: The unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio. Harmonic force fields are obtained using Density Functional Theory (DFT), MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set. DFT calculations use the Local Spin Density Approximation (LSDA), BLYP, and Becke3LYP (B3LYP) density functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with experiment. The MP2 force field yields spectra in slightly worse agreement with experiment than the B3LYP force field. The SCF force field yields spectra in poor agreement with experiment.The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreements with experiment. jg

Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields

Time-Dependent Density Functional Theory (TD-DFT) has become the most widely-used theoretical approach to simulate the optical properties of both organic and inorganic molecules. In this contribution, we review TD-DFT benchmarks that have been performed during the last decade. The aim is often to pinpoint the most accurate or adequate exchangecorrelation functional(s). We present both the different strategies used to assess the functionals and the main results obtained in terms of accuracy. In particular, we discuss both vertical and adiabatic benchmarks and comparisons with both experimental and theoretical reference transition energies. More specific benchmarks (oscillator strengths, excited-state geometries, dipole moments, vibronic shapes, etc.) are summarized as well. V C 2013 Wiley Periodicals, Inc.

https://onlinelibrary.wiley.com/doi/pdf/10.1002/qua.24438

TD-DFT benchmarks: A review

Reactive oxygen, nitrogen, and sulfur species, referred to as ROS, RNS, and RSS, respectively, are produced during normal cell function and in response to various stimuli. An imbalance in the metabolism of these reactive intermediates results in the phenomenon known as oxidative stress. If left unchecked, oxidative molecules can inflict damage on all classes of biological macromolecules and eventually lead to cell death. Indeed, sustained elevated levels of reactive species have been implicated in the etiology (e.g., atherosclerosis, hypertension, diabetes) or the progression (e.g., stroke, cancer, and neurodegenerative disorders) of a number of human diseases.1 Over the past several decades, however, a new paradigm has emerged in which the aforementioned species have also been shown to function as targeted, intracellular second messengers with regulatory roles in an array of physiological processes.2 Against this backdrop, it is not surprising that considerable ongoing efforts are aimed at elucidating the role that these reactive intermediates play in health and disease.

Site-specific, covalent modification of proteins represents a prominent molecular mechanism for transforming an oxidant signal into a biological response. Amino acids that are candidates for reversible modification include cysteines whose thiol (i.e., sulfhydryl) side chain is deprotonated at physiological pH, which is an important attribute for enhancing reactivity. While reactive species can modify other amino acids (e.g., histidine, methionine, tryptophan, and tyrosine), this Review will focus exclusively on cysteine, whose identity as cellular target or “sensor” of reactive intermediates is most prevalent and established.3 Oxidation of thiols results in a range of sulfur-containing products, not just disulfide bridges, as typically presented in biochemistry textbooks. An overview of the most relevant forms of oxidized sulfur species found in vivo is presented in Chart 1.






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Chart 1

Biologically Relevant Cysteine Chemotypesa

aRed, irreversible modifications. Green, unique enzyme intermediates. Note: Additional modifications can form as enzyme intermediates including thiyl radicals, disulfides, and persulfides.

Cysteine-Mediated Redox Signaling: Chemistry, Biology, and Tools for Discovery

Lung Wa Chung,† W. M. C. Sameera,‡ Romain Ramozzi,‡ Alister J. Page, Miho Hatanaka,‡ Galina P. Petrova, Travis V. Harris,‡,⊥ Xin Li, Zhuofeng Ke, Fengyi Liu, Hai-Bei Li, Lina Ding, and Keiji Morokuma*,‡ †Department of Chemistry, South University of Science and Technology of China, Shenzhen 518055, China ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan Newcastle Institute for Energy and Resources, The University of Newcastle, Callaghan 2308, Australia Faculty of Chemistry and Pharmacy, University of Sofia, Bulgaria Boulevard James Bourchier 1, 1164 Sofia, Bulgaria Department of Chemistry, State University of New York at Oswego, Oswego, New York 13126, United States State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou 510275, China Key Laboratory of Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an, Shaanxi 710119, China School of Ocean, Shandong University, Weihai 264209, China School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China

The ONIOM Method and Its Applications

The development of femtosecond time-resolved methods for the study of gas-phase molecular dynamics is founded upon the seminal studies of Zewail and co-workers, as recognized in 1999 by the Nobel Prize in Chemistry.1 This methodology has been applied to chemical reactions ranging in complexity from bond-breaking in diatomic molecules to dynamics in larger organic and biological molecules, and has led to breakthroughs in our understanding of fundamental chemical processes. Photoexcited polyatomic molecules and anions often exhibit quite complex dynamics involving the redistribution of both charge and energy.2-6 These processes are the primary steps in the photochemistry of many polyatomic systems,7 are important in photobiological processes such as vision and photosynthesis,8 and underlie many concepts in molecular electronics.9 Femtosecond time-resolved methods involve a pump-probe configuration in which an ultrafast pump pulse initiates a reaction or, more generally, creates a nonstationary state or wave packet, the evolution of which is monitored as a function of time by means of a suitable probe pulse. Time-resolved or wave packet methods offer a view complementary to the usual spectroscopic approach and often yield a physically intuitive picture. Wave packets can behave as zeroth-order or even classical-like states and are therefore very helpful in discerning underlying dynamics. The information obtained from these experiments is very much dependent on the nature of the final state chosen in a given probe scheme. Transient absorption and nonlinear wave mixing are often the methods of choice in condensed-phase experiments because of their generality. In studies of molecules and clusters in the gas phase, the most popular methods, laser-induced fluorescence and resonant multiphoton ionization, usually require the probe laser to be resonant with an electronic transition in the species being monitored. However, as a chemical reaction initiated by the pump pulse evolves toward products, one expects that both the electronic and vibrational structures of the species under observation will change. Hence, these probe methods can be * To whom corresondence should be addressed. A.S.: telephone (613) 993-7388, fax (613) 991-3437, E-mail albert.stolow@nrc.ca. D.M.N.: telephone (510) 642-3505, fax (510) 642-3635, E-mail dan@radon.cchem.berkeley.edu. 1719 Chem. Rev. 2004, 104, 1719−1757

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Femtosecond time-resolved photoelectron spectroscopy.

Photophysical characterization of triazole-substituted coumarin fluorophores

High-level ab initio calculations employing the CCSD and CCSD(T) coupled cluster methods with a series of systematically convergent correlation-consistent basis sets have been performed to obtain accurate molecular geometry and energetic properties of the simplest S-nitrosothiol (RSNO), HSNO. The properties of the S–N bond, which are central to the physiological role of RSNOs in the storage and transport of nitric oxide, are highlighted. Following corrections for quadruple excitations, core-valence correlation and relativistic effects, the CCSD(T) method extrapolated to the complete basis set (CBS) limit yielded values of 1.85 A and 29.2 kcal mol−1 for the S–N bond length and the dissociation energy for homolysis of the S–N bond, respectively, in the energetically most stable trans-conformer of HSNO. The properties of the S–N bond strongly depend on the basis-set size and the inclusion of triple, and, to a lesser extent, quadruple excitations in the coupled cluster expansion. CCSD calculations systematically underestimate the S–N equilibrium distance and S–N bond dissociation energy by 0.05–0.07 A and 6–7 kcal mol−1, respectively. The significant differences between the CCSD(T) and CCSD descriptions of HSNO, the high values of the coupled clusterT1 (0.027) and D1 (0.076) diagnostics, as well as the instability of the reference restricted Hartree–Fock (RHF) wavefunction indicate that the electronic structure of the SNO group possesses multireference character. Previous quantum-chemical data on RSNOs are reexamined based on the new insight into the SNO electronic structure obtained from the present high-level calculations on HSNO.

Structure and stability of HSNO, the simplest S-nitrosothiol

Poly-p-phenylenes (PPs) are prototype systems for understanding the charge transport in π-conjugated polymers. In a combined computational and experimental study, we demonstrate that the smooth evolution of redox and optoelectronic properties of PP cation radicals toward the polymeric limit can be significantly altered by electron-donating iso-alkyl and iso-alkoxy end-capping groups. A multiparabolic model (MPM) developed and validated here rationalizes this unexpected effect by interplay of the two modes of hole stabilization: due to the framework of equivalent p-phenylene units and due to the electron-donating end-capping groups. A symmetric, bell-shaped hole in unsubstituted PPs becomes either slightly skewed and shifted toward an end of the molecule in iso-alkyl-capped PPs or highly deformed and concentrated on a terminal unit in PPs with strongly electron-donating iso-alkoxy capping groups. The MPM shows that the observed linear 1/n evolution of the PP cation radical properties toward the polymer limit originates from the hole stabilization due to the growing chain of p-phenylene units, while shifting of the hole toward electron-donating end-capping groups leads to early breakdown of these 1/n dependencies. These insights, along with the readily applicable and flexible multistate parabolic model, can guide studies of complex donor–spacer–acceptor systems and doped molecular wires to aid the design of the next generation materials for long-range charge transport and photovoltaic applications.

Key Role of End-Capping Groups in Optoelectronic Properties of Poly-p-phenylene Cation Radicals

There is currently great interest in S-nitrosothiols (RSNOs) because formation of protein-based RSNOs—protein S-nitrosation—has been recently recognized as a major pathway of the biological function of nitric oxide, NO. Despite the growing number of S-nitrosated proteins identified in vivo, enzymatic processes that control reactions of biological RSNOs are still not well understood. In this article, we use a range of models to computationally demonstrate that specific interactions of RSNOs with charged and polar residues in proteins can result in dramatic modification of RSNO structure, stability, and reactivity. This unprecedented sensitivity of the −SNO group toward interactions with charged species is related to their unusual electronic structure that can be elegantly expressed in terms of antagonistic resonance structures. We propose a ‘ligand effect map’ (LEM) approach as an efficient way to estimate the environment effects on the −SNO groups in proteins without performing electronic structure calcul...

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Qadir K. Timerghazin

Papers

Photophysical characterization of triazole-substituted coumarin fluorophores

Structure and stability of HSNO, the simplest S-nitrosothiol

Key Role of End-Capping Groups in Optoelectronic Properties of Poly-p-phenylene Cation Radicals

Protein Control of S-Nitrosothiol Reactivity: Interplay of Antagonistic Resonance Structures

Resonance description of S-nitrosothiols: insights into reactivity.