Ultrafast two-dimensional infrared vibrational echo chemical exchange experiments and theory

Ultrafast two-dimensional (2D) infrared vibrational echo experiments and theory are used to examine chemical exchange between solute-solvent complexes and the free solute for the solute phenol and three solvent complex partners, p-xylene, benzene, and bromobenzene, in mixed solvents of the partner and CCl4. The experiments measure the time evolution of the 2D spectra of the hydroxyl (OD) stretching mode of the phenol. The time-dependent 2D spectra are analyzed using time-dependent diagrammatic perturbation theory with a model that includes the chemical exchange (formation and dissociation of the complexes), spectral diffusion of both the complex and the free phenol, orientational relaxation of the complexes and free phenol, and the vibrational lifetimes. The detailed calculations are able to reproduce the experimental results and demonstrate that a method employed previously that used a kinetic model for the volumes of the peaks is adequate to extract the exchange kinetics. The current analysis also yields the spectral diffusion (time evolution of the dynamic line widths) and shows that the spectral diffusion is significantly different for phenol complexes and free phenol.     

Solute-solvent complex switching dynamics of chloroform between acetone and dimethylsulfoxide-two-dimensional IR chemical exchange spectroscopy

Hydrogen bonds formed between C-H and various hydrogen bond acceptors play important roles in the structure of proteins and organic crystals, and the mechanisms of C-H bond cleavage reactions. Chloroform, a C-H hydrogen bond donor, can form weak hydrogen-bonded complexes with acetone and with dimethylsulfoxide (DMSO). When chloroform is dissolved in a mixed solvent consisting of acetone and DMSO, both types of hydrogen-bonded complexes exist. The two complexes, chloroform-acetone and chloroform-DMSO, are in equilibrium, and they rapidly interconvert by chloroform exchanging hydrogen bond acceptors. This fast hydrogen bond acceptor substitution reaction is probed using ultrafast two-dimensional infrared (2D-IR) vibrational echo chemical exchange spectroscopy. Deuterated chloroform is used in the experiments, and the 2D-IR spectrum of the C-D stretching mode is measured. The chemical exchange of the chloroform hydrogen bonding partners is tracked by observing the time-dependent growth of off-diagonal peaks in the 2D-IR spectra. The measured substitution rate is 1/30 ps for an acetone molecule to replace a DMSO molecule in a chloroform-DMSO complex and 1/45 ps for a DMSO molecule to replace an acetone molecule in a chloroform-acetone complex. Free chloroform exists in the mixed solvent, and it acts as a reactive intermediate in the substitution reaction, analogous to a SN1 type reaction. From the measured rates and the equilibrium concentrations of acetone and DMSO, the dissociation rates for the chloroform-DMSO and chloroform-acetone complexes are found to be 1/24 ps and 1/5.5 ps, respectively. The difference between the measured rate for the complete substitution reaction and the rate for complex dissociation corresponds to the diffusion limited rate. The estimated diffusion limited rate agrees well with the result from a Smoluchowski treatment of diffusive reactions.     

Phenol-benzene complexation dynamics: quantum chemistry calculation, molecular dynamics simulations, and two dimensional IR spectroscopy

Molecular dynamics (MD) simulations and quantum mechanical electronic structure calculations are used to investigate the nature and dynamics of the phenol-benzene complex in the mixed solvent, benzene/CCl4. Under thermal equilibrium conditions, the complexes are continuously dissociating and forming. The MD simulations are used to calculate the experimental observables related to the phenol hydroxyl stretching mode, i.e., the two dimensional infrared vibrational echo spectrum as a function of time, which directly displays the formation and dissociation of the complex through the growth of off-diagonal peaks, and the linear absorption spectrum, which displays two hydroxyl stretch peaks, one for the complex and one for the free phenol. The results of the simulations are compared to previously reported experimental data and are found to be in quite reasonable agreement. The electronic structure calculations show that the complex is T shaped. The classical potential used for the phenol-benzene interaction in the MD simulations is in good accord with the highest level of the electronic structure calculations. A variety of other features is extracted from the simulations including the relationship between the structure and the projection of the electric field on the hydroxyl group. The fluctuating electric field is used to determine the hydroxyl stretch frequency-frequency correlation function (FFCF). The simulations are also used to examine the number distribution of benzene and CCl4 molecules in the first solvent shell around the phenol. It is found that the distribution is not that of the solvent mole fraction of benzene. There are substantial probabilities of finding a phenol in either a pure benzene environment or a pure CCl4 environment. A conjecture is made that relates the FFCF to the local number of benzene molecules in phenol's first solvent shell.     

Solute-solvent complex kinetics and thermodynamics probed by 2D-IR vibrational echo chemical exchange spectroscopy

The formation and dissociation kinetics of a series of triethylsilanol/solvent weakly hydrogen bonding complexes with enthalpies of formation ranging from -1.4 to -3.3 kcal/mol are measured with ultrafast two-dimensional infrared (2D IR) chemical exchange spectroscopy in liquid solutions at room temperature. The correlation between the complex enthalpies of formation and dissociation rate constants can be expressed with an equation similar to the Arrhenius equation. The experimental results are in accord with previous observations on eight phenol/solvent complexes with enthalpies of formation from -0.6 to -2.5 kcal/mol. It was found that the inverse of the solute-solvent complex dissociation rate constant is linearly related to exp(-DeltaH0/RT) where DeltaH0 is the complex enthalpy of formation. It is shown here, that the triethylsilanol-solvent complexes obey the same relationship with the identical proportionality constant, that is, all 13 points, five silanol complexes and eight phenol complexes, fall on the same line. In addition, features of 2D IR chemical exchange spectra at long reaction times (spectral diffusion complete) are explicated using the triethylsilanol systems. It is shown that the off-diagonal chemical exchange peaks have shapes that are a combination (outer product) of the absorption line shapes of the species that give rise to the diagonal peaks.     

Probing dynamics of complex molecular systems with ultrafast 2D IR vibrational echo spectroscopy

Ultrafast 2D IR vibrational echo spectroscopy is described and a number of experimental examples are given. Details of the experimental method including the pulse sequence, heterodyne detection, and determination of the absorptive component of the 2D spectrum are outlined. As an initial example, the 2D spectrum of the stretching mode of CO bound to the protein myoglobin (MbCO) is presented. The time dependence of the 2D spectrum of MbCO, which is caused by protein structural evolution, is presented and its relationship to the frequency-frequency correlation function is described and used to make protein structural assignments based on comparisons to molecular dynamics simulations. The 2D vibrational echo experiments on the protein horseradish peroxidase are presented. The time dependence of the 2D spectra of the enzyme in the free form and with a substrate bound at the active site are compared and used to examine the influence of substrate binding on the protein's structural dynamics. The application of 2D vibrational echo spectroscopy to the study of chemical exchange under thermal equilibrium conditions is described. 2D vibrational echo chemical exchange spectroscopy is applied to the study of formation and dissociation of organic solute-solvent complexes and to the isomerization around a carbon-carbon single bond of an ethane derivative.     

Vibrational spectroscopy and density functional theory of transition-metal ion-benzene and dibenzene complexes in the gas phase

Metal-benzene complexes of the form M(benzene)(n) (M = Ti, V, Fe, Co, Ni) are produced in the gas-phase environment of a molecular beam by laser vaporization in a pulsed nozzle cluster source. These complexes are photoionized with an ArF excimer laser, producing the corresponding cations. The respective mono- and dibenzene complex ions are isolated in an ion-trap mass spectrometer and studied with infrared resonance enhanced multiple-photon dissociation (IR-REMPD) spectroscopy using a tunable free electron laser. Photodissociation of all complexes occurs by the elimination of intact neutral benzene molecules, and this process is enhanced on resonances in the vibrational spectrum, making it possible to measure vibrational spectroscopy for size-selected complexes. Vibrational bands in the 600-1700 cm(-1) region are characteristic of the benzene molecular moiety with systematic shifts caused by the metal bonding. The spectra in this solvent-free environment exhibit periodic trends in band shifts and intensities relative to the free benzene molecule that varies with the metal. Density functional theory calculations are employed to investigate the structures, energetics, and vibrational frequencies of these complexes. The comparison between experiment and theory provides fascinating new insight into the bonding in these prototypical organometallic complexes.     

Cation-pi interactions with a model for the side chain of tryptophan: structures and absolute binding energies of alkali metal cation-indole complexes

Threshold collision-induced dissociation techniques are employed to determine bond dissociation energies (BDEs) of mono- and bis-complexes of alkali metal cations, Li+, Na+, K+, Rb+, and Cs+, with indole, C8H7N. The primary and lowest energy dissociation pathway in all cases is endothermic loss of an intact indole ligand. Sequential loss of a second indole ligand is observed at elevated energies for the bis-complexes. Density functional theory calculations at the B3LYP/6-31G level of theory are used to determine the structures, vibrational frequencies, and rotational constants of these complexes. Theoretical BDEs are determined from single point energy calculations at the MP2(full)/6-311+G(2d,2p) level using the B3LYP/6-31G* geometries. The agreement between theory and experiment is very good for all complexes except Li+ (C8H7N), where theory underestimates the strength of the binding. The trends in the BDEs of these alkali metal cation-indole complexes are compared with the analogous benzene and naphthalene complexes to examine the influence of the extended pi network and heteroatom on the strength of the cation-pi interaction. The Na+ and K+ binding affinities of benzene, phenol, and indole are also compared to those of the aromatic amino acids, phenylalanine, tyrosine, and tryptophan to elucidate the factors that contribute to the binding in complexes to the aromatic amino acids. The nature of the binding and trends in the BDEs of cation-pi complexes between alkali metal cations and benzene, phenol, and indole are examined to help understand nature's preference for engaging tryptophan over phenylalanine and tyrosine in cation-pi interactions in biological systems.     

Formation and dissociation of intra-intermolecular hydrogen-bonded solute-solvent complexes: chemical exchange two-dimensional infrared vibrational echo spectroscopy

2-Methoxyphenol (2MP) solutes form weak complexes with toluene solvent molecules. The complexes are unusual in that the 2MP hydroxyl has an intramolecular hydrogen bond and simultaneously forms an intermolecular hydrogen bond with toluene and other aromatic solvents. In the equilibrated solute-solvent solution, there exists approximately the same concentration of 2MP-toluene complex and free 2MP. The very fast formation and dissociation (chemical exchange) of this type of three-centered hydrogen bond complex were observed in real time under thermal equilibrium conditions with two-dimensional (2D) infrared vibrational echo spectroscopy. Chemical exchange is manifested in the 2D spectrum by the growth of off-diagonal peaks. Both the formation and dissociation can be characterized in terms of the dissociation time constant, which was determined to be 3 ps for the 2MP-toluene complex. The intra-intermolecular hydrogen bond formation is influenced by subtle details of the molecular structure. Although 2MP forms a complex with toluene, it is demonstrated that 2-ethoxyphenol (2EP) does not form complexes to any significant extent. Density functional calculations at the B3LYP/6-31+G(d,p) level suggest that steric effects caused by the extra methyl group in 2EP are responsible for the difference.     

Taking apart the two-dimensional infrared vibrational echo spectra: more information and elimination of distortions

Ultrafast two-dimensional infrared (2D-IR) vibrational echo spectroscopy can probe the fast structural evolution of molecular systems under thermal equilibrium conditions. Structural dynamics are tracked by observing the time evolution of the 2D-IR spectrum, which is caused by frequency fluctuations of vibrational mode(s) excited during the experiment. However, there are a variety of effects that can produce line shape distortions and prevent the correct determination of the frequency-frequency correlation function (FFCF), which describes the frequency fluctuations and connects the experimental observables to a molecular level depiction of dynamics. In addition, it can be useful to analyze different parts of the 2D spectrum to determine if dynamics are different for subensembles of molecules that have different initial absorption frequencies in the inhomogeneously broadened absorption line. Here, an important extension to a theoretical method for extraction of the FFCF from 2D-IR spectra is described. The experimental observable is the center line slope (CLSomega(m)) of the 2D-IR spectrum. The CLSomega(m) is obtained by taking slices through the 2D spectrum parallel to the detection frequency axis (omega(m)). Each slice is a spectrum. The slope of the line connecting the frequencies of the maxima of the sliced spectra is the CLSomega(m). The change in slope of the CLSomega(m) as a function of time is directly related to the FFCF and can be used to obtain the complete FFCF. CLSomega(m) is immune to line shape distortions caused by destructive interference between bands arising from vibrational echo emission, from the 0-1 vibrational transition (positive), and from the 1-2 vibrational transition (negative) in the 2D-IR spectrum. The immunity to the destructive interference enables the CLSomega(m) method to compare different parts of the bands as well as comparing the 0-1 and 1-2 bands. Also, line shape distortions caused by solvent background absorption and finite pulse durations do not affect the determination of the FFCF with the CLSomega(m) method. The CLSomega(m) can also provide information on the cross correlation between frequency fluctuations of the 0-1 and 1-2 vibrational transitions.     

Temperature-dependent solvent effect on the kinetic energy distribution on p-cresol molecule as building block of calixarene capsules

The solvent effect on the kinetic energy distribution of p-cresol molecule was investigated by quantum-chemical (QM) method and molecular dynamics (MD) simulations, then the consequences were checked experimentally by photoluminescence (PL) and differential scanning calorimetry (DSC) methods. Results of QM calculations highlight the coupling of two vibrational normalmodes of p-cresol molecule in the presence of ethanol while no similar coupling was observed in methanol. MD simulations show that the normalmode coupling in ethanol is more pronounced at higher temperature and it is preferably based on the molecular friction of the cresol molecule with its environment. The theoretical observations were also proved experimentally. The dissociation rate of calixarene–phenol complexes were measured by DSC method. The decreased dissociation rate of the calixarene–phenol complexes observed in ethanol reflects the increased motion of the methyl groups of cresol units of calixarene in the ethanol solvent, a property which was predicted by the theoretical results. Our findings are applicable to many areas of chemistry where the formation and dissociation rates play important role: e.g., in the development of chemical molecular sensors or developing molecular containers for drugs towards pharmaceutical applications.     

Electrical effects on the vibrational transitions of hydrogen fluoride due to hydrogen bonding and applied fields

Derivative Hartree-Fock (DHF) theory has been used to study the transition dipole moment of hydrogen fluoride in several hydrogen-bonded complexes and in the presence of applied fields. DHF is an open-ended, analytical means for finding energy derivatives with respect to any number of parameters, and large basis set calculations going through the seventh dipole hyperpolarizability (ninth derivative) are reported. Using multipole moments, multipole polarizabilities and hyperpolarizabilities, the intermolecular electrical influence on vibrational transitions is analyzed.     

Heterodyned fifth-order 2D-IR spectroscopy of the azide ion in an ionic glass

A heterodyned fifth-order infrared pulse sequence has been used to measure a two-dimensional infrared (2D-IR) spectrum of azide in the ionic glass 3KNO3:2Ca(NO3)2. By rephasing a two-quantum coherence, a process not possible with third-order spectroscopy, the 2D-IR spectra are line narrowed, allowing the frequencies, anharmonicities, and their correlations to be measured for the first four (nu=0-3) antisymmetric stretch vibrational levels. In this glass, the vibrational levels are extremely inhomogeneously broadened. Furthermore, the glass shifts the energy of the nu=3 state more than the others, causing an inhomogeneous distribution in the anharmonic constants that are partially correlated to the inhomogeneous distribution of the fundamental frequency. These effects are discussed in light of the strong interactions that exist between the charged solute and solvent. Since this is the first example of a heterodyned fifth-order infrared pulse sequence, possible cascaded contributions to the signal are investigated. No evidence of cascaded signals is found. Compared to third-order spectroscopies, fifth-order pulse sequences provide advanced control over vibrational coherence and population times that promise to extend the capabilities of ultrafast infrared spectroscopy.     

计量置换参数Z值分量的测定(英文)

 以计量置换吸附理论(SDT A)为基础,从理论上推导出计量吸附模型中表征溶质对固定相亲合势大小的参数βa值与流动相中强置换剂浓度的对数呈线性关系。计量置换模型中的参数n和q(n和q分别代表1摩尔溶剂化溶质被吸附时,从吸附剂表面和从溶质分子表面所释放出的溶剂的物质的量)是计量置换参数Z值的分量,是两个非常有用的参数,可以从这个定量关系中直接获得。推导出的方程用苯的衍生物进行了实验验证,获得了较满意的结果。将这种方法计算得到的分量值与SDT A与计量置换保留模型(SDT R)相结合的方法得到的分量值进行了比较。     

Pronounced non-Condon effects in the ultrafast infrared spectroscopy of water

In the context of vibrational spectroscopy in liquids, non-Condon effects refer to the dependence of the vibrational transition dipole moment of a particular molecule on the rotational and translational coordinates of all the molecules in the liquid. For strongly hydrogen-bonded systems, such as liquid water, non-Condon effects are large. That is, the bond dipole derivative of an OH stretch depends strongly on its hydrogen-bonding environment. Previous calculations of nonlinear vibrational spectroscopy in liquids have not included these non-Condon effects. We find that for water, inclusion of these effects is important for an accurate calculation of, for example, homodyned and heterodyned three-pulse echoes. Such echo experiments have been "inverted" to obtain the OH stretch frequency time-correlation function, but by necessity the Condon and other approximations are made in this inversion procedure. Our conclusion is that for water, primarily because of strong non-Condon effects, this inversion may not lead to the correct frequency time-correlation function. Nevertheless, one can still make comparison between theory and experiment by calculating the experimental echo observables themselves.     

Native and unfolded cytochrome c--comparison of dynamics using 2D-IR vibrational echo spectroscopy

Unfolded vs native CO-coordinated horse heart cytochrome c (h-cyt c) and a heme axial methionine mutant cyt c552 from Hydrogenobacter thermophilus ( Ht-M61A) are studied by IR absorption spectroscopy and ultrafast 2D-IR vibrational echo spectroscopy of the CO stretching mode. The unfolding is induced by guanidinium hydrochloride (GuHCl). The CO IR absorption spectra for both h-cyt c and Ht-M61A shift to the red as the GuHCl concentration is increased through the concentration region over which unfolding occurs. The spectra for the unfolded state are substantially broader than the spectra for the native proteins. A plot of the CO peak position vs GuHCl concentration produces a sigmoidal curve that overlays the concentration-dependent circular dichroism (CD) data of the CO-coordinated forms of both Ht-M61A and h-cyt c within experimental error. The coincidence of the CO peak shift curve with the CD curves demonstrates that the CO vibrational frequency is sensitive to the structural changes induced by the denaturant. 2D-IR vibrational echo experiments are performed on native Ht-M61A and on the protein in low- and high-concentration GuHCl solutions. The 2D-IR vibrational echo is sensitive to the global protein structural dynamics on time scales from subpicosecond to greater than 100 ps through the change in the shape of the 2D spectrum with time (spectral diffusion). At the high GuHCl concentration (5.1 M), at which Ht-M61A is essentially fully denatured as judged by CD, a very large reduction in dynamics is observed compared to the native protein within the approximately 100 ps time window of the experiment. The results suggest the denatured protein may be in a glassy-like state involving hydrophobic collapse around the heme.     

Influence of the d orbital occupation on the nature and strength of copper cation-pi interactions: threshold collision-induced dissociation and theoretical studies

Threshold collision-induced dissociation techniques are employed to determine the bond dissociation energies of a wide variety of copper cation-pi complexes, Cu(+)(pi-ligand), where pi-ligand = benzene, flurobenzene, chlorobenzene, bromobenzene, iodobenzene, phenol, toluene, anisole, pyrrole, N-methylpyrrole, indole, naphthalene, aniline, N-methylaniline, and N,N-dimethylaniline. The primary and lowest energy dissociation pathway corresponds to the endothermic loss of the intact neutral pi-ligand for all complexes except those to N-methylpyrrole, indole, aniline, N-methylaniline, and N,N-dimethylaniline. In the latter complexes, the primary dissociation pathway corresponds to loss of the intact ligand accompanied by charge transfer, thereby producing a neutral copper atom and ionized pi-ligand. Fragmentation of the pi-ligands is also observed at elevated energies in several cases. Theoretical calculations at the B3LYP/6-311G(d,p) level of theory are used to determine the structures, vibrational frequencies, and rotational constants of these complexes. Multiple low-energy conformers are found for all of the copper cation-pi complexes. Theoretical bond dissociation energies are determined from single point energy calculations at the B3LYP/6-311+G(3df,2p) level of theory using the B3LYP/6-311G(d,p) optimized geometries. The agreement between theory and experiment is very good for most complexes. The nature and strength of the binding in these copper cation-pi complexes are studied and compared with the corresponding cation-pi complexes to Na(+). Natural bond orbital analyses are carried out to examine the influence of the d orbital occupation on copper cation-pi interactions.     

Comparative study of the hydrogen-bonded complexes of phenol and o-cyanophenol with CO Ab initio and DFT approachs

The structures, stability and vibrational spectra of the hydrogen-bonded complexes of carbon monoxide (CO) with phenol and o-cyanophenol (syn and anti) have been studied using ab initio and DFT calculations. Full geometry optimization has been performed for the studied complexes by DFT (BLYP/6-311++G(d,p)) calculations. The calculations show that the hydrogen-bond formation of carbon monoxide (CO) with phenol and o-cyanophenol (syn and anti) leads to the following stable structures: C6H5OH...CO (1A); C6H5OH...OC (1B); (syn) o-CNC6H4OH...CO (2A-syn); (syn) o-CNC6H4OH...OC (2B-syn); (anti) o-CNC6H4 OH...CO (2A-anti) and (anti) o-CNC6H4OH...OC (2B-anti). Having in mind the corrected values of the dissociation energy, the studied hydrogen-bonded complexes can be ordered according their stability as follows: 2A-anti>2A-syn>1A>2B-anti>1B>2B-syn. The predicted red-shifts for the nuOH vibration with the B3LYP/6-311++G(d,p) calculations for the structures 1A (-46 cm-1), 2A-syn (-60 cm-1) and 2A-anti (-73 cm-1) are in very good agreement with the experimentally observed. The magnitudes of the wavenumber shifts are indicative of relatively weak OH...C hydrogen-bonded interactions. The calculations predict an increase of the IR intensity of the nuOH vibration in the complexes 1A, 2A-anti and 2A-syn up to five times.     

Theoretical study of the structures and vibrational spectra of the hydrogen-bonded systems of 4-cyanophenol with N-bases

The structural and vibrational features of the hydrogen bonded complexes of 1,5,7-triazabicyclo [4.4.0] dec-5-ene (TBD) with one and two 4-CNPhOH molecules have been studied extensively by ab initio SCF/6-31G(d,p) and BLYP calculations with various basis sets: 6-31G(d,p), 6-31+G(d,p) and 6-31++G(d,p). Full geometry optimization was made for the complexes studied. The nature of the hydrogen bonding and the influence of the hydrogen bonding on the structural and vibrational characteristics of the monomers have been investigated. The corrected values of the dissociation energy for the hydrogen-bonded complexes have been calculated in order to estimate their stability. The calculated values of the dissociation energy per phenol molecule indicate that the complex: TBD: 4-CNPhOH (1:1) is more stable than the complex: TBD: 4-CNPhOH (1:2). The changes in the structural and vibrational characteristics upon hydrogen bonding depend on the strength of the hydrogen bonds. In agreement with the experiment, the calculations show that the complexation between TBD and 4-CNPhOH leads to considerably changes in the vibrational characteristics of the stretching O-H vibration. The vibrational frequency of the O-H stretching vibration is shifted to lower wave numbers upon hydrogen bonding. The predicted frequency shifts Deltanu(O-H) for the complexes--TBD: 4-CNPhOH (1:1) and TBD: 4-CNPhOH (1:2) are in the range from -190 cm(-1) to -586 cm(-1). In the same time the IR intensity of the O-H stretching vibration increases dramatically in the hydrogen-bonded complexes.     

Solvent–solute and solute–solute interactions from NMR in nematic phases

Abstract

The use of NMR spectroscopy of molecules oriented in liquid-crystalline media to study solvent–solute and solute–solute interactions in π-systems such as benzene–chloroform and in charge transfer complexes, for example pyridineiodine, is illustrated. Changes in molecular order and chemical shifts as a result of complexation are employed in such studies. The extraordinary symmetry of C₆₀ has also been investigated by using a mixture of liquid crystals of opposite diamagnetic anisotropies indicating, thereby, negligible solvent–solute/solute–solute interactions.     

Influence of the solvent representation on vibrational entropy calculations: Generalized born versus distance‐dependent dielectric model

The harmonic model is the most popular approximation for estimating the “configurational” entropy of a solute in molecular mechanics/Poisson‐Boltzmann solvent accessible surface area (MM/PBSA)‐type binding free energy calculations. Here, we investigate the influence of the solvent representation in the harmonic model by comparing estimates of changes in the vibrational entropies for 30 trypsin/ligand complexes on ligand binding. Second derivatives of Amber generalized Born (GB) solvation models are available in the nucleic acid builder code. They allow one to use these models for the calculation of vibrational entropies instead of using a simpler solvation model based on a distance‐dependent dielectric (DDD) constant. Estimates of changes in the vibrational entropies obtained with a DDD model are systematically and significantly larger, by on average, 6 kcal mol^?1 (at T = 300 K), than estimates obtained with a GB model and so are more favorable for complex formation. The difference becomes larger the more the vibrational entropy contribution disfavors complex formation, that is, the larger the ligand is (for the complexes considered here). A structural decomposition of the estimates into per‐residue contributions reveals polar interactions between the ligand and the surrounding protein, in particular involving charged nitrogens, as a main source of the differences. Snapshots minimized with the DDD model showed a structural deviation from snapshots minimized in explicit water that is larger by, on average, 0.5 Å RMSD compared to snapshots that were minimized with GB^HCT. As experimental vibrational entropies of biomacromolecules are elusive, there is no direct way to establish a solvent model's superiority. Thus, we can only recommend using the GB harmonic model for vibrational entropy calculations based on the reasoning that smaller structural deviations should point to the implicit solvent model that closer approximates the energy landscape of the solute in explicit solvent. © 2012 Wiley Periodicals, Inc.