Synthesis, optical, electrochemical, and computational study of benzene/thiophene based D-π-A chromophores.

We report the design, synthesis, electrochemical, UV-vis, fluorescence, and computational study of nine π-linked donor-acceptor (D-π-A) chromophores. The series of novel compounds comprises a terphenyl, terthiophene, or 2,5-diphenyl thiophene linker, with one electron-donating group (methyl or ,-diethyl) and one electron-withdrawing group (nitrone, formyl, or dicyanovinyl) at opposite ends of the molecule. The HOMO-LUMO gaps were determined cyclic voltammetry and found to correspond well to DFT-calculated values.

Unexpectedly Regioselective Diels-Alder Reactions of New Unsymmetrical Benzoquinones: A Convenient Synthetic Entry to Uniquely Substituted Decalins.

We report flexible synthesis of new unsymmetrically 2,6-disubstituted benzoquinones (33 examples) and a systematic study of their reactivity in the Diels-Alder reaction. The Diels-Alder reactions of selected unsymmetrical benzoquinones with seemingly similar substituents were found to proceed with high regioselectivity and the formation of selected experimentally observed main products was rationalized by theoretical (DFT) calculations. The findings can be exploited in the convenient preparation of densely substituted and stereochemically defined decalins with unique angular substituents at ring fusion.

Mechanisms of Ligand Hyperfine Coupling in Transition-Metal Complexes: σ and π Transmission Pathways.

Theoretical interpretation of hyperfine interactions was pioneered in the 1950s-1960s by the seminal works of McConnell, Karplus, and others for organic radicals and by Watson and Freeman for transition-metal (TM) complexes. In this work, we investigate a series of octahedral Ru(III) complexes with aromatic ligands to understand the mechanism of transmission of the spin density from the d-orbital of the metal to the s-orbitals of the ligand atoms. Spin densities and spin populations underlying ligand hyperfine couplings are analyzed in terms of π-conjugative or σ-hyperconjugative delocalization vs spin polarization based on symmetry considerations and restricted open-shell vs unrestricted wave function analysis.

Mechanistic Analysis of Alkyne Haloboration: A DFT, MP2, and DLPNO-CCSD(T) Study.

Stereocontrol of the alkyne haloboration reaction has received attention in many experimental but few theoretical studies. Here we present a detailed quantum-chemical study of mechanisms leading to versus isomers of haloboration products, considering acetylene and propyne combined with BCl, BBr, and BI. Calculations using B3LYP-D3, MP2, and DLPNO-CCSD(T) methods are used to study polar reactions between the alkyne and BX in the absence and presence of an additional halide anion whose content in the reaction mixture can be controlled experimentally.

Free Radical Isomerizations in Acetylene Bromoboration Reaction.

The experimentally motivated question of the acetylene bromoboration mechanism was addressed in order to suggest possible radical isomerization pathways for the -adduct. Addition-elimination mechanisms starting with a bromine radical attack at the "bromine end" or the "boron end" of the C=C bond were considered. Dispersion-corrected DFT and MP2 methods with the SMD solvation model were employed using three all-electron bases as well as the ECP28MWB ansatz.

Stereoselective Bromoboration of Acetylene with Boron Tribromide: Preparation and Cross-Coupling Reactions of ()-Bromovinylboronates.

The mechanism of acetylene bromoboration in neat boron tribromide was studied carefully by means of experiment and theory. Besides the -addition mechanism through a four-center transition state, radical and polar -addition mechanisms are postulated, both triggered by HBr, which is evidenced also to take part in the isomerization of the product. The proposed mechanism is well supported by calculations at the MP2/6-31+G* level with Ahlrichs' SVP all-electron basis for Br.

The influence of Mg2+ coordination on 13C and 15N chemical shifts in CKI1RD protein domain from experiment and molecular dynamics/density functional theory calculations.

Sequence dependence of (13) C and (15) N chemical shifts in the receiver domain of CKI1 protein from Arabidopsis thaliana, CKI1RD , and its complexed form, CKI1RD •Mg(2+), was studied by means of MD/DFT calculations. MD simulations of a 20-ns production run length were performed. Nine explicitly hydrated structures of increasing complexity were explored, up to a 40-amino-acid structure.

Understanding the Electronic Factors Responsible for Ligand Spin-Orbit NMR Shielding in Transition-Metal Complexes.

The significant role of relativistic effects in altering the NMR chemical shifts of light nuclei in heavy-element compounds has been recognized for a long time; however, full understanding of this phenomenon in relation to the electronic structure has not been achieved. In this study, the recently observed qualitative differences between the platinum and gold compounds in the magnitude and the sign of spin-orbit-induced (SO) nuclear magnetic shielding at the vicinal light atom ((13)C, (15)N), σ(SO)(LA), are explained by the contractions of 6s and 6p atomic orbitals in Au complexes, originating in the larger Au nuclear charge and stronger scalar relativistic effects in gold complexes. This leads to the chemical activation of metal 6s and 6p atomic orbitals in Au complexes and their larger participation in bonding with the ligand, which modulates the propagation of metal-induced SO effects on the NMR signal of the LA via the Spin-Orbit/Fermi Contact (SO/FC) mechanism.

Mechanism of Spin-Orbit Effects on the Ligand NMR Chemical Shift in Transition-Metal Complexes: Linking NMR to EPR.

Relativistic effects play an essential role in understanding the nuclear magnetic resonance (NMR) chemical shifts in heavy-atom compounds. Particularly interesting from the chemical point of view are the relativistic effects due to heavy atom (HA) on the NMR chemical shifts of the nearby light atoms (LA), referred to as the HALA effects. The effect of Spin-Orbit (SO) interaction originating from HA on the nuclear magnetic shielding at a neighboring LA, σ(SO), is explored here in detail for a series of d(6) complexes of iridium.

Toward Reproducing Sequence Trends in Phosphorus Chemical Shifts for Nucleic Acids by MD/DFT Calculations.

This work addresses the question of the ability of the molecular dynamics-density functional theory (MD/DFT) approach to reproduce sequence trend in (31)P chemical shifts (δP) in the backbone of nucleic acids. δP for [d(CGCGAATTCGCG)]2, a canonical B-DNA, have been computed using density functional theory calculations on model compounds with geometries cut out of snapshots of classical molecular dynamics (MD) simulations. The values of (31)P chemical shifts for two distinct B-DNA subfamilies BI and BII, δP/BI and δP/BII, have been determined as averages over the BI and BII subparts of the MD trajectory.

Validation of Relativistic DFT Approaches to the Calculation of NMR Chemical Shifts in Square-Planar Pt(2+) and Au(3+) Complexes.

Recently implemented hybrid density functional methods of calculating nuclear magnetic shielding using the two-component zeroth-order regular approximation approach (J. Phys. Chem.

Phosphorus chemical shifts in a nucleic acid backbone from combined molecular dynamics and density functional calculations.

A comprehensive quantum chemical analysis of the influence of backbone torsion angles on (31)P chemical shifts in DNAs has been carried out. An extensive DFT study employed snapshots obtained from the molecular dynamics simulation of [d(CGCGAATTCGCG)]2 to construct geometries of a hydrated dimethyl phosphate, which was used as a model for the phosphodiester linkage. Our calculations provided differences of 2.

31P chemical shift tensors for canonical and non-canonical conformations of nucleic acids: a DFT study and NMR implications.

31P chemical shift anisotropy (CSA) tensors have been calculated for a set of selected DNA and RNA backbone conformations using density functional theory. The set includes canonical A-RNA, A-DNA, BI-DNA, BII-DNA, ZI-DNA, and ZII-DNA as well as four A-RNA-type, seven non-A-RNA-type, and three non-canonical DNA conformations. Hexahydrated dimethyl phosphate has been employed as a model.

Relationships between 31P chemical shift tensors and conformation of nucleic acid backbone: a DFT study.

Density functional theory (DFT) has been applied to study the conformational dependence of 31P chemical shift tensors in B-DNA. The gg and gt conformations of backbone phosphate groups representing BI- and BII-DNA have been examined. Calculations have been carried out on static models of dimethyl phosphate (dmp) and dinucleoside-3',5'-monophosphate with bases replaced by hydrogen atoms in vacuo as well as in an explicit solvent.

Comparative density-functional study of the electron paramagnetic resonance parameters of amavadin.

Electronic g tensors and hyperfine coupling tensors have been calculated for amavadin, an unusual eight-coordinate vanadium(IV) complex isolated from Amanita muscaria mushrooms. Different density-functional methods have been compared, ranging from local via gradient-corrected to hybrid functionals with a variable Hartree-Fock exchange admixture. For both electron paramagnetic resonance (EPR) properties, hybrid functionals with an appreciable exact-exchange admixture provide the closest agreement with experimental data.

Measurement of long-range 1H-19F scalar coupling constants and their glycosidic torsion dependence in 5-fluoropyrimidine-substituted RNA.

Long-range scalar 5J(H1',F) couplings were observed in 5-fluoropyrimidine-substituted RNA. We developed a novel S3E-19F-alpha,beta-edited NOESY experiment for quantitation of these long-range scalar 5J(H1',F) couplings, where the J-couplings can be extracted from inspection of intraresidual (H1',H6) NOE cross-peaks. Quantum chemical calculations were exploited to investigate the relation between scalar couplings and conformations around the glycosidic bond in oligonucleotides.

Experiments for correlating quaternary carbons in RNA bases.

The paper presents a set of triple-resonance two-dimensional experiments for correlating all quaternary carbons in RNA bases to one or more of the base protons. The experiments make use of either three-bond proton-carbon couplings and one selective INEPT step (the long-range selective HSQC experiment) to transfer the magnetization between a proton and the carbon of interest and back, or they rely on one- and/or two-bond heteronuclear (the H(CN)C and H(N)C experiments) or carbon-carbon (the H(C)C experiment) couplings and multiple INEPT transfer steps. The effect of the large one-bond carbon-carbon coupling in t(1) is removed by a constant time evolution or by a selective refocusing.

DFT analysis of NMR scalar interactions across the glycosidic bond in DNA.

The relationship between the glycosidic torsion angle chi, the three-bond couplings (3)J(C2/4-H1') and (3)J(C6/8-H1'), and the one-bond coupling (1)J(C1'-H1') in deoxyribonucleosides and a number of uracil cyclo-nucleosides has been analyzed using density functional theory. The influence of the sugar pucker and the hydroxymethyl conformation has also been considered. The parameters of the Karplus relationships between the three-bond couplings and chi depend strongly on the aromatic base.

Three-bond sugar-base couplings in purine versus pyrimidine nucleosides: a DFT study of Karplus relationships for (3)J(C2/4-H1') and (3)J(C6/8-H1') in DNA.

(3)J(C2/4-H1') and (3)J(C6/8-H1') scalar spin-spin coupling constants have been calculated for deoxyadenosine, deoxyguanosine, deoxycytidine, and deoxythymidine as functions of the glycosidic torsion angle chi by means of density functional theory. Except for deoxythymidine, (3)J(C2/4-H1') depends little on the base type. On the contrary, (3)J(C6/8-H1') follows the usual trans to cis ratio ((3)J(C-H(cis)) < (3)J(C-H(trans))) for purine nucleosides, but reveals the opposite relation ((3)J(C-H(cis)) > (3)J(C-H(trans))) for pyrimidine nucleosides.

Strong electronic consequences of intercalation in cuprate superconductors: the case of a trigonal planar AuI(3) complex stabilized in the Bi(2)Sr(2)CaCu(2)O(y) lattice.

Recently, a molecular AuI(3) complex was stabilized in the interlayer space of the Bi(2)Sr(2)CaCu(2)O(y) (Bi2212) high-T(c) superconducting phase, adopting an exceptional D(3)(h) structure (Choy, J.-H.; et al.

Electron-rich three-center bonding: role of s,p interactions across the p-block.

This paper analyzes the importance of s,p mixing-a necessary addition to the simplest Rundle-Pimentel picture-and periodic and group trends in electron-rich three-center bonding. Our analysis proceeds through a detailed quantum chemical study of the stability of electron-rich three-center bonding in triatomic 22-valence electron anions. To provide interpretations, a perturbational molecular orbital (MO) analysis of s,p mixing is carried out.