Showing papers on "Solvation published in 2000"
TL;DR: An overview of one such approximation, the generalized Born model, which is simple and fast enough to be used for molecular dynamics simulations of proteins and nucleic acids, and focuses particularly on versions of the generalized born model that have a pair-wise analytical form, and therefore fit most naturally into conventional molecular mechanics calculations.
Abstract: It would often be useful in computer simulations to use a simple description of solvation effects, instead of explicitly representing the individual solvent molecules. Continuum dielectric models often work well in describing the thermodynamic aspects of aqueous solvation, and approximations to such models that avoid the need to solve the Poisson equation are attractive because of their computational efficiency. Here we give an overview of one such approximation, the generalized Born model, which is simple and fast enough to be used for molecular dynamics simulations of proteins and nucleic acids. We discuss its strengths and weaknesses, both for its fidelity to the underlying continuum model and for its ability to replace explicit consideration of solvent molecules in macromolecular simulations. We focus particularly on versions of the generalized Born model that have a pair-wise analytical form, and therefore fit most naturally into conventional molecular mechanics calculations.
1,054 citations
TL;DR: This work compares results using the GB model (or GB plus a surface‐area based “hydrophobic” term) to explicit solvent simulations for a 10 base‐pair DNA oligomer, and for the 108‐residue protein thioredoxin.
Abstract: Generalized Born (GB) models provide an attractive way to include some thermodynamic aspects of aqueous solvation into simulations that do not explicitly model the solvent molecules. Here we discuss our recent experience with this model, presenting in detail the way it is implemented and parallelized in the AMBER molecular modeling code. We compare results using the GB model (or GB plus a surface-area based "hydrophobic" term) to explicit solvent simulations for a 10 base-pair DNA oligomer, and for the 108-residue protein thioredoxin. A slight modification of our earlier suggested parameters makes the GB results more like those found in explicit solvent, primarily by slightly increasing the strength of NH [bond] O and NH [bond] N internal hydrogen bonds. Timing and energy stability results are reported, with an eye toward using these model for simulations of larger macromolecular systems and longer time scales.
944 citations
858 citations
TL;DR: In this paper, a computational scanning mutagenesis method was proposed to identify the 'hotspots' in binding interfaces from a single trajectory of a wild type complex, which can be also used as a tool to optimize the interacting species for the binding, or as a ranking procedure in high throughput screening.
Abstract: Significant progress has been achieved in computational methods to treat solvent effects in recent years. Among various techniques, the continuum solvent approach appears to be practically promising because it can be used to calculate reliable interaction and solvation energies in complex systems. A computational scanning mutagenesis method, one of such new approaches, has been recently developed. It combines the molecular mechanical and continuum solvent approaches and allows one to identify the `hotspots' in binding interfaces from a single trajectory of a wild type complex. Such techniques can be also used as a tool to optimize the interacting species for the binding, or as a ranking procedure in high throughput screening.
812 citations
TL;DR: An overview of the title paper by Miertus, Scrocco and Tomasi, including the impact that it has had on the theoretical description of solvation by means of continuum models, can be found in this paper.
Abstract: This paper provides an overview of the title paper by Miertus, Scrocco and Tomasi, including the impact that it has had on the theoretical description of solvation by means of continuum models.
636 citations
TL;DR: Calculations of free energies of binding, DeltaG(bind), between a diverse set of nine ligands and avidin as well as between a peptide and streptavidin using the recently developed MM/PBSA approach are reported.
Abstract: We report calculations of free energies of binding, ΔGbind, between a diverse set of nine ligands and avidin as well as between a peptide and streptavidin using the recently developed MM/PBSA approach. This method makes use of a molecular dynamics simulation of the ligand−protein complex to generate a thermally averaged ensemble of conformations of the molecules that are involved in the complex formation. Based on this set of structures, a free energy of binding is calculated using molecular mechanical and continuum solvent energies as well as including estimates of the nonpolar solvation free energy and solute entropy. We compare in our simulations different classes of ligands, involving biotin derivatives, the dye 2-(4‘-hydroxyazobenzene)benzoic acid (HABA), and a cyclic hexapeptide, which cover a large range of binding free energies from −5 to −20 kcal/mol. Our calculations are able to reproduce experimental ΔGbind values with a very good correlation coefficient of r2 = 0.92. This agreement is consider...
495 citations
TL;DR: In this article, Monte Carlo statistical mechanics simulations have been carried out for more than 200 organic solutes, including 125 drugs and related heterocycles, in aqueous solution, using the OPLS-AA force field augmented with CM1P partial charges.
Abstract: Monte Carlo (MC) statistical mechanics simulations have been carried out for more than 200 organic solutes, including 125 drugs and related heterocycles, in aqueous solution. The calculations were highly automated and used the OPLS-AA force field augmented with CM1P partial charges. Configurationally averaged results were obtained for a variety of physically significant quantities including the solute−water Coulomb and Lennard-Jones interaction energies, solvent-accessible surface area (SASA), and numbers of donor and acceptor hydrogen bonds. Correlations were then obtained between these descriptors and gas to liquid free energies of solvation in hexadecane, octanol, and water and octanol/water partition coefficients. Linear regressions with three or four descriptors yielded fits with correlation coefficients, r2, of 0.9 in all cases. The regression equation for log P(octanol/water) only needs four descriptors to provide an rms error of 0.55 for 200 diverse compounds, which is competitive with the best fr...
428 citations
TL;DR: In this paper, a causal relationship between the hydrogen-bonding ability of the liquid and the colloidal microstructure observed was investigated in a range of polar organic media and it was shown that the silica forms stable low-viscosity sols exhibiting shear thickening behavior in a host of liquids, including ethylene glycol and its oligomers and short-chain alcohols, such as n-propanol.
Abstract: Dispersions of hydrophilic fumed silica are investigated in a range of polar organic media. The silica forms stable, low-viscosity sols exhibiting shear thickening behavior in a host of liquids, including ethylene glycol and its oligomers and short-chain alcohols, such as n-propanol. In contrast, the silica flocculates into colloidal gels in other liquids, such as glycols with methyl end-caps and longer-chain alcohols. We suggest that there is a causal relationship between the hydrogen-bonding ability of the liquid and the colloidal microstructure observed. In strongly hydrogen-bonding liquids, a solvation layer is envisioned to form on the silica surface through hydrogen bonding between liquid molecules and surface silanol groups (Si−OH). This gives rise to short-range, non-DLVO repulsions (“solvation forces”) which stabilize the silica particles. In contrast, in the case of liquids with limited hydrogen-bonding ability, silanols on adjacent silica particles are envisioned to interact directly by hydroge...
399 citations
TL;DR: In this paper, a general formalism for nonequilibrium electrostatic solvation is developed, applicable to all PCM versions, and a recent procedure for the quantum-mechanical computation of dispersion and repulsion solute-solvent interactions is implemented and used for the first time in this context.
Abstract: A recent extension of the polarizable continuum solvation model (PCM) to excited electronic states is applied to the study of solvent effects on electronic transitions, accounting for both electrostatic and nonelectrostatic solute–solvent interactions. A general formalism for nonequilibrium electrostatic solvation is developed, applicable to all PCM versions, and a recent procedure for the quantum-mechanical computation of dispersion and repulsion solute–solvent interactions is implemented and used for the first time in this context. The procedure is applied to the study of the n→π* transition of acetone in aqueous and nonaqueous solvents: nonequilibrium effects are very important in polar environments; also, the inclusion of dispersion and repulsion is mandatory to obtain the correct trend of the solvatochromic shifts. The effect of adding some explicit solvent molecules is also analyzed.
386 citations
TL;DR: Two important contributions to the evolution of charge transfer states in condensed phase are revealed, one that is strongly coupled to the surrounding environment and another that follows a potential internal to the molecule.
Abstract: Molecular dynamics occurring in the earliest stages following photo-induced charge transfer were investigated. Femtosecond time-resolved absorption anisotropy measurements on [Ru(bpy) 3 ] 2+ , where bpy is 2,2′-bipyridine, reveal a time dependence in nitrile solutions attributed to initial delocalization of the excited state over all three ligands followed by charge localization onto a single ligand. The localization process is proposed to be coupled to nondiffusive solvation dynamics. In contrast, measurements sampling population dynamics show spectral evolution associated with wave packet motion on the excited state surface that is independent of solvent. The results therefore reveal two important contributions to the evolution of charge transfer states in condensed phase, one that is strongly coupled to the surrounding environment and another that follows a potential internal to the molecule.
345 citations
TL;DR: The first complete description of the solution thermodynamics of a series of linear, branched, and cyclic alkanes in water by computer simulations, including the enthalpy and entropy changes in addition to the solvation free energies, was reported in this paper.
Abstract: This study reports the first complete description of the solution thermodynamics of a series of linear, branched, and cyclic alkanes in water by computer simulations, including the enthalpy and entropy changes in addition to the solvation free energies. We have also obtained a complete thermodynamic description of the solvation of the associated alkane cavities. Our results lead to the following key observations: (i) The theoretical prediction that hydration entropy and solvent reorganization are weakly coupled to solute−solvent dispersion interactions is confirmed by computer simulations. (ii) The weak correlation between solute−solvent dispersion interaction energies with solute surface area explains the large relative solubilities of cyclic alkanes and the large difference between the free energy/surface area relations observed for gas to water transfer processes compared to processes involving conformational rearrangements. (iii) The work of cavity formation in water is determined in about equal meas...
TL;DR: It is shown that the solvent non-locality typically results in somewhat stronger dielectric exclusion, however, its most important effect is slowing down the decline of dielectrics exclusion with increasing bulk electrolyte concentration.
TL;DR: The results show the importance of molecular vibration in promoting electron transfer reactions, a class of chemistry important to molecular electronics devices, solar energy conversion, and many biological processes.
Abstract: By using laser methods to prepare specific quantum states of gas-phase nitric oxide molecules, we examined the role of vibrational motion in electron transfer to a molecule from a metal surface free from the complicating influence of solvation effects. The signature of the electron transfer process is a highly efficient multiquantum vibrational relaxation event, where the nitrogen oxide loses hundreds of kilojoules per mole of energy on a subpicosecond time scale. These results cannot be explained simply on the basis of Franck-Condon factors. The large-amplitude vibrational motion associated with molecules in high vibrational states strongly modulates the energetic driving force of the electron transfer reaction. These results show the importance of molecular vibration in promoting electron transfer reactions, a class of chemistry important to molecular electronics devices, solar energy conversion, and many biological processes.
15 Aug 2000
TL;DR: In this article, a quasi-chemical description of hydrophobic hydration was developed that incorporates the hydration structure and permits quantum-mechanical treatment of the solute.
Abstract: Recent breakthroughs in the theory of hydrophobic effects permit new analyses of several characteristics of hydrophobic hydration and interaction. Heat capacities of non-polar solvation, and their temperature dependences, are analyzed within an information theory approach, using experimental information available from bulk liquid water. Non-polar solvation in aqueous electrolytes is studied by computer simulations, and interpreted within the information theory. We also study the preferential solvation of small non-polar molecules in heavy water (D2O) relative to light water (H2O) and find that this revealing difference can be explained by the higher compressibility of D2O. We develop a quasi-chemical description of hydrophobic hydration that incorporates the hydration structure and permits quantum-mechanical treatment of the solute. Finally, these new results are discussed in the context of hydrophobic effects in protein stability and folding, and of mesoscopic hydrophobic effects such as dewetting.
TL;DR: The model described here offers a structure on to which large molecules can be mapped in order to offer insights into their interactions and allows explanation of many of the anomalous properties of water including its temperature-density and pressure-viscosity behaviour.
TL;DR: In this article, collision cross sections have been measured for a series of N- and C-methylated glycines cationized by alkali ions using ion mobility methods, and the measured cross sections are in excellent agreement with model structures obtained from a number of different theoretical approaches.
Abstract: Collision cross sections have been measured for a series of N- and C-methylated glycines cationized by alkali ions using ion mobility methods. In all cases the measured cross sections are in excellent agreement with model structures obtained from a number of different theoretical approaches. Unfortunately both charge solvation and zwitterion structures are predicted to have nearly identical cross sections. On the basis of a conformational search by molecular mechanics methods and density functional theory calculations at the B3LYP/DZVP level it is found that the lowest energy forms of alkali cationized glycine and alanine are charge solvation structures, whereas lowest energy singly and doubly N-methylated glycines are salt bridges independent of metal ion. α-Amino isobutyric acid forms a salt bridge when sodiated and a charge solvation structure when rubidiated. In the most stable charge solvation structures rubidium is bound to one or both carboxyl oxygens, while sodium is bound to both the N- and the C...
TL;DR: In this article, the 3D-RISM integral equations are solved by using the supercell technique and the solvation chemical potential is obtained for the three-dimensional hypernetted chain (3D-HNC) closure as well as for its partial linearization.
Abstract: We adapt the three-dimensional reference interaction site model (3D-RISM) to calculate the potentials of mean force for ion–molecular solution as a difference between the chemical potential of solvation of a cluster of solutes and of individual ones. The method yields the solvation structure around the cluster of solutes in detail. The solvation chemical potential is obtained for the three-dimensional hypernetted chain (3D-HNC) closure as well as for its partial linearization (3D-PLHNC approximation). The solvation chemical potential is obtained in a closed analytical form for both the 3D-HNC and 3D-PLHNC closures. The 3D-RISM integral equations are solved by using the supercell technique. A straightforward supercell treatment of ionic solute in polar molecular solvent leads to a big error in the potential of mean force as well as the solvation chemical potential, which for simple ions in water amounts to about 35 kcal/mol. We elaborated corrections to the 3D-RISM integral equations, alleviating the artifact of the supercell periodicity with an accuracy of 0.05 kcal/mol or better and restoring the long-range asymptotics of the solute–solvent correlation functions. The dielectrically consistent site–site RISM/HNC theory (DRISM/HNC) is employed for the solvent correlations to provide a proper description of the dielectric properties of solution. This allowed us to extend the description to solution at a finite salt concentration. We converge both the 3D-RISM and site–site DRISM integral equations by using the method of modified direct inversion in the iterative subspace. Owing to the proper initial guess of the correlation functions, iteration begins at once for a given temperature and full molecular charge, avoiding a gradual decrease of the temperature and increase of the site charges, which greatly reduces the computation time. We calculate and discuss the potentials of mean force for sodium chloride in ambient water at infinite dilution as well as at a finite concentration.
TL;DR: In this article, an empirically calculated parameter LogPo/w, the log10 of the coefficient for solvent partitioning between 1-octanol and water, has been used to provide the key data for a unique non-covalent interaction force field called HINT (Hydropathic INTeractions).
TL;DR: In this paper, first-principles molecular dynamics simulations have been performed on the solvation of Na+ in water, and it was shown that the first solvation shell of the Na+ contains on average 5.2 water molecules.
Abstract: First-principles molecular dynamics simulations have been performed on the solvation of Na+ in water. Consistent with the available experimental data, we find that the first solvation shell of Na+ contains on average 5.2 water molecules. A significant number of water exchanges between the first and second solvation shells are observed. However, the simulations are not long enough to reliably measure the rate of water exchange. Contrary to several previous studies, we do not find any effect of Na+ on the orientation of water molecules outside of the first solvation shell. Furthermore, the complete set of structural properties determined by first-principles molecular dynamics is not predicted by any of the known classical simulations.
TL;DR: It was found that the adsorption of anionic surfactants alone on alumina was initially highly exothermic due to the electrostatic interaction with the substrate, and further adsOrption leading to a solloid (hemimicelle) formation is proposed to be mainly an entropy-driven process.
TL;DR: Improvements to force-fields and treatments of long-range interactions have significantly increased the reliability of simulations and new studies of sequence effects, axis bending, solvation and conformational transitions have appeared.
TL;DR: In this paper, the free energies of isomerization between hexa-and tetracoordinated structures containing Zn2+ bound to water and ligands of biological interest were evaluated.
Abstract: To elucidate the most preferable, ground-state coordination geometry for zinc complexes in a protein environment, the free energies of isomerization between hexa- and tetracoordinated structures containing Zn2+ bound to water and ligands of biological interest were evaluated. Density functional theory using the 6-31++G(2d,2p) basis set was employed in calculating isomerization free energies in the gas phase, while continuum dielectric theory was used to compute solvation free energies of the zinc clusters in different dielectric media. The results show that the lowest-energy ground-state coordination number of zinc bound to one acidic or two or more neutral protein ligands is 4. The observed decrease in the coordination number of zinc upon protein binding reflects primarily the requirements of the metal and ligands, rather than the constraints of the protein matrix on the metal. Our finding that the tetrahedral zinc complexes in protein cavities generally represent the optimal, least strained structures a...
TL;DR: In this article, a stretched geometry of the fluorocarbon skeleton with tortuosity of 2.4 was reached by energy optimization starting from the regular conformation with all CCCC angles in the trans position.
Abstract: Molecular mechanics and molecular dynamics simulation studies of conformation and solvation of perfluorosulfate oligomers, representing fragments of Nafion membrane, have been performed. Two typical conformations of the oligomer, composed of 10 monomer units, have been found in a vacuum. A stretched geometry of the fluorocarbon skeleton with tortuosity of 2.4 was reached by energy optimization starting from the regular conformation with all CCCC angles in the trans position. A highly folded spiral-like configuration was obtained when the randomly bent chain was taken as the initial configuration. Molecular dynamics simulations of shorter oligomers solvated in water and methanol revealed a noticeable difference between the geometries of the fluorocarbon skeleton in different solvents. The skeleton structure in water was substantially more folded than in methanol. The side chain of the Nafion oligomers was found to be quite stiff; only a few conformational transitions in the side chain were detected. Both w...
TL;DR: In this paper, the authors used a simplified statistical mechanical model of water, the Mercedes Benz (MB) model, in NPT Monte Carlo simulations to predict qualitatively the volume anomalies of pure water and the free energy, enthalpy, entropy, heat capacity, and volume change for inserting a nonpolar solute into water.
Abstract: We model the aqueous solvation of a nonpolar solute as a function of its radius. We use a simplified statistical mechanical model of water, the Mercedes Benz (MB) model, in NPT Monte Carlo simulations. This model has previously been shown to predict qualitatively the volume anomalies of pure water and the free energy, enthalpy, entropy, heat capacity, and volume change for inserting a nonpolar solute into water. We find a very different mechanism for the aqueous solvation of large nonpolar solutes (much larger than a water) than for smaller solutes. Small solute transfer involves a large hydrophobic heat capacity; its disaffinity for cold water (room temperature or below) is due to the ordering of the neighboring waters (entropic), while its disaffinity for hot water is due to the breaking of hydrogen bonds among the neighboring waters (enthalpic). In contrast, transferring large nonpolar solutes into water involves no such large changes in heat capacity or entropy. In this regard, large nonpolar solutes ...
TL;DR: This work investigates the stability of three different ensembles of the 36‐mer villin headpiece subdomain, the native, a compact folding intermediate, and the random coil, finding the native ensemble to be ≈26 kcal/mol more stable than the folding intermediate and ≈39 kcal/ mol morestable than the random Coil ensemble.
Abstract: We investigated the stability of three different ensembles of the 36-mer villin headpiece subdomain, the native, a compact folding intermediate, and the random coil. Structures were taken from a 1-micros molecular dynamics folding simulation and a 100-ns control simulation on the native structure. Our approach for each conformation is to first determine the solute internal energy from the molecular mechanics potential and then to add the change resulting from solvation (DeltaG(solv)). Explicit water was used to run the simulation, and a continuum model was used to estimate DeltaG(solv) with the finite difference Poisson-Boltzmann model accounting for the polarization part and a linearly surface area-dependent term for the non-polar part. We leave out the solute vibrational entropy from these values but demonstrate that there is no statistical difference among the native, folding intermediate, and random coil ensembles. We find the native ensemble to be approximately 26 kcal/mol more stable than the folding intermediate and approximately 39 kcal/mol more stable than the random coil ensemble. With an experimental estimate for the free energy of denaturation equal to 3 kcal/mol, we approximate the non-native degeneracy to lie between 10(16) and 10.(25) We also present a possible scheme for the mechanism of folding, first-order exponential decay of a putative transition state, with an estimate for the t(1/2) of folding of approximately 1 micros.
TL;DR: In this article, the authors studied the properties of propylene carbonate (4methyl-1,3-dioxolan-2-one) in the concentration range from 0.0 to 3.29 M and found that the maximum conductivity at about 0.8 M is explained by the concentration dependence of the solution viscosity.
Abstract: Solutions of lithium hexafluorophosphate, LiPF6, in propylene carbonate (4-methyl-1,3-dioxolan-2-one; denoted by PC hereafter) in the concentration range from 0.0 to 3.29 M (M = mol dm-3) have been studied regarding their conductivities, viscosities, and self-diffusion coefficients of PC by the NMR field gradient technique, Raman spectra, and NMR spectra. Walden's products are almost constant in the range up to and over 3.0 M. Therefore, Li ions are considered to be quite free from the firm interaction with anions even in such concentrated solutions. The appearance of the maximum conductivity at about 0.8 M is explained by associating with the concentration dependence of the solution viscosity. A remarkable increase in the solution viscosity was observed in a concentration beyond 2.0 M, and it can be ascribed to the cluster formation of lithium ions with PC molecules of the solvent. Such an idea of clusters can reasonably interpret some of the characteristic changes of the viscosities, the diffusion coeff...
TL;DR: In this paper, the authors compared the ultrafast dynamics following one-photon UV photodetachment of I− ions in aqueous solution with those following two-phase ionization of the solvent and concluded that the ejected electron in the halide detachment is merely separated from the halogen atom within the same solvent shell.
Abstract: The ultrafast dynamics following one-photon UV photodetachment of I− ions in aqueous solution are compared with those following two-photon ionization of the solvent. Ultrafast pump–probe experiments employing 50 fs ultraviolet pulses reveal similar and very rapid time scales for electron ejection. However, the electron ejection process from water pumped into the conduction band and from iodide ions detached at threshold are readily distinguishable. The observed picosecond timescale geminate recombination and electron escape dynamics are reconstructed using two different models, a diffusion-limited return of the electron from ∼15 A to its parent and a competing kinetics model governed by the reverse electron transfer rate. We conclude that the “ejected” electron in the halide detachment is merely separated from the halogen atom within the same solvent shell. The assignment of detachment into a contact pair is based on the recombination profile rather than by the postulate of any new spectral absorption due...
TL;DR: The ultrafast ultrafast relaxation of p -nitroaniline (PNA) in water and acetonitrile is studied experimentally and theoretically in this article, where transient absorption spectra are measured by the pump-supercontinuum probe technique (PSCP) after 50 fs excitation at 400 nm.
TL;DR: The database-screening tool SLIDE is presented, which is capable of screening large data sets of organic compounds for potential ligands to a given binding site of a target protein, and its main feature is the modeling of induced complementarity by making adjustments in the protein side chains and ligand upon binding.
Abstract: We present our database-screening tool SLIDE, which is capable of screening large data sets of organic compounds for potential ligands to a given binding site of a target protein. Its main feature is the modeling of induced complementarity by making adjustments in the protein side chains and ligand upon binding. Mean-field theory is used to balance the conformational changes in both molecules in order to generate a shape-complementary interface. Solvation is considered by prediction of water molecules likely to be conserved from the crystal structure of the ligand-free protein, and allowing them to mediate ligand interactions, if possible, or including a desolvation penalty when they are displaced by ligand atoms that do not replace the lost hydrogen bonds.A data set of over 175 000 organic molecules was screened for potential ligands to the progesterone receptor, dihydrofolate reductase, and a DNA-repair enzyme. In all cases the screening time was less than a day on a Pentium II processor, and known ligands as well as highly complementary new potential ligands were found.
TL;DR: In this paper, supermolecular calculations that treat both the solute and the solvent quantum-mechanically are performed to analyze the solvatochromism of the first emission transition of formaldehyde in water.
Abstract: Supermolecular calculations that treat both the solute and the solvent quantum-mechanically are performed to analyze the solvatochromism of the first emission transition of formaldehyde in water. The liquid structures are generated by NVT Metropolis Monte Carlo simulation assuming a fully relaxed excited state. The autocorrelation function is calculated to obtain an efficient ensemble average. A detailed analysis of the hydrogen bonds and their contribution to the solvation shift is presented. On average, 0.7 hydrogen bonds are formed in the excited state, about three times less than in the ground state. Quantum-mechanical calculations using the intermediate neglect of differential overlap with singly excited configuration interaction (INDO/CIS) are then performed in the supermolecular clusters corresponding to the hydrogen bond shell and the first, second, and third solvation shells. The third solvation shell extends up to 10 A from the center of mass of formaldehyde, showing the very long-range effects on the solvation shift of this polar molecule. The largest cluster includes one formaldehyde and 142 water molecules. INDO/CIS calculations are performed on this cluster with a properly antisymmetric reference ground state wave function involving all valence electrons. The estimated limit value for the solvatochromic shift of the n-π* emission transition of fully relaxed formaldehyde in water, compared to the gas phase, is ≈1650 cm−1. The total Stokes shift of formaldehyde in water is calculated as ≈550 cm−1.