Proton magnetic shielding in H2O and (H2O)2

The proton magnetic shielding constants in the water molecule and its linear perpendicular dimer are computed from SCF-MO-LCGO wave functions by using the uncoupled Hartree-Fock variation-perturbation procedure due to Karplus and Kolker. The convergence of the calculated shielding constants as well as their gauge dependence is studied. The final results for 17-term polynomial variation function indicate that the best choice for the gauge origin corresponds to the molecular electronic centroid.The calculated proton magnetic shielding constant in the water molecule is in remarkable agreement with experimental data and favourably compares with the best coupled Hartree-Fock results. It follows from the calculations for the water dimer that the H-bond NMR-shift amounts in this case —1.0 ppm and qualitatively agrees with the experimental data for the liquid water.     

Effect of small cations on the hydrogen bond between an N-aromatic heterocycle and amine

The influence of an Li⁺ ion on the structure and bonding of the H-bond interaction of an N-aromatic heterocycle and a singly bonded N-amine is studied by ab initio SCF calculations with imidazole (Imh) and NH₃ serving as models of the two families. Full optimization of structures have been carried out for DZ, DZP and TZP basis sets. The computed H-bond energy for Imh/ NH₃ of −6.4 kcal/mol is in close agreement with a recent experiment. An appreciable three-body interaction of −3.8 kcal/mol is found for the complex Imh/NH₃/Li⁺.     

An EPR/ENDOR study of the asymmetric hydrogen bond between the quinone electron acceptor and the protein backbone in Photosystem I

Hydrogen bonding to the photoaccumulated secondary acceptor radical anion A₁^√− in photosystem (PS) I has been studied using pulsed Q-band ENDOR spectroscopy. With deuterated quinone in protonated PS I particles it is demonstrated that the observed radical anion has only one hydrogen-bond hyperfine coupling (hfc) tensor with tensor components above the 2 MHz range. Below 2 MHz the protein matrix protons dominate and a second weak H-bond could not be detected. The spectral resolution of pulsed Q-band ENDOR is critically required to separate the signals of the H-bond proton from those of the primary chlorophyll acceptor, A₀^√−, which cannot be avoided to be formed to some extent in the photoaccumulation procedure. The determined H-bond hfc tensor of A₁^√− is found to be close to axial symmetry with a small isotropic component, as expected from a predominantly dipolar electron–proton spin interaction in a hydrogen-bond. The principal tensor components are A=(+)7.7, MHz A=(−)4.9 MHz, A_iso=(−)0.7 MHz. The magnitude of the dipolar tensor corresponds to an unusually short H-bond which can be estimated from the point-dipole approximation (1.5±0.1 Å). Based on previous studies with A- and B-branch specific site-directed mutants of the A₁ site of PS I and the chosen photoaccumulation protocol, the observed A₁^√− radical anion can be assigned to the Q_K–A site of the A-branch. The observed H-bond hfc tensor is compared to those determined for related quinone radical anions observed in frozen protic solution as well as in the Q_A site of type II bacterial reaction centers.     

双碳醇水溶液的1H NMR实验与理论分析

In this study, ¹H nuclear magnetic resonance (NMR) measurements and quantum chemistry (QC) studies of ethanol (ET)-water mixtures and ethylene glycol (EG)-water mixtures are carried out at different temperatures to discuss the interactions between water and the alcohols present in the mixtures. From ¹H NMR spectra, it is observed that the chemical shift of the water proton shows two different trends in the ET-water mixtures and the EG-water mixtures. With increasing water concentration, the water proton chemical shift decreases dramatically for ET-water mixtures, while the chemical shift increases slowly for EG-water mixtures. The alcohol hydroxyl proton resonance peaks of both ET and EG shift to lower field with decreasing water concentration. It is found that the resonance peaks of all alkyl protons shift monotonically to low field with increasing alcohol concentration at different temperatures. The geometry optimization results indicate the formation of H-bonds between the water molecules and the hydroxyl groups of the alcohols alongside the weakening of O-H bonds in the alcohols, which results in an O-H bond length decrease. It is interesting to note that the bond length values computed for C-C, C-H and O-H bond in both ET and EG are larger when calculated at the density functional theory (DFT) (B3LYP) level than when calculated using Hartree-Fock (HF) level of theory with the same polarization function and diffusion function. However, the O-H…O H-bond computed at HF level of theory is stronger than that calculated at DFT level of theory. The theoretical results are in good agreement with the experimental ones. In the calculation of NMR chemical shift, DFT(B3LYP) is better than HF, which implies that for the same method, the larger the basis sets are, the more accurate are the calculated values.     

Protonation of group 14 oxides: the proton affinity of SnO

Molecular orbital calculations are reported for the monoxides, XO, of group 14 elements (X = C, Si, Ge and Sn) and for both isomers, XOH⁺ and HXO⁺, of the protonated monoxides. Structure optimisation has been carried out using the Density Functional Theory employing the B3LYP procedure and at both Hartree-Fock and MP2 (full) levels, all with a variety of medium-sized Gaussian basis sets. In all XO molecules the oxygen atom is the preferred site for protonation, except when X = C where HCO⁺ is the lower energy isomer. Barriers to interconversion between the two isomers XOH⁺ and HXO⁺ are over-estimated by the Hartree-Fock calculations, but with wave functions that include electron correlations they generally fall into the range 27-44 kcal mol⁻¹. Proton affinities increase as the atomic number of X increases, and values calculated by averaging over all wave functions that include electron correlation, give the following proton affinities: for CO, 141.5; for SiO, 189.3; for GeO, 196.1; and for SnO, 215.6 (all in kcal mol⁻¹).     

Theoretical investigations of structure and enzymatic mechanisms of aspartyl proteinases : Part I. Ab-initio calculations on an active site model: hydrogen diformiate with H2O and H3O

The active site of aspartyl proteinases (Asp) was modelled as two formiates connected with a proton and set in geometry corresponding to Asp 32 and Asp 215 side chain carboxylate groups of endothiapepsin. The shared solvent molecule was alternatively H₂O and H₃O⁺. Their positions and those of hydrogen-bonded protons were optimized using the STO-3G basis set. Full geometry optimizations were made of the hydrogen diformiate complexes with H₂O and H₃O⁺. Asymmetric hydrogen-bonded structures resulted from these calculations, except for the fully optimized complex with H₂O. In the complexes with H₃O⁺, one proton moved consistently to the proximate carboxylic oxygen yielding a neutral, hydrated formic acid dimer. Interaction energies and proton potential energy curves were calculated using the 4-31G basis set. The interaction energy with H₂O was found to be 20.49 kcal mol⁻¹ and 202.75 kcal mol⁻¹ with H₃O⁺.     

Outline of a transition-state hydrogen-bond theory

Though the H-bond is well characterized as a D–H:A three-center-four-electron interaction, the formulation of a general H-bond theory has turned out to be a rather formidable problem because of the extreme variability of the bonds formed (for instance, O–HO energies range from 0.1 to 31 kcal mol⁻¹). This paper surveys our previous contributions to the problem, including: (a) the H-bond chemical leitmotifs (CLs), showing that there are only four classes of strong H-bonds and one of moderately strong ones; (b) the PA/pK_a equalization principle, showing that the four CLs forming strong H-bonds are actually molecular devices apt to equalize the acid–base properties (PA or pK_a) of the H-bond donor and acceptor groups; (c) the driving variable of the H-bond strength, which remains so identified as the difference ΔpK_a=pK_AH(D–H)−pK_BH(A–H⁺) or, alternatively, ΔPA=PA(D⁻)−PA(A); and, in particular, (d) the transition-state H-bond theory (TSHBT), which interprets the H-bond as a stationary point along the complete proton transfer pathway going from D–HA to DH–A via the DHA transition state. TSHBT is verified in connection with a series of seven 1-(X-phenylazo)-2-naphthols, a class of compounds forming a strong intramolecular resonance-assisted H-bond (RAHB), which is switched from N–HO to NH–O by the decreasing electron-withdrawing properties of the substituent X. The system is studied in terms of: (i) variable-temperature X-ray crystallography; (ii) DFT emulation of stationary points and full PT pathways; (iii) Marcus rate-equilibrium analysis correlated with substituent LFER Hammett parameters.     

Theoretical Study on Ionic Liquid Based on 1-Ethyl-3-Methyl- Imidazolium Cation and Hexafluorophosphate or Tetrafluoroborate

The Hartree-Fock and DFT/B3LYP methods have been employed to investigate the electronic structures of 1-ethy1-3-methyl-imidazolium cation(EMIM~ ),BF_4~-,PF_6~-,EMIM~ -BF_4~-,and EMIM~ -PF_6~- using the Gaussian-94 soft-package at 6-31 G(d,p)basis set level for hydrogen,carbon,nitrogen,boron, phosphorus,and fluorine atoms.Comparison of the electronic structures of the lowest energy of EMIM~ - BF_4~- and EMIM~ -PF_6~- pairs,and single EMIM~ ,BF_4~- and PF_6~- showed that the optimized EMIM~ -BF_4~- and EMIM~ -PF_6~- pair conformers were BF_4~- and PF_6~- outside the 5-ring plane between the ethyl group and the methyl group.The cohesion of C—H…F hydrogen bond between cation and anion is reinforced by charge assistance.The interaction energy between EMIM~ and PF_6~- is 328.8 kJ/mol at the B3LYP level and 326.6 kJ/mol at the Hartree-Fock level,whereas that between EMIM~ and BF_4~- is 353.5 kJ/mol at the B3LYP level and 350.5 kJ/mol at the Hartree-Fock level.The low energy interactions caused by bulky asymmetric EMIM~ ,and charge dispersion of cation and anion give rise to the low melting point of ionic liquid EMIM~ -BF_4~- and EMIM~ -PF_6~-.The two hydrogen bonding models of single hydrogen bond formation,and the hydrogen transfer between C_2 in EMIM~ and F in BF_4~- or PF_6~- were principally depicted.     

A Hartree-Fock SCF calculation of the activation energies for two SN2 reactions

Roothaan Hartree-Fock SCF calculations for points on the F⁻ + CH₃F and CN⁻ + CH₃F minimum potential energy surfaces are reported. Considerable care has been taken in the choice of basis sets used to describe these systems.     

Cooperative two-photon-induced chemical bond formation during a Kr+F2 collision to form KrF

The reactive Kr⁺F₂⁻ potential energy surface is probed by two-photon, laser-induced chemical bond formation during a Kr+F₂ collision. This is compared with the pulsed laser excitation (two-photon) of Kr(2p₉) followed by collision with F₂ leading to the formation of KrF(B, C). In addition to reporting the excitation spectrum for the two-phonon-induced collision process, these techniques were used to determine quenching rate constants of Kr₂F^*. Quenching by Xe gives XeF(B, C) with rate constant (1.5±0.2)×10⁻¹⁰ cm³ s⁻¹; the quenching rate constant for F₂ is (1.5±0.2)×10⁻¹⁰ cm³ s⁻¹, and the radiative lifetime of Kr₂F^* is 240±35 ns. The quenching rate constant for the coupled Kr(2p₈) and Kr(2p₉) levels by F₂ is (13±2)×10⁻¹⁰ cm³ s⁻¹.     

Infrared matrix isolation and quantum chemical studies of the nitrous acid complexes with water

The 1:1 and 2:1 complexes between water and trans- and cis-isomers of nitrous acid have been isolated in argon matrices and studied using FTIR spectroscopy and DFT(B3LYP) calculations with a 6-311++G(2d,2p) basis set. The analysis of the experimental spectra indicate that 1:1 complexes trapped in solid argon involve very strong hydrogen bond in which acid acts as the proton donor and water as the proton acceptor. The perturbed OH stretches are −248, −228 cm⁻¹ red shifted from their free-molecules values in complexes formed by trans- and cis-HONO isomers, respectively. The calculated spectral parameters for the two complexes are in good agreement with experimental data. The calculations also predict stability of two more 1:1 weakly bound complexes formed by each isomer. In these the water acts as the proton donor and one of the two oxygen atoms of the acid as the acceptor. The experimental spectra demonstrate also formation of 2:1 complex between water and trans-HONO isomer in an argon matrix. The performed calculations indicate that the complex involves a seven-membered ring in which OH group of HONO forms very strong hydrogen bond with the oxygen atom of one water molecule and nitrogen atom acts as a weak proton acceptor for the hydrogen atom of the second water molecule of the water dimer. The observed perturbations of the OH stretch of trans-HONO (750 cm⁻¹ red shift) is much larger than that predicted by calculations (556 cm⁻¹ red shift); this difference is attributed to strong solvation effect of argon matrix on very strong hydrogen bond.     

Calculation of binary magnetic properties and potential energy curve in xenon dimer: second virial coefficient of (129)Xe nuclear shielding

Quantum chemical calculations of the nuclear shielding tensor, the nuclear quadrupole coupling tensor, and the spin-rotation tensor are reported for the Xe dimer using ab initio quantum chemical methods. The binary chemical shift delta, the anisotropy of the shielding tensor Delta sigma, the nuclear quadrupole coupling tensor component along the internuclear axis chi( parallel ), and the spin-rotation constant C( perpendicular ) are presented as a function of internuclear distance. The basis set superposition error is approximately corrected for by using the counterpoise correction (CP) method. Electron correlation effects are systematically studied via the Hartree-Fock, complete active space self-consistent field, second-order M?ller-Plesset many-body perturbation, and coupled-cluster singles and doubles (CCSD) theories, the last one without and with noniterative triples, at the nonrelativistic all-electron level. We also report a high-quality theoretical interatomic potential for the Xe dimer, gained using the relativistic effective potential/core polarization potential scheme. These calculations used valence basis set of cc-pVQZ quality supplemented with a set of midbond functions. The second virial coefficient of Xe nuclear shielding, which is probably the experimentally best-characterized intermolecular interaction effect in nuclear magnetic resonance spectroscopy, is computed as a function of temperature, and compared to experiment and earlier theoretical results. The best results for the second virial coefficient, obtained using the CCSD(CP) binary chemical shift curve and either our best theoretical potential or the empirical potentials from the literature, are in good agreement with experiment. Zero-point vibrational corrections of delta, Delta sigma, chi (parallel), and C (perpendicular) in the nu=0, J=0 rovibrational ground state of the xenon dimer are also reported.     

Heteroleptic platinum(II) complexes of macrocyclic thioethers and halides: the crystal structures of [Pt(9S3)Cl2], [Pt(9S3)Br2], and [Pt(9S3)I2]

The synthesis, spectroscopic, and crystal structures of three heteroleptic thioether/halide platinum(II) (Pt(II)) complexes of the general formula [Pt(9S3)X₂] (9S3=1,4,7-trithiacyclononane, X=Cl⁻, Br⁻, I⁻) are presented. All three 9S3/dihalo complexes form very similar structures in which the Pt(II) center is surrounded by a cis arrangement of two halides and two sulfur atoms from the 9S3 ligand. The third sulfur from the 9S3 forms a long distance interaction with the Pt center resulting in an elongated square pyramidal structure with a S₂X₂+S₁ coordination geometry. The distances between the Pt(II) center and axial sulfur shorten with larger halide ions (Cl⁻=3.260(3) Å>Br⁻=3.243(2) Å>I⁻=3.207(2) Å). These distances are consistent with the halides functioning as π donor ligands, and their Pt---S axial distances fall intermediate between Pt(II) thioether complexes involving π acceptor and σ donor ligands. The ¹⁹⁵Pt NMR chemical shift values follow a similar trend with an increased shielding of the platinum ion with larger halide ions. The 9S3 ligand is fluxional in all of these complexes, producing a single carbon resonance. Additionally, a related series of homoleptic crown thioether complexes have been studied using ¹⁹⁵Pt NMR, and there is a strong correlation between the chemical shift and complex structure. Homoleptic crown thioethers show the anticipated upfield chemical shifts with increasing number of coordinated sulfurs. Complexes containing four coordinated sulfur donors have chemical shifts that fall in the range of −4000 to −4800 ppm while a value near −5900 ppm is indicative of five coordinated sulfurs. However, for S₄ crown thioether complexes, differences in the stereochemical orientation of lone pair electrons on the sulfur donors can greatly influence the observed ¹⁹⁵Pt NMR chemical shifts, often by several hundred ppm.     

Calculation of the hydrogen-bond NMR shift in the water dimer

The shielding constant of the hydrogen-bonded proton in the linear perpendicular water dimer is calculated from the SCF MO LCGO wavefunction unsing the uncoupled Hartree-Fock variation-perturbation procedure of Karplus and Kolker. The obtained result (27.61 ppm) is compared with the experimental estimate of the proton shielding in the liquid water (25.62 ppm). Comparing with the proton shielding in the water molecule, calculated previously within the same approximation (28.30 ppm), the non-empirical hydrogen-bond shift of −0.69 ppm is found.     

A theoretical investigation on the effect of π–π stacking interaction on 1H isotropic chemical shielding in certain homo- and hetero-nuclear aromatic systems

Significant changes in the proton chemical shielding (and hence the chemical shift) are predicted in going from the monomer to the dimer of benzene, naphthalene, pyridine and quinoline systems and also the trimer of benzene and pyridine. The computed NMR spectra show additional splitting in going from the monomer to the dimer and the trimer of different species. The aromatic protons show a significant upfield shift due to the enhancement of anisotropic shielding by the π electron cloud of the neighboring molecule(s). The nature of the NMR spectra also changes with the orientation of the stacked conformers. The results obtained using M?ller-Plesset second-order perturbation theory along with the GIAO method show the changes in isotropic shielding, in a reasonable basis set independent fashion.     

Analysis of the vibrational spectra of 1-methyluracil and its isotopic derivatives by ab initio calculations

The vibrational spectrum of 1-methyluracil trapped in an argon matrix has been analysed based on ab initio Hartree—Fock SCF calculations with a split-valence 4–21 basis set. The directly computed theoretical harmonic force field was scaled with empirical scale factors which were transferred from uracil (except for the methyl vibrational modes) to provide an a priori prediction of fundamental frequencies and intensities. The average deviations between experiment and prediction were 9.8 cm⁻¹ for the in-plane vibrations and 18.3 cm⁻¹ for the ring out-of-plane modes. After a few corrections of assignment of the observed spectrum, a new set of scale factors was optimized to give the best force field available from combined consideration of the experimental and theoretical information. These scale factors reduced the average deviations to 6.7 cm⁻¹ for the in-plane modes and to 11.7 cm⁻¹ for the out-of-plane ones. The vibrational spectra of seven isotopic derivatives (-2¹⁸0, -4¹⁸0, -3d, -5d, -6d, -5, 6d₂ and -CD₃) of 1-methyluracil were predicted with the force field resulting from the optimized set of scale factors, and compared with the crystal-phase experimental data. A few misassignments in the experimental isotopic spectra have been corrected. Vibrational absorption intensities have been computed and compared with experiment and with an earlier calculation.     

Hydrogen-bonding effect on C NMR chemical shifts of amino acid residue carbonyl carbons of some peptides in the crystalline state

¹³C cross polarization-magic angle spinning NMR spectra were measured for a series of peptides containing -valine, -leucine and -aspartic acid residues, for which the crystal structures were already determined by X-ray diffraction, in order to investigate the relationship between hydrogen-bond lengths (R_N…O) and ¹³C chemical shifts of amide carbonyl carbons in the peptides. From these experimental results, it was found that the isotropic ¹³C chemical shifts (δ_iso) of the amino acid residues move linearly downfield with a decrease in R_N…O within the hydrogen-bonded length range considered here and also shown in our previous work on glycine and -alanine residues as expressed by δ_iso(ppm) = a − bR_N…O(Å) where a and b are 215.4 (ppm) and 14.2 (ppm Å⁻¹) for the -valine residue, 202.2 (ppm) and 10.0 (ppm Å⁻¹) for the -leucine residue, and 199.0 (ppm) and 9.6 (ppm Å⁻¹) for the -aspartic acid residue, respectively. Using these relations, the R_N…O values of some polypeptides in the crystalline state were determined through the observation of the amide carbonyl carbon chemical shifts. These values were compared with those determined by the X-ray diffraction method. Furthermore, quantum-chemical calculation of the ¹³C shielding constant for a model compound was carried out by the finite perturbation theory INDO method in order to ascertain the ¹³C shielding behavior in the formation of hydrogen bonds.     

Theoretical study of some 1,3-substituted (1,3-diketonato)borondifluorides. Potential energy curve relevant to the barrier crossing reaction

Ab initio Hartree-Fock calculations utilising STO-3G, 3-21G^* and 6-31G^* basis sets have been performed on three neutral and highly polar molecules, (diformylmethine)borondifluoride, (acetylacetonato)borondifluoride and (dibenzylmethine) borondifluoride. The calculated and experimental structures are well correlated when using the HF/3-21G^* basis set, except for the structure parameters involving the boron atom. The HF/6-31G^* basis set does not improve the accuracy in structure calculations. The conformational analysis is in agreement with the experimentally observed C_2v symmetrical structures, where the boron atom is tetrahedrally coordinated. The calculations support a one-dimensional ground state barrier crossing reaction for (dibenzylmethine)borondifluoride, where the phenyl torsion is the most likely reaction coordinate. Both HF/6-31G^* calculations and the second-order Møller-Plesset correction with the 3-21G^* basis set suggest an activation energy of the ground state reaction of about 30 kJ mol⁻¹. The ground state barrier crossing reaction kinetics is evaluated by the Kramers theory. The calculated ground state parameters relevant to the barrier crossing reaction are compared with the experimentally observed excited state values.     

The beryllium dimer potential

The convergence of ab initio calculations of the beryllium dimer potential is examined with several basis sets orders of perturbation theory. When the atomic pair natural orbital basis set calculations are extrapolated to the complete basis set and full CI limits, the calculated parameters: R_e=2.447 Å, D_e=827 cm⁻¹, ν₀₁=212.7 cm⁻¹, ν₁₂=167.2 cm⁻¹, ν₂₃=121.5 cm⁻¹ and ν₃₄=77.7 cm⁻¹ are in good agreement with the experimental parameters: R_e=2.45 Å, D_e=839±10 cm⁻¹, ν₀₁=223.2 cm⁻¹, ν₁₂=169.7 cm⁻¹, ν₂₃=122.5 cm⁻¹, and ν₃₄=79 cm⁻¹.     

C CP MAS NMR, FTIR, X-ray diffraction and PM3 studies of some N-(ω-carboxyalkyl)morpholine hydrohalides

N-(ω-carboxyalkyl)morpholine hydrochlorides, OC₄H₈N(CH₂)_nCOOH·HCl, n=1–5, were obtained and analyzed by ¹³C cross polarization (CP) magic angle spinning (MAS) NMR, FTIR and PM3 calculations. The structure of N-(3-carboxypropyl)morpholine hydrochloride (n=3) has been solved by X-ray diffraction method at 100 K and refined to the R=0.031. The crystals are monoclinic, space group P2₁/c, a=14.307(3), b=9.879(2), c=7.166(1) Å, β=93.20(3)°, V=1011.3(3) ų, Z=4. In this compound the nitrogen atom is protonated and two molecules form a centrosymmetric dimer, connected by two N⁺–HCl⁻ (3.095(1) Å) and two O–HCl⁻ (3.003(1) Å) hydrogen bonds. ¹³C CP MAS NMR spectra, contrary to the solution, showed non-equivalence of the ring carbon atoms. The PM3 calculations predict a molecular dimer without proton transfer for an HCl complex, while for an HBr complex an ion pairs with proton transfer, and reproduces correctly the conformation of both dimers but overestimates H-bond distances. Shielding constants calculated from the PM3 geometry of ion pairs gave a linear correlation with the ¹³C chemical shifts in solids.