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Leach A.R. Ч Molecular Modelling Principles and Applications
Leach A.R. Ч Molecular Modelling Principles and Applications

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Ќазвание: Molecular Modelling Principles and Applications

јвтор: Leach A.R.


Preface to the Second Edition The impetus for this second edition is a desire to include some of the new techniques that have emerged in recent years and also extend the scope of the book to cover certain areas that were under-represented (even neglected) in the first edition. In this second volume there are three topics that fall into the first category (density functional theory, bioinformatics/protein structure analysis and chemoinformatics) and one main area in the second category (modelling of the solid state). In addition, of course, a new edition provides an opportunity to take a critical view of the text and to re-organise and update the material. Thus whilst much remains from the first edition, and this second book follows much the same path through the subject, readers familiar with the first edition will find some changes which I hope they will agree are for the better. As with the first edition we initially consider quantum mechanics, but this is now split into two chapters. Thus Chapter 2 provides an introduction to the ab initio and semi-empirical approaches together with some examples of the uses of quantum mechanics. Chapter 3 covers more advanced aspects of the ab initio approach, density functional theory and the particular problems of the solid state. Molecular mechanics is the subject of Chapter 4 and then in Chapter 5 we consider energy minimisation and other 'static' techniques. Chapters 6, 7 and 8 deal with the two main simulation methods (molecular dynamics and Monte Carlo). Chapter 9 is devoted to the conformational analysis of 'small' molecules but also includes some topics (e.g. cluster analysis, principal components analysis) that are widely used in informatics. In Chapter 10 the problems of protein structure prediction and protein folding are considered; this chapter also contains an introduction to some of the more widely used methods in bioinformatics. In Chapter 11 we draw upon material from the previous chapters in a discussion of free energy calculations, continuum solvent models, and methods for simulating chemical reactions and defects in solids. Finally, Chapter 12 is concerned with modelling and chemoinformatics techniques for discovering and designing new molecules, including database searching, docking, de novo design, quantitative structure-activity relationships and combinatorial library design. As in the first edition, the inexorable pace of change means that what is currently considered 'cutting edge' will soon become routine. The examples are thus chosen primarily because they illuminate the underlying theory rather than because they are the first application of a particular technique or are the most recent available. In a similar vein, it is impossible in a volume such as this to even attempt to cover everything and so there are undoubtedly areas which are under-represented. This is not intended to be a definitive historical account or a review of the current state-of-the-art. Thus, whilst I have tried to include many literature references it is possible that the invention of some technique may appear to be incorrectly attributed or a 'classic' application may be missing. A general guiding principle has been to focus on those techniques that are in widespread use rather than those which are the province of one particular research group. Despite these caveats I hope that the coverage is sufficient to provide a solid introduction to the main areas and also that those readers who are 'experts' will find something new to interest them.

язык: en

–убрика: ’ими€/

—татус предметного указател€: √отов указатель с номерами страниц

ed2k: ed2k stats

»здание: 2-nd

√од издани€: 2001

 оличество страниц: 774

ƒобавлена в каталог: 21.02.2007

ќперации: ѕоложить на полку | —копировать ссылку дл€ форума | —копировать ID
ѕредметный указатель
$Q^2$ (cross-validated R2)      701
$r^2$      699
$S_N2$ reaction, potential of mean force      612Ч614
$S_N2$ reaction, transition state of      280Ч282
$\alpha$-Helix      513Ч515
$\beta$-strand structures      513Ч514
$\beta$-turns      513
$\pi$ systems      197Ч199
$\pi$ systems, benzene      126
$\pi$ systems, delocalised      233Ч234
1, 2-dichloroethane      387Ч388
1, 3, 5-trifluorobenzene      198Ч199
1-octanol and water, partition between      668Ч669
2-methyl propane      644
2D substructure searching      642Ч647
4-acetamido benzoic acid      661
4-methyl-2 oxetanone      137
ab initio defined      65
ab initio molecular dynamics      616Ч622
ab initio potentials for water      216Ч218
ab initio quantum mechanics, calculating properties using      74Ч86 (see also УAdvanced ab initio methodsФ)
Absolute free energies      573Ч574
Accessible surface      7
ACE (angiotensin converting enzyme)      649Ч651
Acetaldehyde      180 578
Acetamide      573
Acetic acid      504Ч505 573 643
Acetic acid, SMILES notation      644 645
Acetonitrile      597
Acetylcholine      678
Acronyms and abbreviations      104Ч105 553Ч554
Adenine      227
Adiabatic mapping      286
Adjacency matrix      647
Adjoint matrix      15
Adsorption processes, Monte Carlo simulations of      441Ч442
Advanced ab initio methods      108Ч164
Advanced ab initio methods, density functional theory      126Ч137
Advanced ab initio methods, electron correlation      110Ч117
Advanced ab initio methods, energy component analysis      122Ч124
Advanced ab initio methods, open-shell systems      108Ч110
Advanced ab initio methods, practical considerations      117Ч122
Advanced ab initio methods, solid state quantum mechanics      138Ч160
Advanced ab initio methods, valence bond theories      124Ч126
Agglomerative cluster analysis methods      493Ч494
Agonists      640
AINT function      350
Alanines      169 459 511 525 542 546 556Ч557
Alanines, energy minimisation methods      277 280 286
Alanines, free energy calculations      583Ч584
Aldehyde      610Ч611
Aldol reactions      610Ч612
Aliovalent substitution      623
Alkaline earth oxides      147
Alkanes      449Ч450
AMBER force field      169Ч170 175Ч176 191 211 230Ч232
AMI      86 97Ч98 102Ч103 230
Amino acids      511 549 602
Amino acids, computer simulation      329Ч330
Amino acids, conformational analysis      459 487
Amino acids, energy minimisation methods      277 280 286
Amino acids, force fields      169Ч170 221
Amino acids, free energy calculations      572 583Ч584
Amino acids, motifs      522
Amino acids, PAM matrices      524Ч526 531 556Ч557
Amino acids, torsion angles      515 (see also УPeptides; proteinsФ)
Amino acids, ТthreadingТ      546
Aminothlazoles      716
AMP AC program      8 99
Amphiphiles, molecular dynamics simulation of      394Ч404
Angiotension converting enzyme      649Ч651
Angle bending      166 173
Annealing, simulated      483Ч489 504Ч505 519 691
Annotations      513
Antagonists      640
Antisymmetry principle      35
Arbitrary step energy minimisation      264
Argand diagram      17
Arginme      329Ч330 510 525 556Ч557
Argon      253 323
Argon, force fields      205 214
Argon, J-walking      434Ч435
Argon, time-steps      361Ч362
Argon, velocity autocorrelation      377
Arithmetic mean      20
Aromatic systems and charge schemes      197Ч199
Asparagine      330 510 525 546 556Ч557
Aspartic acid      510 525 556Ч557
Atoms in molecules theory      80Ч81
Atoms/atomic, charges      157Ч159 181 192Ч195
Atoms/atomic, marker      329Ч330
Atoms/atomic, one-electron      30Ч34
Atoms/atomic, orbitals      41Ч42 56 100 241
Atoms/atomic, polyelectronic      34Ч41
Atoms/atomic, type      169
Atoms/atomic, units      29
Aufbau principle      35
Austin Model I (AMI)      86 97Ч98 102Ч103
Autocorrelation function      376Ч378
Automated protein modelling      548Ч549
Autoscaling      681
Availability      300
Axilrod Ч Teller term (triple-dipole)      213Ч215 239
Azimuthal quantum number      31
B3LYP density function      615
Backtracking      462
Backward sampling      567
band theory      141Ч142
Band theory, orbital-based approach      142Ч146
Barker Ч Fisher Ч Watts potential      214
Basic Local Alignment Search Tool      see УBLASTФ
Basic Local Alignment Search Tool, basis sets/functions      56 85 123
Basic Local Alignment Search Tool, computational quantum mechanics      65Ч74
Basic Local Alignment Search Tool, Gaussian functions      65Ч73 passim 120 137 195
Basic Local Alignment Search Tool, superposition error      121Ч122 (see also УSTOsФ)
BCUT method      686Ч687
Bead model of polymers      428
Becke      see УBLYPФ
BeemanТs algorithm      357
Bending      166 173 176Ч178
Benperidol      675
Benzamidine      586Ч588
benzene      123
Benzene, force fields      170 174 178 186 197Ч198
Benzene, Huckel theory      99 100
Benzene, ring      81 170 178
Benzene, SMILES notation      644
Benzene, spin-coupled valence bond theory      126
Benzyl bromide      670
Beryllium      40 113
BFGS(Broyden-Fletcher-Goldfarb-Shanno) method      269Ч270
Bilinear model      702
Binding site      662 689Ч691
Binomial expansion      11
Bioinformatics      513 (see also УAmino acidsФ УDNAФ УProteinsФ)
Bioisosteres      648
Biotin      576 641
bitstring      645Ч647
BLAST (Basic Local Alignment Search Tool)      521 524 531Ч534 548
BlochТs theorem/function      142Ч145 146 148 161
Block-diagonal Newton Ч Raphson minimisation      268
BLOSUM matrices      526
BLYP (Becke gradient-exchange correction and Lee Ч Yang Ч Parr correlation functional)      135 136 137
Bohr radius      31
Boltzmann distribution      192 214 274 483 611
Boltzmann distribution, computer simulation      306Ч307 347
Boltzmann distribution, conformational analysis      457
Boltzmann distribution, Monte Carlo simulation      415Ч416 433 435Ч436 445Ч446
Boltzmann factor      306Ч307 413
Boltzmann weighted average      576 581
Bond fluctuation model      424Ч425
Bond/bonding      644
Bond/bonding, inorganic molecules      234Ч235
Bond/bonding, lack of      see УNon-bonded interactionsФ
Bond/bonding, orders      81Ч83
Bond/bonding, stretching      166 170Ч173
Bond/bonding, valence      124Ч126 (see also УUnder carbonФ УHydrogenФ)
Born equation/model      238 593Ч594 598Ч601 609
Born Ч Oppenheimer approximation      4 35Ч36 50
Boundary, computer simulation      317Ч321
Boundary, element method      598
Bravais lattices      138Ч139
BrillouinТs theorem      112Ч113 115
Brilloum zone      140Ч141 145Ч146 150Ч151 157Ч158 298Ч299
Bromine      571
Broyden Ч Fletcher Ч Goldfarb Ч Shanno method      269Ч270
BSSE (basis set superposition error)      121Ч122
Buckingham potential      209 238
Build-up approach      517
Butadiene      233 294Ч295
Butane      85Ч86 186 449Ч450 582
Butanone      611Ч612
Cage structure of liquids      377
Calcium      589 626
Calix[4]arene      291Ч292
Cambridge structural database      see УCSDФ
canonical ensemble      563 569
Canonical genetic algorithms      479Ч480
Canonical representation      644
Canonical structures      541
Captopril      649
Car Ч Parrinello scheme      610 617Ч619
Carbo index      678Ч679
Carbon dioxide      181 316 616Ч617
Carbon, bonds      4Ч5 98 362 612 652
Carbon, bonds, energy minimisation methods      253 280Ч281
Carbon, bonds, force fields      167 180 211 233 236
Carbon, five-carbon fragment      472
Carbon, force fields      167 180 211 233 236 244
Carbon, valence electron density      160
Carbonic anhydrase      616
Carboxylic acid      660
Cartesian coordinates      2Ч4
Cartesian coordinates, conformational analysis      466Ч468
Cartesian coordinates, energy minimisation methods      255 257Ч258 275 290
Cartesian coordinates, molecular dynamics simulation      370 372 379 393
Cartesian coordinates, Monte Carlo simulation      417 420Ч421 423
Cartesian coordinates, vectors      11Ч12
CASP3      548
CASSCF (complete active-space SCF)      113 295
CAVEAT program      689
CBMC (configurational bias Monte Carlo) simulation      443Ч50
Cell, cubic      315Ч319
Cell, index method      326
Cell, multipole method      341Ч343
Cell, unit      138
Cell, Wigner Ч Seitz      140 350
Central dogma      509 512
Central multipole expansion      181Ч187
CFF (consistent force field)      231
Chain amphiphiles and molecular dynamics      394Ч404
Charge      187
Charge, atomic      157Ч159 181 191Ч195
Charge, density matrix      58Ч59
Charge, image simulation      340Ч341
Charge, oscillating      201Ч202
Charge, schemes      197Ч199
CHELP procedure      191
Chemical potential calculation in Monte Carlo simulation      442Ч443
Chemical reactions      610Ч622
Chemical reactions, molecular dynamics      616Ч622
Chemical reactions, potential of mean force of      612Ч614
Chemical reactions, quantum and molecular mechanics combined      614Ч616
Chemical reactions, simulation empirically      610Ч612
Chemokine      475
Chi molecular connectivity indices      672
Chi-squared test      344Ч345
Chiral constraints      473Ч474
Chlorides      238 612Ч613 614 676Ч677
Chlorine      181 231 280Ч281 571 612 620Ч621
Chloroform      227 573
Chlorpromazine      678
Chymosin      545
Chymotrypsin      522Ч523
CI (configuration interaction)      111Ч113 120
CID (configuration interaction doubles)      112 113
CISD (configuration interaction singles and doubles)      112 113
City block      see УHammingФ
Clausius Ч Mosotti relationship      238Ч239
Clausius, virial theorem of      309
Clique detection      653Ч656
CLOGP program      669Ч670
Closed-shell systems      51 56Ч9 86Ч88 109
Cluster analysis      494 534 682Ч683
Clustering algorithms      491Ч497
CMR program      671
CNDO (complete neglect of differential overlap)      86 89Ч92 93 94 95
Coefficients      148Ч149 374
Coefficients, new molecules      676Ч678 680Ч681 685
Coefficients, partition      572Ч573 668Ч671
Cofactor      14Ч15
Combination generator      420 453Ч454
Combinatorial explosion      460Ч461
Combinatorial libraries      711Ч719
CoMFA (comparative molecular field analysis)      679 708Ч711
Comparative modelling of proteins      539Ч545
Comparative molecular field analysis      679 708Ч711
Complete active-space SCF      113 295
Complete neglect of differential overlap      86 89Ч92 93 94 95
Complete-linkage (furthest-neighbour) cluster algorithm      493Ч494
complex numbers      16Ч18
Computational quantum mechanics      26Ч107
Computational quantum mechanics, acronyms used in      104Ч105
Computational quantum mechanics, approximate orbital theories      86
Computational quantum mechanics, atomic units      29
Computational quantum mechanics, basis sets      65Ч74
Computational quantum mechanics, calculating properties      74Ч86
Computational quantum mechanics, Huckel theory      99Ч102
Computational quantum mechanics, one-electron atoms      30Ч34
Computational quantum mechanics, operators      28Ч29
Computational quantum mechanics, polyelectroruc atoms and molecules      34Ч41
Computational quantum mechanics, semi-empirical methods      65 86Ч99 102Ч103 УHartree
Computer simulation      303Ч352
Computer simulation, boundaries      317Ч321
Computer simulation, equilibration, monitoring      321Ч323
Computer simulation, free energy calculation difficulties      563Ч564
Computer simulation, long-range forces      334Ч343
Computer simulation, molecular dynamics      305Ч306 307
Computer simulation, phase space      312Ч315
Computer simulation, practical aspects      315Ч316
Computer simulation, real gas contribution to virial      309 349Ч350
Computer simulation, results and errors      343Ч347
Computer simulation, statistical mechanics      347Ч348
Computer simulation, thermodynamic properties, simple      307Ч312
Computer simulation, time and ensemble averages      303Ч305
Computer simulation, translating particle back into control box      350
Computer simulation, truncating potential and minimum image convention      324Ч334 (see also УMolecular dynamics simulation Monte
Computers, hardware      8Ч9
Computers, Internet and World Wide Web      9Ч10 548 553
Computers, software      8Ч9 99
concepts      1Ч25 (see also УCoordinatesФ УMathematical
CONCORD program      659
Conditionally convergent series      336
Conduction band      142
Conductor-like screening model      597
Configuration interaction      see УCIФ УCIDФ УCISDФ
Configurational bias      see УCBMCФ
Conformational analysis      457Ч508
Conformational analysis and NMR/x-ray crystallography      468 474Ч475 483Ч489
Conformational analysis, choice of method      476Ч477
1 2 3 4 5 6
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