Papers by Roberto Gomperts
Multiple sequence alignments represent a class of powerful bioinformatics tools with many uses in... more Multiple sequence alignments represent a class of powerful bioinformatics tools with many uses in computational biology. Knowledge of multiple alignments (MA) helps to predict secondary and tertiary structures and to detect homologies between newly sequenced genes and existing gene (protein) families. With the adoption of high-throughput (HT) automation, offering scientists significantly more data with which to make better decisions, it is increasingly important to run MA calculations as quickly as possible to allow real-time decision making in the lab. The popular MA application Clustal W (1) provides a very good example of how the resources of multiprocessor shared memory computers can be utilized more efficiently. This paper first outlines the efforts undertaken by SGI to parallelize the Clustal W application. The parallel version shows speedups of up to 10x when running Clustal W on 16 CPUs and significantly reduces the time required for data analysis. Second, the development of a high-throughput version of Clustal W called HT Clustal and the different methods of scheduling multiple MA jobs in HT Clustal are discussed. Third, improvements in the recently introduced MULTICLUSTAL algorithm (2) and its efficient use of Parallel Clustal W are reviewed.
Transparent distribution and execution of data in a multiprocessor environment
Parallel Computing, 2000
In this study we report the implementation of Gaussian 98 using OpenMP. OpenMP is a standard for ... more In this study we report the implementation of Gaussian 98 using OpenMP. OpenMP is a standard for parallel programming on shared memory computers. We compare the performance of OpenMP with methods such as Hartree±Fock (HF) and density functional theory (DFT), including ®rst and second derivatives of the energy. In addition we also look at CIsingles (CIS). Performance was investigated with up to 32 processors and compared against the standard version of Gaussian 98. Ó
Parallel processing and computational chemistry
Proteins, 1991
Scalability of Gaussian 03 on SGI Altix: The Importance of Data Locality on CC-NUMA Architecture
Lecture Notes in Computer Science, 2009
Performance anomalies when running Gaussian frequency calculations in parallel on SGI Altix compu... more Performance anomalies when running Gaussian frequency calculations in parallel on SGI Altix computers with CC-NUMA memory architecture are analyzed using performance tools that access hardware counters. The bottleneck is the frequent and nearly simultaneous data-loads of all threads involved in the calculation of data allocated in the node where the master thread runs. Code changes that ensure these data-loads are
The Journal of Physical Chemistry A, 1998
We report herein the results of a high-level ab initio study of the D 2d and C 2h structures of 1... more We report herein the results of a high-level ab initio study of the D 2d and C 2h structures of 1,3,5,7cyclooctatetraene, COT, and bicyclo[4.2.0]octa-2,4,7-triene, BOT. This information has been used to obtain, seemingly for the first time, the standard heat of formation of COT in the gas phase. Values obtained by means of standard atomization reaction are higher than the experimental value (4.7 kcal mol -1 at the G2 level). When isodesmic or homodesmotic reactions are used, the computational and experimental values agree well within the experimental uncertainties.
Ab initia MO calculation in terms of localized orbitals of the 14N electric field gradient in nitriles
Theoretica Chimica Acta, 1988
The contributions of each localized orbital of the CN group and of the molecular remainder to the... more The contributions of each localized orbital of the CN group and of the molecular remainder to the N electric field gradient (EFG) were calculated for nitriles with R = H, F, CH3, OH, NH2, CCH, COH, NO, CN and the E and Z forms of iminoacetonitrile. The changes in the EFG ...
Interaction of CO Molecule with Au/MOR Catalyst: ONIOM-PM6 Study, Active Sites, Thermodynamic and Vibrational Frequencies
The Journal of Physical Chemistry A, 2010
ONIOM calculations have been carried out to determine geometries, adsorption energies, and vibrat... more ONIOM calculations have been carried out to determine geometries, adsorption energies, and vibrational frequencies of CO on a model for Au-exchanged mordenite catalysts, Au/MOR. The CO-calculated vibrational frequencies (upsilon(CO)) are in good agreement with the reported experimental values. We proposed to interpret the frequency results. CH(3)COCH(3) and CH(3)SH adsorption enthalpy calculations on Au/MOR model show that the Au/MOR catalyst behaves like a soft acid according to Pearson's rule. A higher structural deformation degree of the mordenite was found in the calculations with PM6 than with universal force field approach approach. A new pseudopotential (ACEP-121) was developed to improve the Au-Au distance, and Au ionization potential.
The Journal of Physical Chemistry A, 1999
The standard molar enthalpy of formation of gaseous 1-adamantyl chloride (1Cl,g) was determined e... more The standard molar enthalpy of formation of gaseous 1-adamantyl chloride (1Cl,g) was determined experimentally by means of thermochemical techniques. Ab initio quantum-chemical calculations at the G2-(MP2) level were performed on adamantyl cation (1 + ) and on 1Cl. Combination of these data with other experimental and computational results for adamantane (1H), isobutane (2H), tert-butyl cation (2 + ), and tertbutyl chloride (2Cl) provided purely experimental and purely computational, independent values for the standard enthalpy and Gibbs energy changes for reactions 1 and 2:
The Journal of Organic Chemistry, 2002
The standard enthalpy of formation of gaseous 2-adamantyl chloride(2-Ad-Cl) was determined by cal... more The standard enthalpy of formation of gaseous 2-adamantyl chloride(2-Ad-Cl) was determined by calorimetric techniques. The standard Gibbs energy change for the chloride anion exchange between 1-adamantyl (1-Ad + ) and 2-adamantyl (2-Ad + ) cations in the gas phase was obtained by Fourier transform ion cyclotron resonance spectroscopy (FT ICR). Theoretical calculations at the G2(MP2) level were performed on these and other relevant species. This and data from the literature provided three highly consistent independent estimates of the relative stabilities of 2-Ad + and 1-Ad + . This difference in gas-phase stability was compared to the differential structural effects on the rates of solvolysis of the corresponding chlorides and tosylates, and it was shown that the thermodynamic stability of the secondary cation is the leading factor determining the solvolytic reactivity of the precursors in the absence of solvent effects. Thus, under these conditions, the previously established linear free energy correlation between carbenium ion stability and solvolytic reactivity of bridgehead derivatives applies also to secondary derivatives.
The Journal of Organic Chemistry, 1999
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Conformational analysis of HIV-1 protease inhibitors: 2. Thioproline P1? Residue in the potent inhibitor KNI-272
Journal of Computational Chemistry, 1997
ABSTRACT The very potent HIV-1 protease (HIV-PR) inhibitor, KNI-272, contains a norstatine–thiopr... more ABSTRACT The very potent HIV-1 protease (HIV-PR) inhibitor, KNI-272, contains a norstatine–thioproline linkage at P1–P1′. The three-dimensional crystal structure of this compound bound to HIV-PR has recently been determined [Baldwin et al., Structure, 3, 581 (1995)]. The crystal structure reveals a number of interesting interactions previously unseen in bound HIV-PR inhibitors. Here, we employ high-level ab initio calculations and molecular modeling to ascertain the strain energy of the bound conformation of the norstatine–thioproline portion of KNI-272. Baldwin et al. suggested that two of the reasons for the high potency of KNI-272 are the rigidity of its backbone and a strong preference for the norstatine–thioproline amide linkage to adopt a trans conformation. Our analysis shows that, on the contrary, there is still considerable flexibility in the backbone of the norstatine-based inhibitor. Furthermore, in the gas phase and in solution, there are both cis and trans conformations of the norstatine–thioproline amide linkage which are low in energy. However, when bound in the active site of HIV-PR, KNI-272 clearly has a strong preference for a trans conformation, which enables the formation of hydrogen bonds to the flap water. Our calculations, at level up to MP2/6-31++G//HF/6-31G*, suggest that the bound, trans amide conformation of the norstatine–thioproline “core” is still strained by 2–3 kcal/mol, primarily due to the placement of the P1′ thioproline carboxamide. This result is consistent with those previously obtained for the related protease inhibitor Ro 31-8959 (Saquinovir), which also requires a carboxamide to adopt a high-energy rotamer to preserve a good hydrogen bond to the flap water. However, the strain of the bound conformation of KNI-272 is clearly lower than that of Saquinovir. In addition, because the norstatine linkage does not contain a basic amine (as do Saquinovir and JG-365, for example) it should be easier to desolvate, which also assists in binding. The relationship between KNI-272, JG-365, Saquinovir, and P1′ proline-containing substrate also is discussed. © 1997 John Wiley & Sons, Inc. J Comput Chem18: 1151–1166
Investigation of Salt Bridge Stability in a Generalized Born Solvent Model
Journal of Chemical Theory and Computation, 2006
Potentials of mean force (PMFs) of salt bridge formation between oppositely charged amino acid si... more Potentials of mean force (PMFs) of salt bridge formation between oppositely charged amino acid side chains were calculated both in explicit solvent and in a Generalized Born (GB) continuum solvent model to quantify the potential overstabilization of side chain ion pairs in GB relative to explicit solvation. These show that salt bridges are too stable by as much as 3-4 kcal/mol in the GB solvent models that we tested, consistent with previously reported observations of significantly different structural ensembles in GB models and explicit solvent for proteins containing ionizable groups. We thus investigated a simple empirical correction, wherein the intrinsic GB radii of hydrogen atoms bound to charged nitrogen atoms are reduced, effectively increasing the desolvation penalty of the positively charged groups. The thermodynamics of salt bridge formation were considerably improved, as exemplified by the close match of the corrected GB PMF to the reference explicit solvent PMF, and more significantly by our ability to closely reproduce the experimental temperature melting profile of the TC5b Trp-cage miniprotein, which is otherwise highly distorted by prevalent non-native salt bridges when using standard GB parameters.
Potential energy surface of cyclooctatetraene
The Journal of Chemical Physics, 1998
[The Journal of Chemical Physics 108, 203 (1998)]. José L. Andrés, Obis Castaño, Antonio Morreale... more [The Journal of Chemical Physics 108, 203 (1998)]. José L. Andrés, Obis Castaño, Antonio Morreale, Raul Palmeiro, Roberto Gomperts. Abstract. ... BS Tsukerblat, Group Theory in Chemistry and Spectroscopy (Academic, New York, 1994). WT Borden and ER Davidson, Acc. ...
Molybdenum Phosphide as ano-Propylaniline Hydrodenitrogenation Catalyst: A First Principles Study
Chemistry - A European Journal, 2004
MoP has been shown experimentally to be an active catalyst in the hydrodenitrogenation of o-propy... more MoP has been shown experimentally to be an active catalyst in the hydrodenitrogenation of o-propylaniline. We investigate the structure and the energetics of the o-propylaniline adsorption on the Mo-terminated MoP(001) surface. Detailed information on the structure of the free MoP(001) surface and on the structure and adsorption energy of o-propylaniline on MoP(001) is obtained by using density functional theory. The transition state, reaction path, and the energy barrier are reported for one of the branches of the HDN reaction network that leads to the formation of propylbenzene by hydrogenolysis of the C-N bond.
Chemical Physics Letters, 2001
SGI ChemBio
Multiple sequence alignments represent a class of powerful bioinformatics tools with many uses in... more Multiple sequence alignments represent a class of powerful bioinformatics tools with many uses in computational biology. Knowledge of multiple alignments (MA) helps to predict secondary and tertiary structures and to detect homologies between newly sequenced genes and existing gene (protein) families. With the adoption of high-throughput (HT) automation, offering scientists significantly more data with which to make better decisions, it is increasingly important to run MA calculations as quickly as possible to allow real-time decision making in the lab. The popular MA application Clustal W (1) provides a very good example of how the resources of multiprocessor shared memory computers can be utilized more efficiently. This paper first outlines the efforts undertaken by SGI to parallelize the Clustal W application. The parallel version shows speedups of up to 10x when running Clustal W on 16 CPUs and significantly reduces the time required for data analysis. Second, the development of a high-throughput version of Clustal W called HT Clustal and the different methods of scheduling multiple MA jobs in HT Clustal are discussed. Third, improvements in the recently introduced MULTICLUSTAL algorithm (2) and its efficient use of Parallel Clustal W are reviewed.
Die Valenzisomerisierung von Cyclooctatetraen zu Semibullvalen
Angewandte Chemie, 2000
Castaño, O., Frutos, L.-M., Palmeiro, R., Notario, R., Andrés, J.-L., Gomperts, R., Blancafort, L... more Castaño, O., Frutos, L.-M., Palmeiro, R., Notario, R., Andrés, J.-L., Gomperts, R., Blancafort, L. and Robb, M.(2000), Die Valenzisomerisierung von Cyclooctatetraen zu Semibullvalen. Angewandte Chemie, 112: 21682170. doi: 10.1002/1521-3757 (20000616) 112: 12< ...
Angewandte Chemie International Edition, 2000
Tricyclo[3.2.1.0 2,8 ]octa-2,6-diene or semibullvalene (SBV; 1), an isomer of 1,3,5,7-cyclooctate... more Tricyclo[3.2.1.0 2,8 ]octa-2,6-diene or semibullvalene (SBV; 1), an isomer of 1,3,5,7-cyclooctatetraene (COT; 2) was isolated by Zimmerman and Grunewald. At À 140 8C, it has the lowest energy barrier of any presently known compound capable of undergoing the Cope rearrangement of the double bond system. This barrier to the thermal isomerization has been determined experimentally to be 5.5 AE 0.1 kcal mol À1 . High level theoretical studies of the Cope rearrangement have been recently reported. Martin, Urbanek, and Walsh established that COT should be the principal product of thermal decomposition of SBV. Further, the heat of formation of SBV was estimated to be D f H 0 73.6 AE 1.0 kcal mol À1 (298 K), a value close to the experimental value of COT D f H 0 71.1 AE 0.3 kcal mol À1 (298 K). The experimental results clearly show that SBV and COT lie close in energy and that COT is involved in two reversible valence isomerization processes: The isomerization at about 100 8C produces bicyclo[4.2.0]octa-2,4,7 triene and has been extensively studied. The other isomerization is observed at 300 8C and leads to SBV. Martin, Urbanek, and Walsh postulated that the mechanism of the conversion of SBV to COT probably involves the intermediate bicyclo[3.3.0.0]octa-2,6-dien-4,8-diyl diradical 3, which suggests a stepwise mechanism for the reaction. From a thermochemical estimate, they established a value of D f H 0 95 AE 4 kcal mol À1 for this intermediate but, in their conclusions, the authors also stated its formation is not rate determining for the higher temperature COT rearrangement.
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Papers by Roberto Gomperts