QM/MM study of the structure, energy storage, and origin of the bathochromic shift in vertebrate and invertebrate bathorhodopsins

By comparing the results from a hybrid quantum mechanics/molecular mechanics method (SORCI+Q//B3LYP/6-31G*:Amber) between vertebrate (bovine) and invertebrate (squid) visual pigments, the mechanism of molecular rearrangements, energy storage, and origin of the bathochromic shift accompanying the transformation of rhodopsin to bathorhodopsin have been evaluated. The analysis reveals that, in the presence of an unrelaxed binding site, bathorhodopsin was found to carry almost 27 kcal/mol energy in both visual pigments and absorb (λ(max)) at 528 nm in bovine and 554 nm in squid. However, when the residues within 4.0 ? radius of the retinal are relaxed during the isomerization event, almost ～16 kcal/mol energy is lost in squid compared to only ～8 kcal/mol in bovine. Loss of a larger amount of energy in squid is attributed to the presence of a flexible binding site compared to a rigid binding site in bovine. Structure of the squid bathorhodopsin is characterized by formation of a direct H-bond between the Schiff base and Asn87.     

Experimental and theoretical investigation of the 13C and 15N chemical shift tensors in melanostatin-exploring the chemical shift tensor as a structural probe

The determination of backbone conformations in powdered peptides using 13C and 15N shift tensor information is explored. The 13C and 15N principal shift values in natural abundance 13C and 15N melanostatin (L-Pro-L-Leu-Gly amide) are measured using the FIREMAT technique. Furthermore, the orientation of the C-N bond in the 13C shift principal axis system for the backbone carbons is obtained from the presence of the 13C-14N dipolar coupling. The Ramachandran angles for the title compound are obtained from solid-state NMR data by comparing the experimentally determined shift tensor information to systematic theoretical shielding calculations on N-formyl-L-amino acid-amide models. The effects of geometry optimization and neglect of intermolecular interactions on the theoretical shielding values in the model compounds are investigated. The sets of NMR derived Ramachandran angles are assembled in a set of test structures that are compared to the available single-crystal X-ray structure. Shift tensor calculations on the test structures and the X-ray structure are used to further assess the importance of intermolecular interactions when the shift tensor is used as a structural probe in powdered peptides.     

A high-field solid-state 35/37Cl NMR and quantum chemical investigation of the chlorine quadrupolar and chemical shift tensors in amino acid hydrochlorides

A series of six L-amino acid hydrochloride salts has been studied by 35/37Cl solid-state NMR spectroscopy (at 11.75 and 21.1 T) and complementary quantum chemical calculations. Analyses of NMR spectra acquired under static and magic-angle-spinning conditions for the six hydrochloride salts, those of aspartic acid, alanine, cysteine, histidine, methionine and threonine, allowed the extraction of information regarding the chlorine electric field gradient (EFG) and chemical shift tensors, including their relative orientation. Both tensors are found to be highly dependent on the local environment, with chlorine-35 quadrupolar coupling constants (CQ) ranging from -7.1 to 4.41 MHz and chemical shift tensor spans ranging from 60 to 100 ppm; the value of CQ for aspartic acid hydrochloride is the largest in magnitude observed to date for an organic hydrochloride salt. Quantum chemical calculations performed on cluster models of the chloride ion environment demonstrated agreement between experiment and theory, reproducing CQ to within 18%. In addition, the accuracy of the calculated values of the NMR parameters as a function of the quality of the input structure was explored. Selected X-ray structures were determined (L-Asp HCl; L-Thr HCl) or re-determined (L-Cys HCl.H2O) to demonstrate the benefits of having accurate crystal structures for calculations. The self-consistent charge field perturbation model was also employed and was found to improve the accuracy of calculated quadrupolar coupling constants, demonstrating the impact of the neighbouring ions on the EFG tensor of the central chloride ion. Taken together, the present work contributes to an improved understanding of the factors influencing 35/37Cl NMR interaction tensors in organic hydrochlorides.     

Mechanism of CO oxidation by oxygen in the presence of palladium(ii) bromide complexes: a quantum chemical modeling

Russian Chemical Bulletin - Mechanisms of CO oxidation by oxygen in the PdBr2-LiBr-MeCN-H2O system in the absence and in the presence of iron(ii) phthalocyaninate (PcFe) as co-catalyst were studied...     

Stabilization, injection and control of quantum cascade lasers, and their application to chemical sensing in the infrared

Quantum cascade lasers (QCLs) are a relatively new type of semiconductor laser operating in the mid- to long-wave infrared. These monopolar multilayered quantum well structures can be fabricated to operate anywhere between 3.5 and 20 microm, which includes the molecular fingerprint region of the infrared. This makes them an ideal choice for infrared chemical sensing, a topic of great interest at present. Frequency stabilization and injection locking increase the utility of QCLs. We present results of locking QCLs to optical cavities, achieving relative linewidths down to 5.6 Hz. We report injection locking of one distributed feedback grating QCL with light from a similar QCL, demonstrating capture ranges of up to +/-500 MHz, and suppression of amplitude modulation by up to 49 dB. We also present various cavity-enhanced chemical sensors employing the frequency stabilization techniques developed, including the resonant sideband technique known as NICE-OHMS. Sensitivities of 9.7 x 10(-11) cm(-1) Hz(-1/2) have been achieved in pure nitrous oxide.     

Fluorescence properties of organic dyes: quantum chemical studies on the green/blue neutral and protonated DMA-DPH emitters in polymer matrices

The absorption and fluorescence spectra of the green emitter DMA-DPH {1-[4-(dimethylamino)phenyl]-6-phenylhexa-1,3,5-triene} and its protonated blue-emitter form have been studied theoretically through time-dependent density functional theory (TD-DFT) and resolution-of-identity 2nd order perturbative coupled cluster (RI-CC2) calculations with basis sets up to augmented triple-ζ quality, in the gas phase and in solvents of different polarity. These systems dispersed in a polymer matrix are of interest for applications in organic light emitting diode devices (OLEDs). Calculations show that the observed absorption and emission spectra correspond to transitions between the S(0) and S(1) states, in both systems. The nature and characteristics of these transitions are discussed. Excellent agreement with experimental data is obtained, both for absorption and emission, provided that the state-specific polarized continuum model (SS-PCM) method is employed for the inclusion of the solvent.     

A multidimensional approach to the analysis of chemical shift titration experiments in the frame of a multiple reaction scheme

We present a method for fitting curves acquired by chemical shift titration experiments, in the frame of a three‐step complexation mechanism. To that end, we have implemented a fitting procedure, based on a nonlinear least squares fitting method, that determines the best fitting curve using a “coarse grid search” approach and provides distributions for the different parameters of the complexation model that are compatible with the experimental precision. The resulting analysis protocol is first described and validated on a theoretical data set. We show its ability to converge to the true parameter values of the simulated reaction scheme and to evaluate complexation constants together with multidimensional uncertainties. Then, we apply this protocol to the study of the supramolecular interactions, in aqueous solution, between a lanthanide complex and three different model molecules, using NMR titration experiments. We show that within the uncertainty that can be evaluated from the parameter distributions generated during our analysis, the affinities between the lanthanide derivative and each model molecule can be discriminated, and we propose values for the corresponding thermodynamic constants. Copyright © 2013 John Wiley & Sons, Ltd.     

Nucleophilic addition of methanol and methanethiol to acetylene in the superbasic system KOH-DMSO: a quantum chemical model

Cluster-continuum models (KOH·nDMSO, n = 1, 5) were used to model the superbasic system “alkali metal hydroxide-dimethyl sulfoxide” within the framework of MP2/6-311++G**/ and B3LYP/6-31G* methods. The KOH molecule surrounded by five DMSO molecules exists as “solvate-loosened” ion pair with elongated K-O distance. It is proposed to consider the “solvate-loosened” ion pair of potassium cation with hydroxide anion in the surroundings of five solvent molecules as the catalytic coordination sphere of the superbasic system KOH-DMSO. Methanol and methanethiol molecules can be incorporated with ease into the first coordination sphere of potassium cation to form methoxide and methanethiolate ions. The possibility of nucleophilic attack of methoxide and methanethiolate ions on acetylene molecule in the first coordination sphere of potassium cation was studied. The model reaction system C₂H₂-CH₃OK-H₂O with one DMSO molecule included explicitly to maintain the “solvate-loosened” [CH₃O]^?...K⁺ ion pair and additional inclusion of solvent effects within the framework of the IEFPCM continuum model is the most preferable for serial calculations.     

Polymer electrolytes based on poly(ester diacrylate), ethylene carbonate, and LiClO4: a relationship of the conductivity and structure of the polymer according to IR spectroscopy and quantum chemical modeling data

New polymer electrolytes based on poly(ester diacrylate) (PEDA), LiClO₄, and additives of ethylene carbonate (EC) have a Li⁺ ion conductivity comparable with that of liquid electrolytes. The conductivity first decreases by an order of magnitude at an EC content of ??5 wt.% and then increases by three orders of magnitude at 55 wt.% EC. To understand the nature of this extreme dependence, a comprehensive study using IR spectroscopy and quantum chemical modeling was performed. It was found that the changes in the IR spectra with an increase in the EC content were stepwise to form at final stage the same absorption peaks that were observed for the IR spectra of LiClO₄ solutions in EC. The density functional theory studies of the energy and structures of mixed Li⁺ complexes and LiClO₄ with EC and PEDA, which was modeled by oligomers H-((CH₂)₂COO(CH₂)₂O) _n -CH₃ (n ?? 10) showed a stronger binding of the lithium ion with the polymer matrix in the mixed complexes with one EC molecule at a low content of EC resulting, most likely, in a decrease in the conductivity. Less stable mixed complexes with three EC molecules can be formed with an increase in the EC fraction and they become unstable in EC excess because of the transition of the Li⁺ ions to solvate complexes containing only EC molecules.     

Contribution of the nido-[7,8-C2B9H10]- anion to the chemical stability, basicity, and 31P NMR chemical shift in nido-o-carboranylmonophosphines

The icosahedral dicarboranes and their decapitated anion, 1-R'-1,2-C(2)B(10)H(10) (closo) and [7-R'-7,8-C(2)B(9)H(10)](-) (nido), exert a distict influence at the alpha position of substituents attached to the cage carbon atom. The closo fragment is electron-withdrawing while the nido anion is electron-releasing. These effects are studied by (31)P NMR, phosphorus oxidation, and phosphorus protonation in [7-PR(2)-8-R'-7,8-C(2)B(9)H(10)](-) species. The (31)P NMR chemical shift dependence is related to the R alkyl or aryl nature of [7-PR(2)-8-R'-7,8-C(2)B(9)H(10)](-). No direct relationship to the nature of the R substituent on the nido-carboranylmonphosphine toward oxidation has been found. The basicity of the nido-alkylcarboranylmonophosphines is the highest while the lowest corresponds to the nido-arylcarboranylmonophosphines. Interpretation can be carried out qualitatively by considering the electronic properties of the cluster and the nature of the R groups. The influence of R' is less relevant. Confirmation of the molecular structure of the oxidated and protonated nido-carboranylmonophosphine compounds was obtained by X-ray diffraction analysis of [NBu(4)][7-P(O)Ph(2)-8-Ph-7,8-C(2)B(9)H(10)] and [7-PH((i)Pr)(2)-8-Me-7,8-C(2)B(9)H(10)].     

Differential transition-state stabilization in enzyme catalysis: quantum chemical analysis of interactions in the chorismate mutase reaction and prediction of the optimal catalytic field

Chorismate mutase is a key model system in the development of theories of enzyme catalysis. To analyze the physical nature of catalytic interactions within the enzyme active site and to estimate the stabilization of the transition state (TS) relative to the substrate (differential transition state stabilization, DTSS), we have carried out nonempirical variation-perturbation analysis of the electrostatic, exchange, delocalization, and correlation interactions of the enzyme-bound substrate and transition-state structures derived from ab initio QM/MM modeling of Bacillus subtilis chorismate mutase. Significant TS stabilization by approximately -23 kcal/mol [MP2/6-31G(d)] relative to the bound substrate is in agreement with that of previous QM/MM modeling and contrasts with suggestions that catalysis by this enzyme arises purely from conformational selection effects. The most important contributions to DTSS come from the residues, Arg90, Arg7, Glu78, a crystallographic water molecule, Arg116, and Arg63, and are dominated by electrostatic effects. Analysis of the differential electrostatic potential of the TS and substrate allows calculation of the catalytic field, predicting the optimal location of charged groups to achieve maximal DTSS. Comparison with the active site of the enzyme from those of several species shows that the positions of charged active site residues correspond closely to the optimal catalytic field, showing that the enzyme has evolved specifically to stabilize the TS relative to the substrate.     

A quantum chemical study of the generation of a potential prebiotic compound, cyanoacetaldehyde, and related sulfur containing species

Cyanoacetaldehyde (NCCH 2CHO), which may have played a role in the prebiotic formation of the pyrimidine bases cytosine and uracil, is formed in water solutions by addition of water to cyanoacetylene (HCC-CN), a compound that exists in interstellar space, in comets, and planetary atmospheres. A gas-phase model of the uncatalyzed addition of water to cyanoacetylene is explored by ab initio calculations at the MP2/6-311++G** level of theory. A reaction path consisting of several steps was found in these calculations, but the activation energy of the first step is relatively high, which makes it unlikely that cyanoacetaldehyde is formed in an uncatalyzed reaction. Similar calculations were also performed for the uncatalyzed reaction of water to protonated cyanoacetylene (HCCCNH (+)), a component of the interstellar medium, forming protonated cyanoacetaldehyde (HNCCH 2CHO (+)), but a high activation energy was found for this reaction as well. Moreover, the corresponding addition reactions of hydrogen sulfide (H 2S) to HCCCN, as well as to HCCCNH (+), have been explored with similar results.     

Orientation of a key glutamine residue in the BLUF domain from AppA revealed by mutagenesis, spectroscopy, and quantum chemical calculations

The flavin-adenine-dinucleotide-binding BLUF domain constitutes a new class of blue-light receptors, and the N-terminal domain of AppA is a representative of this family. A crystal structure of the BLUF domain from AppA suggested that a conserved Gln63 forms a hydrogen bond with the flavin N5 atom. Upon light excitation, this residue is proposed to undergo a approximately 180 degrees rotation that leads to a rearrangement of a hydrogen bonding network. However, crystallographic studies on the other BLUF proteins claimed an opposite orientation for the glutamine residue. In this communication, we have revealed the presence of a Gln63-to-N5 hydrogen bond in the dark state of AppA by a combined approach of mutagenesis, spectroscopy, and quantum chemical calculations. The present finding supports the view that the reorientation of the Gln63 side chain is a key event in the signaling state formation of BLUF proteins.     

Importance of structural tightening, as opposed to partially bound States, in the determination of chemical shift changes at noncovalently bonded interfaces

Two models (A and B) have been proposed to account for decreased downfield chemical shifts of a proton bound by noncovalent interactions at a ligand/antibiotic interface as the number of ligand/antibiotic interactions is decreased. In model A, the proton involved in the noncovalent bond suffers a smaller downfield shift because the bond is, with a relatively large probability, broken, and not because it is longer. In model B, the proton involved in the noncovalent bond suffers a smaller downfield shift because the bond is longer, and not because it is, with a relatively large probability, broken. We show that model A cannot account for the chemical shift changes. Model B accounts for the process of positively cooperative binding, in which noncovalent bonds are reduced in length and thereby increase the stability of the organized state.     

Probing the structural properties,binding mode and intermolecular interactions of herbacetin against H1N1 neuraminidase using vibrational spectroscopic,quantum chemical calculation and molecular docking studies

Research on Chemical Intermediates - Herbacetin (HBN) is an antiviral agent of H1N1 influenza virus which was reported to inhibit H1N1 neuraminidase (NA) enzyme with IC50 value of...     

Possibility of quantum chemical evaluation of the probability of various chemical transformations in syntheses of phosphorus-, titanium-, silicon-, and vanadium-containing structures on the silica surface

Application of minimum quantum-chemical models for predicting chemical transformations in syntheses of phosphorus-, titanium-, silicon-, and vanadium-containing structures on the silica gel surface by molecular layering is considered. Possible pathways for transformation of the groups synthesized under the action of water vapor and hydrogen chloride are analyzed in terms of the models constructed.     

A study of the electronic structure of octavinylsilsesquioxane and dendron with chromium based compounds by X-ray photoelectron spectroscopy and quantum chemical modeling in the DFT approximation

The electronic structure and some features of octavinylsilsesquioxane interaction with sulfene chloride chromium acetylacetonate complex were studied by means of XPS and DFT. According to XPS, spectrum lines have close positions for all the studied compounds, half-width for dendrons not exceeding 2 eV. For octavinylsilsesquioxane, the broader lines appear due to the action of substrate atoms. Chemical composition of a dendron was determined by analyzing the concentrations of atoms in different chemical states and a residual content of chlorine atoms. Chemical bonding between the complex and octavinylsilsesquioxane is provided by the covalent interaction of carbon and sulfur atoms.     

Toward calculations of the 129Xe chemical shift in Xe@C60 at experimental conditions: relativity, correlation, and dynamics

We calculate the 129Xe chemical shift in endohedral Xe@C60 with systematic inclusion of the contributing physical effects to model the real experimental conditions. These are relativistic effects, electron correlation, the temperature-dependent dynamics, and solvent effects. The ultimate task is to obtain the right result for the right reason and to develop a physically justified methodological model for calculations and simulations of endohedral Xe fullerenes and other confined Xe systems. We use the smaller Xe...C6H6 model to calibrate density functional theory approaches against accurate correlated wave function methods. Relativistic effects as well as the coupling of relativity and electron correlation are evaluated using the leading-order Breit-Pauli perturbation theory. The dynamic effects are treated in two ways. In the first approximation, quantum dynamics of the Xe atom in a rigid cage takes advantage of the centrosymmetric potential for Xe within the thermally accessible distance range from the center of the cage. This reduces the problem of obtaining the solution of a diatomic rovibrational problem. In the second approach, first-principles classical molecular dynamics on the density functional potential energy hypersurface is used to produce the dynamical trajectory for the whole system, including the dynamic cage. Snapshots from the trajectory are used for calculations of the dynamic contribution to the absorption 129Xe chemical shift. The calculated nonrelativistic Xe shift is found to be highly sensitive to the optimized molecular structure and to the choice of the exchange-correlation functional. Relativistic and dynamic effects are significant and represent each about 10% of the nonrelativistic static shift at the minimum structure. While the role of the Xe dynamics inside of the rigid cage is negligible, the cage dynamics turns out to be responsible for most of the dynamical correction to the 129Xe shift. Solvent effects evaluated with a polarized continuum model are found to be very small.