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Experimental methods capable of selectively probing water at the DNA minor groove, major groove, and phosphate backbone are crucial for understanding how hydration influences DNA structure and function. Chiral-selective sum frequency generation spectroscopy (chiral SFG) is unique among vibrational spectroscopies because it can selectively probe water molecules that form chiral hydration structures around biomolecules. However, interpreting chiral SFG spectra is challenging since both water and the biomolecule can produce chiral SFG signals. Here, we combine experiment and computation to establish a theoretical framework for the rigorous interpretation of chiral SFG spectra of DNA. We demonstrate that chiral SFG detects the N-H stretch of DNA base pairs and the O-H stretch of water, exclusively probing water molecules in the DNA first hydration shell. Our analysis reveals that DNA transfers chirality to water molecules only within the first hydration shell, so they can be probed by chiral SFG spectroscopy. Beyond the first hydration shell, the electric field-induced water structure is symmetric and, therefore, precludes chiral SFG response. Furthermore, we find that chiral SFG can differentiate chiral subpopulations of first hydration shell water molecules at the minor groove, major groove, and phosphate backbone. Our findings challenge the scientific perspective dominant for more than 40 years that the minor groove "spine of hydration" is the only chiral water structure surrounding the DNA double helix. By identifying the molecular origins of the DNA chiral SFG spectrum, we lay a robust experimental and theoretical foundation for applying chiral SFG to explore the chemical and biological physics of DNA hydration., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

This paper is dedicated to the quantum chemical package Jaguar, which is commercial software developed and distributed by Schrödinger, Inc. We discuss Jaguar's scientific features that are relevant to chemical research as well as describe those aspects of the program that are pertinent to the user interface, the organization of the computer code, and its maintenance and testing. Among the scientific topics that feature prominently in this paper are the quantum chemical methods grounded in the pseudospectral approach. A number of multistep workflows dependent on Jaguar are covered: prediction of protonation equilibria in aqueous solutions (particularly calculations of tautomeric stability and pKa), reactivity predictions based on automated transition state search, assembly of Boltzmann-averaged spectra such as vibrational and electronic circular dichroism, as well as nuclear magnetic resonance. Discussed also are quantum chemical calculations that are oriented toward materials science applications, in particular, prediction of properties of optoelectronic materials and organic semiconductors, and molecular catalyst design. The topic of treatment of conformations inevitably comes up in real world research projects and is considered as part of all the workflows mentioned above. In addition, we examine the role of machine learning methods in quantum chemical calculations performed by Jaguar, from auxiliary functions that return the approximate calculation runtime in a user interface, to prediction of actual molecular properties. The current work is second in a series of reviews of Jaguar, the first having been published more than ten years ago. Thus, this paper serves as a rare milestone on the path that is being traversed by Jaguar's development in more than thirty years of its existence., (© 2024 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International (CC BY-NC-ND) license (https://creativecommons.org/licenses/by-nc-nd/4.0/).)

We describe the synthesis and characterization of a versatile platform for gold functionalization, based on self-assembled monolayers (SAMs) of distal-pyridine-functionalized N-heterocyclic carbenes (NHC) derived from bis(NHC) Au(I) complexes. The SAMs are characterized using polarization-modulation infrared reflectance-absorption spectroscopy, surface-enhanced Raman spectroscopy, and X-ray photoelectron spectroscopy. The binding mode is examined computationally using density functional theory, including calculations of vibrational spectra and direct comparisons to the experimental spectroscopic signatures of the monolayers. Our joint computational and experimental analyses provide structural information about the SAM binding geometries under ambient conditions. Additionally, we examine the reactivity of the pyridine-functionalized SAMs toward H 2 SO 4 and W(CO) 5 (THF) and verify the preservation of the introduced functionality at the interface. Our results demonstrate the versatility of N-heterocyclic carbenes as robust platforms for on-surface acid-base and ligand exchange reactions.

Understanding the dynamics of proton transfer along low-barrier hydrogen bonds remains an outstanding challenge of great fundamental and practical interest, reflecting the central role of quantum effects in reactions of chemical and biological importance. Here, we combine ab initio calculations with the semiclassical ring-polymer instanton method to investigate tunneling processes on the ground electronic state of 6-hydroxy-2-formylfulvene (HFF), a prototypical neutral molecule supporting low-barrier hydrogen-bonding. The results emerging from a full-dimensional ab initio instanton analysis reveal that the tunneling path does not pass through the instantaneous transition-state geometry. Instead, the tunneling process involves a multidimensional reaction coordinate with concerted reorganization of the heavy-atom skeletal framework to substantially reduce the donor-acceptor distance and drive the ensuing intramolecular proton-transfer event. The predicted tunneling-induced splittings for HFF isotopologues are in good agreement with experimental findings, leading to percentage deviations of only 20-40%. Our full-dimensional results allow us to characterize vibrational contributions along the tunneling path, highlighting the intrinsically multidimensional nature of the attendant hydron-migration dynamics.

We introduce a semi-classical approximation for calculating generalized multi-time correlation functions based on Matsubara dynamics, a classical dynamics approach that conserves the quantum Boltzmann distribution. This method is exact for the zero time and harmonic limits and reduces to classical dynamics when only one Matsubara mode is considered (i.e., the centroid). Generalized multi-time correlation functions can be expressed as canonical phase-space integrals, involving classically evolved observables coupled through Poisson brackets in a smooth Matsubara space. Numerical tests on a simple potential show that the Matsubara approximation exhibits better agreement with exact results than classical dynamics, providing a bridge between the purely quantum and classical descriptions of multi-time correlation functions. Despite the phase problem that prevents practical applications of Matsubara dynamics, the reported work provides a benchmark theory for the future development of quantum-Boltzmann-preserving semi-classical approximations for studies of chemical dynamics in condensed phase systems., (© 2023 Author(s). Published under an exclusive license by AIP Publishing.)

An exact representation of quantum mechanics using the language of phase-space variables provides a natural starting point to introduce and develop semiclassical approximations for the calculation of time correlation functions. Here, we introduce an exact path-integral formalism for calculations of multi-time quantum correlation functions as canonical averages over ring-polymer dynamics in imaginary time. The formulation provides a general formalism that exploits the symmetry of path integrals with respect to permutations in imaginary time, expressing correlations as products of imaginary-time-translation-invariant phase-space functions coupled through Poisson bracket operators. The method naturally recovers the classical limit of multi-time correlation functions and provides an interpretation of quantum dynamics in terms of "interfering trajectories" of the ring-polymer in phase space. The introduced phase-space formulation provides a rigorous framework for the future development of quantum dynamics methods that exploit the invariance of imaginary time path integrals to cyclic permutations.

We present results from machine-learning-based path integral molecular dynamics simulations that describe isomerization paths articulated via collective proton transfers along mixed, cyclic tetramers combining water and ammonia at cryogenic conditions. The net result of such isomerizations is a reverse of the chirality of the global hydrogen-bonding architecture along the different cyclic moieties. In monocomponent tetramers, the classical free energy profiles associated with these isomerizations present the usual symmetric double-well characteristics whereas the reactive paths exhibit full concertedness among the different intermolecular transfer processes. Contrastingly, in mixed water/ammonia tetramers, the incorporation of a second component introduces imbalances in the strengths of the different hydrogen bonds leading to a partial loss of concertedness, most notably at the vicinity of the transition state. As such, the highest and lowest degrees of progression are registered along OH···N and O···HN coordinations, respectively. These characteristics lead to polarized transition state scenarios akin to solvent-separated ion-pair configurations. The explicit incorporation of nuclear quantum effects promotes drastic depletions in the activation free energies and modifications in the overall shape of the profiles which include central plateau-like stages, indicating the prevalence of deep tunneling regimes. On the other hand, the quantum treatment of the nuclei partially restores the degree of concertedness among the evolutions of the individual transfers.

Proton-coupled electron transfer (PCET) is the underlying mechanism governing important reactions ranging from water splitting in photosynthesis to oxygen reduction in hydrogen fuel cells. The interplay of proton and electronic charge distribution motions can vary from sequential to concerted schemes, with elementary steps occurring on ultrafast time scales. We demonstrate with a simulation study that femtosecond soft-X-ray spectroscopy provides key insights into the PCET mechanism of a photoinduced intramolecular enol* → keto* tautomerization reaction. A full quantum treatment of the electronic and nuclear dynamics of 2-(2'-hydroxyphenyl)benzothiazole upon electronic excitation reveals how spectral signatures of local excitations from core to frontier orbitals display the distinctly different stages of charge relocation for the H atom, donating, and accepting sites. Our findings indicate that ultraviolet/X-ray pump-probe spectroscopy provides a unique way to probe ultrafast electronic structure rearrangements in photoinduced chemical reactions essential to understanding the mechanism of PCET.

The characterization of electrical double layers is important since the interfacial electric field and electrolyte environment directly affect the reaction mechanisms and catalytic rates of electrochemical processes. In this work, we introduce a spectroscopic method based on a Stark shift ruler that enables mapping the electric field strength across the electric double layer of electrode/electrolyte interfaces. We use the tungsten-pentacarbonyl(1,4-phenelenediisocyanide) complex attached to the gold surface as a molecular ruler. The carbonyl (CO) and isocyanide (NC) groups of the self-assembled monolayer (SAM) provide multiple vibrational reporters situated at different distances from the electrode. Measurements of Stark shifts under operando electrochemical conditions and direct comparisons to density functional theory (DFT) simulations reveal distance-dependent electric field strength from the electrode surface. This electric field profile can be described by the Gouy-Chapman-Stern model with Stern layer thickness of ∼4.5 Å, indicating substantial solvent and electrolyte penetration within the SAM. Significant electro-induction effect is observed on the W center that is ∼1.2 nm away from the surface despite rapid decay of the electric field (∼90%) within 1 nm. The applied methodology and reported findings should be particularly valuable for the characterization of a wide range of microenvironments surrounding molecular electrocatalysts at electrode interfaces and the positioning of electrocatalysts at specific distances from the electrode surface for optimal functionality.

We present path integral molecular dynamics results that describe the effects of nuclear quantum fluctuations on equilibrium and dynamical characteristics pertaining to bifurcation pathways in hydrogen bonded dimers combining water and ammonia, at cryogenic temperatures of the order of 20 K. Along these isomerizations, the hydrogen atoms in the molecules acting as hydrogen-bond donors interchange their original dangling/connective characters. Our results reveal that the resulting quantum transition paths comprise three stages: the initial and final ones involve overall rotations during which the two protons retain their classical-like characteristics. Effects from quantum fluctuation are clearly manifested in the changes operated at the intermediate passages over transition states, as the spatial extents of the protons stretch over typical lengths comparable to the distances between connective and dangling basins of attractions. Consequently, the classical over-the-hill path is replaced by a tunneling controlled mechanism which, within the path integral perspective, can be cast in terms of concerted inter-basin migrations of polymer beads from dangling-to-connective and from connective-to-dangling, at practically no energy costs. We also estimated the characteristic timescales describing such interconversions within the approximate ring polymer rate theory. Effects derived from full and partial deuteration are also discussed.

External control of chemical processes is a subject of widespread interest in chemical research, including control of electrocatalytic processes with significant promise in energy research. The electrochemical double-layer is the nanoscale region next to the electrode/electrolyte interface where chemical reactions typically occur. Understanding the effects of electric fields within the electrochemical double layer requires a combination of synthesis, electrochemistry, spectroscopy, and theory. In particular, vibrational sum frequency generation (VSFG) spectroscopy is a powerful technique to probe the response of molecular catalysts at the electrode interface under bias. Fundamental understanding can be obtained via synthetic tuning of the adsorbed molecular catalysts on the electrode surface and by combining experimental VSFG data with theoretical modelling of the Stark shift response. The resulting insights at the molecular level are particularly valuable for the development of new methodologies to control and characterize catalysts confined to electrode surfaces. This Perspective article is focused on how systematic modifications of molecules anchored to surfaces report information concerning the geometric, energetic, and electronic parameters of catalysts under bias attached to electrode surfaces., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)

Ultrafast UV-pump/soft-X-ray-probe spectroscopy is a subject of great interest since it can provide detailed information about dynamical photochemical processes with ultrafast resolution and atomic specificity. Here, we focus on the photodissociation of ICN in the 1 Π 1 excited state, with emphasis on the transient response in the soft-X-ray spectral region as described by the ab initio spectral lineshape averaged over the nuclear wavepacket probability density. We find that the carbon K-edge spectral region reveals a rich transient response that provides direct insights into the dynamics of frontier orbitals during the I-CN bond cleavage process. The simulated UV-pump/soft-X-ray-probe spectra exhibit detailed dynamical information, including a time-domain signature for coherent vibration associated with the photogenerated CN fragment., (© 2020 The Authors. Published by Wiley-VCH GmbH.)

Based on a recently developed generalization of Matsubara dynamics to the multi-time realm, we present a formal derivation of multi-time generalizations of ring-polymer molecular dynamics, thermostatted ring-polymer molecular dynamics (TRPMD), centroid molecular dynamics (CMD), and mean-field Matsubara dynamics. Additionally, we analyze the short-time accuracy of each methodology. We find that for multi-time correlation functions of linear operators, (T)RPMD is accurate up to order t 3 , while CMD is only correct up to t, indicating a degradation in the accuracy of these methodologies with respect to the single-time counterparts. The present work provides a firm justification for the use of path-integral-based approximations for the calculation of multi-time correlation functions.

The simulation of multidimensional vibrational spectroscopy of condensed-phase systems including nuclear quantum effects is challenging since full quantum-mechanical calculations are still intractable for large systems comprising many degrees of freedom. Here, we apply the recently developed double Kubo transform (DKT) methodology in combination with ring-polymer molecular dynamics (RPMD) for evaluating multi-time correlation functions [K. A. Jung et al., J. Chem. Phys. 148, 244105 (2018)], providing a practical method for incorporating nuclear quantum effects in nonlinear spectroscopy of condensed-phase systems. We showcase the DKT approach in the simulation of the fifth-order two-dimensional (2D) Raman spectroscopy of Lennard-Jones liquids as a prototypical example, which involves nontrivial nonlinear spectroscopic observables of systems described by anharmonic potentials. Our results show that the DKT can faithfully reproduce the 2D Raman response of liquid xenon at high temperatures, where the system behaves classically. In contrast, liquid neon at low temperatures exhibits moderate but discernible nuclear quantum effects in the 2D Raman response compared to the responses obtained with classical molecular dynamics approaches. Thus, the DKT formalism in combination with RPMD simulations enables simulations of multidimensional optical spectroscopy of condensed-phase systems that partially account for nuclear quantum effects.

Heterogenization of homogenous catalysts on electrode surfaces provides a valuable approach for characterization of catalytic processes in operando conditions using surface selective spectroelectrochemistry methods. Ligand design plays a central role in the attachment mode and the resulting functionality of the heterogenized catalyst as determined by the orientation of the catalyst relative to the surface and the nature of specific interactions that modulate the redox properties under the heterogeneous electrode conditions. Here, we introduce new [Re(L)(CO) 3 Cl] catalysts for CO 2 reduction with sulfur-based anchoring groups on a bipyridyl ligand, where L = 3,3'-disulfide-2,2'-bipyridine (SSbpy) and 3,3'-thio-2,2'-bipyridine (Sbpy). Spectroscopic and electrochemical analysis complemented by computational modeling at the density functional theory level identify the complex [Re(SSbpy)(CO) 3 Cl] as a multi-electron acceptor that combines the redox properties of both the rhenium tricarbonyl core and the disulfide functional group on the bipyridyl ligand. The first reduction at -0.85 V (vs. SCE) involves a two-electron process that breaks the disulfide bond, activating it for surface attachment. The heterogenized complex exhibits robust anchoring on gold surfaces, as probed by vibrational sum-frequency generation (SFG) spectroscopy. The binding configuration is normal to the surface, exposing the active site to the CO 2 substrate in solution. The attachment mode is thus particularly suitable for electrocatalytic CO 2 reduction., (Copyright © 2020 Cattaneo, Guo, Kelly, Videla, Kiefer, Gebre, Ge, Liu, Wu, Lian and Batista.)

Matsubara dynamics has recently emerged as the most general form of a quantum-Boltzmann-conserving classical dynamics theory for the calculation of single-time correlation functions. Here, we present a generalization of Matsubara dynamics for the evaluation of multitime correlation functions. We first show that the Matsubara approximation can also be used to approximate the two-time symmetrized double Kubo transformed correlation function. By a straightforward extension of these ideas to the multitime realm, a multitime Matsubara dynamics approximation can be obtained for the multitime fully symmetrized Kubo transformed correlation function. Although not a practical method, due to the presence of a phase-term, this multitime formulation of Matsubara dynamics represents a benchmark theory for future development of Boltzmann preserving semiclassical approximations to general higher order multitime correlation functions. It also reveals a connection between imaginary time-ordering in the path integral and the classical dynamics of multitime correlation functions.

A parallel study of protein variants with all (l-), all (d-), or mixed (l-)/(d-) amino acids can be used to assess how backbone architecture versus side chain identity determines protein structure. Here, we investigate the secondary structure and side chain orientation dynamics of the antiparallel β-sheet peptide LK 7 β (Ac-Leu-Lys-Leu-Lys-Leu-Lys-Leu-NH 2 ) composed of all (l-), all (d-), or alternating (l-Leu)/(d-Lys) amino acids. Using interface-selective vibrational sum frequency generation spectroscopy (VSFG), we observe that the alternating (l-)/(d-) peptide lacks a resonant C-H stretching mode compared to the (l-) and (d-) variants and does not form antiparallel β-sheets. We rationalize our observations on the basis of density functional theory calculations and molecular dynamics (MD) simulations of LK 7 β at the air-water interface. Irrespective of the handedness of the amino acids, leucine side chains prefer to orient toward the hydrophobic air phase while lysine side chains prefer the hydrophilic water phase. These preferences dictate the backbone configuration of LK 7 β and thereby the folding of the peptide. Our MD simulations show that the preferred side chain orientations can force the backbone of a single strand of (l-) LK 7 β at the air-water interface to adopt β-sheet Ramachandran angles. However, denaturation of the β-sheets at pH = 2 results in a negligible chiral VSFG amide I response. The combined computational and experimental results lend critical support to the theory that a chiral VSFG response requires macroscopic chirality, such as in β-sheets. Our results can guide expectations about the VSFG optical responses of proteins and should improve understanding of how amino acid chirality modulates the structure and function of natural and de novo proteins at biological interfaces.

Rhenium and manganese bipyridyl tricarbonyl complexes have attracted intense interest for their promising applications in photocatalytic and electrocatalytic CO 2 reduction in both homogeneous and heterogenized systems. To date, there have been extensive studies on immobilizing Re catalysts on solid surfaces for higher catalytic efficiency, reduced catalyst loading, and convenient product separation. However, in order for the heterogenized molecular catalysts to achieve the combination of the best aspects of homogeneous and heterogeneous catalysts, it is essential to understand the fundamental physicochemical properties of such heterogeneous systems, such as surface-bound structures of Re/Mn catalysts, substrate-adsorbate interactions, and photoinduced or electric-field-induced effects on Re/Mn catalysts. For example, the surface may act to (un)block substrates, (un)trap charges, (de)stabilize particular intermediates (and thus affect scaling relations), and shift potentials in different directions, just as protein environments do. The close collaboration between the Lian, Batista, and Kubiak groups has resulted in an integrated approach to investigate how the semiconductor or metal surface affects the properties of the attached catalyst. Synthetic strategies to achieve stable and controlled attachment of Re/Mn molecular catalysts have been developed. Steady-state, time-resolved, and electrochemical vibrational sum-frequency generation (SFG) spectroscopic studies have provided insight into the effects of interfacial structures, ultrafast vibrational energy relaxation, and electric field on the Re/Mn catalysts, respectively. Various computational methods utilizing density functional theory (DFT) have been developed and applied to determine the molecular orientation by direct comparison to spectroscopy, unravel vibrational energy relaxation mechanisms, and quantify the interfacial electric field strength of the Re/Mn catalyst systems. This Account starts with a discussion of the recent progress in determining the surface-bound structures of Re catalysts on semiconductor and Au surfaces by a combined vibrational SFG and DFT study. The effects of crystal facet, length of anchoring ligands, and doping of the semiconductor on the bound structures of Re catalysts and of the substrate itself are discussed. This is followed by a summary of the progress in understanding the vibrational relaxation (VR) dynamics of Re catalysts covalently adsorbed on semiconductor and metal surfaces. The VR processes of Re catalysts on TiO 2 films and TiO 2 single crystals and a Re catalyst tethered on Au, particularly the role of electron-hole pair (EHP)-induced coupling on the VR of the Re catalyst bound on Au, are discussed. The Account also summarizes recent studies in quantifying the electric field strength experienced by the catalytically active site of the Re/Mn catalyst bound on a Au electrode based on a combined electrochemical SFG and DFT study of the Stark tuning of the CO stretching modes of these catalysts. Finally, future research directions on surface-immobilized molecular catalyst systems are discussed.

Attaching molecular catalysts to metal and semiconductor electrodes is a promising approach to developing new catalytic electrodes with combined advantages of molecular and heterogeneous catalysts. However, the effect of the interfacial electric field on the stability, activity, and selectivity of the catalysts is often poorly understood due to the complexity of interfaces. In this work, we examine the strength of the interfacial field at the binding site of CO 2 reduction catalysts including Re(S-2,2'-bipyridine)(CO) 3 Cl and Mn(S-2,2'-bipyridine)(CO) 3 Br immobilized on Au electrodes. The vibrational spectra are probed by sum frequency generation spectroscopy (SFG), showing pronounced potential-dependent frequency shifts of the carbonyl stretching modes. Calculations of SFG spectra and Stark tuning rates based on density functional theory allow for direct interpretation of the configurations of the catalysts bound to the surfaces and the influence of the interfacial electric field. We find that electrocatalysts supported on Au electrodes have tilt angles of about 65-75° relative to the surface normal with one of the carbonyl ligands in direct contact with the surface. Large interfacial electric fields of 10 8 -10 9 V/m are determined through the analysis of experimental frequency shifts and theoretical Stark tuning rates of the symmetric CO stretching mode. These large electric fields thus significantly influence the CO 2 binding site.

The computation and interpretation of nonlinear vibrational spectroscopy is of vital importance for understanding a wide range of dynamical processes in molecular systems. Here, we introduce an approach to evaluate multi-time response functions in terms of multi-time double symmetrized Kubo transformed thermal correlation functions. Furthermore, we introduce a multi-time extension of ring polymer molecular dynamics to evaluate these Kubo transforms. Benchmark calculations show that the approximations are useful for short times even for nonlinear operators, providing a consistent improvement over classical simulations of multi-time correlation functions. The introduced methodology thus provides a practical way of including nuclear quantum effects in multi-time response functions of non-linear optical spectroscopy.

We present a path-integral-molecular-dynamics study of the thermodynamic stabilities of DOH⋯ X - and HOD⋯ X - (X = F, Cl, Br, I) coordination in aqueous solutions at ambient conditions. In agreement with experimental evidence, our results for the F - case reveal a clear stabilization of the latter motif, whereas, in the rest of the halogen series, the former articulation prevails. The DOH⋯ X - preference becomes more marked the larger the size of the ionic solute. A physical interpretation of these tendencies is provided in terms of an analysis of the global quantum kinetic energies of the light atoms and their geometrical decomposition. The stabilization of the alternative ionic coordination geometries is the result of a delicate balance arising from quantum spatial dispersions along parallel and perpendicular directions with respect to the relevant O-H⋯X - axis, as the strength of the water-halide H-bond varies. This interpretation is corroborated by a complementary analysis performed on the different spectroscopic signals of the corresponding IR spectra.

Understanding how to control reaction dynamics of polyatomic systems by using ultrafast laser technology is a fundamental challenge of great technological interest. Here, we report a Floquet theoretical study of the effect of light-induced potentials on the ultrafast cis-trans photoisomerization dynamics of rhodopsin. The Floquet Hamiltonian involves an empirical 3-state 25-mode model with frequencies and excited-state gradients parametrized to reproduce the rhodopsin electronic vertical excitation energy, the resonance Raman spectrum, and the photoisomerization time and efficiency as probed by ultrafast spectroscopy. We simulate the excited state relaxation dynamics using the time-dependent self-consistent field method, as described by a 3-state 2-mode nuclear wavepacket coupled to a Gaussian ansatz of 23 vibronic modes. We analyze the reaction time and product yield obtained with pulses of various widths and intensity profiles, defining 'dressed states' where the perturbational effect of the pulses is naturally decoupled along the different reaction channels. We find pulses that delay the excited-state photoisomerization for hundreds of femtoseconds, and we gain insights on the underlying control mechanisms. The reported findings provide understanding of quantum control, particularly valuable for the development of ultrafast optical switches based on visual pigments.

By combining path-integrals molecular dynamics simulations with the accurate MB-pol potential energy surface, we investigate the role of alternative potential models on isotopic fractionation ratios between H and D atoms at dangling positions in water clusters at low temperatures. Our results show clear stabilizations of the lighter isotope at dangling sites, characterized by free energy differences ΔG that become comparable to or larger than k B T for temperatures below ∼75 K. The comparison between these results to those previously reported using the empirical q-TIP4P/F water model [P. E. Videla et al., J. Phys. Chem. Lett. 5, 2375 (2014)] reveals that the latter Hamiltonian overestimates the H stabilization by ∼25%. Moreover, predictions from the MB-pol model are in much better agreement with measured results reported for similar isotope equilibria at ice surfaces. The dissection of the quantum kinetic energies into orthogonal directions shows that the dominant differences between the two models are to be found in the anharmonic characteristics of the potential energy surfaces along OH bond directions involved in hydrogen bonds.

Aligned protein α-helix dipoles have been implicated in protein function and structure. The recent breakthroughs in high-resolution electron microscopy (EM) of macromolecules makes it possible to explore fundamental aspects of structural biology at the detailed molecular level. The electrostatic potential (ESP) generated by aligned protein α-helix dipole should be observable in high-resolution EM maps despite the fact that the effect may be partially screened by induced electric fields. Here, we show that aligned backbone dipoles in protein α-helices account for long-range features in the protein ESP functions. Our results are consistent with experimental EM maps and density functional theory calculations, including direct Fourier summation for proper calculation of the ESP due to the nonlocal nature of the ESP function from aligned dipoles and other partial atomic charges., (© 2017 The Protein Society.)

We recently reported a very unusual temperature dependence of the rate of thermal reaction of wild type bovine rhodopsin: the Arrhenius plot exhibits a sharp "elbow" at 47 °C and, in the upper temperature range, an unexpectedly large activation energy (114 ± 8 kcal/mol) and an enormous prefactor (10 72±5 s -1 ). In this report, we present new measurements and a theoretical model that establish convincingly that this behavior results from a collective, entropy-driven breakup of the rigid hydrogen bonding networks (HBNs) that hinder the reaction at lower temperatures. For E181Q and S186A, two rhodopsin mutants that disrupt the HBNs near the binding pocket of the 11-cis retinyl chromophore, we observe significant decreases in the activation energy (∼90 kcal/mol) and prefactor (∼10 60 s -1 ), consistent with the conclusion that the reaction rate is enhanced by breakup of the HBN. The results provide insights into the molecular mechanism of dim-light vision and eye diseases caused by inherited mutations in the rhodopsin gene that perturb the HBNs.

We present molecular dynamics simulation results describing proton/deuteron exchange equilibria along hydrogen bonds at the vicinity of HX acids (X = F, I) in aqueous clusters at low temperatures. To allow for an adequate description of proton transfer processes, our simulation scheme resorted on the implementation of a multistate empirical valence bond hamiltonian coupled to a path integral scheme to account for effects derived from nuclear quantum fluctuations. We focused attention on clusters comprising a number of water molecules close to the threshold values necessary to stabilize contact-ion-pairs. For X = F, our results reveal a clear propensity of the heavy isotope to lie at the bond bridging the halide to the nearest water molecule. Contrasting, for X = I, the thermodynamic stability is reversed and the former connectivity is preferentially articulated via the light isotope. These trends remain valid for undissociated and ionic descriptions of the stable valence bond states. The preferences are rationalized in terms of differences in the quantum kinetic energies of the isotopes which, in turn, reflect the extent of the local spatial confinements prevailing along the different hydrogen bonds in the clusters. In most cases, these features are also clearly reflected in the characteristics of the corresponding stretching bands of the simulated infrared spectra. This opens interesting possibilities to gauge the extent of the isotopic thermodynamic stabilizations and the strengths of the different hydrogen bonds by following the magnitudes and shifts of the spectral signals in temperature-controlled experiments, performed on mixed clusters combining H2O and HOD.

We present results of ring polymer molecular dynamics simulations that shed light on the effects of nuclear quantum fluctuations on tunneling motions in cyclic [H2O]3 and [D2O]3, at the representative temperature of T = 75 K. In particular, we focus attention on free energies associated with two key isomerization processes: The first one corresponds to flipping transitions of dangling OH bonds, between up and down positions with respect to the O-O-O plane of the cluster; the second involves the interchange between connecting and dangling hydrogen bond character of the H-atoms in a tagged water molecule. Zero point energy and tunneling effects lead to sensible reductions of the free energy barriers. Due to the lighter nature of the H nuclei, these modifications are more marked in [H2O]3 than in [D2O]3. Estimates of the characteristic time scales describing the flipping transitions are consistent with those predicted based on standard transition-state-approximation arguments.

We present results from ring polymer molecular dynamics experiments that provide microscopic insights into the characteristics of the isotopic stabilizations of H and D aqueous species in the first solvation shell of a halide I(-) ion in water nanoclusters at low temperatures. The analysis of the simplest I(-)·(HOD) dimer shows a clear propensity for the light isotope to lie at the non-hydrogen-bonded dangling position. Our results predict that, at T ∼ 50 K, I(-)·(DOH) isomers are three times more abundant than I(-)·(HOD) ones. The reasons for such stabilization can be traced back to differences in the nuclear kinetic energy projected along directions perpendicular to the plane of the water molecule. Dynamical implications of these imbalances are shown to be reflected in the characteristics of the corresponding bands of the infrared spectroscopic signals. A similar analysis performed in larger aggregates containing ∼20 water molecules reveals, in contrast, a stabilization of the light isotope along I(-)···HO hydrogen bonds. Effects derived from the consideration of smaller halide anions with larger electric fields at the surface are also examined.

Using ring polymer molecular dynamics simulations, we examine equilibrium and dynamical characteristics of solid-like, aqueous clusters that combine isotopic mixtures of HDO dilute in H2O, at temperatures intermediate between 50 and 175 K. In particular, we focus attention on the relative thermodynamic stabilities of the two isotopes at dangling hydrogen bond sites. The water octamer is analyzed as a reference system. For this aggregate, decreasing temperature yields a gradual stabilization of the light isotope at dangling sites in molecules acting as single-donor-double-acceptors of hydrogen bonds. At T ∼ 50 K, the imbalance between the corresponding quantum kinetic energies leads to a free energy difference between dangling and hydrogen bonded sites of the order of ∼2kBT. Similar free energy differences were found at dangling sites in Nw = 50 water clusters. The extent of the H/D segregation can be adequately monitored by modifications in the peak intensity of the high frequency shoulder of the stretching band of the infrared spectrum. These signals, in turn, represent a potential experimental signature of the elusive temperature of clusters in molecular beams.

We use ring-polymer-molecular-dynamics (RPMD) techniques and the semi-empirical q-TIP4P/F water model to investigate the relationship between hydrogen bond connectivity and the characteristics of nuclear position fluctuations, including explicit incorporation of quantum effects, for the energetically low lying isomers of the prototype cluster [H2O]8 at T = 50 K and at 150 K. Our results reveal that tunneling and zero-point energy effects lead to sensible increments in the magnitudes of the fluctuations of intra and intermolecular distances. The degree of proton spatial delocalization is found to map logically with the hydrogen-bond connectivity pattern of the cluster. Dangling hydrogen bonds exhibit the largest extent of spatial delocalization and participate in shorter intramolecular O-H bonds. Combined effects from quantum and polarization fluctuations on the resulting individual dipole moments are also examined. From the dynamical side, we analyze the characteristics of the infrared absorption spectrum. The incorporation of nuclear quantum fluctuations promotes red shifts and sensible broadening relative to the classical profile, bringing the simulation results in much more satisfactory agreement with direct experimental information in the mid and high frequency range of the stretching band. While RPMD predictions overestimate the peak position of the low frequency shoulder, the overall agreement with that reported using an accurate, parameterized, many-body potential is reasonable, and far superior to that one obtains by implementing a partially adiabatic centroid molecular dynamics approach. Quantum effects on the collective dynamics, as reported by instantaneous normal modes, are also discussed.

Ring polymer molecular dynamics experiments have been carried out to examine effects derived from nuclear quantum fluctuations at ambient conditions on equilibrium and non-equilibrium dynamical characteristics of charge solvation by a popular simple, rigid, water model, SPC/E , and for a more recent, and flexible, q-TIP4P/F model, to examine the generality of conclusions. In particular, we have recorded the relaxation of the solvent energy gap following instantaneous, ±e charge jumps in an initially uncharged Lennard-Jones-like solute. In both charge cases, quantum effects are reflected in sharper decays at the initial stages of the relaxation, which produce up to a ∼20% reduction in the characteristic timescales describing the solvation processes. For anionic solvation, the magnitude of polarization fluctuations controlling the extent of the water proton localization in the first solvation shell is somewhat more marked than for cations, bringing the quantum solvation process closer to the classical case. Effects on the solvation response from the explicit incorporation of flexibility in the water Hamiltonian are also examined. Predictions from linear response theories for the overall relaxation profile and for the corresponding characteristic timescales are reasonably accurate for the solvation of cations, whereas we find that they are much less satisfactory for the anionic case.

Molecular dynamics simulations have been carried out to investigate structural and dynamical characteristics of NaCl aqueous solutions confined within silica nanopores in contact with a "bulk-like" reservoir. Two types of pores, with diameters intermediate between 20 Å and 37.5 Å, were investigated: The first one corresponded to hydrophobic cavities, in which the prevailing wall-solution interactions were of the Lennard-Jones type. In addition, we also examined the behavior of solutions trapped within hydrophilic cavities, in which a set of unsaturated O-sites at the wall were transformed in polar silanol Si-OH groups. In all cases, the overall concentrations of the trapped electrolytes exhibited important reductions that, in the case of the narrowest pores, attained 50% of the bulk value. Local concentrations within the pores also showed important fluctuations. In hydrophobic cavities, the close vicinity of the pore wall was coated exclusively by the solvent, whereas in hydrophilic pores, selective adsorption of Na(+) ions was also observed. Mass and charge transport were also investigated. Individual diffusion coefficients did not present large modifications from what is perceived in the bulk; contrasting, the electrical conductivity exhibited important reductions. The qualitative differences are rationalized in terms of simple geometrical considerations., (© 2011 American Institute of Physics)