Simplified Sum-Over-States Approach for Predicting Resonance Raman Spectra. Application to Nucleic Acid Bases

Resonance Raman spectra provide a valuable probe into molecular excited-state structures and properties. Moreover, resonance enhancement is of importance for the chemical contribution to surface-enhanced Raman scattering. In this work, we introduce a simplified sum-over-states scheme for computing Raman spectra and Raman excitation profiles. The proposed sum-over-states approach uses derivatives of electronic excitation energies and transition dipole moments, which can be efficiently computed from time-dependent density functional theory. We analyze and interpret the resonance Raman spectra and Raman excitation profiles of nucleic acid bases using the present approach. Contributions of individual excited states under strictly resonant and non-resonant conditions are investigated, and smooth interpolation between both limiting cases is obtained.Chemistry and Chemical Biolog

Modeling Coherent Anti-Stokes Raman Scattering with Time-Dependent Density Functional Theory: Vacuum and Surface Enhancement

We present the first density functional simulations of coherent anti-Stokes Raman scattering (CARS) and an analysis of the chemical effects upon binding to a metal surface. Spectra are obtained from first-principles electronic structure calculations and are compared with available experiments and previously available theoretical results following from Hartree–Fock polarizability derivatives. A first approximation to the nonresonant portion of the CARS signal is also explored. We examine the silver pyridine cluster models of the surface chemical signal enhancement, previously introduced for surface-enhanced Raman scattering. Chemical resonant intensity enhancements of roughly $10^2$ are found for several model clusters. The prospects of realizing further enhancement of CARS signal with metal surfaces is discussed in light of the predicted chemical enhancements.Chemistry and Chemical Biolog

Complex Chemical Reaction Networks from Heuristics-Aided Quantum Chemistry

While structures and reactivities of many small molecules can be computed efficiently and accurately using quantum chemical methods, heuristic approaches remain essential for modeling complex structures and large-scale chemical systems. Here, we present a heuristics-aided quantum chemical methodology applicable to complex chemical reaction networks such as those arising in cell metabolism and prebiotic chemistry. Chemical heuristics offer an expedient way of traversing high-dimensional reactive potential energy surfaces and are combined here with quantum chemical structure optimizations, which yield the structures and energies of the reaction intermediates and products. Application of heuristics-aided quantum chemical methodology to the formose reaction reproduces the experimentally observed reaction products, major reaction pathways, and autocatalytic cycles.Chemistry and Chemical BiologyPhysic

Separation of Electromagnetic and Chemical Contributions to Surface-Enhanced Raman Spectra on Nanoengineered Plasmonic Substrates

Raman signals from molecules adsorbed on a noble metal surface are enhanced by many orders of magnitude due to the plasmon resonances of the substrate. Additionally, the enhanced spectra are modified compared to the spectra of neat molecules; many vibrational frequencies are shifted, and relative intensities undergo significant changes upon attachment to the metal. With the goal of devising an effective scheme for separating the electromagnetic and chemical effects, we explore the origin of the Raman spectra modification of benzenethiol adsorbed on nanostructured gold surfaces. The spectral modifications are attributed to the frequency dependence of the electromagnetic enhancement and to the effect of chemical binding. The latter contribution can be reproduced computationally using molecule−metal cluster models. We present evidence that the effect of chemical binding is mostly due to changes in the electronic structure of the molecule rather than to the fixed orientation of molecules relative to the substrate.Chemistry and Chemical BiologyEngineering and Applied Science

Synthesis and Stereochemical Properties of Chiral Square Complexes of Iron(II)

Der hexadentate und ditopische Ligand 2,5-Bis([2,2']bipyridin-6-yl)pyrazin bildet bei der Selbstorganisationsreaktion mit Fe²⁺-Ionen einen chiralen, quadratförmigen Tetramerkomplex. Das Racemat dieses Komplexes wurde mit Hilfe von Antimonyltartrat in die Enantiomere getrennt. Die Reinheit des Enantiomers wurde durch NMR-Spektroskopie unter Zuhilfenahme eines chiralen, diamagnetischen Shift-Reagenzes untersucht, wie auch duch die Beobachtung des Circulardichroismus (CD). Das CD-Spektrum wurde zudem mit zeitabhängiger Dichtefunktionaltheorie berechnet, wobei die vorhergesagte Korrelation zwischen CD-Spektrum und Konfiguration des Komplexes durch Röntgenstrukturanalyse bestätigt wurde. Die Verwendung einer chiralisierten Variante des Liganden ergab den entsprechenden Eisenkomplex in diastereomerenreiner Form.The hexadentate, and ditopic ligand 2,5-bis([2,2']bipyridin-6-yl)pyrazine yields a chiral, tetrameric, square-shaped, self-assembled species upon complexation with Fe²⁺ ions. The racemate of this complex was resolved with antimonyl tatrate as the chiral auxiliary. The purity of the enantiomer was determined by NMR spectroscopy, by using a chiral, diamagnetic shift reagent, and by circular dichroism (CD). The CD spectrum was also calculated by time-dependent density functional theory, and the correlation that was found between CD spectrum and configuration was confirmed by X-ray cristallography. When a chiralised version of the ligand was used instead, the corresponding iron complex was obtained in diastereomerically pure form

Electronic Structure Calculations in Arbitrary Electrostatic Environment

Modeling of electronic structure of molecules in electrostatic environments is of considerable relevance for surface-enhanced spectroscopy and molecular electronics. We have developed and implemented a novel approach to the molecular electronic structure in arbitrary electrostatic environments that is compatible with standard quantum chemical methods and can be applied to medium-sized and large molecules. The scheme denoted CheESE (chemistry in electrostatic environments) is based on the description of molecular electronic structure subject to a boundary condition on the system/environment interface. Thus, it is particularly suited to study molecules on metallic surfaces. The proposed model is capable of describing both electrostatic effects near nanostructured metallic surfaces and image-charge effects. We present an implementation of the CheESE model as a library module and show example applications to neutral and negatively charged molecules.Chemistry and Chemical Biolog

Quantum Chemical Approach to Estimating the Thermodynamics of Metabolic Reactions

Thermodynamics plays an increasingly important role in modeling and engineering metabolism. We present the first nonempirical computational method for estimating standard Gibbs reaction energies of metabolic reactions based on quantum chemistry, which can help fill in the gaps in the existing thermodynamic data. When applied to a test set of reactions from core metabolism, the quantum chemical approach is comparable in accuracy to group contribution methods for isomerization and group transfer reactions and for reactions not including multiply charged anions. The errors in standard Gibbs reaction energy estimates are correlated with the charges of the participating molecules. The quantum chemical approach is amenable to systematic improvements and holds potential for providing thermodynamic data for all of metabolism.Chemistry and Chemical Biolog

Electronic Transition Moments of 6-methyl Isoxanthopterin—A Fluorescent Analogue of the Nucleic Acid Base Guanine

Fluorescent nucleic acid base analogues are important spectroscopic tools for understanding local structure and dynamics of DNA and RNA. We studied the orientations and magnitudes of the electric dipole transition moments (EDTMs) of 6-methyl isoxanthopterin (6-MI), a fluorescent analogue of guanine that has been particularly useful in biological studies. Using a combination of absorption spectroscopy, linear dichroism (LD) and quantum chemical calculations, we identified six electronic transitions that occur within the 25 000–50 000 $cm^{−1}$ spectral range. Our results indicate that the two experimentally observed lowest-energy transitions, which occur at 29 687 $cm^{−1}$ (337 nm) and 34 596 $cm^{−1}$ (289 nm), are each polarized within the plane of the 6-MI base. A third in-plane polarized transition is experimentally observed at 47 547 $cm^{−1}$ (210 nm). The theoretically predicted orientation of the lowest-energy transition moment agrees well with experiment. Based on these results, we constructed an exciton model to describe the absorption spectra of a 6-MI dinucleotide–substituted double-stranded DNA construct. This model is in good agreement with the experimental data. The orientations and intensities of the low-energy electronic transitions of 6-MI reported here should be useful for studying local conformations of DNA and RNA in biologically important complexes.Chemistry and Chemical Biolog