Theoretical Investigation of Glycine Micro-Solvated. Energy and NMR Spin Spin Coupling Constants Calculations

Glycine in its neutral form can exist in the gas phase while its zwitterion form is more stable in water solution, but how many waters are actually necessary to stabilize the zwitterionic structure in the gas phase? Are the intramolecular isotropic spin spin coupling constants sensitive enough to accuse the change in the environment? or the conformer observed? These and related questions have been investigated by a computational study at the level of density functional theory employing the B3LYP functional and the 6-31++G**-J basis set. We found that at least two water molecules explicitly accounted for in the super-molecule structure are necessary to stabilize both conformers of glycine within a water polarizable continuum model. At least half of the SSCCs of both conformers are very stable to changes in the environment and at least four of them differ significantly between Neutral and Zwitterion conformation.

Nitroisatin dithiocarbazate: Synthesis, structural characterization, DFT, and docking studies

The reaction between 5-nitroisatin with S-benzyl dithiocarbazate affords a new isatindithio carbazate so-called NO2Isadtc (Benzyl 2-(5-nitro-2-oxoindolin-3-ylidene)hydrazinecarbodi thioate) which was characterized by means of 1H NMR, FT-IR, UV-visible and single crystal X-ray diffraction - Crystal data for C16H12N4O3S2 (M =372.42 g/mol): triclinic space group P-1, (n°. 02), a = 6.640 Å, b = 8.256 Å, c = 15.908 Å, V = 849.6 Å3, Z = 2, T = 293 K, μ(MoKα) = 0.337 mm-1, Dcalc = 1.456 g/cm3, 27515 reflections measured (2.499° ≤ 2Θ ≤ 26.524°), 3518 unique (Rint = 0.0533, Rsigma =0.0222) which were used in all calculations. The final R1 was 0.0367 (I > 2σ(I)) and wR2 was 0.1045 (all data). Computational methods were applied to NO2Isadtc and its nonsubstituted parent compound Isadtc for structure optimization, electronic distribution, and infrared calculations using B3LYP functional with 6-31G(d,p) basis set in ethanol as a polarizable continuum model. Furthermore, docking studies using human thioredoxin reductase 1 (TrxR) as enzyme target also were performed using NO2Isadtc and the optimized structure of Isadtc. The results demonstrated that both NO2Isadtc and Isadtc may act as inhibitors of TrxR, having different interactions detected, highlighting the contact between the NO2 group and the S111 at the helix which is found for NO2Isadtc.

High-pressure reaction profiles and activation volumes of 1,3-cyclohexadiene dimerizations computed by the extreme pressure-polarizable continuum model (XP-PCM)

Quantum chemical calculations are reported for the thermal dimerizations of 1,3-cyclohexadiene at 1 atm and high pressures up to 6 GPa. Previous experiments [Klärner et al. Angew. Chem. Int. Ed. 1986, 25, 108], based on measured activation energies and activation volumes, suggested concerted mechanisms for the formation of the endo [4+2] cycloadduct and a [6+4]-ene adduct, and stepwise mechanisms for the formation of the exo [4+2] cycloadduct and two [2+2] cycloadducts. Computed activation enthalpies (ωB97XD, CCSD(T) and SC-NEVPT2) of plausible dimerization pathways at 1 atm agree well with the experiment activation energies and the values from previous calculations [Ess et al. J. Org. Chem. 2008, 73, 7586]. High-pressure reaction profiles, computed by the recently-developed extreme pressure-polarizable continuum model (XP-PCM), show that the reduction of reaction barrier is more profound in concerted reactions than in stepwise reactions, which is rationalized on the basis of the volume profiles of different mechanisms. A clear shift of the transition state towards the reactant by high pressure is revealed for the [6+4]-ene reaction by the calculations. The computed activation volumes by XP-PCM agree excellently with the experimental values, confirming the existence of competing mechanisms in the thermal dimerizations of 1,3-cyclohexadiene.

Transient Absorption of DNA bases in the gas phase and in chloroform solution: a comparative quantum mechanical study

We study the excited state absorption (ESA) properties of the four DNA bases (thymine, cytosine, adenine, and guanine) by different single reference quantum mechanical methods, i.e. equation of motion coupled cluster singles and doubles (EOM-CCSD), singles, doubles and perturbative triples (EOM-CC3), and time-dependent density functional theory (TD-DFT), with the long-range corrected CAM-B3LYP functional. Preliminary results at the Tamm-Dancoff (TDA) CAM-B3LYP level using the maximum overlap method (MOM) are reported for Thymine. In the gas phase, the three methods predict similar One Photon Absorption (OPA) spectra, which are also consistent with the experimental results and with the most accurate computational studies available in the literature. The ESA spectra are then computed for the pp states (one for pyrimidine, two for purines) associated with the lowest energy absorption band, and for the close-lying np state. The EOM-CC3, EOM-CCSD and CAM-B3LYP methods provide similar ESA spectral patterns, which are also in qualitative agreement with literature RASPT2 results. Once validated in the gas phase, TD-CAM-B3LYP has been used to compute the ESA in chloroform, including solvent effect by the polarizable continuum model (PCM). The predicted OPA and ESA spectra in chloroform are very similar to those in the gas phase, most of the bands shifting by less than 0.1 eV, with a small increase of the intensities and a moderate destabilization of the np state. Finally, ESA spectra have been computed from the minima of the lowest energy pp state, and are consistent with the available experimental transient absorption spectra of the nucleosides in solution, providing a final validation of our computational approach.

Low-Order Scaling Quasiparticle Self-Consistent GW for Molecules

Low-order scaling GW implementations for molecules are usually restricted to approximations with diagonal self-energy. Here, we present an all-electron implementation of quasiparticle self-consistent GW for molecular systems. We use an efficient algorithm for the evaluation of the self-energy in imaginary time, from which a static non-local exchange-correlation potential is calculated via analytical continuation. By using a direct inversion of iterative subspace method, fast and stable convergence is achieved for almost all molecules in the GW100 database. Exceptions are systems which are associated with a breakdown of the single quasiparticle picture in the valence region. The implementation is proven to be starting point independent and good agreement of QP energies with other codes is observed. We demonstrate the computational efficiency of the new implementation by calculating the quasiparticle spectrum of a DNA oligomer with 1,220 electrons using a basis of 6,300 atomic orbitals in less than 4 days on a single compute node with 16 cores. We use then our implementation to study the dependence of quasiparticle energies of DNA oligomers consisting of adenine-thymine pairs on the oligomer size. The first ionization potential in vacuum decreases by nearly 1 electron volt and the electron affinity increases by 0.4 eV going from the smallest to the largest considered oligomer. This shows that the DNA environment stabilizes the hole/electron resulting from photoexcitation/photoattachment. Upon inclusion of the aqueous environment via a polarizable continuum model, the differences between the ionization potentials reduce to 130 meV, demonstrating that the solvent effectively compensates for the stabilizing effect of the DNA environment. The electron affinities of the different oligomers are almost identical in the aqueous environment.

Theoretical Investigation of Glycine Micro-solvated. Energy and NMR Spin Spin Coupling Constants Calculations

Glycine in its neutral form can exist in the gas phase while its zwitterion form is more stable in water solution.But how many waters are actually necessary to stabilize the zwitterionic structure in the gas phase? Are the intramolecular isotropic spin spin coupling constants sensitive enough to accuse the change in the environment? or the conformer observed? These and related questions have been investigated by a computational study at the level of density functional theory employing the B3LYP functional and the 6-31++G**-J basis set. We found that at least two water molecules explicitly accounted in the super-molecule structure are necessary to stabilize both conformers of glycine within a water polarizable continuum model. At least half of the SSCC’s of both conformers are very stable to changes in the environment and at least four of them differ significantly between Neutral and Zwitterion conformation.

NMR Properties of the Cyanide Anion, a Quasisymmetric Two-Faced Hydrogen Bonding Acceptor

The isotopically enriched cyanide anion, (13C≡15N)−, has a great potential as the NMR probe of non-covalent interactions. However, hydrogen cyanide is highly toxic and can decompose explosively. It is therefore desirable to be able to theoretically estimate any valuable results of certain experiments in advance in order to carry out experimental studies only for the most suitable molecular systems. We report the effect of hydrogen bonding on NMR properties of 15N≡13CH···X and 13C≡15NH···X hydrogen bonding complexes in solution, where X = 19F, 15N, and O=31P, calculated at the ωB97XD/def2tzvp and the polarizable continuum model (PCM) approximations. In many cases, the isotropic 13C and 15N chemical shieldings of the cyanide anion are not the most informative NMR properties of such complexes. Instead, the anisotropy of these chemical shieldings and the values of scalar coupling constants, including those across hydrogen bonds, can be used to characterize the geometry of such complexes in solids and solutions. 1J(15N13C) strongly correlates with the length of the N≡C bond.

Solvent Effect on the Stability and Reverse Substituent Effect in Nitropurine Tautomers

The solvent effect on the stability and electron-accepting properties (EA) of the nitro group attached to the C2, C6, or C8 position of nitropurine NH tautomers is investigated. For this purpose, the density functional theory (DFT) and the polarizable continuum model (PCM) of solvation in a wide range of solvents (1 < ε < 109) are used. We show that the EA properties of the NO2 group, described by the charge of the substituent active region (cSAR) model, are linearly dependent on the reciprocal of the solvent dielectric constant; in all cases, solvation enhances the EA properties of this group. Furthermore, the sensitivity of EA properties of the nitro group to the solvent effect depends on the proximity effects. It has been shown that the proximity of two endocyclic N atoms (two repulsive interactions) results in higher sensitivity than the asymmetric proximity of the endocyclic N atom and NH group (one repulsive and one attractive interaction). To explain this phenomenon, the geometry of the nitro group in coplanar form and after forcing its rotation around the CN bond is discussed. Relative stabilities of nitropurine tautomers in different solvents are also presented. Differences in the stabilities and solvation energies are explained by aromaticity, electronic structure, and intramolecular interactions of the nitropurine tautomers.

Non-Linear Optical Properties and Global Reactivity Descriptors by ab initio Hartree-Fock (H.F.) Calculations of Simple Coumarins

In this present analysis, the measurement of optimized molecular structure and molecular hyperpolarizability (βtotal) of simple coumarin molecules were investigated using the HF method at 6-311G basis set level Gaussian09W. The measured nonlinear optical parameters (NLO); polarizability (α), the anisotropy of the polarizability (Δα), and first-order molecular hyperpolarizability (βtotal) of the studied coumarins indicate promising optical properties. The energy difference between HOMO and LUMO helped determine the molecular descriptors; global hardness (η), softness (σ) electronegativity (χ) Chemical potential (μ), and electrophilicity index (ω) in gas and different solvents. The molecular hyperpolarizability (βtotal) and descriptors that have been calculated in the solvent medium were taken into consideration through the Polarizable Continuum Model (PCM), This study shows the high static hyperpolarizability exhibited by HNR, FXT, and CNT and offers the potential the materials may have for NLO devices. The molecular descriptors, hardness, and chemical potential values are high for CNT and UCAcompared to other studied coumarins. This suggested that CNT and CA have the most significant chemical potential resistance to change the number of electrons among the other molecules.