A global optimization perspective on molecular clusters.

Although there is a long history behind the idea of chemical structure, this is a key concept that continues to challenge chemists. Chemical structure is fundamental to understanding most of the properties of matter and its knowledge for complex systems requires the use of state-of-the-art techniques, either experimental or theoretical. From the theoretical view point, one needs to establish the interaction potential among the atoms or molecules of the system, which contains all the information regarding the energy landscape, and employ optimization algorithms to discover the relevant stationary points. In particular, global optimization methods are of major importance to search for the low-energy structures of molecular aggregates. We review the application of global optimization techniques to several molecular clusters; some new results are also reported. Emphasis is given to evolutionary algorithms and their application in the study of the microsolvation of alkali-metal and Ca2+ ions with various types of solvents.This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'.

Microsolvation of the potassium ion with aromatic rings: comparison between hexafluorobenzene and benzene.

We employ a recently developed methodology to study structural and energetic properties of the first solvation shells of the potassium ion in nonpolar environments due to aromatic rings, which is important to understand the selectivity of several biochemical phenomena. Our evolutionary algorithm is used in the global optimization study of clusters formed of K(+) solvated with hexafluorobenzene (HFBz) molecules. The global intermolecular interaction for these clusters has been decomposed in HFBz-HFBz and in K(+)-HFBz contributions, using a potential model based on different decompositions of the molecular polarizability of hexafluorobenzene. Putative global minimum structures of microsolvation clusters up to 21 hexafluorobenzene molecules were obtained and compared with the analogous K(+)-benzene clusters reported in our previous work (J. Phys. Chem. A 2012, 116, 4947-4956). We have found that both K(+)-(Bz)n and K(+)-(HFBz)n clusters show a strong magic number around the closure of the first solvation shell. Nonetheless, all K(+)-benzene clusters have essentially the same first solvation shell geometry with four solvent molecules around the ion, whereas the corresponding one for K(+)-(HFBz)n is completed with nine HFBz species, and its structural motif varies as n increases. This is attributed to the ion-solvent interaction that has a larger magnitude for K(+)-Bz than in the case of K(+)-HFBz. In addition, the ability of having more HFBz than Bz molecules around K(+) in the first solvation shell is intimately related to the inversion in the sign of the quadrupole moment of the two solvent species, which leads to a distinct ion-solvent geometry of approach.

Alkali-ion microsolvation with benzene molecules.

The target of this investigation is to characterize by a recently developed methodology, the main features of the first solvation shells of alkaline ions in nonpolar environments due to aromatic rings, which is of crucial relevance to understand the selectivity of several biochemical phenomena. We employ an evolutionary algorithm to obtain putative global minima of clusters formed with alkali-ions (M(+)) solvated with n benzene (Bz) molecules, i.e., M(+)-(Bz)(n). The global intermolecular interaction has been decomposed in Bz-Bz and in M(+)-Bz contributions, using a potential model based on different decompositions of the molecular polarizability of benzene. Specifically, we have studied the microsolvation of Na(+), K(+), and Cs(+) with benzene molecules. Microsolvation clusters up to n = 21 benzene molecules are involved in this work and the achieved global minimum structures are reported and discussed in detail. We observe that the number of benzene molecules allocated in the first solvation shell increases with the size of the cation, showing three molecules for Na(+) and four for both K(+) and Cs(+). The structure of this solvation shell keeps approximately unchanged as more benzene molecules are added to the cluster, which is independent of the ion. Particularly stable structures, so-called "magic numbers", arise for various nuclearities of the three alkali-ions. Strong "magic numbers" appear at n = 2, 3, and 4 for Na(+), K(+), and Cs(+), respectively. In addition, another set of weaker "magic numbers" (three per alkali-ion) are reported for larger nuclearities.

An evolutionary algorithm for the global optimization of molecular clusters: application to water, benzene, and benzene cation.

We have developed an evolutionary algorithm (EA) for the global minimum search of molecular clusters. The EA is able to discover all the putative global minima of water clusters up to (H(2)O)(20) and benzene clusters up to (C(6)H(6))(30). Then, the EA was applied to search for the global minima structures of (C(6)H(6))(n)(+) with n = 2-20, some of which were theoretically studied for the first time. Our results for n = 2-6 are consistent with previous theoretical work that uses a similar interaction potential. Excluding the very symmetric global minimum structure for n = 9, the growth pattern of (C(6)H(6))(n)(+) with n ≥ 7 involves the (C(6)H(6))(2)(+) dimer motif, which is placed off-center in the cluster. Such observation indicates that potentials commonly used in the literature for (C(6)H(6))(n)(+) cannot reproduce the icosahedral-type packing suggested by the available experimental data.

First-line bevacizumab plus taxane-based chemotherapy for locally recurrent or metastatic breast cancer: safety and efficacy in an open-label study in 2,251 patients.

BACKGROUND: First-line bevacizumab combined with chemotherapy significantly improves efficacy versus chemotherapy alone in human epidermal growth factor receptor 2 (HER2)-negative locally recurrent or metastatic breast cancer (LR/mBC). This large, open-label study further assesses first-line bevacizumab with taxane-based chemotherapy in routine oncology practice. PATIENTS AND METHODS: Patients with HER2-negative LR/mBC, Eastern Cooperative Oncology Group (ECOG) performance status (PS) of zero to two and no prior chemotherapy for LR/mBC received bevacizumab 10 mg/kg every 2 weeks or 15 mg/kg every 3 weeks plus taxane-based chemotherapy (or other non-anthracycline chemotherapy) until disease progression, unacceptable toxicity or patient withdrawal. The primary end point was safety; time to progression (TtP) was a secondary end point. RESULTS: Median follow-up in 2251 treated patients was 12.7 months. Median age was 53 years and 94% of patients had ECOG PS of zero or one. Bevacizumab was most commonly administered with single-agent paclitaxel (35%), single-agent docetaxel (33%) or taxane-based combination therapy (10%). The most frequent grade ≥3 adverse event (AE) was neutropenia (5.4%). Grade ≥3 AEs previously associated with bevacizumab included hypertension (4.4%), arterial/venous thromboembolism (3.2%), proteinuria (1.7%) and bleeding (1.4%). No new bevacizumab safety signals were observed. Median TtP was 9.5 months (95% confidence interval 9.1-9.9). CONCLUSIONS: The study population in ATHENA was more representative of general oncology practice than populations enrolled into randomised trials, although there may have been some bias towards younger, fitter patients. The safety and efficacy of bevacizumab-taxane therapy in this large study were consistent with results from randomised first-line trials.

How different are two chemical structures?

We extend the scope of a recent method for superimposing two molecules ( J. Chem. Phys. 2009, 131, 124126-1-124126-10 ) to include the identification of chiral structures. This methodology is tested by applying it to several organic molecules and water clusters that were subjected to geometry optimization. The accuracy of four simpler, non-superimposing approaches is then analyzed by comparing pairs of structures for argon and water clusters. The structures considered in this work were obtained by a Markovian walk in the coordinate space. First, a random geometry is generated, and then, the iterative application of a mutation operator ensures the creation of increasingly dissimilar structures. The discriminating power of the non-superimposing approaches is tested by comparing the corresponding dissimilarity measures with the root-mean-square distance obtained from the superimposing method. Finally, we showcase the application of those methods to characterize the diversity of solutions in global geometry optimization by evolutionary algorithms.

Raman spectroscopy and multivariate analysis of serum samples from breast cancer patients.

Serum samples were studied using Raman spectroscopy and analyzed through the multivariate statistical methods of principal component analysis (PCA) and linear discriminant analysis (LDA). The blood samples were obtained from 11 patients who were clinically diagnosed with breast cancer and 12 healthy volunteer controls. The PCA allowed us to define the wavelength differences between the spectral bands of the control and patient groups. However, since the differences in the involved molecules were in their tertiary or quaternary structure, it was not possible to determine what molecule caused the observed differences in the spectra. The ratio of the corresponding band intensities were analyzed by calculating the p values and it was found that only seven of these band ratios were significant and corresponded to proteins, phospholipids, and polysaccharides. These specific bands might be helpful during screening for breast cancer using Raman Spectroscopy of serum samples. It is also shown that serum samples from patients with breast cancer and from the control group can be discriminated when the LDA is applied to their Raman spectra.

Apparent higher frequency of phenylketonuria in the Mexican state of Jalisco.

The geographic origin of Mexican patients with phenylketonuria (PKU) in Mexico City and in southern California was studied. Compared to patients with other metabolic disorders, patients with PKU were significantly more likely to have originated from the Los Altos region of the state of Jalisco and its environs. The incidence of PKU among mentally retarded students attending special education schools was found to be significantly higher in Jalisco (particularly the Los Altos region) than in the neighboring state of Guanajuato (1.09% vs 0.3%). These results strongly suggest a "population of origin" effect, the mutant allele(s) having been introduced by the Spanish ancestors of the current population. Our findings also support the addition of PKU to the neonatal screening program for this region of Mexico.

[Uterine activity in primiparous and multiparous women in spontaneous labor and induced labor with oxytocin]. / Uterine Aktivität bei Erst- und Mehrgebärenden bei Spontangeburten sowie nach Geburtseinleitung mit Oxytocin.

An analysis was performed of 5187 intra-amniotically measured labor pressure curves in 40 births with spontaneous labour (20 primiparae and 20 multiparae) and 40 births births in which labor was induced with oxytocin (20 primiparae and 20 multiparae). The dilatation of the os uteri was divided into three phases--Phase 1, dilatation of the cervix to 2 cm; Phase 2, dilatation of the cervix from 2 to 4 cm, and Phase 3, dilatation from 4 cm onwards until complete. During the active phase, from 2 cm until dilatation of the os uteri was complete, no differences were observed between induced and spontaneous labor with regard to frequency and amplitude of contractions. In the induced-labor cases, the parameters for uterine activity, maximum contraction and dilatation speed were higher in all three phases of labor, and those for total duration of labor lower than in the spontaneous labor cases. The contraction/dilatation speed is an important parameter for monitoring the effect of drug-induced stimulation of labor. In the latency phase in spontaneous labor, more contractions were observed in multiparae than in primiparae. This fact which should be reason enough to intensify monitoring of both mother and fetus during this phase. In light of these results it would appear advisable, in the absence of progress in labor, to make a clear distinction between the goals of cervical maturity and promotion of uterine activity, and to institute different drug therapy accordingly.

Quaternary structure of pig liver phosphofructokinase.

The quaternary structure of phosphofructokinase from pig liver has been studied by electron microscopy. Particles ranging in size from tetramers to long flexible chains of tetramers were commonly observed. Phosphofructokinase tetramers are square planar and approximately 110 A on a side; individual subunits are roughly spherical, with a mean radius of 28 A. Chains are formed by end-to-end association of tetramers rather than by tetramer stacking. The geometry of association implies that phosphofructokinase tetramers possess D2 symmetry, with distinct isologous bonding domains for dimer, tetramer, and chain formation.