The dynamics of water are examined using ultrafast IR stimulated vibrational echo correlation spectroscopy. OD hydroxyl stretch HOD in H2O is probed with 45-fs pulses that have sufficient bandwidth (>400 cm-1) to span the entire broad spectrum. High-quality 2D spectra obtained having correct phase relations across band. found evolve on multiple time scales. evolution spectrum reflects structural hydrogen bond networks. extended lifetime facilitates measurement for longer times than possible...

Vibrational echo correlation spectroscopy experiments on the OD stretch of dilute HOD in H(2)O are used to probe structural dynamics water. A method is demonstrated for combining spectra taken with different infrared pulse bandwidths (pulse durations), making it possible use data collected from many which laser properties not identical. Accurate measurements anharmonicity (162 cm(-1)) presented and analysis. In addition, recent accurate determination vibrational lifetime (1.45 ps) time scale...

The mutational repertoire of cancers creates the neoepitopes that make immunogenic. Here, we introduce two novel tools identify, with relatively high accuracy, small proportion (among hundreds potential neoepitopes) protect host through an antitumor T cell response. consist (a) numerical difference in NetMHC scores between mutated sequences and their unmutated counterparts, termed differential agretopic index, (b) conformational stability MHC I–peptide interaction. Mechanistically, these...

We present a new approach that combines electronic structure methods and molecular dynamics simulations to investigate the infrared spectroscopy of condensed phase systems. This is applied OH stretch band dilute HOD in liquid D2O OD H2O for two commonly employed models water, TIP4P SPC/E. Ab initio anharmonic transition frequencies are calculated 100 x (D2O)n x(H2O)n (n = 4-9) clusters randomly selected from water simulations. A linear empirical relationship between ab component electric...

The iconic helical structure of DNA is stabilized by the solvation environment, where a change in hydration state can lead to dramatic changes structure. X-ray diffraction experiments at cryogenic temperatures have shown crystallographic water molecules minor groove DNA, which has led notion spine DNA. Here, chiral nonlinear vibrational spectroscopy two sequences shows that not only do such structural exist solution ambient conditions but they form superstructure: hydration. This first...

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 H2O, respectively. The quantities needed compute were obtained from density functional theory calculations performed on clusters, generated liquid-state configurations, containing an molecule along with 4−9 solvent water molecules. frequency, transition dipole, polarizability each empirically related electric field due (or OD)...

In the context of vibrational spectroscopy in liquids, non-Condon effects refer to dependence transition dipole moment a particular molecule on rotational and translational coordinates all molecules liquid. For strongly hydrogen-bonded systems, such as liquid water, are large. That is, bond derivative an OH stretch depends its hydrogen-bonding environment. Previous calculations nonlinear liquids have not included these effects. We find that for inclusion is important accurate calculation of,...

Kwac and Cho [J. Chem. Phys. 119, 2247 (2003)] have recently developed a combined electronic structure/molecular dynamics approach to vibrational spectroscopy in liquids. The method involves fitting ab initio frequencies for solute cluster of solvent molecules linear combination the electrostatic potentials on atoms due charges molecules. These authors applied their N-methylacetamide-D/D(2)O system. We (S. A. Corcelli, C. P. Lawrence, J. L. Skinner, 120, 8107 (2004)]) explored closely...

Textbooks describe excess protons in liquid water as hydronium (H3O+) ions, although their true structure remains lively debated. To address this question, we have combined Raman and infrared (IR) multivariate curve resolution spectroscopy with ab initio molecular dynamics anharmonic vibrational spectroscopic calculations. Our results are used to resolve, for the first time, spectra of hydrated counterions reveal that there is little ion-pairing below 2 M. Moreover, find isolated strongly IR...

Together, spectroscopy combined with computational studies that relate directly to the experimental measurements have potential provide unprecedented insight into dynamics of important biological processes. Recent time-resolved fluorescence experiments shown time scales for collective reorganization at interface proteins and DNA water are more than an order magnitude slower in bulk aqueous solution. The molecular interpretation this change response is somewhat controversial some attribute...

We use temperature-dependent ultrafast infrared spectroscopy of dilute HOD in H2O to study the picosecond reorganization hydrogen bond network liquid water. Temperature-dependent two-dimensional (2D IR), pump−probe, and linear absorption measurements are self-consistently analyzed with a response function formalism that includes effects spectral diffusion, population lifetime, reorientational motion, nonequilibrium heating local environment upon vibrational relaxation. Over range 278−345 K,...

The C≡N bond is a powerful probe of protein structure and dynamics because it absorbs in region the infrared spectrum apart from other vibrations that occur naturally proteins, its absorption line shape sensitive to specific characteristics local environment. Since polarity experienced by can differ dramatically within protein, spectroscopy site-specifically labeled residue be used infer environment protein. It has been shown experimentally acetonitrile water different terms peak position...

Time-dependent Stokes shift experiments of fluorescent probe molecules incorporated into DNA have uncovered a broad range time scales from femtoseconds to tens nanoseconds. A series recent molecular dynamics simulations investigated the longest solvation with sometimes conflicting interpretations. The conclusions these computational studies are reviewed along theoretical methodologies that utilized decompose calculated responses in terms components present system: water, DNA, and ions....

Maps that relate spectroscopic properties of a vibrational mode and collective solvent coordinates have proven useful in theoretical spectroscopy condensed-phase systems. It has been realized the predictive power such an approach is limited there no clear systematic way to improve its accuracy. Here, we propose adaptation Δ-machine-learning methodology goes beyond maps. The machine-learning part our combines Gaussian process regression used generate data set with artificial neural network...

We apply the combined electronic structure/molecular dynamics approach of Corcelli, Lawrence, and Skinner [J. Chem. Phys. 120, 8107 (2004)] to fluctuating charge (SPC-FQ) model liquid water developed by Rick, Stuart, Berne 101, 6141 (1994)]. For HOD in H(2)O time scale for long-time decay OD stretch frequency time-correlation function, which corresponds hydrogen-bond rearrangement liquid, is about 1.5 ps. This result significantly longer than 0.9 ps previously calculated nonpolarizable SPC/E...

Abstract The preparation of 7‐Fc + ‐8‐Fc‐7,8‐ nido ‐[C 2 B 9 H 10 ] − (Fc FcC ) demonstrates the successful incorporation a carborane cage as an internal counteranion bridging between ferrocene and ferrocenium units. This neutral mixed‐valence Fe II /Fe III complex overcomes proximal electronic bias imposed by external counterions, practical limitation in use molecular switches. A combination UV/Vis‐NIR spectroscopic TD‐DFT computational studies indicate that electron transfer within Fc is...

T cell receptor (TCR) recognition of antigenic peptides bound and presented by class I major histocompatibility complex (MHC) proteins underlies the cytotoxic immune response to diseased cells. Crystallographic structures TCR-peptide/MHC complexes have demonstrated how TCRs simultaneously interact with both peptide MHC protein. However, it is increasingly recognized that, beyond serving as a static platform for presentation, physical properties are tuned different in ways that not always...

Although DNA-ligand binding is pervasive in biology, little known about molecular-level mechanisms. Using all-atom, explicit-solvent molecular dynamics simulations conjunction with weighted ensemble (WE)-enhanced sampling, an of 2562 trajectories Hoechst 33258 (H33258) to d(CGC AAA TTT GCG) was generated from which the mechanism extracted. In particular, electrostatic interaction between positively charged H33258 and negatively DNA backbone drives formation initial H33258-DNA contacts. After...

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 challenge is to calculate instantaneous frequencies a molecule in contact molecular environment, accurately quickly, this end number different methods have been developed. In paper we critically analyze these by comparing their results accurate benchmark...