bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computational modeling of tetrahydroimidazo‐[4,5,1‐jk][1,4]‐benzodiazepinone derivatives: An atomistic drug design approach using Kier‐Hall electrotopological state (E‐state) indices
Authors: Sapre Nitin S. , Pancholi Nilanjana , Gupta Swagata , Sapre Neelima 
Published: March 2008

AbstractQuantitative structure‐activity relationships (QSAR), based on E‐state indices have been developed for a series of tetrahydroimidazo‐[4,5,1‐jk]‐benzodiazepinone derivatives against HIV‐1 reverse transcriptase (HIV‐1 RT). Statistical modeling using multiple linear regression technique in predicting the anti‐HIV activity yielded a good correlation for the training set (R2 = 0.913, R = 0.897, Q2 = 0.849, MSE = 0.190, F‐ratio = 59.97, PRESS = 18.05, SSE = 0.926, and p value = 0.00). Leave‐one‐out cross‐validation also reaffirmed the predictions (R2 = 0.850, R = 0.824, Q2 = 0.849, MSE = 0.328, and PRESS = 18.05). The predictive ability of the training set was also cross‐validated by a test set (R2 = 0.812, R = 0.799, Q2 = 0.765, MSE = 0.347, F‐ratio = 64.69, PRESS = 7.37, SSE = 0.975, and p value = 0.00), which ascertained a satisfactory quality of fit. The results reflect the substitution pattern and suggest that the presence of a bulky and electropositive group in the five‐member ring and electron withdrawing groups in the seven‐member ring will have a positive impact on the antiviral activity of the derivatives. Bulky groups in the six‐member ring do not show an activity‐enhancing impact. Outlier analysis too reconfirms our findings. The E‐state descriptors indicate their importance in quantifying the electronic characteristics of a molecule and thus can be used in chemical interpretation of electronic and steric factors affecting the biological activity of compounds. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008
Reference energy extremal optimization: A stochastic search algorithm applied to computational protein design
Authors: Zhang Naigong , Zeng Chen 
Published: March 2008

AbstractWe adapt a combinatorial optimization algorithm, extremal optimization (EO), for the search problem in computational protein design. This algorithm takes advantage of the knowledge of local energy information and systematically improves on the residues that have high local energies. Power‐law probability distributions are used to select the backbone sites to be improved on and the rotamer choices to be changed to. We compare this method with simulated annealing (SA) and motivate and present an improved method, which we call reference energy extremal optimization (REEO). REEO uses reference energies to convert a problem with a structured local‐energy profile to one with more random profile, and extremal optimization proves to be extremely efficient for the latter problem. We show in detail the large improvement we have achieved using REEO as compared to simulated annealing and discuss a number of other heuristics we have attempted to date. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008
A dynamic lattice searching method with interior operation for unbiased optimization of large Lennard‐Jones clusters
Authors: Shao Xueguang , Yang Xiaoli , Cai Wensheng 
Published: March 2008

AbstractFor improving the efficiency of dynamic lattice searching (DLS) method for unbiased optimization of large Lennard‐Jones (LJ) clusters, a variant of the interior operation (IO) proposed by Takeuchi was combined with DLS. The method is named as DLS‐IO. In the method, the IO moves outer atoms with higher energy toward the coordinates center, i.e., (0, 0, 0), of a cluster and a local minimization (LM) follows each IO. This makes the interior atoms more compact and the outer atoms more uniformly distributed with lower potential energy. Therefore, the starting structure for DLS operations is closer to the global optimum compared with the randomly generated structures. On the other hand, a method to identify the central atom is proposed for the central vacancy problem. Optimizations of LJ500, LJ561, LJ660, LJ665, and LJ670 were investigated with the DLS‐IO, and the structural transition during the optimization was analyzed. It was found that the method is efficient and unbiased for optimization of large LJ clusters, and it may be a promising approach to be universally used for structural optimizations. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008
The equivalent potential of water for electronic structure of aspartic acid
Authors: Zhang Tian , Zheng Haoping , Yan Shu 
Published: March 2008

AbstractThe equivalent potential of water for the electronic structure of aspartic acid (Asp−) in solution is constructed by the first‐principles, all‐electrons, ab initio calculations. Aspartic acid is a hydrophilic amino acid which is negatively charged in neutral water solution. The main process of calculation consists of three steps. Firstly, the geometric structure of the cluster containing Asp− and water molecules is calculated by the free cluster calculation. Then, based on the obtained geometric structure, the electronic structure of Asp− with the potential of water molecules is calculated using the self‐consistent cluster‐embedding method. Finally, the electronic structure of Asp− with the potential of dipoles is calculated. The results show that the major effect of water on Asp−'s electronic structure is lowering the occupied molecular orbitals by about 0.02 Ry on average, and narrowing energy gap by 10.8%. The effect of water on the electronic structure of Asp− can be simulated by dipoles potential. © 2008 Wiley Periodicals, Inc.J Comput Chem, 2008.
Prediction of densities for solid energetic molecules with molecular surface electrostatic potentials
Authors: Kim Chan Kyung , Cho Soo Gyeong , Kim Chang Kon , Park Hyung‐Yeon , Zhang Hui , Lee Hai Whang 
Published: March 2008

AbstractThe densities of high energetic molecules in the solid state were calculated with a simplified scheme based on molecular surface electrostatic potentials (MSEP). The MSEP scheme for density estimation, originally developed by Politzer et al., was further modified to calculate electrostatic potential on a simpler van der Waals surface. Forty‐one energetic molecules containing at least one nitro group were selected from among a variety of molecular types and density values, and were used to test the suitability of the MSEP scheme for predicting the densities of solid energetic molecules. For comparison purposes, we utilized the group additivity method (GAM) incorporating the parameter sets developed by Stine (Stine‐81) and by Ammon (Ammon‐98 and ‐00). The absolute average error in densities from our MSEP scheme was 0.039 g/cc. The results based on our MSEP scheme were slightly better than the GAM results. In addition, the errors in densities generated by the MSEP scheme were almost the same for various molecule types, while those predicted by GAM were somewhat dependent upon the molecule types. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008
CHARMM‐GUI: A web‐based graphical user interface for CHARMM
Authors: Jo Sunhwan , Kim Taehoon , Iyer Vidyashankara G. , Im Wonpil 
Published: March 2008

AbstractCHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM‐GUI, http://www.charmm‐gui.org, has been developed to provide a web‐based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM‐GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM‐GUI development project are also discussed briefly together with other features in the CHARMM‐GUI website, such as Archive and Movie Gallery. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008
Time‐dependent density functional theory study on hydrogen‐bonded intramolecular charge‐transfer excited state of 4‐dimethylamino‐benzonitrile in methanol
Authors: Zhao Guang‐Jiu , Han Ke‐Li 
Published: March 2008

AbstractThe time‐dependent density functional theory (TDDFT) method was carried out to investigate the hydrogen‐bonded intramolecular charge‐transfer (ICT) excited state of 4‐dimethylaminobenzonitrile (DMABN) in methanol (MeOH) solvent. We demonstrated that the intermolecular hydrogen bond C≡N···HO formed between DMABN and MeOH can induce the C≡N stretching mode shift to the blue in both the ground state and the twisted intramolecular charge‐transfer (TICT) state of DMABN. Therefore, the two components at 2091 and 2109 cm−1 observed in the time‐resolved infrared (TRIR) absorption spectra of DMABN in MeOH solvent were reassigned in this work. The hydrogen‐bonded TICT state should correspond to the blue‐side component at 2109 cm−1, whereas not the red‐side component at 2091 cm−1 designated in the previous study. It was also demonstrated that the intermolecular hydrogen bond C≡N···HO is significantly strengthened in the TICT state. The intermolecular hydrogen bond strengthening in the TICT state can facilitate the deactivation of the excited state via internal conversion (IC), and thus account for the fluorescence quenching of DMABN in protic solvents. Furthermore, the dynamic equilibrium of these electronically excited states is explained by the hydrogen bond strengthening in the TICT state. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008
Structures and stability of lithium monosilicide clusters SiLin (n = 4–16): What is the maximum number, magic number, and core number for lithium coordination to silicon?
Authors: He Ning , Xie Hong‐Bin , Ding Yi‐Hong 
Published: March 2008

AbstractIn the coordination, hypervalent and cluster chemistry, three important characteristic properties are the maximum coordination number, magic number, and core coordination number. Yet, few studies have considered these three numbers at the same time for an MLn cluster with n larger than 8. In this article, we systematically studied the three properties of SiLin (n = 4–16) clusters at the B3LYP/6‐31G(d), B3LYP/6‐311++G(2d), and CCSD(T)/6‐311++G(3df)//B3LYP/6‐311++G(2d) (for energy only) levels. Various isomeric forms with different symmetries were calculated. For each SiLin (n = 4–9), silicon cohesive energy (cE) from SiLin → Si + Lin reaction, vertical ionization potential (vIP), and vertical electron affinity (vEA) were obtained for the lowest‐energy isomer. We found that the maximum Li‐coordination number of Si is 9, which is the largest number among the known MLin clusters. All cE, vIP, and vEA values predicted that 6 is the magic Li‐coordination number of Si. For small SiLin (n ≤ 6) clusters, Li atoms favor direct coordination to Si, whereas for larger SiLin (n ≥ 7) clusters, there is a core cluster that is surrounded by excessive Li atoms. The core Li‐coordination number is 6 for SiLin (n = 7,8), 7 for SiLin (n = 9,10), 8 for SiLin (n = 11–15) and 9 for SiLin (n ≥ 16). Through the calculations, we verified the relationship between the structure and stability of SiLin with the maximum coordination number, magic number, and core coordination number. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008
Role of structural water molecule in HIV protease‐inhibitor complexes: A QM/MM study
Authors: Suresh Cherumuttathu H. , Vargheese Aswathy Mary , Vijayalakshmi K. Periya , Mohan Neetha , Koga Nobuaki 
Published: March 2008

AbstractStructural water molecule 301 found at the interface of HIV protease‐inhibitor complexes function as a hydrogen bond (H‐bond) donor to carbonyl groups of the inhibitor as well as H‐bond acceptor to amide/amine groups of the flap region of the protease. In this study, six systems of HIV protease‐inhibitor complexes were analyzed, which have the presence of this “conserved” structural water molecule using a two‐layer QM/MM ONIOM method. The combination of QM/MM and QM method enabled the calculation of strain energies of the bound ligands as well as the determination of their binding energies in the ligand–water and ligand–water–protease complexes. Although the ligand experiences considerable strain in the protein bound structure, the H‐bond interactions through the structural water overcomes this strain effect to give a net stability in the range of 16–24 kcal/mol. For instance, in 1HIV system, the strain energy of the ligand was 12.2 kcal/mol, whereas the binding energy associated with the structural water molecule was 20.8 kcal/mol. In most of the cases, the calculated binding energy of structural water molecule showed the same trend as that of the experimental binding free energy values. Further, the classical MD simulations carried out on 1HVL system with and without structural water 301 showed that this conserved water molecule enhances the H‐bond dynamics occurring at the Asp‐bound active site region of the protease‐inhibitor system, and therefore it will have a direct influence on the mechanism of drug action. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008
The amphioxus Hox cluster: characterization, comparative genomics, and evolution
Authors: Amemiya Chris T. , Prohaska Sonja J. , Hill‐Force Alicia , Cook April , Wasserscheid Jessica , Ferrier David E.K. , Pascual‐Anaya Juan , Garcia‐Fernàndez Jordi , Dewar Ken , Stadler Peter F. 
Published: March 2008

AbstractThe amphioxus Hox cluster is often viewed as “archetypal” for the chordate lineage. Here, we present a descriptive account of the 448 kb region spanning the Hox cluster of the amphioxus Branchiostoma floridae from Hox14 to Hox1. We provide complete coding sequences of all 14 previously described amphioxus sequences and give a detailed analysis of the conserved noncoding regulatory sequence elements. We find that the posterior part of the Hox cluster is so highly derived that even the complete genomic sequence is insufficient to decide whether the posterior Hox genes arose by independent duplications or whether they are true orthologs of the corresponding gnathostome paralog groups. In contrast, the anterior region is much better conserved. The amphioxus Hox cluster strongly excludes repetitive elements with the exception of two repeat islands in the posterior region. Repeat exclusion is also observed in gnathostomes, but not protostome Hox clusters. We thus hypothesize that the much shorter vertebrate Hox clusters are the result of extensive resolution of the redundancy of regulatory DNA after the genome duplications rather than the consequence of a selection pressure to remove nonfunctional sequence from the Hox cluster. J. Exp. Zool. (Mol. Dev. Evol.) 310B:465–477, 2008. © 2008 Wiley‐Liss, Inc.
Sensitivity of the regional climate of East/Southeast Asia to convective parameterizations in the RegCM3 modelling system. Part 1: Focus on the Korean peninsula
Authors: Im Eun‐Soon , Ahn Joong‐Bae , Remedio Armelle Reca , Kwon Won‐Tae 
Published: March 2008

AbstractThis study investigates the capability of the regional climate model, RegCM3, to simulate fine‐scale regional climate over a narrow peninsula or archipelago. The model is run in one‐way double‐nested mode with one mother domain and two nested domains. The mother domain encompasses the eastern and southern regions of Asia and adjacent oceans with a grid spacing of 60 km. The first nested domain focuses on the Korean peninsula and the second one covers the Philippine archipelago with a grid spacing of 20 km. The simulation spans a period of 5 years and 1 month, from November 2000 to December 2004. The sensitivity of the two convection schemes, namely, the Grell scheme (Grell) and the MIT‐Emanuel scheme (EMU), is studied.Model results obtained with both the Grell and EMU show reasonable performance in capturing the seasonal variation and the spatial characteristics of the East Asian monsoon. However, the Grell simulation appears to have persistent cold and dry biases in the summer season. There is a definite improvement in these model deficiencies by the implementation of EMU. Although the temperature fields in the Grell and EMU simulations are essentially the same in terms of the spatial distribution, the EMU simulation is quantitatively in better agreement with the observed estimates, indicating a substantial reduction in the cold bias. Further, in comparison with the Grell simulation, the EMU simulation shows an improvement in the timing and amplitude of the rain band propagating northward. The spatial distributions of precipitation also have good quality, capturing the localized maxima over Korea. The frequency distributions of daily temperature and precipitation simulated by EMU are closer to observations than those of the Grell simulation. It is found that the convective precipitation derived from different convection parameterizations is a major contributor to the performance of the model in summer. Copyright © 2008 Royal Meteorological Society
Investigating the climatic impact of urban planning strategies through the use of regional climate modelling: a case study for Melbourne, Australia
Authors: Coutts Andrew M. , Beringer Jason , Tapper Nigel J. 
Published: March 2008

AbstractUrban planning is a useful method for improving local climate and human health in cities through purposefully modifying urban land surface characteristics. This can reduce the potential risks of elevated city temperatures due to the urban heat island (UHI). Unfortunately, simple tools are not readily available for urban planners to assess the climatological impacts of various urban development scenarios. Urban modelling could be developed into such a tool to achieve this. This study attempts to design and evaluate a suitable tool for application in Melbourne, Australia. The Air Pollution Model (TAPM) was chosen to assess the impact of a long‐term urban planning strategy on local climate and the above canopy UHI in Melbourne. Improvements were made to TAPM by increasing the number of urban land‐use classes in the model and creating a higher resolution land cover database focused on housing density. This modified version of TAPM showed a good performance in replicating the surface energy balance compared with an observational flux tower site in suburban Melbourne during summer. TAPM simulated a mean maximum UHI intensity of 3–4 °C at 2 a.m. in January. A future UHI scenario was then examined (year 2030) using an urban land cover database derived from plans in the Melbourne 2030 urban planning strategy. Results highlighted specific areas where planning intervention would be particularly useful to improve local climates, namely activity centres and growth areas. The appropriateness of the use of TAPM and climate models as a tool in urban planning is also discussed. Copyright © 2008 Royal Meteorological Society
Keeping it real: anticounterfeiting strategies in the pharmaceutical industry
Authors: Lybecker Kristina M. 
Published: March 2008

AbstractAlthough pharmaceutical counterfeiting incidents can be traced back thousands of years, it has been downplayed and even dismissed by pharmaceutical manufacturers in the past. That has changed. Pharmaceutical firms are newly dedicated to eradicate counterfeits globally and spending more money on anticounterfeiting efforts than ever before. The confluence of three factors seems to have drastically changed the existing paradigm for the pharmaceutical industry: increasing globalization, advancing technology, and the controversies surrounding the WTO Trade‐related Aspects of Intellectual Property Rights Agreement and access to medicines. Given that counterfeit pharmaceuticals slip into the supply chain at every link, multinational pharmaceutical firms are searching for global solutions through increased interfirm cooperation along the supply chain. This research presents a theoretical model for characterizing the implications of these interventions on the motivations driving counterfeiters. The interventions are shown to increase the share of real pharmaceuticals and decrease the welfare losses attributable to counterfeiting. In practice, it is too early to evaluate the success of these new measures, but this research reflects on the extent of cooperation both across the supply chain and national boundaries and examines the likely long‐run implications of these measures. Copyright © 2008 John Wiley & Sons, Ltd.
The entry and exit decisions of foreign banks in Hong Kong
Authors: Leung Man K. , Young Trevor , Fung Michael K. 
Published: March 2008

AbstractThis paper presents a theoretical framework for explaining the entry and exit decisions of a firm, motivated by the differential returns in its home and a host market. Within this framework, the factors underpinning the entry and exit decisions of foreign banks in Hong Kong are examined, using a duration (accelerated failure time) model. It can be seen that a foreign bank, with international experience from having more overseas markets will take a shorter (longer) time to enter (exit) the Hong Kong market. Faster (slower) growth both in home trade with Hong Kong and in the Hong Kong banking sector itself will increase the likelihood of entry (exit). Ceteris paribus, Asian banks enter at a faster rate and survive longer in the Hong Kong market. Copyright © 2008 John Wiley & Sons, Ltd.
Measurement of turbulence intensity profile by a mini‐sodar
Authors: Chan P. W. 
Published: March 2008

AbstractLow‐level turbulence can bring about rapid bumps and jolts to an aircraft. In severe turbulence, the aircraft may suffer momentary loss of control. In accordance with the practice of the International Civil Aviation Organization (ICAO), turbulence intensity is expressed in terms of the cube root of the eddy dissipation rate (EDR). Measurement of the EDR is an important component in the provision of turbulence alerting services for arriving and departing aircraft at an airport. This article describes a method to calculate the EDR profile using the wind measurements from a ground‐based mini‐sodar located near the Hong Kong International Airport (HKIA). The method makes use of the vertical wind data at 0.25 or 0.5 Hz provided by the mini‐sodar (depending on the maximum measurement range) and searches for the inertial sub‐range in the frequency spectrum of the vertical wind. The accuracy of the wind and EDR measurements of the mini‐sodar is first established by comparison with meteorological tower data in a field experiment. The potential application of the EDR profiles in terrain‐disrupted airflow at HKIA is then demonstrated through two case studies. The EDR profiles obtained from the mini‐sodar are found to be of good quality and could be useful in the monitoring of low‐level turbulence for aviation applications. Copyright © 2008 Royal Meteorological Society