Onsager Continuum Research Articles

Thermodynamic study of solvent effects on nanostructures: phosphatidylserine and phosphatidylinositol membranes

At present, quantum chemistry is almost universally applicable to the interpretation of physical and chemical properties of various compounds. Phospholipids are an important part of biological lipids and are commonly used in biophysical studies. A quantum calculation for two phospholipids PS and PI was performed using the ab initio software. Geometry optimisation and thermodynamic data over the 304–340 K temperature range are included in the supporting information. The effect of the polarity of the environment on the conformation of the membrane lipid PS and PI head groups has been investigated with calculation at the Hartree-Fock level using the STO-3G, 3-21G, 6-31G and 6-31G* basis sets together with the Onsager continuum solvation model with the program GAUSSIAN 98. The different basis sets were used in order to understand the effects of environmental polarity on the conformation and geometry optimisation of PS and PI in various solvents by SCRF theory. Further, the solvent effect on the stability of PS and PI molecules were discussed using Onsager model.

Theoretical study of solvent effect on NMR shielding tensors of luciferin derivatives

Luciferins as the substrates of protein enzyme luciferase are oxidised in the presence of the enzyme luciferase to produce oxyluciferin and energy in the form of light. The solvent effect in biological media and interactions between solvents and luciferin are major points to explain bioluminescence reaction. In this study, we have focussed on the Hartree–Fock calculations of solvent-induced effects on the structural changes of keto and enolate and twisted intra-molecular charge transfer forms of oxyluciferin in different solvent media including water, dimethyl sulphoxide, acetonitryl, ethanol, aniline and cyclohexane using 6-311++G** basis set considering Onsager continuum solvation model, frequency analysis and nuclear magnetic resonance shielding calculation with gauge-included atomic orbital method. The polarity of the environment imposed a significant effect on the relative atomic charge distribution on the selected atoms of luciferin and its derivatives. So, this fact motivated us to report the changes of the relative CHELP – charges from electrostatic potentials – atomic charges of each luciferin derivatives. Among different employed solvents, water as a protic solvent could be suggested as the most suitable solvent. All solvents had no effect on the geometry conformation of luciferin; however, the results have shown that the case of keto luciferin was obviously different and ethanol could affect more the keto luciferin form. This investigation has given useful information about the improved potential activity of luciferin derivatives and its dependence on the environment that are known as the remarkable factors in colour shift.

Quantum studies on the deprotection mechanism of 2-phenyl-1,3-dioxolane catalyzed by α,β-cyclodextrins

The inclusion processes of α,β-cyclodextrins (α,β-CDs) with 2-phenyl-1,3-dioxolane (d), its dihydrate (e) and tetrahydrate (f) have been investigated using PM3, B3LYP and ONIOM2 methods. Solvent effects on the inclusion processes have been corrected using Onsager continuum solvation model combining with B3LYP/6-31G(d). The calculated results indicated that the inclusion complex of head down had an obvious energy advantage over the corresponding head up, and the continuum solvent effect disfavored the formation of inclusion complexes in water. The stability difference between (f)/α-CD head down (−2.90 kcal mol −1) and (f)/β-CD head down (−21.36 kcal mol −1) was closely relative to the yield and the selectivity of the studied deprotection reaction. The deprotection reaction of (d) in water might proceed in a three-step mechanism as follows. Firstly, (d) integrated with four H 2O molecules to form the tetrahydrate (f). Then, (f) entered the hydrophobic cavity of α,β-CDs from secondary hydroxyl rim (S–OH) to yield the complexes of (f)/α,β-CDs head down with different stabilities. Finally, the more stable (f)/β-CD head down were transformed into benzaldehyde, H 2O and β-CD.

THEORETICAL STUDY OF SOLVENT EFFECTS AND NMR SHIELDING TENSORS OF DLPC

The effect of the polarity of the environment on the conformation zwitterionic membrane dilauroyl phosphatidylcholine (DLPC) has been investigated with calculation at the Hatree-Fock level using the 6-31G* basis set with Onsager continuum solvation model. The ‘Gauge Including Atomic Orbital' (GIAO) approach is used to investigate Ab initio GIAO calculations of NMR chemical shielding tensors carried out within SCF-Hartree-Fock approximation are described. In order to compare the calculated chemical shifts with experimental ones, it is important to use consistent nuclear shielding for NMR reference compounds like TMS. Conformation of DLPC was evaluated with four different solvents with different dielectric constant (Water (ε = 78.39), Dimethyl Sulfoxide (ε = 46.7), Acetone (ε = 20.7) and Heptane (ε = 1.92). In concern with conformational energy, Water could be the most suitable solvent for DLPC. Moreover, as the polarity of the medium increase, the conformational stability of this molecule increases faster than that of DLPC in the gas phase. Consequently, the relative energy of DLPC also depends on the polarity of the environment. This subject was considered as well as the most variable in some dihedral angles degree and NMR isotropic shift were in the less dielectric constant (ε = 1.92). It could be in polar medium DLPC conformer becomes additionally stabilized by intermolecular ionic and hydrogen bond interactions with polar neighboring molecules. On the basis of this work it can be concluded that the effect of the polarity of the environment clearly are influenced on the isotropic values by geometry variation due to intermolecular motion in molecule. Keywords: Onsager continuum model, DLPC ,NMR shielding, isotropic, solvent models, anisotropic

NMR shielding and a thermodynamic study of the effect of environmental exposure to petrochemical solvent on DPPC, an important component of lung surfactant

The chemical and petrochemical industries are the major air polluters. Millions of workers are exposed to toxic chemicals on the job, and it is becoming more toxic, causing much damage to respiratory system, today. One of the main components of lung alveoli is a surfactant. DPPC (Dipalmitolphosphatidylcholine) is the predominant lipid component in the lung surfactant, which is responsible for lowering surface tension in alveoli. In this article, we used an approximate model and ab initio computations to describe interactions between DPPC and some chemical solvents, such as benzene, toluene, heptane, acetone, chloroform, ether, and ethanol, which cause lung injuries and lead to respiratory distress such as ARDS. The effect of these solvents on the conformation and disordering of the DPPC head group was investigated by calculations at the Hatree-Fock level using the 6–31G basis set with the Onsager continuum solvation, GAIO, and frequency models. The simulation model was confirmed by accurate NMR measurements as concerns conformational energy. Water can be the most suitable solvent for DPPC. Furthermore, this study shows that ethanol has the most destructive effect on the conformation and lipid disorder of the DPPC head group of the lung surfactant in our model. Our finding will be useful for detecting the dysfunction of DPPC in the lung surfactant caused by acute or chronic exposures to air toxics from petrochemical organic solvent emission source and chronic alcohol consumption, which may lead to ARDS.

Role of hydration in determining the structure and vibrational spectra of L-alanine and N-acetyl L-alanine N′-methylamide in aqueous solution: a combined theoretical and experimental approach

In this work we have utilized recent density functional theory Born-Oppenheimer molecular dynamics simulations to determine the first principles locations of the water molecules in the first solvation shell which are responsible for stabilizing the zwitterionic structure of L-alanine. Previous works have used chemical intuition or classical molecular dynamics simulations to position the water molecules. In addition, a complete shell of water molecules was not previously used, only the water molecules which were thought to be strongly interacting (H-bonded) with the zwitterionic species. In a previous work by Tajkhorshid et al. (J Phys Chem B 102:5899) the L-alanine zwitterion was stabilized by 4 water molecules, and a subsequent work by Frimand et al. (Chem Phys 255:165) the number was increased to 9 water molecules. Here we found that 20 water molecules are necessary to fully encapsulate the zwitterionic species when the molecule is embedded within a droplet of water, while 11 water molecules are necessary to encapsulate the polar region with the methyl group exposed to the surface, where it migrates during the MD simulation. Here we present our vibrational absorption, vibrational circular dichroism and Raman and Raman optical activity simulations, which we compare to the previous simulations and experimental results. In addition, we report new VA, VCD, Raman and ROA measurements for L-alanine in aqueous solution with the latest commercially available FTIR VA/VCD instrument (Biotools, Jupiter, FL, USA) and Raman/ROA instrument (Biotools). The signal to noise of the spectra of L-alanine measured with these new instruments is significantly better than the previously reported spectra. Finally we reinvestigate the causes for the stability of the Pπ structure of the alanine dipeptide, also called N-acetyl-L-alanine N′-methylamide, in aqueous solution. Previously we utilized the B3LYP/6-31G* + Onsager continuum level of theory to investigate the stability of the NALANMA4WC Han et al. (J Phys Chem B 102:2587) Here we use the B3PW91 and B3LYP hybrid exchange correlation functionals, the aug-cc-pVDZ basis set and the PCM and CPCM (COSMO) continuum solvent models, in addition to the Onsager and no continuum solvent model. Here by the comparison of the VA, VCD, Raman and ROA spectra we can confirm the stability of the NALANMA4WC due to the strong hydrogen bonding between the four water molecules and the peptide polar groups. Hence we advocate the use of explicit water molecules and continuum solvent treatment for all future spectral simulations of amino acids, peptides and proteins in aqueous solution, as even the structure (conformer) present cannot always be found without this level of theory.

Comparison of Experimental and Theoretical study of Solvent effect on Interfacial head group and hydrocarbon chains of DPPC molecule.

The bilayer's lipids head groups and hydrocarbon chains affect solvent transport activity.The dielectric constant of solvent can affect both of these interfacial regions. The present article will focus on the effects of solvents on DPPC, 1, 2 - dipalmito l- sn - glycero - 3- phosphatidylcholine, as an important component of lipid membrane and its head group. We could detect and effectively mimic a ten-dielectric model for conformational analysis, in which the obtained results on DPPC compared with its head group results. The effect of solvents on the conformation and disordering of DPPC molecule has been investigated with calculation at the Hatree-Fock level using the 6-31G basis set with Onsager continuum solution, Frequency and GIAO models. Furthermore, the simulated model in solvents was confirmed experimentally by solution nmr technique. Results show that some of the obtained results on DPPC and its head group were different obviously. On the other hand hydrophobic force in tail group caused most atoms to show ordinary constant behavior.And high disordering in main transition temperature was shown for head group region. Therefore, the hydrophobic interaction of solvent partitioning into DPPC is the predominant force involved in DPPC packaging and has the most effect on dielectric constant and also it's totally related to temperature.

The FT-IR spectra of glycine and glycylglycine zwitterions isolated in alkali halide matrices

The infrared absorption spectra of glycine and the dipeptide glycylglycine have been measured using a novel spray-sampling technique which leads to better resolved spectra than the traditional crystal and solution methods. Spectra were recorded for a number of different alkali halide matrices. Theoretical predictions of the spectra have been undertaken using the self-consistent reaction field Onsager continuum model, without the inclusion of specific solute solvent interactions. Good agreement has been achieved between measured and predicted structures and spectra. For the glycine zwitterion in alkali halide matrices, the measured spectra suggest a trans structure about the NC bond, while for the dipeptide the conformation about the peptide bond is trans as in the crystal. The DSD spectra showed little dependence on the alkali halide matrix used to isolate the amino acid zwitterions in support of the theoretical approach adopted.

Theoretical study of the nucleophilic 5-endo-trigonal cyclization of 1,1-difluoro-1-alkenes.

The nucleophilic 5-endo-trigonal cyclization of 1,1-difluoro-1-alkenes has been studied at the B3LYP/6-31+G(d) level in an Onsager continuum model for DMF. The reaction takes an addition-elimination path. Both the transition-state structures and the IRC analyses suggest the delocalization of the negative charge to highly electronegative two fluorine atoms during the addition reaction is the origin of the high reactivity of 1,1-difluoro-1-alkenes. Judging from the activation energies, both dichloro and dibromo counterparts are much less reactive for 5-endo-trigonal cyclization. In these substrates, the cyclization reaction is promoted by chlorine or bromine atom with their good leaving-group ability, and the addition of oxyanion to the pi-bond occurs along with the simultaneous elimination of halogen atom. The study on the cyclizations of beta-monofluoro-o-hydroxystyrenes and beta-bromo-beta-fluoro counterparts shows that one fluorine atom is not enough to delocalize the negative charge in the addition step.

L-Alanyl-L-alanine in the zwitterionic state: structures determined in the presence of explicit water molecules and with continuum models using density functional theory

Abstract The structures and relative energies for L-alanyl-L-alanine (LALA) in the presence of explicit water molecules have been determined by using the density functional theory (DFT) Becke3–Lee–Yang–Parr functional and the 6-31G* basis set (B3LYP/6-31G*). In aqueous solution the dominant state of LALA is the zwitterionic form, while its neutral form is dominant in vacuo. Attempts to locate or determine a gas-phase zwitterionic species failed. That is, on the B3LYP/6-31G* potential energy surface, there is no barrier to proton transfer from the positively charged ammonium group to the negatively charged carboxylate group, or from the ammonium group to the adjacent carbonyl oxygen and from the amide nitrogen to the carboxylate group. To stabilize the zwitterion, we modelled the system by adding explicit water molecules and by placing the zwitterion within a sphere surrounded by a medium with a dielectric constant of 78.5, that is, within the Onsager continuum model, where the recommended cavity radius is obtained from a solute volume calculation. The zwitterionic species is only stable in the presence of water at the B3LYP/6-31G* level. This makes it imperative to include water molecules to model the zwitterionic species of LALA, peptides and amino acids at the B3LYP/6-31G* level. Finally, the zwitterionic structure stabilized by explicit water molecules has also been modelled within the Onsager theory. Here the Onsager model represents the effects due to the bulk water and the explicit water molecules stand for the effect due to direct H-bonding between the zwitterion and the solvent, that is, the first solvation shell. We used molecular dynamics simulations utilizing the CHARMm force field to produce structural input for the subsequent quantum-mechanical simulations. The structures determined using various methods to model the LALA zwitterionic form in aqueous solution were compared. We were able to find additional stable structures for LALA by adding water molecules and optimizing it which could not be obtained by using the Onsager theory. This shows that one must be careful when using continuum models to study peptides and proteins or other methods which do not take into account the explicit interactions between the solute and the first solvent shell.

Structure and Vibrational Spectra of the Zwitterion l-Alanine in the Presence of Explicit Water Molecules: A Density Functional Analysis

Ab initio B3LYP/6-31G* optimized geometries, vibrational frequencies, and absorption intensities have been calculated for the l-alanine zwitterion (ALAZW) structures stabilized by four neighboring water molecules. The ALAZW structures were stabilized by the addition of four neighboring water molecules because at the B3LYP/6-31G* level of theory the ALAZW is not stable in the absence of the water molecules and will be converted to the nonionized species. The ALAZW was not stable at this level of theory within the Onsager continuum model using the recommended cavity radius obtained from the solute volume calculations. Geometry optimization of the ALAZW in the presence of the explicit water molecules resulted in different optimized structures for the amino acid itself. The distributed origin gauge atomic axial tensors and the electric dipole−electric dipole polarizability derivatives calculated at the RHF level of theory were combined with the B3LYP normal modes, frequencies, and atomic polar tensors to calc...

Effect of a Polar Environment on the Conformation of Phospholipid Head Groups Analyzed with the Onsager Continuum Solvation Model

The effect of the polarity of the environment on the conformation of the zwitterionic membrane lipid head groups phosphoethanolamine (PE) and phosphocholine (PC) has been investigated with calculations at the Hartree−Fock level using the 3-21G(*), 6-31G*, and 6-31+G* basis sets together with the Onsager continuum solvation model. Results suggest that in the gas phase both PE and PC adopt cyclic minimum energy conformations, in which an ammonium or N-methyl hydrogen closely approaches one of the nonesterified phosphate oxygens. In the case of PE, intramolecular interactions result in a proton transfer from the ammonium group to the phosphate oxygen, which however is suppressed by a moderate increase in the polarity of the surrounding medium. With increasing polarity of the environment, the cyclic structures of PE and PC still remain low-energy conformers but simultaneously for both head groups an almost identical extended conformer, typical of crystal structures, becomes increasingly favored. Already at ε = 10, the extended conformer of PC is favored (−2.4 kcal/mol) relative to the cyclic one, while for PE the relative energy of the extended conformer approaches that of the cyclic one at ε = 80. The similarity and increasing stability of the extended PE/PC conformers in the monomeric state and the fact that this conformer is also adopted in all crystal structures of PE/PC lipids, regardless of hydration and interaction pattern, indicate that the geometry of this conformer is determined by energetics intrinsic to the phosphoethanolammonium backbone. In lipid aggregates or a membrane environment the extended conformer becomes additionally stabilized by intermolecular ionic and hydrogen bond interactions with neighboring molecules substituting for the internal interaction that in the monomeric state constrains the zwitterionic dipole into a cyclic structure.

Photophysical properties of a highly fluorescent push-pull stilbene

A new push-pull stilbene was synthesized, and its photophysical properties investigated by spectroscopic and theoretical methods. Solvatochromic shifts in the fluorescence were in accordance with Onsager's continuum model, whereas shifts in the absorption spectra only correlated with the polarizability of the solvents. Excited state dipole moments were determined and compared to semi-empirically calculated values. With increasing solvent polarity the fluorescence quantum yield increases steeply as the solvent dielectric permittivity exceeds 8. It is concluded that a strongly luminescent and highly dipolar π, π ∗ state becomes the lowest excited state in polar solvents, and radiative deactivation therefore competes effectively with non-radiative pathways. Preventing internal rotation of molecular subunits is thus no prerequisite for obtaining highly fluorescent push-pull stilbenes.

Theory of geminate recombination as a molecular process: the low-field regime

The lattice random walk theory of geminate recombination is applied to the low-field behavior of the dissociation probability η of photogenerated charge carrier pairs. It is demonstrated that this theory predicts a zero value of the slope-to-intercept ratio of η( E) for isotropic initial electron distributions, in contrast to the prediction of the Onsager continuum theory. It is further shown that the apparent slope-to-intercept ratio, given by a linear fit to data points calculated from the random walk approach, can have a wide range of values, including the Onsager value. The apparent slope-to-intercept ratio is controlled by the molecular parameters of the system. This behavior is consistent with the recent discovery of systems in which the Onsager prediction is violated.

The Minimum in the Mobility-Density Curve for Electrons Injected into Insulating Dense Gases

Abstract Average force and force-force correlation formulae both point to the same result that the mobility μ of electrons injected into dense gases like Ar, Xe, CH4 and C2H6 ought to exhibit at least gross regularities with respect to changes in gas density n. This is the motivation for focussing here on the mobility minimum characterized by dμ/dn = 0. At this minimum, a formula for μmin is obtained from which the scattering length a has been eliminated in favour of its density derivative (da/dn). This density derivative, it is argued, must have the form a gasωt, where ωt, is a ‘characteristic volume for transport’ while a gas is the scattering length in the dilute gas limit. The Onsager continuum model, plus the Bottcher-Onsager formula for the dielectric constant, can be used as a first estimate of ωt, which is shown to be proportional to the cube of the ‘cavity radius’ in this model. The formula for μmin is finally brought into direct contact with experiment.

Local field in liquid dielectrics: A two-parameter mean field approach

In the molecular field approximation, one derives an expression of the static dielectric constant of an isotropic liquid involving renormalized expressions of the molecular dipole and polarizability. The long-range moderate attractive forces are treated as a perturbation of the short-range intense repulsions, so that two parameters λ and η describe the short-range correlations and the long-range order, respectively. On the condition of a superposition hypothesis, the model is compared in its hard-sphere limit (λ=0, η=1) with the available experimental data about a series of organic liquids and with Onsager's continuum approach.