Rotation Of Amino Group Research Articles

Dopamine Adsorption on Rutile TiO2(110): Geometry, Thermodynamics, and Core-Level Shifts from First Principles.

The modification of the rutile TiO2(110) surface with dopamine represents the best example of the functionalization of TiO2-based nanoparticles with catecholamines, which is of great interest for sunlight harvesting and drug delivery. However, there is little information on the dopamine–TiO2(110) adsorption complex in terms of thermodynamic properties and structural parameters such as bond coordination and orientation of the terminal ethyl–amino group. Here, we report a density functional theory (DFT) investigation of dopamine adsorption on the TiO2(110) surface using the optB86b-vdW functional with a Hubbard-type correction to the Ti 3d orbitals, where Ueff = 3 eV. Guided by available X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine structure (NEXAFS) data, our simulations identify enolate species with bidentate coordination at a submonolayer coverage, which are bonded to two neighboring 5-fold-coordinated Ti atoms at the TiO2(110) surface through both deprotonated oxygen atoms of the dopamine, i.e., in a bridging fashion. The process is highly exothermic, involving an adsorption energy of −2.90 eV. Calculated structural parameters suggest that the molecule sits approximately upright on the surface with the amino group interacting with the π-like orbitals of the aromatic ring, leading to a gauche-like configuration. The resulting NH···π hydrogen bond in this configuration can be broken by overcoming an energy barrier of 0.22 eV; in this way, the amino group rotation leads to an anti-like conformation, making this terminal group able to bind to other biomolecules. This mechanism is endothermic by 0.07 eV. Comparison of existing spectroscopic data with DFT modeling shows that our computational setup can reproduce most experimentally determined parameters such as tilt angles from NEXAFS and chemical shifts in XPS, which allows us to identify the preferred mode of adsorption of dopamine on the TiO2(110) surface.

Evolution of the atomic valence observed by the reaction fragility spectra on the reaction path

The computational fragility spectra of atoms on the reaction path are presented for a selection of canonical processes represented by an amino group rotation around the (X)HC–NH(Y) bond (X = O, S; Y=H, CH3). Calculated spectra are found to very accurately describe the variation of atomic valence. Significant linear correlation is also demonstrated between the Wiberg bond indices and the corresponding elements of the connectivity matrix, instrumental for calculation of the spectra. Demonstrated atomic fragility spectra contain rich and subtle information on the variation of the bonding status of all atoms, including the weak interacting individual hydrogens. Correlation with the atomic valences confirm the earlier finding that the spectra contain a picture of the electron density flow upon a reaction.

Pressure-Induced Conformer Modifications and Electronic Structural Changes in 1,3,5-Triamino-2,4,6-trinitrobenzene (TATB) up to 20 GPa

To probe the behavior of structural evolution and optical properties in solid energetic material TATB, X-ray diffraction (XRD) and Raman and absorption spectroscopy were performed under high pressure up to 20 GPa. The absorption edge shifts to red, and the color significantly varies with increasing pressure for TATB. The XRD patterns under high pressure indicate that TATB maintains the triclinic structure within this pressure range. An electronic structural change is observed at ∼5 GPa, resulting from the modification of conformers of TATB, which is associated with the rotation of nitro and amino groups under high pressure. The current experimental results clarified the absence of phase transition below 20 GPa and confirmed that the pressure-induced color change originates from the enhancing conjugation of π orbital due to the shorting C–NO2 bonds and the rotation of nitro groups with increasing pressure. The third-order Birch–Murnaghan equation of state is obtained up to 16.5 GPa, which is helpful for ca...

Rotation of Guanine Amino Groups in G-Quadruplexes: A Probe for Local Structure and Ligand Binding

Nucleic acids are dynamic molecules whose functions may depend on their conformational fluctuations and local motions. In particular, amino groups are dynamic components of nucleic acids that participate in the formation of various secondary structures such as G-quadruplexes. Here, we present a cost-efficient NMR method to quantify the rotational dynamics of guanine amino groups in G-quadruplex nucleic acids. An isolated spectrum of amino protons from a specific tetrad-bound guanine can be extracted from the nuclear Overhauser effect spectroscopy spectrum based on the close proximity between the intra-residue imino and amino protons. We apply the method in different structural contexts of G-quadruplexes and their complexes. Our results highlight the role of stacking and hydrogen-bond interactions in restraining amino-group rotation. The measurement of the rotation rate of individual amino groups could give insight into the dynamic processes occurring at specific locations within G-quadruplex nucleic acids, providing valuable probes for local structure, dynamics, and ligand binding.

β- and γ-relaxations of low density polyethylene: Study by fluorescent probes

The temperatures of γ- and β-relaxation processes in low density polyethylene are studied by means of fluorescence spectroscopy. In this work, the fluorescent sensors employed, p-vinyliden derivatives of N, N-dialkylaminoaryl compounds, were adsorbed in polymer films, and their fluorescence analysed over the temperature range from −200 to 0 °C. In general, the fluorescence of the probes adsorbed in polyethylene decreases as temperature increases, as a consequence of the enhancement of the free volume fraction that favours the radiationless process of the lowest excited singlet state. Slope changes are observed in the temperature ranges −160 to −130 and −70 to −30 °C, attributed to the γ- and β-transitions, respectively. All fluorescent probes exhibit higher sensitivity at β- than at γ-relaxation. Since the former involves longer range segmental motion, and a greater decrease in rigidity of the probe surrounding allows the amino group rotation around the N C Ar bond to happen in probes. The results correlated well with those obtained by means of dynamic mechanical analyses, which indicated the ability of these molecular rotors to sense the weak differences in chain mobility due to β- and γ-transitions of LDPE.

Coupling characteristics and proton transfer mechanisms of guanine–Na + monohydrate

The coupling characteristics and the proton transfer mechanisms of guanine–Na + monohydrate are determined in this investigation after the implementation of the geometry optimization and the harmonic vibrational frequency calculations. There are two elementary coupling modes: the interaction of monohydrated sodium ion with two heteroatoms which form a ringed coupling, and hydrogen-bond involved coupling mode. Two potential reaction pathways, coupling mode and hydration have been taken into account, and the accurate values of binding energy are corrected for basis set superposition error (BSSE) and zero-point vibrational energy (ZPVE). Relative energies of the hydrated guanine–sodium ion complexes indicate that the ringed-coupling complexes are predominant geometries with much lower energies. Monohydrated sodium ion coupling with O6 and N7 generates the most stable geometry with a five-member cycle. Sodium ion plays an important role in the tautomerization for guanine–sodium ion complexes. This investigation indicates that the stable cation-π complexes cannot be optimized for guanine–sodium ion monohydrate. Amino-involved coupling often gives rise to a twisted four-membered cycle with unrealistic distribution of positive charge and higher energies. The rotation of amino group is likely to lead to the redistribution of the base pair hydration bonding. Effective distribution of the positive charge is an important factor in the stabilization of biological systems and binding energies for the monohydrated guanine–sodium ion complexes. The enolic coupling complex has the higher energy than the keto type due to the hindrance for the positive charge.

Creatinine and creatininium cation in DMSO-d6 solution. Structure and restricted internal rotation of NH2 group.

Investigation of 15N NMR spectra of isotopically enriched creatinine has unequivocally shown that in DMSO-d6 solution it exists as amino tautomer (2-amino-1-methylimidazoline-4-one), which in the presence of acid is protonated at N-3. Free energies of activation of the amino group rotation in creatinine and its cation have been determined to be 56 kJ/mol and 60 kJ/mol, respectively, at 298 K, by performing the simultaneous analysis of the lineshapes of -NH2 proton signals in the whole set of 1H NMR spectra recorded at various temperatures and magnetic fields. These results have been theoretically reproduced by the calculations of molecular structures and energies of creatinine and creatininium cation in their ground states and transition states of the amino group rotation, using DFT (B3LYP) method, involving the influence of the solvent.

Influence of local molecular motions on the determination of 1H– 1H internuclear distances measured by 2D 1H spin-exchange experiments

Analysis of spin-exchange build-up curves obtained by measurement of 2D 1H CRAMPS spectra of α-glycine was performed to evaluate the rate of 1H– 1H spin-exchange process with respect to the influence of variation in internal molecular motion. Differences in local motions significantly affect spin-exchange constants even in highly rigid organic solids with virtually uniform motion behavior. The polarization transfer between nonequivalent α-protons is described by the spin-exchange constant D=0.77 nm 2 ms −1, while the polarization transfer involving spin exchange between αH and NH 3 + protons is characterized by D=0.24–0.21 nm 2 ms −1. This significant decrease corresponds to rotation of hydrogen-bonded amino groups. Neglecting this variation in local spin-exchange constants the resulting calculated 1H– 1H distance can be overestimated by up to 100%. Complications following from relayed and back polarization transfer involving the nearest spins within one functional group (e.g., CH 2 and/or NH 3 +) and intermolecular spin exchange are discussed. It was shown that 2H quadrupolar splitting determined for selected sites directly correlates with the experimentally observed differences in spin-exchange coefficients. It is also demonstrated that a medium level quantum chemical calculation of molecular dynamics provides relevant data that can be used to estimate differences in molecular motions.

Electron spin–lattice relaxation in radicals containing two methyl groups, generated by γ-irradiation of polycrystalline solids

The effects of methyl rotation on electron spin–lattice relaxation times were examined by pulsed electron paramagnetic resonance for the major radicals in γ-irradiated polycrystalline α-amino isobutyric acid, dimethyl-malonic acid, and l-valine. The dominant radical is the same in irradiated dimethyl-malonic acid and α-amino isobutyric acid. Continuous wave saturation recovery was measured between 10 and 295 K at S-band and X-band. Inversion recovery, echo-detected saturation recovery, and pulsed electron–electron double resonance (ELDOR) data were obtained between 77 and 295 K. For the radicals in the three solids, recovery time constants measured by the various techniques were not the same, because spectral diffusion processes contribute differently for each measurement. Hyperfine splitting due to the protons of two methyl groups is resolved in the EPR spectra for each of the samples. Pulsed ELDOR data were obtained to characterize the spectral diffusion processes that transfer magnetization between hyperfine lines. Time constants were obtained for electron spin–lattice relaxation ( T 1e), nuclear spin relaxation ( T 1n), cross-relaxation ( T x1), and spin diffusion ( T s). Between 77 and 295 K rapid cross-relaxation (Δ M s=±1, Δ M I=∓1) was observed for each sample, which is attributed to methyl rotation at a rate that is approximately equal to the electron Larmor frequency. The large temperature range over which cross-relaxation was observed suggests that methyl groups in the radical and in the lattice, with different activation energies for rotation, contribute to the rapid cross-relaxation. Activation energies for methyl and amino group rotation between 160 and 1900 K (1.3–16 kJ/mol) were obtained by analysis of the temperature dependence of 1/ T 1e at S-band and X-band in the temperature intervals where the dynamic process dominates T 1e.

Internal Rotation of Amino and Nitro Groups in TATB: MP2 Versus DFT (B3LYP)

We report second-order Moller−Plesset (MP2) and density functional (B3LYP) fully optimized amino and nitro group torsional potential barriers in 1,3,5-triamino-2,4,6-trinitrobenzene (TATB), a molecule with unusually strong intramolecular hydrogen bonding. The calculated barriers show optimum values of 17.0 (25.5) kcal/mol for the amino group and 5.6 (10.5) kcal/mol for the nitro group rotation at the MP2 (B3LYP) level. The large barrier associated with the amino rotation is due to the double-bond character of the respective C−N bond. Because the B3LYP results are 50−87% higher in energy than those provided by MP2, a more detailed comparison with other functionals and higher-level ab initio methods is needed for an accurate description of these intramolecular motions.

Structural peculiarities of 6-azacytosine and its derivatives imply intramolecular H-bonds

The study of 6-azaCyt, 6-azaC, a number of their derivatives and related compounds was performed by PMR and IR spectroscopies. The doublet splitting of amino group signals in PMR spectrum of 6-azaCyt (unlike the cases of the canonical base Cyt, nucleosides C and dC under the same experimental conditions) indicates non-equivalence of amino protons caused by the greater asymmetry of 6-azaCyt electronic structure, which increases on ring substitution at the 1 and 5 positions and by enhanced barrier of amino group rotation. The downfield component is insensitive to the 5-methyl substitution, which is probably related to the involvement of one amino proton into the intramolecular H-bond with the N3 atom. The inverse (as compared to Cyt) specificity of interactions of 6-azaCyt with amino acid carboxylic group and carboxylate ion has been shown in anhydrous dimethylsulfoxide (DMSO). IR spectroscopy data support the conclusion that investigated compounds with nonsubstituted amino group exist as keto–amino tautomers in DMSO and in solid state.

Rotational Dynamics of Adenine Amino Groups in a DNA Double Helix

Exocyclic amino groups of the bases undergo conformational fluctuations that affect the recognition and reactivity of nucleic acid molecules. Among these fluctuations, rotation of amino groups around C-N bonds is of special interest. In the present paper, we report the first determination of the rates and energetic parameters for rotation of the N6-amino group of adenine in a DNA double helix. The DNA molecule studied is the dodecamer [d(CGCGAGCTCGCG)] 2. The adenine in each A · T basepair of the dodecamer was labeled with 15N at the N6 position, and the NMR resonances of the two protons in the adenine amino group were selectively observed by 15N-editing methods. The rates of rotation of the amino group were obtained from experiments of transfer of magnetization between the two protons in the same group and from lineshape analysis of 15N-edited amino proton NMR resonances. The results show that, over the temperature range from 0 to 70°C, the rates of rotation of adenine amino groups range from 60 to 24,000 s −1. Formation of the activated state during rotation has a standard enthalpy change of 15.3 ± 0.2 kcal/mol and a standard entropy change of 6.0 ± 0.7 cal/(mol · K). Analysis of the results suggests that rotation of the amino group occurs in the paired, closed state of the adenine in the A · T basepair of the double-helical DNA structure.

1H NMR investigation on 6-azacytidine and its derivatives

The study of 6-azaCyt, 6-azaC, a number of their derivatives and related compounds was performed by 1H NMR spectroscopy. The doublet splitting of amino group signals in 1H NMR spectrum of 6-azaCyt (unlike the cases of the canonical base Cyt, nucleosides C and dC under the same experimental conditions) indicates non-equivalence of amino protons caused by the greater asymmetry of 6-azaCyt electronic structure, which increases on ring substitution at the 1 and 5 positions, and by enhanced barrier of amino group rotation. The downfield component is insensitive to the 5-methyl substitution, which is probably related to the involvement of one amino proton into the intramolecular H-bond with the N3 atom. The inverse (as compared to Cyt) specificity of interactions of 6-azaCyt with amino acid carboxylic group and carboxylate ion is shown in anhydrous DMSO.

The structure of N-aminopyrazole in the solid state and in solution: an experimental and computational study

The title compound N-aminopyrazole (AMPZ) has been studied both theoretically and experimentally using abinitio methods, low-temperature X-ray crystallography, differential scanning calorimetry, IR spectroscopy, liquid state 1H NMR, broadband solid state 2H NMR and high resolution solid state 15N NMR spectroscopy, focussing on the structure and dynamics of the amino group and the characteristics of hydrogen bond (HB) association. The complete amino group rotation–inversion surface of AMPZ and, for comparison, also of the aniline monomer were calculated at the B3LYP/6-31G* level. The results indicate that monomeric AMPZ exhibits an s hybridized pyramidal amino group where the HH-distance vector is located perpendicular to the pyrazole ring and the hydrogen atoms bent towards the pyrazole ring nitrogen atom, i.e. with the lone electron pair anti to the latter. Both inversion at the nitrogen atom and the 180° rotation of the amino group lead to a metastable structure, where the inversion barrier is much larger than the rotational barrier. These results contrast with those obtained for aniline where the amino group is almost planar and subject to a degenerate 180° rotation. Further calculations of the hydrogen bonded cyclic AMPZ dimer indicate that hydrogen bond association does not substantially perturb the geometry of the amino group, where one of the amino group protons and the ring nitrogen atoms are involved in hydrogen bonding. The X-ray structure was determined at -173°C (100 K) on a monocrystal obtained by zone crystallization. DSC shows that on cooling, neat liquid AMPZ exhibits a solid–solid phase transition around -45°C to a low-temperature phase. In this phase AMPZ forms a weakly hydrogen bonded chain where the structure is similar to the one calculated for the monomer. Only one of the amino protons is involved in hydrogen bonding, where the NH stretch of the hydrogen bonded proton appears at 3197 cm-1 and of the non-hydrogen bonded proton at 3314 cm-1. Solid state 2H NMR spectroscopy of [ND2]AMPZ shows low-temperature structures with rigid ND vectors below and isotropically rotating vectors above the solid–solid phase transition. Hydrogen bond association was further studied by solid state 15N CPMAS (cross polarization magic angle spinning) NMR and by low-temperature liquid state 1H NMR of AMPZ specifically 15N labelled in the amino group. In contrast to the solid state, hydrogen bond exchange rendering the two amino group protons equivalent was found to be fast in the NMR timescale even at 100 K.

Proton and carbon NMR measurements of the effects of hydration on the wheat protein ω-gliadin

The wheat protein ω-gliadin consists of a simple repeat sequence composed mainly of proline and glutamine. It thus represents a simple model for many cereal proteins and other proline and glutamine rich sequences which occur in multiple repeats. The behaviour on hydration has been examined by the measurement of proton NMR relaxation times. Sidechain motions (methyl and amino group rotation, proline ring puckering) were largely responsible for T 1 relaxation. It was found that the glass transition does not affect T 1 and T 1 ρ relaxation and only affects transverse relaxation. Magic angle spinning experiments have been used to observe line narrowed proton spectra as well as carbon cross polarisation spectra. In the proton spectra, at high levels of hydration, backbone and sidechain NH groups are observed indicating that whole segments of the protein chain are in the mobile regime. The carbon spectra are characterised by a loss of the proline C δ signal intensity at high levels of hydration indicating the involvement of proline in the hydration process. It is concluded that the behaviour of ω-gliadin on hydration may be explained by the formation of mobile protein loops together with residual regions of strong interprotein interaction.

Proton NMR relaxation studies of solid L-leucinamide

Proton NMR relaxation time measurements were carried out on solid L-leucinamide. Transverse relaxation, spin-lattice relaxation in the laboratory and rotating frame, and spin lattice relaxation in the dipolar field were measured. The effects of deuteration of the amino groups were also examined. It was found that, unusually for a simple solid, transverse relaxation consisted of two Gaussian components which could be assigned separately to aliphatic and amino groups. Spin-lattice relaxation was driven mainly by methyl group rotation at low temperatures and amino group rotation at high temperatures.

Proton NMR relaxation studies of solid l-leucinamide

Proton NMR relaxation time measurements were carried out on solid L-leucinamide. Transverse relaxation, spin-lattice relaxation in the laboratory and rotating frame, and spin lattice relaxation in the dipolar field were measured. The effects of deuteration of the amino groups were also examined. It was found that, unusually for a simple solid, transverse relaxation consisted of two Gaussian components which could be assigned separately to aliphatic and amino groups. Spin-lattice relaxation was driven mainly by methyl group rotation at low temperatures and amino group rotation at high temperatures.

Structure and dynamics of interstrand guanine association in quadruplex telomeric DNA.

Exchanges of the amino and imino protons in guanine quartets of telomeric DNA have been time-resolved by laser Raman spectroscopy. The Raman dynamic probe has been applied to parallel and antiparallel quadruplexes formed by the telomeric repeat of Oxytricha nova, d(T4G4)4, and to the highly thermostable parallel quadruplex formed by d(G12). Time-dependent Raman spectra of the d(G12) quadruplex reveal two characteristic exchange reactions for guanine N2 amino groups. At 10 degrees C, the pseudo-first-order exchange rates are kN2H(10 degrees C) = 5.7 x 10(-3) and k'N2H'(10 degrees C) = 1.2 x 10(-2) min-1, assignable to Hoogsteen-hydrogen-bonded and non-hydrogen-bonded N2 protons, respectively. These measurements provide the first quantitative determination of two kinetically distinct N2 amino proton exchange reactions in the guanine quartet and demonstrate that amino group rotation about the C2-N2 bond is highly restricted in the quadruplex. No exchange of guanine N1 imino sites occurs in d(G12) at 10 degrees C, and N1 exchange remains slow even at 95 degrees C [kN1H(95 degrees C) = 2.7 x 10(-2) min-1], indicating severe suppression of imino exchange in guanine quartets. For both parallel and antiparallel quadruplexes of d(T4G4)4, proton exchange rates decrease in the order thymine N3 imino > guanine N2 amino > guanine N1 imino. The rapid exchange of thymine N3 imino sites indicates that thymine quartets are not stabilized in Oxytricha quadruplexes. The protium-->deuterium exchange experiments also establish new guanine Raman band assignments. Importantly, the 1603 cm-1 band is due to in-plane bending of N1-H, while the 1644 cm-1 band involves scissoring of the N2 amino group. Accordingly, the 1603 and 1644 cm-1 bands are potentially valuable markers of hydrogen-bonding interactions specific to guanine imino and amino sites, respectively. The present findings also show that guanine hydrogen bonding and exchange dynamics are not interrelated in a simple manner. Despite extraordinary retardation of N1 imino proton exchange, Raman markers suggest that Hoogsteen-type guanine-guanine hydrogen bonding (N1-H...O=C6) is comparable in strength to hydrogen bonding of N1-H with water and, surprisingly, much weaker than hydrogen bonding between N1-H and the cytosine N3 acceptor of Watson-Crick B DNA.

The thermodynamic properties of 2-methylaniline and trans-(R,S)-decahydroquinoline

Measurements leading to the calculation of the ideal-gas thermodynamic properties for 2-methylaniline (Chemical Abstract registry number [95-53-4]) and trans-(R,S)-decahydroquinoline (registry number [767-92-0]) are reported. Experimental methods included combustion calorimetry, adiabatic heat-capacity calorimetry, vibrating-tube densitometry, comparative ebulliometry, inclined-piston gauge manometry, and differential-scanning calorimetry (d.s.c.). Standard molar entropies, enthalpies, and Gibbs free energies of formation were derived for the ideal gas at selected temperatures for both compounds. The critical temperature was determined for 2-methylaniline with the d.s.c. and the critical pressure and density were derived. Measured enthalpies of combustion, densities, vapor pressures, critical properties, and standard ideal-gas thermodynamic functions at p = p o = 101.325 kPa were compared with estimated and experimentally determined literature values. The experimental results were used to estimate magnitudes of methyl-group and amino-group rotation barriers in 2-methylaniline. The barriers are shown to be much larger than had been assumed in literature statistical thermodynamic-property evaluations.

On the mechanism of radiationless deactivation of rhodamines

Absorption and emission (fluorescence spectra and radiative decay curves) spectroscopies are used to determine the photophysical properties of rhodamines with non-alkylated amino groups (rhodamine 110 and 123) in water and in ethanol. The results are compared to those previously reported for rhodamines with alkylamino groups. Different mechanisms for internal conversion such as the amino group rotation hindered by solvent viscosity, amino NH vibrations, the formation of a twisted intramolecular charge transfer state (TICT) and the open-close umbrella-like motion model (ULM) are considered. Both the TICT and the ULM models can explain the experimental results if an intramolecular xanthene-COOR interaction and specific rhodamine-solvent interactions are taken into account.