Computationally-designed phenylephrine prodrugs – a model for enhancing bioavailability

DFT calculations at B3LYP 6-31G (d,p) for intramolecular proton transfer in a number of Kirby's enzyme models demonstrated that the driving force for the proton transfer efficiency is the distance between the two reactive centres (r_GM) and the attack angle (α); and the rate of the reaction is linearly correlated with r_GM² and sin (180°- α). Based on these results three phenylephrine prodrugs were designed to provide phenylephrine with higher bioavailability than their parent drug. Using the experimental t_1/2 (the time needed for the conversion of 50% of the reactants to products) and EM (effective molarity) values for these processes the t_1/2 values for the conversion of the three prodrugs to the parent drug, phenylephrine were calculated. The calculated t_1/2 values for ProD 1 and ProD 2 were very high (145 days and several years, respectively) whereas that of ProD 3 was found to be about 35 hours. Therefore, the intra-conversion rates of the phenylephrine prodrugs to phenylephrine can be programmed according to the nature of the prodrug linker.     

Theoretical study of keto–enol tautomerism by quantum mechanical calculations (the QM/MC/FEP method)

In this study, the tautomeric equilibrium between the keto and enol forms has been studied for five typical ketones and aldehydes: i‐butanal, acetaldehyde, acetone, acetylacetone, and dimedone. The level of theory used in the gas‐phase calculation was Becke, three‐parameter, Lee–Yang–Parr/6‐311G(d,p)//Becke, three‐parameter, Lee–Yang–Parr/6‐31G(d). The free energies of solvation were included in the calculation by using the free‐energy perturbation method based on Monte Carlo simulation, that is, the quantum mechanical/Monte Carlo/free‐energy perturbation method. Three different models, incorporating no‐water, one‐water, and two‐waters, were adopted. The results showed that in the gas phase the addition of water molecules to the reaction mechanism caused the activation barriers (ΔG^?_gas) to decrease by half relative to the water‐free mechanism, but there was no effect on the relative difference in free energy, ΔG_gas. The solvation effects (ΔG_sol), based on quantum mechanical/Monte Carlo/free‐energy perturbation calculations, were added to those of the gas‐phase results of the one‐water and two‐waters models. The two‐waters model produced values that were very consistent with the experimental data for all of the tautomers. The differences in the relative Gibbs free energy (ΔG_rxn) were less than 1.0 kcal mol^–1. In summary, the inclusion of solvent molecules in gas‐phase calculations plays a very important role in producing results consistent with experimental data. Copyright © 2012 John Wiley & Sons, Ltd.     

A high‐level theoretical study into the atmospheric phase hydration,bond dissociation enthalpies,and acidity of aldehydes

CBS‐Q//B3, G4(MP2), and G4 composite method calculations were used to estimate atmospheric phase standard state (298.15 K, 1 atm) free energies of hydration (Δ_hydrG°_(g)), hydration equilibrium constants (log K_hydr,(g)), bond dissociation enthalpies (BDEs), and enthalpies (Δ_dH°_(g)) and free energies (Δ_dG°_(g)) of aldehydic proton acid dissociation for various substituted aldehydes with electron withdrawing and electron releasing groups. Good quality log K_hydr,(g) correlations with the Swain–Lupton resonance effect parameters R and R⁺ were found, allowing extension of the model to predict log K_hydr,(g) values for 487 substituted aldehydes having available R‐values and 108 substituted aldehydes having available R⁺ values. Good correlations were also found between experimental aqueous phase hydration equilibrium constants (log K_hydr,(aq)) and summative R/R⁺ values for peripheral substituents on a range of carbonyl derivatives (aldehydes, ketones, esters, and amides), suggesting that the structure–reactivity modeling approach can be extended to include all possible combinations of R₁C(O)R₂ carbonyl substitution in both gas and aqueous systems. Computationally derived BDEs and Δ_dH°_(g)/Δ_dG°_(g) were in good agreement with the limited experimental and theoretical datasets. BDEs did not generally correlate with any of the Hammett substituent constants or Swain–Lupton parameters considered. Gas phase acidities exhibited high correlation coefficients with Hammett inductive substituent constants (σ_I) and field effect parameters (F), allowing these to be employed as surrogates for estimating the gas phase aldehydic proton acidities of a larger potential compound range. The resulting models will be of use in predicting the environmental behavior for a broad range of environmentally relevant compounds containing carbonyl functionalities. Copyright © 2016 John Wiley & Sons, Ltd.     

Spectroscopic studies on the molecular interaction between salicylic acid and riboflavin (B2) in micellar solution

The interaction between salicylic acid (SA) and riboflavin (RF) was studied by Fluorescence Resonance Energy Transfer (FRET) in micellar solution. The riboflavin strongly quenches the intrinsic fluorescence of SA by radiative energy transfer. The extent of energy transfer in sodium dodecyl sulphate (SDS) micellar solution of different concentration is quantified from the energy transfer efficiency data. It is seen that the energy transfer is more efficient in the micellar solution. The critical energy transfer distance (R₀) was determined from which the mean distance between SA and RF molecules was calculated. The quenching was found to fit into Stern-Volmer relation. The results on variation of Stern-Volmer constant (K_sv) with quencher concentration obtained at different temperatures suggested the formation of complex between SA and RF. The association constant of complex formation was estimated and found to decrease with temperature. The values of thermodynamic parameters ΔH, ΔG and ΔS at different temperatures were estimated and the results indicated that the molecular interaction between SA and RF is electrostatic in nature.     

Electronic structure,absorption spectra,and hyperpolarisabilities of some novel push–pull zinc porphyrins. A DFT/TDDFT study

DFT/TDDFT calculations have been performed on some novel push–pull zinc porphyrins (denoted ZnPor 1, ZnPor 2, and ZnPor 3). This theoretical work aims to investigate the electronic structure, absorption spectra, and hyperpolarisabilities of these molecules. To examine the effects of the peripheral substituents on the molecular properties, zinc porphine (ZnP) and zinc tetraphenylporphine (ZnTPP) were also included in the study. The orbital energy level patterns of the substituted zinc porphyrins are indeed rather different from those of ZnP and ZnTPP. The peripheral substitution breaks the molecular D_4h symmetry of the porphyrin, thereby leading to the splitting of the absorption Q band. On the other hand, the B band in the spectra may not arise only from a single excited state; instead, it could be made up of several states that are close in energy. The calculated hyperpolarisabilities (β _vec) increase strongly from ZnPor 1 to ZnPor 2 to ZnPor3. The latter two molecules were predicted to have a large β _vec value and thus may have potential application in the development of nonlinear optical (NLO) materials.     

Molecular magnetism in closo-azadodecaborane supericosahedrons

ABSTRACT

The connection of 12 s = ½ closo-azadodecaborane radical units (NB₁₁H₁₁?), where a hydrogen atom is removed from the nitrogen atom, produces a supericosahedron [(NB₁₁H₆?)₁₂]^(S), S being the total spin of the system. This work describes the study of the low-lying energy spin-projected states of this supericosahedron with two different geometrical arrangements, each nitrogen atom pointing (1) inwards or (2) outwards with respect to radial axes. These spin-projected states are mapped into a Heisenberg spin Hamiltonian, thus allowing the determination of coupling constants between magnetic sites. The eigenvalues of this model Hamiltonian then predict the ground spin state and the corresponding combinations of spin orientations of the magnetic centres. We show that the energy minimum in the [(N_in/outB₁₁H₆?)₁₂]^(S) systems corresponds to a high-spin S = 6 state.     

Ion beam mixing induced by electronic energy deposition in Fe-Si multilayers

Abstract

Spectroscopic properties of Ce³⁺ ions in GdAlO₃ crystal are presented. At least three Ce³⁺ nonequivalent centres (multisites) are present in this crystal. Energy transfer from the Ce³⁺ main in the UV emitting centres to the Ce³⁺ green emitting centres is observed. Ce³⁺ fluorescence decays are either fast (1.5–20 ns) or slower due to complicated processes of energy transfer and migration (Ce³⁺)_i → (Gd³⁺)_n-steps → (Ce³⁺)_j (energy transfer through Gd³⁺ sublattice).     

Conformational fluctuations in a green fluorescent protein-like Akane family protein: a high-pressure fluorescence study at 0.1–700 MPa

ABSTRACT

We have investigated conformational fluctuations in a new green fluorescent protein(GFP)-like protein rb-Akane found in a red-brown-colored octocoral, Scleronephthya gracillima (Kuekenthal)), with high pressure fluorescence spectroscopy at 0.1–700?MPa. Besides the green fluorescence at 510?nm, two red fluorescence peaks are observed at 590 and 629?nm, the relative intensity of which varies reversibly with pressure. The phenomenon is interpreted as representing the cis–trans isomerization of the chromophore accompanied by the conformational transition between two sub-states of the red fluorescence form of rb-Akane. The two sub-states are separated only marginally in free energy (ΔG⁰?=?1.9?±?0.4?kJ?mol^?1), but significantly in partial molar volume (ΔV⁰?=??19.8?±?1.4?ml?mol^?1) at 0.1?MPa (pH 7.5, 25°C). Above 500?MPa, the fluorescence at λ_max 629?nm undergoes another reversible change with pressure, showing the onset of unfolding.     

Swift heavy ions-induced degradation on the electrical characteristics of silicon NPN power transistors

ABSTRACT

The pre- and post-irradiation effects on the DC electrical characteristics of 100?MeV Phosphorous (P⁷⁺) and 80?MeV Nitrogen (N⁶⁺) ion-irradiated NPN transistors were studied in the dose range from 600?krad (Si) to 100?Mrad (Si). The different electrical characteristics, such as Gummel characteristics, excess base current (ΔI_B?=?I_B-Post?–?I_B-Pre), current gain (h_FE), damage constant (K) and output characteristics, were measured in situ after ion irradiation. The considerable increase in the base current (I_B) at lower V_BE and slight decrease in the collector current (I_C) at higher V_BE were observed after ion irradiation. The C–V measurements revealed that the doping concentration (N_d) was found decreased, while the built-in potential (V_bi) increased after irradiation. The ion-irradiated results are compared with ⁶⁰Co gamma-irradiated results in the same dose range. The SRIM simulation was performed to understand the range of ions and energy loss in the transistor structure. The SRIM simulation showed that 100?MeV P⁷⁺ and 80?MeV N⁶⁺ ions can easily pass through the active region of transistors by creating ionization and displacement damages in the device structure. The irradiation results showed that ions induce more degradation in the electrical characteristics when compared to ⁶⁰Co gamma radiation at the same dose range.     

Distance distributions and dynamics of a zinc finger peptide from fluorescence resonance energy transfer measurements

Time-resolved fluorescence resonance energy transfer (FRET) measurements were used to measure distance distributions and intramolecular dynamics (site-to-site diffusion) of a 28-residue single-domain zinc finger peptide in the absence and presence of zinc ion. Energy transfer was measured between TRP₁₄ and a N-terminal DNS group. As expected, the TRP-to-DNS distance distribution for zinc-bound peptide is shorter and narrower (R _av=11.2 Å,hw=2.8 Å) than the metal-free peptide (R _av=20.1 Å,hw=14.5 Å). The degree of mutual donor-to-acceptor diffusion (D) was also determined for these distributions. For zinc-bound peptide there is no detectible diffusion (D0.2 Ų/ns), whereas for metal-free peptide a considerable amount of motion is occurring between the donor and the acceptor (D=12 Ų/ns). These results indicate that the zinc-bound peptide folds into a unique, well-defined conformation, whereas the metal-free conformation is flexible and rapidly changing. The absence of detectible mutual site-to-site diffusion between the donor and the acceptor in the metal-bound zinc finger peptide indicates that intramolecular motion is essentially frozen out, on the FRET time scale, as a consequence of zinc coordination.Dedicated to the memory of Barbara D. Wells.     

Microscopic Analysis of 5d States Splitting and Charge Transfer Energies Dependence on Interionic Distance in Alkaline Earth Fluorides Doped with Light Trivalent Lanthanides

A first principles fully relativistic analysis (K. Ogasawara et al., Phys. Rev. B 2001, 64, 115413) of the dependence of 5d orbitals splitting (10Dq) and charge transfer (CT) energies on interionic distance has been performed for light lanthanides (Ce³⁺, Pr³⁺, Nd³⁺) in CaF₂, SrF₂, BaF₂ crystals. The salient feature of the method is that four‐component molecular orbitals (MO) composed of atomic wave functions are used as the basis set. Without any fitting parameter, the power dependencies for 10Dq and linear dependencies for the CT energies on the distance between rare‐earth (RE) ions and ligands were obtained. A comparison with experimental values is discussed.     

TiO基态 (X 3 Δr) 的势能函数与光谱常数

应用群论及原子分子反应静力学方法推导了TiO分子基态(X³Δ_r)的离解极限.采用不同的计算方法,包括密度泛函B3LYP,B3P86,BP86,B3PW91和MP2,MP4方法,结合不同基组计算了TiO分子基态的平衡核间距、能量和振动频率.研究表明,使用B3LYP方法,对O原子使用6-311+G基组,Ti原子使用6-311+ +G^**基组时计算得到的平衡几何结构、分子离解能和谐振频率与实验值符合得最好.使用优选出的方法和基组对T 关键词： TiO 势能函数 光谱常数 密度泛函理论     

High-pressure studies of solvent viscosity effects on large-amplitude isomerization rates

Abstract

The solvent viscosity effects on the intramolecular excimer (IE) formation of 1,3-di-l-pyrenylpropane (DPP) and the ground-state isomerization of 3.3′-diethyloxadicarbocyanine iodide (DODCI) were studied by means of a high-pressure technique.

Kramers equation is well applied to the former while it is not to the latter, in which the approach of frequency dependent friction was applied. The activation volume due to solvent dynamical effects (αΔV^¦ _η) and the intrinsic activation volume (ΔV^? _i) are also determined.     

Nature of the Electron Excited States and Energy Transfer in Bichromophore Coumarin Molecules

Results of experimental and theoretical research for three bichromophore molecules, trans-stilbene-CH₂-coumarin 120 (I), 4-methylumbelliferone-CH₂-UC 17, and 4-(3-fluoro)-methylumbelliferone-CH₂-UC 17 (II, III), are presented. Schemes of photophysical processes in the bichromophore molecules based on quantum chemical calculations by the INDO method and theory of radiationless transitions in polyatomic organic molecules are suggested. After optical excitation to the strong donor absorption band, the fast internal conversion processes develop there. As a result, the molecule is found in the S ₁ ^* -state localized on the acceptor moiety. It is shown that a mechanism of intramolecular transfer energy in bichromophores different from that proposed by Förster may be realized. Excitation energy, initially located on D, will be transferred from the donor moiety to the acceptor chromophore in convenience of the internal conversion process. The intramolecular electronic energy transfer from energy donor to energy acceptor may be interpreted as the internal conversion process. The rate constants of internal conversion are calculated.     

Electron scattering from an assembly of point scatterers in the presence of a quantizing magnetic field

Summary We have studied the scattering of electrons by a structured target in the presence of a quantizing static magnetic field, under the assumption that the presence of the field does not affect the behaviour of the massive target nuclei, but it influences only the motion of the incident electrons. In this case, the electron motion in the plane perpendicular to the magnetic field is confined within a typical distance given by the cyclotron radius ρ₀=(cℏ/|e|B)^1/2, that for particular values of the intensity of the magnetic field can be comparable with the distance between two scattering centres. The known field-free interference conditions are modified, depending both on the energy of the incident particle and on the intensity and the direction of the magnetic field. The general case of a three-dimensional scattering array has been derived in detail. Numerical results are given for the case of two scattering centres in perpendicular geometry. To speed up publication, the authors of this paper have agreed to not receive the proofs for correction.     

Rotational and rovibrational transitions in the a 1Δ2 and b 1Σ+0+ states of sulfur monoxide radical

ABSTRACT

Sulfur monoxide radical has widely been detected in outer space using ground-state spectroscopy. The a ¹Δ₂ and b ¹Σ⁺₀₊ states of this radical have low excitation energies, and they possibly exist in outer space. In this work, the potential energy curves and dipole moment functions of the two states were evaluated using the complete active space self- consistent field method, followed by the valence internally contracted multireference configuration interaction approach. The transition line positions, oscillator strengths, band transition dipole matrix elements, Einstein A coefficients, and Franck–Condon factors of all transitions were calculated for lower vibrational levels at rotational angular momentum quantum number J up to 150. The transition line positions calculated in this study are in good agreement with the experimental results. The rovibrational transition became noticeably weak at Δυ > 5. Comparing the results of a ¹Δ₂ and b ¹Σ⁺₀₊ states reported in this paper with the previous values, we conclude that these results are the most accurate and complete to date.     

Collisional Energy Transfer of Highly Vibrationally Excited Polyatomic Molecules. The Effect of Excited Molecule Complexity

Collisional relaxation was probed by CO₂ laser activated delayed fluorescence. The experimental information was adopted to determine the average energies transferred per collision (ΔE) from highly vibrationally excited polyatomic molecules to parent collider. The values of (ΔE) decreased with increasing the number of atoms in the excited molecules in line: biacetyl, acetophenone, benzophenone, antraquinone. The dependences of (ΔE) on the number of factors such as: 1) the average vibrational energy residing in the vibrational modes of excited molecules; 2) the potential of intermolecular interaction; 3) the reduced mass, and others were analyzed in details. The general interplay was noticed between (ΔE) and the molecular parameters which determined the increasing interaction strength and the decreasing energy transfer efficiency due to the adiabatic constraints on the energy transfer.     

The Application of Two-dimensional Fluorescence Correlation Spectroscopy on the Interaction Between Bovine Serum Albumin and Paeonolum in the Presence of Fe(III)

The effect of Fe³⁺ on the interaction between bovine serum albumin (BSA) and paeonolum (PAL), which was extracted from the traditional Chinese herb, Paeonia suffruticosa Andr, was investigated by UV and fluorescence spectroscopy. Two-dimensional correlation spectroscopy was applied to the analysis of fluorescence spectra. The results of spectroscopic measurements suggested that PAL had a strong ability to quench the intrinsic fluorescence of BSA through static quenching procedure in the presence of Fe(III). Thermodynamic parameter enthalpy changes (ΔH) and entropy changes (ΔS) were calculated. The binding parameters including binding constant (K), and the distance (r) between PAL and BSA were evaluated on the basis of the theory of Föster energy transfer. Owing to the spectral resolution enhancement in 2D correlation spectroscopy, the structure change of PAL–Fe³⁺ can be observed.     

Investigation of the dynamical behaviour of the FH(CN−) centre in KCl with temperature dependent endor spectroscopy

Abstract

The temperature dependence of the electron nuclear double resonance (ENDOR) spectra of F_H(CN^?) centres in KCl was investigated in the temperature range between 10–220 K. At the lowest temperature of 10 K only one CN^? orientation with respect to the F centre electron is present, in which the nitrogen is thought to be nearer to the F-electron than the carbon. With the very small thermal activation energy of 2.9 meV the opposite orientation is occupied. The superhyperfine interactions of those first shell K nuclei nearest to CN^? and of the ¹³C interaction of the CN^? molecule are strongly temperature dependent between 10 and 60 K, following an exponential law with a thermal activation energy of 4.2 meV. It is assumed that a soft local mode involving those two nearest K nuclei and the CN^? is causing the strong temperature dependence. The shf interactions of ¹⁴N nuclei have not been seen, probably because of the dynamical effects.     

On the influence of singlet oxygen molecules on characteristics of HCCI combustion: A numerical study

Mechanisms of homogeneous charge compression ignition (HCCI) combustion enhancement are investigated numerically when excited O₂(a ¹Δ_g) molecules are produced at different points in the compression stroke. The analysis is conducted with the use of an extended kinetic model involving the submechanism of nitric oxide formation in the presence of singlet oxygen O₂(a ¹Δ_g) or O₂(b ¹Σ_g ⁺) molecules in the methane-air mixture. It is demonstrated that the abundance of excited O₂(a ¹Δ_g) molecules in the mixture even in a small amounts intensifies the ignition and combustion and allows one to control the ignition event in the HCCI engine. Such a method of energy supply in the HCCI engine is much more effective in advancement of combustion timing than mere heating of the mixture, because it leads to acceleration of the chain-branching mechanism. The excitation of O₂ molecules to the a ¹Δ_g electronic state makes it possible to organise the successful combustion in the cylinder at diminished initial temperature of the mixture and increase the effective energy released during HCCI combustion. The advance in the value of this energy is much higher than the energy needed for the excitation of oxygen molecules. Moreover, in this case, the output concentration of NO and CO can be reduced significantly.