Noncovalent Interactions of Hydrated DNA and RNA Mapped by 2D-IR Spectroscopy

Biomolecules couple to their aqueous environment through a variety of noncovalent interactions. Local structures at the surface of DNA and RNA are frequently determined by hydrogen bonds with water molecules, complemented by non-specific electrostatic and many-body interactions. Structural fluctuations of the water shell result in fluctuating Coulomb forces on polar and/or ionic groups of the biomolecular structure and in a breaking and reformation of hydrogen bonds. Two-dimensional infrared (2D-IR) spectroscopy of vibrational modes of DNA and RNA gives insight into local hydration geometries, elementary molecular dynamics, and the mechanisms behind them. In this chapter, recent results from 2D-IR spectroscopy of native and artificial DNA and RNA are presented, together with theoretical calculations of molecular couplings and molecular dynamics simulations. Backbone vibrations of DNA and RNA are established as sensitive noninvasive probes of the complex behavior of hydrated helices. The results reveal the femtosecond fluctuation dynamics of the water shell, the short-range character of Coulomb interactions, and the strength and fluctuation amplitudes of interfacial electric fields.Comment: To appear as Chapter 8 of Springer Series in Optical Sciences: Coherent Multidimensional Spectroscopy -- Editors: Cho, Minhaeng (Ed.), 201

Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction

© 2020 American Chemical Society. Vibrational spectroscopy is an essential tool in chemical analyses, biological assays, and studies of functional materials. Over the past decade, various coherent nonlinear vibrational spectroscopic techniques have been developed and enabled researchers to study time-correlations of the fluctuating frequencies that are directly related to solute-solvent dynamics, dynamical changes in molecular conformations and local electrostatic environments, chemical and biochemical reactions, protein structural dynamics and functions, characteristic processes of functional materials, and so on. In order to gain incisive and quantitative information on the local electrostatic environment, molecular conformation, protein structure and interprotein contacts, ligand binding kinetics, and electric and optical properties of functional materials, a variety of vibrational probes have been developed and site-specifically incorporated into molecular, biological, and material systems for time-resolved vibrational spectroscopic investigation. However, still, an all-encompassing theory that describes the vibrational solvatochromism, electrochromism, and dynamic fluctuation of vibrational frequencies has not been completely established mainly due to the intrinsic complexity of intermolecular interactions in condensed phases. In particular, the amount of data obtained from the linear and nonlinear vibrational spectroscopic experiments has been rapidly increasing, but the lack of a quantitative method to interpret these measurements has been one major obstacle in broadening the applications of these methods. Among various theoretical models, one of the most successful approaches is a semiempirical model generally referred to as the vibrational spectroscopic map that is based on a rigorous theory of intermolecular interactions. Recently, genetic algorithm, neural network, and machine learning approaches have been applied to the development of vibrational solvatochromism theory. In this review, we provide comprehensive descriptions of the theoretical foundation and various examples showing its extraordinary successes in the interpretations of experimental observations. In addition, a brief introduction to a newly created repository Web site (http://frequencymap.org) for vibrational spectroscopic maps is presented. We anticipate that a combination of the vibrational frequency map approach and state-of-the-art multidimensional vibrational spectroscopy will be one of the most fruitful ways to study the structure and dynamics of chemical, biological, and functional molecular systems in the future

On the Origins of Large Interaction-Induced First Hyperpolarizabilities in Hydrogen-Bonded π‑Electronic Complexes

In this article we elucidate the origins of interaction-induced linear and nonlinear electro-optic properties of model hydrogen-bonded π-electronic complexes. In particular we report on contributions due to various interaction energy terms to excess dipole moments (Δμ), electric dipole polarizabilities (Δα), and first hyperpolarizabilities (Δβ), focusing on the latter. The analysis of intermolecular interaction-induced electric properties is performed for selected model systems including quasi-linear dimers of urea, diformamide, 4-pyridone, 4-nitroaniline, and the complex of hydrogen fluoride with nitroacetylene. The nature of intermolecular interactions as well as of the Δμ and Δα is very similar in all studied complexes. However, partitioning of Δβ into physically well-defined components reveals that the origins of this term, the magnitude of which is often comparable to the hyperpolarizabilities of isolated monomers, are different in each case. Our results indicate that, even though hydrogen bonding usually diminishes the nonlinear response of interacting species, the first hyperpolarizability of complexes with the nitro group acting as a proton acceptor is substantially increased, essentially due to field-induced changes of electrostatic interactions between subsystems. However, in the remaining complexes the origins of Δβ are much more involved. Even though at large intermolecular separations the origins of interaction-induced electric properties are essentially due to the field-induced electrostatic and induction interactions, in the vicinity of van der Waals minimum the overlap effects cannot be neglected since they may substantially alter the predicted excess properties or even determine their magnitude and sign. On the other hand the Δβ contribution due to dispersion interactions is usually negligible. Interestingly, the values of interaction-induced first hyperpolarizability in some cases depend strongly on the intermolecular separation in the vicinity of equilibrium geometry

Distributed Multipolar Expansion Approach to Calculation of Excitation Energy Transfer Couplings

We propose a new approach for estimating the electrostatic part of the excitation energy transfer (EET) coupling between electronically excited chromophores based on the transition density-derived cumulative atomic multipole moments (TrCAMM). In this approach, the transition potential of a chromophore is expressed in terms of truncated distributed multipolar expansion and analytical formulas for the TrCAMMs are derived. The accuracy and computational feasibility of the proposed approach is tested against the exact Coulombic couplings, and various multipole expansion truncation schemes are analyzed. The results of preliminary calculations show that the TrCAMM approach is capable of reproducing the exact Coulombic EET couplings accurately and efficiently and is superior to other widely used schemes: the transition charges from electrostatic potential (TrESP) and the transition density cube (TDC) method

Erratum: Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction (Chemical Reviews (2020) 120:15 (7152−7218) DOI: 10.1021/acs.chemrev.9b00813)

The authors make the following additions and corrections to the paper, C. Baiz et al., Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction. Chem. Rev. 2020, 120, 7152?7218. 1. The below funding sources should be added to the Acknowledgments section on pages 7204 and 7205: NHG acknowledges support from the National Science Foundation (CHE-1905395). AT thanks the Advanced Materials for Energy-Water Systems (AMEWS) Center (DE-AC02-06CH11357) for support. Thus, the Acknowledgments should be as follows: This work was supported by IBS-R023-D1 (MC). BB wishes to thank the European Union’s Horizon 2020 under the Marie Sk?odowska-Curie Grant Agreement No. 665778, as well as the National Science Centre, Poland (grant no. 2016/23/P/ST4/01720). CRB acknowledges generous support from the National Science Foundation (CHE-847199, BIO-1815354 ) , the National Ins t i t u tes o f Hea l t h (R35GM133359), and the Welch Foundation (F-1891). NHG acknowledges support from the National Science Foundation (CHE-1905395). MWDH-H and JDH thank the University of Nottingham, Green Chemicals Beacon for funding toward this research. AT thanks the Advanced Materials for Energy-Water Systems (AMEWS) Center (DEAC02-06CH11357) for support. MCT acknowledges support from Department of Energy (DE-SC0018983), National Science Foundation (1552996), and National Institutes of Health (GM114500). AGD would like to thank Prof. Andrei Tokmakoff for discussing amide modes when he was a Ph.D. student. LW acknowledges the support from the National Institutes of Health through Award R01GM130697. SAC acknowledges support from National Science Foundation (CHE-1565471). 2. The affiliations of Minhaeng Cho and Kijeong Kwak on page 7201 should be corrected as follows: Minhaeng Cho ? Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Republic of Korea; Department of Chemistry, Korea University, Seoul 02841, Republic of Korea Kijeong Kwac ? Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Republic of Korea 3. Reference 329 on page 7214 should be replaced with the following paper: (329) Sul, S; Karaiskaj, D.; Jiang Y.; Ge, N.-H. Conformations of N-Acetyl-L-Prolinamide by Two-Dimensional Infrared Spectroscopy. J. Phys. Chem. B 2006, 110, 19891?19905. 4. A correction in the biography of Magnus Hanson-Heine on page 7203 should be made. MH-H received his Ph.D. in 2014, not 2010