Structures and basicity of LiNOH (N = 1 − 5) species

LiOH is one of the strong bases among neutral molecules. What about hydroxides of small Li_n (n = 2 ? 5) clusters? The addition of a single atom to a cluster sometimes has dramatic effects on its reactivity. This fact motivated us to perform an ab initio MP2/6‐311++G(d, p) investigation on Li_nOH species (n = 1 ? 5). These Li_nOH species are stabilized by both ionic as well as covalent interactions, and are found to be stable against elimination of LiOH and OH. We have determined their gas and aqueous phase basicity by considering hypothetical protonation reactions. The calculated proton affinities of Li_nOH (n ≥ 2) suggest their reduced basicity as compared to LiOH by 50–100 kJ/mol. The NBO charges and the highest occupied molecular orbitals also reveal the electride and alkalide characteristics of Li₂OH and Li₃OH, respectively. © 2016 Wiley Periodicals, Inc.     

Excited‐State Intramolecular Proton Transfer: Photoswitching in Salicylidene Methylamine Derivatives

The effect of chemical substitutions on the photophysical properties of the salicylidene methylamine molecule (SMA) (J. Jankowska, M. F. Rode, J. Sadlej, A. L. Sobolewski, ChemPhysChem, 2012 , 13, 4287–4294) is studied with the aid of ab initio electronic structure methods. It is shown that combining π‐electron‐donating and π‐electron‐withdrawing substituents results in an electron‐density push‐and‐pull effect on the energetic landscape of the ground and the lowest excited ππ* and nπ* singlet states of the system. The presented search for the most appropriate SMA derivatives with respect to their photoswitching functionality offers an efficient prescreening tool for finding chemical structures before real synthetic realization.     

Photophysics of Schiff Bases: Theoretical Study of Salicylidene Methylamine

The proton‐transfer reaction in a model aromatic Schiff base, salicylidene methylamine (SMA), in the ground and in the lowest electronically‐excited singlet states, is theoretically analyzed with the aid of second‐order approximate coupled‐cluster model CC2, time‐dependent density functional theory (TD‐DFT) using the Becke, three‐parameter Lee–Yang–Parr (B3LYP) functional, and complete active space perturbation theory CASPT2 electronic structure methods. Computed vertical‐absorption spectra for the stable ground‐state isomers of SMA fully confirm the photochromism of SMA. The potential‐energy profiles of the ground and the lowest excited singlet state are calculated and four photophysically relevant isomeric forms of SMA; α, β, γ, and δ are discussed. The calculations indicate two S₁/S₀ conical intersections which provide non‐adiabatic gates for a radiationless decay to the ground state. The photophysical scheme which emerges from the theoretical study is related to recent experimental results obtained for SMA and its derivatives in the low‐temperature argon matrices (J. Grzegorzek, A. Filarowski, Z. Mielke, Phys. Chem. Chem. Phys. 2011 , 13, 16596–16605). Our results suggest that aromatic Schiff bases are potential candidates for optically driven molecular switches.     

Experimental versus Calculated Proton Affinities for Aromatic Carboxylic Acid Anions and Related Phenide Ions

Herein, we present the comparison of a large set of experimentally measured proton affinity (PA) values for 65 aromatic carboxylate anions with the values calculated by using selected popular DFT (B3LYP, PBE0, and M05‐2X) and composite [G3(MP2), G4(MP2)] quantum chemistry methods. The root‐mean‐square error (RMSE) values for the chosen methods are RMSE_PBE0=1.7, RMSE_B3LYP=4.6, RMSE_M05‐2X=6.6, RMSE_G3MP2=6.3, RMSE_G4MP2=4.5 kJ mol^?1. In the second part of the study, 82 PA values for substituted phenide ions and a few heteroaromatic anions were calculated. Again, very good agreement between the calculated and experimental values has been observed: RMSE_PBE0=1.9, RMSE_B3LYP=4.5, RMSE_M05‐2X=6.3, RMSE_G3MP2=4.9, RMSE_G4MP2=5.5 kJ mol^?1. Our results show that, for medium‐sized carboxylate anions, all tested methods give reliable results and, surprisingly, much more computationally demanding composite methods do not perform significantly better than the time‐efficient DFT methods.     

Excited-state properties and environmental effects for protonated schiff bases: a theoretical study.

Complete active space self-consistent field (CASSCF), multireference configuration interaction (MRCI), density functional theory (DFT), time dependent DFT (TDDFT) and the singles and doubles coupled-cluster (CC2) methodologies have been used to study the ground state and excited states of protonated and neutral Schiff bases (PSB and SB) as models for the retinal chromophore. Systems with two to four conjugated double bonds are investigated. Geometry relaxation effects are studied in the excited pipi* state using the aforementioned methods. Taking the MRCI results as reference we find that CASSCF results are quite reliable even though overshooting of geometry changes is observed. TDDFT does not reproduce bond alternation well in the pipi* state. CC2 takes an intermediate position. Environmental effects due to solvent or protein surroundings have been studied in the excited states of the PSBs and SBs using a water molecule and solvated formate as model cases. Particular emphasis is given to the proton transfer process from the PSB to its solvent partner in the excited state. It is found that its feasibility is significantly enhanced in the excited state as compared to the ground state, which means that a proton transfer could be initiated already at an early step in the photodynamics of PSBs.     

Accurate pKa Calculation of the Conjugate Acids of Alkanolamines,Alkaloids and Nucleotide Bases by Quantum Chemical Methods

The pK_a of the conjugate acids of alkanolamines, neurotransmitters, alkaloid drugs and nucleotide bases are calculated with density functional methods (B3LYP, M08‐HX and M11‐L) and ab initio methods (SCS‐MP2, G3). Implicit solvent effects are included with a conductor‐like polarizable continuum model (CPCM) and universal solvation models (SMD, SM8). G3, SCS‐MP2 and M11‐L methods coupled with SMD and SM8 solvation models perform well for alkanolamines with mean unsigned errors below 0.20 pK_a units, in all cases. Extending this method to the pK_a calculation of 35 nitrogen‐containing compounds spanning 12 pK_a units showed an excellent correlation between experimental and computational pK_a values of these 35 amines with the computationally low‐cost SM8/M11‐L density functional approach.     

Equilibrium geometry and gas‐phase proton affinity of 2‐thiouracil derivatives

The ground‐state geometries of uracil, 6‐hydroxy‐uracil, and 6‐hydroxy‐, 6‐amino‐, 6‐methyl‐, 6‐trifluoro‐, and 6‐phenyl‐2‐thiouracil were optimized at the Hartree–Fock level. The molecular structures were fully optimized using the 6‐31G and 6‐31G* basis sets. The effect of substituents on the geometry and electronic structural features of 2‐thiouracils were examined. The perturbation effects of the OH and NH₂ groups are by far more pronounced on the geometric features and the dipole moment magnitude and direction of 2‐thiouracil. The potential energy per atom criteria was used to compare the relative tightness of binding in the studied series. Proton affinity and deprotonation enthalpy on each of the possible sites in 2‐thiouracil and its derivatives have been calculated at the 6‐31G/MP2 level of theory. The obtained results show that thiouracils behave as bases where they possess a high tendency to abstract protons. Substituents in the 6‐position have the general effect of enhancing the basicity strength of the thiocabonyl site in the order Ph < CH3 ≈ NH2 < OH. The CF3 group has the effect of reducing considerably the basicity strength and enhances the acidity strength at both N1 and N3. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

Chiral Transformation in Protonated and Deprotonated Adipic Acids through Multistep Internal Proton Transfer

Protonated and deprotonated adipic acids (PAA: HOOC? (CH₂)₄? COOH₂⁺ and DAA: HOOC? (CH₂)₄? COO^?) have a charged hydrogen bond under the influence of steric constraint due to the molecular skeleton of a circular ring. Despite the similarity between PAA and DAA, it is surprising that the lowest energy structure of PAA is predicted to have (H₂O???H???OH₂)⁺ Zundel‐like symmetric hydrogen bonding, whereas that of DAA has H₃O⁺ Eigen‐like asymmetric hydrogen bonding. The energy profiles show that direct proton transfer between mirror image structures is unfavorable. Instead, the chiral transformation is possible by subsequent backbone twistings through stepwise proton transfer along multistep intermediate structures, which are Zundel‐like ions for PAA and Eigen‐like ions for DAA. This type of chiral transformation by multistep intramolecular proton transfers is unprecedented. Several prominent OH???O short hydrogen‐bond stretching peaks are predicted in the range of 1000–1700 cm^?1 in the Car–Parrinello molecular dynamics (CPMD) simulations, which show distinctive signatures different from ordinary hydrogen‐bond peaks. The O? H? O stretching peaks in the range of 1800–2700 cm^?1 become insignificant above around 150 K and are almost washed out at about 300 K.     

Proton Transfer in Crystalline Aromatic Schiff Bases and Their Electronic Properties

Abstract

Aromatic Schiff bases having extended II-electron systems and their charge transfer (CT) complexes have been prepared and subjected to structural, optical, and electrical conductivity studies. It is demonstrated by the X-ray crystal-lographic study that the hydroxyl protons form hydrogen bonds to the imino nitrogens, strength of which can be varied by chemical modification of the molecules. Intramolecular proton transfer takes place in solid state and is manifested in the thermochromic spectral changes.     

Proton transfer 200 years after von Grotthuss: insights from ab initio simulations.

In the last decade, ab initio simulations and especially Car-Parrinello molecular dynamics have significantly contributed to the improvement of our understanding of both the physical and chemical properties of water, ice, and hydrogen-bonded systems in general. At the heart of this family of in silico techniques lies the crucial idea of computing the many-body interactions by solving the electronic structure problem "on the fly" as the simulation proceeds, which circumvents the need for pre-parameterized potential models. In particular, the field of proton transfer in hydrogen-bonded networks greatly benefits from these technical advances. Here, several systems of seemingly quite different nature and of increasing complexity, such as Grotthuss diffusion in water, excited-state proton-transfer in solution, phase transitions in ice, and protonated water networks in the membrane protein bacteriorhodopsin, are discussed in the realms of a unifying viewpoint.     

Proton transfer at the carboxylic sites of amino acids: A single water molecule catalyzed process

Ab initio calculations at MP2 level of theory were used to study the proton transfer at the carboxylic sites of amino acids, in the isolated, mono‐ and di‐hydrated forms. In the case of water dimer, two interaction modes with glycine neutral structures (see Fig. 3 ) were explored, corresponding to the concerted and stepwise reaction pathways. Their transition states can be described as (H₂O? H? OH₂)⁺ [Fig. 4 (a)] and (H₂O‐‐‐H? OH₂)⁺ [Fig. 4 (b)], respectively. The energy analysis indicated that the concerted pathway is preferred. In the isolated, mono‐ and di‐hydrated glycine complexes, the activation barriers of the proton transfer at the carboxylic sites were calculated to be 34.49, 16.59, and 13.36 kcal mol^?1, respectively. It was thus shown that the proton transfer is significantly assisted and catalyzed by water monomer so that it can take place at room temperature. Instead, the further addition of water molecules plays solvent effects rather than catalytic effects to this proton transfer process. The above results obtained with discrete water molecules were supported by the solvent continuum calculated data. It was also observed that the heavy dependence of the solvent continuum models on dipole moments may produce misleading results. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

计算脂肪族胺、醇和醚的气相碱性的经验公式

本文给出计算脂肪族胺、醇和醚气相碱性的经验公式。由公式得出的PA值与ICR实验值接近。     

Theoretical studies on electron delocalization in diaminoguanidine

Ab initio MO and density functional methods have been employed to understand the electronic structure and second-order delocalizations in diaminoguanidine. The potential energy surfaces of the three different positional isomers of diaminoguanidine (DAG1, DAG2, and DAG3) have been studied in detail, which suggest greater stability for DAG1 over the other isomers. Natural Population Analysis (NPA) has been employed to understand the primary and the secondary electron delocalizations in diaminoguanidine. The absolute proton affinity of diaminoguanidine is greater than both guanidine as well as aminoguanidine due to the extra stability from the intramolecular interactions in protonated diaminoguanidine. The increase in the electron delocalization upon protonation in diaminoguanidine is similar to that of guanidine and aminoguanidine.     

The sodium ion affinities of cytosine and its methylated derivatives

The sodium ion affinities of cytosine (Cyt), 5-methylcytosine (5MeCyt) and 1-methylcytosine (1MeCyt) have been determined by experimental and quantum chemical methods. Na(+)-bound heterodimers were produced carrying one cytosine or methylated cytosine ligand (designated as C) and one peptide or amino acid reference base (designated as Pep); the Pep molecules included the peptides GlyLeu, GlyPhe, SerGly, and PheGly, and the amino acid His. The dissociation kinetics of these C--Na(+)--Pep ions were determined by collisionally activated dissociation (CAD) and converted to relative and absolute Na(+) affinities via kinetic method approaches. Relative Na(+) affinities increase in the order (kJ/mol): GlyLeu (0) < Cyt (3) < GlyPhe (4) < SerGly (6) < 5MeCyt (8) < PheGly (11) < 1MeCyt (13) < His (17). Anchoring the relative values of the nucleobases to the absolute affinities of the reference bases leads to absolute Na(+) affinities of 214 +/- 8, 219 +/- 8, and 224 +/- 8 kJ/mol for Cyt, 5MeCyt, and 1MeCyt, respectively. Ab initio calculations were used to confirm these results. The computed affinities of Cyt (213 kJ/mol) and 1MeCyt (217 kJ/mol) are in very good agreement with the experiments. These values unambiguously correspond to Na(+) complexes with the keto form of cytosine and its methyl derivatives. Ab initio calculations on tautomerization mechanisms in the gas versus condensed phase are used to discuss why the sodiated keto isomers were formed in the present electrospray ionization (ESI) experiments, but the enol isomers in previous fast atom bombardment (FAB) experiments.