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.

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.

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

In spite of the impressing cytotoxicity of thapsigargin (), 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.

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

Targeting cytotoxic 4β-phorbol esters toward cancer tissue was attempted by conjugating a 4β-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.

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 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.

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).

Phorbol Rearrangements.

An alternative procedure for isolation of 4β-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.

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.

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 Ca-ATPase inhibitor thapsigargin bring promising prospects for Tb to be used in the development of new anti-cancer drugs.

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.

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.

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.

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.

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.

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.

Efficient sampling avoids the exponential wall in classical simulations of fidelity.

We analyze the efficiency of available algorithms for the simulation of classical fidelity and show that their computational costs increase exponentially with the number of degrees of freedom. Then we present an algorithm for which the number of trajectories needed for convergence is independent of the system's dimensionality and show that, within a continuous family of algorithms, this algorithm is the only one with this property. Simultaneously we propose a general analytical approach to estimate efficiency of trajectory-based methods and suggest how to use it to accelerate calculations of other classical correlation functions.

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.

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.

Cisplatin interaction with amino acids cysteine and methionine from gas phase to solutions with constant pH.

This work is focused on the computational studies of reactions of hydrated forms of cisplatin with sulphur-containing amino acids cysteine and methionine. First, the appropriate model for solvation of the examined complexes was searched for. The suggested procedure employs the B3LYP density functional, 6-311++G(2df,2pd) basis set with Stuttgart-Dresden pseudopotentials on heavy atoms, the D-PCM solvation model and the UAKS cavity which uses more realistic NPA partial charges instead of formal partial charges for platinum ligands.

Communications: Evaluation of the nondiabaticity of quantum molecular dynamics with the dephasing representation of quantum fidelity.

We propose an approximate method for evaluating the importance of non-Born-Oppenheimer effects on the quantum dynamics of nuclei. The method uses a generalization of the dephasing representation (DR) of quantum fidelity to several diabatic potential energy surfaces and its computational cost is the cost of dynamics of a classical phase space distribution. It can be implemented easily into any molecular dynamics program and also can utilize on-the-fly ab initio electronic structure information.

Three applications of path integrals: equilibrium and kinetic isotope effects, and the temperature dependence of the rate constant of the [1,5] sigmatropic hydrogen shift in (Z)-1,3-pentadiene.

Recent experiments have confirmed the importance of nuclear quantum effects even in large biomolecules at physiological temperature. Here we describe how the path integral formalism can be used to describe rigorously the nuclear quantum effects on equilibrium and kinetic properties of molecules. Specifically, we explain how path integrals can be employed to evaluate the equilibrium (EIE) and kinetic (KIE) isotope effects, and the temperature dependence of the rate constant.

Reactions of cisplatin with cysteine and methionine at constant pH; a computational study.

Interactions of hydrated cisplatin complexes cis-[Pt(NH(3))(2)Cl(H(2)O)](+) and cis-[Pt(NH(3))(2)(OH)(H(2)O)](+) with cysteine and methionine in an aqueous solution at constant pH were explored using computational methods. Thermodynamic parameters of considered reactions were studied in a broad pH range, taking up to 4 protonation states of each molecule into account. Reaction free energies at constant pH were obtained from standard Gibbs free energies using the Legendre transformation.