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A solvent is a substance that dissolves a solute, resulting in a solution. A solvent is usually a liquid but can also be a solid, a gas, or a supercritical fluid. Water is a solvent for polar molecules and the most common solvent used by living things; all the ions and proteins in a cell are dissolved in water within the cell.
Solvation describes the interaction of a solvent with dissolved molecules. Both ionized and uncharged molecules interact strongly with a solvent, and the strength and nature of this interaction influence many properties of the solute, including solubility, reactivity, and color, as well as influencing the properties of the solvent such as its viscosity and density. If the attractive forces between the solvent and solute particles are greater than the attractive forces holding the solute particles together, the solvent particles pull the solute particles apart and surround them. The surrounded solute particles then move away from the solid solute and out into the solution. Ions are surrounded by a concentric shell of solvent. Solvation is the process of reorganizing solvent and solute molecules into solvation complexes and involves bond formation, hydrogen bonding, and van der Waals forces. Solvation of a solute by water is called hydration.
In chemistry, solubility is the ability of a substance, the solute, to form a solution with another substance, the solvent. Insolubility is the opposite property, the inability of the solute to form such a solution.
Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system. In the most common version, the trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting particles, where forces between the particles and their potential energies are often calculated using interatomic potentials or molecular mechanical force fields. The method is applied mostly in chemical physics, materials science, and biophysics.
A solvation shell or solvation sheath is the solvent interface of any chemical compound or biomolecule that constitutes the solute. When the solvent is water it is called a hydration shell or hydration sphere. The number of solvent molecules surrounding each unit of solute is called the hydration number of the solute.
Molecular mechanics uses classical mechanics to model molecular systems. The Born–Oppenheimer approximation is assumed valid and the potential energy of all systems is calculated as a function of the nuclear coordinates using force fields. Molecular mechanics can be used to study molecule systems ranging in size and complexity from small to large biological systems or material assemblies with many thousands to millions of atoms.
MOLCAS is an ab initio computational chemistry program, developed as a joint project by a number of international institutes. MOLCAS is developed by scientists to be used by scientists. It is not primarily a commercial product and it is not sold in order to produce a fortune for its owner.
The Poisson–Boltzmann equation is a useful equation in many settings, whether it be to understand physiological interfaces, polymer science, electron interactions in a semiconductor, or more. It aims to describe the distribution of the electric potential in solution in the direction normal to a charged surface. This distribution is important to determine how the electrostatic interactions will affect the molecules in solution. The Poisson–Boltzmann equation is derived via mean-field assumptions. From the Poisson–Boltzmann equation many other equations have been derived with a number of different assumptions.
Implicit solvation is a method to represent solvent as a continuous medium instead of individual “explicit” solvent molecules, most often used in molecular dynamics simulations and in other applications of molecular mechanics. The method is often applied to estimate free energy of solute-solvent interactions in structural and chemical processes, such as folding or conformational transitions of proteins, DNA, RNA, and polysaccharides, association of biological macromolecules with ligands, or transport of drugs across biological membranes.
Protein precipitation is widely used in downstream processing of biological products in order to concentrate proteins and purify them from various contaminants. For example, in the biotechnology industry protein precipitation is used to eliminate contaminants commonly contained in blood. The underlying mechanism of precipitation is to alter the solvation potential of the solvent, more specifically, by lowering the solubility of the solute by addition of a reagent.
In computational chemistry, a water model is used to simulate and thermodynamically calculate water clusters, liquid water, and aqueous solutions with explicit solvent. The models are determined from quantum mechanics, molecular mechanics, experimental results, and these combinations. To imitate a specific nature of molecules, many types of models have been developed. In general, these can be classified by the following three points; (i) the number of interaction points called site, (ii) whether the model is rigid or flexible, (iii) whether the model includes polarization effects.
COSMO is a calculation method for determining the electrostatic interaction of a molecule with a solvent. COSMO is a dielectric continuum model. These models can be used in computational chemistry to model solvation effects. COSMO has become a popular method of these solvation models in recent years. The COSMO formalism is similar to the method proposed earlier by Hoshi et al. The COSMO appraoch is based - as many other dielectric continuum models - on the surface segmentation of a molecule surface.
The hybrid QM/MM approach is a molecular simulation method that combines the strengths of ab initio QM calculations (accuracy) and MM (speed) approaches, thus allowing for the study of chemical processes in solution and in proteins. The QM/MM approach was introduced in the 1976 paper of Warshel and Levitt. They, along with Martin Karplus, won the 2013 Nobel Prize in Chemistry for "the development of multiscale models for complex chemical systems".
In chemistry, solvent effects are the influence of a solvent on chemical reactivity or molecular associations. Solvents can have an effect on solubility, stability and reaction rates and choosing the appropriate solvent allows for thermodynamic and kinetic control over a chemical reaction.
Biology Monte Carlo methods (BioMOCA) have been developed at the University of Illinois at Urbana-Champaign to simulate ion transport in an electrolyte environment through ion channels or nano-pores embedded in membranes. It is a 3-D particle-based Monte Carlo simulator for analyzing and studying the ion transport problem in ion channel systems or similar nanopores in wet/biological environments. The system simulated consists of a protein forming an ion channel (or an artificial nanopores like a Carbon Nano Tube, CNT), with a membrane (i.e. lipid bilayer) that separates two ion baths on either side. BioMOCA is based on two methodologies, namely the Boltzmann transport Monte Carlo (BTMC) and particle-particle-particle-mesh (P3M). The first one uses Monte Carlo method to solve the Boltzmann equation, while the later splits the electrostatic forces into short-range and long-range components.
TeraChem is a computational chemistry software program designed for CUDA-enabled Nvidia GPUs. The initial development started at the University of Illinois at Urbana-Champaign and was subsequently commercialized. It is currently distributed by PetaChem, LLC, located in Silicon Valley. As of 2020, the software package is still under active development.
COSMO-RS is a quantum chemistry based equilibrium thermodynamics method with the purpose of predicting chemical potentials µ in liquids. It processes the screening charge density σ on the surface of molecules to calculate the chemical potential µ of each species in solution. Perhaps in dilute solution a constant potential must be considered. As an initial step a quantum chemical COSMO calculation for all molecules is performed and the results are stored in a database. In a separate step COSMO-RS uses the stored COSMO results to calculate the chemical potential of the molecules in a liquid solvent or mixture. The resulting chemical potentials are the basis for other thermodynamic equilibrium properties such as activity coefficients, solubility, partition coefficients, vapor pressure and free energy of solvation. The method was developed to provide a general prediction method with no need for system specific adjustment.
In computational chemistry, a solvent model is a computational method that accounts for the behavior of solvated condensed phases. Solvent models enable simulations and thermodynamic calculations applicable to reactions and processes which take place in solution. These include biological, chemical and environmental processes. Such calculations can lead to new predictions about the physical processes occurring by improved understanding.
Branka Maria Ladanyi was a physical chemist, who spent her career in the Department of Chemistry at Colorado State University. Her research focused on structure and dynamics of liquids, broadly defined, which she studied using theoretical and computational techniques.
Benedetta Mennucci is an Italian theoretical chemist who is professor at the University of Pisa. She is a developer of the Polarizable continuum model.
References
- 1 2 Jacopo Tomasi, Benedetta Mennucci, and Roberto Cammi (2005). "Quantum Mechanical Continuum Solvation Models." Chem. Rev. 105(8): 2999-3094.
- ↑ Maurizio Cossi, Nadia Rega, Giovanni Scalmani, Vincenzo Barone (2003). "Energies, structures, and electronic properties of molecules in solution with the C-PCM solvation model." J. Comput. Chem. 24(6): 669-681.
- 1 2 Hendrik Zipse (9 February 2004). "The Polarizable Continuum Model (PCM)". Archived from the original on September 28, 2011. Retrieved January 25, 2009.
- ↑ B. Mennucci et al. "Polarizable Continuum Model (PCM) Calculations of Solvent Effects on Optical Rotations of Chiral Molecules." J. Phys. Chem. A 2002, 106, 6102-6113. Link to full text
- ↑ Mennucci, B.; Cancès, E.; Tomasi, J. (December 1997). "Evaluation of Solvent Effects in Isotropic and Anisotropic Dielectrics and in Ionic Solutions with a Unified Integral Equation Method: Theoretical Bases, Computational Implementation, and Numerical Applications". The Journal of Physical Chemistry B. 101 (49): 10506–10517. doi:10.1021/jp971959k.
- ↑ Mark S. Gordon "CLUSTER-BASED APPROACHES TO SOLVATION" Iowa State University, Ames Laboratory. Archived 2012-02-28 at the Wayback Machine