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.

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.

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.

Nuclear Magnetic Resonance Studies of Molecular Motion in a Number of Stearates and Oleates

1971 ◽  
Vol 49 (5) ◽  
pp. 731-739 ◽  
Author(s):  
J. A. Ripmeester ◽  
B. A. Dunell
Keyword(s):  
Phase Transition ◽  
Alkali Metal ◽  
Relaxation Times ◽  
Lattice Relaxation ◽  
Relaxation Mechanism ◽  
Spin Lattice Relaxation ◽  
Relaxation Processes ◽  
Lower Phase ◽  
Spin Lattice ◽  
Significant Difference

The broad line p.m.r. spectra of the alkali metal oleates have been observed from 77 °K up to or beyond the crystalline to waxy phase transition. Lower phase transition temperatures are observed in the oleates than in the stearates. This fact is attributed to larger entropies of transition in the oleates than in the stearates. The n.m.r. second moments indicate that in the stearates the packing of chains is probably not closer than in the oleates and consequently that the barriers to chain reorientation are not significantly higher in the stearates than in the oleates. Sodium oleate and stearate both appear to behave irregularly in the series of alkali metal soaps. Spin-lattice relaxation times have been measured by adiabatic rapid passage methods for both alkali metal oleates and stearates. Values of T1 and of the activation energy barrier for the reorientation of end methyl groups are compared with values obtained by other workers. No significant difference is seen between relaxation processes in stearates and oleates, at least in the lower temperature range. Soaps which seem to have some amorphous character have a second relaxation mechanism, in addition to end methyl group rotation, which is evidently important in the region of about 150–250 °K.

Dielectric relaxation of acetyl- and benzoyl-acetones

1989 ◽  
Vol 67 (5) ◽  
pp. 804-808 ◽  
Author(s):  
R. K. Khanna ◽  
Abha Bhatnagar
Keyword(s):  
Dielectric Relaxation ◽  
Dipole Moments ◽  
Relaxation Times ◽  
Weight Fraction ◽  
Relaxation Mechanism ◽  
Relaxation Processes ◽  
Dielectric Absorption ◽  
Molar Polarization ◽  
Distribution Parameters ◽  
Few Data

Dielectric absorption measurements are reported at radio and microwave frequencies (at six different wavelengths) for acetylacetone and benzoylacetone solutions in benzene, in a temperature range 25–60 °C. Analysis of dielectric data in terms of Cole–Cole arc plots and multiple relaxation processes reveals that, at higher temperatures, overall molecular relaxation is the dominant relaxation mechanism in these β-diketones. The observed relaxation times, distribution parameters, and dipole moments are in reasonable agreement with the few data reported for some temperatures, in the literature. The activation energy parameters are also evaluated assuming dielectric relaxation to be a rate process. Molar polarization vs. weight fraction (concentration) plots show anomalous behaviour for acetylacetone. Keywords: dielectric properties, dielectric losses, relaxation times, dipole moment, dielectric absorption and dispersion, microwave measurements.

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 Graphene Oxide: A Smart (Starting) Material for Natural Methylxanthines Adsorption and Detection

Molecules ◽  
2019 ◽  
Vol 24 (23) ◽  
pp. 4247 ◽  
Author(s):  
Rita Petrucci ◽  
Isabella Chiarotto ◽  
Leonardo Mattiello ◽  
Daniele Passeri ◽  
Marco Rossi ◽  
...  
Keyword(s):  
Electrical Conductivity ◽  
Graphene Oxide ◽  
Nucleic Acids ◽  
Reduced Graphene Oxide ◽  
Electrochemical Sensors ◽  
Enzymatic Digestion ◽  
Biologically Active ◽  
Polar Solvents ◽  
Dna And Rna ◽  
Reduced Graphene

Natural methylxanthines, caffeine, theophylline and theobromine, are widespread biologically active alkaloids in human nutrition, found mainly in beverages (coffee, tea, cocoa, energy drinks, etc.). Their detection is thus of extreme importance, and many studies are devoted to this topic. During the last decade, graphene oxide (GO) and reduced graphene oxide (RGO) gained popularity as constituents of sensors (chemical, electrochemical and biosensors) for methylxanthines. The main advantages of GO and RGO with respect to graphene are the easiness and cheapness of synthesis, the notable higher solubility in polar solvents (water, among others), and the higher reactivity towards these targets (mainly due to – interactions); one of the main disadvantages is the lower electrical conductivity, especially when using them in electrochemical sensors. Nonetheless, their use in sensors is becoming more and more common, with the obtainment of very good results in terms of selectivity and sensitivity (up to 5.4 × 10−10 mol L−1 and 1.8 × 10−9 mol L−1 for caffeine and theophylline, respectively). Moreover, the ability of GO to protect DNA and RNA from enzymatic digestion renders it one of the best candidates for biosensors based on these nucleic acids. This is an up-to-date review of the use of GO and RGO in sensors.

scholarly journals Triazole-Modified Nucleic Acids for the Application in Bioorganic and Medicinal Chemistry

Biomedicines ◽  
2021 ◽  
Vol 9 (6) ◽  
pp. 628
Author(s):  
Dagmara Baraniak ◽  
Jerzy Boryski
Keyword(s):  
Nucleic Acids ◽  
State Of The Art ◽  
Modified Oligonucleotides ◽  
Synthetic Genes ◽  
Chemically Modified ◽  
Amide Linkage ◽  
Dna And Rna ◽  
Modified Dna ◽  
Modified Nucleic Acids ◽  
Non Coding Rnas

This review covers studies which exploit triazole-modified nucleic acids in the range of chemistry and biology to medicine. The 1,2,3-triazole unit, which is obtained via click chemistry approach, shows valuable and unique properties. For example, it does not occur in nature, constitutes an additional pharmacophore with attractive properties being resistant to hydrolysis and other reactions at physiological pH, exhibits biological activity (i.e., antibacterial, antitumor, and antiviral), and can be considered as a rigid mimetic of amide linkage. Herein, it is presented a whole area of useful artificial compounds, from the clickable monomers and dimers to modified oligonucleotides, in the field of nucleic acids sciences. Such modifications of internucleotide linkages are designed to increase the hybridization binding affinity toward native DNA or RNA, to enhance resistance to nucleases, and to improve ability to penetrate cell membranes. The insertion of an artificial backbone is used for understanding effects of chemically modified oligonucleotides, and their potential usefulness in therapeutic applications. We describe the state-of-the-art knowledge on their implications for synthetic genes and other large modified DNA and RNA constructs including non-coding RNAs.

Relaxation processes of some simple aliphatic molecules in dilute solutions

1977 ◽  
Vol 55 (4) ◽  
pp. 297-301 ◽  
Author(s):  
M. P. Madan
Keyword(s):  
Carbon Tetrachloride ◽  
Dielectric Relaxation ◽  
Thermodynamic Parameters ◽  
Relaxation Times ◽  
Relaxation Processes ◽  
Dilute Solutions ◽  
Microwave Region ◽  
Nonpolar Solvents ◽  
Dielectric Data ◽  
Intramolecular Rotation

The dielectric relaxation processes of acetone, cyclohexanone, 4-methyl-2-pentanone, and 4-heptanone in dilute nonpolar solvents, n-heptane, cyclohexane, benzene, and carbon tetrachloride have been studied in the microwave region over a temperature range 10 to 60 °C. The relaxation times and the thermodynamic parameters for the activated states have been determined using the measured dielectric data. The results have been discussed in terms of dipole reorientation by molecular and intramolecular rotation and compared, wherever possible, with other similar studies on aliphatic molecules.

Relaxation processes of quinoline, isoquinoline, and their mixtures

1980 ◽  
Vol 58 (1) ◽  
pp. 20-24 ◽  
Author(s):  
M. P. Madan
Keyword(s):  
Thermodynamic Parameters ◽  
Molecular Motion ◽  
Polar Solvent ◽  
Relaxation Times ◽  
Relaxation Processes ◽  
Polar Components ◽  
Dielectric Absorption ◽  
System A ◽  
Dielectric Data ◽  
Activated State

The dielectric absorption of quinoline, isoquinoline, and their binary mixtures has been studied in the microwave region over a range of temperatures in dilute benzene and n-heptane solutions. The relaxation times and the thermodynamic parameters for the activated state have been determined using the measured dielectric data. The results obtained have been discussed in terms of the molecular motion of the system. A relation has been proposed to represent the relaxation behavior of a system of two Debye-type polar components in a non-polar solvent. The relation has been tested by comparing the calculated values with those determined experimentally for a few systems consisting of similar, simple rigid polar molecules.

Temperature Dependence of Dynamic Properties of Elastomers. Relaxation Distributions

1952 ◽  
Vol 25 (4) ◽  
pp. 720-729 ◽  
Author(s):  
John D. Ferry ◽  
Edwin R. Fitzgerald ◽  
Lester D. Grandine ◽  
Malcolm L. Williams
Keyword(s):  
Distribution Function ◽  
Temperature Dependence ◽  
Dynamic Properties ◽  
Relaxation Times ◽  
Dynamic Mechanical Properties ◽  
Relaxation Processes ◽  
The Real ◽  
Reduced Frequency ◽  
Dynamic Rigidity ◽  
Composite Curve

Abstract By the use of reduced variables, the temperature dependence and frequency dependence of dynamic mechanical properties of rubberlike materials can be interrelated without any arbitrary assumptions about the functional form of either The definitions of the reduced variables are based on some simple assumptions regarding the nature of relaxation processes. The real part of the reduced dynamic rigidity, plotted against the reduced frequency, gives a single composite curve for data over wide ranges of frequency and temperature; this is true also for the imaginary part of the rigidity or the dynamic viscosity. The real and imaginary parts of the rigidity, although independent measurements, are interrelated through the distribution function of relaxation times, and this relation provides a check on experimental results. First and second approximation methods of calculating the distribution function from dynamic data are given. The use of the distribution function to predict various types of time-dependent mechanical behavior is illustrated.

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