Quantum Dynamics of Oblique Vibrational States in the Hénon-Heiles System.

In this paper, we study the quantum time evolution of oblique nonstationary vibrational states in a Hénon-Heiles oscillator system with two dissociation channels, which models the stretching vibrational motions of triatomic molecules. The oblique nonstationary states we are interested in are the eigenfunctions of the anharmonic zero-order Hamiltonian operator resulting from the transformation to oblique coordinates, which are defined as those coming from nonorthogonal coordinate rotations that express the matrix representation of the second-order Hamiltonian in a block diagonal form characterized by the polyadic quantum number n = n1 + n2. The survival probabilities calculated show that the oblique nonstationary states evolve within their polyadic group with a high degree of coherence up to the dissociation limits on the short time scale. The degree of coherence is certainly much higher than that exhibited by the local nonstationary states extracted from the conventional orthogonal rotation of the original normal coordinates. We also show that energy exchange between the oblique vibrational modes occurs in a much more regular way than the exchange between the local modes.

NEXMD v2.0 Software Package for Nonadiabatic Excited State Molecular Dynamics Simulations.

We present NEXMD version 2.0, the second release of the NEXMD (Nonadiabatic EXcited-state Molecular Dynamics) software package. Across a variety of new features, NEXMD v2.0 incorporates new implementations of two hybrid quantum-classical dynamics methods, namely, Ehrenfest dynamics (EHR) and the Ab-Initio Multiple Cloning sampling technique for Multiconfigurational Ehrenfest quantum dynamics (MCE-AIMC or simply AIMC), which are alternative options to the previously implemented trajectory surface hopping (TSH) method. To illustrate these methodologies, we outline a direct comparison of these three hybrid quantum-classical dynamics methods as implemented in the same NEXMD framework, discussing their weaknesses and strengths, using the modeled photodynamics of a polyphenylene ethylene dendrimer building block as a representative example. We also describe the expanded normal-mode analysis and constraints for both the ground and excited states, newly implemented in the NEXMD v2.0 framework, which allow for a deeper analysis of the main vibrational motions involved in vibronic dynamics. Overall, NEXMD v2.0 expands the range of applications of NEXMD to a larger variety of multichromophore organic molecules and photophysical processes involving quantum coherences and persistent couplings between electronic excited states and nuclear velocity.

Vibrational Funnels for Energy Transfer in Organic Chromophores.

Photoinduced intramolecular energy transfers in multichromophoric molecules involve nonadiabatic vibronic channels that act as energy transfer funnels. They commonly take place through specific directions of motion dictated by the nonadiabatic coupling vectors. Vibrational funnels may support persistent coherences between electronic states and sometimes delineate the presence of minor alternative energy transfer pathways. The ultimate confirmation of their role on the interchromophoric energy transfer can be achieved by performing nonadiabatic excited-state molecular dynamics simulations by selectively freezing the nuclear motions in question. Our results point out this strategy as a useful tool to identify and evaluate the impact of these vibrational funnels on the energy transfer processes and guide the in silico design of materials with tunable properties and enhanced functionalities. Our work encourages applications of this methodology to different chemical and biochemical processes such as reactive scattering and protein conformational changes, to name a few.

Description of conformational ensembles of disordered proteins by residue-local probabilities.

The study of proteins with intrinsically disordered regions (IDRs) has emerged as an active field of research due to their intriguing nature. Although IDRs lack a well-defined folded structure, they play important functional roles in cells, following biological mechanisms different from those of the traditional structured proteins. Consequently, it has been necessary to re-design experimental and theoretical methods in order to face the challenges introduced by the dynamic nature of IDRs. In this work, we present an accurate and cost-effective method to study the conformational dynamics of IDRs based on the use of residue-local probabilistic expressions that characterize the conformational ensembles obtained from finite-temperature molecular dynamics (MD) simulations. It is shown that the good performance and the high convergence rates achieved with our method are independent of the IDR lengths, since the method takes advantage of the major influence of the identity and conformation of the nearest residue neighbors on the amino-acid conformational preferences to evaluate the IDR conformational ensembles. This allows us to characterize the conformational space of IDRs using a reduced number of probabilities which can be obtained from comparatively short MD simulations or experimental databases. To exemplify the usefulness of our approach, we present an application to directly detect Molecular Recognition Features (MoRFs) in an IDR domain of the protein p53, and to follow the time evolution of the thermodynamic magnitudes of this system during its exploration of the conformational space.

Host-guest complexes vs. supramolecular polymers in chalcogen bonding receptors: an experimental and theoretical study.

We describe here a comparative study between two tripodal anion receptors based on selenophene as the binding motif. The receptors use benzene or perfluorobenzene as a spacer. The presence of the electron-withdrawing ring activates the selenium atom for anion recognition inducing the formation of self-assembled supramolecular structures in the presence of chloride or bromide anions, which are bonded by the cooperative action of hydrogen and chalcogen bonding interactions. DOSY NMR and DLS experiments provided evidence for the formation of the supramolecular structures only in the presence of a perfluorobenzene based anion receptor while the analogous benzene one shows the classical anion/receptor complex without the participation of the selenium atom. The energetic and geometric features of the complexes of both receptors with the Cl and Br anions have been studied in solution. These results combined with the molecular electrostatic potential (MEP) surface plots allow us to rationalize the quite different behaviors of both receptors observed experimentally.

Ab Initio Partition Functions and Thermodynamic Quantities for the Molecular Hydrogen Isotopologues.

In this work, we calculate the partition functions and thermodynamic quantities of molecular hydrogen isotopologues using the rovibrational energy levels provided by the highly accurate ab initio adiabatic potential energy functions recently determined by Pachucki and Komasa (Pachucki, K.; Komasa, J. J. Chem. Phys. 2014, 141, 224103). The partition functions are calculated by including all bound energy levels of the isotopologues, up to their dissociation limits, plus the quasi-bound levels lying below the centrifugal potential barriers. For the homonuclear isotopologues, H2, D2, and T2, we also determine the partition functions and thermodynamic quantities of the normal mixtures using the statistical treatment recently proposed by Colonna et al. (Colonna, G.; D'Angola, A.; Capitelli, M. Int. J. Hydrogen Energy 2012, 37, 9656) based on the definition of the partition function of the mixture, which avoids inconsistencies in the values of the thermodynamic quantities depending directly on the internal partition function, in the high-temperature limit.

On the Role of Entropy in the Stabilization of α-Helices.

Protein folding evolves by exploring the conformational space with a subtle balance between enthalpy and entropy changes which eventually leads to a decrease of free energy upon reaching the folded structure. A complete understanding of this process requires, therefore, a deep insight into both contributions to free energy. In this work, we clarify the role of entropy in favoring the stabilization of folded structures in polyalanine peptides with up to 12 residues. We use a novel method referred to as K2V that allows us to obtain the potential-energy landscapes in terms of residue conformations extracted from molecular dynamics simulations at conformational equilibrium and yields folding thermodynamic magnitudes, which are in agreement with the experimental data available. Our results demonstrate that the folded structures of the larger polyalanine chains are stabilized with respect to the folded structures of the shorter chains by both an energetic contribution coming from the formation of the intramolecular hydrogen bonds and an entropic contribution coming from an increase of the entropy of the solvent with approximate weights of 60 and 40%, respectively, thus unveiling a key piece in the puzzle of protein folding. In addition, the ability of the K2V method to provide the enthalpic and entropic contributions for individual residues along the peptide chain makes it clear that the energetic and entropic stabilizations are basically governed by the nearest neighbor residue conformations, with the folding propensity being rationalized in terms of triads of residues.

Formation of self-assembled supramolecular polymers by anti-electrostatic anion-anion and halogen bonding interactions.

We report here the formation of self-assembled supramolecular polymers in which the cooperative action of anti-electrostatic anion-anion and halogen-bonding interactions serve as a powerful driving force for the formation of large supramolecular polymers. DOSY-NMR, DLS, TEM, SEM and X-ray experiments provide evidence of the formation of supramolecular structures in solution and solid state.

Selective fluorescence sensing of H2PO4- by the anion induced formation of self-assembled supramolecular polymers.

The utilization of anions to induce the formation of self-assembled supramolecular polymers in solution is an undeveloped area of host-guest chemistry. We report in this manuscript a comparative study of two tripodal anion receptors by hydrogen or halogen bonding interactions to form self-assembled supramolecular structures induced by the presence of anions. DOSY NMR and DLS experiments provided evidence for the formation of supramolecular structures in solution in both halogen and hydrogen bond donors with H2PO4- anions. The nucleation and elongation constants obtained using the thermodynamic model indicate that the polymers grow following an isodesmic mechanism. Emission studies demonstrate that only the formation of the supramolecular polymer between the halogen bond donor receptor and H2PO4- anions results in the appearance of the excimer emission band.

Intraresidual Correlated Motions in Peptide Chains.

We investigate the interresidual and intraresidual correlations between dihedral displacements of adjacent residues within model polyalanine peptides by analyzing extensive molecular dynamics trajectories. Correlations are evaluated individually at different residue conformations covering the whole (ϕi,ψi)-space. From these, we draw maps that unveil an unprecedented strong intramolecular correlation displaying opposite (correlated/anticorrelated) behaviors at different conformations. Both interresidual and intraresidual correlations arise from the propensity of the peptide to minimize the overall atomic displacements.

Energetic Self-Folding Mechanism in α-Helices.

A novel energetic route driving the folding of a polyalanine peptide from an extended conformation to its α-helix native conformation is described, supported by a new method to compute mean potential energy surfaces accurately in terms of the dihedral angles of the peptide chain from extensive molecular dynamics simulations. The energetic self-folding (ESF) route arises specifically from the balance between the intrinsic propensity of alanine residues toward the αR conformation and two, opposite, effects: the destabilizing interaction with neighbor residues and the stabilizing formation of native hydrogen bonds, with the latter being dominant for large peptide lengths. The ESF mechanism provides simple but robust support to the nucleation-elongation or zipper models and offers a quantitative energetic funnel picture of the folding process. The mechanism is validated by the reasonable agreement between the computed folding energies and the experimental values.

Interlocked Supramolecular Polymers Created by Combination of Halogen- and Hydrogen-Bonding Interactions through Anion-Template Self-Assembly.

We present the synthesis and oxoanion-assembling properties of a monomer with a naphthalene ring as a central core decorated with two arms containing iodotriazolium rings as anion binding sites. Interactions with SO42-, H2PO4-, and HP2O73- anions, via a cooperative mechanism, afforded new supramolecular materials stabilized by a combination of halogen- and hydrogen-bonding interactions. 1H NMR experiments and solid-state structure provided evidence for the initial formation of a supramolecular linear chain, nucleation step, and then two different supramolecular chains are interpenetrated with each other, elongation steps, involving the formation of hydrogen bonds between two oxygens of the anion from one of the chains and the naphthalene inner protons from the other chain. Scanning electron microscopy studies revealed that the morphology of the crystals changed dramatically with the nature of the anion added.

Understanding the connection between conformational changes of peptides and equilibrium thermal fluctuations.

Despite the increasing evidence that conformational transitions in peptides and proteins are driven by specific vibrational energy pathways along the molecule, the current experimental techniques of analysis do as yet not allow to study these biophysical processes in terms of anisotropic energy flows. Computational methods offer a complementary approach to obtain a more detailed understanding of the vibrational and conformational dynamics of these systems. Accordingly, in this work we investigate jointly the vibrational energy distribution and the conformational dynamics of trialanine peptide in water solution at room temperature by applying the Instantaneous Normal Mode analysis to the results derived from equilibrium molecular dynamics simulations. It is shown that conformational changes in trialanine are triggered by the vibrational energy accumulated in the low-frequency modes of the molecule, and that excitation is caused exclusively by thermal fluctuations of the solute-solvent system, thus excluding the possibility of an intramolecular vibrational energy redistribution process.

Relaxation pathways of the OD stretch fundamental of HOD in liquid H2O.

The molecular dynamics with quantum transitions method is used to study the vibrational relaxation of the OD stretching mode of HOD dissolved in liquid H2O water at 303 K. All the vibrational modes of the solute and solvent molecules that participate in the relaxation process are described by quantum mechanics, while the rotational and translational degrees of freedom are treated classically. A modification of the water intramolecular SPC/E (Simple Point Charge/Extended) force field providing vibrational frequencies in solution closer to the experimental values is proposed to analyze the influence of the vibrational energy gaps on the relaxation channels. The relaxation times obtained are in satisfactory agreement with experimental values. The energy transfer during the relaxation process alters significantly the H-bond network around the HOD molecule. The analysis of the vibrational transitions during the relaxation process reveals a complex mechanism which involves the participation of both intra- and intermolecular channels and provides a compromise for the different interpretations of the experimental data reported for this system in recent years.

Conformational Changes of Trialanine in Water Induced by Vibrational Relaxation of the Amide I Mode.

Most of the protein-based diseases are caused by anomalies in the functionality and stability of these molecules. Experimental and theoretical studies of the conformational dynamics of proteins are becoming in this respect essential to understand the origin of these anomalies. However, a description of the conformational dynamics of proteins based on mechano-energetic principles still remains elusive because of the intrinsic high flexibility of the peptide chains, the participation of weak noncovalent interactions, and the role of the ubiquitous water solvent. In this work, the conformational dynamics of trialanine dissolved in water (D2O) is investigated through Molecular Dynamics (MD) simulations combined with instantaneous normal modes (INMs) analysis both at equilibrium and after the vibrational excitation of the C-terminal amide I mode. The conformational equilibrium between α and pPII conformers is found to be altered by the intramolecular relaxation of the amide I mode as a consequence of the different relaxation pathways of each conformer which modify the amount of vibrational energy stored in the torsional motions of the tripeptide, so the α → pPII and pPII → α conversion rates are increased differently. The selectivity of the process comes from the shifts of the vibrational frequencies with the conformational changes that modify the resonance conditions driving the intramolecular energy flows.

Hydration Effect on Amide I Infrared Bands in Water: An Interpretation Based on an Interaction Energy Decomposition Scheme.

The sensitivity of some infrared bands to the local environment can be exploited to shed light on the structure and the dynamics of biological systems. In particular, the amide I band, which is specifically related to vibrations within the peptide bonds, can give information on the ternary structure of proteins, and can be used as a probe of energy transfer. In this work, we propose a model to quantitatively interpret the frequency shift on the amide I band of a model peptide induced by the formation of hydrogen bonds in the first solvation shell. This method allows us to analyze to what extent the electrostatic interaction, electronic polarization and charge transfer affect the position of the amide I band. The impact of the anharmoniticy of the pontential energy surface on the hydration induced shift is elucidated as well.

Theoretical study of the temperature dependence of the vibrational relaxation of the H2O bend fundamental in liquid water and the subsequent distortion of the hydrogen bond network.

The molecular dynamics with quantum transitions method is used to study the temperature dependence of the relaxation dynamics of the H2O bend fundamental in liquid water in the range from 277 to 348 K and the subsequent variation of the hydrogen bonds network in the liquid. The vibrational bending degrees of freedom of the water molecules are all described by quantum mechanics while the remaining translational and rotational motions are described classically. The participation of the H-bonds in the relaxation process is studied taking into account the dependence of the relaxation lifetimes on the number of H-bonds formed by the initially excited water molecule and the amount of energy transferred into the hindered rotational motions. It is found that the intermolecular vibrational energy transfer plays an important role in the relaxation mechanism, with almost no temperature dependence, and that the energy transfer into the rotational degrees of freedom is favored over the energy transfer into the translational motions. The thermalization of the system after relaxation is completed in a time scale shorter than the time taken for the H-bond network to recover. The relaxation and equilibration times calculated compare well with experimental and previous theoretical results.

Vibrational energy relaxation of the amide I mode of N-methylacetamide in D2O studied through Born-Oppenheimer molecular dynamics.

The vibrational relaxation of the amide I mode of deuterated N-methylacetamide in D2O solution is studied through nonequilibrium simulations using the semiempirical Born-Oppenheimer molecular dynamics (SEBOMD) approach to describe the whole solute-solvent system. Relaxation pathways and lifetimes are determined using the instantaneous normal mode (INM) analysis. The relaxation of the amide I mode is characterized by three different time scales; most of the excess energy (80%) is redistributed through intramolecular vibrational energy redistribution processes, with a smaller contribution (20%) of intermolecular energy flowing into the solvent. The amide II mode is found to contribute modestly (7%) to the relaxation mechanism. The amide I mode and the total vibrational energy decay curves obtained using SEBOMD and INM are in satisfactory agreement with the experimental measurements.

Instantaneous normal mode analysis of the vibrational relaxation of the amide I mode of alanine dipeptide in water.

Nonequilibrium Molecular Dynamics (MD) simulations coupled to instantaneous normal modes (INMs) analysis are used to study the vibrational relaxation of the acetyl and amino-end amide I modes of the alanine dipeptide (AlaD) molecule dissolved in water (D2O). The INMs are assigned in terms of the equilibrium normal modes using the Effective Atomic Min-Cost algorithm as adapted to make use of the outputs of standard MD packages, a method which is well suited for the description of flexible molecules. The relaxation energy curves of both amide I modes show multiexponential decays, in good agreement with the experimental findings. It is found that ~85%-90% of the energy relaxes through intramolecular vibrational redistribution. The main relaxation pathways are also identified. The rate at which energy is transferred into the solvent is similar for the acetyl-end and amino-end amide I modes. The conformational changes occurring during relaxation are investigated, showing that the populations of the alpha and beta region conformers are altered by energy transfer in such a way that it takes 15 ps for the equilibrium conformational populations to be recovered after the initial excitation of the AlaD molecule.

Conformational changes of ß-carotene and zeaxanthin immersed in a model membrane through atomistic molecular dynamics simulations.

In this work, we investigate systems formed by ß-carotene and zeaxanthin embedded separately in a model lipid bilayer of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) through molecular dynamics (MD) simulations. The study is conducted using an all-atoms model and by analyzing the structural changes that occur at both the carotenoid molecule and the membrane during the simulations. We concentrate specifically on the conformation of the conjugated chain, given the relevance that this feature has in modulating the spectroscopic and antioxidant properties of the carotenoids. The force fields of the carotenoids are parametrized accordingly in order to reproduce the rotation potentials of the conjugated chains calculated using quantum DFT methods. A model to quantify the effective conjugated chain length is presented. The MD simulations are carried out using the parameters adjusted for the carotenoids along with those provided by the CHARMM36 force field for the lipids of the membrane. A differentiating dynamic behavior of ß-carotene and zeaxanthin within the bilayer is observed in the simulations, which is analyzed in detail through umbrella sampling techniques. This behavior is driven basically by the interactions of the lipid polar heads with the hydroxyl groups of zeaxanthin, which are absent in ß-carotene. These interactions influence the carotenoid orientation, modify the conformational distribution of the dihedral angles of the conjugated chain significantly, and specifically distort the membrane structure.