Non-adiabatic direct quantum dynamics using force fields: Toward solvation.

Quantum dynamics simulations are becoming a powerful tool for understanding photo-excited molecules. Their poor scaling, however, means that it is hard to study molecules with more than a few atoms accurately, and a major challenge at the moment is the inclusion of the molecular environment. Here, we present a proof of principle for a way to break the two bottlenecks preventing large but accurate simulations. First, the problem of providing the potential energy surfaces for a general system is addressed by parameterizing a standard force field to reproduce the potential surfaces of the molecule's excited-states, including the all-important vibronic coupling. While not shown here, this would trivially enable the use of an explicit solvent. Second, to help the scaling of the nuclear dynamics propagation, a hierarchy of approximations is introduced to the variational multi-configurational Gaussian method that retains the variational quantum wavepacket description of the key quantum degrees of freedom and uses classical trajectories for the remaining in a quantum mechanics/molecular mechanics like approach. The method is referred to as force field quantum dynamics (FF-QD), and a two-state ππ*/nπ* model of uracil, excited to its lowest bright ππ* state, is used as a test case.

Photophysics of Deoxycytidine and 5-Methyldeoxycytidine in Solution: A Comprehensive Picture by Quantum Mechanical Calculations and Femtosecond Fluorescence Spectroscopy.

The study concerns the relaxation of electronic excited states of the DNA nucleoside deoxycytidine (dCyd) and its methylated analogue 5-methyldeoxycytidine (5mdCyd), known to be involved in the formation of UV-induced lesions of the genetic code. Due to the existence of four closely lying and potentially coupled excited states, the deactivation pathways in these systems are particularly complex and have not been assessed so far. Here, we provide a complete mechanistic picture of the excited state relaxation of dCyd/5mdCyd in three solvents-water, acetonitrile, and tetrahydrofuran-by combining femtosecond fluorescence experiments, addressing the effect of solvent proticity on the relaxation dynamics of dCyd and 5mdCyd for the first time, and two complementary quantum mechanical approaches (CASPT2/MM and PCM/TD-CAM-B3LYP). The lowest energy ππ* state is responsible for the sub-picosecond lifetime observed for dCyd in all the solvents. In addition, computed excited state absorption and transient IR spectra allow one, for the first time, to assign the tens of picoseconds time constant, reported previously, to a dark state (nOπ*) involving the carbonyl lone pair. A second low-lying dark state, involving the nitrogen lone pair (nNπ*), does significantly participate in the excited state dynamics. The 267 nm excitation of dCyd leads to a non-negligible population of the second bright ππ* state, which affects the dynamics, acting mainly as a "doorway" state for the nOπ* state. The solvent plays a key role governing the interplay between the different excited states; unexpectedly, water favors population of the dark states. In the case of 5mdCyd, an energy barrier present on the main nonradiative decay route explains the 6-fold lengthening of the excited state lifetime compared to that of dCyd, observed for all the examined solvents. Moreover, C5-methylation destabilizes both nOπ* and nNπ* dark states, thus preventing them from being populated.

Optical absorption and magnetic circular dichroism spectra of thiouracils: a quantum mechanical study in solution.

The excited electronic states of 2-thiouracil, 4-thiouracil and 2,4-dithiouracil, the analogues of uracil where the carbonyl oxygens are substituted by sulphur atoms, have been investigated by computing the magnetic circular dichroism (MCD) and one-photon absorption (OPA) spectra at the time-dependent density functional theory level. Special attention has been paid to solvent effects, included by a mixed discrete/continuum model, and to determining how our results depend on the adopted DFT functional (CAM-B3LYP and B3LYP). Whereas including solvent effects does not dramatically impact the MCD and OPA spectra, though improving the agreement with the experimental spectra, the performances of CAM-B3LYP and B3LYP are remarkably different. CAM-B3LYP captures well the effect of thionation on the uracil excited states and provides spectra in good agreement with the experiments, whereas B3LYP shows some deficiency in describing 2-TU and 2,4-DTU spectra, despite being more accurate than CAM-B3LYP for 4-TU.

Excited states decay of the A-T DNA: A PCM/TD-DFT study in aqueous solution of the (9-methyl-adenine)(2).(1-methyl-thymine)(2) stacked tetramer.

By exploiting some of the most recent advances in the quantum mechanical methods, we have been able to analyze the behavior of the lowest energy excited states of A-T B-DNA using a realistic model, namely a double strand tetramer formed by two thymine-adenine stacked pairs in aqueous solution. The equilibrium structure of the lowest energy bright and dark excited states has been determined and their main properties disclosed. On this ground, our study provides a detailed atomistic picture of the excited state decay and of the emission process, and it highlights the specific roles of base stacking and pairing. While absorption involves excited states delocalized over different stacked bases, emission mainly takes place from individual monomers and it is dominated by thymine bases. We show that fast "monomer-like" excited state decay routes are operative also in the double strand. On the other hand, the long living components of the excited state population of (dA).(dT) oligomers correspond to a dark excimer produced by intermonomer charge transfer between two stacked adenine bases, whereas adenine-thymine proton transfer plays a minor role in the excited state decay.

Photoinduced dynamics of guanosine monophosphate in water from broad-band transient absorption spectroscopy and quantum-chemical calculations.

Guanosine monophosphate (GMP) in aqueous solutions has been studied with femtosecond broad-band transient absorption spectroscopy and by quantum-mechanical calculations. The sample was excited at 267 or 287 nm and probed between 270 and 1000 nm with 100 fs resolution, for various pH values between 2 and 7. At pH 2, when the guanine ring is ground-state protonated (GMPH(+)), we observe isosbestic behavior indicating state-to-state relaxation. The relaxation is biexponential, tau(1) = 0.4 ps, tau(2) = 2.2 ps, and followed by slower internal conversion with tau(3) = 167 ps. For nonprotonated GMP in the pH range 7-4, we find biexponential decay in the region 400-900 nm (tau(1) = 0.22 ps, tau(2) = 0.9 ps), whereas, between 270 and 400 nm, the behavior is triexponential with one growing, tau(1) = 0.25 ps, and two decaying, tau(2) = 1.0 ps, tau(3) = 2.5 ps, components. The excited-state evolution is interpreted with the help of quantum-chemical calculations, performed at the time-dependent PBE0 level accounting for bulk solvent effects and specific solvation. The computed dynamics involves L(a) and L(b) bright excited states, whereas the n(0)pi* and pisigma* dark excited states play a minor role. Independent of the pH, the photoinduced evolution involves ultrafast L(b)-->L(a) conversion (tau(ba) << 100 fs) and exhibits the presence of a wide planar plateau on L(a). For neutral GMP a barrierless path connects this region to a conical intersection (CI) with the ground state, giving an account of the ultrafast decay of this species. For protonated GMPH(+) the system evolves into a stable minimum L(a min) characterized by out-of-plane displacement of NH and CH groups, which explains the longer (167 ps) fluorescence lifetime.

Computing the Absorption and Emission Spectra of 5-Methylcytidine in Different Solvents: A Test-Case for Different Solvation Models.

The optical spectra of 5-methylcytidine in three different solvents (tetrahydrofuran, acetonitrile, and water) is measured, showing that both the absorption and the emission maximum in water are significantly blue-shifted (0.08 eV). The absorption spectra are simulated based on CAM-B3LYP/TD-DFT calculations but including solvent effects with three different approaches: (i) a hybrid implicit/explicit full quantum mechanical approach, (ii) a mixed QM/MM static approach, and (iii) a QM/MM method exploiting the structures issuing from molecular dynamics classical simulations. Ab-initio Molecular dynamics simulations based on CAM-B3LYP functionals have also been performed. The adopted approaches all reproduce the main features of the experimental spectra, giving insights on the chemical-physical effects responsible for the solvent shifts in the spectra of 5-methylcytidine and providing the basis for discussing advantages and limitations of the adopted solvation models.

Serological and clinical markers of autoimmune disease in HCV-infected subjects with different disease conditions.

OBJECTIVE: To investigate whether the serological markers of autoimmunity and the clinical features of autoimmune disease which occur in hepatitis C virus (HCV)-infected subjects are correlated to each other and/or to the clinical pattern of the disease. METHODS: Seventeen symptom-free, anti-HCV antibody positive subjects, 17 patients with chronic hepatitis C, 21 patients with mixed cryoglobulinemia (MC), and as controls 17 anti-HCV negative patients with dyspepsia were enrolled in a prospective study. A patient history, clinical examination, self-administered questionnaire and laboratory investigations (hepatic enzyme levels, serum HCV-RNA and anti-HCV antibody testing, and serum autoantibody profile) were performed to detect liver and/or autoimmune disease. RESULTS: Serological markers of autoimmunity and clinical findings of autoimmune disease were found to be more frequent in the HCV-infected patients considered as a whole than in controls. However, rheumatoid factor and clinical findings of autoimmune disease were more frequent in MC patients, while anti-smooth muscle antibodies not linked to symptoms or signs of autoimmune disease were detected in all groups of HCV-infected individuals, including healthy carriers and subjects who had recovered from a previous HCV infection. CONCLUSION: Anti-smooth muscle antibodies, a serological marker of autoimmunity, are detectable in HCV-infected subjects whatever their clinical status. Clinical findings of autoimmune disease prevalently occur in patients with mixed cryoglobulinemia.

Isolated autoimmune response: definition, analysis of the prevalence in an outpatient rheumatology clinic, relationship to pre-clinical autoimmune disease and infections by hepatotropic viruses.

OBJECTIVE: To define the clinical significance of non-organ specific autoantibody positivity in patients in whom routine clinical and laboratory examinations did not detect any disease that might have caused the serological finding. METHODS: Out of 1,120 patients consecutively admitted to an outpatient rheumatology clinic, 28 were referred for the evaluation of an autoantibody positivity unrelated to the clinical status. These patients and 28 sex- and age-matched controls underwent a specific work-up with the aim of detecting any underlying infection or autoimmune disease. RESULTS: Eight of the 28 patients (28.5%) were found to be affected by a previously undetected disease: 3 chronic hepatitis C, 3 Sjögren's syndrome, and 2 autoimmune thyroiditis. The remaining 20 did not show any autoimmune or hepatic disease, although 4 of them showed active infection by HBV (n = 1) or HGV (n = 3) and 15 had had a previous infection by hepatotropic viruses (HBV, CMV or EBV). After a follow-up lasting 6-54 months, none of the last 20 patients developed any autoimmune or chronic hepatic disease. CONCLUSIONS: A diagnostic work-up is necessary in patients presenting with unexpected autoantibody positivity in order to detect an underlying pre-clinical autoimmune disease and/or unexpected hepatic infection. Patients in whom such a work-up fails to point out any condition should be further followed in order to make an early diagnosis of autoimmune disease.

Vibrationally Resolved Absorption and Emission Spectra of Dithiophene in the Gas Phase and in Solution by First-Principle Quantum Mechanical Calculations.

The absorption and emission spectra of dithiophene have been computed in different environments (gas phase, apolar, and polar solvents) and at different temperatures, including Duschinsky, temperature and solvent effects at full ab initio level, and considering the anharmonicity of the double well potential associated with the inter-ring torsional mode. The computed spectra are in very good agreement with the experimental ones, allowing for a complete assignment of the main vibrational features. Five different density functionals (BLYP, B3LYP, CAM-B3LYP, BHLYP, and PBE0) have been tested, and CAM-B3LYP and PBE0 are the most accurate.

Influence of base stacking on excited-state behavior of polyadenine in water, based on time-dependent density functional calculations.

A thorough study of the excited-state properties of the stacked dimers and trimers of 9-methyladenine in B-DNA conformation has been performed in aqueous solution by using time-dependent density functional calculations and the solvent polarizable continuum model, and results were compared with experimental results on polyadenine oligomers. The effect of base stacking on the absorption and emission spectra is fully reproduced by our calculations. Although light absorption leads to a state (S(B)) delocalized over several nucleobases, excited-state geometry optimization indicates that S(B) subsequently evolves into a state in which the excitation is localized on a single base. Analysis of the excited-state potential energy surfaces shows that S(B) can easily decay into the lowest energy excited state, S(CT), which is a dark excimer produced by intermonomer charge transfer between two stacked bases. The subpicosecond features of the time-resolved experiments are interpreted in terms of ultrafast decay from S(B). After localization, two easy, radiationless decay channels are indeed open for S(B): (i) ground-state recovery, according to the same mechanisms proposed for isolated adenine and/or (ii) decay to S(CT). Our calculations suggest that the slowest part of the excited-state dynamics detected experimentally involves the S(CT) state.

A Theoretical Study on the Factors Influencing Cyanine Photoisomerization: The Case of Thiacyanine in Gas Phase and in Methanol.

The effects influencing cyanine photoisomerization on the S1 surface in the condensed phase have been investigated by an integrated quantum mechanical approach, focused mainly on 3,3'-diEt-2,2'-thiacyanine. After excitation, a barrierless motion, involving the torsion coupled to bond skeletal deformation, leads to a slightly nonplanar local C2 minimum, which we propose to be the fluorescent state. Crossed a barrier of ≈120 cm(-)(1), a steeper path drives to a more stable C1 minimum S1-Min, corresponding to a pseudoperpendicular twisted intramolecular charge transfer (TICT) state. CAS(6,6) optimization allows for locating the lowest energy S1/S0 conical intersection in the isomerization path which is reached from S1-Min by an increased asymmetry of the two rings and a marked pyramidalization at one N center. The S1 surface is rather flat in the Franck-Condon region and suggests that other paths can be competitive with the minimum energy one. The comparison among different cyanines shows how variation of the molecular scaffold and/or of its substituents modulate the dynamics of the photoisomerization. All the indications coming from our computations are in line with and provide an explanation to the available experimental results.

Excited-state behavior of trans and cis isomers of stilbene and stiff stilbene: a TD-DFT study.

The first part of the isomerization path on the two lowest excited states of trans and cis isomers of stilbene and stiff stilbene is investigated by means of TD-PBE0 calculations in the gas phase and in heptane solution. Solvent effects are taken into account by the PCM model. The excited-state optimized structures and the computed absorption and emission frequencies are in good agreement with the available experimental results. In all of the examined compounds, the isomerization process before barrier crossing occurs on the HOMO --> LUMO bright state, whereas the role played by other single-excitation states appears negligible. The relative energy barriers on the isomerization paths are consistent with the experimental excited-state lifetimes, suggesting a unifying picture of the isomerization process in stilbene-like molecules.

Understanding the role of stereoelectronic effects in determining collagen stability. 1. A quantum mechanical study of proline, hydroxyproline, and fluoroproline dipeptide analogues in aqueous solution.

The importance of local (intraresidue) effects in determining the stability of the collagen triple helix has been investigated with special reference to the role played by hydroxyproline. To this end the dipeptide analogues of L-proline (ProDA), 4(R)-hydroxy-L-proline (HypDA), and 4(R)-fluoro-L-proline (FlpDA) have been studied by means of quantum mechanical ab initio calculations, taking into account solvent effects by the polarizable continuum model (PCM). Our results confirm that the relative stability of up puckerings of the pyrrolidine ring increases with the electronegativity of the 4(R) substituent (X), whereas down puckerings are favored by 4(S) electronegative substituents. Calculations on model compounds show that this effect is due to the interaction between vicinal C-H bonding and C-X antibonding orbitals. Electronegative substituents on the pyrrolidine ring affect cis-trans isomerism around the peptidic bond, with trans isomers stabilized by 4(R) substituents and cis isomers by 4(S) substituents. Also the hydrogen bonding power of the carbonyl moiety following the pyrrolidine ring is affected by 4(R) substituents, but this effect is tuned by the polarity of the embedding medium. Finally, up puckering favors smaller values of the backbone dihedrals phi and psi. All these results strongly support the proposal that the stability of triple helices containing fluorinated or hydroxylated prolines in Y positions is related to the necessity of having up puckerings in those positions.

Chromosome markers and karyology of selachians.

Among vertebrates, chondrichthyans exhibit peculiar karyotypes and total amount and composition of DNA very different from those of tetrapods and teleosteans. Selachians have relatively large genome sizes (more than 30 pg/N), which are inversely related to the fraction rich in adenine-thymine. Moreover, they show a high chromosome number (2n = 60-100), decreasing in the most specialized species. The karyotypes of Scyliorhinus stellaris, Torpedo ocellata, and T. marmorata have been investigated by several techniques in order to distinguish particular genome fractions along the chromosome arms. C-banding appears to be positive in most telomeric regions in Scyliorhinus and at the interstitial level in the two torpedo species. Studies with restriction enzymes (RE) have just been started in selachians, employing ALU I and HIND III in Scyliorhinus stellaris. The former digests the whole chromosome except the telomeric regions, revealing patterns similar to the C-bands. The latter cuts the chromosomes into several interstitial regions, producing G-bands. Other RE are being studied, which will allow identification in situ of qualitative differences in the various DNAs.

A plausible mechanism of electron transfer between quinones in photosynthetic reaction centers.

The mechanism of long-range electron transfer between the primary and the secondary quinone of photosynthetic reaction centers has been investigated, with particular attention on the role of the iron-histidine bridge. Computations suggest that in such a system, where the molecular subunits are packed together by H-bonds, a mobile electron, injected on one end of the chain, can be carried to the other end by switching the positions of the H-bonded hydrogens. Energy estimates would suggest that the proposed mechanism is plausible and worthy of further experimental investigations.

Chemical Composition of Two Exopolysaccharides from Bacillus thermoantarcticus.

The thermophilic bacterium Bacillus thermoantarcticus produces two exocellular polysaccharides (EPS 1 and EPS 2), which can be obtained from the supernatant of liquid cultures by cold-ethanol precipitation, in yields as high as 400 mg liter(sup-1). The EPS fraction was produced with all substrates tested, although a higher yield was obtained with mannose as the carbon and energy source. The EPS content was proportional to the total biomass. On a weight basis, EPS 1 and EPS 2 represented about 27 and 71%, respectively, of the total carbohydrate fraction. EPS 1 is a sulfate heteropolysaccharide containing mannose and glucose in a relative molar proportion of 1.0 and 0.7, respectively. EPS 2 is a sulfate homopolysaccharide containing mannose as the major component. The absolute configurations of hexoses were shown to be d for both EPSs. Nuclear magnetic resonance spectra confirmed the presence of (alpha)-d-mannose and (beta)-d-glucose in EPS 1 and only (alpha)-d-mannose in EPS 2. In addition, (sup1)H nuclear magnetic resonance analysis and chemical analysis indicated the presence of pyruvic acid in EPS 2.

Enzymatic synthesis of 2-beta-D-galactopyranosyloxy ethyl methacrylate (GalEMA) by the thermophilic archeon Sulfolobus solfataricus.

beta-Glycosidases catalyze the synthesis of glycosides when a nucleophilic acceptor other than water is present in the reaction medium. We describe the enzymatyc synthesis of 2-beta-D-galactopyranosyloxyethyl methacrylate (GalEMA) starting from 2-hydroxyethyl methacrylate (HEMA) and p-nitrophenyl-beta-D-galactopyranoside (pNPG) using a beta-glycosidase activity present in the thermophilic archaeon Sulfolobus solfataricus. This thermophilic enzyme catalyzes the transfer of the galactopyranosyl unit from pNPG to the HEMA hydroxyl group by the formation of a new beta-glycosidic bond. The conditions of the biocatalytic system have been optimized to obtain high yield of GalEMA. (c) 1996 John Wiley & Sons, Inc.

Structure and conformational behavior of biopolymers by density functional calculations employing periodic boundary conditions. I. The case of polyglycine, polyalanine, and poly-alpha-aminoisobutyric acid in vacuo.

Fully quantum mechanical calculations exploiting periodic boundary conditions (PBC) have been applied to the study of four different regular structures (alpha- and 3(10)-helix, fully extended and repeated gamma-turns) of the infinite polypeptides of glycine, alanine, and alpha-aminoisobutyric acid (Aib) in vacuo. alpha-Helix is predicted to be the most stable conformer for polyalanine and polyglycine, being stabilized over the 3(10)-helix mainly by more favorable dipole-dipole interactions. Contrary to previous suggestions, steric effects and hydrogen-bond strengths are comparable for both helix structures. 3(10)-Helix is preferred for poly-Aib, since in this case alpha-helix is strongly distorted due to unfavorable intrachain repulsions. Extended structures and repeated gamma-turns are much less stable than helix structures for all of the polypeptides examined, mainly due to the absence of favorable long-range interactions. The optimized geometries are in good agreement with the available experimental data and reveal a remarkable dependence on the nature of the residue forming the polypeptides; at the same time the electronic and structural parameters of each residue strongly depend on the secondary structure of the polypeptides.

Nucleophilic cyclopropane ring opening in duocarmycin SA derivatives by methanol under acid conditions: a quantum mechanical study in the gas-phase and in solution.

We present a quantum-mechanical study of the S(N)2 acid-catalyzed solvolysis with methanol of seven simplified duocarmycin SA (DNA alkylating agent) derivatives characterized by spirocyclic systems of increasing complexity, all containing the cyclopropyl/cyclohexadienone substrate. The reaction has been studied at the DFT-PBE0/6-31G(d) level in the gas phase and in methanol solution, using in the latter case the polarizable continuum model (PCM) to describe solvent effects. The results delivered by this computational protocol are in full agreement with the available experimental evidences and are not modified by extension of the basis set or by using a second-order many-body treatment (MP2) in place of DFT. This allows investigation of substituent effects in terms of structure/reactivity relationships and evaluation of the role of stereoelectronic effects. Furthermore, reactivity indices (hardness, electrophilicity) have been computed and shown to correlate well with activation energies. Together with their intrinsic interest, the details of the mechanism of the acid-catalyzed nucleophilic addition to the activated cyclopropane issuing from the present study pave the route for a deeper understanding of the molecular basis for the remarkable profile of the DNA-alkylation by DSA derivatives.

Antinuclear antibodies in first-degree relatives of patients with polymyositis-dermatomyositis: analysis of the relationship with HLA haplotypes.

Antinuclear antibodies (ANA), as detected by indirect immunofluorescence on HEp-2 cells, have been investigated in five spouses and 41 first-degree relatives of nine probands with polymyositis-dermatomyositis (PM-DM) and in 41 sex- and age-matched controls. ANA were detected in 12 out of the 41 first-degree relatives and in two controls (chi 2 = 6.97; P less than 0.01). HLA typing was done in four out of the nine families; in two of them only, ANA segregated with a haplotype. ANA positivity was not correlated either to sex or to age or to household contact. Our results show that ANA occur in a significant percentage of first-degree relatives of patients with PM-DM. The finding seems to be genetically conditioned.