Anharmonic excited state frequencies of para-difluorobenzene, toluene and catechol using analytic RI-CC2 second derivatives.

Analytic second nuclear derivatives for excited electronic state energies have been implemented for the resolution-of-the-identity accelerated CC2, CIS(D∞) and ADC(2) models. Our efficient implementation with O(N2) memory demands enables the treatment of medium sized molecules with large basis sets and high numerical precision and thereby paves the way for semi-numerical evaluation of the higher-order derivatives required for anharmonic corrections to excited state vibrational frequencies. We compare CC2 harmonic and anharmonic excited state frequencies with experimental values for para-difluorobenzene, toluene and catechol. Basis set problems occur for out-of-plane bending vibrations due to intramolecular basis set superposition error. For non-planar molecules and in plane modes of planar molecules, the agreement between theory and experiment is better than 30 cm-1 on average and we reassign a number of experimental bands on the basis of the ab initio predictions.

Excited state polarizabilities for CC2 using the resolution-of-the-identity approximation.

We report an implementation of static and frequency-dependent excited state polarizabilities for the approximate coupled cluster single and doubles model CC2 as analytic second derivatives of an excited state quasienergy Lagrangian. By including appropriate conditions for the normalization and the phase of the eigenvectors, divergent secular terms are avoided. This leads to response equations in a subspace orthogonal to the unperturbed eigenvectors. It is shown how these projected equations can be solved without storage of the double excitation part of the eigenvectors. By exploiting the resolution-of-the-identity approximation and a numerical Laplace transformation, the quadratic scaling of the main memory demands of RI-CC2 with the system size could be preserved. This enables calculations of excited state polarizabilities for large molecules, e.g., linear polyacenes up to decacene with almost 2500 basis functions on a single compute node within a few days. For a test set of molecules where measurements are available as reference data, we compare the orbital-relaxed and unrelaxed CC2 approaches with experiment to validate its accuracy. The approach can be easily extended to other response methods, in particular CIS(D∞). The latter gives results which, in the orbital-relaxed case, are within a few percent of the CC2 values, while coupled cluster singles results deviate typically by about 20% from orbital-relaxed CC2 and experimental reference data.

Benchmarks for 0-0 transitions of aromatic organic molecules: DFT/B3LYP, ADC(2), CC2, SOS-CC2 and SCS-CC2 compared to high-resolution gas-phase data.

In the present study a benchmark set of medium-sized and large aromatic organic molecules with 10-78 atoms is presented. For this test set 0-0 transition energies measured in supersonic jets are compared to those calculated with DFT and the B3LYP functional, ADC(2), CC2 and the spin-scaled CC2 variants SOS-CC2 and SCS-CC2. Geometries of the ground and excited states have been optimized with these methods in polarized triple zeta basis sets. Zero-point vibrational corrections have been calculated with the same methods and basis sets. In addition the energies have been corrected by single point calculations with a triple zeta basis augmented with diffuse functions, aug-cc-pVTZ. The deviations of the theoretical results from experimental electronic origins, which have all been measured in the gas phase with high-resolution techniques, were evaluated. The accuracy of SOS-CC2 is comparable to that of unscaled CC2, whereas ADC(2) has slightly larger errors. The lowest errors were found for SCS-CC2. All correlated wave function methods provide significantly better results than DFT with the B3LYP functional. The effects of the energy corrections from the augmented basis set and the method-consistent calculation of the zero-point vibrational corrections are small. With this benchmark set reliable reference data for 0-0 transition energies for larger organic chromophores are available that can be used to benchmark the accuracy of other quantum chemical methods such as new DFT functionals or semi-empirical methods for excitation energies and structures and thereby augments available benchmark sets augments present benchmark sets which include mainly smaller molecules.

Methylation of recombinant mononucleosomes by DNMT3A demonstrates efficient linker DNA methylation and a role of H3K36me3.

Recently, the structure of the DNMT3A2/3B3 heterotetramer complex bound to a mononucleosome was reported. Here, we investigate DNA methylation of recombinant unmodified, H3KC4me3 and H3KC36me3 containing mononucleosomes by DNMT3A2, DNMT3A catalytic domain (DNMT3AC) and the DNMT3AC/3B3C complex. We show strong protection of the nucleosomal bound DNA against methylation, but efficient linker-DNA methylation next to the nucleosome core. High and low methylation levels of two specific CpG sites next to the nucleosome core agree well with details of the DNMT3A2/3B3-nucleosome structure. Linker DNA methylation next to the nucleosome is increased in the absence of H3K4me3, likely caused by binding of the H3-tail to the ADD domain leading to relief of autoinhibition. Our data demonstrate a strong stimulatory effect of H3K36me3 on linker DNA methylation, which is independent of the DNMT3A-PWWP domain. This observation reveals a direct functional role of H3K36me3 on the stimulation of DNA methylation, which could be explained by hindering the interaction of the H3-tail and the linker DNA. We propose an evolutionary model in which the direct stimulatory effect of H3K36me3 on DNA methylation preceded its signaling function, which could explain the evolutionary origin of the widely distributed "active gene body-H3K36me3-DNA methylation" connection.

Role of endonucleases XPF and XPG in nucleotide excision repair of platinated DNA and cisplatin/oxaliplatin cytotoxicity.

Resistance of tumor cells to platinum anticancer agents poses a major problem in cancer chemotherapy. One of the mechanisms associated with platinum-based drug resistance is the enhanced capacity of the cell to carry out nucleotide excision repair (NER) on platinum-damaged DNA. Endonucleases XPF and XPG are critical components of NER, responsible for excising the damaged DNA strand to remove the DNA lesion. Here, we investigated possible consequences of down-regulation of XPF and XPG gene expression in osteosarcoma cancer cells (U2OS) and the impact on cellular transcription and DNA repair. We further evaluated the sensitivity of such cells toward the platinum anticancer drugs cisplatin and oxaliplatin.

Self-assembled monolayers of aromatic omega-aminothiols on gold: surface chemistry and reactivity.

Amino-terminated self-assembled monolayers on gold substrates were studied by X-ray photoelectron spectroscopy (XPS), near-edge X-ray absorption fine structure (NEXAFS) measurements, and atomic force microscopy (AFM). Two different omega-amino-4,4'-terphenyl substituted alkanethiols of the general structure H(2)N-(C(6)H(4))(3)-(CH(2))(n)-SH (ATPn) were used: 2-(4''-amino-1,1':4',1''-terphenyl-4-yl)ethane-1-thiol (n = 2, ATP2) and 3-(4''-amino-1,1':4',1''-terphenyl-4-yl)propane-1-thiol (n = 3, ATP3). Moreover, the addressability of amino groups within the films was investigated by chemical derivatization of ATPn SAMs with 3,5-bis(trifluoromethyl)phenyl isothiocyanate (ITC) forming fluorinated thiourea ATPn-F films. Evaluation of high-resolution C 1s and N 1s XPS data revealed successful derivatization of at least 50% of surface amino species. Furthermore, it could be demonstrated by angle-resolved NEXAFS spectroscopy that chemical derivatization with ITC has no noticeable influence on the preferential upright orientation of the molecules in the SAMs.

Determination of accessible amino groups on surfaces by chemical derivatization with 3,5-bis(trifluoromethyl)phenyl isothiocyanate and XPS/NEXAFS analysis.

The determination of amino groups on surfaces capable of binding biomolecules is important for the understanding and optimization of technologically relevant coupling processes. In this study, three different types of amino-functionalized model surfaces, amino thiolate on Au, amino siloxane on Si, and polyethylene (PE) foils and films reacted with 1,2-diaminoethane (DAE) were derivatized with 3,5-bis(trifluoromethyl)phenyl isothiocyanate. Subsequently, these samples were analyzed by chemical derivatization X-ray photoelectron spectroscopy (CD-XPS) and near-edge X-ray absorption fine structure spectroscopy (NEXAFS). The determination of amino groups by this analytical approach allows gaining insight into the availability of groups on surfaces that can actually serve as attachment sites for biomolecules in technical applications. In the case of the amino thiolate on Au, almost 90% of the expected amino groups were detected by CD-XPS. Investigation of the amino siloxane films revealed lower yields for the derivatization reaction in the order of 30%. The lowered reaction yields are thought to be due to interactions between the amino siloxane's amino and silanol groups or the underlying substrate, making them inaccessible to the derivatization agent. The aminated PE samples are characterized by a complex surface chemistry and structure, and reaction yields of the derivatization reaction cannot be unequivocally derived. However, 1-3% of the total carbon atoms in the surface layer were found to be bound to amino groups accessible to the derivatization agent. It can be concluded that, depending on the detailed character of the investigated amino-terminated surface, the amount of amino groups accessible to CD-XPS can be substantially lower than the total amount of amino groups present at the surface.

Application of XPS and ToF-SIMS for surface chemical analysis of DNA microarrays and their substrates.

The chemical composition of the functional surfaces of substrates used for microarrays is one of the important parameters that determine the quality of a microarray experiment. In addition to the commonly used contact angle measurements to determine the wettability of functionalized supports, X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS) are more specific methods to elucidate details about the chemical surface constitution. XPS yields information about the atomic composition of the surface, whereas from ToF-SIMS, information on the molecular species on the surface can be concluded. Applied on printed DNA microarrays, both techniques provide impressive chemical images down to the micrometer scale and can be utilized for label-free spot detection and characterization. Detailed information about the chemical constitution of single spots of microarrays can be obtained by high-resolution XPS imaging.

Using enzymatic amplification by aldolase for the optical detection of DNA by an artificial signal cascade.

A two-step reaction cascade is applied to the sequence-specific detection of single-stranded DNA, including analyte-triggered re-activation of apo-aldolase by its cofactor Zn(2+) and catalytic conversion of a chromophore.

Enzymatic amplification in a bioinspired, autonomous signal cascade.

A two-step reaction cascade is applied to the sequence-specific detection of DNA by enzymatic amplification of the molecular into an optical signal.

Redox activation of metal-based prodrugs as a strategy for drug delivery.

This review provides an overview of metal-based anticancer drugs and drug candidates. In particular, we focus on metal complexes that can be activated in the reducing environment of cancer cells, thus serving as prodrugs. There are many reports of Pt and Ru complexes as redox-activatable drug candidates, but other d-block elements with variable oxidation states have a similar potential to serve as prodrugs in this manner. In this context are compounds based on Fe, Co, or Cu chemistry, which are also covered. A trend in the field of medicinal inorganic chemistry has been toward molecularly targeted, metal-based drugs obtained by functionalizing complexes with biologically active ligands. Another recent activity is the use of nanomaterials for drug delivery, exploiting passive targeting of tumors with nano-sized constructs made from Au, Fe, carbon, or organic polymers. Although complexes of all of the above mentioned metals will be described, this review focuses primarily on Pt compounds, including constructs containing nanomaterials.

Platinum(IV)-chlorotoxin (CTX) conjugates for targeting cancer cells.

Cisplatin is one of the most widely used anticancer drugs. Its side effects, however, have motivated researchers to search for equally effective analogs that are better tolerated. Selectively targeting cancer tissue is one promising strategy. For this purpose, a platinum(IV) complex was conjugated to the cancer-targeting peptide chlorotoxin (CTX, TM601) in order to deliver cisplatin selectively to cancer cells. The 1:1 Pt-CTX conjugate was characterized by mass spectrometry and gel electrophoresis. Like most platinum(IV) derivatives, the cytotoxicity of the conjugate was lower in cell culture than that of cisplatin, but greater than those of its Pt(IV) precursor and CTX in several cancer cell lines.

α(V)ß(3) integrin-targeted PLGA-PEG nanoparticles for enhanced anti-tumor efficacy of a Pt(IV) prodrug.

Targeted delivery of therapeutics to tumor neovasculature is potentially a powerful approach for selective cancer treatment. Integrins are heterodimeric transmembrane proteins involved in cell adhesion and cell signaling, and their expression is commonly upregulated in cancers and inflammatory diseases. The α(v)ß(3) integrin is differentially upregulated on angiogenic endothelial cells as well as on many cancer cells. Here we demonstrate the differential targeting of cisplatin prodrug-encapsulated poly(d,l-lactic-co-glycolic acid)-block-polyethylene glycol (PLGA-PEG) nanoparticles (NPs) to the α(v)ß(3) integrin on cancer cells using the cyclic pentapeptide c(RGDfK). Cisplatin is one of the most widely used anticancer drugs, and approaches that can improve its therapeutic index are of broad importance. The RGD-targeted Pt(IV)-encapsulated NPs displayed enhanced cytotoxicity as compared to cisplatin administered in its conventional dosage form in model prostate and breast cancer epithelial cells in vitro. Cytotoxicities were also elevated in comparison to those of previously reported systems, a small molecule Pt(IV)-RGD conjugate and a Pt(IV) nanoscale coordination polymer carrying RGD moieties. This result encouraged us also to evaluate the anticancer effect of the new construct in an animal model. The RGD-targeted PLGA-PEG NPs were more efficacious and better tolerated by comparison to cisplatin in an orthotopic human breast cancer xenograft model in vivo.