrogen temperatures, but the relaxation mechanisms mediated by aromatic C<sub>5</sub> rings have not been fully established. Here we synthesise a <i>bis</i>-monophospholyl dysprosium SMM [Dy(Dtp)<sub>2</sub>][Al{OC(CF<sub>3</sub>)<sub>3</sub>}<sub>4</sub>] (<b>1</b>, Dtp = {P(C<sup>t</sup>BuCMe)<sub>2</sub>}) by the treatment of <i>in situ</i>-prepared “[Dy(Dtp)<sub>2</sub>(C<sub>3</sub>H<sub>5</sub>)]” with [HNEt<sub>3</sub>][Al{OC(CF<sub>3</sub>)<sub>3</sub>}<sub>4</sub>]. SQUID magnetometry reveals that <b>1</b> has an effective barrier to magnetisation reversal of 1,760 K (1,223 cm<sup>–1</sup>) and magnetic hysteresis up to 48 K. <i>Ab initio</i> calculation of the spin dynamics reveal that transitions out of the ground state are slower in <b>1</b> than in the first reported dysprosocenium SMM, [Dy(Cp<sup>ttt</sup>)<sub>2</sub>][B(C<sub>6</sub>F<sub>5</sub>)<sub>4</sub>] (Cp<sup>ttt</sup> = C<sub>5</sub>H<sub>2</sub><sup>t</sup>Bu<sub>3</sub>-1,2,4), however relaxation is faster in <b>1</b> overall due to the compression of electronic energies and to vibrational modes being brought on-resonance by the chemical and structural changes introduced by the <i>bis</i>-Dtp framework. With the preparation and analysis of <b>1</b> we are thus able to further refine our understanding of relaxation processes operating in <i>bis</i>-C<sub>5</sub>/C<sub>4</sub>P sandwich lanthanide SMMs, which is the necessary first step towards rationally achieving higher magnetic blocking temperatures in these systems in future.

scholarly journals Twisting DNA by Salt

2021 ◽  
Author(s):  
Sergio Cruz-Le&oacuten ◽  
Willem Vanderlinden ◽  
Peter Müller ◽  
Tobias Forster ◽  
Georgina Staudt ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Charge Density ◽  
Molecular Dynamics Simulations ◽  
Structural Changes ◽  
Dna Nanotechnology ◽  
Metal Cations ◽  
Ion Concentration ◽  
Preferential Binding ◽  
Dynamics Simulations ◽  
Dna Twist

DNA structure and properties sensitively depend on its environment, in particular on the ion atmosphere. One of the most fundamental properties of DNA is its helicity and here we investigate how it changes with concentration and identity of the surrounding ions. To resolve how metal cations influence the helical twist, we have combined magnetic tweezer experiments and extensive all-atom molecular dynamics simulations. Two interconnected trends are observed for monovalent alkali and divalent alkaline earth cations. First, DNA twist increases with increasing ion concentration. Secondly, for a given salt concentration, DNA twist strongly depends on cation identity. Metal cations with high charge density (such as Li+ or Ca2+) are most efficient at inducing DNA twist and lead to overwinding. By contrast, metals with intermediate charge density (such as Na+ or Ba2+) reduce the twist and underwind the helix compared to higher density ions. Our molecular dynamics simulations reveal that preferential binding of the metals to the DNA backbone and the nucleobases has opposing effects on DNA twist and provide a microscopic explanation of the observed ion specificity. The comprehensive view gained from our combined approach provides a foundation to understand and predict metal-induced structural changes in nature or in DNA nanotechnology.

Dielectric studies. Part XXV. Methoxy group rotation in anisole and three para-substituted anisoles

1969 ◽  
Vol 47 (24) ◽  
pp. 4645-4650 ◽  
Author(s):  
D. B. Farmer ◽  
S. Walker
Keyword(s):  
Relaxation Process ◽  
Methoxy Group ◽  
Relaxation Times ◽  
Pure Liquid ◽  
Relaxation Processes ◽  
Molecular Relaxation ◽  
Microwave Frequencies ◽  
Dielectric Absorption ◽  
Weight Factors ◽  
Group Rotation

The dielectric absorption at several microwave frequencies of anisole, p-methylanisole, and p-bromoanisole in the solvent p-xylene, and p-dimethoxybenzene in the solvent cyclohexane has been investigated at 4 to 6 temperatures. Anisole, p-methylanisole, and p-dimethoxybenzene were all found to relax mainly by methoxy group rotation, whereas the relaxation process in p-bromoanisole was very largely molecular relaxation. In the literature, considerable divergence exists for the analyses of the dielectric data of anisole and substituted anisoles into contributions from two relaxation times and the magnitude of the weight factors governing each relaxation process. Such divergencies have been explored and justifiable analyses established for these systems where the weight factors governing the relaxation processes are shown to be roughly of the same order as those estimated from group moment data. The weight factor for molecular relaxation in the pure liquid appears considerably greater than that for a dilute solution of it in a non-polar solvent.

Molecular Relaxation Processes in Nucleic Acids Components as Probed with Raman Spectroscopy

2017 ◽  
Vol 68 (10) ◽  
Author(s):  
Cristina M. Muntean ◽  
Ioan Bratu ◽  
Carmen Tripon ◽  
Konstantinos Nalpantidis ◽  
Monica A. P. Purcaru ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Solid Phase ◽  
Dynamical Behavior ◽  
Relaxation Times ◽  
Relaxation Mechanism ◽  
Disodium Salt ◽  
Relaxation Processes ◽  
Molecular Relaxation ◽  
Salt Hydrate ◽  
Dna And Rna

In this work the Raman total half bandwidths of five free nucleic acids components (cytidine-5`- monophosphate, 2`- deoxycytidine 5`- monophosphate, 2`- deoxyguanosine-5`- monophosphate, thymidine - 5� - monophosphate disodium salt hydrate and uridine-5`- monophosphate disodium salt) have been measured, respectively. Raman scattering can be used to study the fast molecular relaxation processes of free nucleic acids components in solid phase. The dependencies of the total half bandwidths and of the corresponding global relaxation times, on functional groups and on the type of DNA and RNA constituents, are reported. In our study, the full widths at half-maximum (FWHMs) for the Raman bands of these nucleic acids components, are typically in the wavenumber range from 9 to 28 cm-1. Besides, it can be observed that the (sub)picosecond dynamics studied in this work, has a global relaxation time value smaller than 1.18 ps and larger than 0.38 ps. We have found that the band centered at 1264 cm-1 for cytidine -5`- monophosphate, the profile near 1373 cm-1 attributed to thymidine -5`- monophosphate disodium salt hydrate and the band around 1233 cm-1 attributed to uridine -5`- monophosphate disodium salt, respectively, are suitable for studying the dynamical behavior of molecular fragments in nucleic acids components. For the case of solid phase samples of nucleic acids components, we can suppose that the dominant relaxation mechanism is of the vibrational type one.

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