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The Perturbed Matrix Method (PMM) approach to be used in combination with Molecular Dynamics (MD) trajectories (MD-PMM) has been recoded from scratch, improved in several aspects, and implemented in the Gaussian suite of programs for allowing a user-friendly and yet flexible tool to estimate quantum chemistry observables in complex systems in condensed phases. Particular attention has been devoted to a description of rigid and flexible quantum centers together with powerful essential dynamics and clustering approaches. The default implementation is fully black-box and does not require any external action concerning both MD and PMM sections. At the same time, fine-tuning of different parameters and use of external data are allowed in all the steps of the procedure. Two specific systems (Tyrosine and Uridine) have been reinvestigated with the new version of the code in order to validate the implementation, check the performances, and illustrate some new features.

Flavoproteins, containing flavin chromophores, are enzymes capable of transferring electrons at very high speeds. The ultrafast photoinduced electron-transfer (ET) kinetics of riboflavin binding protein to the excited riboflavin was studied by femtosecond spectroscopy and found to occur within a few hundred femtoseconds [ Zhong and Zewail, Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 11867-11872 ]. This ultrafast kinetics was attributed to the presence of two aromatic rings that could transfer the electron to riboflavin: the side chains of tryptophan 156 and tyrosine 75. However, the underlying ET mechanism remained unclear. Here, using a hybrid quantum mechanical-molecular dynamics approach, we perform ET dynamics simulations taking into account the motion of the protein and the solvent upon ET. This approach reveals that ET occurs via a major reaction channel involving tyrosine 75 (83%) and a minor one involving tryptophan 156 (17%). We also show that the protein environment is designed to ensure the fast quenching of the riboflavin excited state.

We present here the calculation of the absorption spectrum of riboflavin in acetonitrile and dimethyl sulfoxide using a hybrid quantum/classical approach, namely the perturbed matrix method, based on quantum mechanical calculations and molecular dynamics simulations. The calculated spectra are compared to the absorption spectrum of riboflavin previously calculated in water and to the experimental spectra obtained in all three solvents. The experimentally observed variations in the absorption spectra upon change of the solvent environment are well reproduced by the calculated spectra. In addition, the nature of the excited states of riboflavin interacting with different solvents is investigated, showing that environment effects determine a recombination of the gas-phase electronic states and that such a recombination is strongly affected by the polarity of the solvent inducing significant changes in the absorption spectra. (C) 2017 Elsevier B.V. All rights reserved.

In this study we report the modeling of the absorption spectrum of riboflavin in water using a hybrid quantum/classical mechanical approach, the MD-PMM methodology. By means of MD-PMM calculations, with which the effect of riboflavin internal motions and of solvent interactions on the spectroscopic properties can be explicitly taken into account, we obtain an absorption spectrum in very good agreement with the experimental spectrum. In particular, the calculated peak maxima show a consistent improvement with respect to previous computational approaches. Moreover, the calculations show that the interaction with the environment may cause a relevant recombination of the gas-phase electronic states.

A theoretical–computational study based on Molecular Dynamics simulations and Perturbed Matrix Method (MD–PMM) calculations was carried out for evaluating some properties of solvated Ferrocene including the UV–Vis spectrum and the redox potential. The results, in rather good agreement with the experimental values, display that Ferrocene low-lying excited states are scarcely affected by the change of solvent polarity. On the other hand, the Ferrocene/Ferricinum redox potential show a sharp, although not dramatic, dependency on the nature of the solvent essentially because of the sensitivity of the charged Ferricinium species to the solvent electric field fluctuation. The present study is the first one theoretically addressing, with the use of explicit solvent calculations, the Ferrocene UV spectrum and the Ferricinium/Ferrocene couple redox potential, a quantity proposed by the IUPAC Electrochemical Commission as reference electrode potential for non-aqueous solutions.

Theoretical modeling of the photophysical properties of materials (both low-weighted and polymeric) for energy harvesting represents an attractive area of fundamental and applied research. In this area meaningful results can be obtained only in the presence of realistic models keeping intact the atomistic complexity which, in this system, is usually very high. Herein we propose a model study, carried out on a typical building block for energy harvesting materials, 4,7-dithien-2-yl-2,1,3-benzothiadiazole (DTB), with the precise aim to theoretically reproduce the charge-transfer S0–S1 UV–vis signal in different solvents and also to provide some hints for interpreting the large Stokes-shift observed in its fluorescence spectra. Results show that the DTB spectral (absorption) features are the result of an intimate interplay between chromophore thermal fluctuations and environmental dynamical (electrostatic) perturbation. Deep inspection of the results also confirms the possibility of modulating the chromophor...

In this paper we present a general theoretical-computational model for treating electron transfer reactions in complex atomic-molecular systems. The underlying idea of the approach, based on unbiased first-principles calculations at the atomistic level, utilizes the definition and the construction of the Diabatic Perturbed states of the involved reactive partners (i.e. the quantum centres in our perturbation approach) as provided by the interaction with their environment, including their mutual interaction. In this way we reconstruct the true Adiabatic states of the reactive partners characterizing the electron transfer process as the fluctuation of the electronic density due to the fluctuating perturbation. Results obtained by using a combination of Molecular Dynamics simulation and the Perturbed Matrix Method on a prototypical intramolecular electron transfer (from 2-(9,9'-dimethyl)fluorene to the 2-naphthalene group separated by a steroidal 5-α-androstane skeleton) well illustrate the accuracy of the method in reproducing both the thermodynamics and the kinetics of the process.

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.

Intramolecular charge transfer (ICT) of gaseous π-conjugated oligo-phenyleneethynylenes (OPE) induced by a homogeneous applied electric field has been theoretically investigated using a combined approach integrating molecular dynamics (MD) simulations and Perturbed Matrix Method calculations. In line with recent investigations, our results indicate the peculiar role of conformational transitions on OPE electronic properties which reflects on a strong temperature effect on ICT. Electron transfer reactions inducing chemical alteration on OPE, also taken into account in this study, revealed extremely important for explaining non-linear ICT effects and probably plays a central role in the mechanisms underlying molecular transport junctions. Our study further points out the necessity of using MD-based approach for modelling molecular electronics, even when relatively rigid molecular systems are concerned.

In this work we characterize the thermodynamics of two simple chemical reactions in water. Applying the quasi-gaussian entropy theory to the molecular dynamics calculations, we model the equilibrium constant and its temperature dependence along the typical water isochore. Such a theoretical–computational approach could be useful to predict the optimal condition for chemical reactions in condensed phase at a very low computational cost. 2007 Published by Elsevier B.V.

In this work, we address the problem of the role and relevance of the aqueous environment configurational sampling on acetone electronic properties: the (vertical) absorption spectrum and corresponding excitation Helmholtz free energy. By comparing the results obtained by applying the perturbed matrix method (PMM) on molecular dynamics (MD) trajectories of different sampling efficiency, we specifically quantify the effects of the phase space sampling on acetone vertical electronic excitations. Results confirm that PMM provides an accurate and physically consistent description of the electronic excitation processes and show the crucial importance of an extended configurational sampling of the solvent environment in order to obtain a reliable (chromophore) absorption behaviour.

The free energy profile and the (classical) kinetics of chemical reactions in (soft) condensed phase are modeled theoretically by means of molecular dynamics simulations, the Perturbed Matrix Method (PMM) and the quasi Gaussian entropy (QGE) theory. In this paper we describe the theoretical framework and apply the model to the intramolecular proton transfer reaction of aqueous malonaldehyde. Although in the present application we disregard the quantum effects for the proton dynamics along the reaction coordinate (i.e., tunneling), the classical-like view of the proton transition over the reaction free energy surface seems to properly describe the kinetic process and shows that water acts lowering the reaction free energy barrier. Moreover, a weak temperature dependence of the free energy surface is obtained, implying small entropy variations in the transition. Interestingly the activation entropy, as provided by the QGE model, is negative in the whole temperature range considered, thus indicating an entropy reduction at the transition structure. Finally, by comparing our results with theoretical and experimental literature data, we critically address the actual role of tunneling in this reaction and discuss the emerging kinetic scheme. Copyright (c) 2006 John Wiley & Sons, Ltd.

In this Letter, we use the recently introduced perturbed matrix method (PMM) to study in detail the electronic properties of formaldehyde in water, as obtained by applying this method to Molecular Dynamics simulation data. Results show that PMM provides an accurate description at relatively low computational costs.

Here, we extend a recently introduced theoretical-computational procedure [M. D'Alessandro, M. Aschi, C. Mazzuca, A. Palleschi, and A. Amadei, J. Chem. Phys. 139, 114102 (2013)] to include quantum vibrational transitions in modelling electronic spectra of atomic molecular systems in condensed phase. The method is based on the combination of Molecular Dynamics simulations and quantum chemical calculations within the Perturbed Matrix Method approach. The main aim of the presented approach is to reproduce as much as possible the spectral line shape which results from a subtle combination of environmental and intrinsic (chromophore) mechanical-dynamical features. As a case study, we were able to model the low energy UV-vis transitions of pyrene in liquid acetonitrile in good agreement with the experimental data.

In this study, we present an extension of the theoretical–computational approach developed in our group and based on molecular dynamics simulations, quantum chemical calculations, perturbed matrix method, and essential dynamics analysis for taking into account the cybotactic effect in the computational modeling of absorption spectra of molecular systems in condensed phase. The low-energy UV–Vis spectra of para-nitroaniline in water, methanol, and in the presence of a zwitterionic micelle have been computationally addressed and compared to the experimental data. The approach, considering all the systematic errors deriving from the intrinsic limitations of the computational setup (force field, quantum chemical calculations, and the approximations of the method), satisfactorily reproduces the experimental spectral shifts and peaks shapes and provides a promising tool of investigation for reproducing spectral observables of very complex systems.

A benchmark biochemical reaction is here theoretically investigated by means of a perturbative approach in order to model each reaction step. The reaction is the flavin-indole electron transfer, involving also a spin-state relaxation of the ionic complex. The whole reaction path is modeled and the kinetics of the process is studied. The dipolar interaction between the two radicals is explicitly considered during the dynamic evolution of the system in order to investigate the proper conditions for the triplet-to-singlet transition to occur.

Firefly luciferin and its oxidated form, oxyluciferin, are two heterocyclic compounds involved in the enzymatic reaction, catalyzed by redox proteins called luciferases, which provides the bioluminescence in a wide group of arthropods. Whereas the electronic absorption spectra of d -luciferin in water at different pHs are known since 1960s, only recently reliable experimental electronic spectra of oxyluciferin have become available. In addition oxyluciferin is involved in a triple chemical equilibria (deprotonation of the two hydroxyl groups and keto-enol tautomerism of the 4-hydroxythiazole ring), that obligates to select during an experiment a predominant species, tuning pH or solvent polarity besides introducing chemical modifications. In this study we report the absorption spectra of luciferin and oxyluciferin in each principal chemical form, calculated by means of perturbed matrix method (PMM), which allowed us to successfully introduce the effect of the solvent on the spectroscopic absorption properties, and compare the result with available experimental data.

The absorption spectra in dilute dichloromethane solution at 300 K of four Oligotiophenes (OT), namely 2,2′:5′,2″-Terthiophene, 2,2′:5′,2″:5″,2″′-Quaterthiophene, 4,4″′-Didodecyl-2,2′:5′,2″:5″,2″′-quaterthiophene and 5,5′′′′′-Dihexyl-2,2′:5′,2′′:5′′,2′′′:5′′′,2′′′′:5′′′′,2′′′′′-sexithiophene, have been studied both experimentally and theoretically by using a combination of molecular dynamics simulations, time-dependent density functional theory (TD-DFT) and perturbed matrix method calculations. A deep analysis of the theoretical results, affected by a systematic although not dramatic underestimation of the absorption maxima due to the well-documented TD-DFT limitations, clearly indicates that both the environmental (solvent) and thermal effects significantly alter the Oligotiophenes photophysical properties mainly because of the wide repertoire of the S0–S1 energy gaps and electronic densities experienced in solution by the different conformers actually populated. In particular, all the investigated OT display a very high flexibility resulting in a very high repertoire of sampled conformations. The comparison of the calculated and experimental lineshape of the S0–S1 electronic transition has clearly indicated that for a correct modeling of OT spectral features, the lack of an exhaustive sampling of semiclassical configurational space of the overall system, i.e., solute in interaction with the solvent, might result in an incomplete picture even in the presence of well-documented important aspects such as reliable definition of excited electronic states and the inclusion of quantum vibronic effects.

The effect of a zwitterionic micelle environment on the efficiency of the ketoenol interconversion of 2-pheny- lacetylthiophene has been investigated by means of a joint application of experimental and theoretical/computational approaches. Results have revealed a reduction of the reaction rate constant if compared with bulk water essentially because of the different solvation conditions experienced by the reactant species, including water molecules, in the micelle environment. The slight inhibiting effect due to the application of a static electric field has also been theoretically investigated and presented.

The charge transfer thermodynamics of a simple model of DNA, a single stranded 10-mer poly-adenine oligonucleotide, in water is investigated by means of a computational/theoretical procedure, in which all the relevant environmental effects are considered. Our data indicate that water and counterions ultimately dominate the DNA reduction and oxidation free energies, which are also strongly influenced by the base position along the strand. In fact, we estimated that reduction free energies are large and negative, particularly for the bases close to the 5' and 3' positions, whereas the electron detachment is thermodynamically unfavoured all along the strand, but with a higher free energy cost in the central region of the molecule. Further investigation on double charging, i.e. one nucleobase is oxidized and one is reduced within the strand, predicts that charge-separated states are possible and thermodynamically largely stable when the ionic forms are separated by several nucleobases.

Quantitative characterization of quantum states in complex molecular systems is a rather complicated task because of the necessity of maintaining the pure quantum definition of a state interacting with a configurationally complex molecular environment. Unfortunately, many of the "observables" that are of interest for a chemist, typically dealing with "complex objects", belong to the above class and their theoretical modeling may represent a hard task. In this respect, we have developed a new theoretical methodology, "perturbed matrix method", essentially based on the perturbation theory whose main aim is the characterization of the quantum states of a predefined portion of a complex molecular system, e.g., a solute, classically interacting with the environment, e.g., the solvent. This method has been used in this study to systematically characterize, for the first time and in conjunction with experimental observations, the intrinsic nature of pyrene whose vibrational and electronic states are highly sensitive to the nature of molecular environment. More precisely, pyrene shows a strong alteration of spectral intensities upon modification of polarity of the solvent. This property has been extensively used in many experimental studies and has been interpreted in the present study by characterizing pyrene electronic states as fluctuating states strictly connected to the polarity and the fluctuations of the surrounding medium. A correct theoretical modeling has been also obtained and commented for the vertical transitions in different media and also for the vibronic structure for the first transition in water.

In this study the question as to whether and to what extent horseradish peroxidase (HRP) enzyme structural flexibility affects the free energy barrier for the formation of the key intermediate compound 0 (Cpd0) is addressed by the use of a combined application of molecular dynamics simulations and perturbed matrix method calculations. Results are intriguing and indicate that, within the simulated conditions, free energy profiles are substantially affected by structural fluctuations of the whole surrounding biological environment (i.e. HRP enzyme and solvent). In this respect our results show that the combined effect of enzyme and solvent provides a substantial lowering of the free energy barrier to the formation of Cpd0, with respect to both gas-phase and QM/MM results carried out at a comparable level of theory. A careful inspection of such observations and their general implications in currently employed methodological approaches to the modelling of enzyme reactions, is also discussed.

The state-of-the-art of theoretical-computational modelling of infrared (IR) spectra in peptides and proteins is able to reproduce the main spectral features involved in the secondary-structure organisation. The results so far collected, clearly show that the complexity of the atomic processes inherent to the IR spectra makes the often used empirical secondary-structure/frequency correlations inaccurate and possibly misleading. The use of extended configurational sampling as provided by, for example, molecular dynamics simulations and of a physically coherent treatment of both the quantum degrees of freedom and their coupling with the semiclassical atomic motions, promises to open the way to interpret and predict IR temperature-dependent and time-dependent spectral signals, in particular for the study of folding/unfolding transitions.

The free-energy profile and the classical kinetics of the heme carbomonoxide binding-unbinding reaction have been derived by means of a theoretical method for the separated chains of human (HbA) and Trematomus newnesi major component (HbTn) hemoglobin. The results reveal that the alpha- and beta-chains of HbA have similar values of kinetic constants for the dissociation of the Fe-CO state, in agreement with experimental data. Comparisons of the present findings with the data obtained for the alpha- and beta-chains of HbTn and with theoretical and experimental results previously collected on myoglobin provide a detailed picture of this important biochemical reaction in globins. The sequence and structural differences among the globins are not reflected in meaningful variations in the rate of CO dissociation. These data support the conclusion that the differences observed for the reaction with CO of globins, if any, involve the rate of ligand migration to the solvent, rather than the Fe-CO complex formation/rupture. Furthermore, our results agree with the recent discovery that globin family proteins exhibit common dynamics, thus confirming the observation that the dynamic properties of proteins are strongly related to their overall architecture.

Irreversible redox-induced relaxation processes occurring in a synthetic thread for rotaxane-based molecular devices are investigated; the results show that such a system in solution allows chemists to efficiently realize a nanosecond timescale/electrochemically-driven "conformational shaping" through simple control of non-covalent interactions.

In this article we characterize, by means of the perturbed matrix method, the response of the electronic states of a chemical system to the perturbing environment. In the theory section we describe in detail the basic derivations and implications of the method, extending its theoretical framework to treat possible excitonic effects, and we show how to characterize the perturbed electronic states. Finally, by using a set of chemical systems interacting with complex atomic-molecular environments, we describe the nature and general features of the electronic state mixing and transitions as caused by atomic and molecular interactions.

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.

In a recent paper [Aschi et al., ChemPhysChem 6, 53 (2005)], we characterized, by means of theoretical-computational procedures, the electronic excitation of water along the typical liquid state isochore (55.32 mol/l) for a large range of temperature. In that paper we were able to accurately reproduce the experimental absorption maximum at room temperature and to provide a detailed description of the temperature dependence of the excitation spectrum along the isochore. In a recent experimental work by Marin et al. [J. Chem. Phys. 125, 104314 (2006)], water electronic excitation energy was carefully analyzed in a broad range of density and temperature, finding a remarkable agreement of the temperature behavior of the experimental data with our theoretical results. Here, by means of the same theoretical-computational procedures (molecular dynamics simulations and the perturbed matrix method), we investigate water electronic absorption exactly in the same density-temperature range used in the experimental work, hence, now considering also the absorption density dependence. Our results point out that, (1) for all the densities and temperatures investigated, our calculated absorption spectra are in very good agreement with the experimental ones and (2) the gradual maxima redshift observed increasing the temperature or decreasing the density has to be ascribed to a real shift of the lowest X--A electronic transition, supporting the conclusions of Marin et al.

Here we report that at room temperature in acetonitrile after the reduction of the naphthalimide-site, a synthetic molecular thread undergoes a complete conformational change which makes possible an efficient conversion of chemical energy into mechanical work; such results point out the ability of the thread to act as a molecular device under electrochemical control.

In a previous paper we introduced a new Hamiltonian model for polarizable water, based on the atomic charge density expansion, whose reliability should in principle be independent of the system conditions. In this work we refine and apply this model to describe the structural and energetical features of clusters of increasing dimension and to evaluate the second virial coefficient. Results show that, despite its simplicity, such Hamiltonian provides an efficient and rather accurate description of the systems studied.

Contradictory data in the huge literature on microwaves bio-effects may result from a poor understanding of the mechanisms of interaction between microwaves and biological systems. Molecular simulations of biochemical processes seem to be a promising tool to comprehend microwave induced bio-effects. Molecular simulations of classical and quantum events involved in relevant biochemical processes enable to follow the dynamic evolution of a biochemical reaction in the presence of microwave fields. In this paper, the action of a microwave signal (1 GHz) on the covalent binding process of a ligand (carbon monoxide) to a protein (myoglobin) has been studied. Our results indicate that microwave fields, with intensities much below the atomic/molecular electric interactions, cannot affect such biochemical process.

In this article we use the perturbed matrix method and an extended molecular dynamics sampling of the carbon monoxide (CO) in the myoglobin distal pocket to characterize the CO vibrational spectrum and hence to relate its spectroscopic features with the atomic-molecular behavior. Results show the accuracy of the method employed and confirm the assignment of the spectroscopic B1 and B2 states proposed by Lim et al.

In this Letter, we use the perturbed matrix method, in combination with molecular dynamics and statistical mechanics, in order to describe in details the electric field induced intramolecular charge transfer (ICT) in two π-conjugated oligomers of nanotechnological interest. Results show a relevant relationship between the extent of ICT and molecular conformation, pointing out the highly non-linear charge transfer field response.

The free energy profile and the (classical) kinetics of chemical reactions in (soft) condensed phase may be well modelled theoretically by means of molecular dynamics simulations, the perturbed matrix method (PMM) and statistical mechanics, as we provided in previous articles. In this paper, we describe the theoretical framework, discussing thoroughly its crucial points, and apply the model to an important biochemical reaction: the Haem carbon monoxide binding–unbinding reaction in Myoglobin, specifically investigating the reaction step involving the carbon–iron chemical bond formation (disruption) which is of particular biochemical interest.

The synthetic peptide Vitr-p-13 (YPIVGQELLGAIK-NH2), derived from the bacterial dimeric Vitreoscilla haemoglobin (VHb) in the position 95–107, is characterized by a pre-eminent “statistical coil” conformation in water as demonstrated by CD experiments and long time-scale MD simulations. In particular, Vitr-p-13 does not spontaneously adopt an alpha-helix folding in water, but it is rather preferentially found in beta-hairpin-like conformations. Long time-scale MD simulations have also shown that Vitr-p-13 displays a “topological-trigger” which initiates alpha-helix folding within residues 7–10, exactly like seen in the temporins, a group of linear, membrane-active antimicrobial peptides of similar length. At variance with temporins, in Vitr-p-13 such a process is energetically very demanding (+10 kJ/mol) in water at 300 K, and the peptide was found to be unable to bind model membranes in vitro and was devoid of antimicrobial activity. The present results, compared with previous studies on similar systems, strengthen the hypothesis of the requirement of a partial folding when still in aqueous environment to allow a peptide to interact with cell-membranes and eventually exert membrane perturbation-related antibiotic effects on target microbial cells. © 2007 Wiley Periodicals, Inc. Biopolymers 87: 85–92, 2007. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com

In this paper, we investigate the effects of a point mutation on the enzymatic activity of copper−zinc superoxide dismutase, which we recently studied in detail by means of a theoretical-computational procedure (J. Phys. Chem. B 2004, 108, 16255). Comparison of the reactivity of the initial catalytic steps in this mutant (G93A mutation far from the active site) with our previous data, reveals the beautiful mechanical-dynamical architecture of the enzyme, altered by such an apparently irrelevant mutation. Finally, our results suggest a possible atomic-molecular-based explanation for the mutant-pathology correlation, in line with the most recent experimental data.

Molecular dynamics (MD) simulations and circular dichroism (CD) experiments were carried out on aqueous temporin A and L, two short peptides belonging to an interesting class of natural substances known to be active mainly against Gram-positive/negative bacteria and fungi. Experimental results indicate the higher propensity of temporin L, with respect to temporin A, in forming a-helical structures. These results were revisited by long-timescale MD simulations, in which their a-helical propensity was investigated in the absence of trifluoroethanol. Results clearly show the higher stability of a-helix conformations in temporin L; moreover, an interestingly strong mechanical analogy emerges since both temporins show the same residue interval (from 7 to 10) as the most energetically accessible for a-helix formation. Such studies provide some intriguing struc- tural and mechanical evidence that may help in better understanding and rationalizing the confor- mational behaviour of temporins in water solution and, ultimately, the inner principles of their microbial targets selectivity and mechanism of action at the level of cell membranes. # 2005 Wiley

By using the quasi Gaussian entropy theory in combination with molecular dynamics simulations and the perturbed matrix method, we investigate the ground and excited state thermodynamics of aqueous carbon monoxide. Results show that the model used is rather accurate and provides a great detail in the description of the excitation thermodynamics.

Because of its central role in basically all aspects of science,water is certainly one of the most extensively investigated sub-stances, from a theoretical point of view. Many properties havebeen, in fact, theoretically addressed both in the isolated andcondensed phases. Nevertheless, many aspects are still notcompletely understood and represent the focus of active theo-retical interest. Among them, one of the most appealing is cer-tainly the understanding of the electronic properties, in partic-ular the photoabsorption features, in condensed phase. Liquidwater experimentally shows, under ambient conditions, the0–1 absorption maximum at 147 nm, that is, 88 kJmol

The zwitterionic form of aqueous L-alanine is chosen as a benchmark for the theoretical evaluation of the optical rotatory dispersion (ORD) in solution, as provided by a simple application of the perturbed matrix method (PMM). Results show the applicability of this procedure, suggesting that its use might provide a general theoretical-computational tool for describing, at atomic–molecular level, the optical activity of a molecule in a complex environment. 2005 Elsevier B.V. All rights reserved.

A theoretical study of the conformational properties of a small heme peptide in aqueous solution is carried out by classical, long-timescale molecular dynamics simulations. The electronic properties of this species, that is, the relative energies of its excited electronic states and the redox potential, are reproduced and related to the conformational behavior using the perturbed matrix method and basic statistical mechanics. Our results show an interesting coupling between the conformational transitions and the electronic properties. These investigations, beyond the biophysically relevant results addressing the long-standing question of the actual role of the enzyme structure on the enzyme activity, are also of some methodological interest since they offer a further computational perspective for including the electronic degrees of freedom into the modeling of rather complex molecular systems.

In this paper we extend the perturbed matrix method by explicitly including the nuclear degrees of freedom, in order to treat quantum vibrational states in a perturbed molecule. In a previous paper we showed how to include, in a simple way, nuclear degrees of freedom for the calculation of molecular polarizability. In the present work we extend and generalize this approach to model vibroelectronic transitions, requiring a more sophisticated treatment.

The electronic properties of peridinin (Per) are investigated using density functional theory (DFT) with a time dependent (TD) treatment for transitions from the ground state to the low-lying electronic excited states. The use of a TD-DFT approach was first tested on the simpler beta-carotene molecule in order to see the performances of different functionals. It turns out from the present study that a TD-DFT approach provides a rather good qualitative picture for the electronic properties of this system for which the use of highly correlated ab initio methods with the needed prescriptions, for example, a large enough basis set and/or active space, is still prevented by its large dimension. The vertical transitions of Per obtained in vacuo using TD-DFT are in good agreement with experimental data available in a nonpolar solvent like n-hexane. Vertical energies obtained for the minimum energy structure of Per were also refined, spanning the Per in vacuo conformational space using ab initio molecular dynamics on its ground state hypersurface. These calculations also confirm the reliability of TD-DFT calculations at least on properties available from a dynamical sampling, that is, possible state inversion and partial explanation of bandwidth. Hence, combining these results with TD-DFT calculations, it is possible to better understand some spectroscopic properties of peridinin.

In this paper, the perturbed matrix method (PMM) is used in combination with basic statistical mechanics, to develop a general theoretical method to model chemical reactions and related molecular processes in complex systems, i.e., liquids, biochemical systems, macromolecules, etc. The main feature of this approach consists of the explicit treatment of the coupling between the reaction center and the fluctuating atomic-molecular environment, providing a rigorous statistical mechanical description of the chemical event. A special attention is dedicated to the approximations and assumptions necessary to use such a theoretical procedure in combination with simulation data.

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.

In this paper we describe in detail a general and efficient methodology, based on the perturbed matrix method and molecular dynamics simulations, to model UV-Vis absorption and emission spectra including vibrational and conformational effects. The basic approximation used is to consider all the chromophore atomic coordinates as semiclassical degrees of freedom, hence allowing the calculation of the complete spectral signal by using the electronic vertical transitions as obtained at each possible chromophore configuration, thus including the contributions of vibrations and conformational transitions into the spectrum. As shown for the model system utilized in this paper, solvated 1-phenyl-naphthalene, such an approximation can be rather accurate to reproduce the absorption and emission spectral line shape and properties when, as it often occurs, the vertical vibronic transition largely overlaps the other non-negligible vibronic transitions.

Assessment of the perturbed matrix method (PMM) ability in reproducing valence UV absorption spectra is carried out on two model systems: 1,2,3-triazine in methanol solution and uracil in water solution. Results show that even using the simplest definition of the quantum center, i.e. the portion of the system explicitly treated quantum mechanically, PMM provides rather good results. This paper further confirms the possibility of using PMM as a theoretical-computational tool, complementary to other methodologies, for addressing the electronic properties in molecular systems of high complexity.