pH dependence of the electronic structure of glycine

The carbon, nitrogen, and oxygen K-edge spectra were measured for aqueous solutions of glycine by total electron yield near-edge X-ray absorption fine structure (TEY NEXAFS) spectroscopy. The bulk solution pH was systematically varied while maintaining a constant amino acid concentration. Spectra were assigned through comparisons with both previous studies and ab initio computed spectra of isolated glycine molecules and hydrated glycine clusters. Nitrogen K-edge solution spectra recorded at low and moderate pH are nearly identical to those of solid glycine, whereas basic solution spectra strongly resemble those of the gas phase. The carbon 1s --> pi*(C=O) transition exhibits a 0.2 eV red shift at high pH due to the deprotonation of the amine terminus. This deprotonation also effects a 1.4 eV red shift in the nitrogen K-edge at high pH. Two sharp preedge features at 401.3 and 402.5 eV are also observed at high pH. These resonances, previously observed in the vapor-phase ISEELS spectrum of glycine, have been reassigned as transitions to sigma* bound states. The observation of these peaks indicates that the amine moiety is in an acceptor-only hydrogen bond configuration at high pH. At low pH, the oxygen 1s --> pi*(C=O) transition exhibits a 0.25-eV red shift due to the protonation of the carboxylic acid terminus. These spectral differences indicate that the variations in electronic structure observed in the NEXAFS spectra are determined by the internal charge state and hydration environment of the molecule in solution.     

Local hydration environments of amino acids and dipeptides studied by X-ray spectroscopy of liquid microjets

The nitrogen K-edge spectra of aqueous proline and diglycine solutions have been measured by total electron yield near-edge X-ray absorption fine structure (NEXAFS) spectroscopy at neutral and high pH. All observed spectral features have been assigned by comparison to the recently reported spectrum of aqueous glycine and calculated spectra of isolated amino acids and hydrated amino acid clusters. The sharp preedge resonances at 401.3 and 402.6 eV observed in the spectrum of anionic glycine indicate that the nitrogen terminus is in an "acceptor-only" configuration, wherein neither amine proton is involved in hydrogen bonding to the solvent, at high pH. The analogous 1s --> sigma(NH) preedge transitions are absent in the NEXAFS spectrum of anionic proline, implying that the acceptor-only conformation observed in anionic glycine arises from steric shielding induced by free rotation of the amine terminus about the glycine CN bond. Anionic diglycine solutions exhibit a broadened 1s --> pi(CN) resonance at 401.2 eV and a broad shoulder resonance at 403 eV, also suggesting the presence of an acceptor-only species. Although this assignment is not as unambiguous as for glycine, it implies that the nitrogen terminus of most proteins is capable of existing in an acceptor-only conformation at high pH. The NEXAFS spectrum of zwitterionic lysine solution was also measured, exhibiting features similar to those of both anionic and zwitterionic glycine, and leading us to conclude that the alpha amine group is present in an acceptor-only configuration, while the end of the butylammonium side chain is fully solvated.     

Density functional study of the interaction between small Au clusters, Au(n) (n=1-7) and the rutile TiO(2) surface. I. Adsorption on the stoichiometric surface

This is the first paper in a series of four dealing with the adsorption site, electronic structure, and chemistry of small Au clusters, Au(n) (n=1-7), supported on stoichiometric, partially reduced, or partially hydroxylated rutile TiO(2)(110) surfaces. Analysis of the electronic structure reveals that the main contribution to the binding energy is the overlap between the highest occupied molecular orbitals of Au clusters and the Kohn-Sham orbitals localized on the bridging and the in-plane oxygen of the rutile TiO(2)(110) surface. The structure of adsorbed Au(n) differs from that in the gas phase mostly because the cluster wants to maximize this orbital overlap and to increase the number of Au-O bonds. For example, the equilibrium structures of Au(5) and Au(7) are planar in the gas phase, while the adsorbed Au(5) has a distorted two-dimensional structure and the adsorbed Au(7) is three-dimensional. The dissociation of an adsorbed cluster into two adsorbed fragments is endothermic, for all clusters, by at least 0.8 eV. This does not mean that the gas-phase clusters hitting the surface with kinetic energy greater than 0.8 eV will fragment. To place enough energy in the reaction coordinate for fragmentation, the impact kinetic energy needs to be substantially higher than 0.8 eV. We have also calculated the interaction energy between all pairs of Au clusters. These interactions are small except when a Au monomer is coadsorbed with a Au(n) with odd n. In this case the interaction energy is of the order of 0.7 eV and the two clusters interact through the support even when they are fairly far apart. This happens because the adsorption of a Au(n) cluster places electrons in the states of the bottom of the conduction band and these electrons help the Au monomer to bind to the five-coordinated Ti atoms on the surface.     

Electronic and geometric characterization of the L-cysteine paired-row phase on Au(110)

We have studied the vapor-phase deposition of L-cysteine on the Au(110) surface by means of synchrotron-based techniques. Relying on a comparison with previous X-ray photoemission analysis, we have assigned the fine structure of the C K-shell X-ray absorption spectra to the nonequivalent carbon bonds within the molecule. In particular, the C1s --> sigma* transition, where the sigma* state is mainly localized on the C-S bond, is shifted well below the ionization threshold, at approximately -5 eV from the characteristic pi* transition line related to carboxylic group. From the polarization dependence of the absorption spectra in the monolayer coverage range, the molecules are found to lay flat on the surface with both the C-S bond and the carboxylic group almost parallel to the surface. We performed in situ complementary surface X-ray diffraction, SXRD, measurements to probe the rearrangement of the Au atoms beneath the L-cysteine molecules. Since the early stage of deposition, L-cysteine domains are formed which display an intermediate fourfold symmetry along [001]. The self-assembly of molecules into paired rows, extending along the [1(-)10] direction, is fully compatible with our observations, as has been reported for the case of D-cysteine molecules grown on Au(110) [Kühnle, A. et al. Phys. Rev. Lett. 2004, 93, 086101.]     

Gas phase formation of dense alkanethiol layers on GaAs(110)

We present a study of the growth and thermal stability of hexanethiol (C6) films on GaAs(110) by direct recoil spectroscopy with time-of-flight analysis. We compare our results with the better known case of C6 adsorption on Au(111). In contrast to the two-step adsorption kinetics observed for Au surfaces after lengthy exposures, data for C6 adsorption on the GaAs(110) surface are consistent with the formation of a single dense phase of C6 molecules at lower exposures. On the contrary, in solution preparation, dense phases can only be obtained on GaAs for long alkanethiols and after lengthy immersions. The C6 layer has a first desorption peak at 325 K, where partial desorption of the alkanethiol molecules takes place. Fits to the desorption curves result in a 1 eV adsorption energy, in agreement with a chemisorption process. Increasing the temperature to 500 K results in the S-C bond scission with only S remaining on the GaAs(110) surface. The possibility of forming dense, short-alkanethiol layers on semiconductor surfaces from the vapor phase could have a strong impact for a wide range of self-assembled monolayer applications, with only minimal care not to surpass room temperature once the layer has been formed in order to avoid molecular desorption.     

Stereoselective and Chiroselective Surface Plasmon Resonance (SPR) Analysis of Amino Acids by Molecularly Imprinted Au‐Nanoparticle Composites

Au nanoparticles (NPs) functionalized with thioaniline and cysteine are used to assemble bis‐aniline‐bridged Au‐NP composites on Au surfaces using an electropolymerization process. During the polymerization of the functionalized Au NPs in the presence of different amino acids, for example, L ‐glutamic acid, L ‐aspartic acid, L ‐histidine, and L ‐phenylalanine, zwitterionic interactions between the amino acids and the cysteine units linked to the particles lead to the formation of molecularly imprinted sites in the electropolymerized Au‐NP composites. Following the elimination of the template amino acid molecules, the electropolymerized matrices reveal selective recognition and binding capabilities toward the imprinted amino acid. Furthermore, by imprinting of L ‐glutamic or D ‐glutamic acids, chiroselective imprinted sites are generated in the Au‐NP composites. The binding of amino acids to the imprinted recognition sites was followed by surface plasmon resonance spectroscopy. The refractive index changes occurring upon the binding of the amino acids to the imprinted sites are amplified by the coupling between the localized plasmon associated with the Au NPs and the surface plasmon wave.     

Nature of the aqueous hydroxide ion probed by X-ray absorption spectroscopy

X-ray absorption spectra of aqueous 4 and 6 M potassium hydroxide solutions have been measured near the oxygen K edge. Upon addition of KOH to water, a new spectral feature (532.5 eV) emerges at energies well below the liquid water pre-edge feature (535 eV) and is attributed to OH- ions. In addition to spectral changes explicitly due to absorption by solvated OH- ions, calculated XA spectra indicate that first-solvation-shell water molecules exhibit an absorption spectrum that is unique from that of bulk liquid water. It is suggested that this spectral change results primarily from direct electronic perturbation of the unoccupied molecular orbitals of first-shell water molecules and only secondarily from geometric distortion of the local hydrogen bond network within the first hydration shell. Both the experimental and the calculated XA spectra indicate that the nature of the interaction between the OH- ion and the solvating water molecules is fundamentally different than the corresponding interactions of aqueous halide anions with respect to this direct orbital distortion. Analysis of the Mulliken charge populations suggests that the origin of this difference is a disparity in the charge asymmetry between the hydrogen atoms of the solvating water molecules. The charge asymmetry is induced both by electric field effects due to the presence of the anion and by charge transfer from the respective ions. The computational results also indicate that the OH- ion exists with a predominately "hyper-coordinated" solvation shell and that the OH- ion does not readily donate hydrogen bonds to the surrounding water molecules.     

Interaction of amino acids with gold and silver clusters

Binding of gold and silver clusters with amino acids (glycine and cysteine) was studied using density functional theory (DFT). Geometries of neutral, anionic, and cationic amino acids with Au3 and Ag3 clusters were optimized using the DFT-B3LYP approach. The mixed basis set used here was denoted by 6-31+G** (union or logical sum)LANL2DZ. This work demonstrated that the interaction of amino acids with gold and silver clusters is governed by two major bonding factors: (a) the anchoring N-Au(Ag), O-Au(Ag), and S-Au(Ag) bonds and (b) the nonconventional N-H...Au(Ag) and O-H...Au(Ag) hydrogen bonds. Among the three forms of amino acids, anionic ones exhibited the most tendency to interact with the Au and Ag clusters. Natural bond orbital analysis was performed to calculate charge transfer, natural population analysis, and Wiberg bond indices of the complexes. Atoms-in-molecules theory was also applied to determine the nature of interactions. It was shown that these bonds are partially electrostatic and partially covalent.     

Structure and bonding of the multifunctional amino acid L-DOPA on Au(110)

In investigations of the proteins which are responsible for the surface adhesion of the blue mussel Mytilus edulis, an unusually frequent appearance of the otherwise rare amino acid 3-(3,4-dihydroxyphenyl)-L-alanine (L-DOPA) has been observed. This amino acid is thought to play a major role in the mechanism of mussel adhesion. Here we report a detailed structural and spectroscopic investigation of the interface between L-DOPA and a single-crystalline Au(110) model surface, with the aim of understanding fundamentals about the surface bonding of this amino acid and its role in mussel adhesion. Molecular layers are deposited by organic molecular beam deposition (OMBD) in an ultrahigh-vacuum environment. The following experimental techniques have been applied: ex situ Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), low-energy electron diffraction (LEED), high-resolution electron energy loss spectroscopy (HREELS), and scanning tunneling microscopy (STM). Vibrational spectra of isolated L-DOPA molecules and the zwitterionic bulk have been calculated using density functional theory (DFT). The predicted modes are assigned to observed spectra, allowing conclusions regarding the molecule-substrate and molecule-molecule interactions at the L-DOPA/Au(110) interface. We find that zwitterionic L-DOPA forms a monochiral, one-domain commensurate monolayer on Au(110), with the catechol rings on top of [110] gold rows, oriented parallel to the surface. The (2 x 1)-Au(110) surface reconstruction is not lifted. The carboxylate group is found in a bidentate or bridging configuration, the amino group is tilted out of the surface plane, and the hydroxyl groups do not dehydrogenate on Au(110). Similar to the case for the bulk, molecules form dimers on Au(110). However, the number of hydrogen bridge bonds between L-DOPA molecules is reduced as compared to the bulk. Thicker layers which are deposited onto the commensurate interface do not order in the bulk structure. In conclusion, our study shows that the aromatic ring system of L-DOPA functions as a surface anchor. Since it is also known that the hydroxyl groups support cross-link reactions between L-DOPA residues in the mussel glue protein, we can conclude that the catechol ring supports surface adhesion of mussel proteins via two independent functions.     

Homocysteine-mediated reactivity and assembly of gold nanoparticles

This paper reports the findings of an investigation of the reactivity and assembly of gold nanoparticles mediated by homocysteine (Hcys), a thiol-containing amino acid found in plasma. The aim is to gain insight into the interparticle interaction and reactivity, which has potential application for the detection of thiol-containing amino acids. By monitoring the evolution of the surface plasmon resonance absorption and the dynamic light scattering of gold nanoparticles in the presence of Hcys, the assembly was shown to be dependent on the nature and concentration of the electrolytes, reflecting an effective screening of the diffuse layer around the initial citrate-capped nanoparticles that decreases the barrier to the Hcys adsorption onto the surface, and around the subsequent Hcys-capped nanoparticles that facilitate the zwitterion-type electrostatic interactions between amino acid groups of Hcys bound to different nanoparticles. A key element of the finding is that the interparticle zwitterion interaction of the Hcys-Au system is much stronger than the expectation for a simple Hcys or Au solution, a new phenomenon originating from the unique nanoscale interparticle interaction. The strength and reversibility of the interparticle zwitterion-type electrostatic interactions between amino acid groups are evidenced by the slow disassembly upon increasing pH at ambient temperatures and its acceleration at elevated temperature. These findings provide new insight into the precise control of interfacial interactions and reactivities between amino acids anchored to nanoparticles and have broad implications in the development of colorimetric nanoprobes for amino acids.     

Electroreduction activity of hydrogen peroxide on Pt and Au electrodes

Hydrogen peroxide electroreduction on both catalytically active Pt and inactive Au surfaces are studied by using both surface-enhanced Raman spectroscopy (SERS) and density functional theory (DFT) calculations. SERS measurements on Pt show the presence of Pt-OH at negative potentials, which suggests that hydroxide is formed as an intermediate during the electroreduction process. Additionally, the O-O stretch mode of H(2)O(2) is observed on Pt, which shifts to lower energy as potential is swept negatively, indicating that the O-O bond is elongated. For comparison, there is no variation in the energy of the same O-O mode on Au surfaces, and there is no observation of Au-OH. DFT calculations show that H(2)O(2) adsorption on Pt(110) results in the dissociation of O-O bond and the formation of Pt-OH bond. On Au, O-O bond elongation is calculated to occur only on the (110) face. However, the magnitude of the elongation is much smaller than that found on Pt(110).     

Photoluminescence of oxygen-deficient defects in germanium oxides: a quantum chemical study

The photoabsorption and photoluminescence (PL) properties of the surface E(') center, -GeX(3), and the combined E(')-center-oxygen vacancy, X(3)Ge-GeX(2), defects in substoichiometric germanium oxides have been investigated by high-level ab initio calculations, including complete active space self-consistent field, multireference configuration interaction, and symmetry-adapted cluster configuration interaction methods. Both defects have been shown to give rise to photoabsorption bands between 4 and 6 eV. Geometry relaxation is significant and the Stokes shifts are large for all calculated excited states. A removal of an electron from the Ge-Ge bond leads to its destruction, whereas the creation of an electron hole at lone pairs of O atoms results in elongations of the Ge-O-Ge bonds in the corresponding bridges. Most often, deexcitations of excited electronic states proceed radiationlessly, through crossing points of their potential energy surfaces with those of the lower states. The -GeX(3) defect is able to generate several PL bands in the UV ( approximately 3 eV) and IR (1.2-1.4 and 0.5-0.6 eV) spectral ranges, whereas the X(3)Ge-GeX(2) defect gives only one red/orange PL band at 2.0-2.1 eV. No intense PL band was found in the blue spectral region of 2.5-2.7 eV, and the two defects are not likely to contribute to the intense blue photoluminescence observed for GeO(2) nanowires.     

Adsorption of water on sodium chloride surfaces: electrostatics – guided ab initio studies

Water adsorption is studied on medium-sized clusters of sodium chloride representing (100) and (110) surfaces at the ab initio level. Topographical features of molecular electrostatic potential (MESP) have been employed for predicting the potent sites for binding of one to four water molecules on these surfaces. Such guess geometries are initially optimized using an electrostatics-based model, electrostatic potential for intermolecular complexation (EPIC) and further at the Hartree–Fock and B3LYP/6-31G(d, p) levels. The corresponding interaction energies are examined for assessing co-operative binding effects. The geometry and interaction energy of four water molecules adsorbed on NaCl(100) clearly brings out the co-operative binding among the water molecules. Further, water binding to (110) surface is stronger than that with (100) surface. This is also in confirmation with the electrostatic properties of (110) surface. Many-body decomposition analysis brings out the stronger interaction between NaCl clusters with water molecules vis-a-vis water–water interaction.     

Dual-scale modeling of benzene adsorption onto Ni(111) and Au(111) surfaces in explicit water.

We present a multiscale modeling approach for studying interactions of organic molecules with metal surfaces in explicit water. The approach is based on combining adsorption energies of isolated molecules on transition metal surfaces calculated by ab initio density functional methods and classical molecular dynamics simulations using atomistically detailed force fields. The interaction of benzene with Ni(111) and Au(111) surfaces was studied. It is shown that a strong affinity of water for the hydrophilic surfaces makes benzene adsorption on Au thermodynamically unfavorable, while on Ni there is no preference. The work presented here serves as a first step in modeling the interactions of larger organic molecules with metal surfaces.     

DFT study of gas-phase adsorption of benzotriazole on Cu(111), Cu(100), Cu(110), and low coordinated defects thereon

The adsorption of benzotriazole--an outstanding corrosion inhibitor for copper--on Cu(111), Cu(100), Cu(110), and low coordinated defects thereon has been studied and characterized using density functional theory (DFT) calculations. We find that benzotriazole can either chemisorb in an upright geometry or physisorb with the molecular plane being nearly parallel to the surface. While the magnitude of chemisorption energy increases as passing from densely packed Cu(111) to more open surfaces and low coordinated defects, the physisorption energy is instead rather similar on all three low Miller index surfaces. It is pointed out that due to a large dipole moment of benzotriazole the dipole-dipole interactions are rather important. For perpendicular chemisorption modes the lateral repulsion is very long ranged, extending up to the nearest-neighbor distance of about 60 bohrs, whereas for parallel adsorption modes the lateral interactions are far less pronounced and the molecules experience a weak attraction at distances ?25 bohrs. The chemisorption energies were therefore extrapolated to zero coverage by a recently developed scheme and the resulting values are -0.60, -0.73, and -0.92 eV for Cu(111), Cu(100), and Cu(110), respectively, whereas the zero-coverage physisorption energy is about -0.7 eV irrespective of the surface plane. While the more densely packed surfaces are not reactive enough to interact with the molecular π-system, the reactivity of Cu(110) appears to be at the onset of such interaction, resulting in a very stable parallel adsorption structure with an adsorption energy of -1.3 eV that is ascribed as an apparent chemisorption+physisorption mode.     

Filled and empty states of carbon nanotubes in water: Dependence on nanotube diameter, wall thickness and dispersion interactions

We have carried out a series of molecular dynamics simulations of water containing a narrow carbon nanotube as a solute to investigate the filling and emptying of the nanotube and also the modifications of the density and hydrogen bond distributions of water inside and also in the vicinity of the outer surfaces of the nanotube. Our primary goal is to look at the effects of varying nanotube diameter, wall thickness and also solute-solvent interactions on the solvent structure in the confined region also near the outer surfaces of the solute. The thickness of the walls is varied by considering single and multi-walled nanotubes and the interaction potential is varied by tuning the attractive strength of the 12–6 pair interaction potential between a carbon atom of the nanotubes and a water molecule. The calculations are done for many different values of the tuning parameter ranging from fully Lennard-Jones to pure repulsive pair interactions. It is found that both the solvation characteristics and hydrogen bond distributions can depend rather strongly on the strength of the attractive part of the solute-water interaction potential. The thickness of the nanotube wall, however, is found to have only minor effects on the density profiles, hydrogen bond network and the wetting characteristics. This indicates that the long range electrostatic interactions between water molecules inside and on the outer side of the nanotube do not make any significant contribution to the overall solvation structure of these hydrophobic solutes. The solvation characteristics are primarily determined by the balance between the loss of energy due to hydrogen bond network disruption, cavity repulsion potential and offset of the same by attractive component of the solute-water interactions. Our studies with different system sizes show that the essential features of wetting and dewetting characteristics of narrow nanotubes for different diameter and interaction potentials are also present in relatively smaller systems consisting of about five hundred molecules. We dedicate this work to Professor Debashis Mukherjee on his 60th Birthday.     

Theoretical study of the dynamics of AR collisions with C2H6 and C2F6 at hyperthermal energy

We present a classical-trajectory study of the dynamics of high-energy (5-12 eV) collisions between Ar atoms and the C2H6 and C2F6 molecules. We have constructed the potential-energy surfaces for these systems considering separately the Ar-molecule interactions (intermolecular potential) and the interactions within the molecule (intramolecular potential). The intermolecular surfaces consist of pairwise empirical potentials derived from high-accuracy ab initio calculations. The intramolecular potentials for C2H6 and C2F6 are described using specific-reaction-parameters semiempirical Hamiltonians and are calculated "on the fly", i.e., while the trajectories are evolving. Trajectory analysis shows that C2F6 absorbs more energy than C2H6 and is more susceptible to collision-induced dissociation (CID). C-C bond-breakage processes are more important than C-H or C-F bond breakage at the energies explored in this work. Analysis of the reaction mechanism for CID processes indicates that, although C-C breakage is mostly produced by side-on collisions, head-on collisions are more efficient in producing C-F or C-H dissociation. Our results suggest that high-energy collisions between closed-shell species of the natural low-Earth-orbit environment and spacecraft can contribute to the observed degradation of polymers that coat spacecraft surfaces.     

Adsorption of genetically engineered proteins studied by time‐of‐flight secondary ion mass spectrometry (TOF‐SIMS). Part A: data acquisition and principal component analysis (PCA)

Recent progress in the adaptation of combinatorial biology selection protocols to materials science has created a new class of polypeptides with specific affinity to inorganics. Here, we use one of the genetically engineered proteins, a gold binding protein (GBP‐1), to assess quantitatively its binding specificity to Au, Ag and Pd surfaces by using time‐of‐flight secondary ion mass spectroscopy (TOF‐SIMS). The GBP‐1, originally selected using cell‐surface display techniques, consisting of 14 amino acids with a sequence of MHGKTQATSGTIQS, was used in this study. Three‐repeat and single‐repeat forms of GBP‐1 were prepared. In earlier studies, GBP‐1 was shown to bind to Au particles and self‐assemble on flat Au surfaces. Through the fingerprint analysis of these specific peptides, their role in binding can be investigated in terms of their contribution to surface interaction possibly forming the right molecular architecture for binding. To achieve this purpose, a large‐sized data matrix produced by TOF‐SIMS must be properly treated for analysis. In Part A, we use principal component analysis (PCA) to visualize the spectral variations for a variety of adsorption conditions and suggest possible contribution of the specific types of amino acids (binding site) to the interactions. Copyright © 2007 John Wiley & Sons, Ltd.     

Effect of lattice-gas atoms on the adsorption behaviour of thioether molecules

Using STM topographic imaging and spectroscopy, we have investigated the adsorption of two thioether molecules, 1,2-bis(phenylthio)benzene and (bis(3-phenylthio)-phenyl)sulfane, on noble and transition metal surfaces. The two substrates show nearly antipodal behaviour. Whereas complexes with one or two protruding centres are observed on Au(111), only flat and uniform ad-structures are found on NiAl(110). The difference is ascribed to the possibility of the thioethers to form metal-organic complexes by coordinating lattice-gas atoms on the Au(111), while only the pristine molecules adsorb on the alloy surface. The metal coordination in the first case is driven by the formation of strong Au-S bonds and enables the formation of characteristic monomer, dimer and chain-like structures of the thioethers, using the Au atoms as linkers. A similar mechanism is not available on the NiAl, because no lattice gas develops at this surface at room temperature. Our work demonstrates how surface properties, i.e. the availability of mobile ad-species, determine the interaction of organic molecules with metallic substrates.     

Water‐mediated Spectral Shifts in Rhodopsin and Bathorhodopsin†

The role of water molecules in spectral tuning of proteins has been left largely unexplored. This topic is important because changing hydrogen bond patterns during the activation process may lead to spectral shifts which can be of diagnostic value for the underlying structures. Arguments put forward in this article are based on spectral shift calculations of the rhodopsin and bathorhodopsin chromophore due to wat2a and 2b in the presence and absence of the counterion and of the amino acids lining the rhodopsin binding pocket. They show, among others, that a single water molecule can shift the absorbance by up to 0.1 eV or 34 nm depending on the environment of the chromophore.