A polarizable force field for computing the infrared spectra of the polypeptide backbone

The shapes of the amide bands in the infrared (IR) spectra of proteins and peptides are caused by electrostatically coupled vibrations within the polypeptide backbone and code the structures of these biopolymers. A structural decoding of the amide bands has to resort to simplified models because the huge size of these macromolecules prevents the application of accurate quantum mechanical methods such as density functional theory (DFT). Previous models employed transition-dipole coupling methods that are of limited accuracy. Here we propose a concept for the computation of protein IR spectra, which describes the molecular mechanics (MM) of polypeptide backbones by a polarizable force field of "type II". By extending the concepts of conventional polarizable MM force fields, such a PMM/II approach employs field-dependent parameters not only for the electrostatic signatures of the molecular components but also for the local potentials modeling the stiffness of chemical bonds with respect to elongations, angle deformations, and torsions. Using a PMM/II force field, the IR spectra of the polypeptide backbone can be efficiently calculated from the time dependence of the backbone's dipole moment during a short (e.g., 100 ps) MD simulation by Fourier transformation. PMM/II parameters are derived for harmonic bonding potentials of amide groups in polypeptides from a series of DFT calculations on the model molecule N-methylacetamide (NMA) exposed to homogeneous external electric fields. The amide force constants are shown to vary by as much as 20% for relevant field strengths. As a proof of principle, it is shown that the large solvatochromic effects observed in the IR spectra of NMA upon transfer from the gas phase into aqueous solution are not only excellently reproduced by DFT/MM simulations but are also nicely modeled by the PMM/II approach. The tasks remaining for a proof of practice are specified.     

Identification of 2D-gel proteins: a comparison of MALDI/TOF peptide mass mapping to mu LC-ESI tandem mass spectrometry

A comparative analysis of protein identification for a total of 162 protein spots separated by two-dimensional gel electrophoresis from two fully sequenced archaea, Methanococcus jannaschii and Pyrococcus furiosus, using MALDI-TOF peptide mass mapping (PMM) and mu LC-MS/MS is presented. 100% of the gel spots analyzed were successfully matched to the predicted proteins in the two corresponding open reading frame databases by mu LC-MS/MS while 97% of them were identified by MALDI-TOF PMM. The high success rate from the PMM resulted from sample desalting/concentrating with ZipTip(C18) and optimization of several PMM search parameters including a 25 ppm average mass tolerance and the application of two different protein molecular weight search windows. By using this strategy, low-molecular weight (<23 kDa) proteins could be identified unambiguously with less than 5 peptide matches. Nine percent of spots were identified as containing multiple proteins. By using mu LC-MS/MS, 50% of the spots analyzed were identified as containing multiple proteins. mu LC-MS/MS demonstrated better protein sequence coverage than MALDI-TOF PMM over the entire mass range of proteins identified. MALDI-TOF and PMM produced unique peptide molecular weight matches that were not identified by mu LC-MS/MS. By incorporating amino acid sequence modifications into database searches, combined sequence coverage obtained from these two complimentary ionization methods exceeded 50% for approximately 70% of the 162 spots analyzed. This improved sequence coverage in combination with enzymatic digestions of different specificity is proposed as a method for analysis of post-translational modification from 2D-gel separated proteins.     

Tyrosine absorption spectroscopy: Backbone protonation effects on the side chain electronic properties

The UV–vis spectrum of Tyrosine and its response to different backbone protonation states have been studied by applying the Perturbed Matrix Method (PMM) in conjunction with molecular dynamics (MD) simulations. Herein, we theoretically reproduce the UV–vis absorption spectrum of aqueous solution of Tyrosine in its zwitterionic, anionic and cationic forms, as well as of aqua‐p‐Cresol (i.e., the moiety that constitutes the side chain portion of Tyrosine). To achieve a better accuracy in the MD sampling, the Tyrosine Force Field (FF) parameters were derived de novo via quantum mechanical calculations. The UV–vis absorption spectra are computed considering the occurring electronic transitions in the vertical approximation for each of the chromophore configurations sampled by the classical MD simulations, thus including the effects of the chromophore semiclassical structural fluctuations. Finally, the explicit treatment of the perturbing effect of the embedding environment permits to fully model the inhomogeneous bandwidth of the electronic spectra. Comparison between our theoretical–computational results and experimental data shows that the used model captures the essential features of the spectroscopic process, thus allowing to perform further analysis on the strict relationship between the quantum properties of the chromophore and the different embedding environments. © 2018 Wiley Periodicals, Inc.     

Comparison of a quantum random number generator with pseudorandom number generators for their use in molecular Monte Carlo simulations

Four pseudorandom number generators were compared with a physical, quantum‐based random number generator using the NIST suite of statistical tests, which only the quantum‐based random number generator could successfully pass. We then measured the effect of the five random number generators on various calculated properties in different Markov‐chain Monte Carlo simulations. Two types of systems were tested: conformational sampling of a small molecule in aqueous solution and liquid methanol under constant temperature and pressure. The results show that poor quality pseudorandom number generators produce results that deviate significantly from those obtained with the quantum‐based random number generator, particularly in the case of the small molecule in aqueous solution setup. In contrast, the widely used Mersenne Twister pseudorandom generator and a 64‐bit Linear Congruential Generator with a scrambler produce results that are statistically indistinguishable from those obtained with the quantum‐based random number generator. © 2017 Wiley Periodicals, Inc.     

Coupled and decoupled dual quantum systems in one semiconductor nanocrystal

Dual quantum systems, 0-dimensional quantum dot, and 2-dimensional quantum wells were constructed in one II-VI semiconductor nanocrystal by the epitaxial growth of a barrier (ZnS) layer between the systems in solution. By alteration of the thickness of the barrier layer, the two quantum systems were controlled to either electronically coupled or decoupled. Evidence of optical coupling between the two band gap emissions was also observed. The position and relative intensity of the two emissions can be independently tuned by reaction conditions. Total photoluminescence quantum efficiency of the dual emitting bands reached as high as 30% at room temperature under synthetic conditions not optimized for high emission.     

Quantum chemistry simulation on quantum computers: theories and experiments

It has been claimed that quantum computers can mimic quantum systems efficiently in the polynomial scale. Traditionally, those simulations are carried out numerically on classical computers, which are inevitably confronted with the exponential growth of required resources, with the increasing size of quantum systems. Quantum computers avoid this problem, and thus provide a possible solution for large quantum systems. In this paper, we first discuss the ideas of quantum simulation, the background of quantum simulators, their categories, and the development in both theories and experiments. We then present a brief introduction to quantum chemistry evaluated via classical computers followed by typical procedures of quantum simulation towards quantum chemistry. Reviewed are not only theoretical proposals but also proof-of-principle experimental implementations, via a small quantum computer, which include the evaluation of the static molecular eigenenergy and the simulation of chemical reaction dynamics. Although the experimental development is still behind the theory, we give prospects and suggestions for future experiments. We anticipate that in the near future quantum simulation will become a powerful tool for quantum chemistry over classical computations.     

Semiclassical initial value series solution of the spin boson problem

A numerical solution for the quantum dynamics of the spin boson problem is obtained using the semiclassical initial value series representation approach to the quantum dynamics. The zeroth order term of the series is computed using the new forward-backward representation for correlation functions presented in the preceding adjacent paper. This leads to a rapid convergence of the Monte Carlo sampling, as compared to previous attempts. The zeroth order results are already quite accurate. The first order term of the series is small, demonstrating the rapid convergence of the semiclassical initial value representation series. This is the first time that the first order term in the semiclassical initial value representation series has been converged for systems with the order of 50 degrees of freedom.     

Partial waves in the nonspherical case

Many quantum mechanical problems are separable in one or several of the standard classifications of general coordinate systems. The associated solution is most conveniently evaluated using expansions in Lamé wave functions. We give here some preliminary numerical results displaying the continuous distortion of an s-, p-, and d-wave spherical harmonic. The results indicate rather surprising features which may be useful in general quantum mechanical contexts. © 1996 John Wiley & Sons, Inc.     

Digital image colorimetry method for determination of glucose using silver nanoparticles immobilized into polymethacrylate matrix

We suggest Ag⁰ nanoparticles immobilized into transparent polymethacrylate matrix (PMM–Ag⁰) as a simple colorimetric sensor for determination of glucose. We demonstrate the capabilities of a smartphone to process the images and further analyze the information obtained by determination of glucose using PMM–Ag⁰ sensor. The method can be employed for glucose concentrations of 0.1–4.3 mmol dm⁻³, while its detection limit is 0.05 mmol dm⁻³.     

Hyperconjugative and inductive perturbations in poly(p-phenylene vinylenes)

New polymers having high solid-state fluorescence quantum yields and the ability to tune their electron affinity without effecting their band gap using hyperconjugative interactions is reported. The novel three-dimensional poly(phenylene vinylenes) having [2.2.2] bicyclic ring systems shown were synthesized, and the different hyperconjugative perturbations provide differential fluorescence sensory quenching responses to electron-rich and electron-deficient analytes in solution and solid thin films.     

The Strength of the Macromonomer Strategy for Complex Macromolecular Architecture: Molecular Characterization,Properties and Applications of Polymacromonomers

The efficiency of the macromonomer (MM) synthetic strategy for the creation of nonlinear complex macromolecular architectures (miktoarm stars, α,ω‐branched polymers, random/exact comb and graft copolymers, dendritic polymers, molecular brushes) is reviewed. In addition, the solution/bulk properties and the potential applications of polymacromonomers (PMM), as well as new synthetic ideas are presented. The synthesis of macromonomers and living polymacromonomers in situ leads to many novel linear and nonlinear structures, as for example PMM‐b‐PS‐b‐PMM, (PS)₂PMM. The use of multichlorosilylstyrenes as monomer/linking agents opens new ways for structures with multichain macromonomeric building blocks.

The use of multichlorosilylstyrenes as monomer/linking agents opens new ways for structures having multichain macromonomeric building blocks.     

Adiabatic passage in a three-state system with non-Markovian relaxation: the role of excited-state absorption and two-exciton processes

The influence of excited-state absorption (ESA) and two-exciton processes on a coherent population transfer with intense ultrashort chirped pulses in molecular systems in solution has been studied. A unified treatment of adiabatic rapid passage (ARP) in such systems has been developed using a three-state electronic system with relaxation treated as a diffusion on electronic potential energy surfaces. We have shown that ESA has a profound effect on coherent population transfer in large molecules that necessitates a more accurate interpretation of experimental data. A simple and physically clear model for ARP in molecules with three electronic states in solution has been developed by extending the Landau-Zener calculations putting in a third level to random crossing of levels. A method for quantum control of two-exciton states in molecular complexes has been proposed.     

Including quantum effects in the dynamics of complex (i.e., large) molecular systems

The development in the 1950s and 1960s of crossed molecular beam methods for studying chemical reactions at the single-collision molecular level stimulated the need and desire for theoretical methods to describe these and other dynamical processes in molecular systems. Chemical dynamics theory has made great strides in the ensuing decades, so that methods are now available for treating the quantum dynamics of small molecular systems essentially completely. For the large molecular systems that are of so much interest nowadays (e.g., chemical reactions in solution, in clusters, in nanostructures, in biological systems, etc.), however, the only generally available theoretical approach is classical molecular dynamics (MD) simulations. Much effort is currently being devoted to the development of approaches for describing the quantum dynamics of these complex systems. This paper reviews some of these approaches, especially the use of semiclassical approximations for adding quantum effects to classical MD simulations, also showing some new versions that should make these semiclassical approaches even more practical and accurate.     

Theoretical modeling of enzyme reactions: the thermodynamics of formation of compound 0 in horseradish peroxidase

In this paper, by using the perturbed matrix method (PMM) in combination with basic statistical mechanical relations both based on nanosecond time-scale molecular dynamics (MD) simulations, we quantitatively address the thermodynamics of compound 0 (Cpd 0) formation in horseradish peroxidase (HRP) enzyme. Our results, in the same trend of low-temperature experimental data, obtained in cryoenzymology studies indicate that such a reaction can be described essentially as a stepwise spontaneous process: a first step mechanically constrained, strongly exothermic proton transfer from the heme-H2O2 complex to the conserved His42, followed by a solvent-protein relaxation involving a large entropy increase. Critical evaluation of PMM/MD data also reveals the crucial role played by specific residues in the reaction pocket and, more in general, by the conformational fluctuations of the overall environment in physiological conditions.     

New insight into the IR-spectra/structure relationship in amyloid fibrils: a theoretical study on a prion peptide

Molecular-level structural information on amyloid aggregates is of great importance for the understanding of protein-misfolding-related deseases. Nevertheless, this kind of information is experimentally difficult to obtain. In this work, we used molecular dynamics (MD) simulations combined with a mixed quantum mechanics/molecular mechanics theoretical methodology, the perturbed matrix method (PMM), in order to study the amide I' IR spectrum of fibrils formed by a short peptide, the H1 peptide, derived from residues 109 through 122 of the Syrian hamster prion protein. The PMM/MD approach allows isolation of the amide I' signal arising from any desired peptide group of the polypeptide chain and quantification of the effect of the excitonic coupling on the frequency position. The calculated single-residue signals were found to be in good agreement with the experimental site-specific spectra obtained by means of isotope-labeled IR spectroscopy, providing a means for their interpretation at the molecular level. In particular, our results confirm the experimental hypothesis that residues ala117 are aligned in all strands and that the alignment gives rise to a red shift of the corresponding site-specific amide I' mode due to strong excitonic coupling among the ala117 peptide groups. In addition, our data show that a red shift of the amide I' band due to strong excitonic coupling can also occur for amino acids adjacent in sequence to the aligned ones. Thus, a red shift of the signal of a given isotope-labeled amino acid does not necessarily imply that the peptide groups under consideration are aligned in the β-sheet.     

On the photolysis of simple anions and neutral molecules as sources of O-/OH, SO(x)- and Cl in aqueous solution

This contribution examines the aqueous phase photolysis processes of simple anions such as nitrate, nitrite, peroxodisulfate and neutral molecules such as H2O2. The review includes new results on absolute effective quantum yields for the photodissociation processes of NO3(-), NO2(-), S2O8(2-), HSO5(-), S2O6(2-), HOCl, and chloroacetone in an aqueous solution. The quantum yields for the photolysis of nitrate and nitrite have also been determined as a function of temperature. Models to interpret the wavelength and the temperature dependencies of the quantum yields for the different systems are discussed and a simple model treatment is developed to quantify the effects of (i) impulse conservation, (ii) electrostatic interaction (e.g., ion-dipole, dipole-dipole and coulomb interaction between the photofragments directly after photolytic fragmentation), and (iii) diffusion and recombination. The combined impulse-interaction-diffusion (IID) model is compared to the experimentally observed effective radical formation quantum yields and reasonable agreement is found for a number of systems. It is shown that the temperature dependencies for effective quantum yields of photolysis processes in aqueous solution are not only governed by the temperature dependence of the viscosity of water but also determined by the temperature dependence of the rate constants of the photofragment recombination reactions.     

Conformational fluctuations and electronic properties in myoglobin

In this article we use the recently developed perturbed matrix method (PMM) to investigate the effect of conformational fluctuations on the electronic properties of heme in Myoglobin. This widely studied biomolecule has been chosen as a benchmark for evaluating the accuracy of PMM in a large and complex system. Using a long, 80-ns, molecular dynamics simulation and unperturbed Configuration Interaction (CISD) calculations in PMM, we reproduced the main spectroscopic features of deoxy-Myoglobin. Moreover, in line with our previous results on a photosensitive protein, this study reveals a clear dynamical coupling between electronic properties and conformational fluctuations, suggesting that this correlation could be a general feature of proteins.     

BENZOPHENONE-SENSITIZED LIPID PEROXIDATION IN LINOLEATE MICELLES

Abstract— Benzophenone-photosensitized peroxidation in linoleic acid micelles (Type I reaction) has been investigated and quantum yields of both sensitizer photolysis and lipid peroxidation have been obtained. Benzophenone as well as its derivative, benzophenone-4'-heptyl-4-pentanoic acid (BHPA) have been utilized as sensitizers in this study. A quantum yield of 1.2 for hydroperoxide formation, compared with a benzophenone disappearance quantum yield of 0.41 (in the same linoleate micellar solution) was obtained; yields of 1.3 and 0.6 were found for comparable systems in which BHPA was the sensitizer. Although such data are consistent with the peroxidation mechanism of chain reaction, it is necessary to know the yields of initiating species to arrive at chain reaction lengths in these systems. Such yields have been determined by flash photolysis. The dependencies of sensitizer photolysis and hydroperoxide yields on linoleate concentration have also been determined in order to elucidate the effects of micelle formation or molecular organization on the peroxidative process. Additionally, for comparison in a saturated surfactant (lipid) system hydrogen abstraction was investigated by photolysis techniques in sodium dodecyl sulfate alone using these two sensitizers.     

Some iterative techniques for large CI matrices. II. Singular systems of linear equations

An interative technique to solve nearly singular systems of linear equations of quantum chemical interest is described and tested. The solution is split into regular and singular parts, the last being the resonating eigenvector.