Growth mechanism prediction for nanoparticles via structure matching polymerization.

Exploring structural and component evolution remains a challenging scientific problem for nanoscience. We propose a novel approach called principle of minimization of structure matching polymerization (SMP) change to rapidly explore the global minimum structure on the potential energy surface (PES). The new method can map low-dimensional stable structures to high-dimensional local minima, and this will make it possible for us to study the growth mechanisms of nanoparticles. Some new lowest-energy structures were found by SMP methods for sulfuric acid (SA)-dimethylamine (DMA) systems relative to previous studies. Additionally, we found that the growth process of boron clusters is mainly that the small-size boron clusters are continuously added to large-size boron clusters by structure matching for Bn (n = 2-36) systems, Bm + Bk → Bn, where m + k = n and 1 ≤ k ≤ 3. The SMP approach can greatly improve the search efficiency of other unbiased global optimization algorithms, such as basin-hopping (BH) and genetic algorithm (GA), with an enhancement of up to 19- and 7-fold relative to traditional BH and GA algorithms for searching the global minima of Bn (n = 14-22) systems. The SMP approach is general and flexible and can be applied to different kinds of problems, such as material structure design, crystal structure prediction, and new drug generation.

Experiment-theory hybrid method for studying the formation mechanism of atmospheric new particle formation.

Atmospheric aerosols have a significant influence on climate change through their effect on the cloud lifetime and the radiative balance of the Earth's atmosphere. Despite its importance, the mechanism of aerosol nucleation is still poorly understood. Based on the low-energy structure of cluster molecules, quantum chemical (QC) computations can help us to directly calculate the formation mechanism of atmospheric clusters and formation rates at the molecular level. However, deciphering the formation mechanism of pre-nucleated clusters, especially those close to the critical size (∼1.7 nm), remains extremely challenging because many millions of configuration spaces might need to be explored to find the low-energy structure. We present a new idea that establishes a comprehensive experimental and computational hybrid calculation protocol to integrate experimental data, isomer distributions, hydrogen bond interactions, and interaction sites for exploring the configuration spaces and clarifying the nucleation mechanism of acid-base clusters, whose maximum size can exceed 1.7 nm. This protocol can effectively and accurately explore the configuration space of complex large nucleation clusters on the potential energy surface (PES). The consistency of the cluster concentration and the formation rate between the experiment and the in situ measurement is much better than that of the previous studies and proves its accuracy. In addition, we found that malic acid (MA) can enhance sulfuric acid-dimethylamine (SA-DMA)-based particle formation rates in the atmospheric boundary layer, for example, in Shanghai and Beijing in the summer, with an enhancement of up to 700- and 135-fold, respectively. The enhancement in atmospheric particle formation by MA is critical for new particle formation in the boundary layer with relatively low SA and DMA concentrations and at high temperature. This model greatly improves our understanding of the complex aerosol nucleation mechanism of large-scale multicomponent cluster molecules.

Ion formation mechanism of cortisone molecules and clusters in charged nanodroplets.

Mass spectrometry measurements coupled with classical molecular dynamics (MD) simulations have been conducted in recent years to understand the final stage of ion formation in electrospray ionization (ESI). Here, to characterize the ion formation mechanism in the recently developed droplet-assisted ionization (DAI) source, MD simulations with various conditions (solute number, temperature, ions, composition) were performed to help explain DAI-based measurements. The specific binding ability of cortisone with preformed ions (ions of sodium, cesium and iodide) in evaporating nanodroplets makes the ion formation process characteristic of both the ion evaporation and charge residue models (IEM and CRM, respectively). Most preformed ions are ejected with dozens of solvent molecules to form gas-phase ions by IEM, while clusters of one or more cortisone molecules with one or more preformed ions remain in the evaporating droplet to form gas-phase ions by CRM. As the ratio of cortisone molecules to preformed ions increases, the number of preformed ions held in the droplet without ejection by the IEM increases. In other words, increasing the molecular solute to preformed ion ratio in the droplet increases the fraction of gas-phase ions formed by CRM relative to IEM. The increase in CRM relative to IEM is accompanied by an increase in the calculated activation energy barrier, which can explain the activation energy measurements by DAI, where droplets without preformed ions exhibit higher activation energies for gas-phase ion formation than droplets containing large numbers of preformed ions.

Association of PNPLA3 rs738409 G/C gene polymorphism with nonalcoholic fatty liver disease in children: a meta-analysis.

BACKGROUND: Nonalcoholic fatty liver disease (NAFLD) is one of the most common causes of chronic liver disease worldwide. Current studies have shown that PNPLA3 (Patatin-like phospholipase domain containing 3) rs738409 G/C gene polymorphism is associated with adult nonalcoholic fatty liver disease [1, 2].But there is no consensus on the relationship between PNPLA3 rs738409 G/C gene polymorphism and children NAFLD due to differences in population samples. To this end, a meta-analysis of published research is conducted to comprehensively assess the relationship between PNPLA3 gene polymorphism and NAFLD in children. METHODS: We searched MEDLINE, PubMed, EMBASE, and CENTRAL databases from inception to May 2019. Case-control studies assessing the relationship between PNPLA3 rs738409 G/C gene polymorphism with non-alcoholic fatty liver disease in children were selected according to inclusion and exclusion criteria. Random effects model was used to quantify the association between the PNPLA3 rs738409 G/C gene polymorphism and the susceptibility of children's NAFLD. Fixed effects model was used to quantify the relationship between the PNPLA3 rs738409 G/C gene polymorphism and the severity of NAFLD in children. The Stata 12.0 software was employed for data analysis. RESULTS: A total of nine case-control studies were included in this meta-analysis containing data of 1173 children with NAFLD and 1792 healthy controls. Five studies compared NAFLD children and non-NAFLD healthy populations. Statistical analysis showed that PNPLA3 gene polymorphism was significantly associated with children's NAFLD in the allele contrast, dominant, recessive and over dominant models (G vs C,OR = 3.343, 95% CI = 1.524-7.334; GG + GC vs CC,OR = 3.157, 95% CI = 1.446-6.892;GG vs GC + CC,OR = 5.692, 95% CI = 1.941-16.689; GG + CC vs GC,OR = 2.756, 95% CI = 1.729-4.392). Four case-control studies compared Children with nonalcoholic fatty liver (NAFL) and children with nonalcoholic steatohepatitis (NASH). The results showed that the PNPLA3 gene polymorphism was also significantly associated with the severity of NAFLD in children in recessive gene model (GG vs GC + CC,OR = 14.43, 95% CI = 5.985-34.997); The Egger's test revealed no significant publication bias. CONCLUSIONS: Meta-analysis showed that PNPLA3 gene polymorphism was significantly associated with susceptibility and severity of NAFLD in children.

Association of TM6SF2 rs58542926 T/C gene polymorphism with hepatocellular carcinoma: a meta-analysis.

BACKGROUND: Hepatocellular carcinoma (HCC) is the sixth-most common malignancy worldwide. Multiple previous studies have assessed the relationship between TM6SF2 gene polymorphism and the risk of developing HCC, with discrepant conclusions reached. To assess the association of TM6SF2 rs58542926 T/C gene polymorphism with liver cancer, we performed the current meta-analysis. METHODS: This study queried the MEDLINE, PubMed, EMBASE, and CENTRAL databases from inception to April 2019. Case-control studies assessing the relationship between TM6SF2 rs5854292 locus polymorphism and liver cancer were selected according to inclusion and exclusion criteria. The Stata 12.0 software was employed for data analysis. RESULTS: A total of 5 articles, encompassing 6873 patients, met inclusion criteria and were included in the meta-analysis. Statistical analysis showed that the TM6SF2 gene polymorphism was significantly associated with liver cancer in the allele contrast, dominant, recessive and over dominant models (T vs C, OR = 1.621, 95%CI 1.379-1.905; CT + TT vs CC. OR = 1.541, 95%CI 1.351-1.758; TT vs CT + CC, OR = 2.897, 95%CI 1.690-4.966; CC + TT vs TC, OR = 0.693, 95%CI 0.576-0.834). The Egger's test revealed no significant publication bias. CONCLUSION: The present findings suggest a significant association of TM6SF2 gene polymorphism with HCC risk in the entire population studied.

Enhancement of Atmospheric Nucleation by Highly Oxygenated Organic Molecules: A Density Functional Theory Study.

New particle formation (NPF) by gas-particle conversion is the main source of atmospheric aerosols. Highly oxygenated organic molecules (HOMs) and sulfuric acid (SA) are important NPF participants. 2-Methylglyceric acid (MGA), a kind of HOMs, is a tracer of isoprene-derived secondary organic aerosols. The nucleation mechanisms of MGA with SA were studied using density functional theory and atmospheric cluster dynamics simulation in this study, along with that of MGA with methanesulfonic acid (MSA) as a comparison. Our theoretical works indicate that the (MGA)(SA) and (MGA)(MSA) clusters are the most stable ones in the (MGA) i(SA) j ( i = 1-2, j = 1-2) and (MGA) i(MSA) j ( i = 1-2, j = 1-2) clusters, respectively. Both the formation rates of (MGA)(SA) and (MGA)(MSA) clusters are quite large and could have significant contributions to NPF. The results imply that the homomolecular nucleation of MGA is unlikely to occur in the atmosphere, and MGA and SA can effectively contribute to heteromolecular nucleation mainly in the form of heterodimers. MSA exhibits properties similar to SA in its ability to form clusters with MGA but is slightly weaker than SA.

Hydration of 3-hydroxy-4,4-dimethylglutaric acid with dimethylamine complex and its atmospheric implications.

Atmospheric aerosols have a tremendous influence on visibility, climate, and human health. New particle formation (NPF) is a crucial source of atmospheric aerosols. At present, certain field observations and experiments have discovered the presence of 3-hydroxy-4,4-dimethylglutaric acid (HDMGA), which may participate in NPF events. However, the nucleation mechanism of HDMGA has not been clearly understood. In addition, dimethylamine (DMA) is an important precursor of nucleation. The nucleation mechanism involving HDMGA and DMA has not been studied. In this study, the most stable structures of (HDMGA)(H2O)n (n = 0-3) and (HDMGA)(DMA)(H2O)n (n = 0-3) were obtained by using M06-2X coupled with the 6-311++G(3df,3pd) basis set. The α-carboxyl group is directly attached to the amino group in all the most stable configurations. Proton transfer enhances the strength of a hydrogen bond, as well as promotes the generation of a global minimum structure. Temperature has a considerable influence on the distribution of isomers for (HDMGA)(DMA)(H2O)3 as compared to the other investigated clusters. The Gibbs free energy values reveal that most of the clusters can exist in NPF, except for (HDMGA)(H2O)1. The process of adding a cluster of (H2O)n more likely occurs in the atmosphere than gradually adding a single water molecule.

Synergistic Effect of Ammonia and Methylamine on Nucleation in the Earth's Atmosphere. A Theoretical Study.

Ammonia and amines are important common trace atmospheric species that can enhance new particle formation (NPF) in the Earth's atmosphere. However, the synergistic effect of these two bases involving nucleation is still lacking. We studied the most stable geometric structures and thermodynamics of quaternary (NH3)(CH3NH2)(H2SO4) m(H2O) n ( m = 1-3, n = 0-4) clusters at the PW91PW91/6-311++G(3df,3pd) level of theory for the first time. We find that the proton transfer from H2SO4 molecule to CH3NH2 molecule is easier than to NH3 molecule in the free or hydrated H2SO4-base clusters, and thus leads to the stability. The energetically favorable formation of the (NH3)(CH3NH2)(H2SO4) m(H2O) n ( n = 0-4) clusters, by hydration or attachment of base or substitution of ammonia by methylamine at 298.15 K, indicate that ammonia and methylamine together could enhance the stabilization of small binary clusters. At low RH and an ambient temperature of 298.15 K, the concentration of total hydrated (NH3)(CH3NH2)(H2SO4)2 clusters could reach that of total hydrated (NH3)(H2SO4)2 clusters, which is the most stable ammonia-containing cluster. These results indicate that the synergistic effect of NH3 and CH3NH2 might be important in forming the initial cluster with sulfuric acid and subsequently growth process. In addition, the evaporation rates of (NH3)(CH3NH2)(H2SO4)(H2O), (NH3)(CH3NH2)(H2SO4)2 and (NH3)(CH3NH2)(H2SO4)3 clusters, three relative abundant clusters in (NH3)(CH3NH2)(H2SO4) m(H2O) n system, were calculated. We find the stability increases with the increasing number of H2SO4 molecules.

Clinical and molecular relevance of mutant-allele tumor heterogeneity in breast cancer.

PURPOSE: Intra-tumor heterogeneity (ITH) plays a pivotal role in driving breast cancer progression and therapeutic resistance. We used a mutant-allele tumor heterogeneity (MATH) algorithm to measure ITH and explored its correlation with clinical parameters and multi-omics data. METHODS: We assessed 916 female breast cancer patients from The Cancer Genome Atlas. We calculated the MATH values from whole-exome sequencing data and further investigated their correlation with clinical characteristics, somatic mutations, somatic copy number alterations (SCNAs), and gene enrichment. RESULTS: The patients were divided into low, intermediate, and high MATH groups. High T stage, African American race, and triple-negative or basal-like subtype were associated with a higher MATH level (all P < 0.001). In hormone receptor-positive and human epidermal growth factor receptor-negative patients, the high MATH group showed a tendency toward a worse overall survival (P = 0.052); Furthermore, the TP53 mutation rate increased as MATH was elevated (P < 0.001), whereas CDH1 mutations were correlated with a lower level of MATH (P = 0.002). Several focal and arm-level SCNA events were more common in the high MATH group (P < 0.05), including Chr8q24 with only the MYC gene in the "peak" region. Similarly, high MATH was associated with gene set enrichment related to the MYC pathway and proliferation. CONCLUSION: Our integrative analysis reveals the clinical and genetic relevance of ITH in breast cancer. These results also suggest the origin and natural history of clonal evolution and intra-tumor genetic heterogeneity, which warrant further investigation.

Comprehensive transcriptome analysis identifies novel molecular subtypes and subtype-specific RNAs of triple-negative breast cancer.

BACKGROUND: Triple-negative breast cancer (TNBC) is a highly heterogeneous group of cancers, and molecular subtyping is necessary to better identify molecular-based therapies. While some classifiers have been established, no one has integrated the expression profiles of long noncoding RNAs (lncRNAs) into such subtyping criterions. Considering the emerging important role of lncRNAs in cellular processes, a novel classification integrating transcriptome profiles of both messenger RNA (mRNA) and lncRNA would help us better understand the heterogeneity of TNBC. METHODS: Using human transcriptome microarrays, we analyzed the transcriptome profiles of 165 TNBC samples. We used k-means clustering and empirical cumulative distribution function to determine optimal number of TNBC subtypes. Gene Ontology (GO) and pathway analyses were applied to determine the main function of the subtype-specific genes and pathways. We conducted co-expression network analyses to identify interactions between mRNAs and lncRNAs. RESULTS: All of the 165 TNBC tumors were classified into four distinct clusters, including an immunomodulatory subtype (IM), a luminal androgen receptor subtype (LAR), a mesenchymal-like subtype (MES) and a basal-like and immune suppressed (BLIS) subtype. The IM subtype had high expressions of immune cell signaling and cytokine signaling genes. The LAR subtype was characterized by androgen receptor signaling. The MES subtype was enriched with growth factor signaling pathways. The BLIS subtype was characterized by down-regulation of immune response genes, activation of cell cycle, and DNA repair. Patients in this subtype experienced worse recurrence-free survival than others (log rank test, P = 0.045). Subtype-specific lncRNAs were identified, and their possible biological functions were predicted using co-expression network analyses. CONCLUSIONS: We developed a novel TNBC classification system integrating the expression profiles of both mRNAs and lncRNAs and determined subtype-specific lncRNAs that are potential biomarkers and targets. If further validated in a larger population, our novel classification system could facilitate patient counseling and individualize treatment of TNBC.

Examining the structural evolution of bicarbonate-water clusters: insights from photoelectron spectroscopy, basin-hopping structural search, and comparison with available IR spectral studies.

Bicarbonate plays a crucial biochemical role in the physiological pH buffering system and also has important atmospheric implications. In the current study, HCO3(-)(H2O)n (n = 0-13) clusters were successfully produced via electrospray ionization of the corresponding bulk salt solution, and were characterized by negative ion photoelectron spectroscopy and theoretical calculations. Photoelectron spectra reveal that the electron binding energy monotonically increases with the cluster size up to n = 10 and remains largely the same after n > 10. The photo-detaching feature of the solute HCO3(-) itself, which dominates in the small clusters, diminishes with the increase of water coverage. Based on the charge distribution and molecular orbital analyses, the universal high electron binding energy tail that dominates in the larger clusters can be attributed to the ionization of water. Thus, the transition of ionization from the solute to the solvent at a size larger than n = 10 has been observed. Extensive theoretical structural search based on the basin-hopping unbiased method was carried out, and a plethora of low energy isomers have been obtained for each medium and large-sized cluster. By comparing the simulated photoelectron spectra and calculated electron binding energies with the experiments, as well as by comparing the simulated infrared spectra with previously reported IR spectra, the best fit structures and the structural evolutionary routes are presented. The nature of bicarbonate-water interactions is mainly electrostatic as implied by electron localization function (ELF) analysis.

Bidirectional Interaction of Alanine with Sulfuric Acid in the Presence of Water and the Atmospheric Implication.

Amino acids are recognized as important components of atmospheric aerosols, which impact on the Earth's climate directly and indirectly. However, much remains unknown about the initial events of nucleation. In this work, the interaction of alanine [NH2CH(CH3)COOH or Ala], one of the most abundant amino acids in the atmosphere, with sulfuric acid (SA) and water (W) has been investigated at the M06-2X/6-311++G(3df, 3pd) level of theory. We have studied thermodynamics of the hydrated (Ala)(SA) core system with up to four water molecules. We found that Ala, with one amino group and one carboxyl group, can interact with H2SO4 and H2O in two directions and that it has a high cluster stabilizing effect similar to that of ammonia, which is one of the key nucleation precursor. The corresponding Gibbs free energies of the (Ala)(SA)(W)n (n = 0-4) clusters formation at 298.15 K predicted that Ala can contribute to the stabilization of small binary clusters. Our results showed that the hydrate distribution is temperature-dependent and that a higher humidity and temperature can contribute to the formation of hydrated clusters.

Development of triple-negative breast cancer radiosensitive gene signature and validation based on transcriptome analysis.

Triple-negative breast cancer (TNBC) is a heterogeneous disease with highest loco-regional recurrence among breast cancer subtypes. Radiotherapy is indispensable for TNBC loco-regional control. However, intrinsic radiosensitivity differences exist in TNBC patients and RT is still prescribed mainly based on conventional clinicopathologic features of patients without considering the differences. The purpose of the present study is to develop and validate a TNBC radiosensitive gene signature (RSGS) and to guide therapeutic decisions. In this study, we compared transcriptome profiles of 12 locally recurrent TNBCs to 20 non-locally recurrent TNBCs treated with surgery radio-chemotherapy and developed a seven-gene RSGS and a simplified three-gene RSGS by using pathway analysis, univariate Cox proportional hazards regression model and rank-based linear algorithm. They were validated by using transcriptome profiles of 166 TNBC patients. Two gene signatures specifically identified a radiosensitive population that had an improved recurrence-free survival in patients treated with surgery radio-chemotherapy (Radiosensitive patients vs radioresistant patients, for seven-gene RSGS: P = 0.024, HR = 0.35, 95 %CI 0.14­0.87 and for three-gene RSGS: P = 0.035, HR = 0.38, 95 %CI 0.15­0.94). In contrast, there was no significant difference in outcome between predicted radiosensitive and radioresistant patients that treated with other treatment modality. RSGSs provide a useful tool for identification of radiosensitive/radioresistant TNBC patients and they could lead to a better selection of patients for RT protocols.

Different patterns in the prognostic value of age for breast cancer-specific mortality depending on hormone receptor status: a SEER population-based analysis.

BACKGROUND: Few studies have been undertaken to evaluate the prognostic value of age at diagnosis for determining breast cancer survival in a large population. METHODS: Using the U.S. National Cancer Institute's Surveillance, Epidemiology, and End Results (SEER) database consisting of 18 population-based cancer registries, this study identified 331,969 female patients with a diagnosis of breast cancer from 1 January 1990, to 31 December 31. Breast cancer-specific mortality (BCSM) was compared among patients in different age groups using Kaplan-Meier plots. The Cox proportional hazards model was used for multivariate analysis. RESULTS: In the multivariate analysis, the hazard ratios (HRs) of BCSM in the different age groups formed a U-shaped curve, with patients younger than 30 years and patients older than 79 years experiencing the worst survival rates (HR, 1.19; 95 % confidence interval [CI], 1.06-1.33; P = 0.003 and HR, 2.16; 95 % CI, 2.05-2.27; P < 0.001, with age 50-59 years as the reference, respectively). When the interaction between age at diagnosis and hormone receptor (HoR) status for prediction of BCSM was further analyzed, the findings showed that in the HoR-positive group, patients younger than 30 years and patients older than 79 years had the worst survival rates (HR, 1.52; 95 % CI, 1.30-1.76; P < 0.001 and HR, 2.07; 95 % CI, 1.94-2.20; P < 0.001, respectively), whereas patients ages 40 to 49 years had the best survival rate (HR, 0.93; 95 % CI, 0.89-0.98; P = 0.005). This pattern, however, was different in the HoR-negative group. Patients younger than 60 years had nearly the same BCSM (P = 0.356, 0.199, and 0.036 for ages <30 years, 30-39 years, and 40-49 years, respectively), with BCSM starting to increase with age only for patients older than 60 years and peaking for patients older than 79 years (HR, 2.39; 95 % CI, 2.20-2.59; P < 0.001). CONCLUSIONS: The study findings show different patterns in the prognostic value of age for determining BCSM, depending on the HoR status. These data underscore the importance of age-specific studies for different HoR groups to individualize treatment and improve outcomes for breast cancer patients.

Interaction of gas phase oxalic acid with ammonia and its atmospheric implications.

Oxalic acid is believed to play an important role in the formation and growth of atmospheric organic aerosols. However, as a common organic acid, the understanding of the larger clusters formed by gas phase oxalic acid with multiple ammonia molecules is incomplete. In this work, the structural characteristics and thermodynamics of oxalic acid clusters with up to six ammonia molecules have been investigated at the PW91PW91/6-311++G(3df,3pd) level of theory. We found that oxalic acid forms relatively stable clusters with ammonia molecules, and that ionization events play a key role. The analyses of the thermodynamics and atmospheric relevance indicate that the heterodimer (H2C2O4)(NH3) shows an obvious relative concentration in the atmosphere, and thus likely participates in new particle formation. However, with increasing number of ammonia molecules, the concentration of clusters decreases gradually. Additionally, clusters of oxalic acid with ammonia molecules are predicted to form favorably in low temperature conditions and show high Rayleigh scattering intensities.

Stability of Hydrated Methylamine: Structural Characteristics and H2N···H-O Hydrogen Bonds.

Methylamine is the simplest aliphatic amine found in human urine, blood, and tissues. It is thought to play a significant part in central nervous system disturbances observed during renal and hepatic disease. In this work we have investigated the methylamine hydration clusters using a basin hopping (BH) algorithm with the density functional theory (DFT). The results presented herein yield a detailed understanding of the structure and stability for a system consisting of one methylamine molecule and up to seven waters: the most stable geometries arise from a fusion of tetramer or pentamer rings; by the geometrical parameters and topological parameters analysis, the strengths of the H2N···H-O hydrogen bonds of the global minima increase as the sizes of clusters increase, except for n = 5 where there is a slight fluctuation. This work may shed light on the form mechanism of methylamine existing in organisms and the hydration structures of larger molecules containing amino functional groups and their interaction with the water molecules nearby.

Properties of ammonium ion-water clusters: analyses of structure evolution, noncovalent interactions, and temperature and humidity effects.

Although ammonium ion-water clusters are abundant in the biosphere, some information regarding these clusters, such as their growth route, the influence of temperature and humidity, and the concentrations of various hydrated clusters, is lacking. In this study, theoretical calculations are performed on ammonium ion-water clusters. These theoretical calculations are focused on determining the following characteristics: (1) the pattern of cluster growth; (2) the percentages of clusters of the same size at different temperatures and humidities; (3) the distributions of different isomers for the same size clusters at different temperatures; (4) the relative strengths of the noncovalent interactions for clusters of different sizes. The results suggest that the dipole moment may be very significant for the ammonium ion-water system, and some new stable isomers were found. The nucleation of ammonium ions and water molecules is favorable at low temperatures; thus, the clusters observed at high altitudes might not be present at low altitudes. High humidity can contribute to the formation of large ammonium ion-water clusters, whereas the formation of small clusters may be favorable under low-humidity conditions. The potential energy surfaces (PES) of these different sized clusters are complicated and differ according to the distribution of isomers at different temperatures. Some similar structures are observed between NH4(+)(H2O)n and M(H2O)n (where M represents an alkali metal ion or water molecule); when n = 8, the clusters begin to form the closed-cage geometry. As the cluster size increases, these interactions become progressively weaker. The successive binding energy at the DF-MP2-F12/VDZ-F12 level is better than that at the PW91PW91/6-311++G(3df, 3pd) level and is consistent with the experimentally determined values.

Study of Cl(-)(H2O)n (n = 1-4) using basin-hopping method coupled with density functional theory.

Cl(-)(H2O)n (n = 1-4) clusters were investigated using a basin-hopping (BH) algorithm coupled with density functional theory (DFT). Structures, energetics, thermodynamics, vertical detachment energies, and vibrational frequencies were obtained from high-level ab initio calculations. Through comparisons with previous theoretical and experimental data, it was demonstrated that the combination of the BH method and DFT could accurately predict the global and local minima of Cl(-)(H2O)n (n = 1-4). Additionally, to optimize larger Cl(-)(H2O)n (n > 4) clusters, several popular density functionals as well as DF-LMP2 (Schütz et al., J. Chem. Phys. 2004, 121, 737) (second-order Møller-Plesset perturbation theory using local and density fitting approximations) were tested with appropriate basis sets through comparisons with MP2 optimized results. DF-LMP2 will be used in future studies because its overall performance in describing the relative binding energies and the geometrical parameters of Cl(-)(H2O)n (n = 1-4) was outstanding in this study.

Theoretical study of temperature dependence and Rayleigh scattering properties of chloride hydration clusters.

Cl(-)(H2O)n (n = 5-6) clusters were investigated using a basin hopping (BH) method coupled with density functional theory (DFT). Structures, energetics, thermodynamics, and vibrational frequencies were obtained using high level ab initio calculations. DF-LMP2 (second-order Møller-Plesset perturbation theory using local and density fitting approximations) with an appropriate basis set were employed for final optimization and frequency calculation, which has been benchmarked in a recent study. The global minimum of Cl(-)(H2O)5 was verified and the new competitive local minimum of Cl(-)(H2O)6 was offered. Considering the increasing complexity of the large system and the high flexibility of the hydrogen bonding environment, Boltzmann averaged Gibbs free energy was provided taking into account the contributions of local minima on the potential energy surface. Finally, the temperature dependence of the conformational population for isomers of Cl(-)(H2O)n (n = 5-6) and Rayleigh scattering properties of Cl(-)(H2O)n (n = 1-6) have been investigated systematically for the first time.

Structural exploration of water, nitrate/water, and oxalate/water clusters with basin-hopping method using a compressed sampling technique.

Exploration of the low-lying structures of atomic or molecular clusters remains a fundamental problem in nanocluster science. Basin hopping is typically employed in conjunction with random motion, which is a perturbation of a local minimum structure. We have combined two different sampling technologies, "random sampling" and "compressed sampling", to explore the potential energy surface of molecular clusters. We used the method to study water, nitrate/water, and oxalate/water cluster systems at the MP2/aug-cc-pVDZ level of theory. An isomer of the NO3(-)(H2O)3 cluster molecule with a 3D structure was lower in energy than the planar structure, which had previously been reported by experimental study as the lowest-energy structure. The lowest-energy structures of the NO3(-)(H2O)5 and NO3(-)(H2O)7 clusters were found to have structures similar to pure (H2O)8 and (H2O)10 clusters, which contradicts previous experimental result by Wang et al.(J. Chem. Phys. 2002, 116, 561-570). The new minimum energy structures for C2O4(2-)(H2O)5 and C2O4(2-)(H2O)6 are found by our calculations.