Estimation on the intramolecular 10-membered ring NH···OC hydrogen-bonding energies in glycine and alanine peptides

Serum proteins on nanoparticles: early stages of the "protein corona"

Nanoparticles in biological systems such as the bloodstream are exposed to a complex solution of biomolecules. A "corona" monolayer of proteins has historically been thought to form on nanoparticles upon introduction into such environments. To examine the first steps of protein binding, Fluorescence Correlation/Cross Correlation Spectroscopy and Fluorescence Resonance Energy Transfer were used to directly analyze four different nanoparticle systems. CdSe/ZnS core/shell quantum dots, 100 nm diameter polystyrene fluospheres, 200 nm diameter polystyrene fluospheres, and 200 nm diameter PEG-grafted DOTAP liposomes were studied with respect to serum protein binding, using bovine serum albumin as a model. Surface heterogeneity is found to be a key factor in protein binding to these nanoparticles, and as such we present a novel conceptualization of the early hard corona as low-ratio, non-uniform binding rather than a uniform monolayer.

A Critical Check for the Role of Resonance in Intramolecular Hydrogen Bonding

Although resonance-assisted H-bonds (RAHBs) are well recognized, the role of π resonance in RAHBs is controversial, as the seemingly enhanced H-bonds in unsaturated compounds may result from the constraints imposed by the σ skeleton. Herein the block-localized wave function (BLW) method, which can derive optimal yet resonance-quenched structures with related physiochemical properties, was employed to examine the correlation between π resonance and the strength of intramolecular RAHBs. Examination of a series of paradigmatic molecules with RAHBs and their saturated analogues showed that it is inappropriate to compare a conjugated system with its saturated counterpart, as they may have quite different σ frameworks. Nevertheless, comparison between a conjugated system and its resonance-quenched (i.e., electron-localized) state, which have identical σ skeletons, shows that in all studied cases, π resonance unanimously reduces the bonding distance by 0.111-0.477 Å, strengthens the bonding by 40-56 %, and redshifts the D-H vibrational frequency by 104-628 cm^-1 . Furthermore, there is an excellent correlation between hydrogen-bonding strength and the classical Coulomb attraction between the hydrogen-bond donor and the acceptor, which suggests that the dominant role of the electrostatic interaction in H-bonds and RAHBs originates from the charge flow from H-bond donors to acceptors through π conjugation.

The Origin of the Non-Additivity in Resonance-Assisted Hydrogen Bond Systems

The concept of resonance-assisted hydrogen bond (RAHB) has been widely accepted, and its impact on structures and energetics can be best studied computationally using the block-localized wave function (BLW) method, which is a variant of ab initio valence bond (VB) theory and able to derive strictly electron-localized structures self-consistently. In this work, we use the BLW method to examine a few molecules that result from the merging of two malonaldehyde molecules. As each of these molecules contains two hydrogen bonds, these intramolecular hydrogen bonds may be cooperative or anticooperative, depended on their relative orientations, and compared with the hydrogen bond in malonaldehyde. Apart from quantitatively confirming the concept of RAHB, the comparison of the computations with and without π resonance shows that both σ-framework and π-resonance contribute to the nonadditivity in these RAHB systems with multiple hydrogen bonds.

Effects of Structure and Environment on the Spectroscopic Properties of (3-Amino-Substituted-Thieno[2,3-b] Pyridine-2-yl)Pyridine/Quinolin-2-yl)(Phenyl)Methanones: Experimental and Theoretical Study

The electronic absorption, excitation and fluorescence properties of two 3-amino-substituted-thieno[2,3-b]pyridine/quinolin-2-yl)(phenyl)methanones; (referred to as compounds 1-2: where 3-amino-4,5,6-trimethyl-thieno[2,3-b]pyridin-2-yl)(phenyl)methanone (1); and 3-amino-5,6,7,8-tetrahydro-thieno[2,3-b]quinolin-2-yl)(phenyl)methanone (2)) have been investigated in solvents of various polarity and hydrogen-bonding abilities. Results based on the electronic absorption, excitation and emission study of these compounds; indicated that singlets (S1 and S2) excited-states are populated in non-polar and polar protic/aprotic solvents giving dual fluorescence with weak charge transfer separation. The experimental results were interpreted with the aid of quantum chemistry calculations carried out with the DFT and TD-DFT/B3lyp/6-31 + G(d,p) methods. Based on these calculations, compounds 1-2 exist in two rotamers: anti and syn, separated by ca. 5-6 kcal mol(-1) energy barriers in favor of the anti-conformer. The anti-structure, was shown to be stabilized through existence of intramolecular NH…O hydrogen bond (H-b), which plays a dominant role in affecting the energy of the HOMO-1 molecular orbital. Further, methyl/alkyl substitution in the pyridyl-thiophene ring was shown to involve in σ-π hyper-conjugation and destabilization of the HOMO-1 MO's.

Rapid evaluation of the interaction energies for carbohydrate-containing hydrogen-bonded complexes via the polarizable dipole–dipole interaction model combined with NBO or AM1 charge

The polarizable dipole–dipole interaction model has been developed to rapidly and accurately estimate the hydrogen bond distances and interaction energies for carbohydrate-containing hydrogen-bonded complexes.

Homology model and targeted mutagenesis identify critical residues for arachidonic acid inhibition of Kv4 channels

Polyunsaturated fatty acids such as arachidonic acid (AA) exhibit inhibitory modulation of Kv4 potassium channels. Molecular docking approaches using a Kv4.2 homology model predicted a membrane-embedded binding pocket for AA comprised of the S4-S5 linker on one subunit and several hydrophobic residues within S3, S5 and S6 from an adjacent subunit. The pocket is conserved among Kv4 channels. We tested the hypothesis that modulatory effects of AA on Kv4.2/KChIP channels require access to this site. Targeted mutation of a polar residue (K318) and a nonpolar residue (G314) within the S4-S5 linker as well as a nonpolar residue in S3 (V261) significantly impaired the effects of AA on K (+) currents in Xenopus oocytes. These residues may be important in stabilizing (K318) or regulating access to (V261, G314) the negatively charged carboxylate moiety on the fatty acid. Structural specificity was supported by the lack of disruption of AA effects observed with mutations at residues located near, but not within the predicted binding pocket. Furthermore, we found that the crystal structure of the related Kv1.2/2.1 chimera lacks the structural features present in the proposed AA docking site of Kv4.2 and the Kv1.2/2.1 K (+) currents were unaffected by AA. We simulated the mutagenic substitutions in our Kv4.2 model to demonstrate how specific mutations may disrupt the putative AA binding pocket. We conclude that AA inhibits Kv4 channel currents and facilitates current decay by binding within a hydrophobic pocket in the channel in which K318 within the S4-S5 linker is a critical residue for AA interaction.

Electrostatic fields near the active site of human aldose reductase: 2. New inhibitors and complications caused by hydrogen bonds

Vibrational Stark effect spectroscopy was used to measure electrostatic fields in the hydrophobic region of the active site of human aldose reductase (hALR2). A new nitrile-containing inhibitor was designed and synthesized, and the X-ray structure of its complex, along with cofactor NADP(+), with wild-type hALR2 was determined at 1.3 Å resolution. The nitrile is found to be in the proximity of T113, consistent with a hydrogen bond interaction. Two vibrational absorption peaks were observed at room temperature in the nitrile region when the inhibitor binds to wild-type hALR2, indicating that the nitrile probe experiences two different microenvironments, and these could be empirically separated into a hydrogen-bonded and non-hydrogen-bonded population by comparison with the T113A mutant, in which a hydrogen bond to the nitrile is not present. Classical molecular dynamics simulations based on the structure predict a double-peak distribution in protein electric fields projected along the nitrile probe. The interpretation of these two peaks as a hydrogen bond formation-dissociation process between the probe nitrile group and a nearby amino acid side chain is used to explain the observation of two IR bands, and the simulations were used to investigate the molecular details of this conformational change. Hydrogen bonding complicates the simplest analysis of vibrational frequency shifts as being due solely to electrostatic interactions through the vibrational Stark effect, and the consequences of this complication are discussed.

Rapid evaluation of the binding energies in hydrogen-bonded amide-thymine and amide-uracil dimers in gas phase

The binding energies and the equilibrium hydrogen bond distances as well as the potential energy curves of 48 hydrogen-bonded amide-thymine and amide-uracil dimers are evaluated from the analytic potential energy function established in our lab recently. 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 BSSE correction. For all the 48 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 46 dimers, only two differences are larger than 0.50 kcal/mol and the largest one is only 0.60 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 0.050 Å for all the 48 dimers. The analytic potential energy function is further applied to four more complicated hydrogen-bonded amide-base 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 amide-base dimers quickly and accurately.

Estimating the hydrogen bond energy

First, different approaches to detect hydrogen bonds and to evaluate their energies are introduced newly or are extended. Supermolecular interaction energies of 256 dimers, each containing one single hydrogen bond, were correlated to various descriptors by a fit function depending both on the donor and acceptor atoms of the hydrogen bond. On the one hand, descriptors were orbital-based parameters as the two-center or three-center shared electron number, products of ionization potentials and shared electron numbers, and the natural bond orbital interaction energy. On the other hand, integral descriptors examined were the acceptor-proton distance, the hydrogen bond angle, and the IR frequency shift of the donor-proton stretching vibration. Whereas an interaction energy dependence on 1/r(3.8) was established, no correlation was found for the angle. Second, the fit functions are applied to hydrogen bonds in polypeptides, amino acid dimers, and water cluster, thus their reliability is demonstrated. Employing the fit functions to assign intramolecular hydrogen bond energies in polypeptides, several side chain CH...O and CH...N hydrogen bonds were detected on the fly. Also, the fit functions describe rather well intermolecular hydrogen bonds in amino acid dimers and the cooperativity of hydrogen bond energies in water clusters.

An analytic potential energy function for the amide-amide and amide-water intermolecular hydrogen bonds in peptides

An analytic potential energy function is proposed and applied to evaluate the amide-amide and amide-water hydrogen-bonding interaction energies in peptides. The parameters in the analytic function are derived from fitting to the potential energy curves of 10 hydrogen-bonded training dimers. The analytic potential energy function is then employed to calculate the N-H...O=C, C-H...O=C, N-H...OH2, and C=O...HOH hydrogen-bonding interaction energies in amide-amide and amide-water dimers containing N-methylacetamide, acetamide, glycine dipeptide, alanine dipeptide, N-methylformamide, N-methylpropanamide, N-ethylacetamide and/or water molecules. The potential energy curves of these systems are therefore obtained, including the equilibrium hydrogen bond distances R(O...H) and the hydrogen-bonding energies. The function is also applied to calculate the binding energies in models of beta-sheets. The calculation results show that the potential energy curves obtained from the analytic function are in good agreement with those obtained from MP2/6-31+G** calculations by including the BSSE correction, which demonstrate that the analytic function proposed in this work can be used to predict the hydrogen-bonding interaction energies in peptides quickly and accurately.

Estimation of N-H...O=C intramolecular hydrogen bond energy in polypeptides

The previously proposed molecular tailoring approached (MTA) [Deshmukh, M. M.; Gadre, S. R.; Bartolotti, L. J. J. Phys. Chem. A 2006, 110, 12519] for the estimation of intramolecular O-H...O hydrogen bond energy is extended to that for the N-H...O=C bond within polypeptides. The methodology is initially tested on a tetrapeptide containing two types of N-H...O=C hydrogen bonds and is found to distinguish between them. The estimated values are in good agreement with the trends predicted by the geometrical parameters. Furthermore, this methodology is applied to partially as well as fully substituted, capped polyglycines that contain five glycine residues (acetyl-(gly)(5)-NH(2)) to check the effect of substituents on the energetics of hydrogen bonds. The estimated N-H...O=C bond energy values lie in the range of 4-6 kcal/mol. These estimated values are not only in concurrence with the geometric parameters but also able to reflect the subtle effects of substituents for the substituted polypeptides studied in the present work.