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Excitation energy transfer (EET) determines the fate of sunlight energy absorbed by light-harvesting proteins in natural photosynthetic systems and photovoltaic cells. As previously reported (D. Kosenkov, J. Comput. Chem. 2016, 37(19), 1847), PyFREC software enables computation of electronic couplings between organic molecules with a molecular fragmentation approach. The present work reports implementation of direct fragmentation-based computation of the electronic couplings and EET rates in pigment-protein complexes within the Forster theory in PyFREC. The new feature enables assessment of EET pathways in a wide range of photosynthetic complexes, as well as artificial molecular architectures that include light-harvesting proteins or tagged fluorescent biomolecules. The developed methodology has been tested analyzing EET in the Fenna-Matthews-Olson (FMO) pigment-protein complex. The pathways of excitation energy transfer in FMO have been identified based on the kinetics studies. © 2017 Wiley Periodicals, Inc.

The effective fragment potential (EFP) approach, which can be described as a nonempirical polarizable force field, affords an accurate first-principles treatment of noncovalent interactions in extended systems. EFP can also describe the effect of the environment on the electronic properties (e.g., electronic excitation energies and ionization and electron-attachment energies) of a subsystem via the QM/EFP (quantum mechanics/EFP) polarizable embedding scheme. The original formulation of the method assumes that the system can be separated, without breaking covalent bonds, into closed-shell fragments, such as solvent and solute molecules. Here, we present an extension of the EFP method to macromolecules (mEFP). Several schemes for breaking a large molecule into small fragments described by EFP are presented and benchmarked. We focus on the electronic properties of molecules embedded into a protein environment and consider ionization, electron-attachment, and excitation energies (single-point calculations only). The model systems include chromophores of green and red fluorescent proteins surrounded by several nearby amino acid residues and phenolate bound to the T4 lysozyme. All mEFP schemes show robust performance and accurately reproduce the reference full QM calculations. For further applications of mEFP, we recommend either the scheme in which the peptide is cut along the Cα-C bond, giving rise to one fragment per amino acid, or the scheme with two cuts per amino acid, along the Cα-C and Cα-N bonds. While using these fragmentation schemes, the errors in solvatochromic shifts in electronic energy differences (excitation, ionization, electron detachment, or electron-attachment) do not exceed 0.1 eV. The largest error of QM/mEFP against QM/EFP (no fragmentation of the EFP part) is 0.06 eV (in most cases, the errors are 0.01-0.02 eV). The errors in the QM/molecular mechanics calculations with standard point charges can be as large as 0.3 eV.

The laboratory unit demonstrates a project-based approach to teaching physical chemistry laboratory where upper-division undergraduates carry out a transient-absorption experiment investigating the kinetics of cis–trans isomerization of N,N-dimethyl-4,4′-azodianiline. Students participate in modification of a standard flash-photolysis spectrometer by adding a temperature-controlled sample holder. The sample holder design is open-source and can be reproduced with the 3D-printing technology. Students build the experimental setup, perform the transient spectroscopy experiment, and analyze the obtained kinetics data to estimate the activation energy, enthalpy, entropy, and Gibbs free energy of cis–trans isomerization of N,N-dimethyl-4,4′-azodianiline.

This project is designed to improve physical chemistry and instrumental analysis laboratory courses for undergraduate students by employing as teaching tools novel technologies in electronics and data integration using the industrial Internet. The project carried out by upper-division undergraduates is described. Students are exposed to a complete process of building, calibrating, and programming an automatic titrator using an open-source microcontroller platform and standard pH probes, and integrating the instrument into the Internet. The approach is flexible and can be used to enable integration of various laboratory instruments (e.g., temperature, pressure, salinity probes, etc.) into the industrial Internet. The hardware and software are open-source, which makes further modification and development by the academic community possible.

A detailed description of the implementation of the effective fragment potential (EFP) method in the Q-CHEM electronic structure package is presented. The Q-CHEM implementation interfaces EFP with standard quantum mechanical (QM) methods such as Hartree–Fock, density functional theory, perturbation theory, and coupled-cluster methods, as well as with methods for electronically excited and open-shell species, for example, configuration interaction, time-dependent density functional theory, and equation-of-motion coupled-cluster models. In addition to the QM/EFP functionality, a ‘’ feature is also available (when the system is described by effective fragments only). To aid further developments of the EFP methodology, a detailed description of the Cþþ classes and EFP module’s workflow is presented. The EFP input structure and EFP job options are described. To assist setting up and performing EFP calculations, a collection of Perl service scripts is provided. The precomputed EFP parameters for standard fragments such as common solvents are stored in Q-CHEM’s auxiliary library; they can be easily invoked, similar to specifying standard basis sets. The instructions for generating user-defined EFP parameters are given. Fragments positions can be specified by their center of mass coordinates and Euler angles. The interface with the IQMOL and WEBMO software is also described. V C 2013 Wiley Periodicals, Inc.

Noncovalent interactions play an important role in the stabilization of biological molecules. The effective fragment potential (EFP) is a computationally inexpensive ab initio-based method for modeling intermolecular interactions in noncovalently bound systems. The accuracy of EFP is benchmarked against the S22 and S66 data sets for noncovalent interactions [Jurečka, P.; Šponer, J.; Černý, J.; Hobza, P. Phys. Chem. Chem. Phys.2006, 8, 1985; Řezáč, J.; Riley, K. E.; Hobza, P. J. Chem. Theory Comput.2011, 7, 2427]. The mean unsigned error (MUE) of EFP interaction energies with respect to coupled-cluster singles, doubles, and perturbative triples in the complete basis set limit [CCSD(T)/CBS] is 0.9 and 0.6 kcal/mol for S22 and S66, respectively, which is similar to the MUE of MP2 and SCS-MP2 for the same data sets, but with a greatly reduced computational expense. Moreover, EFP outperforms classical force fields and popular DFT functionals such as B3LYP and PBE, while newer dispersion-corrected functionals provide a more accurate description of noncovalent interactions. Comparison of EFP energy components with the symmetry-adapted perturbation theory (SAPT) energies for the S22 data set shows that the main source of errors in EFP comes from Coulomb and polarization terms and provides a valuable benchmark for further improvements in the accuracy of EFP and force fields in general.

The viability of pyrite-pulled metabolism in the ‘iron-sulfur world’ theory was assessed using a simple model of iron–nickel sulfide (Fe–Ni–S) surface and data obtained from quantum chemical calculations. We have investigated how the individual reactions in the carbon fixation cycle (carboxylic acids formation) on an Fe–Ni–S surface could have operated to produce carboxylic acids from carbon oxide and water. The proposed model cycle reveals how the individual reactions might have functioned and provides the thermodynamics of each step of the proposed pathway. The feasibility of individual reactions, as well the whole cycle was considered. The reaction of acetic acid production from CH3SH and CO on an Fe–Ni sulfide surface was revealed to be endergonic with a few partial steps having positive Gibbs free energy. On the other hand, the pyrite formation was found to be slightly exergonic. The significance of the catalytic activity of transition metal sulfides in generation of acetic acid was shown. The Gibbs free energy values indicate that the acetic acid synthesis is unfavorable to proceed on the studied Fe–Ni–S model under simulated conditions. The importance of these results in terms of a primordial chemistry on iron–nickel sulfide surfaces is discussed.

The implementation of the Effective Fragment Potential (EFP) method within the Q-Chem electronic structure package is presented. The EFP method is used to study non-covalent π – π and hydrogen-bonding interactions in DNA strands. Since EFP is a computationally inexpensive alternative to high-level ab initio calculations, it is possible to go beyond the dimers of nucleic acid bases and to investigate the asymptotic behavior of different components of the total interaction energy. The calculations demonstrated that the dispersion energy is a leading component in π-stacked oligomers of all sizes. Exchange-repulsion energy also plays an important role. The contribution of polarization is small in these systems, whereas the magnitude of electrostatics varies. Pairwise fragment interactions (i.e., the sum of dimer binding energies) were found to be a good approximation for the oligomer energy.

International audience; A novel kinetic approach based on ab initio calculated rate constants has been developed and implemented in the kTSim program. The proposed approach allows prediction of the distribution of reactant and product concentrations over time, based exclusively on computationally obtained rate constants. The newly developed methodology was used to simulate the process of evaporation and tautomerization of guanine and cytosine under thermal (T = 490 K, cytosine; T = 620 K, guanine) and laser (T = 1000 K, 24 ns laser pulse) desorption conditions. Both monomolecular and bimolecular mechanisms of the tautomerization were considered simultaneously. The rates of the reactions were estimated using the values of Gibbs free energies calculated at the MPWB1K/aug-cc-pVDZ level and specified in a kTSim input. We expect that the proposed approach can also be used for accurate kinetic simulation of a wide range of processes.

The tautomeric equilibrium and hydrogen bonding in nucleotide 2'-deoxyguanosine monophosphate that interacts with hydrated Mg2+ cation (4H2O.Mg[dGMP]) were studied at the MP2/cc-pVDZ//B3LYP/cc-pVDZ and B3LYP/aug-cc-pVTZ//B3LYP/cc-pVDZ levels of theory. The Mg2+ ion forms two inner-shell contacts with the nucleotide, similar to small phosphorylated molecules under physiological conditions. The presence of the phosphate group and the hydrated magnesium cation leads to a change in guanine tautomeric equilibrium of 4H2O.Mg[dGMP] in comparison to free guanine. The influence of the phosphate group and the magnesium cation on tautomeric equilibrium is larger in the anti conformation where the P=O--Mg and Mg--N7 coordinate bonds are formed. The canonical oxo form of guanine is more stable (by 6-8 kcal/mol) than the O6-hydroxo form in anti conformation. Thus, the interaction with Mg2+ ion is capable of further suppressing the likelihood of a spontaneous transient formation of the rare tautomer. In the syn conformation of 4H2O.Mg[dGMP], the interaction of the guanine nucleobase with the phosphate group and the magnesium cation is not as strong as in the anti conformation, and the relative stability of guanine tautomers is close to those in free guanine.

Naphthalene diimide ligands have the potential to stabilize human telomeric G-quadruplex DNA via noncovalent interactions. Stabilization of G-quadruplex high order structures has become an important strategy to develop novel anticancer therapeutics. In this study four naphthalene diimide based ligands were analyzed in order to elucidate the principal factors determining contributions to G-quadruplex-ligand binding. Three possible modes of binding and their respective Gibbs free energies for two naphthalene diimide based di-N-alkylpyridinium substituted ligands have been determined using a molecular docking technique and compared to experimental results. The structures obtained from the molecular docking calculations, were analyzed using the ab initio based fragment molecular orbital (FMO) method in order to determine the major enthalpic contributions to the binding and types of interactions between the ligand and specific residues of the G-quadruplex. A computational methodology for the efficient and inexpensive ligand optimization as compared to fully ab initio methods based on the estimation of binding affinities of the naphthalene diimide derived ligands to G-quadruplex is proposed.

International audience; A summary of the technical advances that are incorporated in the fourth major release of the Q-Chem quantum chemistry program is provided, covering approximately the last seven years. These include developments in density functional theory methods and algorithms, nuclear magnetic resonance (NMR) property evaluation, coupled cluster and perturbation theories, methods for electronically excited and open-shell species, tools for treating extended environments, algorithms for walking on potential surfaces, analysis tools, energy and electron transfer modelling, parallel computing capabilities, and graphical user interfaces. In addition, a selection of example case studies that illustrate these capabilities is given. These include extensive benchmarks of the comparative accuracy of modern density functionals for bonded and non-bonded interactions, tests of attenuated second order Moller-Plesset (MP2) methods for intermolecular interactions, a variety of parallel performance benchmarks, and tests of the accuracy of implicit solvation models. Some specific chemical examples include calculations on the strongly correlated Cr-2 dimer, exploring zeolite-catalysed ethane dehydrogenation, energy decomposition analysis of a charged ter-molecular complex arising from glycerol photoionisation, and natural transition orbitals for a Frenkel exciton state in a nine-unit model of a self-assembling nanotube.

A detailed description of the implementation of the effective fragment potential (EFP) method in the Q-CHEM electronic structure package is presented. The Q-CHEM implementation interfaces EFP with standard quantum mechanical (QM) methods such as Hartree-Fock, density functional theory, perturbation theory, and coupled-cluster methods, as well as with methods for electronically excited and open-shell species, for example, configuration interaction, time-dependent density functional theory, and equation-of-motion coupled-cluster models. In addition to the QM/EFP functionality, a "fragment-only" feature is also available (when the system is described by effective fragments only). To aid further developments of the EFP methodology, a detailed description of the C++ classes and EFP module's workflow is presented. The EFP input structure and EFP job options are described. To assist setting up and performing EFP calculations, a collection of Perl service scripts is provided. The precomputed EFP parameters for standard fragments such as common solvents are stored in Q-CHEM's auxiliary library; they can be easily invoked, similar to specifying standard basis sets. The instructions for generating user-defined EFP parameters are given. Fragments positions can be specified by their center of mass coordinates and Euler angles. The interface with the IQMOL and WEBMO software is also described.

Members of the green fluorescent protein (GFP) family form chromophores by modifications of three internal amino acid residues. Previously, many key characteristics of chromophores were studied using model compounds. However, no studies of intermolecular excited-state proton transfer (ESPT) with GFP-like synthetic chromophores have been performed because they either are nonfluorescent or lack an ionizable OH group. In this paper we report the synthesis and photochemical study of two highly fluorescent GFP chromophore analogues: p-HOBDI-BF2 and p-HOPyDI:Zn. Among known fluorescent compounds, p-HOBDI-BF(2) is the closest analogue of the native GFP chromophore. These irrreversibly (p-HOBDI-BF(2)) and reversibly (p-HOPyDI:Zn) locked compounds are the first examples of fully planar GFP chromophores, in which photoisomerization-induced deactivation is suppressed and protolytic photodissociation is observed. The photophysical behavior of p-HOBDI-BF2 and p-HOPyDI:Zn (excited state pK(a)'s, solvatochromism, kinetics, and thermodynamics of proton transfer) reveals their high photoacidity, which makes them good models of intermolecular ESPT in fluorescent proteins. Moreover, p-HOPyDI:Zn is a first example of "super" photoacidity in metal-organic complexes.

The single-conformation spectroscopy of two model γ-peptides has been studied under jet-cooled conditions in the gas phase. The methyl-capped triamides, Ac-γ(2)-hPhe-γ(2)-hAla-NHMe and Ac-γ(2)-hAla-γ(2)-hPhe-NHMe, were probed by resonant two-photon ionization (R2PI) and resonant ion-dip infrared (RIDIR) spectroscopies. Four conformers of Ac-γ(2)-hPhe-γ(2)-hAla-NHMe and three of Ac-γ(2)-hAla-γ(2)-hPhe-NHMe were observed and spectroscopically interrogated. On the basis of comparison with the predictions of density functional theory calculations employing a dispersion-corrected functional (ωB97X-D/6-311++G(d,p)), all seven conformers have been assigned to particular conformational families. The preference for formation of nine-membered rings (C9) observed in a previous study [James, W. H., III et al., J. Am. Chem. Soc. 2009, 131, 14243] of the smaller analog, Ac-γ(2)-hPhe-NHMe, carries over to these triamides, with four of the seven conformers forming C9/C9 sequential double-ring structures, and one conformer a C9/C14 bifurcated double ring. The remaining two conformers form C7/C7/C14 H-bonded cycles involving all three amide NH groups, unprecedented in other peptides and peptidomimetics. The amide groups in these structures form a H-bonded triangle with the two trimethylene bridges forming loops above and below the molecule's midsection. The structure is a natural extension of amide stacking, with the two terminal amides blocked from forming the amide tristack by formation of the C14 H-bond. Pair interaction energy decomposition analysis based on the fragment molecular orbital method (FMO-PIEDA) is used to determine the nonbonded contributions to the stabilization of these conformers. Natural bond orbital (NBO) analysis identifies amide stacking with a pair of n → π* interactions between the nitrogen lone pairs and π* orbitals on the carbonyl of the opposing amide groups.

Solvatochromic shifts of the electronic states of a chromophore can be used as a measure of solute-solvent interactions. The shifts of the electronic states of a model organic chromophore, p-nitroaniline (pNA), embedded in solvents with different polarities (water, 1,4-dioxane, and cyclohexane) are studied using a hybrid quantum mechanics/molecular-mechanics-type technique in which the chromophore is described by the configuration interaction singles with perturbative doubles (CIS(D)) method while the solvent is treated by the effective fragment potential (EFP) method. This newly developed CIS(D)/EFP scheme includes the quantum-mechanical coupling of the Coulomb and polarization terms; however, short-range dispersion and exchange-repulsion terms of EFP are not included in the quantum Hamiltonian. The CIS(D)/EFP model is benchmarked against the more accurate equation of motion coupled cluster with singles and doubles (EOM-CCSD)/EFP method on a set of small pNA-water clusters. CIS(D)/EFP accurately predicts the red solvatochromic shift of the charge-transfer π → π* state of pNA in polar water. The shift is underestimated in less polar dioxane and cyclohexane probably because of the omission of the explicit quantum-mechanical treatment of the short-range terms. Different solvation of singlet and triplet states of pNA results in different probabilities of intersystem crossing (ISC) and internal conversion (IC) pathways of energy relaxation in solvents of different polarity. Computed singlet-triplet splittings in water and dioxane qualitatively explain the active ISC channel in dioxane and predict almost no conversion to the triplet manifold in water, in agreement with experimental findings.

Combined experimental and theoretical studies have been carried out to investigate the transformations of the epoxyimides of norbornane into heterocyclic compounds. We established that interaction of the aryl-substituted epoxyimides of norbornane with sodium ethoxide results in the formation of new heterocyclic compounds in preparatively useful yields and with complete regioselectivity. The reactions of epoxyimides, containing aryl electron-donor substituents, result in the formation of endo-9-carbamoyl-exo-2-hydroxy-5-oxo-4-oxatricyclo[4.2.1.0(3,7)]nonanes, while in the case of the absence of an aryl electron-donor group or the presence of aryl electron-withdrawing group in the epoxyimide, exo-2-hydroxy-5-oxo-4-azatricyclo[4.2.1.0(3,7)]nonan-endo-9-carboxylic acids were obtained as products of the ethanolysis reaction. Unexpectedly, the ethanolysis of alkyl-substituted epoxyimides leads to dihydroxyimide formation as the major product. In order to understand the vital role of the imide substituent, a systematic theoretical DFT study at the PCM/B3LYP/6-31+G(d) level was carried out. We found that substituents at the nitrogen atom of epoxyimides exerted remarkable effects on the regioselectivity in the ethanolysis reaction, based on the solvent effects and intramolecular electronic interactions. Particularly, the preference for the formation of dihydroxyimides over heterocyclic systems for alkyl derivatives might be explained by kinetic stability of the formed acetal intermediate over the competitive epoxyamido acid intermediate. The above results provide a convenient and efficient method for predicting the structures of heterocyclic systems formed under basic ethanol conditions depending on the substituent on the nitrogen atom of the norbornane epoxyimides.

The kinetics of chemical reactions characterizes the rates of chemical processes, i.e. distribution of all reactants, intermediates and products over time. This information is of vital importance for all areas of chemistry: chemical technology to control organic or inorganic syntheses, chemical construction of nanomaterials, as well as for the investigation of biochemical processes. The chemical kinetics data provide a possibility to investigate the effect of different chemical, physical and environmental factors on the rate of a reaction, final products and by-products distribution, and even the direction of a chemical process. In the first part of the chapter the general introduction to the kinetics of chemical reactions is given. The classical kinetics of chemical reactions uses the outcome from experimental measurement of reaction rates. However, currently available reliable computational ab initio methods provide an alternative efficient way for estimation of the rate constants even for stepwise and multidirectional reactions. Another benefit of the computational investigations is the possibility to simulate a wide range of processes with duration from picoseconds to hours, days, or even for much longer time scales. Contemporary ab initio methods have been used for estimation and prediction of reaction rates for a number of different chemical reactions. Until recently most of the theoretical studies on kinetic parameters have not been extended beyond the calculations of the rate constants of chemical reactions. In the present review we describe the simulation of the chemical kinetics of proton transfer (tautomerization) in nucleic acid bases and their complexes with metal ions, also in the presence of water molecules. The considered models are based on the ab initio calculated rate constants of chemical reactions. Then, such predicted rate constants are used for further kinetic simulations. Biological consequences of investigated processes are also discussed.

The naturally occurring modified nucleotide queuosine 5'-monophosphate (QMP) related to biochemical regulatory pathways in the cell was investigated using quantum chemical approaches. The relative stability of biologically relevant conformations of QMP in solvent under a pH change was predicted at the BVP86/TZVP and MP2/TZVP levels of theory. Hydrogen bonding in QMP was studied using Bader's approach. The acidity constants of QMP were estimated using the COSMO-RS theory. It has been found that the neutral and anionic forms of QMP are the most stable in the physiological pH range. These forms correspond to the anti/north conformation and exist as zwitterionic tautomers having a negatively charged phosphate group (-1 for neutral and -2 for anionic) and a positively charged secondary amine group in the side chain. It was also found that QMP possesses the syn conformation in the cationic state at pH < 5.0 and undergoes syn to anti conformation transition when the pH increases, remaining in the anti conformation at the higher pH values. The marker IR bands specific for the anionic and neutral QMP forms in the 2300-2700 cm(-1) region were assigned to H-bonded NH groups of the QMP side chain. The bands between 800 and 1300 cm(-1) of the "fingerprint" (400-1500 cm(-1)) region were assigned to the vibrations of the ribose ring, the phosphate group and the side chain of QMP. The predicted IR spectra can be useful for the assignment of vibration bands in the experiential spectra of QMP or identification of the QMP forms. The revealed peculiarities of the QMP conformation sensitivity to a pH change as well as additional formed H-bonds could be responsible for specific nucleotide interactions with enzymes.

High-level ab initio predictions of the tautomerization equilibrium and rate constants of water-assisted proton transfer of 1-methyl-cytosine (MeC) to its MeC* imino tautomeric form in the presence of up to two water molecules (W) and the Na(+) cation were carried out. The calculated energy values were used to obtain the thermodynamic parameters and equilibrium concentration of MeC, its rare tautomer, and their complexes with up to two water molecules and the Na (+) cation. The rate constants for the tautomerization were obtained by using the instanton approach (a quasiclassical method based on the least-action principle). Hydration of MeC by one water molecule leads to an increase of the concentration of the MeC* tautomer in the equilibrium mixture and a decrease of the barrier of the MeC* formation (to 15.6 kcal/mol). If the Na(+) cation is present, the tautomeric form is much less favored, and the tautomerization barrier increases to 25.2 kcal/mol. It was found that MeC monohydrate has both the highest equilibrium (2.9 x 10(-2)) and rate (7.9 x 10(5) s(-1)) constants of tautomerization in comparison to the MeC*NaW and MeC*Na2W complexes containing the Na(+) cation. Moreover, this study also allows one to estimate the concentration of MeC present in the cell during DNA synthesis as the unwanted tautomer, which in forming a mismatched base pair can cause spontaneous point mutations. Kinetic simulations have demonstrated that the low values of equilibrium (10(-14)-10(-13)) and rate constants (10(-17)-10(-16) s(-1)) of tautomerization make contribution of the MeC*Na(+)W and MeC*Na(+)2W complexes to the point mutations in DNA unlikely. In contrast to these Na(+) complexes, MeC*W can reach an equilibrium concentration of 2.9 x 10(-2) within 10(-7) s; thus, it can increase the probability of the point mutations.

1,5-Dihydrodiimidazo[4,5-b:4′5′e]pyrazine, 1H-imidazo[4,5-b]pyrazine, and 1H-imidazole were considered as possible products of 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane (CL-20) photodecomposition. Since we took as a reference the product obtained after CL-20 irradiation in methanol solution, the nature of intermolecular bonds between heterocycles under study and methanol molecules was analyzed in detail. Existing hydrogen bonds were found to be quite strong, so dependence of calculations results on an influence of solvent was taken into account using both the polarizable continuum model (PCM) and the supermolecular approach. Electronic spectra of 1,5-dihydrodiimidazo[4,5-b:4′5′e]pyrazine, 1H-imidazo[4,5-b]pyrazine and 1H-imidazole were simulated using time dependent density functional theory (TD-DFT) and single-excitation configuration interaction (CIS) method. We observed that TD-DFT excitation energies are lower if compared to corresponding values obtained by the CIS method. Results of calculations with PCM and the supermolecular approach are very close. It was found that differences between calculated gas phase excitation energies and those values obtained by applying solvent models increases when the number of conjugated bonds in a molecule increases. Oscillator strengths of UV bands of the considered molecules are higher in the gas phase than in modeled methanol solutions. We found that the predicted spectrum of 1H-imidazole is in close agreement with the experimental UV spectrum of the CL-20 photolysis product.

The use of the method of enhancement of infrared absorption by rough metallic surface (surface enhanced infrared absorption — SEIRA) allows one to increase the probability of infrared transitions and to reveal a series of spectral manifestations of structural features of biological molecules. We analyse various experimental techniques that give the possibility to achieve enhancement in the infrared (IR) spectra. We studied the applicability of the SEIRA techniques for conformational analysis of nucleic acids and proteins (bovine serum albumin — BSA) on gold substrate of 200–500 A thickness. Under the conditions of our experiment and according to literature data, there was observed enhancement factor equalled to 3...20 for vibrations of various molecular groups. Concentration of BSA solution and thickness of the protein film on gold substrate influence the conformational composition. Conformational state of protein in solution plays a key role after its precipitation on gold substrate. Different roughness of gold surface leads to changes in enhancement factor. Peculiarity of another optical amplifier, namely, colloidal gold that effectively used for enhancement of signal in IR absorption and Raman scattering, have been studied. The structural features of DNA — colloidal gold and BSA — colloidal gold system that obtained in SEIRA and SPR (surface plasmon resonance) experiment are discussed. Atom forth microscopy (AFM) technique was applied to test the roughness of the metal surface. The IR experimental evidence for enhancement of the vibrations of residual graphite on the surface of carbon nanotubes is presented. We made an attempt to model the factor of enhancement of electrical field and their frequency dependence for different metal surfaces and obtained that silver, gold and copper are the best.

Conformation analysis of mutated DNA-bacteriophages (PLys-23, P23-2, P47- the numbers have been assigned by T. Pererva) induced by MS2 virus incorporated in Ecoli AB 259 Hfr 3000 has been done. Surface enhanced infrared absorption (SEIRA) spectroscopy and principal component analysis has been applied for solving this problem. The nucleic acids isolated from the mutated phages had a form of double stranded DNA with different modifications. The nucleic acid from phage P47 was undergone the structural rearrangement in the most degree. The shape and position ofthe fine structure of the Phosphate asymmetrical band at 1071cm-1 as well as the stretching OH vibration at 3370-3390 cm-1 has indicated to the appearance ofadditional OH-groups. The Z-form feature has been found in the base vibration region (1694 cm-1) and the sugar region (932 cm-1). A supposition about modification of structure of DNA by Z-fragments for P47 phage has been proposed. The P23-2 and PLys-23 phages have showed the numerous minor structural changes also. On the basis of SEIRA spectra we have determined the characteristic parameters of the marker bands of nucleic acid used for construction of principal components. Contribution of different spectral parameters of nucleic acids to principal components has been estimated.© (2004) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.