Mechanism of Daunomycin Intercalation into DNA from Enhanced Sampling Simulations.

Daunomycin is a widely used anticancer drug, yet the mechanism underlying how it binds to DNA remains contested. 469 all-atom trajectories of daunomycin binding to the DNA oligonucleotide d(GCG CAC GTG CGC) were collected using weighted ensemble (WE)-enhanced sampling. Mechanistic insights were revealed through analysis of the ensemble of trajectories. Initially, the binding process involves a ubiquitous hydrogen bond between the DNA backbone and the NH3+ group on daunomycin. During the binding process, most trajectories exhibited similar structural changes to DNA, including DNA base pair rise, bending, and minor groove width changes. Variability within the ensemble of binding trajectories illuminates differences in the orientation of daunomycin as it initially intercalates; around 10% of trajectories needed minimal rearrangement from intercalation to reaching the fully bound configuration, whereas most needed an additional 1-5 ns to rearrange. The results here emphasize the utility of generating an ensemble of trajectories to discern biomolecular binding mechanisms.

Molecular Mechanism of Ligand Binding to the Minor Groove of DNA.

Although DNA-ligand binding is pervasive in biology, little is known about molecular-level binding mechanisms. Using all-atom, explicit-solvent molecular dynamics simulations in conjunction with weighted ensemble (WE)-enhanced sampling, an ensemble of 2562 binding trajectories of Hoechst 33258 (H33258) to d(CGC AAA TTT GCG) was generated from which the binding mechanism was extracted. In particular, the electrostatic interaction between the positively charged H33258 and the negatively charged DNA backbone drives the formation of initial H33258-DNA contacts. After this initial contact, a hinge-like intermediate state is formed in which one end of H33258 inserts into the minor groove of DNA. Following hinge state formation is a concerted motion whereby the second end of H33258 swings into the minor groove and the spine of hydration along the minor groove causing dehydration. This study illustrates how WE-enhanced simulations of biomolecular ligation processes can offer novel mechanistic insights by generating ensembles of binding events.

Decompositions of Solvent Response Functions in Ionic Liquids: A Direct Comparison of Equilibrium and Nonequilibrium Methodologies.

Time-dependent Stokes shift (TDSS) measurements provide crucial insights into the dynamics of liquids. The interpretation of TDSS measurements is often aided by molecular dynamics simulations, where solvent response functions are computed either with an equilibrium or nonequilibrium approach. In the nonequilibrium approach, the solvent is at equilibrium with the ground electronic state of the solute and its charge distribution is instantaneously changed to that of the first excited state. The solvation response function is then calculated as a nonequilibrium average of the subsequent evolution of the solvent influence on the electronic energy gap. In the equilibrium approach, the normalized time correlation function of the fluctuations of the solvent-perturbed electronic energy gap is calculated. If the linear response approximation is valid, then the nonequilibrium solvation response function is identical to the equilibrium time correlation function. The nonequilibrium methodology conceptually mimics the experiment, but it is significantly more computationally expensive than the equilibrium approach. In multicomponent systems such as ionic liquids, it is natural to inquire how the various components affect the observed relaxation dynamics. When utilizing the nonequilibrium methodology, the solvation response naturally decomposes into a sum of responses for each component present in the system. However, the equilibrium time correlation function does not decompose unambiguously. Here, we have evaluated a decomposition strategy that is consistent with the linear response approximation for the study of solvation dynamics of coumarin 153 (C153) in the 1-ethyl-3-methyl imidazolium tetrafluoroborate, [emim][BF4], ionic liquid. The agreement of the equilibrium and nonequilibrium solvation response functions demonstrates the validity of the linear response approximation for the C153/[emim][BF4] system. Moreover, decompositions of the equilibrium time correlation function into contributions of the translational and rovibrational motions of the anions and cations are essentially identical to the same decompositions of the nonlinear solvation response.

Nonadiabatic transition path sampling.

Fewest-switches surface hopping (FSSH) is combined with transition path sampling (TPS) to produce a new method called nonadiabatic path sampling (NAPS). The NAPS method is validated on a model electron transfer system coupled to a Langevin bath. Numerically exact rate constants are computed using the reactive flux (RF) method over a broad range of solvent frictions that span from the energy diffusion (low friction) regime to the spatial diffusion (high friction) regime. The NAPS method is shown to quantitatively reproduce the RF benchmark rate constants over the full range of solvent friction. Integrating FSSH within the TPS framework expands the applicability of both approaches and creates a new method that will be helpful in determining detailed mechanisms for nonadiabatic reactions in the condensed-phase.

Thermal equilibrium properties of surface hopping with an implicit Langevin bath.

The ability of fewest switches surface hopping (FSSH) approach, where the classical degrees of freedom are coupled to an implicit Langevin bath, to establish and maintain an appropriate thermal equilibrium was evaluated in the context of a three site model for electron transfer. The electron transfer model consisted of three coupled diabatic states that each depends harmonically on the collective bath coordinate. This results in three states with increasing energy in the adiabatic representation. The adiabatic populations and distributions of the collective solvent coordinate were monitored during the course of 250 ns FSSH-Langevin (FSSH-L) simulations performed at a broad range of temperatures and for three different nonadiabatic coupling strengths. The agreement between the FSSH-L simulations and numerically exact results for the adiabatic population ratios and solvent coordinate distributions was generally favorable. The FSSH-L method produces a correct Boltzmann distribution of the solvent coordinate on each of the adiabats, but the integrated populations are slightly incorrect because FSSH does not rigorously obey detailed balance. The overall agreement is better at high temperatures and for high nonadiabatic coupling, which agrees with a previously reported analytical and simulation analysis [J. R. Schmidt, P. V. Parandekar, and J. C. Tully, J. Chem. Phys. 129, 044104 (2008)] on a two-level system coupled to a classical bath.

Computational Study of Phosphate Vibrations as Reporters of DNA Hydration.

The sensitivity of the phosphate asymmetric stretch vibrational frequency to DNA hydration was investigated with molecular dynamics (MD) simulations and a spectroscopic map relating the vibrational frequency to the electrostatics of its environment. 95% of the phosphate vibrational frequency shift in fully hydrated DNA was due to water within two hydration layers. The phosphate vibration was relatively insensitive to water in the major and minor grooves and to the sodium counterions but was enormously sensitive to water interacting with the DNA backbone. Comparisons to experimental measurements on DNA as a function of relative humidity suggest that one water molecule per phosphate group likely persists at the lowest values of the relative humidity. Finally, the calculated spectral diffusion dynamics show that water in the vicinity of the DNA backbone is slowed by a factor of ∼5, in agreement with NMR and solvation dynamics experiments, as well as previous MD simulations.

Molecular dynamics investigation of the vibrational spectroscopy of isolated water in an ionic liquid.

Experimental studies examining the structure and dynamics of water in ionic liquids (ILs) have revealed local ion rearrangements that occur an order of magnitude faster than complete randomization of the liquid structure. Simulations of an isolated water molecule embedded in 1-butyl-3-methyl imidazolium hexafluorophosphate, [bmim][PF6], were performed to shed insight into the nature of these coupled water-ion dynamics. The theoretical calculations of the spectral diffusion dynamics and the infrared absorption spectra of the OD stretch of isolated HOD in [bmim][PF6] agree well with experiment. The infrared absorption line shape of the OD stretch is narrower and blue-shifted in the IL compared to those in aqueous solution. Decomposition of the OD frequency time correlation function revealed that translational motions of the anions dominate the spectral diffusion dynamics.

On the mechanism of solvation dynamics in imidazolium-based ionic liquids.

Experimental studies of solvation dynamics in imidazolium-based ionic liquids (ILs) have revealed complex kinetics over a broad range of time scales from femtoseconds to tens of nanoseconds. Microsecond-length molecular dynamics (MD) simulations of coumarin 153 (C153) in 1-ethyl-3-methyl imidazolium tetrafluoroborate, [emim][BF4], were performed to reveal the molecular-level mechanism for solvation dynamics in imidazolium-based ILs over the full range of time scales accessed in the experiments. The solvation response of C153 in [emim][BF4] compared favorably with experiment. An analysis of the structure of the IL in the vicinity of the C153 dye revealed preferential solvation by the [emim] cations. Despite this observation, decomposition of the solvation response into components from the anions and cations and also from translational and rotational motions shows that translations of the [BF4] anions are the dominant contributor to solvation dynamics. The kinetics for the translation of the [BF4] anions into and out of the first solvation shell of the dye were found to mimic the kinetic profile of the solvation dynamics response. This mechanism for solvation dynamics contrasts dramatically with conventional polar liquids in which solvent rotations are generally responsible for the response.

Monitoring Intramolecular Proton Transfer with Two-Dimensional Infrared Spectroscopy: A Computational Prediction.

Proton transfer processes are ubiquitous and play a vital role in a broad range of chemical and biochemical phenomena. The ability of two-dimensional infrared (2D IR) spectroscopy with a carbon-deuterium (C-D) reporter to monitor the kinetics of proton transfer in the model compound malonaldehyde was demonstrated computationally. One of the two carbonyl/enol carbon atoms in malonaldehyde was labeled with a C-D bond. The C-D stretch vibrational frequency provides ∼150 cm(-1) of sensitivity to the two tautomers of malonaldehyde. Mixed quantum mechanics/molecular mechanics simulations employing the self-consistent-charge density functional tight binding (SCC-DFTB) method were used to compute 2D IR line shapes for the C-D stretch of labeled malonaldehyde in aqueous solution. The 2D IR spectra reveal cross peaks from the chemical exchange of the proton. The kinetics for the growth of the cross-peaks (and the decay of the diagonal peaks) precisely match the proton transfer rate observed in the SCC-DFTB simulations.

Collective hydrogen bond reorganization in water studied with temperature-dependent ultrafast infrared spectroscopy.

We use temperature-dependent ultrafast infrared spectroscopy of dilute HOD in H(2)O to study the picosecond reorganization of the hydrogen bond network of liquid water. Temperature-dependent two-dimensional infrared (2D IR), pump-probe, and linear absorption measurements are self-consistently analyzed with a response function formalism that includes the effects of spectral diffusion, population lifetime, reorientational motion, and nonequilibrium heating of the local environment upon vibrational relaxation. Over the range 278-345 K, we find the time scales of spectral diffusion and reorientational relaxation decrease from approximately 2.4 to 0.7 ps and 4.6 to 1.2 ps, respectively, which corresponds to barrier heights of 3.4 and 3.7 kcal/mol, respectively. We compare the temperature dependence of the time scales to a number of measures of structural relaxation and find similar effective activation barrier heights and slightly non-Arrhenius behavior, which suggests that the reaction coordinate for the hydrogen bond rearrangement in water is collective. Frequency and orientational correlation functions computed from molecular dynamics (MD) simulations over the same temperature range support our interpretations. Finally, we find the lifetime of the OD stretch is nearly the same from 278 K to room temperature and then increases as the temperature is increased to 345 K.

Effects of an unnatural base pair replacement on the structure and dynamics of DNA and neighboring water and ions.

Incorporating small molecule probes into biomolecular systems to report on local structure and dynamics is a powerful strategy that underlies a wide variety of experimental techniques, including fluorescence, electron paramagnetic resonance (EPR), and Forster resonance energy transfer (FRET) measurements. When an unnatural probe is inserted into a protein or DNA, the degree to which the presence of the probe has perturbed the local structure and dynamics it was intended to study is always an important concern. Here, molecular dynamics (MD) simulations are used to systematically study the effect of replacing a DNA base pair with a fluorescent probe, coumarin 102 deoxyriboside, at six unique sites along an A-tract DNA dodecamer. While the overall structure of the DNA oligonucleotide remains intact, replacement of A*T base pairs leads to widespread structural and dynamic perturbations up to four base pairs away from the probe site, including widening of the minor groove and increased DNA flexibility. New DNA conformations, not observed in the native sequence, are sometimes found in the vicinity of the probe and its partner abasic site analog. Strong correlations are demonstrated between DNA surface topology and water mobility.

Carbon-deuterium vibrational probes of the protonation state of histidine in the gas-phase and in aqueous solution.

The protonation state of ionizable residues is an important contributor to protein stability and function. Histidine is of particular importance because its side chain pK(a) is near physiological pH. The sensitivity of carbon deuterium (C-D) vibrational frequencies to the protonation state of histidine dipeptide (Hdp) was investigated in the gas-phase using density functional theory (DFT) calculations, and in aqueous solution using two-layered integrated molecular orbital and molecular mechanics (ONIOM) calculations. All three C-D vibrational probes on the side chain (C(beta)-D(2), C(delta)-D, and C(epsilon)-D) independently exhibited a striking sensitivity to the gas-phase histidine protonation state, with calculated shifts of up to 40 cm(-1) upon deprotonation of the histidine residue. Simultaneously including all three C-D vibrational probes on the Hdp side chain produced significant shifts of 28 to 43 cm(-1) between the neutral and charged states. The calculated intensities also dropped precipitously upon deprotonation, which is an important factor for the interpretation of experiments employing C-D vibrational probes to investigate side chain protonation. Solvating the labeled Hdp molecule produces an overall blue-shift in the average C-D vibrational frequencies relative to the gas-phase. The C(beta)-D(2), C(delta)-D, and C(epsilon)-D vibrational probes all showed sensitivity to the histidine protonation state, with shifts of up to 40 cm(-1) in the mean frequencies after deprotonation, which bodes well for studies employing C-D probes to study histidine protonation state in peptides and proteins.

Bulk and Surface Properties of Rutile TiO2 from Self-Consistent-Charge Density Functional Tight Binding.

Bulk rutile TiO2 and its (110) surface have been investigated with a computationally efficient semiempirical tight binding method: self-consistent-charge density functional tight binding (SCC-DFTB). Comparisons of energetic, mechanical, and electronic properties are made to density functional theory (DFT) and to experiment to characterize the accuracy of SCC-DFTB for bulk rutile TiO2 and TiO2(110). Despite the fact that the SCC-DFTB parameters for Ti, Ti-Ti, and Ti-O were developed in the context of small biologically relevant Ti containing compounds, SCC-DFTB predicts many properties of bulk TiO2 and the TiO2(110) surface with accuracy similar to local and gradient-corrected DFT. In particular, SCC-DFTB predicts a direct band gap of TiO2 of 2.46 eV, which is in better agreement with experiment, 3.06 eV, than DFT utilizing the local density approximation (LDA), 2.0 eV. SCC-DFTB also performs similar in terms of accuracy as LDA-DFT for the phonon frequencies of the bulk lattice and for the relaxed geometry of the TiO2(110) surface. SCC-DFTB does, however, overestimate the surface energy of TiO2(110) compared to LDA-DFT. Nevertheless, the overall accuracy of SCC-DFTB, which is substantially more computationally efficient than DFT, is encouraging for bulk rutile TiO2 and TiO2(110).

Carbon-deuterium vibrational probes of amino acid protonation state.

The protonation state of titratable amino acid residues has profound effects on protein stability and function. Therefore, correctly determining the acid dissociation constant, pK(a), of charged residues under physiological conditions is an important challenge. The general utility of site-specific carbon-deuterium (C-D) vibrational probes as reporters of the protonation state of arginine, aspartic acid, glutamic acid, and lysine amino acid side chains was examined using density functional theory (DFT) calculations. Substantial shifts were observed in the anharmonic vibrational frequencies of a C-D(2) probe placed immediately adjacent to the titratable group. Lysine exhibited the largest C-D(2) frequency shifts upon protonation, 44.9 cm(-1) (symmetric stretch) and 69.5 cm(-1) (asymmetric stretch). Furthermore, the predicted harmonic intensities of the C-D(2) probe vibrations were extraordinarily sensitive to the protonation state of the nearby acidic or basic group. Accounting for this dramatic change in intensity is essential to the interpretation of an infrared (IR) absorption spectrum that contains the signature of both the neutral and charged states.

Carbon-deuterium vibrational probes of peptide conformation: alanine dipeptide and glycine dipeptide.

The utility of alpha-carbon deuterium-labeled bonds (C(alpha)-D) as infrared reporters of local peptide conformation was investigated for two model dipeptide compounds: C(alpha)-D labeled alanine dipeptide (Adp-d(1)) and C(alpha)-D(2) labeled glycine dipeptide (Gdp-d(2)). These model compounds adopt structures that are analogous to the motifs found in larger peptides and proteins. For both Adp-d(1) and Gdp-d(2), we systematically mapped the entire conformational landscape in the gas phase by optimizing the geometry of the molecule with the values of phi and psi, the two dihedral angles that are typically used to characterize the backbone structure of peptides and proteins, held fixed on a uniform grid with 7.5 degrees spacing. Since the conformations were not generally stationary states in the gas phase, we then calculated anharmonic C(alpha)-D and C(alpha)-D(2) stretch transition frequencies for each structure. For Adp-d(1) the C(alpha)-D stretch frequency exhibited a maximum variability of 39.4 cm(-1) between the six stable structures identified in the gas phase. The C(alpha)-D(2) frequencies of Gdp-d(2) show an even more substantial difference between its three stable conformations: there is a 40.7 cm(-1) maximum difference in the symmetric C(alpha)-D(2) stretch frequencies and an 81.3 cm(-1) maximum difference in the asymmetric C(alpha)-D(2) stretch frequencies. Moreover, the splitting between the symmetric and asymmetric C(alpha)-D(2) stretch frequencies of Gdp-d(2) is remarkably sensitive to its conformation.

Infrared absorption line shapes in the classical limit: a comparison of the classical dipole and fluctuating frequency approximations.

Infrared spectroscopy is a versatile technique for probing the structure and dynamics of condensed-phase systems. Simulating infrared absorption spectra with molecular dynamics (MD) offers a powerful means to establish a molecular-level interpretation of experimental results, as well as a basis for the parametrization of more accurate simulation force-fields. Two distinct methods for the calculation of infrared absorption line shapes of high-frequency (Planck's omega/k(B)T>>1) vibrational probes from MD simulations are examined: The classical dipole approximation (CDA) and the fluctuating frequency approximation (FFA). Although these two formalisms result in expressions for the infrared absorption line shape that appear very different, both approximations are shown to yield identical results for the infrared line shape of a harmonic system in the condensed-phase. The equivalence of the FFA and CDA is also demonstrated in the case where the transition dipole of the oscillator fluctuates in response to the environment (i.e., where the Condon approximation has been relaxed). Finally we examine the effects of solute anharmonicity and demonstrate that the CDA and FFA are not equivalent in general, and the magnitude of the deviations increases with anharmonicity. We conclude that the calculation of infrared absorption line shapes via the CDA is a promising alternative to the FFA approach in cases where it may be difficult or undesirable to employ the latter, particularly when the effects of anharmonicity are small.

Approaches for the calculation of vibrational frequencies in liquids: comparison to benchmarks for azide/water clusters.

Ultrafast vibrational spectroscopy experiments, together with molecular-level theoretical interpretation, can provide important information about the structure and dynamics of complex condensed phase systems, including liquids. The theoretical challenge is to calculate the instantaneous vibrational frequencies of a molecule in contact with a molecular environment, accurately and quickly, and to this end a number of different methods have been developed. In this paper we critically analyze these different methods by comparing their results to accurate benchmark calculations on azide/water clusters. We also propose an optimized quantum mechanics/molecular mechanics method, which for this problem is superior to the other methods.

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.

Infrared and Raman line shapes of dilute HOD in liquid H2O and D2O from 10 to 90 degrees C.

A combined electronic structure/molecular dynamics approach was used to calculate infrared and isotropic Raman spectra for the OH or OD stretches of dilute HOD in D2O or H2O, respectively. The quantities needed to compute the infrared and Raman spectra were obtained from density functional theory calculations performed on clusters, generated from liquid-state configurations, containing an HOD molecule along with 4-9 solvent water molecules. The frequency, transition dipole, and isotropic transition polarizability were each empirically related to the electric field due to the solvent along the OH (or OD) bond, calculated on the H (or D) atom of interest. The frequency and transition dipole moment of the OH (or OD) stretch of the HOD molecule were found to be very sensitive to its instantaneous solvent environment, as opposed to the isotropic transition polarizability, which was found to be relatively insensitive to environment. Infrared and isotropic Raman spectra were computed within a molecular dynamics simulation by using the empirical relationships and semiclassical expressions for the line shapes. The line shapes agree well with experiment over a temperature range from 10 to 90 degrees C.

Dynamics of water probed with vibrational echo correlation spectroscopy.

Vibrational echo correlation spectroscopy experiments on the OD stretch of dilute HOD in H(2)O are used to probe the structural dynamics of water. A method is demonstrated for combining correlation spectra taken with different infrared pulse bandwidths (pulse durations), making it possible to use data collected from many experiments in which the laser pulse properties are not identical. Accurate measurements of the OD stretch anharmonicity (162 cm(-1)) are presented and used in the data analysis. In addition, the recent accurate determination of the OD vibrational lifetime (1.45 ps) and the time scale for the production of vibrational relaxation induced broken hydrogen bond "photoproducts" ( approximately 2 ps) aid in the data analysis. The data are analyzed using time dependent diagrammatic perturbation theory to obtain the frequency time correlation function (FTCF). The results are an improved FTCF compared to that obtained previously with vibrational echo correlation spectroscopy. The experimental data and the experimentally determined FTCF are compared to calculations that employ a polarizable water model (SPC-FQ) to calculate the FTCF. The SPC-FQ derived FTCF is much closer to the experimental results than previously tested nonpolarizable water models which are also presented for comparison.