Why is N···Be distance of NH3H+···DBeH shorter than that of NH3D+···HBeH? paradoxical geometrical isotope effects for partially isotope‐substituted dihydrogen‐bonded isotopomers

The partial isotope substitution for the change of geometrical parameters, interaction energies, and nuclear magnetic shielding tensors (σ) of dihydrogen‐bonded NH₃X⁺···YBeH (X, Y = H, D, and T) systems is analyzed. Based on the theoretical calculation, the distance between heavy atoms R_N···Be of NH₃H⁺···DBeH is clearly found to be shorter than that in NH₃D⁺···HBeH. Such apparently paradoxical geometrical isotope effect (GIE) on R_N···Be is revealed by the cooperative effect of two kinds of (1) primary covalent‐bonded GIE and (2) secondary dihydrogen‐bonded one. We have demonstrated that (1) the covalent bond lengths become shorter by heavier isotope‐substitution and (2) the dihydrogen‐bonded distance R_X···Y becomes shorter by heavier Y and lighter X isotope‐substitution due to the difference of electronic structure reflected by the nuclear distribution. We have also found that interaction energy of NH₃H⁺···DBeH is stronger than that of NH₃D⁺···HBeH and isotopic deshielding effect of magnetic shielding becomes large in lighter isotope. © 2013 Wiley Periodicals, Inc.     

Cooperative influence of water binding to peptides by N?H···OH2 and CO···HOH hydrogen bonds: Study by Ab Initio calculations

In this article, the geometry structures of hydrogen bond chains of formamide and N‐methylacetamide and their hydrogen‐bonded complexes with water were optimized at the MP2/6‐31G* level. Then, we performed Møller–Plesset perturbation method with 6‐311++g**, aug‐cc‐pvtz basis sets to study the cooperative influence to the total hydrogen bond energy by the N? H ··· OH₂ and C?O ··· HOH hydrogen bonds. On the basis of our results, we found that the cooperativity of the hydrogen‐bonded complexes become weaker as N? H ··· OH₂ and C?O ··· HOH hydrogen bonds replacing N? H ··· O?C hydrogen bonds in protein and peptide. It means that the N? H and C?O bonds in peptide prefer to form N? H ··· O?C hydrogen bond rather than to form C?O ··· HOH and N? H ··· OH₂. It is significant for understanding the structures and properties of the helical or sheet structures of protein and peptide in biological systems. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Characterization of the N?H···ON and N?H···NO H‐bonds in nitrosamine dimers

Ab initio molecular orbital and DFT calculations have been carried out for three most stable dimers of parent nitrosamine (NA) in order to elucidate the structures and energetics of the dimers. The structures were optimized using HF, B3LYP, and MP2 methods with 6‐311+G(d,p) and 6‐311++G(2d,2p) basis sets. At the optimized geometries obtained at MP2/6‐311++G(2d,2p) level of theory, the energies were evaluated at QCISD/aug‐cc‐pVDZ and CCSD/aug‐cc‐pVDZ levels. The most stable dimer has two N? H···O?N hydrogen bonds and the least stable dimer has two N? H···N?O hydrogen bonds. The natural bond orbital analysis showed that the lpO(N) → BD*(N? N) and lpO(N) → BD*(N? H_b) interactions play a decisive role in the stabilization of the NH···O(N) hydrogen bonds in dimers. The atoms in molecules results reveal that the intermolecular N? H···O(N) H‐bonds in dimers have electrostatic character. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Theoretical study of the S?H···O blue‐shifted hydrogen bond

Theoretical calculations were performed to study the nature of the hydrogen bonds in the complexes HCHO···HSO, HCOOH···HSO, HCHO···HOO, and HCOOH···HOO. The geometric structures and vibrational frequencies of these four complexes at the MP2/6‐31G(d,p) and MP2/6‐311+G(d,p) levels are calculated by standard and counterpoise‐corrected methods, respectively. The results indicate that in the complexes HCHO···HSO and HCOOH···HSO the S? H bond is strongly contracted. In the S? H···O hydrogen bonds, the calculated blue shifts for the S? H stretching frequencies are in the vicinity of 50 cm^?1. While in the complexes HCHO···HOO and HCOOH···HOO, the O? H bond is elongated and O? H···O red‐shifted hydrogen bonds are found. From the natural bond orbital analysis it can be seen that the X? H bond length in the X? H···Y hydrogen bond is controlled by a balance of four main factors in the opposite directions: hyperconjugation, electron density redistribution, rehybridization, and structural reorganization. Among them hyperconjugation has the effect of elongating the X? H bond. Electron density redistribution and rehybridization belong to the bond shortening effects, while structural reorganization has an uncertain influence on the X? H bond length. In the complexes HCHO···HSO and HCOOH···HSO, the shortening effects dominate which lead to the blue shift of the S? H stretching frequencies. In the complexes HCHO···HOO and HCOOH···HOO where elongating effects are dominant, the O? H···O hydrogen bonds are red‐shifted. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Investigation on the individual contributions of N?H···OC and C?H···OC interactions to the binding energies of β‐sheet models

In this article, the binding energies of 16 antiparallel and parallel β‐sheet models are estimated using the analytic potential energy function we proposed recently and the results are compared with those obtained from MP2, AMBER99, OPLSAA/L, and CHARMM27 calculations. The comparisons indicate that the analytic potential energy function can produce reasonable binding energies for β‐sheet models. Further comparisons suggest that the binding energy of the β‐sheet models might come mainly from dipole–dipole attractive and repulsive interactions and VDW interactions between the two strands. The dipole–dipole attractive and repulsive interactions are further obtained in this article. The total of N? H···H? N and C?O···O?C dipole–dipole repulsive interaction (the secondary electrostatic repulsive interaction) in the small ring of the antiparallel β‐sheet models is estimated to be about 6.0 kcal/mol. The individual N? H···O?C dipole–dipole attractive interaction is predicted to be ?6.2 ± 0.2 kcal/mol in the antiparallel β‐sheet models and ?5.2 ± 0.6 kcal/mol in the parallel β‐sheet models. The individual C^α? H···O?C attractive interaction is ?1.2 ± 0.2 kcal/mol in the antiparallel β‐sheet models and ?1.5 ± 0.2 kcal/mol in the parallel β‐sheet models. These values are important in understanding the interactions at protein–protein interfaces and developing a more accurate force field for peptides and proteins. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010     

N?H···S and S?H···N intramolecular hydrogen bond in β‐thioaminoacrolein: A quantum chemical study

The conformational study of β‐thioaminoacrolein was performed at various theoretical levels, HF, B3LYP, and MP2 with 6‐311++G(d,p) basis set, and the equilibrium conformations were determined. To have more reliable energies, the total energies of all conformers were recomputed at high‐level ab initio methods, G2MP2, G3, and CBS‐QB3. According to these calculations, the intramolecular hydrogen bond is accepted as the origin of conformational preference in thialamine (TAA) and thiolimine groups. The hydrogen bond strength in various resonance‐assisted hydrogen bond systems was evaluated by HB energy, geometrical parameters, topological parameters, and charge transfers corresponding to orbital interactions. Furthermore, our results reveal that the TAA tautomer has extra stability with respect to the other tautomers. The population analyses of the possible conformations by NBO predict that the origin of this preference is mainly due to the π‐electron delocalization in framework of TAA forms, especially usual π_C?C → π*_C?S and Lp (N) → π*_C?C charge transfers. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

A novel single‐electron sodium bond system of H3C···Na?Y (YH,OH, F,CCH, CN,and NC)

A novel single‐electron sodium bond system of H₃C···Na? H (I), H₃C···Na? OH(II), H₃C···Na? F(III), H₃C···Na‐CCH(IV), H₃C···Na? CN (V) and H₃C···Na? NC (VI) complexes has been studied by using MP2/6‐311++G** and MP2/aug‐cc‐pVTZ methods for the first time. We demonstrated that the single‐electron sodium bond H₃C···Na? Y formed between H₃C and Na? Y (Y?H, OH, F, CCH, CN, and NC) could induce the Na? Y increased and stretching frequencies of I–IV and VI are red‐shifted, including the Na? N bond in complex V is blue‐shifted abnormally. The interaction energies are calculated at two levels of theory [MP2, CCSD(T)] with different basis. The results shows that the strength of binding bond in group 2 (IV–VI) with π electrons are stronger than that of group 1 (I–III) without π electrons. For all complexes, the main orbital interactions between moieties H₃C and Na? Y are LP₁(C)→LP*₁(Na). By comparisons with some related systems, it is concluded that the strength of single‐electron bond is increased in the order: hydrogen bond < bromine bond < sodium bond < lithium bond. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

An insight into C?H···N hydrogen bond and stability of the complexes formed by trihalomethanes with ammonia and its monohalogenated derivatives

A theoretical study of the C? H···N hydrogen bond in the interactions of trihalomethanes CHX₃ (X = F, Cl, Br) with ammonia and its halogen derivatives NH₂Y (Y = F, Cl, Br) has been carried out thoroughly. The complexes are quite stable, and their stability increases in going from CHF₃ to CHCl₃ then to CHBr₃ when Y keeps unchanged. With the same CHX₃ proton donor, enhancement of the gas phase basicity of NH₂Y strengthens stability of the CHX₃···NH₂Y complex. The C? H···N hydrogen bond strength is directly proportional to the increase of proton affinity (PA) at N site of NH₂Y and the decrease of deprotonation enthalpy (DPE) of C? H bond in CHX₃. The CHF₃ primarily appears to favor blue shift while the red‐shift is referred to the CHBr₃. The blue‐ or red‐shift of CHCl₃ strongly depends on PA at N site of NH₂Y. We suggest the ratio of DPE/PA as a factor to predict which type of hydrogen bond is observed upon complexation. The SAPT2+ results show that all C? H···N interactions in the complexes are electrostatically driven regardless of the type of hydrogen bond, between 48% and 61% of the total attractive energy, and partly contributed by both induction and dispersion energies.     

Intermolecular interactions in group 14 hydrides: Beyond C?H···H?C contacts

In line with previous work in which we established the factors that enhance attractive C? H···H? C dihydrogen interactions in alkanes, an extended theoretical analysis of noncovalent intermolecular interactions in group 14 hydrides is presented here. Remarkably, these weak interactions may play a major role in determining the crystal structures adopted by several families of molecules. A combined structural and computational analysis at the MP2 level allowed us to identify and characterize different interactions of the type E? H···H? E and E···H? E (E = Si, Ge, Sn, and Pb), and to find also the most suitable scenario for the establishment of each particular type. The nature of the interactions has been analyzed in terms of natural charges of the atoms involved and a topological analysis of the electron density of several dimers confirms the existence of H···H and H···E attractive contacts. We have observed that the interaction strength increases when descending down the periodic group and that silicon has a marked tendency to establish Si···H? Si interactions. A size‐dependent backbone effect that reinforces H···H dihydrogen interactions in polyhedral systems has also been found.     

Tetrabutylammonium salt of the B24F224− anion. Two B12F112− icosahedra linked by a 2c–2e B?B bond and surrounded by a sheath of CH· · ·FB hydrogen bonds

The B₂₄F₂₂⁴⁻ anion, which was formed as a minor by‐product when the B₁₂H₁₂²⁻ anion was treated with F₂ in liquid HF, has been isolated as its N(n‐Bu)₄⁺ salt and characterized by ¹⁰B, ¹¹B, and ¹⁹F NMR spectroscopy, electrospray mass spectrometry, cyclic voltammetry, single‐crystal X‐ray diffraction, and calculations at the DFT level of theory. The B₂₄F₂₂⁴⁻ anion has idealized D₅ symmetry and consists of two B₁₂F₁₁²⁻ icosahedra linked by a 2c–2e boron–boron single bond with a B B distance of 1.725(4) Å. In the solid state, the anion interacts with eight N(n‐Bu)₄⁺ cations via a network of 34 CH···FB hydrogen bonds with H· · ·F distances that range from 2.26 to 2.55 Å. These hydrogen bonds were successfully modeled by DFT calculations, which showed that the hydrogen bonds probably have a measurable, albeit subtle, effect on the structure of the B₂₄F₂₂⁴⁻. © 2006 Wiley Periodicals, Inc. Heteroatom Chem 17:181–187, 2006; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/hc.20220     

A simple model for the band structure and D.C. conductivity of an infinite CO···H?N chain perpendicular to the protein backbone

The¹ Hartree–Fock crystal orbital (CO) method in its linear combination of atomic orbitals form was applied to determine the band structure of histone proteins taking 0.041e charge transfer per nucleotide base from the PO groups of poly(guanilic acid) to the arginine, and lysine side chains in histones (see text). Assuming that there are infinite COs, perpendicular to the main chain, formed by the amide groups of one segment of the protein chain bound together by H‐bonds with the C?O groups of another segment of the chain, we have calculated the band structure. From this, we have determined the mobility using the deformation potential approximation. Multiplying this with the mobile electron concentration due to the charge transfer between the PO groups of DNA and the positive side chains in histones, we have obtained for the direct current (D.C.) electron conductivity σ_fib = 1.07 × 10^?9 Ω^?1 cm for a single fiber and after division by the cross‐section of 9.10 × 10^?16 cm², σ_spec = 1.18 × 10⁶ Ω^?1 cm^?1 for the specific conductivity. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Effect of Al?H···H?O dihydrogen bond on the reaction between diphenylmethanol and pyrazolate‐bridged dialuminum complex. An ONIOM DFT/AM1 study

To elucidate the nature of the Al? H···H? O dihydrogen bond and its effect on the reaction between diphenylmethanol and pyrazolate‐bridged dialuminum complex, a theoretical study was carried out using the ONIOM(B3LYP/6‐31+G(d,p):AM1) method. Calculations indicate that this reaction is a two‐step process. The first step is nucleophilic addition and the resulting intermediate is stabilized by an Al? H···H? O dihydrogen bond. Topology analyses based on the “atoms‐in‐molecules” theory show that the Al? H···H? O dihydrogen bond in dialuminum intermediate is stronger than normal hydrogen bond. This step is not barrierless, which is contrary to the result predicted by using simplified model. The second step, eliminating a molecule of dihydrogen, requires an activation free energy of 9.9 kcal/mol in gas phase, which implies the simplified model underestimates the energy barrier of this elimination step. ONIOM calculations also show that, using the simplified model without zero‐point energy correction, the dihydrogen bonding strength has been underestimated and unreliable results have been obtained. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Effects of Cultivation Conditions on the Production of γ-PGA with <Emphasis Type="Italic">Bacillus subtilis</Emphasis> ZJU-7

Poly-γ-glutamic acid (γ-PGA) is a kind of water-soluble and biodegradable polymer made from d- and l-glutamic acid units, which are linked by amide bonds formed between α-amino and γ-carboxylic acid groups. As a potential targeted biopolymer that can be refined from biomass directly, γ-PGA has been increasingly applied to food, cosmetic, and pharmaceutical industries. In this work, a suitable nitrogen source was screened out for the high and cost-effective production of γ-PGA in Bacillus subtilis ZJU-7. The effects of inoculation time and initial glucose concentration on the γ-PGA production were investigated systematically in both shake flasks and a bench-top 15-l fermentor. Under the optimized culture conditions, a high γ-PGA productivity (46.4 g/l) was obtained after 48 h cultivation at 37 °C. Finally, the large-scale fermentation of γ-PGA production was successfully scaled up to a 100-l fermentor, with the highest γ-PGA productivity for over 54.0 g/l.     

A new unconventional halogen bond C?X···H?M between HCCX (X = Cl and Br) and HMH (M = Be and Mg): An ab initio study

In this article, a new type of halogen‐bonded complex YCCX···HMY (X = Cl, Br; M = Be, Mg; Y = H, F, CH₃) has been predicted and characterized at the MP2/aug‐cc‐pVTZ level. We named it as halogen‐hydride halogen bonding. In each YCCX···HMY complex, a halogen bond is formed between the positively charged X atom and the negatively charged H atom. This new kind of halogen bond has similar characteristics to the conventional halogen bond, such as the elongation of the C? X bond and the red shift of the C? X stretch frequency upon complexation. The interaction strength of this type of halogen bond is in a range of 3.34–10.52 kJ/mol, which is smaller than that of dihydrogen bond and conventional halogen bond. The nature of the electrostatic interaction in this type of halogen bond has also been unveiled by means of the natural bond orbital, atoms in molecules, and energy decomposition analyses. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010     

How good is a Broyden–Fletcher–Goldfarb–Shanno-like update Hessian formula to locate transition structures? Specific reformulation of Broyden–Fletcher–Goldfarb–Shanno for optimizing saddle points

Based on a study of the Broyden–Fletcher–Goldfarb–Shanno (BFGS) update Hessian formula to locate minima on a hypersurface potential energy, we present an updated Hessian formula to locate and optimize saddle points of any order that in some sense preserves the initial structure of the BFGS update formula. The performance and efficiency of this new formula is compared with the previous updated Hessian formulae such as the Powell and MSP ones. We conclude that the proposed update is quite competitive but no more efficient than the normal updates normally used in any optimization of saddle points. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 349–362, 1998     

Is the Excited‐State H‐atom Transfer in Hypericin Concerted?¶

The excited-state intramolecular H-atom transfer of hypericin (Hyp) was investigated as a function of pH in monodispersed reverse micelles formed by sodium bis(2-ethylhexyl)sulfosuccinate/heptane/water and in complexes with Tb3+ under conditions in which one of the two carbonyl groups of Hyp is incapable of accepting a hydrogen atom. The results of pump-probe transient absorption experiments provide no evidence for a concerted H-atom transfer mechanism.     

On the Formation of Cyclobutane Pyrimidine Dimers in UV‐irradiated DNA: Why are Thymines More Reactive?¶

The reaction pathways for thermal and photochemical formation of cyclobutane pyrimidine dimers in DNA are explored using density functional theory techniques. Although it is found that the thermal [2 + 2] cycloadditions of thymine + thymine (T + T --> T x T), cytosine + cytosine (C + C --> C x C) and cytosine + thymine (C + T --> C x T) all are similarly unfavorable in terms of energy barriers and reaction energies, the excited-state energy curves associated with the corresponding photochemical cycloadditions display differences that--in line with experimental findings--unanimously point to the predominance of T x T in UV-irradiated DNA. It is shown that the photocycloaddition of thymines is facilitated by the fact that the S1 state of the corresponding reactant complex lies comparatively high in energy. Moreover, at a nuclear configuration coinciding with the ground-state transition structure, the excited-state energy curve displays an absolute minimum only for the T + T system. Finally, the T + T system is also associated with the most favorable excited-state energy barriers and has the smallest S2-S0 energy gap at the ground-state transition structure.     

Do Liposome‐binding Constants of Porphyrins Correlate with Their Measured and Predicted Partitioning Between Octanol and Water?¶

We tested correlations between lipophilicity parameters and the partitioning of sensitizers into membranes. For this purpose we investigated 17 porphyrins and two chlorins having various chemical structures. Some of these compounds possess an amphiphilic structure (including hematoporphyrin, deuteroporphyrin, mesoporphyrin, chlorin e6 and more). The others are very symmetrical sensitizers [meso-tetra(N-methyl-4-pyridyl)porphyrin, tetra-benzoporphyrin, coproporphyrin I dihydrochloride (CP), meso-tetra(4-carboxyphenyl)porphyrin (TCP) and meso-tetra(m-hydroxyphenyl)chlorin]. Our investigation also included two series of hematoporphyrins and protoporphyrins with varying lengths of alkylcarboxylate side groups. The partitioning of these compounds between the bulk aqueous phase and liposomes was studied by fluorescence methods, and a liposome-binding constant, Kb, was obtained. It was found that CP and TCP do not incorporate into the lipid phase at pH 7.3. An n-octanol-water partition coefficient (log P) and a distribution coefficient (log D) were predicted with a modeling software. The values of log D were also obtained experimentally. We found that for the studied molecules, the predicted log D correlated well with the measured values. The values of log D as well as log P, in turn, did not correlate nicely, for the whole group of studied compounds, with the binding constants to liposomes. However, in the case of porphyrins that share a similar structure, the Kb showed good linear correlation with both log P and log D. For the series of hematoporphyrins and protoporphyrins with different lengths of alkylcarboxyl groups, it was shown that prolongation of this group caused an increase in the lipophilicity and the liposome-binding constant. This effect is more pronounced for the proto- than for the hematoporphyrin series. The results highlight the possible use, as well as limitations, of lipophilicity parameters for the prediction of membrane binding.     

How do UV Photomorphogenic Responses Confer Water Stress Tolerance?¶†

Although ultraviolet-B (UV-B) radiation is potentially harmful, it is an important component of terrestrial radiation to which plants have been exposed since invading land. Since then, plants have evolved mechanisms to avoid and repair UV radiation damage; therefore, it is not surprising that photomorphogenic responses to UV-B are often assumed to be adaptations to harmful radiation. This presupposes that the function of the observed responses is to prevent UV damage. It has been hypothesized that, as with blue light, UV-B provides a signal important for normal plant development and might be perceived within developing plants through nondestructive processes, perhaps through UV-specific signal perception mechanisms. UV signal perception can lead to photomorphogenic responses that may confer adaptive advantages under conditions associated with high-light environments, such as water stress. Plant responses to UV radiation in this regard include changes in leaf area, leaf thickness, stomatal density, photosynthetic pigment production and altered stem elongation and branching patterns. Such responses may lead to altered transpiration rates and water-use efficiencies. For example, we found that the cumulative effect of ambient UV-B radiation upon stomatal density and conductance can lead to altered water-use efficiencies. In field settings, UV might more properly be viewed as a photomorphogenic signal than as a stressor. Hence, it might be insufficient to attempt to fully evaluate the adaptive roles of plant responses to UV-B cues upon stress tolerance by the simultaneous application of UV and drought stress during development. We propose that rather than examining a plant's response to combinations of stressors one might also examine how a plant's response to UV induces tolerance to subsequently applied stresses.