Implementation of Nuclear Velocity Perturbation and Magnetic Field Perturbation Theory in CP2K and Their Application to Vibrational Circular Dichroism.

We present the implementation of nuclear velocity perturbation theory (NVPT), using a pioneering combination of atom-centered (velocity-dependent) Gaussian basis functions and plane waves in the CP2K package. The atomic polar tensors (APTs) and atomic axial tensors (AATs) are evaluated in the velocity representation using efficient density functional perturbation theory. The presence of nonlocal pseudopotentials, the representation of potentials on numerical integration grids, and effects arising from the basis functions being centered on the atoms have been considered in the implementation. The Magnetic Field Perturbation Theory (MFPT) using gauge-including atomic orbitals is implemented in the same code and compared to the NVPT. Our implementation is the first to compare both approaches (MFPT and NVPT) in the same code. The implementation has been verified via sum rules and by investigating the gauge origin dependence of the AATs for a set of small molecules, oxirane, and fluoro-oxirane. We also present vibrational circular dichroism spectra that are related to the APTs and AATs, applying both theories.

Betulinic Acid Decorated with Polar Groups and Blue Emitting BODIPY Dye: Synthesis, Cytotoxicity, Cell-Cycle Analysis and Anti-HIV Profiling.

Betulinic acid (BA) is a potent triterpene, which has shown promising potential in cancer and HIV-1 treatment. Here, we report a synthesis and biological evaluation of 17 new compounds, including BODIPY labelled analogues derived from BA. The analogues terminated by amino moiety showed increased cytotoxicity (e.g., BA had on CCRF-CEM IC50 > 50 µM, amine 3 IC50 0.21 and amine 14 IC50 0.29). The cell-cycle arrest was evaluated and did not show general features for all the tested compounds. A fluorescence microscopy study of six derivatives revealed that only 4 and 6 were detected in living cells. These compounds were colocalized with the endoplasmic reticulum and mitochondria, indicating possible targets in these organelles. The study of anti-HIV-1 activity showed that 8, 10, 16, 17 and 18 have had IC50i > 10 µM. Only completely processed p24 CA was identified in the viruses formed in the presence of compounds 4 and 12. In the cases of 2, 8, 9, 10, 16, 17 and 18, we identified not fully processed p24 CA and p25 CA-SP1 protein. This observation suggests a similar mechanism of inhibition as described for bevirimat.

Steroid Glycosides Hyrcanoside and Deglucohyrcanoside: On Isolation, Structural Identification, and Anticancer Activity.

Cardiac glycosides (CGs) represent a group of sundry compounds of natural origin. Most CGs are potent inhibitors of Na+/K+-ATPase, and some are routinely utilized in the treatment of various cardiac conditions. Biological activities of other lesser known CGs have not been fully explored yet. Interestingly, the anticancer potential of some CGs was revealed and thereby, some of these compounds are now being evaluated for drug repositioning. However, high systemic toxicity and low cancer cell selectivity of the clinically used CGs have severely limited their utilization in cancer treatment so far. Therefore, in this study, we have focused on two poorly described CGs: hyrcanoside and deglucohyrcanoside. We elaborated on their isolation, structural identification, and cytotoxicity evaluation in a panel of cancerous and noncancerous cell lines, and on their potential to induce cell cycle arrest in the G2/M phase. The activity of hyrcanoside and deglucohyrcanoside was compared to three other CGs: ouabain, digitoxin, and cymarin. Furthermore, by in silico modeling, interaction of these CGs with Na+/K+-ATPase was also studied. Hopefully, these compounds could serve not only as a research tool for Na+/K+-ATPase inhibition, but also as novel cancer therapeutics.

Large Scale Conversion of Trilobolide into the Payload of Mipsagargin: 8-O-(12-Aminododecanoyl)-8-O-Debutanoylthapsigargin.

In spite of the impressing cytotoxicity of thapsigargin (Tg), this compound cannot be used as a chemotherapeutic drug because of general toxicity, causing unacceptable side effects. Instead, a prodrug targeted towards tumors, mipsagargin, was brought into clinical trials. What substantially reduces the clinical potential is the limited access to Tg and its derivatives and cost-inefficient syntheses with unacceptably low yields. Laser trilobum, which contains a structurally related sesquiterpene lactone, trilobolide (Tb), is successfully cultivated. Here, we report scalable isolation of Tb from L. trilobum and a transformation of Tb to 8-O-(12-aminododecanoyl)-8-O-debutanoylthapsigargin in seven steps. The use of cultivated L. trilobum offers an unlimited source of the active principle in mipsagargin.

Missing Selectivity of Targeted 4ß-Phorbol Prodrugs Expected to be Potential Chemotherapeutics.

Targeting cytotoxic 4ß-phorbol esters toward cancer tissue was attempted by conjugating a 4ß-pborbol derivative with substrates for the proteases prostate-specific antigen (PSA) and prostate-specific membrane antigen (PSMA) expressed in cancer tissue. The hydrophilic peptide moiety was hypothesized to prevent penetration of the prodrugs into cells and prevent interaction with PKC. Cleavage of the peptide in cancer tumors was envisioned to release lipophilic cytotoxins, which subsequently penetrate into cancer cells. The 4ß-phorbol esters were prepared from 4ß-phorbol isolated from Croton tiglium seeds, while the peptides were prepared by solid-phase synthesis. Cellular assays revealed activation of PKC by the prodrugs and efficient killing of both peptidase positive as well as peptidase negative cells. Consequently no selectivity for enzyme expressing cells was found.

Semiclassical Approach to Photophysics Beyond Kasha's Rule and Vibronic Spectroscopy Beyond the Condon Approximation. The Case of Azulene.

Azulene is a prototypical molecule with an anomalous fluorescence from the second excited electronic state, thus violating Kasha's rule, and with an emission spectrum that cannot be understood within the Condon approximation. To better understand the photophysics and spectroscopy of azulene and other nonconventional molecules, we developed a systematic, general, and efficient computational approach combining the semiclassical dynamics of nuclei with ab initio electronic structure. First, to analyze the nonadiabatic effects, we complement the standard population dynamics by a rigorous measure of adiabaticity, estimated with the multiple-surface dephasing representation. Second, we propose a new semiclassical method for simulating non-Condon spectra, which combines the extended thawed Gaussian approximation with the efficient single-Hessian approach. S1 ← S0 and S2 ← S0 absorption and S2 → S0 emission spectra of azulene, recorded in a new set of experiments, agree very well with our calculations. We find that accuracy of the evaluated spectra requires the treatment of anharmonicity, Herzberg-Teller, and mode-mixing effects.

Stanazolol derived ELISA as a sensitive forensic tool for the detection of multiple 17α-methylated anabolics.

Two valuable forensic tools based on enzyme-linked immunoassays (ELISAs) for the analysis of 17α-methylated steroids were developed using haptens of stanazolol and its conjugates with biotin. Haptens containing terminal carboxylic group were conjugated to bovine serum albumin (BSA), rabbit serum albumin (RSA) or ovalbumin (OVA). Eight batches of antisera (RAbs) obtained by immunization of rabbits were tested in an indirect competitive ELISA system using immobilization of RSA conjugate (RSA/hapten) and competitor immobilization of the biotinylated conjugate (AB-ELISA) to avidin (avidin/hapten). The best results were achieved with the RAb 212 antibodies in RSA/ST-3 and avidin/ST-10 assembled variants. For the RSA/ST-3 system, an IC50 of 0.3 ng/mL and a detection limit of 0.02 ng/mL were measured. In case of avidin/ST-10 variant, IC50 was of 3.9 ng/mL and a detection limit of 0.57 ng/mL were obtained. The effect of solvent was tested as well as the stability of coated microtiter plates over four-month period. The cross-reactivity of the developed assays with other anabolic steroids was tested and high sensitivity towards 17α-methylated steroids was observed. RSA/ST-3 assay showed significant cross-reactivity with 17α-methyltestosterone (81.2%), oxymetholone (30.4%), methandienone (10.0%) and methyl dihydrotestosterone (7.7%). Similarly, in the avidin/ST-10 assay, 17α-methyltestosterone (34.5%), mestanolone (32.1%), oxymetholone (22.7%), methandienone (14.2%), 9-dehydromethyltestosterone (12.5%) and oxandrolone (1.2%) exhibited high cross-reactivity. The functionality of the developed systems was verified by the successful identification of a series of 17α-methylated anabolic steroids in a set of real samples including pharmaceutical preparations seized by the Police of the Czech Republic on the black market.

Phorbol Rearrangements.

An alternative procedure for isolation of 4ß-phorbol from seeds of Croton tiglium has been developed, and an artifact containing a furan ring formed by rearrangement of 12,13,20- O-triacylated phorbol derivatives into (6b S,7 R,8 R,8a S)-2-(hydroxymethyl)-5,7,9,9-tetramethyl-3,7,8,9,9a,9b-hexahydrocyclopropa[3',4']benzo[1',2':3,4]cyclohepta[1,2- b]furan-6b,8,8a-triol (8a) has been characterized. A mechanism involving an oxidative rearrangement and a decarboxylation for formation of the artifact is proposed.

Preparation of Enzyme-Activated Thapsigargin Prodrugs by Solid-Phase Synthesis.

Since cells in solid tumors divide less rapidly than cells in the bone marrow or cells of the immune system, mitotic inhibitors often cause severe side effects when used for treatment of diseases like prostate cancer and breast cancer. One approach to overcome this problem involves attempts at developing drugs based on general cytotoxins, like calicheamicin and thapsigargin, which kill cells at all phases of the cell cycle. However, such toxins can only be used when efficient targeting to the malignant tissue is possible. In the case of thapsigargin, selectivity for tumor-associated cells is achieved by conjugating the drug to a peptide that is only cleaved in the vicinity of tumors to release the cytotoxic drug or an analog with retained activity. Solid-phase synthesis protocols were developed for preparation of three already validated prodrugs of thapsigargin: one prodrug cleavable by human kallikrein 2, one prodrug cleavable by prostate-specific antigen, and one prodrug cleavable by prostate-specific membrane antigen.

Immunoassay for determination of trilobolide.

Trilobolide (Tb) is a pharmacologically interesting sesquiterpene lactone isolated from Laser trilobum (L.) Borkh. Structural relation to a sarco/endoplasmic reticulum Ca2+-ATPase inhibitor thapsigargin bring promising prospects for Tb to be used in the development of new anti-cancer drugs. As long as there are still unanswered questions regarding its investigation, a need for novel analytical tools emerge. Since immunoassays serve as one of powerful tools within the investigation of natural products, the development of indirect competitive enzyme-linked immunosorbent assay (ELISA) utilizing coating based on avidin-biotin technology is described. In our set-up of ELISA, newly synthesized biotinylated Tb served as immobilized competitor. Tb-carboxymethyloxime-bovine serum albumin (BSA) and Tb-succinoyl-BSA conjugates were used separately for immunization of rabbits. Two sets of polyclonal antibodies (RAbs) were obtained. Antibodies against Tb-succinoyl-BSA conjugate (RAb No. 206) were chosen as the best. Under optimized conditions, limit of detection and 50% intercept of our ELISA were 849pg/mL and 8.89ng/mL, respectively. The cross-reactivity (CR) was tested on 10 structurally related compounds and CR did not exceed 6.1%. The reproducibility of the system is expressed as intra- and inter-assay coefficients of variation (9.7% and 11.4%, respectively). Based on conducted experiments, we proposed the use of ELISA for quantification of Tb in complex biological matrices such as plant extracts. A method was applied to analyze three extracts obtained from different parts of L. trilobum. Data obtained were compared to those acquired by UHPLC-MS/MS. The concordance between the methods (103-87%) showed the ability of ELISA to quantify Tb.

Nonadiabatic effects in electronic and nuclear dynamics.

Due to their very nature, ultrafast phenomena are often accompanied by the occurrence of nonadiabatic effects. From a theoretical perspective, the treatment of nonadiabatic processes makes it necessary to go beyond the (quasi) static picture provided by the time-independent Schrödinger equation within the Born-Oppenheimer approximation and to find ways to tackle instead the full time-dependent electronic and nuclear quantum problem. In this review, we give an overview of different nonadiabatic processes that manifest themselves in electronic and nuclear dynamics ranging from the nonadiabatic phenomena taking place during tunnel ionization of atoms in strong laser fields to the radiationless relaxation through conical intersections and the nonadiabatic coupling of vibrational modes and discuss the computational approaches that have been developed to describe such phenomena. These methods range from the full solution of the combined nuclear-electronic quantum problem to a hierarchy of semiclassical approaches and even purely classical frameworks. The power of these simulation tools is illustrated by representative applications and the direct confrontation with experimental measurements performed in the National Centre of Competence for Molecular Ultrafast Science and Technology.

Tunneling Time and Weak Measurement in Strong Field Ionization.

Tunneling delays represent a hotly debated topic, with many conflicting definitions and little consensus on when and if such definitions accurately describe the physical observables. Here, we relate these different definitions to distinct experimental observables in strong field ionization, finding that two definitions, Larmor time and Bohmian time, are compatible with the attoclock observable and the resonance lifetime of a bound state, respectively. Both of these definitions are closely connected to the theory of weak measurement, with Larmor time being the weak measurement value of tunneling time and Bohmian trajectory corresponding to the average particle trajectory, which has been recently reconstructed using weak measurement in a two-slit experiment [S. Kocsis, B. Braverman, S. Ravets, M. J. Stevens, R. P. Mirin, L. K. Shalm, and A. M. Steinberg, Science 332, 1170 (2011)]. We demonstrate a big discrepancy in strong field ionization between the Bohmian and weak measurement values of tunneling time, and we suggest this arises because the tunneling time is calculated for a small probability postselected ensemble of electrons. Our results have important implications for the interpretation of experiments in attosecond science, suggesting that tunneling is unlikely to be an instantaneous process.

Efficient on-the-fly ab initio semiclassical method for computing time-resolved nonadiabatic electronic spectra with surface hopping or Ehrenfest dynamics.

We derive a somewhat crude, yet very efficient semiclassical approximation for computing nonadiabatic spectra. The resulting method, which is a generalization of the multiple-surface dephasing representation, includes quantum effects through interference of mixed quantum-classical trajectories and through quantum treatment of the collective electronic degree of freedom. The method requires very little computational effort beyond the fewest-switches surface hopping or Ehrenfest locally mean-field dynamics and is very easy to implement. The proposed approximation is tested by computing the absorption and time-resolved stimulated emission spectra of pyrazine using the four-dimensional three-surface model which allows for comparison with the numerically exact quantum spectra. As expected, the multiple-surface dephasing representation is not suitable for high-resolution linear spectra, yet it seems to capture all the important features of pump-probe spectra. Finally, the method is combined with on-the-fly ab initio evaluation of the electronic structure (i.e., energies, forces, electric-dipole, and nonadiabatic couplings) in order to compute fully dimensional nonadiabatic spectra of pyrazine without approximations inherent to analytical, including vibronic-coupling models. The Appendix provides derivations of perturbative expressions for linear and pump-probe spectra of arbitrary mixed states and for arbitrary laser pulse shapes.

Role of sampling in evaluating classical time autocorrelation functions.

We analyze how the choice of the sampling weight affects efficiency of the Monte Carlo evaluation of classical time autocorrelation functions. Assuming uncorrelated sampling or sampling with constant correlation length, we propose a sampling weight for which the number of trajectories needed for convergence is independent of the correlated quantity, dimensionality, dynamics, and phase-space density. By contrast, it is shown that the computational cost of the "standard" algorithm sampling from the phase-space density may scale exponentially with the number of degrees of freedom. Yet, for the stationary Gaussian distribution of harmonic systems and for the autocorrelation function of a linear function of phase-space coordinates, the computational cost of this standard algorithm is also independent of dimensionality.

Can Satraplatin be hydrated before the reduction process occurs? The DFT computational study.

Hydration reactions of two anticancer Pt(IV) complexes JM149 and JM216 (Satraplatin) were studied computationally together with the hydration of the Pt(II) complex JM118, which is a product of the Satraplatin reduction. Thermodynamic and kinetic parameters of the reactions were determined at the B3LYP/6-311++G(2df.2pd)//B3LYP/6-31 + G(d)) level of theory. The water solution was modeled using the COSMO implicit solvation model, with cavities constructed using Klamt's atomic radii. It was found that hydration of the Pt(IV) complexes is an endergonic/endothermic reaction. It follows the (pseudo)associative mechanism is substantially slower (k ≈ 10(-11) s(-1)) than the corresponding reaction of Pt(II) analogues ((k ≈ 10(-5) s(-1)). Such a low value of the reaction constant signifies that the hydration of JM149 and Satraplatin is with high probability a kinetically forbidden reaction. Similarly to JM149 and Satraplatin, the hydration of JM118 is an endothermic/endoergic reaction. On the other hand, the kinetic parameters are similar to those of cisplatin Zimmermann et al. (J Mol Model 17:2385-2393, 2011), allowing the hydration reaction to occur at physiological conditions. These results suggest that in order to become active Satraplatin has to be first reduced to JM118, which may be subsequently hydrated to yield the active species.

Evaluation of the importance of spin-orbit couplings in the nonadiabatic quantum dynamics with quantum fidelity and with its efficient "on-the-fly" ab initio semiclassical approximation.

We propose to measure the importance of spin-orbit couplings (SOCs) in the nonadiabatic molecular quantum dynamics rigorously with quantum fidelity. To make the criterion practical, quantum fidelity is estimated efficiently with the multiple-surface dephasing representation (MSDR). The MSDR is a semiclassical method that includes nuclear quantum effects through interference of mixed quantum-classical trajectories without the need for the Hessian of potential energy surfaces. Two variants of the MSDR are studied, in which the nuclei are propagated either with the fewest-switches surface hopping or with the locally mean field dynamics. The fidelity criterion and MSDR are first tested on one-dimensional model systems amenable to numerically exact quantum dynamics. Then, the MSDR is combined with "on-the-fly" computed electronic structure to measure the importance of SOCs and nonadiabatic couplings in the photoisomerization dynamics of CH(2)NH(2)(+) considering 20 electronic states and in the collision of F + H(2) considering six electronic states.

Measuring nonadiabaticity of molecular quantum dynamics with quantum fidelity and with its efficient semiclassical approximation.

We propose to measure nonadiabaticity of molecular quantum dynamics rigorously with the quantum fidelity between the Born-Oppenheimer and fully nonadiabatic dynamics. It is shown that this measure of nonadiabaticity applies in situations where other criteria, such as the energy gap criterion or the extent of population transfer, fail. We further propose to estimate this quantum fidelity efficiently with a generalization of the dephasing representation to multiple surfaces. Two variants of the multiple-surface dephasing representation (MSDR) are introduced, in which the nuclei are propagated either with the fewest-switches surface hopping or with the locally mean field dynamics (LMFD). The LMFD can be interpreted as the Ehrenfest dynamics of an ensemble of nuclear trajectories, and has been used previously in the nonadiabatic semiclassical initial value representation. In addition to propagating an ensemble of classical trajectories, the MSDR requires evaluating nonadiabatic couplings and solving the Schrödinger (or more generally, the quantum Liouville-von Neumann) equation for a single discrete degree of freedom. The MSDR can be also used in the diabatic basis to measure the importance of the diabatic couplings. The method is tested on three model problems introduced by Tully and on a two-surface model of dissociation of NaI.

Self-assembled molecular rafts at liquid|liquid interfaces for four-electron oxygen reduction.

The self-assembly of the oppositely charged water-soluble porphyrins, cobalt tetramethylpyridinium porphyrin (CoTMPyP(4+)) and cobalt tetrasulphonatophenyl porphyrin (CoTPPS(4-)), at the interface with an organic solvent to form molecular "rafts", provides an excellent catalyst to perform the interfacial four-electron reduction of oxygen by lipophilic electron donors such as tetrathiafulvalene (TTF). The catalytic activity and selectivity of the self-assembled catalyst toward the four-electron pathway was found to be as good as that of the Pacman type cofacial cobalt porphyrins. The assembly has been characterized by UV-visible spectroscopy, Surface Second Harmonic Generation, and Scanning Electron Microscopy. Density functional theory calculations confirm the possibility of formation of the catalytic CoTMPyP(4+)/ CoTPPS(4-) complex and its capability to bind oxygen.

Activation of the cisplatin and transplatin complexes in solution with constant pH and concentration of chloride anions; quantum chemical study.

The thermodynamics of cisplatin and transplatin hydration is studied within the model of constant pH solution. Several implicit solvation models were chosen for the determination of pK(a) and pK constants of the hydration reactions. The polarizable dielectric model (DPCM), integral equation formalism polarizable model (IEFPCM), and polarizable conductor model (CPCM) were combined with the 'united atom model for Hartree-Fock' (UAHF) method for cavity construction and the B3LYP/6-31++G(2dp,2pd) level of calculations for the determination of electronic energies. The results were compared with the COSMO-RS and SM8 model developed by Truhlar (with M06 and MPWX functionals and the charge model CM4). The RMS difference between experimental and calculated pK(a) values of cis/transplatin, water, HCl, and NH (4) (+) was used to evaluate accuracy of calculations. The DPCM model was confirmed to perform the best. The predicted pK(a) constants were used in Legendre transformation for the estimation of the ΔG' energies in the constant-pH model. The dependence of the pK constant on pH is plotted and compared with experimental value at pH=7.4. The influence of various chloride concentrations on the molar fractions of dissolved forms of cisplatin is examined for the DPCM model. The increased ratio of cisplatin active aqua-forms is clearly visible for 4 mM chloride solution in comparison with 104 mM Cl(-) concentration.