A non-perturbative pairwise-additive analysis of charge transfer contributions to intermolecular interaction energies.

Energy decomposition analysis (EDA) based on absolutely localized molecular orbitals (ALMOs) decomposes the interaction energy between molecules into physically interpretable components like geometry distortion, frozen interactions, polarization, and charge transfer (CT, also sometimes called charge delocalization) interactions. In this work, a numerically exact scheme to decompose the CT interaction energy into pairwise additive terms is introduced for the ALMO-EDA using density functional theory. Unlike perturbative pairwise charge-decomposition analysis, the new approach does not break down for strongly interacting systems, or show significant exchange-correlation functional dependence in the decomposed energy components. Both the energy lowering and the charge flow associated with CT can be decomposed. Complementary occupied-virtual orbital pairs (COVPs) that capture the dominant donor and acceptor CT orbitals are obtained for the new decomposition. It is applied to systems with different types of interactions including DNA base-pairs, borane-ammonia adducts, and transition metal hexacarbonyls. While consistent with most existing understanding of the nature of CT in these systems, the results also reveal some new insights into the origin of trends in donor-acceptor interactions.

DNA Analogues Modified at the Nonlinking Positions of Phosphorus.

Chemically modified oligonucleotides are being developed as a new class of medicines for curing conditions that previously remained untreatable. Three primary classes of therapeutic oligonucleotides are single-stranded antisense oligonucleotides (ASOs), double stranded small interfering RNAs (siRNAs), and oligonucleotides that induce exon skipping. Recently, ASOs, siRNAs, and exon skipping oligonucleotides have been approved for patients with unmet medical needs, and many other candidates are being tested in late stage clinical trials. In coming years, therapeutic oligonucleotides may match the promise of small molecules and antibodies. Interestingly, in the 1980s when we developed chemical methods for synthesizing oligonucleotides, no one would have imagined that these highly charged macromolecules could become future medicines. Indeed, the anionic nature and poor metabolic stability of the natural phosphodiester backbone provided a major challenge for the use of oligonucleotides as therapeutic drugs. Thus, chemical modifications of oligonucleotides were essential in order to improve their pharmacokinetic properties. Keeping this view in mind, my laboratory has developed a series of novel oligonucleotides where one or both nonbridging oxygens in the phosphodiester backbone are replaced with an atom or molecule that introduces molecular properties that enhance biological activity. We followed two complementary approaches. One was the use of phosphoramidites that could act directly as synthons for the solid phase synthesis of oligonucleotide analogues. This approach sometimes was not feasible due to instability of various synthons toward the reagents used during synthesis of oligonucleotides. Therefore, using a complementary approach, we developed phosphoramidite synthons that can be incorporated into oligonucleotides with minimum changes in the solid phase DNA synthesis protocols but contain a handle for generating appropriate analogues postsynthetically.This Account summarizes our efforts toward preparing these types of analogues over the past three decades and discusses synthesis and properties of backbone modified oligonucleotides that originated from the Caruthers' laboratory. For example, by replacing one of the internucleotide oxygens with an acetate group, we obtained so-called phosphonoacetate oligonucleotides that were stable to nucleases and, when delivered as esters, entered into cells unaided. Alternatively oligonucleotides bearing borane phosphonate linkages were found to be RNase H active and compatible with the endogenous RNA induced silencing complex (RISC). Oligonucleotides containing an alkyne group directly linked to phosphorus in the backbone were prepared as well and used to attach molecules such as amino acids and peptides.

Boron clusters as a platform for new materials: composites of nucleic acids and oligofunctionalized carboranes (C2B10H12) and their assembly into functional nanoparticles.

Nucleic acids are key biomolecules in all life forms. These biomolecules can encode and transfer information via Watson-Crick base-pairing interactions and can form double-stranded structures between complementary sequences with high precision. These properties make nucleic acids extremely successful in applications in materials science as nanoconstruction materials. Herein, we describe a method for the automated synthesis of "oligopeds", which are building blocks based on the boron cluster structure equipped with short DNA adapters; these building blocks assemble into functional nanoparticles. The obtained, well defined, torus-like structures are the first DNA nanoconstructs based on a boron cluster scaffold. The results indicate the potential of boron clusters in DNA nanoconstruction and open the way for the design of entirely new types of buildings blocks based on polyhedral heteroborane geometry and its unique properties. The use of antisense oligonucleotides as DNA adapters illustrates one of the possible applications of the obtained nanoconstructs as vectors for therapeutic nucleic acids.

Solid-Phase Synthesis of Phosphate/Boranophosphate Chimeric DNAs Using the H-Phosphonate-H-Boranophosphonate Method.

Boranophosphate (PB) DNAs are promising antisense oligonucleotide candidates because of their attractive features, such as high nuclease resistance and low toxicity. However, a full boranophosphate backbone modification to antisense DNAs causes reduced duplex formation with complementary RNAs and reduced antisense activity. In this study, an efficient solid-phase synthesis of phosphate/boranophosphate (PO/PB) chimeric DNA was achieved by the combination of the H-phosphonate and H-boranophosphonate methods. The physiological and biological properties of the synthesized PO/PB chimeric DNAs were also evaluated. The strategy employed herein can facilitate the design and synthesis of PO/PB chimeric DNAs containing site-specific boranophosphate modifications.

Metallacarborane Sulfamides: Unconventional, Specific, and Highly Selective Inhibitors of Carbonic Anhydrase IX.

Carbonic anhydrase IX (CAIX) is a transmembrane enzyme that regulates pH in hypoxic tumors and promotes tumor cell survival. Its expression is associated with the occurrence of metastases and poor prognosis. Here, we present nine derivatives of the cobalt bis(dicarbollide)(1-) anion substituted at the boron or carbon sites by alkysulfamide group(s) as highly specific and selective inhibitors of CAIX. Interactions of these compounds with the active site of CAIX were explored on the atomic level using protein crystallography. Two selected derivatives display subnanomolar or picomolar inhibition constants and high selectivity for the tumor-specific CAIX over cytosolic isoform CAII. Both derivatives had a time-dependent effect on the growth of multicellular spheroids of HT-29 and HCT116 colorectal cancer cells, facilitated penetration and/or accumulation of doxorubicin into spheroids, and displayed low toxicity and showed promising pharmacokinetics and a significant inhibitory effect on tumor growth in syngenic breast 4T1 and colorectal HT-29 cancer xenotransplants.

Hydrogen gas improves photothermal therapy of tumor and restrains the relapse of distant dormant tumor.

Inflammation during photothermal therapy (PTT) of tumor usually results in adverse consequences. Here, a biomembrane camouflaged nanomedicine (mPDAB) containing polydopamine and ammonia borane was designed to enhance PTT efficacy and mitigate inflammation. Polydopamine, a biocompatible photothermal agent, can effectively convert light into heat for PTT. Ammonia borane was linked to the surface of polydopamine through the interaction of hydrogen bonding, which could destroy redox homoeostasis in tumor cells and reduce inflammation by H2 release in tumor microenvironment. Owing to the same origin of outer biomembranes, mPDAB showed excellent tumor accumulation and low systemic toxicity in a breast tumor model. Excellent PTT efficacy and inflammation reduction made the mPDAB completely eliminate the primary tumors, while also restraining the outgrowth of distant dormant tumors. The biomimetic nanomedicine shows potentials as a universal inflammation-self-alleviated platform to ameliorate inflammation-related disease treatment, including but not limited to PTT for tumor.

Optimization and validation of a derivatization method with boron trifluoride in ethanol for analysis of aromatic carboxylic acids in water.

Gas-chromatography (GC) analysis of carboxylic acids is limited by the high polarity and low volatility of most of these compounds. Boron trifluoride (BF3) mediated alkylation reactions is one of the most commonly used derivatization methods for making carboxylic acids GC compatible. A semi-automated BF3·EtOH (ethanol) derivatization method was optimized for comprehensive two-dimensional gas chromatography high-resolution mass spectrometry (GC × GC-HR MS) analysis of carboxylic acids in solid phase extraction (SPE) extracts of oil polluted water. The optimal derivatization method were found to be with addition of 300 µL BF3·EtOH per 200 µL sample and reaction at 75 °C for 24 h. Derivatives of eight selected acids (aliphatic, mono- and di-aromatic) were stable over 12 h with relative standard deviations (RSDs) of 2.0-10.7 %, the derivatization method was repeatable (RSDs of 3.2-17.2 %), detection limits (DL) and limit of detections (LODs) was in the range of DL = 0.53-1.63 ppb and LOD = 0.19-2.51 ppb for pure acid standards, and DL = 0.18-3.41 ppb and LOD = 0.28-5.46 ppb for matrix matched acid standards. Finally, the method was validated on the acidic fraction of a mixed anion-exchange SPE of oil polluted water. Thousands of degradation products from parent alkylated polycyclic aromatic hydrocarbons (PAHs) and aliphatic hydrocarbons, such as aliphatic acids and mono-, di- and tri- aromatic acids were analyzed by the applied method and compound groups were tentatively identified.

Potentiality of PARAFAC approaches for simultaneous determination of N-acetylcysteine and acetaminophen based on the second-order data obtained from differential pulse voltammetry.

N-acetylcysteine (N-AC) has widespread application such as pharmaceutical drug and nutritional supplement. Its adverse effects are rash, urticaria, and itchiness and large doses of N-AC could potentially cause damage to the heart and lungs. Therefore, in this work, a sensitive voltammetric sensor based on a carbon paste electrode modified with silica nano particles (i.e. Mobil Composition of Matter (No. 41) modified with Boron Trifluoride or BF3@MCM-41) with a combination of 4,4'-dihydroxybiphenyl (DHB) (BF3@MCM-41/DHB/CPE) was designed for determination of N-AC. The electrochemical oxidation of N-AC was examined using various techniques such as cyclic voltammetry (CV), chronoamperometry and differential pulse voltammetry (DPV). Under the optimum conditions, some parameters such as electron transfer coefficient (α) and heterogeneous rate constant (ks) were estimated for N-AC. Due to the use of N-AC for the treatment of acetaminophen (AC) overdose, the application of modified electrode was investigated for the simultaneous determination of N-AC and AC in blood serum and tablet samples. Since, the signals of these species overlap and due to the presence of interfering species in blood samples, the simultaneous determination of mentioned species is difficult or impossible. To overcome this challenge, parallel factor analysis (PARAFAC) was used for the analysis of the complex matrices to obtain the spectral profile of each component and interference. To achieve this goal, electrochemical second-order data were generated using a simple change in pulse height of differential pulse voltammetry. The results of the presently proposed strategy for the real samples analysis are similar to those obtained with HPLC. Thus, the proposed method has acceptable performance for simultaneous determination of the two species in real samples.

P-N Cooperative Borane Activation and Catalytic Hydroboration by a Distorted Phosphorous Triamide Platform.

Studies of the stoichiometric and catalytic reactivity of a geometrically constrained phosphorous triamide 1 with pinacolborane (HBpin) are reported. The addition of HBpin to phosphorous triamide 1 results in cleavage of the B-H bond of pinacolborane through addition across the electrophilic phosphorus and nucleophilic N-methylanilide sites in a cooperative fashion. The kinetics of this process of were investigated by NMR spectroscopy, with the determined overall second-order empirical rate law given by ν = -k[1][HBpin], where k = 4.76 × 10-5 M-1 s-1 at 25 °C. The B-H bond activation process produces P-hydrido-1,3,2-diazaphospholene intermediate 2, which exhibits hydridic reactivity capable of reacting with imines to give phosphorous triamide intermediates, as confirmed by independent synthesis. These phosphorous triamide intermediates are typically short lived, evolving with elimination of the N-borylamine product of imine hydroboration with regeneration of the deformed phosphorous triamide 1. The kinetics of this latter process are shown to be first-order, indicative of a unimolecular mechanism. Consequently, catalytic hydroboration of a variety of imine substrates can be realized with 1 as the catalyst and HBpin as the terminal reagent. A mechanistic proposal implicating a P-N cooperative mechanism for catalysis that incorporates the various independently verified stoichiometric steps is presented, and a comparison to related phosphorus-based systems is offered.

Fatty acid microemulsion for the treatment of neonatal conjunctivitis: quantification, characterisation and evaluation of antimicrobial activity.

Fatty acids (FAs) are used by many organisms as defence mechanism against virulent bacteria. The high safety profile and broad spectrum of activity make them potential alternatives to currently used topical antibiotics for the treatment of eye infections in neonates. The current study utilised a Design of Experiment approach to optimise the quantification of five fatty acids namely; lauric acid, tridecanoic acid, myristoleic acid, palmitoleic acid and α-linolenic acid. The significance of the influence of the experimental parameters such as volume of catalyst, volume of n-hexane, incubation temperature, incubation time and the number of extraction steps on derivatisation was established by statistical screening with a factorial approach. Derivatisation was confirmed using attenuated total reflectance infrared (ATR) and 1H NMR spectrum. A gas chromatographic method (GC-FID) was developed and validated according to ICH guidelines for the identification and quantification of fatty acids. The results were found to be linear over the concentration range studied with coefficient of variation greater than 0.99 and high recovery values and low intra-day and inter-day variation values for all FAs. Then, different α-linolenic acid-based microemulsions (MEs) were prepared using Tween 80 as surfactant, polyethylene glycol 400 (PEG 400) as co surfactant and water as aqueous phase. The developed GC method was used to quantify the FA content in ME formulations. The results indicated that the developed GC method is very effective to quantify the FA content in the ME formulations. The antimicrobial efficacy of FA-based MEs were tested against Staphylococcus aureus. It was concluded that the FA-based MEs have strong antimicrobial effect against S. aureus.

Efficient Preparation of Various O-Methylquercetins by Selective Demethylation.

penia-O-Methylquercetin (2) was prepared by permethylation of quercetin (1). Selective demethylation of 2 using either BBr or BCl3/TBAI (tetrabutylammonium iodide) gave five O-methylquercetins (3-6), with satisfactory yields. The reaction can be easily scaled-up. We established an efficient and large-scale preparation of O-methylquercetins.

Face to face activation of a phenylselenium borane with α,ß-unsaturated carbonyl substrates: facile synthesis of C-Se bonds.

Activated olefins directly react with a phenylselenium borane, at room temperature, without any metal or organocatalytic assistance. Up to 10 examples of ß-(phenylseleno) substituted ketones and aldehydes have been prepared and theoretical evidence for the mechanism opens up non-existing pathways to create C-heteroatom bonds as a general tool.

Solid-phase synthesis of P-boronated oligonucleotides by the H-boranophosphonate method.

Recently, P-boronated oligonucleotides have been attracting much attention as potential therapeutic oligonucleotides. In this study, we developed H-boranophosphonate oligonucleotide bearing a borano group and hydrogen atom on the internucleotidic phosphorus and demonstrated that this novel P-boronated oligonucleotide is a versatile precursor to various P-boronated oligonucleotides such as boranophosphate, boranophosphorothioate, and boranophosphoramidate. The method was also applicable to the synthesis of a locked nucleic acid-modified boranophosphate oligonucleotide, which exhibited a dramatically enhanced affinity to complementary oligonucleotides.

Pnicogen-bonded cyclic trimers (PH2X)3 with X = F, Cl, OH, NC, CN, CH3, H, and BH2.

Ab initio MP2/aug'-cc-pVTZ calculations have been carried out to determine the structures and binding energies of cyclic trimers (PH2X)3 with X = F, Cl, OH, NC, CN, CH3, H, and BH2. Except for [PH2(CH3)]3, these complexes have C3h symmetry and binding energies between -17 and -63 kJ mol(-1). Many-body interaction energy analyses indicate that the two-body terms are dominant, accounting for 97-103% of the total binding energy. Except for the trimer [PH2(OH)]3, the three-body terms are stabilizing. Charge transfer from the lone pair on one P atom to an antibonding σ* orbital of the P atom adjacent to the lone pair plays a very significant role in stabilization. The charge-transfer energies correlate linearly with the trimer binding energies. NBO, AIM, and ELF analyses have been used to characterize bonds, lone pairs, and the degree of covalency of the P···P pnicogen bonds. The NMR properties of chemical shielding and (31)P-(31)P coupling constants have also been evaluated. Although the (31)P chemical shieldings in the five most strongly bound trimers increase relative to the corresponding isolated monomers, there is no correlation between the chemical shieldings and the charges on the P atoms. EOM-CCSD (31)P-(31)P spin-spin coupling constants computed for four (PH2X)3 trimers fit nicely onto a plot of (1p)J(P-P) versus the P-P distance for (PH2X)2 dimers. A coupling constant versus distance plot for the four trimers has a second-order trendline which has been used to predict the values of (1p)J(P-P) for the remaining trimers.

Stereodivergent SN2@P reactions of borane oxazaphospholidines: experimental and theoretical studies.

The stereodivergent ring-opening of 2-phenyl oxazaphospholidines with alkyl lithium reagents is reported. N-H oxazaphospholidines derived from both (+)-cis-1-amino-2-indanol and (-)-norephedrine provide inversion products in a highly stereoselective process. In contrast, N-Me oxazaphospholidines yield ring-opening products with retention of configuration at the P center, as previously reported by Jugé and co-workers. As a result, from a single amino alcohol auxiliary, both enantiomers of key P-stereogenic intermediates could be synthesized. Theoretical studies of ring-opening with model oxazaphospholidines at the DFT level have elucidated the streochemical course of this process. N-H substrates react in a single step via preferential backside S(N)2@P substitution with inversion at phosphorus. N-methylated substrates react preferentially via a two-step frontside S(N)2@P, yielding a ring-opened product in which the nucleophilic methyl binds to P with retention of configuration. DFT calculations have shown that the BH3 unit is a potent directing group to which the methyl lithium reagent coordinates via Li in all the reactions studied.

Stoichiometric and catalytic synthesis of alkynylphosphines.

Alkynylphosphines or their borane complexes are available either through C-P bond forming reactions or through modification of the phosphorus or the alkynyl function of various alkynyl phosphorus derivatives. The latter strategy, and in particular the one involving phosphoryl reduction by alanes or silanes, is the method of choice for preparing primary and secondary alkynylphosphines, while the former strategy is usually employed for the synthesis of tertiary alkynylphosphines or their borane complexes. The classical C-P bond forming methods rely on the reaction between halophosphines or their borane complexes with terminal acetylenes in the presence of a stoichiometric amount of organometallic bases, which precludes the access to alkynylphosphines bearing sensitive functional groups. In less than a decade, efficient catalytic procedures, mostly involving copper complexes and either an electrophilic or a nucleophilic phosphorus reagent, have emerged. By proceeding under mild conditions, these new methods have allowed a significant broadening of the substituent scope and structure complexity.

Electrochemical detection of DNA hybridization using metallacarborane unit.

The evaluation of novel electrochemically active label for electrochemical detection of DNA hybridization is presented. Metallacarborane units modified with iron, cobalt or chromium were investigated. The value of redox potential and relatively strong current signal facilitate usage of Fe-carborane as marker covalently attached to the ssDNA. In electrochemical genosensor the sequence complementary to UL55 gene was labeled and used as a target for biosensor device. Interactions were investigated using electrochemical and piezoelectric methods. Obtained results confirm usefulness of the designed label in electrochemical detection of DNA hybridization.

Characterization of doped amorphous silicon thin films through the investigation of dopant elements by glow discharge spectrometry: a correlation of conductivity and bandgap energy measurements.

The determination of optical parameters, such as absorption and extinction coefficients, refractive index and the bandgap energy, is crucial to understand the behavior and final efficiency of thin film solar cells based on hydrogenated amorphous silicon (a-Si:H). The influence of small variations of the gas flow rates used for the preparation of the p-a-SiC:H layer on the bandgap energy, as well as on the dopant elements concentration, thickness and conductivity of the p-layer, is investigated in this work using several complementary techniques. UV-NIR spectrophotometry and ellipsometry were used for the determination of bandgap energies of four p-a-SiC:H thin films, prepared by using different B(2)H(6) and SiH(4) fluxes (B(2)H(6) from 12 sccm to 20 sccm and SiH(4) from 6 sccm to 10 sccm). Moreover, radiofrequency glow discharge optical emission spectrometry technique was used for depth profiling characterization of p-a-SiC:H thin films and valuable information about dopant elements concentration and distribution throughout the coating was found. Finally, a direct relationship between the conductivity of p-a-SiC:H thin films and the dopant elements concentration, particularly boron and carbon, was observed for the four selected samples.

Solid-phase synthesis, thermal denaturation studies, nuclease resistance, and cellular uptake of (oligodeoxyribonucleoside)methylborane phosphine-DNA chimeras.

The major hurdle associated with utilizing oligodeoxyribonucleotides for therapeutic purposes is their poor delivery into cells coupled with high nuclease susceptibility. In an attempt to combine the nonionic nature and high nuclease stability of the P-C bond of methylphosphonates with the high membrane permeability, low toxicity, and improved gene silencing ability of borane phosphonates, we have focused our research on the relatively unexplored methylborane phosphine (Me-P-BH(3)) modification. This Article describes the automated solid-phase synthesis of mixed-backbone oligodeoxynucleotides (ODNs) consisting of methylborane phosphine and phosphate or thiophosphate linkages (16-mers). Nuclease stability assays show that methylborane phosphine ODNs are highly resistant to 5' and 3' exonucleases. When hybridized to a complementary strand, the ODN:RNA duplex was more stable than its corresponding ODN:DNA duplex. The binding affinity of ODN:RNA duplex increased at lower salt concentration and approached that of a native DNA:RNA duplex under conditions close to physiological saline, indicating that the Me-P-BH(3) linkage is positively charged. Cellular uptake measurements indicate that these ODNs are efficiently taken up by cells even when the strand is 13% modified. Treatment of HeLa cells and WM-239A cells with fluorescently labeled ODNs shows significant cytoplasmic fluorescence when viewed under a microscope. Our results suggest that methylborane phosphine ODNs may prove very valuable as potential candidates in antisense research and RNAi.