Determination of side‐chain‐rotamer and side‐chain and backbone virtual‐bond‐stretching potentials of mean force from AM1 energy surfaces of terminally‐blocked amino‐acid residues,for coarse‐grained simulations of protein structure and folding. I. The method

In this and the accompanying article, we report the development of new physics‐based side‐chain‐rotamer and virtual‐bond‐deformation potentials which now replace the respective statistical potentials used so far in our physics‐based united‐reside UNRES force field for large‐scale simulations of protein structure and dynamics. In this article, we describe the methodology for determining the corresponding potentials of mean force (PMF's) from the energy surfaces of terminally‐blocked amino‐acid residues calculated with the AM1 quantum‐mechanical semiempirical method. The approach is based on minimization of the AM1 energy for fixed values of the angles λ for rotation of the peptide groups about the C^α ··· C^α virtual bonds, and for fixed values of the side‐chain dihedral angles χ, which formed a multidimensional grid. A harmonic‐approximation approach was developed to extrapolate from the energy at a given grid point to other points of the conformational space to compute the respective contributions to the PMF. To test the applicability of the harmonic approximation, the rotamer PMF's of alanine and valine obtained with this approach have been compared with those obtained by using a Metropolis Monte Carlo method. The PMF surfaces computed with the harmonic approximation are more rugged and have more pronounced minima than the MC‐calculated surfaces but the harmonic‐approximation‐and MC‐calculated PMF values are linearly correlated. The potentials derived with the harmonic approximation are, therefore, appropriate for UNRES for which the weights (scaling factors) of the energy terms are determined by force‐field optimization for foldability. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Optical charge transfer transitions in supramolecular fullerene and porphyrin compounds

By the DFT method with the planar wave basis set and in the PAW approximation the geometric and electronic structures of four supramolecular compounds of porphyrin and fullerene molecules in the crystalline state are performed: H₂TPP·C₆₀·3 toluene, H₂T_pivPP·C₆₀, H₂T_3,5-dimethylPP·C₇₀·4 toluene, and NiT_4-methylPP·2C₇₀·2 toluene. The geometry is optimized using the PBE functional and the Grimme DFT-D2 dispersion interaction correction. The electronic structure and absorbance spectra are calculated using the HSE functional. It is shown that the H₂TPP·C₆₀·3 toluene structure having a sufficiently wide absorbance wavelength range, which results in a photoinduced electron transition from the higher occupied states formed by porphyrin molecules to the lower unoccupied states formed by fullerene molecules, is most promising for the design of photogalvanic elements.     

Structure electronique des complexes acide-base de Lewis. I. Structure electronique et conformation moléculaire des molécules F3P·BH3 et F2HP·BH3

The electronic structure and preferred conformations of F₃P·BH₃ and F₂HP·BH₃ are investigated in the framework of the CNDO /2 approximation. In complete agreement with microwave data, the staggered conformations are predicted to be the most stable ones. The barriers to internal rotation are in good agreement with experimental values (F₃P·BH₃: calc. = 3.03 kcal/mole, exp. = 3.24 ± 0.15 kcal/mole; F₂HP·BH₃: calc. = 3.63 kcal/mole, exp. = 4.05 ± 0.45 kcal/mole) and a bicentric energy partitioning shows that the variations of the total energy are completely reflected by the only variation of the interaction energy between phosphorus and H atoms bonded to boron. The analysis of the electron densities reveals the importance of the 3s(P) → 2p_x(B) transfer in the formation of the co-ordination. Finally, the computed dipole moment value and direction agree with corresponding experimental data.     

Heteroatom Effects on Electronic Excited State Hydrogen Bonding of Fluorenone‐Based Molecular Materials

In this work, the geometry optimizations in the ground state and electronic excitation energies and corresponding oscillation strengths of the low‐lying electronically excited states for the isolated fluorenone (FN) and FN‐based molecular monomers, the relatively hydrogen‐bonded dimers, and doubly hydrogen‐bonded trimers, are calculated by the density functional theory and time‐dependent density functional theory methods, respectively. We find the intermolecular hydrogen bond CO···H O is strengthened in some of the electronically excited states of the hydrogen‐bonded dimers and doubly hydrogen‐bonded trimers, because the excitation energy in a related excited state decrease and electronic spectral redshift are induced. Similarly, the hydrogen bond CO···H O is weakened in other excited states. On this basis, owing to the important difference of electronegativity, heteroatoms S, Se, and Te that substitute for the O atom in the carbonyl group of the FN molecule have a significant effect on the strength of the hydrogen bond and the spectral shift. It is observed that the hydrogen bond CTe···H O is too weak to be formed. When the CS and CSe substitute for CO, the strength of the hydrogen bonds and electronic spectra frequency shift are significantly changed in the electronic excited state due to the electron transition type transformation from the ππ* feature to σπ* feature. © 2013 Wiley Periodicals, Inc. Heteroatom Chem 24:153–162, 2013; View this article online at wileyonlinelibrary.com . DOI 10.1002/hc.21075     

Effects of Hydrogen Bonding on the Transition Properties of Ethanol–Water Clusters: A TD-DFT Study

In this work, time-dependent density functional theory method was used to study the electronic transitions of hydrogen-bonded ethanol–water complexes Dimer-I, Dimer-II and Trimer. The intermolecular hydrogen bonds H₁···O₁ and O···H₂ were demonstrated by the optimized geometric structures of the three hydrogen-bonded ethanol–water complexes. It is demonstrated that the S₁-state electronic transitions for ethanol monomer and the hydrogen-bonded complex Dimer-I (through HB-I) should be of LE nature on the ethanol molecule, while those of complexes Dimer-II and Trimer should be of CT character from the hydrogen-bonded water molecule (through HB-II) to the ethanol moiety. The different electronic transition types should be the reasons for the tiny redshift of the S₁-state electronic energy for Dimer-I and the large blueshifts for Dimer-II and the Trimer compared with that of the ethanol monomer.     

Time-Dependent Density Functional Theory Study on Excited-State Hydrogen Bonding Dynamics of Acetic Acid Hydrates

The time-dependent density functional theory (TDDFT) method was performed to investigate the hydrogen-bonding dynamics of acetic acid (AA) hydrates in aqueous solution. For AA, it tends to be both active hydrogen acceptor and donor and denote double H-bonds as O_A···H_W and H_A···O_W, resulting in ring structure hydrates. The ground-state geometry optimizations and electronic transition energies and corresponding oscillation strengths of the low-lying electronically excited states for the isolated AA monomer and the hydrogen-bonded ring structure hydrates are calculated by the density functional theory and TDDFT methods, respectively. Different types of intermolecular hydrogen bonds are formed between one AA molecule and water molecules. According to Zhao’s rule on the excited-state hydrogen bonding dynamics, it can be found that the intermolecular hydrogen bonds O_A···H_W and H_A···O_W are strengthened in electronically excited states of the hydrogen-bonded ring structure hydrates, with the excitation energy of a related excited state being lowered and electronic spectral redshifts being induced. Moreover, the hydrogen bond strengthening in the electronically excited state is crucial to the photophysics and photochemistry of hydrates with AA in aqueous solution.     

Energy of planar autoassociation of xanthine and spatial structure of poly(riboxanthylic acid)

First- and second-order perturbation theory in a polarization approximation was employed to calculate interaction energies of planar xanthine–xanthine pairs in stable configurations. Electrostatic energy was obtained in the atomic-dipole approximation. The results provided a basis for formulation of a four-stranded model of poly(xanthylic acid) that allows two hydrogen bonds per base. The model accounts satisfactorily for the unusual thermal stability and the observed pH transition of the polymer. The latter is due to the gradual dissociation of the N₃ protons accompanying by disrupture of the weak N₃? H ··· O₆ hydrogen bonds. However, the structure is only moderately weakened since the configuration of the coplanar bases remains stabilized by four N₁? H ··· O₂ hydrogen bonds.     

Electronic structure and hydrogen bond in the crystal of paracetamol drugs

We study the density of state (DOS), band structure (BS), and atomic orbit projected density of state (PDOS) of paracetamol crystal adopting the density functional theory (DFT) technique in the local density approximation (LDA). The band structure around the Fermi level and the contributions from p-type orbit of C, N, O, and s-type orbit of H to the total density of state (TDOS) are addressed, and we find that the electronic characteristic is the key to form the hydrogen bond between O and H atoms. We show that the structure of paracetamol crystal consists of the –OH···O=C and –NH···OH hydrogen-bonding cycle by studying a single paracetamol molecule as well as the PDOS graph of O and H atoms in the crystal.     

Molecular Adducts of Isoniazid: Crystal Structure,Electronic Properties,and Hirshfeld Surface Analysis

Three molecular adducts of the antituberculosis drug isoniazid (INH) are synthesized with γ-resorcylic acid (γRA), phloroglucinol (PG), and gallic acid (GA). The new solid phases are preliminarily characterized by the thermal analysis (DSC/TGA) and powder X-ray diffraction. The formation of new solid phases is confirmed by single crystal X-ray diffraction, infrared (FT-IR) and Raman spectroscopy. All three new solid crystalline forms are stabilized by various hydrogen bonding interactions such as N⁺···H–O^–, N···H–O, O···H–O, and π–π stacking. The FT-IR analysis puts forward that the solid form of INH1 is a salt whereas the INH2 and INH3 molecular complexes are cocrystals. We have also investigated the density of states (DOS), band structure, and atomic orbit projected density of state (PDOS) of title compounds by adopting the density functional theory (DFT) technique in the local density approximation (LDA). The electronic structure calculations show that energy states are delocalized in the k-space due the hydrogen and covalent bonds in the crystals. The frontier molecular orbital (FMO) analysis reveals that charge transfer takes place within the compounds. The Hirshfeld analysis shows that H–H and N?H–O hydrogen bonding interactions are dominant in all three molecular adducts of INH.     

Reinvestigation of intramolecular hydrogen bond in malonaldehyde derivatives: An ab initio,AIM and NBO study

The RAHB systems in malonaldehyde and its derivatives at MP2/ 6‐311++G(d,p) level of theory were studied and their intramolecular hydrogen bond energies by using the related rotamers method was obtained. The topological properties of electron density distribution in O? H···O intramolecular hydrogen bond have been analyzed in term of quantum theory of atoms in molecules (QTAIM). Correlations between the H‐bond strength and topological parameters are probed. The results of QTAIM clearly showed that the linear correlation between the electron density distribution at HB critical point and RAHB ring critical point with the corresponding hydrogen bond energies was obtained. Moreover, it was found a linear correlation between the electronic potential energy density, V(r_cp), and hydrogen bond energy which can be used as a simple equation for evaluation of HB energy in complex RAHB systems. Finally, the similar linear treatment between the geometrical parameters, such as O···O or O? H distance, and Lp(O)→σ*_OH charge transfer energy with the intramolecular hydrogen bond energy is observed. © 2010 Wiley Periodicals, Inc., Int J Quantum Chem, 2011     

Decoupling approximations for quantum vibrational predissociation dynamics: The tests on the low-level golden rule approaches for some rare gas—Cl2, ICl complexes

Vibrational and rotational decoupling approximations are tested in three-dimensional Fermi Golden Rule calculations on energies, lifetimes, and product state distributions of the vibrationally predissociating atom—diatom van der Waals complexes. The validity of approximate separations of diatom vibration, decoupling of stretching and bending intermolecular motions, and rotational infinite order sudden approximation for product scattering is characterized by comparison with the results of accurate calculations on the Ne ··· Cl₂, Ne ··· ICl, and He ··· ICl systems. The most accurate approximate schemes are recommended. © 1996 by John Wiley & Sons, Inc.     

Time-Dependent Density Functional Theory Study on Electronic Excited-State Hydrogen Bonding of Benzonitrile in Methanol Solution

In this work, the time dependent density functional theory (TDDFT) method was used to investigate the hydrogen bonding dynamics of benzonitrile (PhCN) as hydrogen acceptor in hydrogen donating solvent methanol (MeOH). The ground-state geometry optimizations and the electronic transition energies of the isolated PhCN and MeOH monomers and the two hydrogen-bonded PhCN–MeOH dimers are calculated by the DFT and TDDFT method respectively. According to the results, the hydrogen bond takes the responsibility of the geometric structure change and electronic transfer of the molecules involved. As well, the intermolecular hydrogen-bond C≡N···H–O is strengthened in electronically excited states of the hydrogen-bonded PhCN–MeOH^a (planar structure) and PhCN–MeOH^b (perpendicular structure) as a result of the lower excitation energy and the electronic spectral redshifts. Despite the different structure, the effects of hydrogen bond on PhCN–MeOH^a and PhCN–MeOH^b are considered the same, which serves as a proof that geometric structure has little contribution to the structural and energy change in hydrogen-bonded complexes. However, in high-lying singlet states, the structure can cause the divergence of electronic transition rate between the two hydrogen-bonded complexes, even if within the same transition path. What’s more, the extent of hydrogen bond effect on PhCN and MeOH is different between the low-lying excited states and the high-lying excited states.     

Inverse hydrogen migration in arginine-containing peptide ions upon electron transfer

Collisional electron transfer from gaseous Cs atoms was studied for singly and doubly protonated peptides Gly-Arg (GR) and Ala-Arg (AR) at 50- and 100-keV kinetic energies. Singly protonated GR and AR were discharged to radicals that in part rearranged by migration of a C_α hydrogen atom onto the guanidine group. The C_α-radical isomers formed were detected as stable anions following transfer of a second electron. In addition to the stabilizing rearrangements, the radicals underwent side-chain and backbone dissociations. The latter formed z fragments that were detected as the corresponding anions. Analysis of the (GR+H)^· radical potential energy surface using electronic structure theory in combination with Rice-Ramsperger-Kassel-Marcus calculations of rate constants indicated that the arginine C_α hydrogen atom was likely to be transferred to the arginine side-chain on the experimental timescale of ≤200 ns. Transfer of the Gly C_α-H was calculated to have a higher transition-state energy and was not kinetically competitive. Collisional electron transfer to doubly protonated GR and AR resulted in complete dissociation of (GR+2H)^+· and (AR+2H)^+· ions by loss of H, ammonia, and N-C_α bond cleavage. Electronic structure theory analysis of (GR+2H)^+· indicated the presence of multiple conformers and electronic states that differed in reactivity and steered the dissociations to distinct channels. Electron attachment to (GR+2H)²⁺ resulted in the formation of closely spaced electronic states of (GR+2H)^+· in which the electron density was delocalized over the guanidinium, ammonium, amide, and carboxyl groups. The different behavior of (GR+H)^· and (GR+2H)^+· is explained by the different timescales for dissociation and different internal energies acquired upon electron transfer.     

Watson-crick base pairs with thiocarbonyl groups: How sulfur changes the hydrogen bonds in DNA

We have theoretically analyzed mimics of Watson-Crick AT and GC base pairs in which N-H···O hydrogen bonds are replaced by N-H···S, using the generalized gradient approximation (GGA) of density functional theory at BP86/TZ2P level. The general effect of the above substitutions is an elongation and a slight weakening of the hydrogen bonds that hold together the base pairs. However, the precise effects depend on how many, and in particular, on which hydrogen bonds AT and GC are substituted.. Another purpose of this work is to clarify the relative importance of electrostatic attraction versus orbital interaction in the hydrogen bonds involved in the mimics, using a quantitative bond energy decomposition scheme. At variance with widespread believe, the orbital interaction component in these hydrogen bonds is found to contribute more than 40% of the attractive interactions and is thus of the same order of magnitude as the electrostatic component, which provides the remaining attraction.      

O–H···C hydrogen bond in the methane–water complex

Quantum chemical calculations were performed at different levels of theory (SCF, DFT, MP2, and CCSD(T)) to determine the geometry and electronic structure of the HOH···CH₄ complex formed by water and methane molecules, in which water is a proton donor and methane carbon (sp³) is an acceptor. The charge distribution on the atoms of the complex was analyzed by the CHelpG method and Hirshfeld population analysis; both methods revealed the transfer of electron charge from methane to water. According to the natural bond orbital (NBO) analysis data, the charge transfer upon complexation is caused by the interaction between the σ orbital of the axial С–H bond of methane directed along the line of the O–H···C hydrogen bridge and the antibonding σ* orbital of the О–H bond of the water molecule. Topological analysis of electron density in the HOH···CH₄ complex by the AIM method showed that the parameters of the critical point of the bond between hydrogen and acceptor (carbon atom) for the O–H···C interaction are typical for Н-bonded systems (the magnitude of electron density at the critical point of the bond, the sign and value of the Laplacian). It was concluded that the intermolecular interaction in the complex can be defined as an Н bond of O–H···σ(С–H) type, whose energy was found to be 0.9 kcal/mol in MP2/aug-cc-pVQZ calculations including the basis set superposition error (BSSE).     

Off‐center shallow donors in a spherical Si quantum dot with dielectric border

Within the effective mass approximation and using a finite element method, the ground state energy and electron cloud localization of the shallow donors in a Si quantum dot (QD) with dielectric border are calculated. Simultaneous effects of dielectric mismatch (DM) at the core–shell interface, the impurity radial position, and the external electric field on the electronic properties are investigated. We found that (i) for a freestanding QD, the binding energy is strongly enhanced due to the additional interactions of the electron with the polarization charges; (ii) the electron cloud distribution can be easily modulated by varying the impurity position; (iii) the electric field‐induced shift in energy levels increases with the DM. Therefore, the electronic energy levels of the nanocrystal could be tuned by properly tailoring the heterostructure parameters (DM with the surrounding matrix, impurity location) as well as by varying the electric field strength. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

A comparative study of the dimers of selected hydroxybenzenes

Hydroxybenzenes are the parent compounds of large classes of derivatives, many of which exhibit biological activities. This work presents the results of a comparative study of the dimers of selected hydroxybenzenes, considering all the possible mutual geometrical arrangements of the two monomers and comparing their relative stabilities and interaction energies. The OH···OH hydrogen bond between the two monomers is the dominant stabilizing factor, with frequent preference for mutual perpendicularity of the two aromatic rings. C? H···O unconventional H‐bonds, OH···π unconventional H‐bonds, H···π interactions and π··π interactions also may play significant roles. The factors stabilizing individual hydroxybenzenes (presence of intramolecular hydrogen bonds; number, positioning and orientation of the OH groups; symmetry features) have greater influence on the dimers' relative energy than on the interaction energy between monomers. While results from different calculations methods (HF, MP2, and DFT/B3LYP) show consistency for all the features just‐mentioned, they show some relevant differences in the way they take into account different types of interactions between monomers, resulting in some differences in the geometry arrangements of the monomers in the lowest energy dimers and in differences in the relative preferences among higher‐energy dimer geometries. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

TATB与二氟甲烷以及与聚偏二氟乙烯的分子间相互作用

动用密度泛函理论(SFT)B3LYP方法,取3－21G*基组,求得TATB(1,3,5-三氨基-2,4,6-三硝基苯)与CH~2F~2混合体系的三种优化构型以Boys-Bernardi方案校正基组叠加误差求得结合能。在B3LYP/6----311G*//B3LYP/3---21G*水TATB与CH~2F~2间的最大结合能为4.62kJ·mol^-1,还用MO－PM3方法计算TATB与---（CF~2CH~2}－(N=1,2,3,4,5,)的混合体系,由色散校正电子相关近似地求得其结合能力。当n＝5时,求得TATB与－（CF~2CH~2）--~n的最大结合能约为52.97kJ·MOL^-1。此外,自然键轨道分析用于讨论TATB与CH~2F~2之间的电荷转移。     

Rapid evaluation of the binding energies between peptide amide and DNA base

The binding energies and the equilibrium hydrogen bond distances as well as the potential energy curves of 20 hydrogen‐bonded amide–base dimers are evaluated from the analytic potential energy function established in our laboratory recently. The analytic potential energy function is used to calculate the N? H···N, N? H···O?C, C? H···N, and C? H···O?C dipole–dipole attractive interaction energies and C?O···O?C, N? H···H? N, and N? H···H? C dipole–dipole repulsive interaction energies in the 20 dimers composed of DNA bases adenine, guanine, cytosine, or thymine and peptide amide. The calculation results show that the potential energy curves obtained from the analytic potential energy function are in good agreement with those obtained from MP2/6‐311+G** calculations by including the basis set superposition error (BSSE) correction. For all the 20 dimers, the analytic potential energy function yields the binding energies of the MP2/6‐311+G** with BSSE correction within the error limits of 0.50 kcal/mol for 19 dimers, only one difference is larger than 0.50 kcal/mol and the difference is only 0.61 kcal/mol. The analytic potential energy function produces the equilibrium hydrogen bond distances of the MP2/6‐311+G** with BSSE correction within the error limits of 0.030 Å for all the 20 dimers. The analytic potential energy function is further applied to four more complicated DNA base‐peptide amide systems involving amino acid side chain and β‐sheet. The values of the binding energies and equilibrium hydrogen bond distances obtained from the analytic potential energy function are also in good agreement with those obtained from MP2 calculations with the BSSE correction. These results demonstrate that the analytic potential energy function can be used to evaluate the binding energies in hydrogen‐bonded peptide amide–DNA base dimers quickly and accurately. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011