Theoretical Study on Hydrogen‐Bond Effects in IR Spectra of High‐ and Low‐Temperature Phases of Nitric Acid Dihydrate

The low‐ and high‐temperature phases (α and β, respectively) of solid nitric acid dihydrate (NAD) are studied in depth by DFT methods. Each phase contains two types of complex structures (H₃O⁺) ? (H₂O), designated A and B, with different hydrogen‐bonding (HB) characteristics. The theoretical study reveals that type A complexes are weakly bound and could be described as (H₃O)⁺ and H₂O aggregates, with decoupled vibrational modes, whereas in type B structures the proton is situated close to the centre of the O ??? O bond and induces strong vibrational coupling. The proton‐transfer mode is predicted at quite different wavenumbers in each complex, which provides an important differentiating spectral feature, together with splitting of some bands in β‐NAD. Theoretical spectra are estimated by using two GGA parameterizations, namely, PBE and BLYP. The potential‐energy surface for each type of HB in NAD is also studied, as is the spectral influence of displacement of the shared H atom along the O? O bond. The results are compared to literature infrared spectra recorded by different techniques, namely, transmission and reflection–absorption, with both normal and tilted incident radiation. This work provides a thorough assignment of the observed spectra, and predictions for some spectra not yet available. The usefulness of high‐level theoretical calculations as performed herein to discriminate between two phases of a solid crystal is thus evidenced.     

Identifying Protein β‐Turns with Vibrational Raman Optical Activity

β‐turns belong to the most important secondary structure elements in proteins. On the basis of density functional calculations, vibrational Raman optical activity signatures of different types of β‐turns are established and compared as well as related to other signatures proposed in the literature earlier. Our findings indicate that there are much more characteristic ROA signals of β‐turns than have been hitherto suggested. These suggested signatures are, however, found to be valid for the most important type of β‐turns. Moreover, we compare the influence of different amino acid side chains on these signatures and investigate the discrimination of β‐turns from other secondary structure elements, namely α‐ and 3₁₀‐helices.     

Can Raman Optical Activity Separate Axial from Local Chirality? A Theoretical Study of Helical Deca‐Alanine

Motivated by experimental work on the distinction of protein secondary structure motifs by Raman optical activity (ROA) spectroscopy, we demonstrate using density functional theory that axial chirality in structures with different local chirality can be filtered out by ROA spectroscopy. To this purpose, two diastereomers of right-handed helical deca-alanine, the (all-S) and the (R,S,R,S,R,S,R,S,R,S) form, are compared. Furthermore, we suggest to interpret calculated ROA spectra of large molecules in terms of vibrational bands rather than individual peaks. This is due to the non-homogeneous effect of the harmonic approximation as well as of the chosen electronic structure method onto the vibrational frequencies, which in a dense region of many vibrations will strongly determine the shape of the spectrum. In addition, the calculated ROA spectrum of (all-S)-deca-alanine is compared to the experimental spectrum of poly-(L)-alanine in solution.     

Synthesis,Spectroscopy, and Computational Analysis of Photoluminescent Bis(aminophenyl)‐Substituted Thiophene Derivatives

Substituted oligothiophenes have a long history in the field of organic electronics, as they often combine outstanding electro‐optical properties with the ease of synthesis. To assist the rational selection of the most promising structures to be synthesized, there is the demand for tools that allow prediction of the properties of the materials. In this study, we present strategies for synthesis and computational characterization, with respect to the fluorescence behavior of oligothiophene‐based materials for organoelectronic applications. In a combined approach, sophisticated computational methodologies are directly compared to experimental results. The M06‐2X functional in combination with the polarizable continuum model in a state‐specific formulation for excited‐state solvation proved to be particularly reliable. In addition, a semiclassical approach for describing the vibrational broadening of the spectra is employed. As a result, a robust procedure for the prediction of the fluorescence spectra of oligothiophene derivatives is presented.     

Prediction of Raman Optical Activity Spectra of Chiral 3‐Acetylcamphorato‐Cobalt Complexes

We examine calculated vibrational Raman optical activity (ROA) spectra of octahedral cobalt complexes containing different combinations of acetylacetonato and 3‐acetylcamphorato ligands. Starting from the Δ‐tris(acetylacetonato)cobalt(III) complex, the ROA spectra of isomers generated by successive replacement of acetylacetonato ligands by chiral (+)‐ or (?)‐3‐acetylcamphorato ligands are investigated. In this way, it is possible to assess the influence of the degree of ligand substitution, ligand chirality, and geometrical isomerism on the ROA spectra. In addition, the effect of the Λ‐configuration is studied. It is found that the ROA spectra contain features that make it possible to identify each of the isomers, demonstrating the great sensitivity of ROA spectroscopy to the chiral nature of the various complexes.     

Vibrational Property of α-Borophene Determined by Tip-Enhanced Raman Spectroscopy

We report a Raman characterization of the α borophene polymorph by scanning tunneling microscopy combined with tip-enhanced Raman spectroscopy. A series of Raman peaks were discovered, which can be well related with the phonon modes calculated based on an asymmetric buckled α structure. The unusual enhancement of high-frequency Raman peaks in TERS spectra of α borophene is found and associated with its unique buckling when landed on the Ag(111) surface. Our paper demonstrates the advantages of TERS, namely high spatial resolution and selective enhancement rule, in studying the local vibrational properties of materials in nanoscale.     

Understanding the Supramolecular Self‐Assembly of the Fullerene Derivative PCBM on Gold Surfaces

We report a DFT study on the self‐assembly of the fullerene derivative PCBM on the Au(111) surface. Recent STM experiments (Angew. Chem. 2007 , 119, 8020–8023^[1]) show a coverage‐dependent transition of the adsorption and self‐assembly of PCBM on this surface. To understand the origin of this observation, we compute the geometries and relative energies of ten PCBM dimers and four tetramers. The calculations show that the self‐assembly of PCBM at high coverage is mainly controlled by hydrogen bonding between the PCBM tails. Due to the large size of the fullerene cage, the hydrogen bonds are formed far away from the surface; hence they are very similar to those found in the gas phase. This picture successfully explains the observed site‐insensitive adsorption at high coverage and the 2D arrangement of PCBM on the surface.     

The Nature of Activated Non‐classical Hydrogen Bonds: A Case Study on Acetylcholinesterase–Ligand Complexes

Molecular recognition events in biological systems are driven by non‐covalent interactions between interacting species. Here, we have studied hydrogen bonds of the CH???Y type involving electron‐deficient CH donors using dispersion‐corrected density functional theory (DFT) calculations applied to acetylcholinesterase–ligand complexes. The strengths of CH???Y interactions activated by a proximal cation were considerably strong; comparable to or greater than those of classical hydrogen bonds. Significant differences in the energetic components compared to classical hydrogen bonds and non‐activated CH???Y interactions were observed. Comparison between DFT and molecular mechanics calculations showed that common force fields could not reproduce the interaction energy values of the studied hydrogen bonds. The presented results highlight the importance of considering CH???Y interactions when analysing protein–ligand complexes, call for a review of current force fields, and opens up possibilities for the development of improved design tools for drug discovery.     

Visualization of Vibrational Modes in Real Space by Tip‐Enhanced Non‐Resonant Raman Spectroscopy

We present a general theory to model the spatially resolved non‐resonant Raman images of molecules. It is predicted that the vibrational motions of different Raman modes can be fully visualized in real space by tip‐enhanced non‐resonant Raman scattering. As an example, the non‐resonant Raman images of water clusters were simulated by combining the new theory and first‐principles calculations. Each individual normal mode gives rise its own distinct Raman image, which resembles the expected vibrational motions of the atoms very well. The characteristics of intermolecular vibrations in supermolecules could also be identified. The effects of the spatial distribution of the plasmon as well as nonlinear scattering processes were also addressed. Our study not only suggests a feasible approach to spatially visualize vibrational modes, but also provides new insights in the field of nonlinear plasmonic spectroscopy.     

Interactions of Molecules with cis and trans Double Bonds: A Theoretical Study of cis‐ and trans‐2‐Butene

Noncovalent interactions of cis‐ and trans‐2‐butene, as the smallest model systems of molecules with cis and trans double bonds, were studied to find potential differences in interactions of these molecules. The study was performed using quantum chemical methods including very accurate CCSD(T)/CBS method. We studied parallel and displaced parallel interactions in 2‐butene dimers, in butane dimers, and between 2‐butene and saturated butane. The results show the trend that interactions of 2‐butene with butane are the strongest, followed by interactions in butane dimers, whereas the interaction in 2‐butene dimers are the weakest. The strongest calculated interaction energy is between trans‐2‐butene and butane, with a CCSD(T)/CBS energy of ?2.80 kcal mol^?1. Interactions in cis‐2‐butene dimers are stronger than interactions in trans‐2‐butene dimers. Interestingly, some of the interactions involving 2‐butene are as strong as interactions in a benzene dimer. These insights into interactions of cis‐ and trans‐2‐butene can improve understanding of the properties and processes that involve molecules with cis and trans double bonds, such as fatty acids and polymers.     

Environmental Effects in Computational Spectroscopy: Accuracy and Interpretation

Spectroscopic techniques are valuable tools for understanding the structure and dynamics of complex systems, such as biomolecules or nanomaterials. Most of the current research is devoted to the development of new experimental techniques for improving the intrinsic resolution of different spectra. However, the subtle interplay of several different effects acting at different length and time scales still makes the interpretation and analysis of such spectra a very difficult task. In this respect, computational spectroscopy is becoming a needful and versatile tool for the assignment and interpretation of experimental spectra. It is in fact possible nowadays to model with relatively high accuracy the physical–chemical properties of complex molecules in different environments, and to link spectroscopic evidence directly to the structural and dynamical properties of optically or magnetically active solvated probes. In this Review, significant steps toward the simulation of entire spectra in condensed phases are presented together with some basic aspects of computational spectroscopy, which highlight how intramolecular and intermolecular degrees of freedom influence several spectroscopic parameters.