Bent Hydrogen Bonds Research Articles

Electronic Excitation of ortho-Fluorothiophenol.

ortho-Fluorothiophenol (o-FTP) photodissociates through the well-known πσ* process. The fluorine atom of o-FTP introduces a feature in the photodissociation of o-FTP that does not occur in most other πσ* processes because the fluorine atom can form a hydrogen bond with the hydrogen atom of the SH group. Theoretical computations can serve as a good way to study these reactions because they usually proceed very quickly, and the current spectroscopies cannot probe the details of the processes as thoroughly as theory can. Here we use completely renormalized equation-of-motion coupled cluster theory with single and double excitations and a quasiperturbative treatment of connected triple excitations (CR-EOM-CCSD(T)) and quasidegenerate perturbation theory, in particular extended multistate complete-active-space second-order perturbation theory (XMS- CASPT2), to calculate the four lowest singlet states of o-FTP and hybrid density functional theory to optimize the geometries of the two lowest singlet states. We find that ten active electrons in nine active orbitals are sufficient to provide a good reference function for all four states. We find that the ground electronic state and the first excited singlet state both exhibit strongly bent hydrogen bonds. We also use density functional theory with the Tamm-Dancoff approximation and the SMD solvation model to successfully simulate the electronic spectrum of o-FTP in n-hexane solvent.

A Transferable Polarizable Force Field for Urea Crystals and Aqueous Solutions.

Urea is an important chemical with many biological and industrial applications. In this work, we develop a first-principles polarizable force field for urea crystals and aqueous solutions within the symmetry-adapted perturbation theory (SAPT) protocol with the SWM4-NDP model for water. We make three adjustments to the SAPT force field protocol: We augment the carbonyl oxygen atom of urea with additional interaction sites in order to address the "chelated" bent double hydrogen bonds in urea, we reduce the polarizability of urea by a factor of 0.70 to reproduce experimental in-crystal dipole moments, and we re-fit atomic pre-exponential parameters to correct the predicted liquid structure. We find that the resulting force field is in good agreement for the static and dynamic properties of aqueous urea solutions when compared to experiment or first-principles molecular dynamics simulations. The polarizable urea model accurately reproduces the crystal-solution phase diagram in the temperature range of 261 to 310 K; for which, it is superior to non-polarizable models. We expect that this force field will be useful in the modeling of complex biomolecular systems and enable studies of polarizability effects of solid-liquid phase behavior of complex fluids.

Local structure of dilute aqueous DMSO solutions, as seen from molecular dynamics simulations.

The information about the structure of dimethyl sulfoxide (DMSO)-water mixtures at relatively low DMSO mole fractions is an important step in order to understand their cryoprotective properties as well as the solvation process of proteins and amino acids. Classical MD simulations, using the potential model combination that best reproduces the free energy of mixing of these compounds, are used to analyze the local structure of DMSO-water mixtures at DMSO mole fractions below 0.2. Significant changes in the local structure of DMSO are observed around the DMSO mole fraction of 0.1. The array of evidence, based on the cluster and the metric and topological parameters of the Voronoi polyhedra distributions, indicates that these changes are associated with the simultaneous increase of the number of DMSO-water and decrease of water-water hydrogen bonds with increasing DMSO concentration. The inversion between the dominance of these two types of H-bonds occurs around XDMSO = 0.1, above which the DMSO-DMSO interactions also start playing an important role. In other words, below the DMSO mole fraction of 0.1, DMSO molecules are mainly solvated by water molecules, while above it, their solvation shell consists of a mixture of water and DMSO. The trigonal, tetrahedral, and trigonal bipyramidal distributions of water shift to lower corresponding order parameter values indicating the loosening of these orientations. Adding DMSO does not affect the hydrogen bonding between a reference water molecule and its first neighbor hydrogen bonded water molecules, while it increases the bent hydrogen bond geometry involving the second ones. The close-packed local structure of the third, fourth, and fifth water neighbors also is reinforced. In accordance with previous theoretical and experimental data, the hydrogen bonding between water and the first, the second, and the third DMSO neighbors is stronger than that with its corresponding water neighbors. At a given DMSO mole fraction, the behavior of the intensity of the high orientational order parameter values indicates that water molecules are more ordered in the vicinity of the hydrophilic group while their structure is close-packed near the hydrophobic group of DMSO.

Intramolecular competition between n-pair and π-pair hydrogen bonding: Microwave spectrum and internal dynamics of the pyridine-acetylene hydrogen-bonded complex.

a-type rotational spectra of the hydrogen-bonded complex formed from pyridine and acetylene are reported. Rotational and (14)N hyperfine constants indicate that the complex is planar with an acetylenic hydrogen directed toward the nitrogen. However, unlike the complexes of pyridine with HCl and HBr, the acetylene moiety in HCCH-NC5H5 does not lie along the symmetry axis of the nitrogen lone pair, but rather, forms an average angle of 46° with the C2 axis of the pyridine. The a-type spectra of HCCH-NC5H5 and DCCD-NC5H5 are doubled, suggesting the existence of a low lying pair of tunneling states. This doubling persists in the spectra of HCCD-NC5H5, DCCH-NC5H5, indicating that the underlying motion does not involve interchange of the two hydrogens of the acetylene. Single (13)C substitution in either the ortho- or meta-position of the pyridine eliminates the doubling and gives rise to separate sets of spectra that are well predicted by a bent geometry with the (13)C on either the same side ("inner") or the opposite side ("outer") as the acetylene. High level ab initio calculations are presented which indicate a binding energy of 1.2 kcal/mol and a potential energy barrier of 44 cm(-1) in the C2v configuration. Taken together, these results reveal a complex with a bent hydrogen bond and large amplitude rocking of the acetylene moiety. It is likely that the bent equilibrium structure arises from a competition between a weak hydrogen bond to the nitrogen (an n-pair hydrogen bond) and a secondary interaction between the ortho-hydrogens of the pyridine and the π electron density of the acetylene.

Phase transitions and hydrogen bonding in deuterated calcium hydroxide: High-pressure and high-temperature neutron diffraction measurements

In situ neutron diffraction measurements combined with the pulsed neutron source at the Japan Proton Accelerator Research Complex (J-PARC) were conducted on high-pressure polymorphs of deuterated portlandite (Ca(OD)2) using a Paris–Edinburgh cell and a multi-anvil press. The atomic positions including hydrogen for the unquenchable high-pressure phase at room temperature (phase II′) were first clarified. The bent hydrogen bonds under high pressure were consistent with results from Raman spectroscopy. The structure of the high-pressure and high-temperature phase (Phase II) was concordant with that observed previously by another group for a recovered sample. The observations elucidate the phase transition mechanism among the polymorphs, which involves the sliding of CaO polyhedral layers, position modulations of Ca atoms, and recombination of Ca–O bonds accompanied by the reorientation of hydrogen to form more stable hydrogen bonds.

Synthesis and Characterization of the Crystal and Magnetic Structures and Properties of the Hydroxyfluorides Fe(OH)F and Co(OH)F

The title compounds were synthesized by a hydrothermal route from a 1:1 molar ratio of lithium fluoride and transition-metal acetate in an excess of water. The crystal structures were determined using a combination of powder and/or single-crystal X-ray and neutron powder diffraction (NPD) measurements. The magnetic structure and properties of Co(OH)F were characterized by magnetic susceptibility and low-temperature NPD measurements. M(OH)F (M = Fe and Co) crystallizes with structures related to diaspore-type α-AlOOH, with the Pnma space group, Z = 4, a = 10.471(3) Å, b = 3.2059(10) Å, and c = 4.6977(14) Å and a = 10.2753(3) Å, b = 3.11813(7) Å, and c = 4.68437(14) Å for the iron and cobalt phases, respectively. The structures consist of double chains of edge-sharing M(F,O)6 octahedra running along the b axis. These infinite chains share corners and give rise to channels. The protons are located in the channels and form O-H···F bent hydrogen bonds. The magnetic susceptibility indicates an antiferromagnetic ordering at ∼40 K, and the NPD measurements at 3 K show that the ferromagnetic rutile-type chains with spins parallel to the short b axis are antiferromagnetically coupled to each other, similarly to the magnetic structure of goethite α-FeOOH.

Synthesis and characterization of the crystal structure and magnetic properties of the hydroxyfluoride MnF2−x(OH)x (x ∼ 0.8)

The new compound MnF(2-x)(OH)x (x ~ 0.8) was synthesized by a hydrothermal route from a 1 : 1 molar ratio of lithium fluoride and manganese acetate in an excess of water. The crystal structure was determined using the combination of single crystal X-ray and neutron powder diffraction measurements. The magnetic properties of the title compound were characterized by magnetic susceptibility and low-temperature neutron powder diffraction measurements. MnF(2-x)(OH)x (x ~ 0.8) crystallizes with orthorhombic symmetry, space group Pnn2 (no. 34), a = 4.7127(18), b = 5.203(2), c = 3.2439(13) Å, V = 79.54(5) Å(3) and Z = 2. The crystal structure is a distorted rutile-type with [Mn(F,O)4] infinite edge-sharing chains along the c-direction. The protons are located in the channels and form O-HF bent hydrogen bonds. The magnetic susceptibility measurements indicate an antiferromagnetic ordering at ~70 K and the neutron powder diffraction measurements at 3 K show that the ferromagnetic chains with spins parallel to the c-axis are antiferromagnetically coupled to each other, similarly to the magnetic structure of tetragonal rutile-type MnF2 with isoelectronic Mn(2+). MnF(2-x)(OH)x (x ~ 0.8) is expected to be of great interest as a positive electrode for Li cells if the protons could be exchanged for lithium.

Salt effects on solvent features of coexisting phases in aqueous polymer/polymer two-phase systems

The solvatochromic parameters characterizing the solvent dipolarity/polarizability (π*), solvent hydrogen-bond donor acidity (α), and solvent hydrogen-bond acceptor basicity (β) of aqueous media were measured in the coexisting phases of aqueous Dextran-Ficoll, Dextran-Ucon, Dextran-PEG, PEG-Ucon, Ficoll-Ucon, and Ficoll-PEG two-phase systems (ATPS). Ionic composition of each ATPS included 0.15M KCl, 0.15M KBr, 0.15M NaBr, 0.1M Na2SO4, and 0.1M Li2SO4 in 0.01M sodium phosphate buffer (NaPB), pH 7.4; and 0.01M and 0.11M sodium phosphate buffer, pH 7.4. Partition ratios of sodium salts of dinitrophenylated (DNP) amino acids with aliphatic side-chains (glycine, alanine, norvaline, norleucine, and α-amino-n-caprylic acid) were measured in all ATPSs, and the results were evaluated in terms of the differences between the relative hydrophobicity (parameter E) and the electrostatic properties (parameter C) of the aqueous media of the coexisting phases. It was established that parameter E is described by a linear combination of the differences between the solvent dipolarity/polarizability (Δπ*) and between the solvent hydrogen-bond acidity (Δα) of the media in the coexisting phases. Parameter C depends on the phase forming polymer pair and is shown to be described by a linear combination of three parameters: the differences between the solvent hydrogen-bond acidity (Δα) and between the solvent hydrogen-bond basicity (Δβ) of the media in the coexisting phases, and a measure of the effect of a given salt additive on the hydrogen bonds in water. This effect was represented by a parameter (Kb−l), characterizing the equilibrium between populations of hydrogen bonds with a bent hydrogen bond conformation and with linear hydrogen bond conformation affected by a given salt additive.

Kinetics of the Hydrogen Abstraction from Carbon-3 of 1-Butanol by Hydroperoxyl Radical: Multi-Structural Variational Transition-State Calculations of a Reaction with 262 Conformations of the Transition State.

We estimated rate constants for the hydrogen abstraction from carbon-3 of 1-butanol by hydroperoxyl radical, a critically important reaction in the combustion of biofuel. We employed the recently developed multi-structural variational transition-state theory (MS-VTST), which utilizes a multifaceted dividing surface that allows us to include the contributions of multiple structures for reacting species and transition states. First, multiconfigurational Shepard interpolation-based on molecular-mechanics-guided interpolation of electronic-structure Hessian data obtained by the M08 HX/jun-cc-pVTZ electronic model chemistry-was used to obtain the portion of the potential energy surface needed for single-structure variational transition-state theory rate constants including multidimensional tunneling; then, the M08-HX/MG3S electronic model chemistry was used to calculate multi-structural torsional anharmonicity factors to complete the MS-VTST rate constant calculations. The lowest-energy structures of the transition state have strongly bent hydrogen bonds. Our results indicate that neglect of multi-structural anharmonicity would lead to errors of factors of 0.3, 46, and 171 at 200, 1000, and 2400 K for this reaction.

Pressure Effects on the Quasi-1-D Molecular Ferromagnet 2-(4,5,6,7-Tetrafluorobenzimidazol-2-yl)-4,4,5,5-tetramethyl-4,5-dihydro-1H-imidazole-3-oxide-1-oxyl

Crystallographic lattice compression and magnetic variations in the quasi-1-D ferromagnet 2-(4,5,6,7-tetrafluorobenzimidazol-2-yl)-4,4,5,5-tetramethyl-4,5-dihydro-1H-imidazole-3-oxide-1-oxyl (F4BImNN) were studied under hydrostatic pressure for polycrystalline samples. The crystallographic c-axis—along which F4BImNN forms hydrogen bonds—was compressed by 3% at 10 kbar and by 4% at 17.8 kbar. The overall lattice volume contracts by 12% from ambient pressure to 17.8 kbar. The axis of the hydrogen bonded chain propagation is compressed, since the bent F4BImNN hydrogen bonds accommodate geometric compression. The magnetic susceptibility measured over 1.8–300 K showed an increase in ferromagnetic exchange interactions as pressure increased. Curie–Weiss 1/χ vs T analyses showed an increase in Weiss constant from (+)10.4 K to (+)15.3 K from ambient pressure to 9.85 kbar. Fitting of the χT vs T data indicated predominantly 1-D Heisenberg chain type behavior at all pressures, increasing from J/k = (+)19 K at room pressure to (+)25 K at 4.77 kbar and (+)30 K at 9.85 kbar. The increase in exchange strength is attributed to pressure-increased overlap of spin orbitals in the hydrogen bonded chains, which favors 1-D ferromagnetic interaction. There was no indication of a phase change, either crystallographically or in discontinuities of the magnetic behavior.

Investigation of hydrogen sites of wadsleyite: A neutron diffraction study

A neutron powder diffraction experiment was conducted to refine the hydrogen position of Mg-endmember deuterated wadsleyite. Preliminary refinement using the dry-structure determined by single crystal X-ray diffraction reveals a maximum peak Q1 of nuclear density in the difference Fourier map at the M3 octahedral edge, between the O1 and O4 atoms (3.071(3) Å). Full Rietveld refinement was conducted assuming that the maximum peak corresponds to deuterium atom. The deuterium position was determined as (0.096, 0.289, 0.315) with occupancy of 8.2%. The O1–D1 vector lies along M3 octahedral edge pointing O4 atom, and the bond length is determined as 1.037(15) Å for O1–D1, and 2.041(15) Å for D1⋯O4. The O1–D1⋯O4 geometry is almost linear with angle of 171.7(5) °. The residual peak Q2 was found in the map at (0, 0.172, 0.268), suggesting the existence of a bent hydrogen bond between O1⋯O3 (3.035 Å) of the M3 octahedral edge. The respective distances from the surrounding oxygen atoms are 0.97 and 2.13 Å for O1–Q2 and Q2⋯O3. The O1–Q2⋯O3 configuration is nonlinear, with angle of 154.4 °. These results reveal that the dominant site of protonation in wadsleyite is the O1 site, which is consistent with the previous prediction.

GIAO, DFT, AIM and NBO analysis of the NH···O intramolecular hydrogen‐bond influence on the1J(N,H) coupling constant in push–pull diaminoenones

In the series of diaminoenones, large high-frequency shifts of the (1)H NMR of the N-H group in the cis-position relative to the carbonyl group suggests strong N-H...O intramolecular hydrogen bonding comprising a six-membered chelate ring. The N-H...O hydrogen bond causes an increase of the (1)J(N,H) coupling constant by 2-4 Hz and high-frequency shift of the (15)N signal by 9-10 ppm despite of the lengthening of the relevant N-H bond. These experimental trends are substantiated by gauge-independent atomic orbital and density functional theory calculations of the shielding and coupling constants in the 3,3-bis(isopropylamino)-1-(aryl)prop-2-en-1-one (12) for conformations with the Z- and E-orientations of the carbonyl group relative to the N-H group. The effects of the N-H...O hydrogen-bond on the NMR parameters are analyzed with the atoms-in-molecules (AIM) and natural bond orbital (NBO) methods. The AIM method indicates a weakening of the N-H...O hydrogen bond as compared with that of 1,1-di(pyrrol-2-yl)-2-formylethene (13) where N-H...O hydrogen bridge establishes a seven-membered chelate ring, and the corresponding (1)J(N,H) coupling constant decreases. The NBO method reveals that the LP(O) --> sigma*(N-H) hyperconjugative interaction is weakened on going from the six-membered chelate ring to the seven-membered one due to a more bent hydrogen bond in the former case. A dominating effect of the N-H bond rehybridization, owing to an electrostatic term in the hydrogen bonding, seems to provide an increase of the (1)J(N,H) value as a consequence of the N-H...O hydrogen bonding in the studied diaminoenones.

Water in the Half Shell: Structure of Water, Focusing on Angular Structure and Solvation

Water is a highly polar molecule, consisting of a very electronegative atom, oxygen, bonded to two weakly electropositive hydrogen atoms with two lone pairs of electrons. These features give water remarkable physical properties, some of which are anomalous, such as its lower density in the solid phase compared with the liquid phase. Its ability to serve as both a hydrogen bond donor and hydrogen bond acceptor governs its role as a solvent, a role that is of central interest for biological chemists. In this Account, we focus on water's properties as a solvent. Water dissolves a vast range of solutes with solubilities that range over 10 orders of magnitude. Differences in solubility define the fundamental dichotomy between polar, or hydrophilic, solutes and apolar, or hydrophobic, solutes. This important distinction plays a large part in the structure, stability, and function of biological macromolecules. The strength of hydrogen bonding depends on the H-O...O H-bond angle, and the angular distribution is bimodal. Changes in the width and frequency of infrared spectral lines and in the heat capacity of the solution provide a measure of the changes in the strength and distribution of angles of the hydrogen bonds. Polar solutes and inorganic ions increase the population of bent hydrogen bonds at the expense of the more linear population, while apolar solutes or groups have the opposite effect. We examine how protein denaturants might alter the solvation behavior of water. Urea has very little effect on water's hydrogen bond network, while guanidinium ions promote more linear hydrogen bonds. These results point to fundamental differences in the protein denaturation mechanisms of these molecules. We also suggest a mechanism of action for antifreeze (or thermal hysteresis) proteins: ordering of water around the surface of these proteins prior to freezing appears to interfere with ice formation.

On Water Structure in Concentrated Salt Solutions

In concentrated salt solutions the average distances between the ions, dav=1.1844⋅(∑νici)−1/3 nm, are commensurate with the sizes of the solvated ions, so that no ‘bulk solvent’ remains. This is illustrated with two saturated aqueous solutions, where 16.67 mol⋅dm−3 CsF at 75 °C has dav(Cs–F)=0.368 nm and 14.54 mol⋅dm−3 LiI at 80 °C has dav(Li–I)=0.385 nm. The minimal distance required for the bare ions (sum of their radii) are 0.303 nm for CsF and 0.289 nm for LiI. Hence no water molecule, diameter 0.276 nm, can be fitted between the ions to form linear or slightly bent hydrogen bonds. Some recent work ignoring such constraints, even in 3–6 mol⋅dm−3 solutions, is criticized on this account.

Theoretical study of bifurcated bent blue-shifted hydrogen bonds CH2···Y

Ab initio quantum chemistry methods were applied to study the bifurcated bent hydrogen bonds Y··· H2CZ (Z = O, S, Se) and Y···H2CZ2 (Z = F, Cl, Br) (Y = Cl−, Br−) at the MP2/6-311++G(d,p) and MP2/6-311++G(2df,2p) levels. The results show that in each complex there are two equivalent blue-shifted H-bonds Y···H-C, and that the interaction energies and blue shifts are large, the energy of each Y···H-C H-bond is 15–27 kJ/mol, and Δr(CH) = −0.1 − −0.5 pm and Δv(CH) = 30 − 80 cm−1. The natural bond orbital analysis shows that these blue-shifted H-bonds are caused by three factors: large rehybridization; small direct intermolecular hyperconjugation and larger indirect intermolecular hyperconjugation; large decrease of intramolecular hyperconjugation. The topological analysis of electron density shows that in each complex there are three intermolecular critical points: there is one bond critical point between the acceptor atom Y and each hydrogen, and there is a ring critical point inside the tetragon YHCH, so these interactions are exactly H-bonding.

The shape of the potential energy curves for NHN+ hydrogen bonds and the influence of non-linearity

The potential energy curves for proton motion in NHN(+) hydrogen bonds have been calculated to investigate whether different methods of evaluation give different results: for linear H bonds most curves calculated along the NH direction are, as expected, identical with those along NN; for intramolecular H bonds it is very important to take into account the non-linearity and the potential energy curve calculated along the NH direction can be very far from the curve correctly describing the proton transfer. Other factors which influence the proton-transfer process are steric hindrance and presence of anions which modify the proton motion. In the analysis of the proton transfer process it is very important to take changes in the structure of the rest of the molecule into account, which is connected with exchange of energy with the surroundings. Comparison of adiabatic and non-adiabatic curves shows that they are significantly different for very bent hydrogen bonds and for hydrogen bonds with steric constraints for which the proton transfer process must be accompanied with relaxation of the whole molecule. Comparison of the potential-energy curves for compounds with very short H bonds emphasizes that the term 'strong H bond' needs to be qualified. For intermolecular H bonds shortening of the bond is connected with linearization. But for intramolecular H bonds the NN distance cannot be used as the only measure of H bond strength.

The 10 Å phase at high pressure by first principles calculations and implications for the petrology of subduction zones

The structure and the physical properties of the 10 Å phase, Mg 3Si 4O 10(OH) 2· nH 2O, with n = 0, n = 1 and n = 2 is explored over a wide range of pressure with density functional theory in the local density (LDA) and generalized gradient approximations (GGA). The static equation of state depends strongly on the amount of water ( n = 0: V 0 = 218.1(4) Å 3, K 0 = 37.0(6) GPa, K 0′ = 14.0(2); n = 1: V 0 = 226.6(3) Å 3, K 0 = 54.2(5) GPa, K 0′ = 17.2(2), n = 2: V 0 = 238.9(4) Å 3, K 0 = 38.2(12) GPa, K 0′ = 24.0(6)). All the investigated structures present a layer offset with respect to the ideal phlogopite like stacking along the x direction that influences the beta angle: tetrahedral rings and water molecules are not exactly aligned along the c nor the c ⁎ directions in the n = 1 and n = 2 structures. Water is bound to the tetrahedral sheets and is located off the mid-plane of the interlayer. The water dipole vector lies almost parallel to the tetrahedral sheets at zero pressure; the angle it forms with the ab plane increases with pressure in both n = 1 (up to 80°) and n = 2 (up to 50°) structures. Water molecules act both as acceptor and donor oxygen groups for hydrogen bonds. Water oxygens accept hydrogen from the intra-layer hydroxyls, leading to H-bonds at the boundary between the weak and the strong limit, in agreement with the relatively high Raman frequency at 3620 cm − 1 assigned to this vibrational mode. Water molecules donate hydrogen to basal oxygens of the tetrahedral sheet. Interactions between water molecules and basal oxygens are complicated by the occurrence of polifurcated, mainly asymmetric, bent hydrogen bonds. Nonetheless, within the stability field of the 10 Å phase, LDA results yield distances between basal oxygens and water hydrogen that fall between the weak and strong limit in agreement with Raman signals at 3672 and 3593 cm − 1 . GGA simulations suggest even stronger interactions between water molecules and basal oxygens.

Electronic properties of multifurcated bent hydrogen bonds CH3⋯Y and CH2⋯Y

H-bonding angle angleYHX has an important effect on the electronic properties of the H-bond Y...HX, such as intra- and intermolecular hyperconjugations and rehybridization, and topological properties of electron density. We studied the multifurcated bent H-bonds of the proton donors H3CZ (Z = F, Cl, Br), H2CO and H2CF2 with the proton acceptors Cl(-) and Br(-) at the four high levels of theory: MP2/6-311++G(d,p), MP2/6-311++G(2df,2p), MP2/6-311++G(3df,3pd) and QCISD/6-311++G(d,p), and found that they are all blue-shifted. These complexes have large interaction energies, 7-12 kcal mol(-1), and large blue shifts, delta r(HC) = -0.0025 --0.006 A and delta v(HC) = 30-90 cm(-1). The natural bond orbital analysis shows that the blue shifts of these H-bonds Y...HnCZ are mainly caused by three factors: rehybridization; indirect intermolecular hyperconjugation n(Y) -->sigma*(CZ), in that the electron density from n(Y) of the proton acceptor is transferred not to sigma*(CH), but to sigma*(CZ) of the donor; intramolecular hyperconjugation n(Z) -->sigma*(CH), in that the electron density in sigma*(CH) comes back to n(Z) of the donor such that the occupancy in sigma*(CH) decreases. The topological properties of the electron density of the bifurcated H-bonds Y...H2CZ are similar to those of the usual linear H-bonds, there is a bond critical point between Y and each hydrogen, and a ring critical point inside the tetragon YHCH. However, the topological properties of electron density of the trifurcated H-bonds Y...H3CZ are essentially different from those of linear H-bonds, in that the intermolecular bond critical point, which represents a closed-shell interaction, is not between Y and hydrogen, but between Y and carbon.

Theoretical Investigation of Hydrogen Bonds between CO and HNF2, H2NF, and HNO

Ab initio quantum mechanics methods were applied to investigate the hydrogen bonds between CO and HNF2, H2NF, and HNO. We use the Hartree-Fock, MP2, and MP4(SDQ) theories with three basis sets 6-311++G(d,p), 6-311++G(2df,2p), and AUG-cc-pVDZ, and both the standard gradient and counterpoise-corrected gradient techniques to optimize the geometries in order to explore the effects of the theories, basis sets, and different optimization methods on this type of H bond. Eight complexes are obtained, including the two types of C...H-N and O...H-N hydrogen bonds: OC...HNF2(C(s)), OC...H2NF(C(s) and C1), and OC...HNO(C(s)), and CO...HNF2(C(s)), CO...H2NF(C(s) and C1), and CO...HNO(C(s)). The vibrational analysis shows that they have no imaginary frequencies and are minima in potential energy surfaces. The N-H bonds exhibit a small decrease with a concomitant blue shift of the N-H stretch frequency on complexation, except for OC...HNF2 and OC...H2NF(C1), which are red-shifting at high levels of theory and with large basis sets. The O...H-N hydrogen bonds are very weak, with 0 K dissociation energies of only 0.2-2.5 kJ/mol, but the C...H-N hydrogen bonds are stronger with dissociation energies of 2.7-7.0 kJ/mol at the MP2/AUG-cc-pVDZ level. It is notable that the IR intensity of the N-H stretch vibration decreases on complexation for the proton donor HNO but increases for HNF2 and H2NF. A calculation investigation of the dipole moment derivative leads to the conclusion that a negative permanent dipole moment derivative of the proton donor is not a necessary condition for the formation of the blue-shifting hydrogen bond. Natural bond orbital analysis shows that for the C...H-N hydrogen bonds a large electron density is transferred from CO to the donors, but for the O...H-N hydrogen bonds a small electron density transfer exists from the proton donor to the acceptor CO, which is unusual except for CO...H2NF(C(s)). From the fact that the bent hydrogen bonds in OC(CO)...H2NF(C(s)) are quite different from those in the others, we conclude that a greatly bent H-bond configuration shall inhibit both hyperconjugation and rehybridization.

Estimation of strength in different extra Watson–Crick hydrogen bonds in DNA double helices through quantum chemical studies

It was shown earlier, from database analysis, model building studies, and molecular dynamics simulations that formation of cross-strand bifurcated or Extra Watson-Crick hydrogen (EWC) bonds between successive base pairs may lead to extra rigidity to DNA double helices of certain sequences. The strengths of these hydrogen bonds are debatable, however, as they do not have standard linear geometry criterion. We have therefore carried out detailed ab initio quantum chemical studies using RHF/6-31G(2d,2p) and B3LYP/6-31G(2p,2d) basis sets to determine strengths of several bent hydrogen bonds with different donor and acceptors. Interaction energy calculations, corrected for the basis set superposition errors, suggest that N-H...O type bent EWC hydrogen bonds are possible along same strands or across the strands between successive base pairs, leading to significant stability (ca. 4-9 kcal/mol). The N-H...N and C-H...O type interactions, however, are not so stabilizing. Hence, consideration of EWC N-H...O H-bonds can lead to a better understanding of DNA sequence directed structural features.