Properties Of Molecules In Solution Research Articles

Non-linear Hamiltonian models for DNA.

Nucleic acids' physical properties have been investigated by theoretical methods based both on fully atomistic representations and on coarse-grained models, e.g., the worm-like-chain, taken from polymer physics. In this review article, I discuss an intermediate (mesoscopic) approach and show how to build a three-dimensional Hamiltonian model which accounts for the main interactions responsible for the stability of the helical molecules. While the 3D mesoscopic model yields a sufficiently detailed description of the helix at the level of the base pair, it also allows one to predict the thermodynamical and structural properties of molecules in solution. Relying on the idea that the base pair fluctuations can be conceived as trajectories, I have built over the past years a computational method based on the time-dependent path integral formalism to derive the partition function. While the main features of the method are presented, I focus here in particular on a newly developed statistical method to set the maximum amplitude of the base pair fluctuations, a key parameter of the theory. Some applications to the calculation of DNA flexibility properties are discussed together with the available experimental data.

The prediction of pKa values for phenolic compounds by the DFT theory

The acid dissociation constant is an important parameter that affects the physicochemical properties of molecules in solution. A set of 20 phenolic compounds were used to establish a model to predict values of phenolic compounds. Calculations in aqueous medium were performed with a polarizable continuum solvent model (PCM) and three hybrid DFT functionals (B3LYP, PBE0, ωB97XD and M062X) with the basis set 6-311++G(d,p). The directly calculated value of gives less accurate results with an average absolute error (MAE) of 1.74 units when using the ωB97XD functional and phenol as reference compound. In the case of using statistical correction, the accuracy of is greatly improved. In the case of using statistical correction, the accuracy of is greatly improved with the lowest MAE value of 0.14 units (M062X; ). The calculated results of in this study have the same accuracy as the experimental measurements.The acid dissociation constant is an important parameter that affects the physicochemical properties of molecules in solution. A set of 20 phenolic compounds were used to establish a model to predict values of phenolic compounds. Calculations in aqueous medium were performed with a polarizable continuum solvent model (PCM) and three hybrid DFT functionals (B3LYP, PBE0, ωB97XD and M062X) with the basis set 6-311++G(d,p). The directly calculated value of gives less accurate results with an average absolute error (MAE) of 1.74 units when using the ωB97XD functional and phenol as reference compound. In the case of using statistical correction, the accuracy of is greatly improved. In the case of using statistical correction, the accuracy of is greatly improved with the lowest MAE value of 0.14 units (M062X; ). The calculated results of in this study have the same accuracy as the experimental measurements.

Accurate Absorption Energy Calculations in Solution Using the Reference Interaction Site Model Self-Consistent Field Including the Constrained Spatial Electron Density Distribution

The solvation effect is an important factor determining the properties of molecules in solution. The reference interaction site model (RISM) is a powerful method to treat the solvation effect with pair-correlation functions, such as a radial distribution function. This study developed a hybrid method between quantum mechanics and RISM using the spatial electron density distributions on each atomic site (RISM-SCF-cSED). Sophisticated quantum mechanical approaches can be used to consider the solvation effect because the computational cost of RISM-SCF-cSED is reasonable. In this study, the absorption energies of 5-(dimethylamino)-2,4-pentadienal in various solutions were calculated using RISM-SCF-cSED. The experimental data were well reproduced with an average errors of ∼0.06 eV, using multi-reference perturbation theory.

Optimization of the Substitution Pattern of 1,3‐Disubstituted Imidazo[1,5‐a]Pyridines and ‐Quinolines for Electro‐Optical Applications

A series of recently synthesized 1,3‐disubstituted imidazo[1,5‐a]pyridines (IPs) and ‐quinolines (IQs) targeting at increased efficiency of luminescence is investigated. The properties of molecules in solution as well as their change in the solid state are reported and assessed regarding possible application in organic electronics. The influence of increased ring size by substitution, e.g., exchanging phenyl to naphthalenyl, as well as pyridyl to quinolinyl moieties, and by means of a larger IQ fluorophore is discussed. A higher oscillator strength and quantum yield can be achieved. Frontier orbital energies are estimated based on cyclic voltammetry and density functional theory (DFT) calculations. Single crystals of molecules are grown. A red‐shift in the photoluminescence spectra found for crystals of IQs compared with those in solution is proposed to be caused by intermolecular coupling based on the parallel stacking of the enlarged fluorophore units. Thin films deposited by physical vapor deposition exhibit similar effects, showing promise as active layers in organic light‐emitting diodes (OLEDs). An amorphous morphology is inferred for these films from both spectral broadening in photoluminescence and atomic force microscopy. An OLED test structure is prepared, using the most efficient IQ lumophore and demonstrating the feasibility of obtaining electroluminescence from such thin films.

Information Content in Fluorescence Correlation Spectroscopy: Binary Mixtures and Detection Volume Distortion

When properly implemented, fluorescence correlation spectroscopy (FCS) reveals numerous static and dynamic properties of molecules in solution. However, complications arise whenever the measurement scenario is complex. Specific limitations occur when the detection region does not match the ideal Gaussian geometry ubiquitously assumed by FCS theory, or when properties of multiple fluorescent species are assessed simultaneously. A simple binary solution of diffusers, where both mole fraction and diffusion constants are sought, can face interpretive difficulty. In order to better understand the limits of FCS, this study systematically explores the relationship between detection-volume distortion, diffusion constants, species mole fraction, and fitting methodology in analyses that utilize a two-component autocorrelation model. FCS measurements from solution mixtures of dye-labeled protein and free dye are compared to simulations, which predict the performance of FCS under a variety of experimental circumstances. The results reveal a range of conditions necessary for performing accurate measurements and describe experimental scenarios that should be avoided. The findings also provide guidelines for obtaining meaningful measurements when grossly distorted detection volumes are utilized and generally assess the latent information contained in FCS datasets.

Dual-Focus Confocal Microscopy for Flow and Brightness Measurements

Fluorescence correlation spectroscopy (FCS) is a confocal microscopy method mostly used to measure the dynamic properties of molecules in solution and in biological membranes. In 2007, Dertinger et al. introduced a new two-beam confocal method called dual-focus fluorescence correlation spectroscopy (2f-FCS). [1] This development has been extremely important to the field because it overcomes major artifacts that limit conventional FCS as a quantitative measurement technique. In this poster we present two applications of 2f-FCS. One is measuring the velocity profile in a microfluidic channel with high accuracy and sub-micrometer spatial resolution. Second, we present a scheme to measure the absolute brightness of single fluorescent molecules, and thereby directly observe the heterogeneity intrinsic to biological systems.View Large Image | View Hi-Res Image | Download PowerPoint Slide Measured velocity profile in a 300-by-300 micrometer-squared capillary.1. Dertinger, T., et al., ChemPhysChem, 2007. 8(3): p. 433-443.

An ab initio investigation of the Buckingham birefringence of furan, thiophene, and selenophene in cyclohexane solution

Using a recently developed quadratic response methodology for the calculation of frequency-dependent third-order properties of molecules in solution, we investigate the Buckingham birefringence of furan, thiophene, and selenophene in cyclohexane solution. These systems are chosen since accurate experimental data are available, allowing for a direct comparison of experimental observations with our theoretical estimates. Our model for describing the solvent effects is based on a dielectric continuum approach for the solvent, and uses a molecule-shaped cavity. Our results show qualitatively different Buckingham constants and effective quadrupole centers calculated with and without the solvent, and only when the solvent is included are the qualitative trends observed experimentally reproduced. It is demonstrated that a significant part of this effect arises from the geometry relaxation of the molecules in the solvent.

Theoretical modeling of spectroscopic properties of molecules in solution: toward an effective dynamical discrete/continuum approach

In this work, we present an effective and flexible computational approach, which is the result of an on-going development conducted in our group, for simulating complex solute–solvent systems and computing relevant spectroscopic observables. Such an approach is based on QM/MM molecular dynamics techniques using non-periodic conductor boundary conditions and localized basis sets, combined with a posteriori high-level quantum mechanical methods for the calculation of spectroscopic parameters. As illustrative applications, we report structural and spectroscopic analyses of acetone, acrolein and glycine radical in aqueous solutions, where solvent effects on the NMR chemical shifts, UV absorption spectrum and EPR hyperfine coupling constants, respectively, are investigated and favorably compared to experimental measurements. In particular, it will be shown the importance of including dynamical effects in order to reproduce experimental data accurately. Moreover, we present an infrared analysis of formamide in both gas phase and acetonitrile from first-principle molecular dynamics simulations.

Reversing-pulse electric birefringence of multicomponent systems: The formulation and signal simulation for two axially symmetric components in equilibrium and the appearance of unusual signal patterns

This paper consists of two parts on reversing-pulse electric birefringence (RPEB) signal patterns. The first is the theoretical formulation of two axially symmetric models coexisting in equilibrium in solution. The present RPEB theory is based on the original Tinoco–Yamaoka theory with classical electric dipole moments, which was recently modified and extended by Yamaoka, Sasai, and Kohno to include various electric and optical parameters and most importantly the ion-fluctuation dipole moment 〈 m 3 2 〉 1 / 2 along the longitudinal direction of axially symmetric molecules. The theory contains the electric polarizability anisotropy Δ α′, which can be either positive or negative in relation to the shape of components. The overall signal can be expressed as the sum of the fractions of two components in proportions to the coefficient F 1 or F 2 (=1 − F 1). The second part is the simulation of theoretical RPEB curves for the two-component system with various sets of electric and hydrodynamic parameters for hypothetical but interesting cases. In consideration of the decay behavior, calculated decay curves were compared with experimentally conceivable signals, classifying them into three categories according to cases: F 1 > 1, 0 < F 1 < 1, and F 1 < 0. Showing humps and/or dips in profiles the simulated RPEB signal in buildup and reverse transients reveals the mechanism of field orientation and electro-optic properties of molecules in solution. The ratio q = 〈 m 3 2 〉 / k t Δ α ′ is the crucial factor that controls the pattern of RPEB signals. If q value of one component is positive and the other is negative, the simulated RPEB curves are characterized by three cases: q > 0, q < −1, and −1 < q < 0. If q > 0 or q < −1, the resultant patterns are often encountered with experimental signals. If −1 < q < 0, many anomalous signal patterns appears.

Hydrodynamic and conformational properties of cellulose myristate molecules in solution

Cellulose myristate samples with a degree of substitution of 230–250 have been studied by the methods of molecular hydrodynamics (viscometry, analytical ultracentrifugation (flotation), and isothermal translational diffusion) in chloroform in the range M = (56–652) × 103. The experimental evidence has been interpreted within the framework of the generalized wormlike Yamakawa-Fuji model with the following parameters: the persistence length a = 115 × 10−8 cm, the chain diameter d = 45 × 10−8 cm, and the molecular mass per unit chain length M L = 270 × 108 cm−1. It has been inferred that the polymer dissolves in chloroform in the form of dimers.

Chemical Applications of Hyper-Rayleigh Scattering in Solution

Hyper-Rayleigh or second harmonic Rayleigh scattering (HRS or SHLS) has been employed to measure equilibrium physical properties of molecules in solution. It has been utilized in our laboratory to obtain the dissociation constants of weak organic acids such as substituted benzoic and cinnamic acids in solution. Partition coefficient, supramolecular structure formation and stoichiometry, critical micelle concentration, and binding or association constant of a molecule with another molecule have all been measured by the HRS technique by us. We find that both the symmetry of the molecule and its concentration in the medium play an important role in finding new chemical applications of the technique.

Circular dichroism spectrum of [Co(en)3]3+ in water: A discrete solvent reaction field study

AbstractIn this work we investigate the circular dichroism (CD) spectrum of [Co(en)3]3+ in water, using the discrete solvent reaction field (DRF) model. The DRF model is a polarizable quantum mechanics/molecular mechanics (QM/MM) model. The implementation of the DRF model for CD spectra calculations based on time‐dependent density functional theory (TDDFT) is presented. The combination of DRF with TDDFT allows for a computationally attractive solution for calculating chirooptical properties of molecules in solution when explicit solvent structures are of interest. Using a mixed coarse/fine‐grained parallel computation, we show that average CD spectra from snapshots of the solvent structure can be obtained routinely. Classical polarizable molecular dynamics (MD) simulations have been used to obtain the solvent structure around the [Co(en)3]3+ (en = ethyldiamine) solute. We show that the final spectrum converges quickly with respect to the number of configurations. The DRF results were compared with results obtained from the much simpler conductor‐like screening model (COSMO). Both models predicted similar blue shifts of the CD bands, but none of the models is in perfect agreement with the experiments. For instance, the calculated intensities are larger than what is found experimentally if reasonable empirical line width parameters are applied. From the DRF computations, we further show that almost all the solvent effects arise from ground‐state solvation. Thus, ignoring the dynamic solvent response is a good approximation for a system like [Co(en)3]3+, where the solute is highly charged and the solvent is very polar. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006

Investigation of the Chromatographic Process via Pulsed-Gradient Spin−Echo Nuclear Magnetic Resonance. Role of the Solvent Composition in Partitioning Chromatography

The diffusional properties of molecules in solution vary dramatically upon addition of a solid chromatographic phase. This effect can be monitored via pulsed-gradient spin-echo NMR used in conjunction with moderately fast rotation of the sample (high-resolution magic angle spinning) to produce exploitable spectra. The molecular diffusion coefficients observed in this condition are averages reflecting the equilibrium population distribution among the different phases. It is thus possible to use this information for investigating a crucial step of reversed-phase chromatography, namely, the partitioning of the analyte between different phases. In this work, we describe the evolution of the apparent diffusion coefficient of typical solutes for water/acetonitrile solvent mixtures of varying proportions.

Optical properties of molecules in solution via hybrid TDDFT/MM simulations

AbstractThe optical properties of molecules in complex environments were investigated within hybrid time‐dependent density functional theory / molecular mechanics (TDDFT/MM) simulation studies. The potential energy surface in the excited state is described within time‐dependent density functional theory (TDDFT). The solvent is described through a molecular mechanics approach and the effects due to the inhomogeneities of the electric field of the solvent molecules are fully included. The results for different systems including both n → π* and π → π* transitions are discussed. We apply this TDDFT/MM technique to the study of the properties of the ground state and of the first excited singlet state of two different systems: acetone in water and aminocoumarins in water and acetonitrile. Our approach yields quantitative information on the solvent‐induced shifts, both batho‐ and hypsochromic, of the electronic absorption spectra, and on the effect of a protic and an aprotic solvent on the spectral shift. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005

On the performance of time-dependent density functional theory and polarizable continuum model in the study of aqueous formaldehyde

In this paper Time-Dependent Density Functional Theory (TD-DFT) with Becke's three-parameter hybrid method using the Lee–Yang–Parr correlation functional (B3LYP) in conjunction with different basis sets is applied to calculate the solvatochromic shift on the lowest singlet transition of formaldehyde in vacuum and in solution. Our results, in excellent agreement with solvent excitation energy shift of acetone in water at 298–300 K (no experimental data on formaldehyde in water are available so far) and with previous high level quantum chemical calculations, help in appreciating the potentialities of the combined DFT/PCM approach on aquo-complexes for the study of structural and spectroscopic properties of molecule in solution.

A discrete solvent reaction field model for calculating molecular linear response properties in solution

A discrete solvent reaction field model for calculating frequency-dependent molecular linear response properties of molecules in solution is presented. The model combines a time-dependent density functional theory (QM) description of the solute molecule with a classical (MM) description of the discrete solvent molecules. The classical solvent molecules are represented using distributed atomic charges and polarizabilities. All the atomic parameters have been chosen so as to describe molecular gas phase properties of the solvent molecule, i.e., the atomic charges reproduce the molecular dipole moment and the atomic polarizabilities reproduce the molecular polarizability tensor using a modified dipole interaction model. The QM/MM interactions are introduced into the Kohn–Sham equations and all interactions are solved self-consistently, thereby allowing for the solute to be polarized by the solvent. Furthermore, the inclusion of polarizabilities in the MM part allows for the solvent molecules to be polarized by the solute and by interactions with other solvent molecules. Initial applications of the model to calculate the vertical electronic excitation energies and frequency-dependent molecular polarizability of a water molecule in a cluster of 127 classical water molecules are presented. The effect of using different exchange correlation (xc)-potentials is investigated and the results are compared with results from wave function methods combined with a similar solvent model both at the correlated and uncorrelated level of theory. It is shown that accurate results in agreement with correlated wave function results can be obtained using xc-potentials with the correct asymptotic behavior.

Energies, structures, and electronic properties of molecules in solution with the C-PCM solvation model.

The conductor-like solvation model, as developed in the framework of the polarizable continuum model (PCM), has been reformulated and newly implemented in order to compute energies, geometric structures, harmonic frequencies, and electronic properties in solution for any chemical system that can be studied in vacuo. Particular attention is devoted to large systems requiring suitable iterative algorithms to compute the solvation charges: the fast multipole method (FMM) has been extensively used to ensure a linear scaling of the computational times with the size of the solute. A number of test applications are presented to evaluate the performances of the method.

A Monte Carlo–quantum mechanics study of the spectroscopic properties of molecules in solution

A combination of Monte Carlo simulation and quantum mechanics calculation is used to study properties, structure and spectroscopy of molecules in solution. All properties are obtained as statistical averages using uncorrelated structures generated by the Monte Carlo simulation. The auto-correlation function of the energy is calculated and used in the correlation analysis. Examples include the solvatochromic shift of the n–π∗ transition of formaldehyde and pyridine in water. A detailed and systematic analysis is made starting from the hydrogen bond shell and extending up to the bulk limit. Long range effects are found to be of importance for the total solvatochromic shift. Short range, hydrogen bond, effects are seen to alter the dipole moment of the chromophore both in direction and module, having an effect on the outer solvation shells.A careful analysis is made of the possible structural changes induced by a solvent in merocyanine dyes. The hyperpolarizability of phenol blue is shown to vary with the resonance between the two, neutral and charge-separated, forms, having a pronounced maximum as obtained experimentally. This indicates that phenol blue undergoes structural changes in polar solvents.

A semiclassical approximation model for properties of molecules in solution

We propose a simple semiclassical approximation model for frequency-independent properties of molecules in solution using the cavity/dielectric approach. The model is applied to test systems comprising nonpolar, polar, and charged solutes, and is compared with the perturbation expansion method and the self-consistent reaction field theory method. Considering the simplicity of the model, the results compare well with the full self-consistent reaction field theory results, especially for the linear properties. Since the model relies only on gas phase calculations, it can be used for any electronic structure method that is implemented for static properties.

General parameterization of a reaction field theory combined with the boundary element method

AbstractWe described various technical aspects in applying reaction field theories using continuum models to practical problems. It was investigated how solvent‐dependent properties of solute molecules are influenced by the following factors: difference in quantum‐chemical description of solute–solvent (continuum dielectric) interaction, difference in values of empirically determinable parameters such as atomic radii to define a size of a cavity created in a dielectric to accommodate a solute, and difference in the sophistication level of molecular orbital calculation, including electron correlation and different parameter sets (MNDO, AM1, and PM3). Through these investigations, the better parameter sets were found to evaluate accurately physicochemically important parameters such as hydration enthalpy. © 1994 by John Wiley &amp; Sons, Inc.