An Excited State Density Functional Theory Study of the Rhodopsin Chromophore

An Overview of Molecular Modeling for Drug Discovery with Specific Illustrative Examples of Applications

In this paper we review the current status of high-performance computing applications in the general area of drug discovery. We provide an introduction to the methodologies applied at atomic and molecular scales, followed by three specific examples of implementation of these tools. The first example describes in silico modeling of the adsorption of small molecules to organic and inorganic surfaces, which may be applied to drug delivery issues. The second example involves DNA translocation through nanopores with major significance to DNA sequencing efforts. The final example offers an overview of computer-aided drug design, with some illustrative examples of its usefulness.

Anti-stokes Raman study of vibrational cooling dynamics in the primary photochemistry of rhodopsin

Picosecond Stokes and anti-Stokes Raman spectra are used to probe the structural dynamics and reactive energy flow in the primary cis-to-trans isomerization reaction of rhodopsin. The appearance of characteristic ethylenic, hydrogen out-of-plane (HOOP), and low-wavenumber photoproduct bands in the Raman spectra is instrument-response-limited, consistent with a subpicosecond product appearance time. Intense high and low-frequency anti-Stokes peaks demonstrate that the all-trans photoproduct is produced vibrationally hot on the ground-state surface. Specifically, the low-frequency modes at 282, 350, and 477 cm(-1) are highly vibrationally excited (T > 2000 K) immediately following isomerization, revealing that these low-frequency motions directly participate in the reactive curve-crossing process. The anti-Stokes modes are characterized by a approximately 2.5 ps temporal decay that coincides with the conversion of photorhodopsin to bathorhodopsin. This correspondence shows that the photo-to-batho transition is a ground-state cooling process and that energy storage in the primary visual photoproduct is complete on the picosecond time scale. Finally, unique Stokes vibrations at 290, 992, 1254, 1290, and 1569 cm(-1) arising from the excited state of rhodopsin are observed only at 0 ps delay.

FIRST PRINCIPLES MOLECULAR DYNAMICS INVOLVING EXCITED STATES AND NONADIABATIC TRANSITIONS

Extensions of traditional molecular dynamics to excited electronic states and non-Born–Oppenheimer dynamics are reviewed focusing on applicability to chemical reactions of large molecules, possibly in condensed phases. The latter imposes restrictions on both the level of accuracy of the underlying electronic structure theory and the treatment of nonadiabaticity. This review, therefore, exclusively deals with ab initio "on the fly" molecular dynamics methods. For the same reason, mainly mixed quantum-classical approaches to nonadiabatic dynamics are considered.

Solvent Effects on the Low-Lying Excited States of a Model of Retinal

The low-lying excited states of a solution in alcohol of a five-double-bond model of the rhodopsin protein chromophore, the protonated 11-cis-retinal Schiff base (PSB11), are studied theoretically. We combine a multireference perturbational treatment in the description of the solute molecule with molecular dynamics calculations in the description of the solvent. The geometry, charge distribution, and electronic spectra are strongly influenced by the solvent. The solvent shift values show a marked dependence on the use of relaxed geometries in solution and on the nature of the states involved in the excitation process. The dynamic correlation has a strong effect on the order of the excited states. In solution, the first two excited states almost become degenerate.

Solvent and Protein Effects on the Structure and Dynamics of the Rhodopsin Chromophore

The structure and dynamics of the retinal chromophore of rhodopsin are investigated systematically in different environments (vacuum, methanol solution, and protein binding pocket) and with different computational approaches (classical, quantum, and hybrid quantum mechanics/molecular mechanics (QM/MM) descriptions). Finite temperature effects are taken into account by molecular dynamics simulations. The different components that determine the structure and dynamics of the chromophore in the protein are dissected, both in the dark state and in the early photointermediates. In vacuum and in solution the chromophore displays a very high flexibility, which is significantly reduced by the protein environment. In the 11-cis chromophore, the bond-length alternation, which is correlated with the dipole moment, is found to be similar in solution and in the protein, while it differs greatly with respect to minimum-energy vacuum structures. In the model of the earliest protein photointermediate, the highly twisted chromophore shows a very reduced bond-length alternation.

IntroducingONETEP: Linear-scaling density functional simulations on parallel computers

We present ONETEP (order-N electronic total energy package), a density functional program for parallel computers whose computational cost scales linearly with the number of atoms and the number of processors. ONETEP is based on our reformulation of the plane wave pseudopotential method which exploits the electronic localization that is inherent in systems with a nonvanishing band gap. We summarize the theoretical developments that enable the direct optimization of strictly localized quantities expressed in terms of a delocalized plane wave basis. These same localized quantities lead us to a physical way of dividing the computational effort among many processors to allow calculations to be performed efficiently on parallel supercomputers. We show with examples that ONETEP achieves excellent speedups with increasing numbers of processors and confirm that the time taken by ONETEP as a function of increasing number of atoms for a given number of processors is indeed linear. What distinguishes our approach is that the localization is achieved in a controlled and mathematically consistent manner so that ONETEP obtains the same accuracy as conventional cubic-scaling plane wave approaches and offers fast and stable convergence. We expect that calculations with ONETEP have the potential to provide quantitative theoretical predictions for problems involving thousands of atoms such as those often encountered in nanoscience and biophysics.

QM/MM study of energy storage and molecular rearrangements due to the primary event in vision

The energy storage and the molecular rearrangements due to the primary photochemical event in rhodopsin are investigated by using quantum mechanics/molecular mechanics hybrid methods in conjunction with high-resolution structural data of bovine visual rhodopsin. The analysis of the reactant and product molecular structures reveals the energy storage mechanism as determined by the detailed molecular rearrangements of the retinyl chromophore, including rotation of the (C11-C12) dihedral angle from -11 degrees in the 11-cis isomer to -161 degrees in the all-trans product, where the preferential sense of rotation is determined by the steric interactions between Ala-117 and the polyene chain at the C13 position, torsion of the polyene chain due to steric constraints in the binding pocket, and stretching of the salt bridge between the protonated Schiff base and the Glu-113 counterion by reorientation of the polarized bonds that localize the net positive charge at the Schiff-base linkage. The energy storage, computed at the ONIOM electronic-embedding approach (B3LYP/6-31G*:AMBER) level of theory and the S0-->S1 electronic-excitation energies for the dark and product states, obtained at the ONIOM electronic-embedding approach (TD-B3LYP/6-31G*//B3LYP/6-31G*:AMBER) level of theory, are in very good agreement with experimental data. These results are particularly relevant to the development of a first-principles understanding of the structure-function relations in prototypical G-protein-coupled receptors.

Photodissociation of diiodomethane in acetonitrile solution and fragment recombination into iso-diiodomethane studied with ab initio molecular dynamics simulations

Photodissociation of diiodomethane (CH2I2) in acetonitrile solution has been studied with ab initio molecular dynamics simulations, which show how the iso-diiodomethane photoproduct (CH2I-I) can be formed. The first excited state, described by the "restricted open-shell Kohn-Sham" density functional method, is dissociative and photoexcitation of diiodomethane induces a breaking of one of the C-I bonds. In the simulations, we observe that energy dissipation to the surrounding solvent is essential in the formation of a stable iso-diiodomethane molecule. The caging effect of the solvent results in a recombination of the CH2I and I fragments into iso-diiodomethane on a picosecond time scale. The molecular dynamics simulations enable us to study the cage effect as well as the relaxation of intermediates and the distribution of energy. The CH2I fragment is formed vibrationally excited along the C-I stretching mode. After recombination of the CH2I and I fragments, iso-diiodomethane shows a strong vibration excitation in the CH2 group, which could be used as a fingerprint of the proposed mechanism.

Patterns of retinal light absorption related to retinitis pigmentosa mutants from in silico model structures of rhodopsin

Changes induced by mutations in rhodopsin that are associated with the degenerative visual disease retinitis pigmentosa result in an altered pattern of light absorption according to quantum mechanical simulations and reference experimental works. Eleven single-point mutations associated with retinitis pigmentosa at and in the proximity to the retinal binding pocket of rhodopsin have been modeled in silico and their spectra calculated with the NDOL (Neglect of Differential Overlap accounting L azimuthal quantum number) a priori method. The altered pattern of absorption found would lead to cumulative consequences in energy dissipation with aging. Different energy balances in the case of mutants at the very molecular level, compared to native nonmutated rhodopsin, can cause permanent cellular stress and would play a role in the progression of the retine degenerative process. It could explain the worsening of the pathological condition mostly in adults and suggests the probable beneficial effects of using quenching drugs and protection devices against excess of light in the early stages of life for avoiding or reducing potential damage.

A global investigation of excited state surfaces within time-dependent density-functional response theory

This work investigates the capability of time-dependent density functional response theory to describe excited state potential energy surfaces of conjugated organic molecules. Applications to linear polyenes, aromatic systems, and the protonated Schiff base of retinal demonstrate the scope of currently used exchange-correlation functionals as local, adiabatic approximations to time-dependent Kohn-Sham theory. The results are compared to experimental and ab initio data of various kinds to attain a critical analysis of common problems concerning charge transfer and long range (nondynamic) correlation effects. This analysis goes beyond a local investigation of electronic properties and incorporates a global view of the excited state potential energy surfaces.

Analysis of the mode-specific excited-state energy distribution and wavelength-dependent photoreaction quantum yield in rhodopsin

The photoreaction quantum yield of rhodopsin is wavelength dependent: phi(lambda) is reduced by up to 5% at wavelengths to the red of 500 nm but is invariant (phi = 0.65 +/- 0.01) between 450 and 500 nm (Kim et al., 2001). To understand this nonstatistical internal conversion process, these results are compared with predictions of a Landau-Zener model for dynamic curve crossing. The initial distribution of excess photon energy in the 28 Franck-Condon active vibrational modes of rhodopsin is defined by a fully thermalized sum-over-states vibronic calculation. This calculation reveals that absorption by high-frequency unreactive modes (e.g., C[double bond]C stretches) increases as the excitation wavelength is shifted from 570 to 450 nm whereas relatively less energy is deposited into reactive low-frequency modes. This result qualitatively explains the experimentally observed wavelength dependence of phi(lambda) for rhodopsin and reveals the importance of delocalized, torsional modes in the reactive pathway.

Early steps of the intramolecular signal transduction in rhodopsin explored by molecular dynamics simulations

We present molecular dynamics simulations of bovine rhodopsin in a membrane mimetic environment based on the recently refined X-ray structure of the pigment. The interactions between the protonated Schiff base and the protein moiety are explored both with the chromophore in the dark-adapted 11-cis and in the photoisomerized all-trans form. Comparison of simulations with Glu181 in different protonation states strongly suggests that this loop residue located close to the 11-cis bond bears a negative charge. Restrained molecular dynamics simulations also provide evidence that the protein tightly confines the absolute conformation of the retinal around the C12-C13 bond to a positive helicity. 11-cis to all-trans isomerization leads to an internally strained chromophore, which relaxes after a few nanoseconds by a switching of the ionone ring to an essentially planar all-trans conformation. This structural transition of the retinal induces in turn significant conformational changes of the protein backbone, especially in helix VI. Our results suggest a possible molecular mechanism for the early steps of intramolecular signal transduction in a prototypical G-protein-coupled receptor.

Ab initio molecular dynamics with density functional theory

Recent applications of density functional theory base ab initio molecular dynamics in chemical relevant systems are reviewed. The emphasis is on the dynamical aspect in the study of structures, reaction mechanisms, and electronic properties in both the molecular and condensed phases. Examples were chosen from fluxional molecules, solution reactions, and biological systems to illustrate the broad potential applications and unique information that can be obtained from ab initio molecular dynamics calculations. Recent advances in the development of efficient numerical algorithms for the prediction of spectroscopic properties are highlighted.

A semiempirical study of the optimized ground and excited state potential energy surfaces of retinal and its protonated Schiff base

The electronic ground and first excited states of retinal and its Schiff base are optimized for the first time using the semiempirical AM1 Hamiltonian. The barrier for rotation about the C(11)-C(12) double bond is characterized by variation of both the twist angle delta(C(10)-C(11)-C(12)-C(13)) and the bond length d(C(11)-C(12)). The potential energy surface is obtained by varying these two parameters. The calculated ground state rotational barrier is equal to 15.6 kcal/mol for retinal and 20.5 kcal/mol for its Schiff base. The all-trans conformation is more stable by 3.7 kcal/mol than the 11-cis geometry. For the first excited state, S(1,) the 90 degrees twisted geometry represents a saddle point for retinal with the rotational barrier of 14.6 kcal/mol. In contrast, this conformation is an energy minimum for the Schiff base. It can be easily reached at room temperature from the planar minima since it is separated from them by a barrier of only 0.6 kcal/mol. The 90 degrees minimum conformation is more stable than the all-trans by 8.6 kcal/mol. We are thus able to present a reaction path on the S(1) surface of the retinal Schiff base with an almost barrier-less geometrical relaxation into a twisted minimum geometry, as observed experimentally. The character of the ground and first excited singlet states underscores the need for the inclusion of double excitations in the calculations.

The rational of catalytic activity of herpes simplex virus thymidine kinase. a combined biochemical and quantum chemical study

Most antiherpes therapies exploit the large substrate acceptance of herpes simplex virus type 1 thymidine kinase (TK(HSV1)) relative to the human isoenzyme. The enzyme selectively phosphorylates nucleoside analogs that can either inhibit viral DNA polymerase or cause toxic effects when incorporated into viral DNA. To relate structural properties of TK(HSV1) ligands to their chemical reactivity we have carried out ab initio quantum chemistry calculations within the density functional theory framework in combination with biochemical studies. Calculations have focused on a set of ligands carrying a representative set of the large spectrum of sugar-mimicking moieties and for which structural information of the TK(HSV1)-ligand complex is available. The k(cat) values of these ligands have been measured under the same experimental conditions using an UV spectrophotometric assay. The calculations point to the crucial role of electric dipole moment of ligands and its interaction with the negatively charged residue Glu(225). A striking correlation is found between the energetics associated with this interaction and the k(cat) values measured under homogeneous conditions. This finding uncovers a fundamental aspect of the mechanism governing substrate diversity and catalytic turnover and thus represents a significant step toward the rational design of novel and powerful prodrugs for antiviral and TK(HSV1)-linked suicide gene therapies.